# Lightweight ET Viewer using PyMOL # Script/plugin by Rhonald Lua (lua@bcm.edu) # Some parts of GUI code based on apbs_tools.py by Michael Lerner. # # THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, # INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN # NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR # CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF # USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR # OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR # PERFORMANCE OF THIS SOFTWARE. # ---------------------------------------------------------------------- # Possible locations of the PyMOL plugins directory: # On Windows, this is usually: # C:\Program Files\DeLano Scientific\PyMOL\modules\pmg_tk\startup # On Macintosh, with the X11/Hybrid version, the location is probably: # PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup # On a linux machine, it might be under: # /var/lib/python-support/python2.4/pmg_tk/startup/ from pymol import cmd # This launches pymol from tkinter import * import os, fnmatch, time, math, colorsys, string, urllib.request, urllib.parse, urllib.error import tkinter, Pmw, tkinter.colorchooser # from tkSimpleDialog import * from threading import Thread, Event import collections # Square of cutoff distance defining adjacency or contact # between residues CONTACT_DISTANCE2 = 16.0 # Enable or disable multithreading on certain operations _ET_THREADING = 0 def _getPyMOLstructuresequence(self, model, structurename, chainindicator): three2one = { "ALA": 'A', "ARG": 'R', "ASN": 'N', "ASP": 'D', "CYS": 'C', "GLN": 'Q', "GLU": 'E', "GLY": 'G', "HIS": 'H', "ILE": 'I', "LEU": 'L', "LYS": 'K', "MET": 'M', "PHE": 'F', "PRO": 'P', "SER": 'S', "THR": 'T', "TRP": 'W', "TYR": 'Y', "VAL": 'V', "A": "A", "G": "G", "T": "T", "U": "U", "C": "C", } # print 'Comparing residue numbers of structure \'%s\' and ranks \'%s\'...' % (structurename+chainindicator, # rankspath) # Check that the residue numbers in the model # and in the ranks file are identical resnumDict = {} resnums = [] restypes = [] # chainup=chainindicator.upper() # Case of chain indicator is relevant if len(chainindicator) > 0: for i in range(len(model.atom)): atomobj = model.atom[i] if chainindicator == atomobj.chain: try: # Does not just look for CA atom name, so we get several atoms with the same residue number and name, hence the dictionary aa1 = three2one[atomobj.resn] # Consider only residues with standard amino acids try: rrr = resnumDict[atomobj.resi] except KeyError: resnumDict[atomobj.resi] = 1 resnums.append(atomobj.resi) restypes.append(aa1) except KeyError: pass else: for i in range(len(model.atom)): try: atomobj = model.atom[i] aa1 = three2one[atomobj.resn] # Consider only residues with standard amino acids try: rrr = resnumDict[atomobj.resi] except KeyError: resnumDict[atomobj.resi] = 1 resnums.append(atomobj.resi) restypes.append(aa1) except KeyError: pass return restypes, resnums ####################################################### # Functions useful for calculating clustering z-score # ####################################################### def _et_calcDist(self, atoms1, atoms2): """return smallest distance (squared) between two groups of atoms""" # (not distant by more than ~100 A) # mind2=CONTACT_DISTANCE2+100 c1 = atoms1[0] # atoms must not be empty c2 = atoms2[0] mind2 = (c1[0] - c2[0]) * (c1[0] - c2[0]) + \ (c1[1] - c2[1]) * (c1[1] - c2[1]) + \ (c1[2] - c2[2]) * (c1[2] - c2[2]) for c1 in atoms1: for c2 in atoms2: d2 = (c1[0] - c2[0]) * (c1[0] - c2[0]) + \ (c1[1] - c2[1]) * (c1[1] - c2[1]) + \ (c1[2] - c2[2]) * (c1[2] - c2[2]) if d2 < mind2: mind2 = d2 return mind2 # Square of distance between most proximate atoms def _et_computeAdjacency(self, structurename): """Compute the pairs of contacting residues A(i,j) implemented as a hash of hash of residue numbers""" # self.adjacencyOK=False try: model = cmd.get_model(structurename) except Exception: print("Structure \'%s\' does not exist!" % structurename) return None, None three2one = { "ALA": 'A', "ARG": 'R', "ASN": 'N', "ASP": 'D', "CYS": 'C', "GLN": 'Q', "GLU": 'E', "GLY": 'G', "HIS": 'H', "ILE": 'I', "LEU": 'L', "LYS": 'K', "MET": 'M', "PHE": 'F', "PRO": 'P', "SER": 'S', "THR": 'T', "TRP": 'W', "TYR": 'Y', "VAL": 'V', "A": "A", "G": "G", "T": "T", "U": "U", "C": "C", } ResAtoms = {} # List of atom coordinates indexed by residue number # atom.resi is a string, convert it to int for i in range(len(model.atom)): atom = model.atom[i] try: # 07/12/10 Test for standard amino acids aa = three2one[atom.resn] except KeyError: continue try: ResAtoms[int(atom.resi)].append(atom.coord) except KeyError: ResAtoms[int(atom.resi)] = [atom.coord] A = {} A_recip = {} for resi in list(ResAtoms.keys()): for resj in list(ResAtoms.keys()): if resi < resj: if (self.calcDist(ResAtoms[resi], ResAtoms[resj]) < CONTACT_DISTANCE2): try: A[resi][resj] = 1 except KeyError: A[resi] = {resj: 1} # 12/21/11 This addition should not break anything(?). 07/24/12 It did, the z-scores will be wrong. try: A_recip[resj][resi] = 1 except KeyError: A_recip[resj] = {resi: 1} # self._A=A # self.adjacencyOK=True return A, ResAtoms, A_recip def _et_calcZScore(self, reslist, L, A, bias=1): """Calculate z-score (z_S) for residue selection reslist=[1,2,...] z_S = (w-_S)/sigma_S The steps are: 1. Calculate Selection Clustering Weight (SCW) 'w' 2. Calculate mean SCW (_S) in the ensemble of random selections of len(reslist) residues 3. Calculate mean square SCW (_S) and standard deviation (sigma_S) Reference: Mihalek, Res, Yao, Lichtarge (2003) reslist - a list of int's of protein residue numbers, e.g. ET residues L - length of protein A - the adjacency matrix implemented as a dictionary. The first key is related to the second key by resi_S and _S. # Use expressions (3),(4),(5),(6) in Reference. M = len(reslist) # L=self.ranksObj1.getSize() pi1 = M * (M - 1.0) / (L * (L - 1.0)) pi2 = pi1 * (M - 2.0) / (L - 2.0) pi3 = pi2 * (M - 3.0) / (L - 3.0) w_ave = 0 w2_ave = 0 if bias == 1: for resi, neighborsj in list(A.items()): for resj in neighborsj: w_ave += (resj - resi) for resk, neighborsl in list(A.items()): for resl in neighborsl: if (resi == resk and resj == resl) or \ (resi == resl and resj == resk): w2_ave += pi1 * (resj - resi) * (resl - resk) elif (resi == resk) or (resj == resl) or \ (resi == resl) or (resj == resk): w2_ave += pi2 * (resj - resi) * (resl - resk) else: w2_ave += pi3 * (resj - resi) * (resl - resk) elif bias == 0: for resi, neighborsj in list(A.items()): w_ave += len(neighborsj) for resj in neighborsj: # w_ave+=1 for resk, neighborsl in list(A.items()): for resl in neighborsl: if (resi == resk and resj == resl) or \ (resi == resl and resj == resk): w2_ave += pi1 elif (resi == resk) or (resj == resl) or \ (resi == resl) or (resj == resk): w2_ave += pi2 else: w2_ave += pi3 w_ave = w_ave * pi1 # print "w_ave", w_ave sigma = math.sqrt(w2_ave - w_ave * w_ave) # print "sigma", sigma if sigma == 0: # Response to Bioinformatics reviewer 08/24/10 return 'NA' return (w - w_ave) / sigma def _et_computeInterface(self, structurename1, structurename2, dist2): """Get the interface residues between structurename1 and structurename2""" try: model1 = cmd.get_model(structurename1) except Exception: print("Structure \'%s\' does not exist!" % structurename1) return None, None, None, None try: model2 = cmd.get_model(structurename2) except Exception: print("Structure \'%s\' does not exist!" % structurename2) return None, None, None, None ResAtoms1 = {} # List of atom coordinates indexed by residue number # atom.resi is a string, leave it as string for i in range(len(model1.atom)): atom = model1.atom[i] try: ResAtoms1[int(atom.resi)].append(atom.coord) except KeyError: ResAtoms1[int(atom.resi)] = [atom.coord] ResAtoms2 = {} # List of atom coordinates indexed by residue number for i in range(len(model2.atom)): atom = model2.atom[i] try: ResAtoms2[int(atom.resi)].append(atom.coord) except KeyError: ResAtoms2[int(atom.resi)] = [atom.coord] A1 = {} A2 = {} for res1 in list(ResAtoms1.keys()): for res2 in list(ResAtoms2.keys()): if (self.calcDist(ResAtoms1[res1], ResAtoms2[res2]) < dist2): try: A1[res1].append(res2) except KeyError: A1[res1] = [res2] try: A2[res2].append(res1) except KeyError: A2[res2] = [res1] return A1, A2, ResAtoms1, ResAtoms2 def _et_computeCoupling(self, reslist1, reslist2, L1, L2, A): """Calculate coupling z-score (z_S) for residue selection reslist1=[1,2,...] and reslist2 z_S = (w-_S)/sigma_S The steps are: 1. Calculate the number of couples ('w') between residues in reslist1 and reslist2 2. Calculate mean number of couples (_S) in the ensemble of random selections of len(reslist) residues on each protein partner 3. Calculate mean square number of couples (_S) and standard deviation (sigma_S) reslist1 and reslist2 - lists of int's of protein residue numbers, e.g. ET residues L1 and L2 - lengths of protein partners A - the adjacency matrix of interface residues implemented as a dictionary""" w = 0 for resi in reslist1: for resj in reslist2: try: if resj in A[resi]: # A is a dictionary of lists of neighbors w += 1 except KeyError: pass # Calculate _S and _S. M1 = len(reslist1) M2 = len(reslist2) c1 = M1 * 1.0 / L1 c2 = M2 * 1.0 / L2 SiSk = c1 * (M1 - 1.0) / (L1 - 1.0) SjSl = c2 * (M2 - 1.0) / (L2 - 1.0) w_ave = 0 w2_ave = 0 for resi, neighborsj in list(A.items()): w_ave += len(neighborsj) # total number of interface couples when the loop ends for resj in neighborsj: for resk, neighborsl in list(A.items()): for resl in neighborsl: if resi == resk: SiSjSkSl = c1 else: SiSjSkSl = SiSk if resj == resl: SiSjSkSl *= c2 else: SiSjSkSl *= SjSl w2_ave += SiSjSkSl w_ave = w_ave * c1 * c2 # print "w_ave", w_ave sigma = math.sqrt(w2_ave - w_ave * w_ave) # print "sigma", sigma return w, w_ave, sigma ################################################################# ##try: ## PYMOL_PATH=os.environ['PYMOL_PATH'] ##except KeyError: ## PYMOL_PATH='.' def __init__(self): self.menuBar.addmenuitem('Plugin', 'command', 'Launch PyETV', label='PyETV version - 1.3', command=lambda s=self: ETTools(s)) class FileDialogButtonClassFactory: def get(fn, filter='*'): """This returns a FileDialogButton class that will call the specified function with the resulting file. """ class FileDialogButton(tkinter.Button): # This is just an ordinary button with special colors. def __init__(self, master=None, cnf={}, **kw): '''when we get a file, we call fn(filename)''' self.fn = fn self.__toggle = 0 tkinter.Button.__init__(*(self, master, cnf), **kw) self.configure(command=self.set) def set(self): fd = PmwFileDialog(self.master, filter=filter) fd.title('Please choose a file') n = fd.askfilename() if n is not None: self.fn(n) return FileDialogButton get = staticmethod(get) # # The classes PmwFileDialog and PmwExistingFileDialog and the _errorpop function # are taken from the Pmw contrib directory. The attribution given in that file # is: ################################################################################ # Filename dialogs using Pmw # # (C) Rob W.W. Hooft, Nonius BV, 1998 # # Modifications: # # J. Willem M. Nissink, Cambridge Crystallographic Data Centre, 8/2002 # Added optional information pane at top of dialog; if option # 'info' is specified, the text given will be shown (in blue). # Modified example to show both file and directory-type dialog # # No Guarantees. Distribute Freely. # Please send bug-fixes/patches/features to # ################################################################################ # import os,fnmatch,time # import Tkinter,Pmw # Pmw.setversion("0.8.5") ##def _errorpop(master,text): ## d=Pmw.MessageDialog(master, ## title="Error", ## message_text=text, ## buttons=("OK",)) ## d.component('message').pack(ipadx=15,ipady=15) ## d.activate() ## d.destroy() class PmwFileDialog(Pmw.Dialog): """File Dialog using Pmw""" def __init__(self, parent=None, **kw): # Define the megawidget options. optiondefs = ( ('filter', '*', self.newfilter), ('directory', os.getcwd(), self.newdir), ('filename', '', self.newfilename), ('historylen', 10, None), ('command', None, None), ('info', None, None), ) self.defineoptions(kw, optiondefs) # Initialise base class (after defining options). Pmw.Dialog.__init__(self, parent) self.withdraw() # Create the components. interior = self.interior() if self['info'] is not None: rowoffset = 1 dn = self.infotxt() dn.grid(row=0, column=0, columnspan=2, padx=3, pady=3) else: rowoffset = 0 dn = self.mkdn() dn.grid(row=0 + rowoffset, column=0, columnspan=2, padx=3, pady=3) del dn # Create the directory list component. dnb = self.mkdnb() dnb.grid(row=1 + rowoffset, column=0, sticky='news', padx=3, pady=3) del dnb # Create the filename list component. fnb = self.mkfnb() fnb.grid(row=1 + rowoffset, column=1, sticky='news', padx=3, pady=3) del fnb # Create the filter entry ft = self.mkft() ft.grid(row=2 + rowoffset, column=0, columnspan=2, padx=3, pady=3) del ft # Create the filename entry fn = self.mkfn() fn.grid(row=3 + rowoffset, column=0, columnspan=2, padx=3, pady=3) fn.bind('', self.okbutton) del fn # Buttonbox already exists bb = self.component('buttonbox') bb.add('OK', command=self.okbutton) bb.add('Cancel', command=self.cancelbutton) del bb Pmw.alignlabels([self.component('filename'), self.component('filter'), self.component('dirname')]) def infotxt(self): """ Make information block component at the top """ return self.createcomponent( 'infobox', (), None, tkinter.Label, (self.interior(),), width=51, relief='groove', foreground='darkblue', justify='left', text=self['info'] ) def mkdn(self): """Make directory name component""" return self.createcomponent( 'dirname', (), None, Pmw.ComboBox, (self.interior(),), entryfield_value=self['directory'], entryfield_entry_width=40, entryfield_validate=self.dirvalidate, selectioncommand=self.setdir, labelpos='w', label_text='Directory:') def mkdnb(self): """Make directory name box""" return self.createcomponent( 'dirnamebox', (), None, Pmw.ScrolledListBox, (self.interior(),), label_text='directories', labelpos='n', hscrollmode='dynamic', # 'none' originally dblclickcommand=self.selectdir) def mkft(self): """Make filter""" return self.createcomponent( 'filter', (), None, Pmw.ComboBox, (self.interior(),), entryfield_value=self['filter'], entryfield_entry_width=40, selectioncommand=self.setfilter, labelpos='w', label_text='Filter:') def mkfnb(self): """Make filename list box""" return self.createcomponent( 'filenamebox', (), None, Pmw.ScrolledListBox, (self.interior(),), label_text='files', labelpos='n', hscrollmode='dynamic', # 'none' originally. 'dynamic' is supposed to be the default selectioncommand=self.singleselectfile, dblclickcommand=self.selectfile) def mkfn(self): """Make file name entry""" return self.createcomponent( 'filename', (), None, Pmw.ComboBox, (self.interior(),), entryfield_value=self['filename'], entryfield_entry_width=40, entryfield_validate=self.filevalidate, selectioncommand=self.setfilename, labelpos='w', label_text='Filename:') def dirvalidate(self, string): if os.path.isdir(string): return Pmw.OK else: return Pmw.PARTIAL def filevalidate(self, string): if string == '': return Pmw.PARTIAL elif os.path.isfile(string): return Pmw.OK elif os.path.exists(string): return Pmw.PARTIAL else: return Pmw.OK def okbutton(self): """OK action: user thinks he has input valid data and wants to proceed. This is also called by in the filename entry""" fn = self.component('filename').get() self.setfilename(fn) if self.validate(fn): self.canceled = 0 self.deactivate() def cancelbutton(self): """Cancel the operation""" self.canceled = 1 self.deactivate() def tidy(self, w, v): """Insert text v into the entry and at the top of the list of the combobox w, remove duplicates""" if not v: return entry = w.component('entry') entry.delete(0, 'end') entry.insert(0, v) list = w.component('scrolledlist') list.insert(0, v) index = 1 while index < list.index('end'): k = list.get(index) if k == v or index > self['historylen']: list.delete(index) else: index = index + 1 w.checkentry() def setfilename(self, value): if not value: return value = os.path.join(self['directory'], value) dir, fil = os.path.split(value) self.configure(directory=dir, filename=value) c = self['command'] if isinstance(c, collections.Callable): c() def newfilename(self): """Make sure a newly set filename makes it into the combobox list""" self.tidy(self.component('filename'), self['filename']) def setfilter(self, value): self.configure(filter=value) def newfilter(self): """Make sure a newly set filter makes it into the combobox list""" self.tidy(self.component('filter'), self['filter']) self.fillit() def setdir(self, value): self.configure(directory=value) def newdir(self): """Make sure a newly set dirname makes it into the combobox list""" self.tidy(self.component('dirname'), self['directory']) self.fillit() def singleselectfile(self): """Single click in file listbox. Move file to "filename" combobox""" cs = self.component('filenamebox').curselection() if cs != (): value = self.component('filenamebox').get(cs) self.setfilename(value) def selectfile(self): """Take the selected file from the filename, normalize it, and OK""" self.singleselectfile() value = self.component('filename').get() self.setfilename(value) if value: self.okbutton() def selectdir(self): """Take selected directory from the dirnamebox into the dirname""" cs = self.component('dirnamebox').curselection() if cs != (): value = self.component('dirnamebox').get(cs) dir = self['directory'] if not dir: dir = os.getcwd() if value: if value == '..': dir = os.path.split(dir)[0] else: dir = os.path.join(dir, value) self.configure(directory=dir) self.fillit() def askfilename(self, directory=None, filter=None): """The actual client function. Activates the dialog, and returns only after a valid filename has been entered (return value is that filename) or when canceled (return value is None)""" if directory != None: self.configure(directory=directory) if filter != None: self.configure(filter=filter) self.fillit() self.canceled = 1 # Needed for when user kills dialog window self.activate() if self.canceled: return None else: return self.component('filename').get() lastdir = "" lastfilter = None lasttime = 0 def fillit(self): """Get the directory list and show it in the two listboxes""" # Do not run unnecesarily if self.lastdir == self['directory'] and self.lastfilter == self['filter'] and self.lasttime > \ os.stat(self.lastdir)[8]: return self.lastdir = self['directory'] self.lastfilter = self['filter'] self.lasttime = time.time() dir = self['directory'] if not dir: dir = os.getcwd() dirs = ['..'] files = [] try: fl = os.listdir(dir) fl.sort() except os.error as arg: if arg[0] in (2, 20): return raise for f in fl: if os.path.isdir(os.path.join(dir, f)): dirs.append(f) else: filter = self['filter'] if not filter: filter = '*' if fnmatch.fnmatch(f, filter): files.append(f) self.component('filenamebox').setlist(files) self.component('dirnamebox').setlist(dirs) def validate(self, filename): """Validation function. Should return 1 if the filename is valid, 0 if invalid. May pop up dialogs to tell user why. Especially suited to subclasses: i.e. only return 1 if the file does/doesn't exist""" return 1 ##class PmwExistingFileDialog(PmwFileDialog): ## def filevalidate(self,string): ## if os.path.isfile(string): ## return Pmw.OK ## else: ## return Pmw.PARTIAL ## def validate(self,filename): ## if os.path.isfile(filename): ## return 1 ## elif os.path.exists(filename): ## _errorpop(self.interior(),"This is not a plain file") ## return 0 ## else: ## _errorpop(self.interior(),"Please select an existing file") ## return 0 ##################### EA Evolutionary Action of a substitution/mutation ########################### # Class representing a list of EA ranks per substitution "R36A 22.66" class EARanks: def __init__(self): self.ranksloaded = False # This method gets called inside mapRanks, after PyMOL structure has been checked and determined 08/25/14 def readRanks(self, rankspath): """Read residue rankings from an EA .predictions file, Substitution on the first column (R36A) and EA coverage on the second column.""" self.resnums = [] self.ranks = [] self.coverages = [] self.ranksloaded = False self.rankspath = rankspath self.resnum_mutpred = {} # Key: the residue number; value: dictionary of mutations and predicted EA scores if True: # rankspath[-7:]=='.simple': FILE = open(rankspath, 'r') types = [] # .simple file has no list of amino acid types try: for line in FILE: if line.find('#') == 0: # comment continue cols = line.split() if len(cols) < 2: continue ara = cols[0].strip() # "R36A" resnum = ara[1:-1] # "36" # aresnum=ara[0:-1] #"R36" atype = ara[0].upper() muta = ara[-1] rho = cols[1].strip() try: self.resnum_mutpred[resnum][muta] = float(rho) except KeyError: self.resnum_mutpred[resnum] = {muta: float(rho)} self.resnums.append(resnum) types.append(atype) finally: FILE.close() if len(self.resnums) > 0: self.sequence = string.join(types, '') self.ranks = [0] * len(self.resnums) self.coverages = [0] * len(self.resnums) atypesmax = [] atypesmin = [] # Find the maximum and minimum EA score for each residue number for r in self.resnums: maxscore = -1 minscore = 1000 atypemax = 'X' atypemin = 'X' mutpred = self.resnum_mutpred[r] for a, s in list(mutpred.items()): if s > maxscore: maxscore = s atypemax = a if s < minscore: minscore = s atypemin = a if maxscore > -1: mutpred['MAX'] = maxscore atypesmax.append(atypemax) else: print("Warning in finding EA maxscore for residue %s!" % r) if minscore < 1000: mutpred['MIN'] = minscore atypesmin.append(atypemin) else: print("Warning in finding EA minscore for residue %s!" % r) # self.computeCoverage() # self.ranksloaded=True self.atypesmax = string.join(atypesmax, '') self.atypesmin = string.join(atypesmin, '') print('***** AMINO ACID SEQUENCE *****') print('ORIGINAL :', self.sequence) print('') print('MAXIMUM ACTION MUTATION:', self.atypesmax) print('') print('MINIMUM ACTION MUTATION:', self.atypesmin) print('') # Panos EA scores are already in a form of a coverage: 0 - neutral, 100 - deleterious/has effect on phenotype def assignRanks(self, option): numres = self.getSize() if option == 0: for i in range(numres): # EA scores of alanine mutations e.g. R36A try: # TODO What to do if the native type is already Alanine? self.ranks[i] = self.resnum_mutpred[self.resnums[i]]['A'] except KeyError: self.ranks[i] = 1.0 print('WARNING: Did not find an Alanine substitution in your input Actions file') self.coverages[i] = 100.0 - self.ranks[i] # self.computeCoverage() self.ranksloaded = True elif option == 1: for i in range(numres): # Maximum EA scores for each residue self.ranks[i] = self.resnum_mutpred[self.resnums[i]]['MAX'] self.coverages[i] = 100.0 - self.ranks[i] # self.computeCoverage() self.ranksloaded = True elif option == 2: for i in range(numres): # Minimum EA scores for each residue self.ranks[i] = self.resnum_mutpred[self.resnums[i]]['MIN'] self.coverages[i] = 100.0 - self.ranks[i] # self.computeCoverage() self.ranksloaded = True def computeCoverage(self): numres = self.getSize() for i in range(numres): self.coverages[i] = 0 for j in range(numres): if self.ranks[i] <= self.ranks[ j]: # TODO Make sure the inequality is correct for the sense of coverage used self.coverages[i] += 1 self.coverages[i] = self.coverages[i] * 100.0 / numres def getSize(self): return len(self.resnums) def ranksLoaded(self): return self.ranksloaded def getResnumCoverageRankTuple(self, i): return self.resnums[i], self.coverages[i], self.ranks[i] def getResnum(self, i): return self.resnums[i] def alignToAnotherSequence(self, restypesstring, resnums): """align the sequence in the actions or ranks file to an external sequence e.g. the sequence in a PyMOL structure. Associate the action or rank with the aligned residue in the external sequence """ from Bio import pairwise2 from Bio.pairwise2 import format_alignment from Bio.SubsMat import MatrixInfo as matlist matrix = matlist.blosum62 gap_open = -10 # TODO gap_extend = -0.5 # TODO # for a in pairwise2.align.globaldx(self.sequence,restypesstring,matrix): # print(format_alignment(*a)) # topalign=pairwise2.align.globaldx(self.sequence,restypesstring,matrix)[0] topalign = pairwise2.align.globalds(self.sequence, restypesstring, matrix, gap_open, gap_extend)[0] print( "The pairwise alignment with matrix=blosum62 and gap_open=%lf and gap_extend=%lf:" % (gap_open, gap_extend)) print((format_alignment(*topalign))) a1 = topalign[0] a2 = topalign[1] gap = '-' shiftedresnums1 = [None] * len(a1) i = 0 for idx, a in enumerate(a1): if a != gap: shiftedresnums1[idx] = self.resnums[i] i += 1 shiftedresnums2 = [None] * len(a2) i = 0 for idx, a in enumerate(a2): if a != gap: shiftedresnums2[idx] = resnums[i] i += 1 self._resnums = [] self._resnum_mutpred = {} self._resnum1_resnum2 = {} # Mapping of residue numbers from the first sequence to the second (e.g. structure) for idx, a in enumerate(a1): print(shiftedresnums1[idx], a, shiftedresnums2[idx], a2[idx]) if shiftedresnums1[idx] is not None and shiftedresnums2[idx] is not None: self._resnums.append(shiftedresnums2[idx]) self._resnum_mutpred[shiftedresnums2[idx]] = self.resnum_mutpred[shiftedresnums1[idx]] self._resnum1_resnum2[shiftedresnums1[idx]] = shiftedresnums2[idx] self._coverages = [0] * len(self._resnums) self._ranks = [0] * len(self._resnums) # print self._resnum_mutpred # TEST TODO check zscores # Replacing the original residue numbers self.resnums = self._resnums self.resnum_mutpred = self._resnum_mutpred self.coverages = self._coverages self.ranks = self._ranks def mapResnum1toResnum2(self, resnum): return self._resnum1_resnum2[resnum] class EAControlGroup: # Reuse some functions useful for calculating clustering z-score # (Assignments made outside of a method such as __init__ make 'self' the first parameter) calcDist = _et_calcDist computeAdjacency = _et_computeAdjacency calcZScore = _et_calcZScore getPyMOLstructuresequence = _getPyMOLstructuresequence def __init__(self, page, groupname='Action', defaultstructurename='', defaultrankspath='.pred', defaultslidercoverage=30, defaultetoption=3, defaultqualitymeasure=0, defaultchain='', defaultactionoption=0, etcolor='red', noetcolor='green', et_colorramp=None, et_colorPrism=None, et_messagebox=None): self.etcolor = etcolor self.noetcolor = noetcolor self.et_colorramp = et_colorramp self.et_colorPrism = et_colorPrism self.et_messagebox = et_messagebox # group = Pmw.Group(page,tag_text=groupname) # Changing to scrollable frame as a response to Bioinformatics reviewer 08/24/10 group = Pmw.ScrolledFrame(page, labelpos='nw', label_text=groupname) self.groupname = groupname self.group = group # self.groupscrolled=group group.pack(fill='both', expand=1, padx=10, pady=5) self.balloon = Pmw.Balloon(group.interior()) self.structureframe = tkinter.Frame(group.interior()) # Field for entering name of structure or model self.structure = Pmw.EntryField(self.structureframe, labelpos='w', label_text='structure to use: ', value=defaultstructurename, ) self.chain = Pmw.EntryField(self.structureframe, labelpos='w', label_text='chain: ', value=defaultchain, ) self.structure.grid(column=0, row=0) self.chain.grid(column=1, row=0) def quickFileValidation(s): if s == '': return Pmw.PARTIAL elif os.path.isfile(s): return Pmw.OK elif os.path.exists(s): return Pmw.PARTIAL else: return Pmw.PARTIAL self.checksequence_var = IntVar() self.checksequence_var.set(1) self.checksequence_checkbutton = Checkbutton(group.interior(), text="check sequence", variable=self.checksequence_var) self.checkalignsequences_var = IntVar() self.checkalignsequences_var.set(1) self.checkalignsequences_checkbutton = Checkbutton(group.interior(), text="align input sequence to the structure", variable=self.checkalignsequences_var) self.selectalign = Pmw.EntryField(group.interior(), labelpos='w', label_text='Select residues: ' # value=defaultchain, ) # Button for assigning ranks to structure self.map_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.map_buttonbox.add('Map Action to structure', command=self.mapRanks) # Field for entering ranks file self.ranksfile = Pmw.EntryField(group.interior(), labelpos='w', label_pyclass=FileDialogButtonClassFactory.get(self.setRanksFileLocation, '*.pred'), validate={'validator': quickFileValidation, }, value=defaultrankspath, # entry_width=50, #This value is set for the sole purpose of making the width of the plugin dialog box large enough label_text='EA predictions file path:') # Tkinter Slider Tkinterfor changing ET residue coverage. # TODO: Use a Pmw implementation? self.slider = Scale(group.interior(), # from_=self.min, to=self.max, from_=0, to=100, showvalue=1, length=200, orient=HORIZONTAL, resolution=0.01, tickinterval=0, # repeatinterval=500, #Dunno what repeatinterval is for... repeatdelay=500 ) self.slider.set(defaultslidercoverage) # self.slider.grid() self.slider.bind("", self.slider_button_release) # self.slider.bind("", self.mousebutton_click) self.slider.bind("", self.mousebutton_click) # For Windows self.slider.bind("", self.mousewheel_roll) # For Linux (for Mac?) self.slider.bind("", self.mousewheel_roll) self.slider.bind("", self.mousewheel_roll) # self.slider.bind("", self.slider_button_release) ## Triggered when the mouse enters a widget ## ## Triggered when a left click is done in a widget ##, <1> ## Triggered when the mouse is dragged over ## ## the widget with the left mouse button being ## held down. ## Triggered when a widget is double-clicked ## ## with the left mouse button ## Triggered when the key producing the letter ##, , , A ## A (caps) is pressed. # Field for displaying ET coverage self.frame1 = tkinter.Frame(group.interior()) self.percentcoverage = Pmw.EntryField(self.frame1, # group.interior(), labelpos='w', label_text='Percent coverage: ', value='', ) self.rankvalue = Pmw.EntryField(self.frame1, # group.interior(), labelpos='w', label_text='Action: ', value='', ) self.percentcoverage.grid(column=0, row=0) self.rankvalue.grid(column=1, row=0) self.frame2 = tkinter.Frame(group.interior()) self.et_options_tuple = ('Colors only(' + self.etcolor + ')', 'as Spheres', 'as Spheres (C-alpha only)', 'Red_to_Green', 'as Sticks', 'Map -1 to +1 to blue-white-red', 'Greyscale', 'Prismatic (Gobstopper)') self.show_et_options = Pmw.OptionMenu(self.frame2, # group.interior(), labelpos='w', label_text='Show EA residues', items=self.et_options_tuple, initialitem=self.et_options_tuple[defaultetoption], command=self.slider_button_release ) ## self.show_et_var=IntVar() ## self.show_et_var.set(0) ## self.show_et_checkbutton = Checkbutton(group.interior(), ## text = "Show EA residues (as spheres)", ## variable = self.show_et_var) self.select_et_var = IntVar() self.select_et_var.set(0) self.select_et_checkbutton = Checkbutton(self.frame2, # group.interior(), text="Select EA residues", variable=self.select_et_var) self.show_et_options.grid(column=0, row=0) self.select_et_checkbutton.grid(column=1, row=0) # self.ETcolor_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) #06/10/11 Experimenting with tkColorChooser # self.ETcolor_buttonbox.add('Choose ET color',command=self.chooseETcolor) self.qualitymeasure_options_tuple = ('3D nobias', '3D bias (j-i)') self.show_qualitymeasure_options = Pmw.OptionMenu(group.interior(), labelpos='w', label_text='quality measure: ', items=self.qualitymeasure_options_tuple, initialitem=self.qualitymeasure_options_tuple[ defaultqualitymeasure], ) self.zscore_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.zscore_buttonbox.add('Compute z-scores', command=self.showZScores) # self.zscore_buttonbox.add('Average neighbor ranks',command=self.averageNeighborRanks) self.zscore_et = Pmw.EntryField(group.interior(), labelpos='w', label_text='z-score EA residues: ', value='', ) self.zscore_notet = Pmw.EntryField(group.interior(), labelpos='w', label_text='z-score non-EA residues: ', value='', ) self.action_options_tuple = ('Alanine substitution', 'Maximum impact', 'Minimum impact') self.show_action_options = Pmw.OptionMenu(group.interior(), labelpos='w', label_text='Select Evolutionary Action: ', items=self.action_options_tuple, initialitem=self.action_options_tuple[defaultactionoption], command=self.reassignEAranks ) for entry in (self.structureframe, self.ranksfile, self.checksequence_checkbutton, self.checkalignsequences_checkbutton, self.selectalign, self.map_buttonbox, self.slider, self.frame1, self.frame2, self.show_action_options, self.zscore_buttonbox, self.show_qualitymeasure_options, self.zscore_et, self.zscore_notet): entry.pack(fill='x', padx=4, pady=1) # vertical # Tool tips (help) for user-interface components and boxes self.balloon.bind(self.structure, "Enter a name from the list of objects in the PyMOL Viewer") self.balloon.bind(self.ranksfile, "Click to open a box for navigating and choosing a file") self.balloon.bind(self.checksequence_checkbutton, "Check this box to verify if the sequence in the structure and EA predictions file match after mapping Action to structure") self.balloon.bind(self.checkalignsequences_checkbutton, "Check this box to align the amino acid sequence in your actions file with the sequence of the PyMOL structure. Requires Biopython installation.") self.balloon.bind(self.selectalign, "Select the residues in the structure that align with these residue numbers (use a comma to separate e.g. 7,23,25)") self.balloon.bind(self.map_buttonbox, "Click to map Action data onto the structure.") self.balloon.bind(self.slider, "Drag slider to vary EA residue selection and coverage of the structure") self.balloon.bind(self.percentcoverage, "Maximum percent-rank (or percentile-rank) in the EA residue selection") self.balloon.bind(self.rankvalue, "Minimum raw Action score in the EA residue selection") self.balloon.bind(self.show_et_options, "Select display style to distinguish EA residue selection from the rest of the structure") self.balloon.bind(self.select_et_checkbutton, "Check box to create a PyMOL selection of the EA residues") self.balloon.bind(self.zscore_buttonbox, "Compute the clustering z-score of the EA residue selection") self.balloon.bind(self.show_qualitymeasure_options, "Select from several measures of clustering quality") self.balloon.bind(self.show_action_options, "Select the substitution to use in assigning an Evolutionary Action score to a residue") self.ranksObj = EARanks() self.ranksStructureOK = False self.adjacencyOK = False def setRanksFileLocation(self, value): self.ranksfile.setvalue(value) def mapRanks(self): structurename = self.structure.getvalue().strip() supper = structurename.upper() for n in cmd.get_names('all'): if supper == n.upper(): break else: print('structure name must be in PyMOL viewer list:') print(cmd.get_names('all')) return chainindicator = self.chain.getvalue().strip() self.ranksStructureOK = False self.adjacencyOK = False # TODO Is this redundant? See cmd.get_names above if len(structurename) < 1: print('Provide structure name!') return try: model = cmd.get_model(structurename) except Exception: print("Structure \'%s\' does not exist!" % structurename) return try: rankspath = self.ranksfile.getvalue().strip() if len(rankspath) < 1: print('Provide path to predictions file!') return self.ranksObj.readRanks(rankspath) if self.checkalignsequences_var.get() == 1: (pymolrestypes, pymolresnums) = self.getPyMOLstructuresequence(model, structurename, chainindicator) print("Aligning the sequence in %s with the sequence in the PyMOL structure %s %s" % ( rankspath, structurename, chainindicator)) # print pymolrestypes, 'n', pymolresnums self.ranksObj.alignToAnotherSequence(string.join(pymolrestypes, ''), pymolresnums) selectresstring = self.selectalign.getvalue().strip() if len(selectresstring) > 0: print("Your list of residues aligned with these residues in the structure:") selectreslist1 = selectresstring.split(',') selectreslist2 = [] for resnum in selectreslist1: try: resnum2 = self.ranksObj.mapResnum1toResnum2(resnum.strip()) selectreslist2.append(resnum2) print("%5s -> %5s" % (resnum.strip(), resnum2)) except KeyError: print("%5s -> %5s" % (resnum.strip(), '-')) if len(selectreslist2) > 0: print("The residue numbers ", selectreslist2, " were selected on the structure, based on your input selection of ", selectreslist1) if len(chainindicator) > 0: cmd.select('selalign_%s%s_PyETV' % (structurename, chainindicator), '%s and chain %s and resi %s' % ( structurename, chainindicator, string.join(selectreslist2, '+'))) else: cmd.select('selalign_%s%s_PyETV' % (structurename), '%s and resi %s' % (structurename, string.join(selectreslist2, '+'))) if self.show_action_options.getvalue() == self.action_options_tuple[0]: self.ranksObj.assignRanks(0) elif self.show_action_options.getvalue() == self.action_options_tuple[1]: self.ranksObj.assignRanks(1) elif self.show_action_options.getvalue() == self.action_options_tuple[2]: self.ranksObj.assignRanks(2) if self.ranksObj.ranksLoaded(): print("Predictions file \'%s\' loaded" % rankspath) else: print("Error loading predictions file \'%s\'!" % rankspath) return if self.checksequence_var.get() == 1: self.checkSequence(model, structurename, chainindicator, rankspath) except Exception as e: print("Exception encountered in EA mapRanks", e) self.structurename = structurename self.chainindicator = chainindicator self.ranksStructureOK = True self.slider_button_release(None) # This check uses the residue numbers, not the amino acid types def checkSequence(self, model, structurename, chainindicator, rankspath): three2one = { "ALA": 'A', "ARG": 'R', "ASN": 'N', "ASP": 'D', "CYS": 'C', "GLN": 'Q', "GLU": 'E', "GLY": 'G', "HIS": 'H', "ILE": 'I', "LEU": 'L', "LYS": 'K', "MET": 'M', "PHE": 'F', "PRO": 'P', "SER": 'S', "THR": 'T', "TRP": 'W', "TYR": 'Y', "VAL": 'V', "A": "A", "G": "G", "T": "T", "U": "U", "C": "C", } print('Comparing residue numbers of structure \'%s\' and ranks \'%s\'...' % (structurename + chainindicator, rankspath)) # Check that the residue numbers in the model # and in the ranks file are identical resnumDict = {} if len(chainindicator) > 0: # chainup=chainindicator.upper() # Case of chain indicator is relevant for i in range(len(model.atom)): atomobj = model.atom[i] if chainindicator == atomobj.chain: try: aa1 = three2one[atomobj.resn] # Consider only residues with standard amino acids resnumDict[atomobj.resi] = 1 except KeyError: pass else: for i in range(len(model.atom)): # TODO check for standard amino acids like the one right above 08/25/14 resnumDict[model.atom[i].resi] = 1 print('Sequence lengths:') print('structure: ', len(resnumDict)) print('ranks: ', self.ranksObj.getSize()) if len(resnumDict) < 1: print('Structure \'%s\' has no residues!' % (structurename + chainindicator)) if len(resnumDict) != self.ranksObj.getSize(): print("Sequence lengths of \'%s\' and \'%s\' are not the same!" % (structurename + chainindicator, rankspath)) missing = 0 for i in range(self.ranksObj.getSize()): try: r = resnumDict[self.ranksObj.getResnum(i)] except KeyError: missing += 1 if missing > 0: print("%d residue numbers in \'%s\' missing in \'%s\'!" % ( missing, rankspath, structurename + chainindicator)) print('...Done.') def mousewheel_roll(self, event): slideval = self.slider.get() # See http://www.daniweb.com/code/snippet217059.html if event.num == 4 or event.delta == -120: self.slider.set(slideval + 1) self.slider_button_release(None) if event.num == 5 or event.delta == 120: self.slider.set(slideval - 1) self.slider_button_release(None) # print event.num, event.delta, slideval def mousebutton_click(self, event): # slideval=self.slider.get() if event.num == 1 or event.num == 2: self.slider_button_release(None) # print event.num, event.delta, slideval def reassignEAranks(self, event): if self.ranksStructureOK: if self.show_action_options.getvalue() == self.action_options_tuple[0]: self.ranksObj.assignRanks(0) elif self.show_action_options.getvalue() == self.action_options_tuple[1]: self.ranksObj.assignRanks(1) elif self.show_action_options.getvalue() == self.action_options_tuple[2]: self.ranksObj.assignRanks(2) self.slider_button_release(event) def slider_button_release(self, event): if self.ranksStructureOK: self.et_messagebox.show() maxcov = 0 maxrank = 0 slideval = self.slider.get() # The following does not work. The colors _et_prism_colorXX are defined only in PyMOL, # not Pmw/Tkinter # self.slider.configure(background=('_et_prism_color%d' % (slideval-0.000001))) if len(self.chainindicator) > 0: structurename = '%s and chain %s' % (self.structurename, self.chainindicator) else: structurename = self.structurename if self.show_et_options.getvalue() == self.et_options_tuple[2]: cmd.hide('spheres', structurename) # Need to hide spheres in case non-CA atoms are displayed for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color(self.etcolor, '%s and resi %s' % (structurename, resnum)) cmd.show('spheres', '%s and resi %s and name CA' % (structurename, resnum)) else: # TODO: Color only the spheres? cmd.color(self.noetcolor, '%s and resi %s' % (structurename, resnum)) cmd.hide('spheres', '%s and resi %s' % (structurename, resnum)) # if self.show_et_var.get()==1: elif self.show_et_options.getvalue() == self.et_options_tuple[1]: # Rong's suggestion # cmd.hide('spheres',structurename) # cmd.show('cartoon',structurename) # cmd.color(self.noetcolor,structurename) for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color(self.etcolor, '%s and resi %s' % (structurename, resnum)) cmd.show('spheres', '%s and resi %s' % (structurename, resnum)) else: # TODO: Color only the spheres? cmd.color(self.noetcolor, '%s and resi %s' % (structurename, resnum)) cmd.hide('spheres', '%s and resi %s' % (structurename, resnum)) elif self.show_et_options.getvalue() == self.et_options_tuple[3]: # Do red green for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color('_et_rg_color%d' % (int(cov - 0.000001)), '%s and resi %s' % (structurename, resnum)) else: cmd.color('white', '%s and resi %s' % (structurename, resnum)) if self.et_colorramp: # print 'show red green ramp' self.et_colorramp.show() elif self.show_et_options.getvalue() == self.et_options_tuple[4]: for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color(self.etcolor, '%s and resi %s' % (structurename, resnum)) cmd.show('sticks', '%s and resi %s' % (structurename, resnum)) else: cmd.color(self.noetcolor, '%s and resi %s' % (structurename, resnum)) cmd.hide('sticks', '%s and resi %s' % (structurename, resnum)) elif self.show_et_options.getvalue() == self.et_options_tuple[5]: # Special mapping for difference ET coverage differentials suggested by Angela for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if cov > maxcov: maxcov = cov maxrank = rank if rank > 0.99999: rank = 0.99999 if rank < -0.99999: rank = -0.99999 if rank > 0.2: cmd.color('_et_red_color%s' % int(10 * (rank - 0.2) / 0.8), '%s and resi %s' % (structurename, resnum)) elif rank < -0.2: cmd.color('_et_blue_color%s' % int(10 * (-rank - 0.2) / 0.8), '%s and resi %s' % (structurename, resnum)) else: cmd.color('white', '%s and resi %s' % (structurename, resnum)) elif self.show_et_options.getvalue() == self.et_options_tuple[6]: # Do Greyscale 09/02/14 for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color('_et_greyscale_color%d' % (int(cov - 0.000001)), '%s and resi %s' % (structurename, resnum)) else: cmd.color('orange', '%s and resi %s' % (structurename, resnum)) elif self.show_et_options.getvalue() == self.et_options_tuple[7]: # Do Prismatic for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color('_et_prism_color%d' % (int(cov - 0.000001)), '%s and resi %s' % (structurename, resnum)) else: cmd.color('white', '%s and resi %s' % (structurename, resnum)) if self.et_colorPrism: # print 'show prismatic ramp' self.et_colorPrism.show() else: # It turns out that calling cmd.color or cmd.select with a list of residues, e.g. 'resi 1+2+...', can crash pymol # if the list is too big (>300) for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color(self.etcolor, '%s and resi %s' % (structurename, resnum)) else: cmd.color(self.noetcolor, '%s and resi %s' % (structurename, resnum)) # See if this is faster # if len(etlist)>0: # cmd.color(self.etcolor,'%s and resi %s' % (structurename,string.join(etlist,'+'))) # if len(notetlist)>0: # cmd.color(self.noetcolor,'%s and resi %s' % (structurename,string.join(noetlist,'+'))) self.percentcoverage.setvalue(maxcov) self.rankvalue.setvalue(maxrank) # Make a selection of the ET residues if self.select_et_var.get() == 1: resnumlist = [] for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: resnumlist.append(resnum) else: # You might want to make a selection for non-ET residues also pass if len(resnumlist) > 0: cmd.select('et_%s_PyETV' % (self.structurename + self.chainindicator), '%s and resi %s' % (structurename, string.join(resnumlist, '+'))) else: cmd.select('et_%s_PyETV' % (self.structurename + self.chainindicator), 'none') self.et_messagebox.withdraw() def showZScores(self): if self.ranksStructureOK: try: self.et_messagebox.show() slideval = self.slider.get() # Get the slider value (ET threshold) early if self.show_qualitymeasure_options.getvalue() == self.qualitymeasure_options_tuple[0]: bias = 0 elif self.show_qualitymeasure_options.getvalue() == self.qualitymeasure_options_tuple[1]: bias = 1 if not self.adjacencyOK: if len(self.chainindicator) > 0: structurename = '%s and chain %s' % (self.structurename, self.chainindicator) else: structurename = self.structurename print("Computing adjacency matrix A(i,j)...") self._A, ResAtoms, self._Ar = self.computeAdjacency(structurename) if self._A == None: self.zscore_et.setvalue('') self.zscore_notet.setvalue('') self.et_messagebox.withdraw() return else: self.adjacencyOK = True print("... done") # Get lists of ET residues et1 = [] notet = [] # slideval=self.slider.get() for i in range(self.ranksObj.getSize()): (resnum1, cov1, rank1) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov1: et1.append(int(resnum1)) else: notet.append(int(resnum1)) print("ET residue selection lists:") print(et1) print("Computing z-scores...") if len(et1) > 0: z1 = self.calcZScore(et1, self.ranksObj.getSize(), self._A, bias) else: z1 = 'NA' if len(notet) > 0: z0 = self.calcZScore(notet, self.ranksObj.getSize(), self._A, bias) else: z0 = 'NA' print("...done") self.zscore_et.setvalue(z1) self.zscore_notet.setvalue(z0) # if len(notet)>0: # print 'Non-ET residue z-score: ', self.calcZScore(notet,self.ranksObj.getSize(),self._A) except Exception as detail: print('An exception occurred in showZScores!') print(detail) self.et_messagebox.withdraw() ########################################################################### ################################# ET ###################################### # Class representing a list of ET ranks (rho), computed coverages, # and residue numbers. class ETRanks: def __init__(self): self.ranksloaded = False def readRanks(self, rankspath): """Read residue rankings from an ET .ranks file, or a .simple file with residue numbers in the first column and ranks on the second column.""" self.resnums = [] self.ranks = [] self.coverages = [] self.ranksloaded = False self.rankspath = rankspath if rankspath[-7:] == '.simple': FILE = open(rankspath, 'r') types = [] # .simple file has no list of amino acid types try: for line in FILE: if line.find('#') == 0: # comment continue cols = line.split() if len(cols) < 2: continue resnum = cols[0].strip() rho = cols[1].strip() if resnum == '-': pass # gap else: self.resnums.append(resnum) self.ranks.append(float(rho)) self.coverages.append(0) finally: FILE.close() else: FILE = open(rankspath, 'r') types = [] split_tup = os.path.splitext(rankspath) if split_tup[-1].lower() == '.ranks': print("ranks file") splitRangeStart = 72 splitRangeEnd = 82 else: print("cov file") splitRangeStart = 82 splitRangeEnd = 92 try: for line in FILE: if line.find('%') == 0: continue if len(line.rstrip()) > 81: resnum = line[10:20].strip() if resnum == '-': pass # gap else: rho = line[splitRangeStart:splitRangeEnd].strip() self.resnums.append(resnum) types.append(line[29]) # One-letter amino acid code self.ranks.append(float(rho)) self.coverages.append(0) # print resnum,rho finally: FILE.close() if len(self.resnums) > 0: self.sequence = string.join(types, '') self.computeCoverage() self.ranksloaded = True # PyMOL already has "spectrum" that can indicate b-factors def getBfactors(self, model): self.resnums = [] self.ranks = [] self.coverages = [] self.ranksloaded = False self.rankspath = "B-factors" resnumBdict = {} for i in range(len(model.atom)): atomobj = model.atom[i] # if atomobj.hetatm==1: # continue try: resnumBdict[atomobj.resi].append(atomobj.b) except KeyError: resnumBdict[atomobj.resi] = [atomobj.b] self.resnums.append(atomobj.resi) for i in range(len(self.resnums)): r = self.resnums[i] bsum = 0 for b in resnumBdict[r]: bsum += b self.ranks.append(bsum * 1.0 / len(resnumBdict[r])) self.coverages.append(0) if len(self.resnums) > 0: # self.sequence=string.join(types,'') self.computeCoverage() self.ranksloaded = True def computeCoverage(self): numres = self.getSize() for i in range(numres): self.coverages[i] = 0 # 12/21/11 for j in range(numres): if self.ranks[i] >= self.ranks[j]: self.coverages[i] += 1 self.coverages[i] = self.coverages[i] * 100.0 / numres def getSize(self): return len(self.resnums) def ranksLoaded(self): return self.ranksloaded def getResnumCoverageRankTuple(self, i): return self.resnums[i], self.coverages[i], self.ranks[i] def getResnum(self, i): return self.resnums[i] def alignToAnotherSequence(self, restypesstring, resnums): """align the sequence in the actions or ranks file to an external sequence e.g. the sequence in a PyMOL structure. Associate the action or rank with the aligned residue in the external sequence """ from Bio import pairwise2 from Bio.pairwise2 import format_alignment from Bio.SubsMat import MatrixInfo as matlist matrix = matlist.blosum62 gap_open = -10 # TODO gap_extend = -0.5 # TODO # for a in pairwise2.align.globaldx(self.sequence,restypesstring,matrix): # print(format_alignment(*a)) topalign = pairwise2.align.globalds(self.sequence, restypesstring, matrix, gap_open, gap_extend)[0] print( "The pairwise alignment with matrix=blosum62 and gap_open=%lf and gap_extend=%lf:" % (gap_open, gap_extend)) print((format_alignment(*topalign))) a1 = topalign[0] a2 = topalign[1] gap = '-' shiftedresnums1 = [None] * len(a1) shiftedcoverages1 = [None] * len(a1) shiftedranks1 = [None] * len(a1) i = 0 for idx, a in enumerate(a1): if a != gap: shiftedresnums1[idx] = self.resnums[i] shiftedcoverages1[idx] = self.coverages[i] shiftedranks1[idx] = self.ranks[i] i += 1 shiftedresnums2 = [None] * len(a2) i = 0 for idx, a in enumerate(a2): if a != gap: shiftedresnums2[idx] = resnums[i] i += 1 self._resnums = [] self._coverages = [] self._ranks = [] for idx, a in enumerate(a1): print(shiftedresnums1[idx], a, shiftedresnums2[idx], a2[idx]) if shiftedresnums1[idx] is not None and shiftedresnums2[idx] is not None: self._resnums.append(shiftedresnums2[idx]) self._coverages.append(shiftedcoverages1[idx]) self._ranks.append(shiftedranks1[idx]) # TEST TODO check zscores # Replacing the original residue numbers self.resnums = self._resnums self.coverages = self._coverages self.ranks = self._ranks class ETControlGroup: # Reuse some functions useful for calculating clustering z-score # (Assignments made outside of a method such as __init__ make 'self' the first parameter) calcDist = _et_calcDist computeAdjacency = _et_computeAdjacency calcZScore = _et_calcZScore computeInterface = _et_computeInterface getPyMOLstructuresequence = _getPyMOLstructuresequence def __init__(self, page, groupname='Trace', defaultstructurename='(pdb)', defaultrankspath='.ranks', defaultslidercoverage=10, defaultetoption=3, defaultqualitymeasure=0, defaultchain='', defaultpartnerstructurename='', etcolor='red', noetcolor='salmon', et_loader_on=True, interface_on=True, et_colorramp=None, et_colorPrism=None, et_messagebox=None): self.etcolor = etcolor self.noetcolor = noetcolor self.et_colorramp = et_colorramp self.et_colorPrism = et_colorPrism self.et_messagebox = et_messagebox group = Pmw.Group(page,tag_text=groupname) # Changing to scrollable frame as a response to Bioinformatics reviewer 08/24/10 '''group = Pmw.ScrolledFrame(page, labelpos='nw', label_text=groupname)''' self.groupname = groupname self.group = group # self.groupscrolled=group group.pack(fill='both', expand=1, padx=10, pady=5) self.balloon = Pmw.Balloon(group.interior()) self.structureframe = tkinter.Frame(group.interior()) # Field for entering name of structure or model self.structure = Pmw.EntryField(self.structureframe, labelpos='w', label_text='structure to use: ', value=defaultstructurename, ) self.chain = Pmw.EntryField(self.structureframe, labelpos='w', label_text='chain: ', value=defaultchain, ) self.structure.grid(column=0, row=0) self.chain.grid(column=1, row=0) def quickFileValidation(s): if s == '': return Pmw.PARTIAL elif os.path.isfile(s): return Pmw.OK elif os.path.exists(s): return Pmw.PARTIAL else: return Pmw.PARTIAL if et_loader_on: # Put ET Loader capability directly into ETControlGroup (03/08/10) self.loadergroup = Pmw.Group(group.interior(), tag_text='(optional) Load structure and precomputed trace') self.pdbnamebox = Pmw.EntryField(self.loadergroup.interior(), labelpos='w', label_text='Enter a 4-digit pdb code + chain id (e.g. 2phyA): ', value='2phyA', ) # Button for assigning ranks to structure self.load_buttonbox = Pmw.ButtonBox(self.loadergroup.interior(), padx=0) self.load_buttonbox.add('Load trace', command=self.loadETVX) self.load_buttonbox.add('View ET Server Page', command=self.viewETServerPage) self.pdbnamebox.pack(fill='x', padx=4, pady=1) # vertical self.load_buttonbox.pack(fill='x', padx=4, pady=1) # vertical self.checksequence_var = IntVar() self.checksequence_var.set(1) self.checksequence_checkbutton = Checkbutton(group.interior(), text="check sequence", variable=self.checksequence_var) self.usebfactor_var = IntVar() self.usebfactor_var.set(0) self.usebfactor_checkbutton = Checkbutton(group.interior(), text="Use b-factor as ranks", variable=self.usebfactor_var) self.checkalignsequences_var = IntVar() self.checkalignsequences_var.set(1) self.checkalignsequences_checkbutton = Checkbutton(group.interior(), text="align input sequence to the structure", variable=self.checkalignsequences_var) # Button for assigning ranks to structure self.map_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.map_buttonbox.add('Map ranks to structure', command=self.mapRanks) # Field for entering ranks file self.ranksfile = Pmw.EntryField(group.interior(), labelpos='w', label_pyclass=FileDialogButtonClassFactory.get(self.setRanksFileLocation,'*'), validate={'validator': quickFileValidation, }, value=defaultrankspath, # entry_width=50, #This value is set for the sole purpose of making the width of the plugin dialog box large enough label_text='ET ranks/Cov file path:') # Tkinter Slider Tkinterfor changing ET residue coverage. # TODO: Use a Pmw implementation? self.slider = Scale(group.interior(), # from_=self.min, to=self.max, from_=0, to=100, showvalue=1, length=175, orient=HORIZONTAL, resolution=0.01, tickinterval=0, # repeatinterval=500, #Dunno what repeatinterval is for... repeatdelay=500 ) self.slider.set(defaultslidercoverage) # self.slider.grid() self.slider.bind("", self.slider_button_release) # self.slider.bind("", self.mousebutton_click) self.slider.bind("", self.mousebutton_click) # For Windows self.slider.bind("", self.mousewheel_roll) # For Linux (for Mac?) self.slider.bind("", self.mousewheel_roll) self.slider.bind("", self.mousewheel_roll) # self.slider.bind("", self.slider_button_release) ## Triggered when the mouse enters a widget ## ## Triggered when a left click is done in a widget ##, <1> ## Triggered when the mouse is dragged over ## ## the widget with the left mouse button being ## held down. ## Triggered when a widget is double-clicked ## ## with the left mouse button ## Triggered when the key producing the letter ##, , , A ## A (caps) is pressed. # Field for displaying ET coverage self.frame1 = tkinter.Frame(group.interior()) self.percentcoverage = Pmw.EntryField(self.frame1, # group.interior(), labelpos='w', label_text='Percent coverage: ', value='', ) self.rankvalue = Pmw.EntryField(self.frame1, # group.interior(), labelpos='w', label_text='Rank/Cov: ', value='', ) self.percentcoverage.grid(column=0, row=0) self.rankvalue.grid(column=1, row=0) self.frame2 = tkinter.Frame(group.interior()) self.et_options_tuple = ('Colors only(' + self.etcolor + ')', 'as Spheres', 'as Spheres (C-alpha only)', 'Red_to_Green', 'as Sticks', 'Map -1 to +1 to blue-white-red', 'Greyscale', 'Prismatic (Gobstopper)') self.show_et_options = Pmw.OptionMenu(self.frame2, # group.interior(), labelpos='w', label_text='Show ET residues', items=self.et_options_tuple, initialitem=self.et_options_tuple[defaultetoption], command=self.slider_button_release ) ## self.show_et_var=IntVar() ## self.show_et_var.set(0) ## self.show_et_checkbutton = Checkbutton(group.interior(), ## text = "Show ET residues (as spheres)", ## variable = self.show_et_var) self.select_et_var = IntVar() self.select_et_var.set(0) self.select_et_checkbutton = Checkbutton(self.frame2, # group.interior(), text="Select ET residues", variable=self.select_et_var) self.show_et_options.grid(column=0, row=0) self.select_et_checkbutton.grid(column=1, row=0) # self.ETcolor_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) #06/10/11 Experimenting with tkColorChooser # self.ETcolor_buttonbox.add('Choose ET color',command=self.chooseETcolor) self.qualitymeasure_options_tuple = ('3D nobias', '3D bias (j-i)') self.show_qualitymeasure_options = Pmw.OptionMenu(group.interior(), labelpos='w', label_text='quality measure: ', items=self.qualitymeasure_options_tuple, initialitem=self.qualitymeasure_options_tuple[ defaultqualitymeasure], ) self.zscore_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.zscore_buttonbox.add('Compute z-scores', command=self.showZScores) self.zscore_buttonbox.add('Average neighbor ranks', command=self.averageNeighborRanks) self.zscore_et = Pmw.EntryField(group.interior(), labelpos='w', label_text='z-score ET residues: ', value='', ) self.zscore_notet = Pmw.EntryField(group.interior(), labelpos='w', label_text='z-score non-ET residues: ', value='', ) if interface_on: # Put Interface/binding site search capability into ETControlGroup (05/18/10) self.interfacegroup = Pmw.Group(group.interior(), tag_text='Find interface with the next structure/molecule') self.partnerstructureframe = tkinter.Frame(self.interfacegroup.interior()) # Field for entering name of structure or model self.partnerstructure = Pmw.EntryField(self.partnerstructureframe, labelpos='w', label_text='structure: ', value=defaultpartnerstructurename, ) self.partnerchain = Pmw.EntryField(self.partnerstructureframe, labelpos='w', label_text='chain: ', value='', ) self.partnerstructure.grid(column=0, row=0) self.partnerchain.grid(column=1, row=0) self.distance = Pmw.EntryField(self.interfacegroup.interior(), labelpos='w', label_text='distance to use for interface: ', validate={'validator': 'real', 'min': 1, 'max': 20}, value=4, ) self.mark_buttonbox = Pmw.ButtonBox(self.interfacegroup.interior(), padx=0) self.mark_buttonbox.add('Mark interface', command=self.markInterface) self.interface_options_tuple = ( # 'Colors only('+self.interfacecolor1+')', 'as Spheres', 'as Sticks', 'as Selection', 'None') self.show_interface_options = Pmw.OptionMenu(self.interfacegroup.interior(), labelpos='w', label_text='Show interface residues', items=self.interface_options_tuple, initialitem=self.interface_options_tuple[0], command=self.updateInterface # Need two arguments for this method ) self.partnerstructureframe.pack(fill='x', padx=4, pady=1) self.distance.pack(fill='x', padx=4, pady=1) self.mark_buttonbox.pack(fill='x', padx=4, pady=1) self.show_interface_options.pack(fill='x', padx=4, pady=1) if et_loader_on: self.loadergroup.pack(fill='x', padx=4, pady=1) for entry in (self.structureframe, self.ranksfile, self.checksequence_checkbutton, self.usebfactor_checkbutton, self.checkalignsequences_checkbutton, self.map_buttonbox, self.slider, self.frame1, self.frame2, # self.percentcoverage, # self.rankvalue, # self.show_et_checkbutton, # self.show_et_options, # self.select_et_checkbutton, # self.ETcolor_buttonbox, self.zscore_buttonbox, self.show_qualitymeasure_options, self.zscore_et, self.zscore_notet): entry.pack(fill='x', padx=4, pady=1) # vertical if interface_on: self.interfacegroup.pack(fill='x', padx=4, pady=1) # Tool tips (help) for user-interface components and boxes self.balloon.bind(self.structure, "Enter a name from the list of objects in the PyMOL Viewer") self.balloon.bind(self.ranksfile, "Click to open a box for navigating and choosing a file") self.balloon.bind(self.checksequence_checkbutton, "Check this box to verify if the sequence in the structure and ranks file match after mapping ranks to structure") self.balloon.bind(self.usebfactor_checkbutton, "Check this box to use the B factor or the temperature factor, averaged over the residue's atoms, as ET ranks") self.balloon.bind(self.checkalignsequences_checkbutton, "Check this box to align the amino acid sequence in your ranks file with the sequence of the PyMOL structure. Requires Biopython installation.") self.balloon.bind(self.map_buttonbox, "Click to map rank data onto the structure. Done automatically when doing 'Load trace'") self.balloon.bind(self.slider, "Drag slider to vary ET residue selection and coverage of the structure") self.balloon.bind(self.percentcoverage, "Maximum percent-rank (or percentile-rank) in the ET residue selection") self.balloon.bind(self.rankvalue, "Maximum raw ET rank score in the ET residue selection") self.balloon.bind(self.show_et_options, "Select display style to distinguish ET residue selection from the rest of the structure") self.balloon.bind(self.select_et_checkbutton, "Check box to create a PyMOL selection of the ET residues") self.balloon.bind(self.zscore_buttonbox, "Compute the clustering z-score of the ET residue selection") self.balloon.bind(self.show_qualitymeasure_options, "Select from several measures of clustering quality") if et_loader_on: self.balloon.bind(self.loadergroup, "Use this to download a PDB chain and precomputed ET rank data") self.balloon.bind(self.load_buttonbox.button(0), "Click to start download") self.balloon.bind(self.load_buttonbox.button(1), "Click to view the ET server entry for this structure if it exists") if interface_on: self.balloon.bind(self.partnerstructure, "A structure with this name must exist from the list of objects in the PyMOL Viewer!") self.balloon.bind(self.distance, "Maximum inter-residue atom-atom distance (Angstroms)") self.balloon.bind(self.mark_buttonbox, "Click to start interface calculation and display") self.balloon.bind(self.show_interface_options, "Select display style to distinguish interface residues from the rest of the structure") self.ranksObj = ETRanks() self.ranksStructureOK = False self.adjacencyOK = False self.interfaceComputed = False self.et_loader_on = et_loader_on self.zscore_button_bg = self.zscore_buttonbox.button(0).cget('background') self.zscore_button_state = self.zscore_buttonbox.button(0).cget('state') # The defaults for zscore_buttonbox could instead be used self.mark_button_bg = self.mark_buttonbox.button(0).cget('background') self.mark_button_state = self.mark_buttonbox.button(0).cget('state') def setRanksObj(self, ranksObj_external): """Ranks file has been read without calling mapRanks. Use the externally-created ranksObj""" structurename = self.structure.getvalue().strip() chainindicator = self.chain.getvalue().strip() self.structurename = structurename self.chainindicator = chainindicator self.ranksStructureOK = True self.ranksObj = ranksObj_external # self.setRanksFileLocation(self.ranksObj.rankspath) # self.slider_button_release(None) # 06/10/11 Experimenting with tkColorChooser def chooseETcolor(self): if self.ranksStructureOK: print(tkinter.colorchooser.askcolor(title="Pick a color for ET residues", parent=self.group.interior())) def mapRanks(self): structurename = self.structure.getvalue().strip() supper = structurename.upper() for n in cmd.get_names('all'): if supper == n.upper(): break else: print('structure name must be in PyMOL viewer list:') print(cmd.get_names('all')) return chainindicator = self.chain.getvalue().strip() self.ranksStructureOK = False self.adjacencyOK = False if len(structurename) < 1: print('Provide structure name!') return try: model = cmd.get_model(structurename) except Exception: print("Structure \'%s\' does not exist!" % structurename) return if self.usebfactor_var.get() == 1: print("Using %s B-factors as ranks" % structurename) self.ranksObj.getBfactors(model) else: rankspath = self.ranksfile.getvalue().strip() if len(rankspath) < 1: print('Provide path to ranks file!') return self.ranksObj.readRanks(rankspath) if self.ranksObj.ranksLoaded(): print("Ranks file \'%s\' loaded" % rankspath) else: print("Error loading ranks file \'%s\'!" % rankspath) return if self.checksequence_var.get() == 1: self.checkSequence(model, structurename, chainindicator, rankspath) # TODO TEST 08/28/14 if self.checkalignsequences_var.get() == 1: (pymolrestypes, pymolresnums) = self.getPyMOLstructuresequence(model, structurename, chainindicator) print("Aligning the sequence in %s with the sequence in the PyMOL structure %s %s" % ( rankspath, structurename, chainindicator)) # print pymolrestypes, 'n', pymolresnums try: # DEBUG self.ranksObj.alignToAnotherSequence(string.join(pymolrestypes, ''), pymolresnums) except Exception as detail: print("An exception occurred while aligning sequences!") print(detail) return self.structurename = structurename self.chainindicator = chainindicator self.ranksStructureOK = True self.recomputeInterface = True # For CouplingGroup self.slider_button_release(None) # This check uses the residue numbers, not the amino acid types def checkSequence(self, model, structurename, chainindicator, rankspath): three2one = { "ALA": 'A', "ARG": 'R', "ASN": 'N', "ASP": 'D', "CYS": 'C', "GLN": 'Q', "GLU": 'E', "GLY": 'G', "HIS": 'H', "ILE": 'I', "LEU": 'L', "LYS": 'K', "MET": 'M', "PHE": 'F', "PRO": 'P', "SER": 'S', "THR": 'T', "TRP": 'W', "TYR": 'Y', "VAL": 'V', "A": "A", "G": "G", "T": "T", "U": "U", "C": "C", } print('Comparing residue numbers of structure \'%s\' and ranks \'%s\'...' % (structurename + chainindicator, rankspath)) # Check that the residue numbers in the model # and in the ranks file are identical resnumDict = {} if len(chainindicator) > 0: # chainup=chainindicator.upper() # Case of chain indicator is relevant for i in range(len(model.atom)): atomobj = model.atom[i] if chainindicator == atomobj.chain: try: aa1 = three2one[atomobj.resn] # Consider only residues with standard amino acids resnumDict[atomobj.resi] = 1 except KeyError: pass else: for i in range(len(model.atom)): resnumDict[model.atom[i].resi] = 1 print('Sequence lengths:') print('structure: ', len(resnumDict)) print('ranks: ', self.ranksObj.getSize()) if len(resnumDict) < 1: print('Structure \'%s\' has no residues!' % (structurename + chainindicator)) if len(resnumDict) != self.ranksObj.getSize(): print("Sequence lengths of \'%s\' and \'%s\' are not the same!" % (structurename + chainindicator, rankspath)) missing = 0 for i in range(self.ranksObj.getSize()): try: r = resnumDict[self.ranksObj.getResnum(i)] except KeyError: missing += 1 if missing > 0: print("%d residue numbers in \'%s\' missing in \'%s\'!" % ( missing, rankspath, structurename + chainindicator)) print('...Done.') def mousewheel_roll(self, event): slideval = self.slider.get() # See http://www.daniweb.com/code/snippet217059.html if event.num == 4 or event.delta == -120: self.slider.set(slideval + 1) self.slider_button_release(None) if event.num == 5 or event.delta == 120: self.slider.set(slideval - 1) self.slider_button_release(None) # print event.num, event.delta, slideval def mousebutton_click(self, event): # slideval=self.slider.get() if event.num == 1 or event.num == 2: self.slider_button_release(None) # print event.num, event.delta, slideval def slider_button_release(self, event): if self.ranksStructureOK: self.et_messagebox.show() maxcov = 0 maxrank = 0 slideval = self.slider.get() # The following does not work. The colors _et_prism_colorXX are defined only in PyMOL, # not Pmw/Tkinter # self.slider.configure(background=('_et_prism_color%d' % (slideval-0.000001))) if len(self.chainindicator) > 0: structurename = '%s and chain %s' % (self.structurename, self.chainindicator) else: structurename = self.structurename if self.show_et_options.getvalue() == self.et_options_tuple[2]: cmd.hide('spheres', structurename) # Need to hide spheres in case non-CA atoms are displayed for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color(self.etcolor, '%s and resi %s' % (structurename, resnum)) cmd.show('spheres', '%s and resi %s and name CA' % (structurename, resnum)) else: # TODO: Color only the spheres? cmd.color(self.noetcolor, '%s and resi %s' % (structurename, resnum)) cmd.hide('spheres', '%s and resi %s' % (structurename, resnum)) # if self.show_et_var.get()==1: elif self.show_et_options.getvalue() == self.et_options_tuple[1]: # Rong's suggestion # cmd.hide('spheres',structurename) # cmd.show('cartoon',structurename) # cmd.color(self.noetcolor,structurename) for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color(self.etcolor, '%s and resi %s' % (structurename, resnum)) cmd.show('spheres', '%s and resi %s' % (structurename, resnum)) else: # TODO: Color only the spheres? cmd.color(self.noetcolor, '%s and resi %s' % (structurename, resnum)) cmd.hide('spheres', '%s and resi %s' % (structurename, resnum)) elif self.show_et_options.getvalue() == self.et_options_tuple[3]: # Do red green for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color('_et_rg_color%d' % (int(cov - 0.000001)), '%s and resi %s' % (structurename, resnum)) else: cmd.color('white', '%s and resi %s' % (structurename, resnum)) if self.et_colorramp: # print 'show red green ramp' self.et_colorramp.show() elif self.show_et_options.getvalue() == self.et_options_tuple[4]: for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color(self.etcolor, '%s and resi %s' % (structurename, resnum)) cmd.show('sticks', '%s and resi %s' % (structurename, resnum)) else: cmd.color(self.noetcolor, '%s and resi %s' % (structurename, resnum)) cmd.hide('sticks', '%s and resi %s' % (structurename, resnum)) elif self.show_et_options.getvalue() == self.et_options_tuple[5]: # Special mapping for difference ET coverage differentials suggested by Angela for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if cov > maxcov: maxcov = cov maxrank = rank if rank > 0.99999: rank = 0.99999 if rank < -0.99999: rank = -0.99999 if rank > 0.2: cmd.color('_et_red_color%s' % int(10 * (rank - 0.2) / 0.8), '%s and resi %s' % (structurename, resnum)) elif rank < -0.2: cmd.color('_et_blue_color%s' % int(10 * (-rank - 0.2) / 0.8), '%s and resi %s' % (structurename, resnum)) else: cmd.color('white', '%s and resi %s' % (structurename, resnum)) elif self.show_et_options.getvalue() == self.et_options_tuple[6]: # Do Greyscale 09/02/14 for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color('_et_greyscale_color%d' % (int(cov - 0.000001)), '%s and resi %s' % (structurename, resnum)) else: cmd.color('orange', '%s and resi %s' % (structurename, resnum)) elif self.show_et_options.getvalue() == self.et_options_tuple[7]: # Do Prismatic for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color('_et_prism_color%d' % (int(cov - 0.000001)), '%s and resi %s' % (structurename, resnum)) else: cmd.color('white', '%s and resi %s' % (structurename, resnum)) if self.et_colorPrism: # print 'show prismatic ramp' self.et_colorPrism.show() else: # It turns out that calling cmd.color or cmd.select with a list of residues, e.g. 'resi 1+2+...', can crash pymol # if the list is too big (>300) for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color(self.etcolor, '%s and resi %s' % (structurename, resnum)) else: cmd.color(self.noetcolor, '%s and resi %s' % (structurename, resnum)) # See if this is faster # if len(etlist)>0: # cmd.color(self.etcolor,'%s and resi %s' % (structurename,string.join(etlist,'+'))) # if len(notetlist)>0: # cmd.color(self.noetcolor,'%s and resi %s' % (structurename,string.join(noetlist,'+'))) self.percentcoverage.setvalue(maxcov) self.rankvalue.setvalue(maxrank) # Make a selection of the ET residues if self.select_et_var.get() == 1: resnumlist = [] for i in range(self.ranksObj.getSize()): (resnum, cov, rank) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov: resnumlist.append(resnum) else: # You might want to make a selection for non-ET residues also pass if len(resnumlist) > 0: cmd.select('et_%s_PyETV' % (self.structurename + self.chainindicator), '%s and resi %s' % (structurename, string.join(resnumlist, '+'))) else: cmd.select('et_%s_PyETV' % (self.structurename + self.chainindicator), 'none') self.et_messagebox.withdraw() def setRanksFileLocation(self, value): self.ranksfile.setvalue(value) def getETselection(self): """Get selection of ET residues at the current slider (percentile) setting""" et1 = [] if self.ranksStructureOK: slideval = self.slider.get() for i in range(self.ranksObj.getSize()): (resnum1, cov1, rank1) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov1: et1.append(int(resnum1)) else: pass # notet.append(int(resnum1)) return et1 # list of ints of residue numbers # Threading as a response to reviewers 08/24/10 if _ET_THREADING: def showZScores(self): if self.ranksStructureOK: self.zscore_buttonbox.button(0).configure(state=DISABLED) if self.et_loader_on: self.load_buttonbox.button(0).configure(state=DISABLED, background='red') self.map_buttonbox.button(0).configure(state=DISABLED, background='red') self.zscoreBusyDoneEvent = Event() self.zscoreDoneEvent = Event() tm = Thread(target=self.zscoreBusyMessage) tm.start() tz = Thread(target=self.showZScores_run) tz.start() else: def showZScores(self): if self.ranksStructureOK: try: self.et_messagebox.show() slideval = self.slider.get() # Get the slider value (ET threshold) early if self.show_qualitymeasure_options.getvalue() == self.qualitymeasure_options_tuple[0]: bias = 0 elif self.show_qualitymeasure_options.getvalue() == self.qualitymeasure_options_tuple[1]: bias = 1 if not self.adjacencyOK: if len(self.chainindicator) > 0: structurename = '%s and chain %s' % (self.structurename, self.chainindicator) else: structurename = self.structurename print("Computing adjacency matrix A(i,j)...") self._A, ResAtoms, self._Ar = self.computeAdjacency(structurename) self._L = len( ResAtoms) # 10/24/12: Peg this to the number of amino acids in the structure, not the number in the ranks file! if self._A == None: self.zscore_et.setvalue('') self.zscore_notet.setvalue('') self.et_messagebox.withdraw() return else: self.adjacencyOK = True print("... done") # Get lists of ET residues et1 = [] notet = [] # slideval=self.slider.get() for i in range(self.ranksObj.getSize()): (resnum1, cov1, rank1) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov1: et1.append(int(resnum1)) else: notet.append(int(resnum1)) # Temporary for grant 10/24/12 ## et1=[44,128,298,73,291,292,272,300, ## 75,307,134,250,138,226,139,230,51,136,55,110,78, ## 135,215,223,267,268,296,306,302, ## 303,79,265,80,121,113,125,124,161,171,174,167,295] print("ET residue selection lists:") print(et1) print("Computing z-scores...") if len(et1) > 0: # z1=self.calcZScore(et1,self.ranksObj.getSize(),self._A,bias) z1 = self.calcZScore(et1, self._L, self._A, bias) else: z1 = 'NA' if len(notet) > 0: # z0=self.calcZScore(notet,self.ranksObj.getSize(),self._A,bias) z0 = self.calcZScore(notet, self._L, self._A, bias) else: z0 = 'NA' print("...done") self.zscore_et.setvalue(z1) self.zscore_notet.setvalue(z0) # if len(notet)>0: # print 'Non-ET residue z-score: ', self.calcZScore(notet,self.ranksObj.getSize(),self._A) except Exception as detail: print('An exception occurred in showZScores!') print(detail) self.et_messagebox.withdraw() ####################### 12/21/11 def averageNeighborRanks(self): if self.ranksStructureOK: try: self.et_messagebox.show() if not self.adjacencyOK: if len(self.chainindicator) > 0: structurename = '%s and chain %s' % (self.structurename, self.chainindicator) else: structurename = self.structurename print("Computing adjacency matrix A(i,j)...") self._A, ResAtoms, self._Ar = self.computeAdjacency(structurename) if self._A == None: self.et_messagebox.withdraw() return else: self.adjacencyOK = True print("... done") self.calcAverageNeighborRanks() print("...done") except Exception as detail: print('An exception occurred in averageNeighborRanks!') print(detail) self.et_messagebox.withdraw() def calcAverageNeighborRanks(self): # Build dictionary (resnum,i) resindex = {} tmpranks = [0] * self.ranksObj.getSize() for i in range(self.ranksObj.getSize()): (resnum1, cov1, rank1) = self.ranksObj.getResnumCoverageRankTuple(i) resindex[int(resnum1)] = i tmpranks[i] = rank1 for i in range(self.ranksObj.getSize()): ranki = tmpranks[i] resi = int(self.ranksObj.getResnum(i)) try: neighborsj = self._A[resi] for resj in neighborsj: j = resindex[resj] rankj = tmpranks[j] ranki += rankj except KeyError: neighborsj = [] try: neighborsj2 = self._Ar[resi] for resj in neighborsj2: j = resindex[resj] rankj = tmpranks[j] ranki += rankj except KeyError: neighborsj2 = [] nall = len(neighborsj) + len(neighborsj2) if nall > 0: self.ranksObj.ranks[i] = ranki / (nall + 1.0) # Update coverage self.ranksObj.computeCoverage() # Update display self.slider_button_release(None) print("ET ranks have been modified!") ####################### def zscoreBusyMessage(self): tog = True # Loop until showZScores_run finishes with calculation while not self.zscoreDoneEvent.isSet(): if tog: self.zscore_buttonbox.button(0).configure(background='green') # self.zscore_et.setvalue('PROCESSING...') # self.zscore_notet.setvalue('PROCESSING...') else: self.zscore_buttonbox.button(0).configure(background=self.zscore_button_bg) # self.zscore_et.setvalue('') # self.zscore_notet.setvalue('') tog = not tog time.sleep(0.5) self.zscore_buttonbox.button(0).configure(background=self.zscore_button_bg) # Notify showZScores_run that pulsing message has ended self.zscoreBusyDoneEvent.set() def showZScores_run(self): try: if 1: # if self.ranksStructureOK: slideval = self.slider.get() # Get the slider value (ET threshold) early if self.show_qualitymeasure_options.getvalue() == self.qualitymeasure_options_tuple[0]: bias = 0 elif self.show_qualitymeasure_options.getvalue() == self.qualitymeasure_options_tuple[1]: bias = 1 if not self.adjacencyOK: if len(self.chainindicator) > 0: structurename = '%s and chain %s' % (self.structurename, self.chainindicator) else: structurename = self.structurename print("Computing adjacency matrix A(i,j)...") self._A, ResAtoms, self._Ar = self.computeAdjacency(structurename) if self._A == None: self.zscoreDoneEvent.set() self.zscoreBusyDoneEvent.wait(5) self.zscore_et.setvalue('') self.zscore_notet.setvalue('') self.zscore_buttonbox.button(0).configure(state=self.zscore_button_state, background=self.zscore_button_bg) if self.et_loader_on: self.load_buttonbox.button(0).configure(state=self.zscore_button_state, background=self.zscore_button_bg) self.map_buttonbox.button(0).configure(state=self.zscore_button_state, background=self.zscore_button_bg) return else: self.adjacencyOK = True print("... done") # Get lists of ET residues et1 = [] notet = [] # slideval=self.slider.get() for i in range(self.ranksObj.getSize()): (resnum1, cov1, rank1) = self.ranksObj.getResnumCoverageRankTuple(i) if slideval >= cov1: et1.append(int(resnum1)) else: notet.append(int(resnum1)) print("ET residue selection lists:") print(et1) print("Computing z-scores...") if len(et1) > 0: z1 = self.calcZScore(et1, self.ranksObj.getSize(), self._A, bias) else: z1 = 'NA' if len(notet) > 0: z0 = self.calcZScore(notet, self.ranksObj.getSize(), self._A, bias) else: z0 = 'NA' print("...done") self.zscoreDoneEvent.set() # Make sure zscoreBusyMessage ends so z-scores # on text/entry fields don't get overwritten self.zscoreBusyDoneEvent.wait(5) self.zscore_et.setvalue(z1) self.zscore_notet.setvalue(z0) # if len(notet)>0: # print 'Non-ET residue z-score: ', self.calcZScore(notet,self.ranksObj.getSize(),self._A) except Exception as detail: print('An exception occurred in showZScores_run!') print(detail) self.zscoreDoneEvent.set() # Place inside a "finally" clause? self.zscore_buttonbox.button(0).configure(state=self.zscore_button_state, background=self.zscore_button_bg) if self.et_loader_on: self.load_buttonbox.button(0).configure(state=self.zscore_button_state, background=self.zscore_button_bg) self.map_buttonbox.button(0).configure(state=self.zscore_button_state, background=self.zscore_button_bg) def loadETVX(self): self.et_messagebox.show() etvxurl = 'http://mammoth.bcm.tmc.edu/ETserver2/pdbeasytrace/' # self.etvxurlbox.getvalue().strip() pdb_chain = self.pdbnamebox.getvalue().strip()[:5] print('Retrieving ' + pdb_chain + '.etvx from ' + etvxurl) try: tmpetvxpath = urllib.request.urlretrieve(etvxurl + pdb_chain + '.etvx')[0] except Exception: print('Error in retrieving trace data! Please check your internet connection.') self.et_messagebox.withdraw() return print(tmpetvxpath) if os.path.getsize(tmpetvxpath) == 0: print(etvxurl + pdb_chain + '.etvx not found') self.et_messagebox.withdraw() return print('Extracting query pdb structure') pdbfilename = self.extractPDB(tmpetvxpath, pdb_chain) if pdbfilename == None: print('Missing structure.', etvxurl + pdb_chain + '.etvx likely non-existent') self.et_messagebox.withdraw() return print(pdbfilename) print('Extracting ranks file') ranksfilename = self.extractRanks(tmpetvxpath, pdb_chain) print(ranksfilename) cmd.load(pdbfilename, object=pdb_chain) self.setRanksFileLocation(ranksfilename) self.structure.setvalue(pdb_chain) self.chain.setvalue('') # Let PyETV (or ET Tools) know about this trace... # cmd._et_tools_structurename=pdb_chain # cmd._et_tools_rankspath1=ranksfilename self.mapRanks() self.et_messagebox.withdraw() def extractPDB(self, etvxpath, pdb_chain): # Get the ATOM records FILE = open(etvxpath, 'r') data = '' try: for line in FILE: if line[:4] == 'ATOM': data += line # TODO: Stop when pdb section is exhausted? finally: FILE.close() if len(data) == 0: return None # Write ATOM lines to file pdbfilename = os.path.dirname(etvxpath) + os.sep + 'query_' + pdb_chain + '.pdb' FILE_PDB = open(pdbfilename, 'w') FILE_PDB.write(data) FILE_PDB.close() return pdbfilename def extractRanks(self, etvxpath, pdb_chain): # Get the ranks section FILE = open(etvxpath, 'r') data = '' ready = False try: for line in FILE: if line[:5] == '~tree': break if ready: data += line if line[:9] == '~ET_ranks': ready = True finally: FILE.close() # Write ranks section to file ranksfilename = os.path.dirname(etvxpath) + os.sep + pdb_chain + '.ranks' FILE_RANKS = open(ranksfilename, 'w') FILE_RANKS.write(data) FILE_RANKS.close() return ranksfilename def viewETServerPage(self): tv = Thread(target=self.viewETServerPage_run) tv.start() def viewETServerPage_run(self): pdb = self.pdbnamebox.getvalue().strip()[:4] import webbrowser webbrowser.open('http://mammoth.bcm.tmc.edu/cgi-bin/report_maker_ls/traceServerResults.pl?identifier=%s' % pdb) if _ET_THREADING: def markInterface(self): if self.ranksStructureOK: self.mark_buttonbox.button(0).configure(state=DISABLED) self.markBusyDoneEvent = Event() self.markDoneEvent = Event() tm = Thread(target=self.markBusyMessage) tm.start() ti = Thread(target=self.markInterface_run) ti.start() else: def markInterface(self): if self.ranksStructureOK: try: chainindicator1 = self.chain.getvalue().strip() structname = self.structure.getvalue().strip() supper = structname.upper() for n in cmd.get_names('all'): if supper == n.upper(): break else: print('structure name must be in PyMOL viewer list:') print(cmd.get_names('all')) return if len(chainindicator1) > 0: structurename1 = structname + ' and chain %s' % chainindicator1 else: structurename1 = structname chainindicator2 = self.partnerchain.getvalue().strip() pstructname = self.partnerstructure.getvalue().strip() psupper = pstructname.upper() for n in cmd.get_names('all'): if psupper == n.upper(): break else: print('partner structure name must be in PyMOL viewer list:') print(cmd.get_names('all')) return if len(chainindicator2) > 0: structurename2 = pstructname + ' and chain %s' % chainindicator2 else: structurename2 = pstructname dist = float(self.distance.getvalue().strip()) self.et_messagebox.show() # In self.interface1, each residue indexes into an array of neighboring residues in the other structure (self.interface1, self.interface2, self.ResAtoms1, self.ResAtoms2) = self.computeInterface(structurename1, structurename2, dist * dist) if (self.interface1 is None) or (self.interface2 is None): print('Interfaces not computed') self.interfaceComputed = False self.et_messagebox.withdraw() return self.interfaceComputed = True print("%d interface residues in %s" % (len(self.interface1), structurename1)) print("%d interface residues in %s" % (len(self.interface2), structurename2)) print("Adjacency lists:") print(structurename1, self.interface1) print(structurename2, self.interface2) self.updateInterface(None) except Exception as detail: print('An exception occurred in markInterface!') print(detail) self.et_messagebox.withdraw() def markBusyMessage(self): tog = True # Loop until markInterface_run finishes with calculation while not self.markDoneEvent.isSet(): if tog: self.mark_buttonbox.button(0).configure(background='green') else: self.mark_buttonbox.button(0).configure(background=self.mark_button_bg) tog = not tog time.sleep(0.5) self.mark_buttonbox.button(0).configure(background=self.mark_button_bg) # Notify markInterface_run that pulsing message has ended self.markBusyDoneEvent.set() def markInterface_run(self): # Response to reviewer 08/24/10 try: chainindicator1 = self.chain.getvalue().strip() structname = self.structure.getvalue().strip() supper = structname.upper() for n in cmd.get_names('all'): if supper == n.upper(): break else: print('structure name must be in PyMOL viewer list:') print(cmd.get_names('all')) self.markDoneEvent.set() self.markBusyDoneEvent.wait(5) self.mark_buttonbox.button(0).configure(state=self.mark_button_state, background=self.mark_button_bg) return if len(chainindicator1) > 0: structurename1 = structname + ' and chain %s' % chainindicator1 else: structurename1 = structname chainindicator2 = self.partnerchain.getvalue().strip() pstructname = self.partnerstructure.getvalue().strip() psupper = pstructname.upper() for n in cmd.get_names('all'): if psupper == n.upper(): break else: print('partner structure name must be in PyMOL viewer list:') print(cmd.get_names('all')) self.markDoneEvent.set() self.markBusyDoneEvent.wait(5) self.mark_buttonbox.button(0).configure(state=self.mark_button_state, background=self.mark_button_bg) return if len(chainindicator2) > 0: structurename2 = pstructname + ' and chain %s' % chainindicator2 else: structurename2 = pstructname dist = float(self.distance.getvalue().strip()) # These are redundant. 08/29/10 ## if len(self.structure.getvalue().strip())<1: ## print 'Provide structure 1 name!' ## self.mark_buttonbox.button(0).configure(state=self.mark_button_state, ## background=self.mark_button_bg) ## return ## if len(self.partnerstructure.getvalue().strip())<1: ## print 'Provide structure 2 name!' ## self.mark_buttonbox.button(0).configure(state=self.mark_button_state, ## background=self.mark_button_bg) ## return # In self.interface1, each residue indexes into an array of neighboring residues in the other structure (self.interface1, self.interface2, self.ResAtoms1, self.ResAtoms2) = self.computeInterface(structurename1, structurename2, dist * dist) if (self.interface1 is None) or (self.interface2 is None): print('Interfaces not computed') self.interfaceComputed = False self.markDoneEvent.set() self.markBusyDoneEvent.wait(5) self.mark_buttonbox.button(0).configure(state=self.mark_button_state, background=self.mark_button_bg) return self.interfaceComputed = True print("%d interface residues in %s" % (len(self.interface1), structurename1)) print("%d interface residues in %s" % (len(self.interface2), structurename2)) print("Adjacency lists:") print(structurename1, self.interface1) print(structurename2, self.interface2) self.updateInterface(None) except Exception as detail: print('An exception occurred in markInterface_run!') print(detail) # self.markDoneEvent.set() self.markDoneEvent.set() self.markBusyDoneEvent.wait(5) self.mark_buttonbox.button(0).configure(state=self.mark_button_state, background=self.mark_button_bg) def updateInterface(self, event): # TODO: Make this method more aware of changes in the viewer if self.interfaceComputed == False: return s1 = self.structure.getvalue().strip() s2 = self.partnerstructure.getvalue().strip() c1 = self.chain.getvalue().strip() c2 = self.partnerchain.getvalue().strip() if len(c1) > 0: structurename1 = s1 + ' and chain %s' % c1 else: structurename1 = s1 if len(c2) > 0: structurename2 = s2 + ' and chain %s' % c2 else: structurename2 = s2 ## if self.show_interface_options1.getvalue()==self.interface_options_tuple[0]: ## for res in self.interface1.keys(): ## cmd.color(self.interfacecolor1,'%s and resi %s' % (structurename1,res)) if self.show_interface_options.getvalue() == self.interface_options_tuple[0]: for res in list(self.interface1.keys()): cmd.show('spheres', '%s and resi %s' % (structurename1, res)) elif self.show_interface_options.getvalue() == self.interface_options_tuple[1]: for res in list(self.interface1.keys()): cmd.show('sticks', '%s and resi %s' % (structurename1, res)) elif self.show_interface_options.getvalue() == self.interface_options_tuple[2]: # Make a selection of the ET residues if len(self.interface1) > 0: cmd.select('%s_%s_PyETV' % (s1 + c1, s2 + c2), '%s and resi %s' % (structurename1, string.join(list(map(str, self.interface1)), '+'))) else: cmd.select('%s_%s_PyETV' % (s1 + c1, s2 + c2), 'none') ##################################################################### # Assembly # 1. Get multimer structure from PISA # 2. Get ranks files of every unique chain from mammoth pdbeasytrace # 3. Map ranks files to the correct chains in the multimer class ETAssemblyControlGroup: def __init__(self, page, groupname='Load Biological Unit', defaultslidercoverage=30, defaultetoption=0, defaultqualitymeasure=0, et_colorramp=None, et_colorPrism=None, et_messagebox=None ): group = Pmw.Group(page, tag_text=groupname) group.pack(fill='both', expand=1, padx=10, pady=5) self.et_colorramp = et_colorramp self.et_colorPrism = et_colorPrism self.et_messagebox = et_messagebox self.slavelist = [] if 1: self.pdbnamebox = Pmw.EntryField(group.interior(), labelpos='w', label_text='Enter a 4-digit pdb code (e.g. 3gcb): ', value='1got', ) # Button for assigning ranks to structure self.load_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.load_buttonbox.add('Load Assembly', command=self.load) self.load_buttonbox.add('View PISA Page', command=self.viewPage) self.pdbnamebox.pack(fill='x', padx=4, pady=1) # vertical self.load_buttonbox.pack(fill='x', padx=4, pady=1) # vertical # Tkinter Slider Tkinterfor changing ET residue coverage. # TODO: Use a Pmw implementation? self.slider = Scale(group.interior(), # from_=self.min, to=self.max, from_=0, to=100, showvalue=1, length=200, orient=HORIZONTAL, resolution=0.01, tickinterval=0, # repeatinterval=500, #Dunno what repeatinterval is for... repeatdelay=500 ) self.slider.set(defaultslidercoverage) # self.slider.grid() # These additional mouse operations might be too costly for large assemblies self.slider.bind("", self.slider_button_release) ## #self.slider.bind("", self.mousebutton_click) ## self.slider.bind("", self.mousebutton_click) ## #For Windows ## self.slider.bind("", self.mousewheel_roll) ## #For Linux (for Mac?) ## self.slider.bind("", self.mousewheel_roll) ## self.slider.bind("", self.mousewheel_roll) # self.slider.bind("", self.slider_button_release) ## Triggered when the mouse enters a widget ## ## Triggered when a left click is done in a widget ##, <1> ## Triggered when the mouse is dragged over ## ## the widget with the left mouse button being ## held down. ## Triggered when a widget is double-clicked ## ## with the left mouse button ## Triggered when the key producing the letter ##, , , A ## A (caps) is pressed. self.frame2 = tkinter.Frame(group.interior()) # This list must be the same as in ETControlGroup self.et_options_tuple = ('Colors only', 'as Spheres', 'as Spheres (C-alpha only)', 'Red_to_Green', 'as Sticks') self.show_et_options = Pmw.OptionMenu(self.frame2, # group.interior(), labelpos='w', label_text='Show ET residues', items=self.et_options_tuple, initialitem=self.et_options_tuple[defaultetoption], command=self.change_options ) self.show_et_options.grid(column=0, row=0) self.notebook = Pmw.NoteBook(group.interior()) self.balloon = Pmw.Balloon(group.interior()) self.balloon.bind(self.slider, "Use this slider to vary the selection of ET residues for all chains in the assembly.") self.balloon.bind(self.load_buttonbox.button(0), "Click to start downloading an assembly and rank data and creating widgets below") self.balloon.bind(self.load_buttonbox.button(1), "Click to view the PISA entry") self.balloon.bind(self.show_et_options, "Select display style to distinguish ET residue selections from the rest of the structure") self.balloon.bind(self.pdbnamebox, "Enter a single PDB code (e.g. 1got) or a PDB code with PISA assembly numbers (1got:1,1)") for entry in (self.pdbnamebox, self.load_buttonbox, self.slider, self.frame2): entry.pack(fill='x', padx=4, pady=1) # vertical self.notebook.pack(fill='x', expand=1, padx=4, pady=1) self.three2one = { "ALA": 'A', "ARG": 'R', "ASN": 'N', "ASP": 'D', "CYS": 'C', "GLN": 'Q', "GLU": 'E', "GLY": 'G', "HIS": 'H', "ILE": 'I', "LEU": 'L', "LYS": 'K', "MET": 'M', "PHE": 'F', "PRO": 'P', "SER": 'S', "THR": 'T', "TRP": 'W', "TYR": 'Y', "VAL": 'V'} self.load_button_bg = self.load_buttonbox.button(0).cget('background') self.load_button_state = self.load_buttonbox.button(0).cget('state') if _ET_THREADING: # Threading as a response to reviewers 08/24/10 def load(self): self.load_buttonbox.button(0).configure(state=DISABLED) # Got errors when the next two loops were placed in load_run and ran # on a new thread for slave in self.slavelist: del slave for name in self.notebook.pagenames(): self.notebook.delete(name) # Clear the previous tabs self.loadBusyDoneEvent = Event() self.loadDoneEvent = Event() tm = Thread(target=self.loadBusyMessage) tm.start() tl = Thread(target=self.load_run) tl.start() else: # Not threaded def load(self): try: self.et_messagebox.show() for slave in self.slavelist: del slave for name in self.notebook.pagenames(): self.notebook.delete(name) # Clear the previous tabs params = self.pdbnamebox.getvalue().strip() if len(params) < 4: print('Enter valid pdb code!') self.et_messagebox.withdraw() return elif len(params) == 4: params = params + ':1,1' else: # User might specify different assembly set, e.g. '3cgb:2,1' pass PISA_url = 'http://www.ebi.ac.uk/msd-srv/pisa/cgi-bin/multimer.pdb?' + params # import urllib try: pdbpath = urllib.request.urlretrieve(PISA_url)[0] except Exception: print('Error in retrieving PISA structure data! Please check your internet connection.') raise Exception() structurename = params[:4] cmd.load(pdbpath, structurename) # Check if structure/pdb is empty try: model = cmd.get_model(structurename) except Exception: print("Structure \'%s\' does not exist!" % structurename) self.et_messagebox.withdraw() return if len(model.atom) == 0: print("Structure \'%s\' has no PISA quaternary structure!" % structurename) self.et_messagebox.withdraw() return self.getRanks(params[:4]) self.matchChaintoRanks(structurename) # Create ET control groups mapping a trace to each chain self.slavelist = [] for c, ranksObj in list(self.chain_ranks_dict.items()): page = self.notebook.add(c) slave = ETControlGroup(page, groupname=structurename + c, defaultstructurename=structurename, defaultchain=c, defaultrankspath=ranksObj.rankspath, # defaultetoption=self.show_et_options.index(Pmw.SELECT), defaultslidercoverage=self.slider.get(), # etcolor=etcolor_, # noetcolor=noetcolor_, defaultpartnerstructurename=structurename, et_loader_on=False, et_colorramp=self.et_colorramp, et_colorPrism=self.et_colorPrism, et_messagebox=self.et_messagebox) slave.setRanksObj(ranksObj) self.slavelist.append(slave) # Add Zcoupling and Interface computation to Assembly tabs (05/20/11) if len(self.chain_ranks_dict) > 1: page = self.notebook.add('Zcoupling') self.couplingCalculatorAssembly = CouplingGroup2(page, groupname='Compute ET coupling z-score', tracelist=self.slavelist, et_messagebox=self.et_messagebox ) self.InterfaceGroupAssembly = InterfaceControlGroup2(page, groupname='Mark interface between structures 1 and 2', tracelist=self.slavelist, defaultinterfaceoption1=1, defaultinterfaceoption2=1, et_messagebox=self.et_messagebox ) self.notebook.pack(fill='both', expand=1, padx=10, pady=10) # self.notebook.setnaturalsize() self.change_options(None) except Exception as detail: print('An exception occurred in load!') print(detail) self.et_messagebox.withdraw() def loadBusyMessage(self): tog = True # Loop until load_run finishes with calculation while not self.loadDoneEvent.isSet(): if tog: self.load_buttonbox.button(0).configure(background='green') else: self.load_buttonbox.button(0).configure(background=self.load_button_bg) tog = not tog time.sleep(0.5) # Notify load_run that pulsing message has ended self.loadBusyDoneEvent.set() def load_run(self): """Download multimer pdb from PISA""" ## for slave in self.slavelist: ## #slave.groupscrolled.configure(hscrollmode='none') ## del slave.groupscrolled try: params = self.pdbnamebox.getvalue().strip() if len(params) < 4: print('Enter valid pdb code!') self.loadDoneEvent.set() self.loadBusyDoneEvent.wait(5) self.load_buttonbox.button(0).configure(state=self.load_button_state, background=self.load_button_bg) return elif len(params) == 4: params = params + ':1,1' else: # User might specify different assembly set, e.g. '3cgb:2,1' pass PISA_url = 'http://www.ebi.ac.uk/msd-srv/pisa/cgi-bin/multimer.pdb?' + params # import urllib pdbpath = urllib.request.urlretrieve(PISA_url)[0] structurename = params[:4] cmd.load(pdbpath, structurename) # Check if structure/pdb is empty try: model = cmd.get_model(structurename) except Exception: print("Structure \'%s\' does not exist!" % structurename) self.loadDoneEvent.set() self.loadBusyDoneEvent.wait(5) self.load_buttonbox.button(0).configure(state=self.load_button_state, background=self.load_button_bg) return if len(model.atom) == 0: print("Structure \'%s\' has no PISA quaternary structure!" % structurename) self.loadDoneEvent.set() self.loadBusyDoneEvent.wait(5) self.load_buttonbox.button(0).configure(state=self.load_button_state, background=self.load_button_bg) return self.getRanks(params[:4]) self.matchChaintoRanks(structurename) # Create ET control groups mapping a trace to each chain self.slavelist = [] for c, ranksObj in list(self.chain_ranks_dict.items()): page = self.notebook.add(c) slave = ETControlGroup(page, groupname=structurename + c, defaultstructurename=structurename, defaultchain=c, defaultrankspath=ranksObj.rankspath, # defaultetoption=self.show_et_options.index(Pmw.SELECT), defaultslidercoverage=self.slider.get(), # etcolor=etcolor_, # noetcolor=noetcolor_, defaultpartnerstructurename=structurename, et_loader_on=False, et_colorramp=self.et_colorramp, et_colorPrism=self.et_colorPrism, et_messagebox=self.et_messagebox) slave.setRanksObj(ranksObj) self.slavelist.append(slave) self.notebook.pack(fill='both', expand=1, padx=10, pady=10) # self.notebook.setnaturalsize() self.change_options(None) except Exception as detail: print('An exception occurred in load_run!') print(detail) # self.loadDoneEvent.set() self.loadDoneEvent.set() self.loadBusyDoneEvent.wait(5) self.load_buttonbox.button(0).configure(state=self.load_button_state, background=self.load_button_bg) def viewPage(self): tv = Thread(target=self.viewPage_run) tv.start() def viewPage_run(self): import webbrowser # http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html # http://www.ebi.ac.uk/msd-srv/prot_int/cgi-bin/piserver # http://www.ebi.ac.uk/msd-srv/pisa/cgi-bin/piserver?qa=1stm params = self.pdbnamebox.getvalue().strip()[:4] PISA_url = 'http://www.ebi.ac.uk/msd-srv/pisa/cgi-bin/piserver?qa=' + params webbrowser.open(PISA_url) # This call blocks in debian linux def matchChaintoRanks(self, structurename): """Get the amino acid sequences in the structure sorted by chain""" try: model = cmd.get_model(structurename) except Exception: print("Structure \'%s\' does not exist!" % structurename) return chain_sequence_dict = {} for i in range(len(model.atom)): atomobj = model.atom[i] if atomobj.name == 'CA': # Caution: Sometimes the CA atom may not be present in a pdb residue try: aa1 = self.three2one[atomobj.resn] # Assume the amino acids are standard except KeyError: pass # Not a standard amino acid else: try: chain_sequence_dict[atomobj.chain].append(aa1) except KeyError: chain_sequence_dict[atomobj.chain] = [aa1] self.chain_ranks_dict = {} for c, s in list(chain_sequence_dict.items()): seq = string.join(s, '') for ranksObj in self.ranksObjlist: if seq.find( ranksObj.sequence) != -1: # Find a 'soft' match. Sequence in trace must be a substring of the PDB chain sequence. self.chain_ranks_dict[c] = ranksObj break print("Structure \'%s\' has %d protein chains:" % (structurename, len(chain_sequence_dict)), list(chain_sequence_dict.keys())) print("Found traces for %d chains" % (len(self.chain_ranks_dict))) def getRanks(self, pdbcode): """Gather all ranks files for this pdbcode from mammoth""" self.ranksObjlist = [] # TODO: This strategy looks like a hack. Get the list of unique chains from the pml file, which contains: # load http://mammoth.bcm.tmc.edu/ETserver2/pdbeasytrace/1ewyA.etvx, 1ewyA # load http://mammoth.bcm.tmc.edu/ETserver2/pdbeasytrace/1ewyC.etvx, 1ewyC # zoom # cmd._et_tools_structurenamelist=['1ewyA', '1ewyC'] # cmd._et_tools_etvxurllist=['http://mammoth.bcm.tmc.edu/ETserver2/pdbeasytrace/1ewyA.etvx', 'http://mammoth.bcm.tmc.edu/ETserver2/pdbeasytrace/1ewyC.etvx'] # cmd._et_tools_selectpage='1ewyA' pml_url = "http://mammoth.bcm.tmc.edu/ETserver2/pdbeasytrace/pmlFiles/%s.pml" % pdbcode try: pmlpath = urllib.request.urlretrieve(pml_url)[0] except Exception: print('Error retrieving trace (pml) data! Please check your internet connection.') raise Exception() FILE = open(pmlpath, 'r') for line in FILE: cols = line.split() if len(cols) == 3: if cols[0] == 'load': etvxurl = cols[1].strip(' ,') chain = etvxurl[-1] try: etvxpath = urllib.request.urlretrieve(etvxurl)[0] except Exception: print('Error retrieving trace data! Please check your internet connection.') raise Exception() ranksfilename = self.extractRanks(etvxpath, cols[2].strip()) ranksObj = ETRanks() ranksObj.readRanks(ranksfilename) self.ranksObjlist.append(ranksObj) FILE.close() def extractRanks(self, etvxpath, pdb_chain): # Get the ranks section FILE = open(etvxpath, 'r') data = '' ready = False try: for line in FILE: if line[:5] == '~tree': break if ready: data += line if line[:9] == '~ET_ranks': ready = True finally: FILE.close() # Write ranks section to file ranksfilename = os.path.dirname(etvxpath) + os.sep + pdb_chain + '.ranks' FILE_RANKS = open(ranksfilename, 'w') FILE_RANKS.write(data) FILE_RANKS.close() return ranksfilename def mousewheel_roll(self, event): slideval = self.slider.get() # See http://www.daniweb.com/code/snippet217059.html if event.num == 4 or event.delta == -120: self.slider.set(slideval + 1) self.slider_button_release(None) if event.num == 5 or event.delta == 120: self.slider.set(slideval - 1) self.slider_button_release(None) # print event.num, event.delta, slideval def mousebutton_click(self, event): # slideval=self.slider.get() if event.num == 1 or event.num == 2: self.slider_button_release(None) # print event.num, event.delta, slideval def slider_button_release(self, event): slideval = self.slider.get() for slave in self.slavelist: slave.slider.set(slideval) slave.slider_button_release(None) def change_options(self, event): for slave in self.slavelist: slave.show_et_options.setvalue(self.show_et_options.getvalue()) slave.slider_button_release(None) ##################################################################### # Complex/multiple chains class ETMasterControlGroup: def __init__(self, page, groupname='ALL', slavelist=[], defaultslidercoverage=30, defaultetoption=0, defaultqualitymeasure=0): group = Pmw.Group(page, tag_text=groupname) group.pack(fill='both', expand=1, padx=10, pady=5) self.slavelist = slavelist # Tkinter Slider Tkinterfor changing ET residue coverage. # TODO: Use a Pmw implementation? self.slider = Scale(group.interior(), # from_=self.min, to=self.max, from_=0, to=100, showvalue=1, length=200, orient=HORIZONTAL, resolution=0.01, tickinterval=0, # repeatinterval=500, #Dunno what repeatinterval is for... repeatdelay=500 ) self.slider.set(defaultslidercoverage) # self.slider.grid() self.slider.bind("", self.slider_button_release) # These mouse operations might be too costly for large assemblies ## #self.slider.bind("", self.mousebutton_click) ## self.slider.bind("", self.mousebutton_click) ## #For Windows ## self.slider.bind("", self.mousewheel_roll) ## #For Linux (for Mac?) ## self.slider.bind("", self.mousewheel_roll) ## self.slider.bind("", self.mousewheel_roll) # self.slider.bind("", self.slider_button_release) ## Triggered when the mouse enters a widget ## ## Triggered when a left click is done in a widget ##, <1> ## Triggered when the mouse is dragged over ## ## the widget with the left mouse button being ## held down. ## Triggered when a widget is double-clicked ## ## with the left mouse button ## Triggered when the key producing the letter ##, , , A ## A (caps) is pressed. self.frame2 = tkinter.Frame(group.interior()) # This list must be the same as in ETControlGroup self.et_options_tuple = ('Colors only', 'as Spheres', 'as Spheres (C-alpha only)', 'Red_to_Green', 'as Sticks') self.show_et_options = Pmw.OptionMenu(self.frame2, # group.interior(), labelpos='w', label_text='Show ET residues', items=self.et_options_tuple, initialitem=self.et_options_tuple[defaultetoption], command=self.change_options ) self.show_et_options.grid(column=0, row=0) self.notebook = Pmw.NoteBook(group.interior()) self.balloon = Pmw.Balloon(group.interior()) self.balloon.bind(self.slider, "Use this slider to vary the selection of ET residues for all chains in the complex.") self.balloon.bind(self.show_et_options, "Select display style to distinguish ET residue selections from the rest of the structure") for entry in (self.slider, self.frame2): entry.pack(fill='x', padx=4, pady=1) # vertical self.notebook.pack(fill='x', expand=1, padx=4, pady=1) def mousewheel_roll(self, event): slideval = self.slider.get() # See http://www.daniweb.com/code/snippet217059.html if event.num == 4 or event.delta == -120: self.slider.set(slideval + 1) self.slider_button_release(None) if event.num == 5 or event.delta == 120: self.slider.set(slideval - 1) self.slider_button_release(None) # print event.num, event.delta, slideval def mousebutton_click(self, event): # slideval=self.slider.get() if event.num == 1 or event.num == 2: self.slider_button_release(None) # print event.num, event.delta, slideval def slider_button_release(self, event): slideval = self.slider.get() for slave in self.slavelist: slave.slider.set(slideval) slave.slider_button_release(None) def change_options(self, event): for slave in self.slavelist: slave.show_et_options.setvalue(self.show_et_options.getvalue()) slave.slider_button_release(None) ##################################################################### # Group for computing the ET coupling z-score # This control interacts with two ETControlGroup pages (ET1 and ET2) class CouplingGroup: # Reuse some functions useful for calculating coupling z-score calcDist = _et_calcDist computeInterface = _et_computeInterface computeCoupling = _et_computeCoupling def __init__(self, page, trace1, trace2, groupname='Coupling z-score', et_messagebox=None): group = Pmw.Group(page, tag_text=groupname) self.et_messagebox = et_messagebox self.trace1 = trace1 self.trace2 = trace2 group.pack(fill='both', expand=1, padx=10, pady=5) self.zscore_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.zscore_buttonbox.add('Update interface', command=self.computeInterface_cb) self.zscore_buttonbox.add('Compute coupling z-score', command=self.showZScores) self.scw = Pmw.EntryField(group.interior(), labelpos='w', label_text='Number of ET couples, c: ', value='', ) self.scw_ave = Pmw.EntryField(group.interior(), labelpos='w', label_text=' average: ', value='', ) self.scw_stdev = Pmw.EntryField(group.interior(), labelpos='w', label_text='c stdev: ', value='', ) self.zscore = Pmw.EntryField(group.interior(), labelpos='w', label_text='z-score: ', value='', ) for entry in (self.zscore_buttonbox, self.zscore, self.scw, self.scw_ave, self.scw_stdev): entry.pack(fill='x', padx=4, pady=1) # vertical self.balloon = Pmw.Balloon(group.interior()) self.balloon.bind(self.zscore_buttonbox.button(0), "Recompute the interface between structures in ET1 and ET2") self.balloon.bind(self.zscore_buttonbox.button(1), "Click to start computing the ET coupling z-score using ET residue selections in ET1 and ET2") self.balloon.bind(self.zscore, "(c-)/stdev") self.interfaceOK = False # Deprecated self.zscore_buttonbox.button(0).configure(state=DISABLED) # Disable Update interface for now self.zscore_button_bg = self.zscore_buttonbox.button(1).cget('background') self.zscore_button_state = self.zscore_buttonbox.button(1).cget('state') def computeInterface_cb(self): # self.interfaceOK=False if self.trace1.ranksStructureOK and self.trace2.ranksStructureOK: if len(self.trace1.chainindicator) > 0: structurename1 = '%s and chain %s' % (self.trace1.structurename, self.trace1.chainindicator) else: structurename1 = self.trace1.structurename if len(self.trace2.chainindicator) > 0: structurename2 = '%s and chain %s' % (self.trace2.structurename, self.trace2.chainindicator) else: structurename2 = self.trace2.structurename print("Computing adjacency matrix for protein-protein interface A(i,j)...") self._A1, self._A2, ResAtoms1, ResAtoms2 = self.computeInterface(structurename1, structurename2, CONTACT_DISTANCE2) if self._A1 == None: return else: # self.interfaceOK=True print("%d interface residues in %s" % (len(self._A1), structurename1)) print("%d interface residues in %s" % (len(self._A2), structurename2)) print("Adjacency lists:") print(structurename1, self._A1) print(structurename2, self._A2) print("... done") else: print("Must provide structures and map trace results first!") if _ET_THREADING: # Threading as a response to reviewers 08/24/10 def showZScores(self): if self.trace1.ranksStructureOK and self.trace2.ranksStructureOK: self.zscore.setvalue('') self.scw.setvalue('') self.scw_ave.setvalue('') self.scw_stdev.setvalue('') self.zscore_buttonbox.button(1).configure(state=DISABLED) # TODO: These may get enabled by another thread, like # the z-score computations in ET1 or ET2 self.trace1.map_buttonbox.button(0).configure(state=DISABLED, background='red') self.trace1.load_buttonbox.button(0).configure(state=DISABLED, background='red') self.trace2.map_buttonbox.button(0).configure(state=DISABLED, background='red') self.trace2.load_buttonbox.button(0).configure(state=DISABLED, background='red') self.zscoreBusyDoneEvent = Event() self.zscoreDoneEvent = Event() tm = Thread(target=self.zscoreBusyMessage) tm.start() tz = Thread(target=self.showZScores_run) tz.start() else: self.zscore.setvalue('') self.scw.setvalue('') self.scw_ave.setvalue('') self.scw_stdev.setvalue('') print("Must provide structures and map trace results in ET1 and ET2!") else: def showZScores(self): if self.trace1.ranksStructureOK and self.trace2.ranksStructureOK: self.zscore.setvalue('') self.scw.setvalue('') self.scw_ave.setvalue('') self.scw_stdev.setvalue('') try: self.et_messagebox.show() # if not self.interfaceOK: if self.trace1.recomputeInterface == False and \ self.trace2.recomputeInterface == False: # Interface between ET1 and ET2 structures was previously computed # after a "Map ranks to structure" on ET1 and ET2 pass else: self.trace1.recomputeInterface = False self.trace2.recomputeInterface = False self.computeInterface_cb() print("Computing coupling z-scores using structures \'%s\' and \'%s\'..." % ( self.trace1.structurename + self.trace1.chainindicator, self.trace2.structurename + self.trace2.chainindicator)) # et1 and et2 are list of ints of residue numbers et1 = self.trace1.getETselection() et2 = self.trace2.getETselection() print("ET selections", et1, et2) if 1: # if len(et1)>0 and len(et2)>0: L1 = self.trace1.ranksObj.getSize() L2 = self.trace2.ranksObj.getSize() w, w_ave, w_stdev = self.computeCoupling(et1, et2, L1, L2, self._A1) self.scw.setvalue(w) self.scw_ave.setvalue(w_ave) self.scw_stdev.setvalue(w_stdev) if w_stdev > 0: self.zscore.setvalue((w - w_ave) / w_stdev) else: self.zscore.setvalue('NA') print("...done") except Exception as detail: print('An exception occurred in showZScores!') print(detail) self.et_messagebox.withdraw() else: self.zscore.setvalue('') self.scw.setvalue('') self.scw_ave.setvalue('') self.scw_stdev.setvalue('') print("Must provide structures and map trace results in ET1 and ET2!") def zscoreBusyMessage(self): tog = True # Loop until showZScores_run finishes with calculation while not self.zscoreDoneEvent.isSet(): if tog: self.zscore_buttonbox.button(1).configure(background='green') # self.zscore.setvalue('PROCESSING...') else: self.zscore_buttonbox.button(1).configure(background=self.zscore_button_bg) # self.zscore.setvalue('') tog = not tog time.sleep(0.5) # Notify showZScores_run that pulsing message has ended self.zscoreBusyDoneEvent.set() def showZScores_run(self): # if self.trace1.ranksStructureOK and self.trace2.ranksStructureOK: try: # if not self.interfaceOK: if self.trace1.recomputeInterface == False and \ self.trace2.recomputeInterface == False: # Interface between ET1 and ET2 structures was previously computed # after a "Map ranks to structure" on ET1 and ET2 pass else: self.trace1.recomputeInterface = False self.trace2.recomputeInterface = False self.computeInterface_cb() ## print "Computing adjacency matrix for protein-protein interface A(i,j)..." ## self._A1,self._A2,ResAtoms1,ResAtoms2=self.computeInterface(self.trace1.structurename, ## self.trace2.structurename, ## CONTACT_DISTANCE2) #(4 A)^2 ## if self._A1==None: ## return ## else: ## self.interfaceOK=True ## print "%d interface residues in %s" % (len(self._A1),self.trace1.structurename) ## print "%d interface residues in %s" % (len(self._A2),self.trace2.structurename) ## print "Adjacency lists:" ## print self.trace1.structurename, self._A1 ## print self.trace2.structurename, self._A2 ## print "... done" print("Computing coupling z-scores using structures \'%s\' and \'%s\'..." % ( self.trace1.structurename + self.trace1.chainindicator, self.trace2.structurename + self.trace2.chainindicator)) # et1 and et2 are list of ints of residue numbers et1 = self.trace1.getETselection() et2 = self.trace2.getETselection() print("ET selections", et1, et2) if 1: # if len(et1)>0 and len(et2)>0: L1 = self.trace1.ranksObj.getSize() L2 = self.trace2.ranksObj.getSize() w, w_ave, w_stdev = self.computeCoupling(et1, et2, L1, L2, self._A1) self.scw.setvalue(w) self.scw_ave.setvalue(w_ave) self.scw_stdev.setvalue(w_stdev) if w_stdev > 0: self.zscore.setvalue((w - w_ave) / w_stdev) else: self.zscore.setvalue('NA') print("...done") except Exception as detail: print('An exception occurred in showZScores_run!') print(detail) # self.markDoneEvent.set() self.zscoreDoneEvent.set() self.zscoreBusyDoneEvent.wait(5) ## self.zscore.setvalue('') ## self.scw.setvalue('') ## self.scw_ave.setvalue('') ## self.scw_stdev.setvalue('') self.zscore_buttonbox.button(1).configure(state=self.zscore_button_state, background=self.zscore_button_bg) self.trace1.map_buttonbox.button(0).configure(state=self.zscore_button_state, background=self.zscore_button_bg) self.trace1.load_buttonbox.button(0).configure(state=self.zscore_button_state, background=self.zscore_button_bg) self.trace2.map_buttonbox.button(0).configure(state=self.zscore_button_state, background=self.zscore_button_bg) self.trace2.load_buttonbox.button(0).configure(state=self.zscore_button_state, background=self.zscore_button_bg) # Modify CouplingGroup to have selectable list of traces class CouplingGroup2: # Reuse some functions useful for calculating coupling z-score calcDist = _et_calcDist computeInterface = _et_computeInterface computeCoupling = _et_computeCoupling def __init__(self, page, tracelist=[], groupname='Coupling z-score', et_messagebox=None): group = Pmw.Group(page, tag_text=groupname) self.et_messagebox = et_messagebox self.tracelist = tracelist group.pack(fill='both', expand=1, padx=10, pady=5) self.zscore_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.zscore_buttonbox.add('Update interface', command=self.computeInterface_cb) self.zscore_buttonbox.add('Compute coupling z-score', command=self.showZScores) self.scw = Pmw.EntryField(group.interior(), labelpos='w', label_text='Number of ET couples, c: ', value='', ) self.scw_ave = Pmw.EntryField(group.interior(), labelpos='w', label_text=' average: ', value='', ) self.scw_stdev = Pmw.EntryField(group.interior(), labelpos='w', label_text='c stdev: ', value='', ) self.zscore = Pmw.EntryField(group.interior(), labelpos='w', label_text='z-score: ', value='', ) self.tracesframe = tkinter.Frame(group.interior()) self.traces_tuple = tuple([t.groupname for t in self.tracelist]) self.show_traces_options1 = Pmw.OptionMenu(self.tracesframe, # group.interior(), labelpos='w', label_text='Select 1st trace', items=self.traces_tuple, initialitem=self.traces_tuple[0], # command=self.slider_button_release ) self.show_traces_options2 = Pmw.OptionMenu(self.tracesframe, # group.interior(), labelpos='w', label_text='Select 2nd trace', items=self.traces_tuple, initialitem=self.traces_tuple[1], # command=self.slider_button_release ) self.show_traces_options1.grid(column=0, row=0) self.show_traces_options2.grid(column=1, row=0) for entry in (self.tracesframe, self.zscore_buttonbox, self.zscore, self.scw, self.scw_ave, self.scw_stdev): entry.pack(fill='x', padx=4, pady=1) # vertical self.balloon = Pmw.Balloon(group.interior()) self.balloon.bind(self.zscore_buttonbox.button(0), "Recompute the interface between structures") self.balloon.bind(self.zscore_buttonbox.button(1), "Click to start computing the ET coupling z-score using ET residue selections in 1st and 2nd trace") self.balloon.bind(self.zscore, "(c-)/stdev") self.interfaceOK = False # Deprecated self.zscore_buttonbox.button(0).configure(state=DISABLED) # Disable Update interface for now self.zscore_button_bg = self.zscore_buttonbox.button(1).cget('background') self.zscore_button_state = self.zscore_buttonbox.button(1).cget('state') def computeInterface_cb(self): # self.interfaceOK=False self.trace1 = self.tracelist[self.show_traces_options1.index(Pmw.SELECT)] self.trace2 = self.tracelist[self.show_traces_options2.index(Pmw.SELECT)] if self.trace1 == self.trace2: print("Cannot compute the coupling z-score for identical structures!") return if self.trace1.ranksStructureOK and self.trace2.ranksStructureOK: if len(self.trace1.chainindicator) > 0: structurename1 = '%s and chain %s' % (self.trace1.structurename, self.trace1.chainindicator) else: structurename1 = self.trace1.structurename if len(self.trace2.chainindicator) > 0: structurename2 = '%s and chain %s' % (self.trace2.structurename, self.trace2.chainindicator) else: structurename2 = self.trace2.structurename print("Computing adjacency matrix for protein-protein interface A(i,j)...") self._A1, self._A2, ResAtoms1, ResAtoms2 = self.computeInterface(structurename1, structurename2, CONTACT_DISTANCE2) if self._A1 == None: return else: # self.interfaceOK=True print("%d interface residues in %s" % (len(self._A1), structurename1)) print("%d interface residues in %s" % (len(self._A2), structurename2)) print("Adjacency lists:") print(structurename1, self._A1) print(structurename2, self._A2) print("... done") else: print("Must provide structures and map trace results first!") def showZScores(self): self.trace1 = self.tracelist[self.show_traces_options1.index(Pmw.SELECT)] self.trace2 = self.tracelist[self.show_traces_options2.index(Pmw.SELECT)] if self.trace1 == self.trace2: print("Cannot compute the coupling z-score for identical structures!") return if self.trace1.ranksStructureOK and self.trace2.ranksStructureOK: self.zscore.setvalue('') self.scw.setvalue('') self.scw_ave.setvalue('') self.scw_stdev.setvalue('') try: self.et_messagebox.show() # if not self.interfaceOK: ## if self.trace1.recomputeInterface==False and \ ## self.trace2.recomputeInterface==False: ## #Interface between ET1 and ET2 structures was previously computed ## #after a "Map ranks to structure" on ET1 and ET2 ## pass ## else: ## self.trace1.recomputeInterface=False ## self.trace2.recomputeInterface=False if 1: self.computeInterface_cb() print("Computing coupling z-scores using structures \'%s\' and \'%s\'..." % ( self.trace1.structurename + self.trace1.chainindicator, self.trace2.structurename + self.trace2.chainindicator)) # et1 and et2 are list of ints of residue numbers et1 = self.trace1.getETselection() et2 = self.trace2.getETselection() print("ET selections", et1, et2) if 1: # if len(et1)>0 and len(et2)>0: L1 = self.trace1.ranksObj.getSize() L2 = self.trace2.ranksObj.getSize() w, w_ave, w_stdev = self.computeCoupling(et1, et2, L1, L2, self._A1) self.scw.setvalue(w) self.scw_ave.setvalue(w_ave) self.scw_stdev.setvalue(w_stdev) if w_stdev > 0: self.zscore.setvalue((w - w_ave) / w_stdev) else: self.zscore.setvalue('NA') print("...done") except Exception as detail: print('An exception occurred in showZScores!') print(detail) self.et_messagebox.withdraw() else: self.zscore.setvalue('') self.scw.setvalue('') self.scw_ave.setvalue('') self.scw_stdev.setvalue('') print("Must provide structures and map trace results in 1st and 2nd trace!") def showZScores_run(self): # if self.trace1.ranksStructureOK and self.trace2.ranksStructureOK: try: # if not self.interfaceOK: if self.trace1.recomputeInterface == False and \ self.trace2.recomputeInterface == False: # Interface between ET1 and ET2 structures was previously computed # after a "Map ranks to structure" on ET1 and ET2 pass else: self.trace1.recomputeInterface = False self.trace2.recomputeInterface = False self.computeInterface_cb() ## print "Computing adjacency matrix for protein-protein interface A(i,j)..." ## self._A1,self._A2,ResAtoms1,ResAtoms2=self.computeInterface(self.trace1.structurename, ## self.trace2.structurename, ## CONTACT_DISTANCE2) #(4 A)^2 ## if self._A1==None: ## return ## else: ## self.interfaceOK=True ## print "%d interface residues in %s" % (len(self._A1),self.trace1.structurename) ## print "%d interface residues in %s" % (len(self._A2),self.trace2.structurename) ## print "Adjacency lists:" ## print self.trace1.structurename, self._A1 ## print self.trace2.structurename, self._A2 ## print "... done" print("Computing coupling z-scores using structures \'%s\' and \'%s\'..." % ( self.trace1.structurename + self.trace1.chainindicator, self.trace2.structurename + self.trace2.chainindicator)) # et1 and et2 are list of ints of residue numbers et1 = self.trace1.getETselection() et2 = self.trace2.getETselection() print("ET selections", et1, et2) if 1: # if len(et1)>0 and len(et2)>0: L1 = self.trace1.ranksObj.getSize() L2 = self.trace2.ranksObj.getSize() w, w_ave, w_stdev = self.computeCoupling(et1, et2, L1, L2, self._A1) self.scw.setvalue(w) self.scw_ave.setvalue(w_ave) self.scw_stdev.setvalue(w_stdev) if w_stdev > 0: self.zscore.setvalue((w - w_ave) / w_stdev) else: self.zscore.setvalue('NA') print("...done") except Exception as detail: print('An exception occurred in showZScores_run!') print(detail) # self.markDoneEvent.set() self.zscoreDoneEvent.set() self.zscoreBusyDoneEvent.wait(5) ## self.zscore.setvalue('') ## self.scw.setvalue('') ## self.scw_ave.setvalue('') ## self.scw_stdev.setvalue('') self.zscore_buttonbox.button(1).configure(state=self.zscore_button_state, background=self.zscore_button_bg) self.trace1.map_buttonbox.button(0).configure(state=self.zscore_button_state, background=self.zscore_button_bg) self.trace1.load_buttonbox.button(0).configure(state=self.zscore_button_state, background=self.zscore_button_bg) self.trace2.map_buttonbox.button(0).configure(state=self.zscore_button_state, background=self.zscore_button_bg) self.trace2.load_buttonbox.button(0).configure(state=self.zscore_button_state, background=self.zscore_button_bg) ########################################################################### # Group for computing the z-score of the # Selection Clustering Weight (SCW) (Mihalek,Res,Yao,Lichtarge,JMB,2003) class SCWGroup: # Reuse some functions useful for calculating clustering z-score calcDist = _et_calcDist computeAdjacency = _et_computeAdjacency # calcZScore=_et_calcZScore def __init__(self, page, groupname='Selection Clustering Weight (SCW)', defaultstructurename='(pdb)', defaultselectionname='(sele)', defaultqualitymeasure=0): group = Pmw.Group(page, tag_text=groupname) group.pack(fill='both', expand=1, padx=10, pady=5) # Field for entering name of structure or model self.structure = Pmw.EntryField(group.interior(), labelpos='w', label_text='structure to use: ', value=defaultstructurename, ) self.selection = Pmw.EntryField(group.interior(), labelpos='w', label_text='residue selection to use: ', value=defaultselectionname, ) self.qualitymeasure_options_tuple = ('3D nobias', '3D bias (j-i)') self.show_qualitymeasure_options = Pmw.OptionMenu(group.interior(), labelpos='w', label_text='quality measure: ', items=self.qualitymeasure_options_tuple, initialitem=self.qualitymeasure_options_tuple[ defaultqualitymeasure], ) self.zscore_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.zscore_buttonbox.add('Compute adjacency', command=self.computeAdjacency_cb) self.zscore_buttonbox.add('Compute z-score', command=self.showZScores) self.scw = Pmw.EntryField(group.interior(), labelpos='w', label_text='SCW: ', value='', ) self.scw_ave = Pmw.EntryField(group.interior(), labelpos='w', label_text=' average: ', value='', ) self.scw_stdev = Pmw.EntryField(group.interior(), labelpos='w', label_text='SCW stdev: ', value='', ) self.zscore = Pmw.EntryField(group.interior(), labelpos='w', label_text='z-score: ', value='', ) for entry in (self.structure, self.selection, self.show_qualitymeasure_options, self.zscore_buttonbox, self.zscore, self.scw, self.scw_ave, self.scw_stdev): entry.pack(fill='x', padx=4, pady=1) # vertical self.adjacencyOK = False def computeAdjacency_cb(self): self.adjacencyOK = False self.structurename = self.structure.getvalue().strip() print("Computing adjacency matrix A(i,j)...") self._A, ResAtoms, self._Ar = self.computeAdjacency(self.structurename) if self._A == None: return else: self.adjacencyOK = True self.numres = len(ResAtoms) print("... done") def showZScores(self): if 1: structurename = self.structure.getvalue().strip() if self.show_qualitymeasure_options.getvalue() == self.qualitymeasure_options_tuple[0]: bias = 0 elif self.show_qualitymeasure_options.getvalue() == self.qualitymeasure_options_tuple[1]: bias = 1 if not self.adjacencyOK or structurename != self.structurename: self.structurename = structurename self.adjacencyOK = False print("Computing adjacency matrix A(i,j)...") self._A, ResAtoms, self._Ar = self.computeAdjacency(structurename) if self._A == None: return else: self.adjacencyOK = True self.numres = len(ResAtoms) print("... done") # Get the list of selected residues selectionname = self.selection.getvalue().strip() try: selemodel = cmd.get_model(selectionname) except Exception: print("Selection \'%s\' does not exist!" % selectionname) # return #Temporary? So we can have "4ch9 and chain B" in the structurename 09/02/14 SeleResAtoms = {} # List of atom coordinates indexed by residue number # atom.resi is a string, convert it to int for i in range(len(selemodel.atom)): atom = selemodel.atom[i] try: SeleResAtoms[int(atom.resi)].append(atom.coord) except KeyError: SeleResAtoms[int(atom.resi)] = [atom.coord] print("Computing z-scores using structure \'%s\' and selection \'%s\'..." % (structurename, selectionname)) print("Residue list = ", list(SeleResAtoms.keys())) zscore, w, w_ave, w_stdev = self.calcZScore(list(SeleResAtoms.keys()), self.numres, bias) self.scw.setvalue(w) self.scw_ave.setvalue(w_ave) self.scw_stdev.setvalue(w_stdev) self.zscore.setvalue(zscore) print("...done") # Calculate z-score (z_S) for residue selection reslist=[1,2,...] # z_S = (w-_S)/sigma_S # The steps are: # 1. Calculate Selection Clustering Weight (SCW) 'w' # 2. Calculate mean SCW (_S) in the ensemble of random # selections of len(reslist) residues # 3. Calculate mean square SCW (_S) and standard deviation (sigma_S) # Reference: Mihalek, Res, Yao, Lichtarge (2003) def calcZScore(self, reslist, L, bias=1): A = self._A # Calculate w w = 0 if bias == 1: for resi in reslist: for resj in reslist: if resi < resj: try: Aij = A[resi][resj] # A(i,j)==1 w += (resj - resi) except KeyError: pass elif bias == 0: for resi in reslist: for resj in reslist: if resi < resj: try: Aij = A[resi][resj] # A(i,j)==1 w += 1 except KeyError: pass # Calculate _S and _S. # Use expressions (3),(4),(5),(6) in Reference. M = len(reslist) # L=self.numres pi1 = M * (M - 1.0) / (L * (L - 1.0)) pi2 = pi1 * (M - 2.0) / (L - 2.0) pi3 = pi2 * (M - 3.0) / (L - 3.0) w_ave = 0 w2_ave = 0 if bias == 1: for resi, neighborsj in list(A.items()): for resj in neighborsj: w_ave += (resj - resi) for resk, neighborsl in list(A.items()): for resl in neighborsl: if (resi == resk and resj == resl) or \ (resi == resl and resj == resk): w2_ave += pi1 * (resj - resi) * (resl - resk) elif (resi == resk) or (resj == resl) or \ (resi == resl) or (resj == resk): w2_ave += pi2 * (resj - resi) * (resl - resk) else: w2_ave += pi3 * (resj - resi) * (resl - resk) elif bias == 0: for resi, neighborsj in list(A.items()): w_ave += len(neighborsj) for resj in neighborsj: # w_ave+=1 for resk, neighborsl in list(A.items()): for resl in neighborsl: if (resi == resk and resj == resl) or \ (resi == resl and resj == resk): w2_ave += pi1 elif (resi == resk) or (resj == resl) or \ (resi == resl) or (resj == resk): w2_ave += pi2 else: w2_ave += pi3 w_ave = w_ave * pi1 # print "w_ave", w_ave sigma = math.sqrt(w2_ave - w_ave * w_ave) # print "sigma", sigma return (w - w_ave) / sigma, w, w_ave, sigma class InterfaceControlGroup: computeInterface = _et_computeInterface calcDist = _et_calcDist def __init__(self, page, groupname='Protein-protein interface', defaultstructurename1='(pdb)', defaultstructurename2='(pdb)', defaultchain1='', defaultchain2='', defaultdistance=4, interfacecolor1='red', interfacecolor2='red', defaultinterfaceoption1=0, defaultinterfaceoption2=0, et_messagebox=None): self.interfacecolor1 = interfacecolor1 self.interfacecolor2 = interfacecolor2 self.et_messagebox = et_messagebox group = Pmw.Group(page, tag_text=groupname) group.pack(fill='both', expand=1, padx=10, pady=5) self.structureframe1 = tkinter.Frame(group.interior()) # Field for entering name of structure or model self.structure1 = Pmw.EntryField(self.structureframe1, labelpos='w', label_text='structure 1: ', value=defaultstructurename1, ) self.chain1 = Pmw.EntryField(self.structureframe1, labelpos='w', label_text='chain: ', value=defaultchain1, ) self.structure1.grid(column=0, row=0) self.chain1.grid(column=1, row=0) self.structureframe2 = tkinter.Frame(group.interior()) self.structure2 = Pmw.EntryField(self.structureframe2, labelpos='w', label_text='structure 2: ', value=defaultstructurename2, ) self.chain2 = Pmw.EntryField(self.structureframe2, labelpos='w', label_text='chain: ', value=defaultchain2, ) self.structure2.grid(column=0, row=0) self.chain2.grid(column=1, row=0) self.distance = Pmw.EntryField(group.interior(), labelpos='w', label_text='distance to use for interface: ', validate={'validator': 'real', 'min': 1, 'max': 20}, value=defaultdistance, ) self.mark_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.mark_buttonbox.add('Mark interface', command=self.markInterface) self.interface_options_tuple1 = ('Colors only(' + self.interfacecolor1 + ')', 'as Spheres', 'as Sticks', 'as Selection', 'None') self.interface_options_tuple2 = ('Colors only(' + self.interfacecolor2 + ')', 'as Spheres', 'as Sticks', 'as Selection', 'None') self.show_interface_options1 = Pmw.OptionMenu(group.interior(), labelpos='w', label_text='Show interface residues (structure 1)', items=self.interface_options_tuple1, initialitem=self.interface_options_tuple1[ defaultinterfaceoption1], command=self.updateInterface # Need two arguments for this method ) self.show_interface_options2 = Pmw.OptionMenu(group.interior(), labelpos='w', label_text='Show interface residues (structure 2)', items=self.interface_options_tuple2, initialitem=self.interface_options_tuple2[ defaultinterfaceoption2], command=self.updateInterface ) for entry in (self.structureframe1, self.structureframe2, self.distance, self.mark_buttonbox, self.show_interface_options1, self.show_interface_options2, ): entry.pack(fill='x', padx=4, pady=1) # vertical self.balloon = Pmw.Balloon(group.interior()) self.balloon.bind(self.structure1, "Enter a name from the list of objects in the PyMOL Viewer") self.balloon.bind(self.structure2, "Enter a name from the list of objects in the PyMOL Viewer") self.balloon.bind(self.distance, "Maximum inter-residue atom-atom distance (Angstroms)") self.balloon.bind(self.mark_buttonbox, "Click to start interface calculation and display") self.balloon.bind(self.show_interface_options1, "Select display style to distinguish interface residues from the rest of structure 1") self.balloon.bind(self.show_interface_options2, "Select display style to distinguish interface residues from the rest of structure 2") self.interfaceComputed = False self.mark_button_bg = self.mark_buttonbox.button(0).cget('background') self.mark_button_state = self.mark_buttonbox.button(0).cget('state') if _ET_THREADING: # Threading as a response to reviewers 08/24/10 def markInterface(self): self.interfaceComputed = False supper1 = self.structure1.getvalue().strip().upper() supper2 = self.structure2.getvalue().strip().upper() for n in cmd.get_names('all'): if supper1 == n.upper(): break else: print('structure 1 name must be in PyMOL viewer list:') print(cmd.get_names('all')) return for n in cmd.get_names('all'): if supper2 == n.upper(): break else: print('structure 2 name must be in PyMOL viewer list:') print(cmd.get_names('all')) return if 1: self.mark_buttonbox.button(0).configure(state=DISABLED) self.markBusyDoneEvent = Event() self.markDoneEvent = Event() tm = Thread(target=self.markBusyMessage) tm.start() tz = Thread(target=self.markInterface_run) tz.start() else: def markInterface(self): try: self.interfaceComputed = False supper1 = self.structure1.getvalue().strip().upper() supper2 = self.structure2.getvalue().strip().upper() for n in cmd.get_names('all'): if supper1 == n.upper(): break else: print('structure 1 name must be in PyMOL viewer list:') print(cmd.get_names('all')) return for n in cmd.get_names('all'): if supper2 == n.upper(): break else: print('structure 2 name must be in PyMOL viewer list:') print(cmd.get_names('all')) return chainindicator1 = self.chain1.getvalue().strip() self.s1 = self.structure1.getvalue().strip() # Save these self.c1 = chainindicator1 if len(chainindicator1) > 0: structurename1 = self.s1 + ' and chain %s' % chainindicator1 else: structurename1 = self.s1 chainindicator2 = self.chain2.getvalue().strip() self.s2 = self.structure2.getvalue().strip() self.c2 = chainindicator2 if len(chainindicator2) > 0: structurename2 = self.s2 + ' and chain %s' % chainindicator2 else: structurename2 = self.s2 dist = float(self.distance.getvalue().strip()) if len(self.structure1.getvalue().strip()) < 1: print('Provide structure 1 name!') return if len(self.structure2.getvalue().strip()) < 1: print('Provide structure 2 name!') return self.et_messagebox.show() # In self.interface1, each residue indexes into an array of neighboring residues in the other structure (self.interface1, self.interface2, self.ResAtoms1, self.ResAtoms2) = self.computeInterface(structurename1, structurename2, dist * dist) if (self.interface1 is None) or (self.interface2 is None): self.interfaceComputed = False self.et_messagebox.withdraw() return self.interfaceComputed = True print("%d interface residues in %s" % (len(self.interface1), structurename1)) print("%d interface residues in %s" % (len(self.interface2), structurename2)) print("Adjacency lists:") print(structurename1, self.interface1) print(structurename2, self.interface2) self.updateInterface(None) except Exception as detail: print('An exception occurred in markInterface!') print(detail) self.et_messagebox.withdraw() def markBusyMessage(self): tog = True # Loop until markInterface_run finishes with calculation while not self.markDoneEvent.isSet(): if tog: self.mark_buttonbox.button(0).configure(background='green') else: self.mark_buttonbox.button(0).configure(background=self.mark_button_bg) tog = not tog time.sleep(0.5) # Notify markInterface_run that pulsing message has ended self.markBusyDoneEvent.set() def markInterface_run(self): try: chainindicator1 = self.chain1.getvalue().strip() self.s1 = self.structure1.getvalue().strip() # Save these self.c1 = chainindicator1 if len(chainindicator1) > 0: structurename1 = self.s1 + ' and chain %s' % chainindicator1 else: structurename1 = self.s1 chainindicator2 = self.chain2.getvalue().strip() self.s2 = self.structure2.getvalue().strip() self.c2 = chainindicator2 if len(chainindicator2) > 0: structurename2 = self.s2 + ' and chain %s' % chainindicator2 else: structurename2 = self.s2 dist = float(self.distance.getvalue().strip()) if len(self.structure1.getvalue().strip()) < 1: print('Provide structure 1 name!') self.markDoneEvent.set() self.markBusyDoneEvent.wait(5) self.mark_buttonbox.button(0).configure(state=self.mark_button_state, background=self.mark_button_bg) return if len(self.structure2.getvalue().strip()) < 1: print('Provide structure 2 name!') self.markDoneEvent.set() self.markBusyDoneEvent.wait(5) self.mark_buttonbox.button(0).configure(state=self.mark_button_state, background=self.mark_button_bg) return # In self.interface1, each residue indexes into an array of neighboring residues in the other structure (self.interface1, self.interface2, self.ResAtoms1, self.ResAtoms2) = self.computeInterface(structurename1, structurename2, dist * dist) if (self.interface1 is None) or (self.interface2 is None): self.interfaceComputed = False self.markDoneEvent.set() self.markBusyDoneEvent.wait(5) self.mark_buttonbox.button(0).configure(state=self.mark_button_state, background=self.mark_button_bg) return self.interfaceComputed = True print("%d interface residues in %s" % (len(self.interface1), structurename1)) print("%d interface residues in %s" % (len(self.interface2), structurename2)) print("Adjacency lists:") print(structurename1, self.interface1) print(structurename2, self.interface2) self.updateInterface(None) except Exception as detail: print('An exception occurred in markInterface_run!') print(detail) # self.markDoneEvent.set() self.markDoneEvent.set() self.markBusyDoneEvent.wait(5) self.mark_buttonbox.button(0).configure(state=self.mark_button_state, background=self.mark_button_bg) def updateInterface(self, event): # TODO: Make this method more aware of changes in the viewer if self.interfaceComputed == False: return ## s1=self.structure1.getvalue().strip() ## s2=self.structure2.getvalue().strip() ## c1=self.chain1.getvalue().strip() ## c2=self.chain2.getvalue().strip() s1 = self.s1 s2 = self.s2 c1 = self.c1 c2 = self.c2 if len(c1) > 0: structurename1 = s1 + ' and chain %s' % c1 else: structurename1 = s1 if len(c2) > 0: structurename2 = s2 + ' and chain %s' % c2 else: structurename2 = s2 if self.show_interface_options1.getvalue() == self.interface_options_tuple1[0]: for res in list(self.interface1.keys()): cmd.color(self.interfacecolor1, '%s and resi %s' % (structurename1, res)) elif self.show_interface_options1.getvalue() == self.interface_options_tuple1[1]: for res in list(self.interface1.keys()): cmd.show('spheres', '%s and resi %s' % (structurename1, res)) elif self.show_interface_options1.getvalue() == self.interface_options_tuple1[2]: for res in list(self.interface1.keys()): cmd.show('sticks', '%s and resi %s' % (structurename1, res)) elif self.show_interface_options1.getvalue() == self.interface_options_tuple1[3]: # Make a selection of the ET residues if len(self.interface1) > 0: cmd.select('%s_%s_PyETV' % (s1 + c1, s2 + c2), '%s and resi %s' % (structurename1, string.join(list(map(str, self.interface1)), '+'))) else: cmd.select('%s_%s_PyETV' % (s1 + c1, s2 + c2), 'none') if self.show_interface_options2.getvalue() == self.interface_options_tuple2[0]: for res in list(self.interface2.keys()): cmd.color(self.interfacecolor2, '%s and resi %s' % (structurename2, res)) elif self.show_interface_options2.getvalue() == self.interface_options_tuple2[1]: for res in list(self.interface2.keys()): cmd.show('spheres', '%s and resi %s' % (structurename2, res)) elif self.show_interface_options2.getvalue() == self.interface_options_tuple2[2]: for res in list(self.interface2.keys()): cmd.show('sticks', '%s and resi %s' % (structurename2, res)) elif self.show_interface_options2.getvalue() == self.interface_options_tuple2[3]: # Make a selection of the ET residues if len(self.interface2) > 0: cmd.select('%s_%s_PyETV' % (s2 + c2, s1 + c1), '%s and resi %s' % (structurename2, string.join(list(map(str, self.interface2)), '+'))) else: cmd.select('%s_%s_PyETV' % (s2 + c2, s1 + c1), 'none') # Compute interface between traces from a selectable list class InterfaceControlGroup2: computeInterface = _et_computeInterface calcDist = _et_calcDist def __init__(self, page, groupname='Protein-protein interface', tracelist=[], defaultstructurename1='(pdb)', defaultstructurename2='(pdb)', defaultchain1='', defaultchain2='', defaultdistance=4, interfacecolor1='red', interfacecolor2='red', defaultinterfaceoption1=0, defaultinterfaceoption2=0, et_messagebox=None): self.interfacecolor1 = interfacecolor1 self.interfacecolor2 = interfacecolor2 self.et_messagebox = et_messagebox group = Pmw.Group(page, tag_text=groupname) group.pack(fill='both', expand=1, padx=10, pady=5) self.structureframe1 = tkinter.Frame(group.interior()) # Field for entering name of structure or model self.structure1 = Pmw.EntryField(self.structureframe1, labelpos='w', label_text='structure 1: ', value=defaultstructurename1, ) self.chain1 = Pmw.EntryField(self.structureframe1, labelpos='w', label_text='chain: ', value=defaultchain1, ) self.structure1.grid(column=0, row=0) self.chain1.grid(column=1, row=0) self.structureframe2 = tkinter.Frame(group.interior()) self.structure2 = Pmw.EntryField(self.structureframe2, labelpos='w', label_text='structure 2: ', value=defaultstructurename2, ) self.chain2 = Pmw.EntryField(self.structureframe2, labelpos='w', label_text='chain: ', value=defaultchain2, ) self.structure2.grid(column=0, row=0) self.chain2.grid(column=1, row=0) self.distance = Pmw.EntryField(group.interior(), labelpos='w', label_text='distance to use for interface: ', validate={'validator': 'real', 'min': 1, 'max': 20}, value=defaultdistance, ) self.mark_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.mark_buttonbox.add('Mark interface', command=self.markInterface) self.interface_options_tuple1 = ('Colors only(' + self.interfacecolor1 + ')', 'as Spheres', 'as Sticks', 'as Selection', 'None') self.interface_options_tuple2 = ('Colors only(' + self.interfacecolor2 + ')', 'as Spheres', 'as Sticks', 'as Selection', 'None') self.show_interface_options1 = Pmw.OptionMenu(group.interior(), labelpos='w', label_text='Show interface residues (structure 1)', items=self.interface_options_tuple1, initialitem=self.interface_options_tuple1[ defaultinterfaceoption1], command=self.updateInterface # Need two arguments for this method ) self.show_interface_options2 = Pmw.OptionMenu(group.interior(), labelpos='w', label_text='Show interface residues (structure 2)', items=self.interface_options_tuple2, initialitem=self.interface_options_tuple2[ defaultinterfaceoption2], command=self.updateInterface ) self.tracelist = tracelist self.tracesframe = tkinter.Frame(group.interior()) self.traces_tuple = tuple([t.groupname for t in self.tracelist]) self.show_traces_options1 = Pmw.OptionMenu(self.tracesframe, # group.interior(), labelpos='w', label_text='Select 1st trace', items=self.traces_tuple, initialitem=self.traces_tuple[0], # command=self.slider_button_release ) self.show_traces_options2 = Pmw.OptionMenu(self.tracesframe, # group.interior(), labelpos='w', label_text='Select 2nd trace', items=self.traces_tuple, initialitem=self.traces_tuple[1], # command=self.slider_button_release ) self.show_traces_options1.grid(column=0, row=0) self.show_traces_options2.grid(column=1, row=0) for entry in (self.tracesframe, # self.structureframe1, # self.structureframe2, self.distance, self.mark_buttonbox, self.show_interface_options1, self.show_interface_options2, ): entry.pack(fill='x', padx=4, pady=1) # vertical self.balloon = Pmw.Balloon(group.interior()) self.balloon.bind(self.structure1, "Enter a name from the list of objects in the PyMOL Viewer") self.balloon.bind(self.structure2, "Enter a name from the list of objects in the PyMOL Viewer") self.balloon.bind(self.distance, "Maximum inter-residue atom-atom distance (Angstroms)") self.balloon.bind(self.mark_buttonbox, "Click to start interface calculation and display") self.balloon.bind(self.show_interface_options1, "Select display style to distinguish interface residues from the rest of structure 1") self.balloon.bind(self.show_interface_options2, "Select display style to distinguish interface residues from the rest of structure 2") self.interfaceComputed = False self.mark_button_bg = self.mark_buttonbox.button(0).cget('background') self.mark_button_state = self.mark_buttonbox.button(0).cget('state') def markInterface(self): try: self.interfaceComputed = False self.trace1 = self.tracelist[self.show_traces_options1.index(Pmw.SELECT)] self.trace2 = self.tracelist[self.show_traces_options2.index(Pmw.SELECT)] if self.trace1 == self.trace2: print("Cannot compute the interface for identical structures!") return supper1 = self.trace1.structurename.upper() supper2 = self.trace2.structurename.upper() # supper1=self.structure1.getvalue().strip().upper() # supper2=self.structure2.getvalue().strip().upper() for n in cmd.get_names('all'): if supper1 == n.upper(): break else: print('structure 1 name must be in PyMOL viewer list:') print(cmd.get_names('all')) return for n in cmd.get_names('all'): if supper2 == n.upper(): break else: print('structure 2 name must be in PyMOL viewer list:') print(cmd.get_names('all')) return chainindicator1 = self.trace1.chainindicator self.s1 = self.trace1.structurename # chainindicator1=self.chain1.getvalue().strip() # self.s1=self.structure1.getvalue().strip() #Save these self.c1 = chainindicator1 if len(chainindicator1) > 0: structurename1 = self.s1 + ' and chain %s' % chainindicator1 else: structurename1 = self.s1 chainindicator2 = self.trace2.chainindicator self.s2 = self.trace2.structurename # chainindicator2=self.chain2.getvalue().strip() # self.s2=self.structure2.getvalue().strip() self.c2 = chainindicator2 if len(chainindicator2) > 0: structurename2 = self.s2 + ' and chain %s' % chainindicator2 else: structurename2 = self.s2 dist = float(self.distance.getvalue().strip()) if len(self.structure1.getvalue().strip()) < 1: print('Provide structure 1 name!') return if len(self.structure2.getvalue().strip()) < 1: print('Provide structure 2 name!') return self.et_messagebox.show() # In self.interface1, each residue indexes into an array of neighboring residues in the other structure (self.interface1, self.interface2, self.ResAtoms1, self.ResAtoms2) = self.computeInterface(structurename1, structurename2, dist * dist) if (self.interface1 is None) or (self.interface2 is None): self.interfaceComputed = False self.et_messagebox.withdraw() return self.interfaceComputed = True print("%d interface residues in %s" % (len(self.interface1), structurename1)) print("%d interface residues in %s" % (len(self.interface2), structurename2)) print("Adjacency lists:") print(structurename1, self.interface1) print(structurename2, self.interface2) self.updateInterface(None) except Exception as detail: print('An exception occurred in markInterface!') print(detail) self.et_messagebox.withdraw() def markInterface_run(self): try: chainindicator1 = self.chain1.getvalue().strip() self.s1 = self.structure1.getvalue().strip() # Save these self.c1 = chainindicator1 if len(chainindicator1) > 0: structurename1 = self.s1 + ' and chain %s' % chainindicator1 else: structurename1 = self.s1 chainindicator2 = self.chain2.getvalue().strip() self.s2 = self.structure2.getvalue().strip() self.c2 = chainindicator2 if len(chainindicator2) > 0: structurename2 = self.s2 + ' and chain %s' % chainindicator2 else: structurename2 = self.s2 dist = float(self.distance.getvalue().strip()) if len(self.structure1.getvalue().strip()) < 1: print('Provide structure 1 name!') self.markDoneEvent.set() self.markBusyDoneEvent.wait(5) self.mark_buttonbox.button(0).configure(state=self.mark_button_state, background=self.mark_button_bg) return if len(self.structure2.getvalue().strip()) < 1: print('Provide structure 2 name!') self.markDoneEvent.set() self.markBusyDoneEvent.wait(5) self.mark_buttonbox.button(0).configure(state=self.mark_button_state, background=self.mark_button_bg) return # In self.interface1, each residue indexes into an array of neighboring residues in the other structure (self.interface1, self.interface2, self.ResAtoms1, self.ResAtoms2) = self.computeInterface(structurename1, structurename2, dist * dist) if (self.interface1 is None) or (self.interface2 is None): self.interfaceComputed = False self.markDoneEvent.set() self.markBusyDoneEvent.wait(5) self.mark_buttonbox.button(0).configure(state=self.mark_button_state, background=self.mark_button_bg) return self.interfaceComputed = True print("%d interface residues in %s" % (len(self.interface1), structurename1)) print("%d interface residues in %s" % (len(self.interface2), structurename2)) print("Adjacency lists:") print(structurename1, self.interface1) print(structurename2, self.interface2) self.updateInterface(None) except Exception as detail: print('An exception occurred in markInterface_run!') print(detail) # self.markDoneEvent.set() self.markDoneEvent.set() self.markBusyDoneEvent.wait(5) self.mark_buttonbox.button(0).configure(state=self.mark_button_state, background=self.mark_button_bg) def updateInterface(self, event): # TODO: Make this method more aware of changes in the viewer if self.interfaceComputed == False: return ## s1=self.structure1.getvalue().strip() ## s2=self.structure2.getvalue().strip() ## c1=self.chain1.getvalue().strip() ## c2=self.chain2.getvalue().strip() s1 = self.s1 s2 = self.s2 c1 = self.c1 c2 = self.c2 if len(c1) > 0: structurename1 = s1 + ' and chain %s' % c1 else: structurename1 = s1 if len(c2) > 0: structurename2 = s2 + ' and chain %s' % c2 else: structurename2 = s2 if self.show_interface_options1.getvalue() == self.interface_options_tuple1[0]: for res in list(self.interface1.keys()): cmd.color(self.interfacecolor1, '%s and resi %s' % (structurename1, res)) elif self.show_interface_options1.getvalue() == self.interface_options_tuple1[1]: for res in list(self.interface1.keys()): cmd.show('spheres', '%s and resi %s' % (structurename1, res)) elif self.show_interface_options1.getvalue() == self.interface_options_tuple1[2]: for res in list(self.interface1.keys()): cmd.show('sticks', '%s and resi %s' % (structurename1, res)) elif self.show_interface_options1.getvalue() == self.interface_options_tuple1[3]: # Make a selection of the ET residues if len(self.interface1) > 0: cmd.select('%s_%s_PyETV' % (s1 + c1, s2 + c2), '%s and resi %s' % (structurename1, string.join(list(map(str, self.interface1)), '+'))) else: cmd.select('%s_%s_PyETV' % (s1 + c1, s2 + c2), 'none') if self.show_interface_options2.getvalue() == self.interface_options_tuple2[0]: for res in list(self.interface2.keys()): cmd.color(self.interfacecolor2, '%s and resi %s' % (structurename2, res)) elif self.show_interface_options2.getvalue() == self.interface_options_tuple2[1]: for res in list(self.interface2.keys()): cmd.show('spheres', '%s and resi %s' % (structurename2, res)) elif self.show_interface_options2.getvalue() == self.interface_options_tuple2[2]: for res in list(self.interface2.keys()): cmd.show('sticks', '%s and resi %s' % (structurename2, res)) elif self.show_interface_options2.getvalue() == self.interface_options_tuple2[3]: # Make a selection of the ET residues if len(self.interface2) > 0: cmd.select('%s_%s_PyETV' % (s2 + c2, s1 + c1), '%s and resi %s' % (structurename2, string.join(list(map(str, self.interface2)), '+'))) else: cmd.select('%s_%s_PyETV' % (s2 + c2, s1 + c1), 'none') class DiffETControlGroup: # Reuse some functions useful for calculating clustering z-score calcDist = _et_calcDist computeAdjacency = _et_computeAdjacency calcZScore = _et_calcZScore def __init__(self, page, groupname='Trace', defaultstructurename='(pdb)', defaultchain='', defaultrankspath1='.ranks', defaultrankspath2='.ranks', defaultqualitymeasure=0, etcolor1='blue', etcolor2='red', etcolor12='orange', noetcolor='white', et_messagebox=None): self.etcolor1 = etcolor1 self.etcolor2 = etcolor2 self.etcolor12 = etcolor12 self.noetcolor = noetcolor self.et_messagebox = et_messagebox group = Pmw.Group(page, tag_text=groupname) group.pack(fill='both', expand=1, padx=10, pady=5) self.balloon = Pmw.Balloon(group.interior()) self.structureframe = tkinter.Frame(group.interior()) # Field for entering name of structure or model self.structure = Pmw.EntryField(self.structureframe, labelpos='w', label_text='structure to use: ', value=defaultstructurename, ) self.chain = Pmw.EntryField(self.structureframe, labelpos='w', label_text='chain: ', value=defaultchain, ) self.structure.grid(column=0, row=0) self.chain.grid(column=1, row=0) def quickFileValidation(s): if s == '': return Pmw.PARTIAL elif os.path.isfile(s): return Pmw.OK elif os.path.exists(s): return Pmw.PARTIAL else: return Pmw.PARTIAL # Button for assigning ranks to structure self.map_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.map_buttonbox.add('Map ranks to structure', command=self.mapRanks) # Field for entering ranks file self.ranksfile1 = Pmw.EntryField(group.interior(), labelpos='w', label_pyclass=FileDialogButtonClassFactory.get(self.setRanksFileLocation1, '*.cov'), validate={'validator': quickFileValidation, }, value=defaultrankspath1, label_text='Superfamily ranks file path:') self.ranksfile2 = Pmw.EntryField(group.interior(), labelpos='w', label_pyclass=FileDialogButtonClassFactory.get(self.setRanksFileLocation2, '*.cov'), validate={'validator': quickFileValidation, }, value=defaultrankspath2, label_text='Subfamily ranks file path:') self.subgroup1 = Pmw.Group(group.interior(), tag_text='Superfamily (blue+orange)') # Tkinter Slider Tkinter for changing ET residue coverage. # TODO: Use a Pmw implementation? self.slider1 = Scale(self.subgroup1.interior(), # from_=self.min, to=self.max, from_=0, to=100, showvalue=1, length=200, orient=HORIZONTAL, resolution=0.01, tickinterval=0, # repeatinterval=500, #Dunno what repeatinterval is for... repeatdelay=500 ) self.slider1.set(30) # self.slider.grid() self.slider1.bind("", self.slider_button_release) # self.slider1.bind("", self.mousebutton_click_slider1) self.slider1.bind("", self.mousebutton_click_slider1) # For Windows self.slider1.bind("", self.mousewheel_roll_slider1) # For Linux (for Mac?) self.slider1.bind("", self.mousewheel_roll_slider1) self.slider1.bind("", self.mousewheel_roll_slider1) # Field for displaying ET coverage self.frame1 = tkinter.Frame(self.subgroup1.interior()) self.percentcoverage1 = Pmw.EntryField(self.frame1, # group.interior(), labelpos='w', label_text='Percent coverage: ', value='', ) self.rankvalue1 = Pmw.EntryField(self.frame1, # group.interior(), labelpos='w', label_text='Rank: ', value='', ) self.percentcoverage1.grid(column=0, row=0) self.rankvalue1.grid(column=1, row=0) self.slider1.pack(fill='x', padx=4, pady=1) # vertical # self.balloon.bind(self.slider1,"Superfamily ranks slider") self.frame1.pack(fill='x', padx=4, pady=1) # vertical # Use options menu (combobox) instead of checkboxes self.et_options_tuple = ('Colors only(' + self.etcolor1 + ',' + self.etcolor12 + ',' + self.etcolor2 + ')', 'as Spheres', 'as Spheres (C-alpha only)', 'Coverage differentials') self.show_et_options = Pmw.OptionMenu(group.interior(), labelpos='w', label_text='Show ET residues', items=self.et_options_tuple, initialitem=self.et_options_tuple[0], command=self.slider_button_release ) ## self.show_et_var=IntVar() ## self.show_et_var.set(0) ## self.show_et_checkbutton = Checkbutton(group.interior(), ## text = "Show ET residues (as spheres)", ## variable = self.show_et_var) self.sync_sliders_var = IntVar() self.sync_sliders_var.set(1) self.sync_sliders_checkbutton = Checkbutton(group.interior(), text="Synchronize Subfamily ranks slider to Superfamily", variable=self.sync_sliders_var) self.subgroup2 = Pmw.Group(group.interior(), tag_text='Subfamily (red+orange)') self.slider2 = Scale(self.subgroup2.interior(), # from_=self.min, to=self.max, from_=0, to=100, showvalue=1, length=200, orient=HORIZONTAL, resolution=0.01, tickinterval=0, # repeatinterval=500, #Dunno what repeatinterval is for... repeatdelay=500 ) self.slider2.set(30) # self.slider.grid() self.slider2.bind("", self.slider_button_release) # self.slider2.bind("", self.mousebutton_click_slider2) self.slider2.bind("", self.mousebutton_click_slider2) # For Windows self.slider2.bind("", self.mousewheel_roll_slider2) # For Linux (for Mac?) self.slider2.bind("", self.mousewheel_roll_slider2) self.slider2.bind("", self.mousewheel_roll_slider2) # Field for displaying ET coverage self.frame2 = tkinter.Frame(self.subgroup2.interior()) self.percentcoverage2 = Pmw.EntryField(self.frame2, # group.interior(), labelpos='w', label_text='Percent coverage: ', value='', ) self.rankvalue2 = Pmw.EntryField(self.frame2, # group.interior(), labelpos='w', label_text='Rank: ', value='', ) self.percentcoverage2.grid(column=0, row=0) self.rankvalue2.grid(column=1, row=0) self.slider2.pack(fill='x', padx=4, pady=1) # vertical # self.balloon.bind(self.slider2,"Subfamily ranks slider") self.frame2.pack(fill='x', padx=4, pady=1) # vertical self.qualitymeasure_options_tuple = ('3D nobias', '3D bias (j-i)') self.show_qualitymeasure_options = Pmw.OptionMenu(group.interior(), labelpos='w', label_text='quality measure: ', items=self.qualitymeasure_options_tuple, initialitem=self.qualitymeasure_options_tuple[ defaultqualitymeasure], ) self.zscore_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.zscore_buttonbox.add('Compute z-scores', command=self.showZScores) self.zscore1only = Pmw.EntryField(group.interior(), labelpos='w', label_text='z-score superfamily only (blue): ', value='', ) self.zscore12 = Pmw.EntryField(group.interior(), labelpos='w', label_text='z-score common (orange): ', value='', ) self.zscore2only = Pmw.EntryField(group.interior(), labelpos='w', label_text='z-score subfamily only (red): ', value='', ) for entry in (self.structureframe, self.ranksfile1, self.ranksfile2, self.map_buttonbox, self.subgroup1, # self.slider1, # self.frame1, # self.percentcoverage1, # self.rankvalue1, self.show_et_options, # self.show_et_checkbutton, self.sync_sliders_checkbutton, self.subgroup2, # self.slider2, # self.frame2, # self.percentcoverage2, # self.rankvalue2, self.zscore_buttonbox, self.show_qualitymeasure_options, self.zscore1only, self.zscore12, self.zscore2only): entry.pack(fill='x', padx=4, pady=1) # vertical self.balloon.bind(self.structure, "Enter a name from the list of objects in the PyMOL Viewer") self.balloon.bind(self.map_buttonbox, "Click once before operating the controls below") self.balloon.bind(self.slider1, "Drag superfamily ranks slider to vary ET residue selection and coverage (blue+orange) of the structure") self.balloon.bind(self.slider2, "Drag subfamily ranks slider to vary ET residue selection and coverage (red+orange) of the structure") self.balloon.bind(self.show_et_options, "Select display style to distinguish ET residue selection from the rest of the structure") self.balloon.bind(self.zscore_buttonbox, "Compute the clustering z-scores of the ET residue selections") self.balloon.bind(self.show_qualitymeasure_options, "Select from several measures of clustering quality") self.ranksObj1 = ETRanks() self.ranksObj2 = ETRanks() self.ranksStructureOK = False self.adjacencyOK = False def mapRanks(self): structurename = self.structure.getvalue().strip() chainindicator = self.chain.getvalue().strip() self.ranksStructureOK = False self.adjacencyOK = False if len(structurename) < 1: print('Provide structure name!') return try: model = cmd.get_model(structurename) except Exception: print("Structure \'%s\' does not exist!" % structurename) return rankspath1 = self.ranksfile1.getvalue().strip() if len(rankspath1) < 1: print('Provide path to superfamily ranks file!') return self.ranksObj1.readRanks(rankspath1) if self.ranksObj1.ranksLoaded(): print("Superfamily ranks file \'%s\' loaded" % rankspath1) else: print("Error loading ranks file \'%s\'!" % rankspath1) return rankspath2 = self.ranksfile2.getvalue().strip() if len(rankspath2) < 1: print('Provide path to subfamily ranks file!') return self.ranksObj2.readRanks(rankspath2) if self.ranksObj2.ranksLoaded(): print("Subfamily ranks file \'%s\' loaded" % rankspath2) else: print("Error loading ranks file \'%s\'!" % rankspath2) return if self.ranksObj1.getSize() != self.ranksObj2.getSize(): print("Residue numbers in \'%s\' and \'%s\' are not the same!" % (rankspath1, rankspath2)) return # TODO: This sanity check is too restrictive. for i in range(self.ranksObj1.getSize()): if self.ranksObj1.getResnum(i) != self.ranksObj2.getResnum(i): print("Residue numbers in \'%s\' and \'%s\' are not the same!" % (rankspath1, rankspath2)) return # TODO: Make this optional # Check that the residue numbers in the model # and in the ranks file are identical ## resnumDict={} ## for i in range(len(model.atom)): ## if chaindicator==atom[i].chain: ## resnumDict[model.atom[i].resi]=1 ## if len(resnumDict)<1: ## print 'Structure \'%s\' has no residues!' % structurename ## return ## if len(resnumDict)!=self.ranksObj1.getSize(): ## print "Residue numbers in \'%s\' and \'%s\' are not the same!" % (structurename, rankspath1) ## return ## for i in range(self.ranksObj1.getSize()): ## try: ## r=resnumDict[self.ranksObj1.getResnum(i)] ## except KeyError: ## print "Residue numbers in \'%s\' and \'%s\' do not match!" % (structurename, rankspath1) return self.structurename = structurename self.chainindicator = chainindicator self.ranksStructureOK = True # print 'Residue numbers checked with structure \'%s\'' % structurename self.slider_button_release(None) # TODO: Use this method to compare the sequences between structure and ranks files # This check uses the residue numbers, not the amino acid types def checkSequence(self, model, structurename, chainindicator, rankspath): three2one = { "ALA": 'A', "ARG": 'R', "ASN": 'N', "ASP": 'D', "CYS": 'C', "GLN": 'Q', "GLU": 'E', "GLY": 'G', "HIS": 'H', "ILE": 'I', "LEU": 'L', "LYS": 'K', "MET": 'M', "PHE": 'F', "PRO": 'P', "SER": 'S', "THR": 'T', "TRP": 'W', "TYR": 'Y', "VAL": 'V', "A": "A", "G": "G", "T": "T", "U": "U", "C": "C", } print('Comparing residue numbers of structure \'%s\' and ranks \'%s\'...' % (structurename + chainindicator, rankspath)) # Check that the residue numbers in the model # and in the ranks file are identical resnumDict = {} if len(chainindicator) > 0: # chainup=chainindicator() # Case of chain indicator is relevant for i in range(len(model.atom)): atomobj = model.atom[i] if chainindicator == atomobj.chain: try: aa1 = three2one[atomobj.resn] # Consider only residues with standard amino acids resnumDict[atomobj.resi] = 1 except KeyError: pass else: for i in range(len(model.atom)): resnumDict[model.atom[i].resi] = 1 print('Sequence lengths:') print('structure: ', len(resnumDict)) print('ranks: ', self.ranksObj.getSize()) if len(resnumDict) < 1: print('Structure \'%s\' has no residues!' % (structurename + chainindicator)) if len(resnumDict) != self.ranksObj.getSize(): print("Sequence lengths of \'%s\' and \'%s\' are not the same!" % (structurename + chainindicator, rankspath)) missing = 0 for i in range(self.ranksObj.getSize()): try: r = resnumDict[self.ranksObj.getResnum(i)] except KeyError: missing += 1 if missing > 0: print("%d residue numbers in \'%s\' missing in \'%s\'!" % ( missing, rankspath, structurename + chainindicator)) print('...Done.') def mousewheel_roll_slider1(self, event): slideval = self.slider1.get() # See http://www.daniweb.com/code/snippet217059.html if event.num == 4 or event.delta == -120: self.slider1.set(slideval + 1) self.slider_button_release(None) if event.num == 5 or event.delta == 120: self.slider1.set(slideval - 1) self.slider_button_release(None) # print event.num, event.delta, slideval def mousebutton_click_slider1(self, event): # slideval=self.slider.get() if event.num == 1 or event.num == 2: self.slider_button_release(None) # print event.num, event.delta, slideval def mousewheel_roll_slider2(self, event): slideval = self.slider2.get() # See http://www.daniweb.com/code/snippet217059.html if event.num == 4 or event.delta == -120: self.slider2.set(slideval + 1) self.slider_button_release(None) if event.num == 5 or event.delta == 120: self.slider2.set(slideval - 1) self.slider_button_release(None) # print event.num, event.delta, slideval def mousebutton_click_slider2(self, event): # slideval=self.slider.get() if event.num == 1 or event.num == 2: self.slider_button_release(None) # print event.num, event.delta, slideval def slider_button_release(self, event): if self.ranksStructureOK: self.et_messagebox.show() if len(self.chainindicator) > 0: structurename = '%s and chain %s' % (self.structurename, self.chainindicator) else: structurename = self.structurename maxcov1 = 0 maxrank1 = 0 maxcov2 = 0 maxrank2 = 0 slideval1 = self.slider1.get() if self.sync_sliders_var.get() == 1: self.slider2.set(slideval1) slideval2 = slideval1 else: slideval2 = self.slider2.get() # if self.show_et_var.get()==1: if self.show_et_options.getvalue() == self.et_options_tuple[3]: for i in range(self.ranksObj1.getSize()): (resnum1, cov1, rank1) = self.ranksObj1.getResnumCoverageRankTuple(i) (resnum2, cov2, rank2) = self.ranksObj2.getResnumCoverageRankTuple(i) if cov1 > maxcov1: maxcov1 = cov1 maxrank1 = rank1 if cov2 > maxcov2: maxcov2 = cov2 maxrank2 = rank2 cd = (cov1 - cov2) / (cov1 + cov2) # SuperfamilyCoverage-SubfamilyCoverage if cd > 0.2: cmd.color('_et_red_color%s' % int(10 * (cd - 0.2) / 0.8), '%s and resi %s' % (structurename, resnum1)) elif cd < -0.2: cmd.color('_et_blue_color%s' % int(10 * (-cd - 0.2) / 0.8), '%s and resi %s' % (structurename, resnum1)) else: cmd.color('white', '%s and resi %s' % (structurename, resnum1)) elif self.show_et_options.getvalue() == self.et_options_tuple[2]: cmd.hide('spheres', structurename) # Need to hide spheres in case non-CA atoms are displayed for i in range(self.ranksObj1.getSize()): (resnum1, cov1, rank1) = self.ranksObj1.getResnumCoverageRankTuple(i) (resnum2, cov2, rank2) = self.ranksObj2.getResnumCoverageRankTuple(i) # assert(resnum1==resnum2) if slideval1 >= cov1: et1 = True if cov1 > maxcov1: maxcov1 = cov1 maxrank1 = rank1 else: et1 = False if slideval2 >= cov2: et2 = True if cov2 > maxcov2: maxcov2 = cov2 maxrank2 = rank2 else: et2 = False if et1 and not et2: cmd.color(self.etcolor1, '%s and resi %s' % (structurename, resnum1)) cmd.show('spheres', '%s and resi %s and name CA' % (structurename, resnum1)) elif et1 and et2: cmd.color(self.etcolor12, '%s and resi %s' % (structurename, resnum1)) cmd.show('spheres', '%s and resi %s and name CA' % (structurename, resnum1)) elif et2 and not et1: cmd.color(self.etcolor2, '%s and resi %s' % (structurename, resnum1)) cmd.show('spheres', '%s and resi %s and name CA' % (structurename, resnum1)) else: cmd.color(self.noetcolor, '%s and resi %s' % (structurename, resnum1)) cmd.hide('spheres', '%s and resi %s' % (structurename, resnum1)) elif self.show_et_options.getvalue() == self.et_options_tuple[1]: for i in range(self.ranksObj1.getSize()): (resnum1, cov1, rank1) = self.ranksObj1.getResnumCoverageRankTuple(i) (resnum2, cov2, rank2) = self.ranksObj2.getResnumCoverageRankTuple(i) # assert(resnum1==resnum2) if slideval1 >= cov1: et1 = True if cov1 > maxcov1: maxcov1 = cov1 maxrank1 = rank1 else: et1 = False if slideval2 >= cov2: et2 = True if cov2 > maxcov2: maxcov2 = cov2 maxrank2 = rank2 else: et2 = False if et1 and not et2: cmd.color(self.etcolor1, '%s and resi %s' % (structurename, resnum1)) cmd.show('spheres', '%s and resi %s' % (structurename, resnum1)) elif et1 and et2: cmd.color(self.etcolor12, '%s and resi %s' % (structurename, resnum1)) cmd.show('spheres', '%s and resi %s' % (structurename, resnum1)) elif et2 and not et1: cmd.color(self.etcolor2, '%s and resi %s' % (structurename, resnum1)) cmd.show('spheres', '%s and resi %s' % (structurename, resnum1)) else: # Still assign the right color even we hide it, in case the user makes # this part visible cmd.color(self.noetcolor, '%s and resi %s' % (structurename, resnum1)) cmd.hide('spheres', '%s and resi %s' % (structurename, resnum1)) # elif self.show_et_options.getvalue()==self.et_options_tuple[0]: else: for i in range(self.ranksObj1.getSize()): (resnum1, cov1, rank1) = self.ranksObj1.getResnumCoverageRankTuple(i) (resnum2, cov2, rank2) = self.ranksObj2.getResnumCoverageRankTuple(i) # assert(resnum1==resnum2) if slideval1 >= cov1: et1 = True if cov1 > maxcov1: maxcov1 = cov1 maxrank1 = rank1 else: et1 = False if slideval2 >= cov2: et2 = True if cov2 > maxcov2: maxcov2 = cov2 maxrank2 = rank2 else: et2 = False if et1 and not et2: cmd.show cmd.color(self.etcolor1, '%s and resi %s' % (structurename, resnum1)) elif et1 and et2: cmd.color(self.etcolor12, '%s and resi %s' % (structurename, resnum1)) elif et2 and not et1: cmd.color(self.etcolor2, '%s and resi %s' % (structurename, resnum1)) else: cmd.color(self.noetcolor, '%s and resi %s' % (structurename, resnum1)) self.percentcoverage1.setvalue(maxcov1) self.rankvalue1.setvalue(maxrank1) self.percentcoverage2.setvalue(maxcov2) self.rankvalue2.setvalue(maxrank2) self.et_messagebox.withdraw() def setRanksFileLocation1(self, value): self.ranksfile1.setvalue(value) def setRanksFileLocation2(self, value): self.ranksfile2.setvalue(value) def showZScores(self): if self.ranksStructureOK: try: self.et_messagebox.show() if self.show_qualitymeasure_options.getvalue() == self.qualitymeasure_options_tuple[0]: bias = 0 elif self.show_qualitymeasure_options.getvalue() == self.qualitymeasure_options_tuple[1]: bias = 1 if not self.adjacencyOK: if len(self.chainindicator) > 0: structurename = '%s and chain %s' % (self.structurename, self.chainindicator) else: structurename = self.structurename print("Computing adjacency matrix A(i,j)...") self._A, ResAtoms, self._Ar = self.computeAdjacency(structurename) if self._A == None: self.et_messagebox.show() return else: self.adjacencyOK = True print("... done") # Get lists of ET residues et1only = [] et12 = [] et2only = [] notet = [] slideval1 = self.slider1.get() slideval2 = self.slider2.get() for i in range(self.ranksObj1.getSize()): (resnum1, cov1, rank1) = self.ranksObj1.getResnumCoverageRankTuple(i) (resnum2, cov2, rank2) = self.ranksObj2.getResnumCoverageRankTuple(i) # assert(resnum1==resnum2) if slideval1 >= cov1: et1 = True else: et1 = False if slideval2 >= cov2: et2 = True else: et2 = False if et1 and not et2: et1only.append(int(resnum1)) elif et1 and et2: et12.append(int(resnum1)) elif et2 and not et1: et2only.append(int(resnum1)) else: notet.append(int(resnum1)) print("ET residue selection lists:") print(et1only) print(et12) print(et2only) print("Computing z-scores...") if len(et1only) > 0: z1only = self.calcZScore(et1only, self.ranksObj1.getSize(), self._A, bias) else: z1only = 'NA' if len(et12) > 0: z12 = self.calcZScore(et12, self.ranksObj1.getSize(), self._A, bias) else: z12 = 'NA' if len(et2only) > 0: z2only = self.calcZScore(et2only, self.ranksObj1.getSize(), self._A, bias) else: z2only = 'NA' self.zscore1only.setvalue(z1only) self.zscore12.setvalue(z12) self.zscore2only.setvalue(z2only) if len(notet) > 0: print('Non-ET residue z-score: ', self.calcZScore(notet, self.ranksObj1.getSize(), self._A, bias)) # Test # Residues with L>0.090000: # cnet=['54', '50', '52', '110', '81', '85', '12', '42'] # Residues with L>0.080000: # cnet=['25', '21', '54', '50', '52', '110', '80', '81', '85', '12', '19', '42', '1', '76'] # Residues with L>0.070000: # cnet=['24', '25', '21', '23', '120', '124', '54', '50', '52', '110', '80', '81', '85', '31', '69', '12', '19', '48', '44', '42', '43', '1', '76'] # Residues with L>0.050000: # cnet=['24', '25', '21', '23', '29', '120', '122', '124', '58', '54', '50', '52', '110', '80', '81', '85', '31', '61', '64', '69', '98', '12', '19', '48', '44', '42', '43', '1', '76'] # Residues with L>0.030000: # cnet=['24', '25', '20', '21', '22', '23', '29', '120', '121', '122', '123', '124', '58', '55', '54', '57', '56', '50', '53', '52', '117', '111', '110', '112', '80', '81', '119', '118', '85', '106', '31', '60', '61', '64', '65', '67', '69', '99', '98', '12', '15', '19', '89', '48', '46', '44', '42', '43', '1', '9', '76', '74', '70', '78'] # print 'Conductivity network z-score: ', self.calcZScore(cnet) # print cnet, len(cnet) print("...done") except Exception as detail: print('An exception occurred in showZScores!') print(detail) self.et_messagebox.withdraw() ############################################################### class InterproteinPairETRanks: def __init__(self): self.dataloaded = False self.maxpairs = 200 def dataLoaded(self): return self.dataloaded def readData(self, datapath): self.network = {} # (resnum1,resnum2) self.coverages = {} self.dataloaded = False FILE = open(datapath, 'r') numpairs = 0 try: for line in FILE: if line.find('%') > -1: continue if len(line.rstrip()) >= 50: ## resnum1=line[36:40].strip() ## resnum2=line[50:54].strip() ## ETpair=float(line[18:29].strip()) resnum1 = line[20:25].strip() # Using new file format of Angela (08/03/11) resnum2 = line[30:35].strip() ETpair = float(line[40:52].strip()) cvg = float(line[52:64].strip()) self.network[(resnum1, resnum2)] = ETpair self.coverages[(resnum1, resnum2)] = cvg print(resnum1, resnum2, ETpair, cvg) numpairs += 1 if numpairs == self.maxpairs: break finally: FILE.close() if len(self.network) > 0: ## for respair1, value1 in self.network.items(): ## for respair2, value2 in self.network.items(): ## if value1>=value2: ## self.coverages[respair1]+=1 ## self.coverages[respair1]=self.coverages[respair1]*100.0/numpairs self.dataloaded = True class InterproteinPairRankControlGroup: def __init__(self, page, groupname='Interprotein ET Pair Ranks Network', defaultstructurename1='(pdb)', defaultstructurename2='(pdb)', defaultrankspath='.ranks', etcolor1='red', noetcolor1='wheat', etcolor2='blue', noetcolor2='palecyan', defaultetoption=2, defaultslidercoverage=0.05): self.etcolor1 = etcolor1 self.noetcolor1 = noetcolor1 self.etcolor2 = etcolor2 self.noetcolor2 = noetcolor2 group = Pmw.Group(page, tag_text=groupname) group.pack(fill='both', expand=1, padx=10, pady=5) # Field for entering name of structure or model self.structure1 = Pmw.EntryField(group.interior(), labelpos='w', label_text='structure to use (chain 1): ', value=defaultstructurename1, ) self.structure2 = Pmw.EntryField(group.interior(), labelpos='w', label_text='structure to use (chain 2): ', value=defaultstructurename2, ) def quickFileValidation(s): if s == '': return Pmw.PARTIAL elif os.path.isfile(s): return Pmw.OK elif os.path.exists(s): return Pmw.PARTIAL else: return Pmw.PARTIAL # Button for assigning ranks to structure self.map_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.map_buttonbox.add('Map pair ranks to structure', command=self.mapRanks) # Field for entering ranks file self.ranksfile = Pmw.EntryField(group.interior(), labelpos='w', label_pyclass=FileDialogButtonClassFactory.get(self.setRanksFileLocation, '*'), validate={'validator': quickFileValidation, }, value=defaultrankspath, label_text='pair ranks file path:') # Tkinter Slider Tkinterfor changing ET residue coverage. # TODO: Use a Pmw implementation? self.slider = Scale(group.interior(), # from_=self.min, to=self.max, from_=0, to=1, showvalue=1, length=200, orient=HORIZONTAL, resolution=0.001, tickinterval=0, # repeatinterval=500, #Dunno what repeatinterval is for... repeatdelay=500 ) self.slider.set(defaultslidercoverage) # self.slider.grid() self.slider.bind("", self.slider_button_release) # self.slider.bind("", self.slider_button_release) # Field for displaying ET coverage self.frame1 = tkinter.Frame(group.interior()) self.percentcoverage = Pmw.EntryField(self.frame1, # group.interior(), labelpos='w', label_text='Percent coverage: ', value='', ) self.rankvalue = Pmw.EntryField(self.frame1, # group.interior(), labelpos='w', label_text='Rank: ', value='', ) self.percentcoverage.grid(column=0, row=0) self.rankvalue.grid(column=1, row=0) self.frame2 = tkinter.Frame(group.interior()) self.et_options_tuple = ('Colors only(' + self.etcolor1 + ',' + self.etcolor2 + ')', 'as Spheres', 'as Spheres (C-alpha only)', 'Red_to_Green') # TODO Prismatic self.show_et_options = Pmw.OptionMenu(self.frame2, # group.interior(), labelpos='w', label_text='Show ET residues', items=self.et_options_tuple, initialitem=self.et_options_tuple[defaultetoption], command=self.slider_button_release ) ## self.show_et_var=IntVar() ## self.show_et_var.set(0) ## self.show_et_checkbutton = Checkbutton(group.interior(), ## text = "Show ET residues (as spheres)", ## variable = self.show_et_var) self.pair_et_var = IntVar() self.pair_et_var.set(0) self.pair_et_checkbutton = Checkbutton(self.frame2, # group.interior(), text='Show pair (CA) distances', variable=self.pair_et_var) self.show_et_options.grid(column=0, row=0) self.pair_et_checkbutton.grid(column=1, row=0) for entry in (self.structure1, self.structure2, self.ranksfile, self.map_buttonbox, self.slider, self.frame1, self.frame2): entry.pack(fill='x', padx=4, pady=1) # vertical self.dataObj = InterproteinPairETRanks() self.ranksStructureOK = False def mapRanks(self): structurename1 = self.structure1.getvalue().strip() self.ranksStructureOK = False if len(structurename1) < 1: print('Provide structure name!') return try: model1 = cmd.get_model(structurename1) except Exception: print("Structure \'%s\' does not exist!" % structurename1) return structurename2 = self.structure2.getvalue().strip() # self.ranksStructureOK=False if len(structurename2) < 1: print('Provide structure name!') return try: model2 = cmd.get_model(structurename2) except Exception: print("Structure \'%s\' does not exist!" % structurename2) return rankspath = self.ranksfile.getvalue().strip() if len(rankspath) < 1: print('Provide path to pair ranks file!') return self.dataObj.readData(rankspath) if self.dataObj.dataLoaded(): print("Pair ranks file \'%s\' loaded" % rankspath) else: print("Error loading pair ranks file \'%s\'!" % rankspath) return # Check that the residue numbers in the model # and in the ranks file are identical ## resnumDict={} ## for i in range(len(model.atom)): ## resnumDict[model.atom[i].resi]=1 ## if len(resnumDict)<1: ## print 'Structure \'%s\' has no residues!' % structurename ## return ## if len(resnumDict)!=self.ranksObj.getSize(): ## print "Residue numbers in \'%s\' and \'%s\' are not the same!" % (structurename, rankspath) ## return ## for i in range(self.ranksObj.getSize()): ## try: ## r=resnumDict[self.ranksObj.getResnum(i)] ## except KeyError: ## print "Residue numbers in \'%s\' and \'%s\' do not match!" % (structurename, rankspath) ## return self.structurename1 = structurename1 self.structurename2 = structurename2 self.ranksStructureOK = True ## print 'Residue numbers checked with structure \'%s\'' % structurename self.slider_button_release(None) def slider_button_release(self, event): if self.ranksStructureOK: maxcov = 0 maxrank = 0 slideval = self.slider.get() if self.show_et_options.getvalue() == self.et_options_tuple[2]: cmd.hide('spheres', self.structurename1) # Need to hide spheres in case non-CA atoms are displayed cmd.hide('spheres', self.structurename2) # Also need to hide spheres first because a residue may appear in more than one pair cmd.color(self.noetcolor1, '%s' % (self.structurename1)) cmd.color(self.noetcolor2, '%s' % (self.structurename2)) for respair, rank in list(self.dataObj.network.items()): cov = self.dataObj.coverages[respair] if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color(self.etcolor1, '%s and resi %s' % (self.structurename1, respair[0])) cmd.show('spheres', '%s and resi %s and name CA' % (self.structurename1, respair[0])) cmd.color(self.etcolor2, '%s and resi %s' % (self.structurename2, respair[1])) cmd.show('spheres', '%s and resi %s and name CA' % (self.structurename2, respair[1])) elif self.show_et_options.getvalue() == self.et_options_tuple[1]: cmd.hide('spheres', '%s' % (self.structurename1)) cmd.hide('spheres', '%s' % (self.structurename2)) cmd.color(self.noetcolor1, '%s' % (self.structurename1)) cmd.color(self.noetcolor2, '%s' % (self.structurename2)) for respair, rank in list(self.dataObj.network.items()): cov = self.dataObj.coverages[respair] if slideval >= cov: if cov > maxcov: maxcov = cov maxrank = rank cmd.color(self.etcolor1, '%s and resi %s' % (self.structurename1, respair[0])) cmd.show('spheres', '%s and resi %s' % (self.structurename1, respair[0])) cmd.color(self.etcolor2, '%s and resi %s' % (self.structurename2, respair[1])) cmd.show('spheres', '%s and resi %s' % (self.structurename2, respair[1])) ## elif self.show_et_options.getvalue()==self.et_options_tuple[3]: #Do Prismatic ## for i in range(self.ranksObj.getSize()): ## (resnum,cov,rank)=self.ranksObj.getResnumCoverageRankTuple(i) ## if slideval>=cov: ## if cov>maxcov: ## maxcov=cov ## maxrank=rank ## cmd.color('_et_prism_color%d'%(int(cov-0.000001)),'%s and resi %s' % (self.structurename,resnum)) ## else: ## cmd.color('white','%s and resi %s' % (self.structurename,resnum)) ## else: ## #It turns out that calling cmd.color or cmd.select with a list of residues, e.g. 'resi 1+2+...', can crash pymol ## #if the list is too big (>300) ## for i in range(self.ranksObj.getSize()): ## (resnum,cov,rank)=self.ranksObj.getResnumCoverageRankTuple(i) ## if slideval>=cov: ## if cov>maxcov: ## maxcov=cov ## maxrank=rank ## cmd.color(self.etcolor,'%s and resi %s' % (self.structurename,resnum)) ## else: ## cmd.color(self.noetcolor,'%s and resi %s' % (self.structurename,resnum)) # Draw lines between residues if self.pair_et_var.get() == 1: pair_distance_name = 'et_pair_%s_%s_PyETV' % (self.structurename1, self.structurename2) cmd.delete(pair_distance_name) for respair, rank in list(self.dataObj.network.items()): cov = self.dataObj.coverages[respair] if slideval >= cov: cmd.distance(pair_distance_name, '%s and resi %s and name CA' % (self.structurename1, respair[0]), '%s and resi %s and name CA' % (self.structurename2, respair[1])) self.percentcoverage.setvalue(maxcov) self.rankvalue.setvalue(maxrank) def setRanksFileLocation(self, value): self.ranksfile.setvalue(value) ####################################################################### # Take the minimum pair rank coverage as the score of a residue # This class is patterned after ConductivityNetwork. class PairETRanks: def __init__(self): self.dataloaded = False def dataLoaded(self): return self.dataloaded def buildCluster(self, seed, neighbors, pcov): remain = neighbors[:] tmpcluster = [seed] for r in neighbors: for t in tmpcluster: try: L = self.network[(r, t)] if L <= pcov: tmpcluster.append(r) remain.remove(r) break except KeyError: pass try: L = self.network[(t, r)] if L <= pcov: tmpcluster.append(r) remain.remove(r) break except KeyError: pass return tmpcluster, remain def clusters(self, pcov): resnumlist = [] for resnum, pcov_ in list(self.resnumsMaxL.items()): if pcov_ <= pcov: resnumlist.append(resnum) if len(resnumlist) == 0: return None clusterlist = [] remain = resnumlist while len(remain) > 0: seed = remain[0] tmpcluster, remain = self.buildCluster(seed, remain[1:], pcov) clusterlist.append(tmpcluster) return clusterlist def readData(self, datapath): self.network = {} # (resnum1,resnum2): L value (resnum1 (maps to) minimum pair coverage value self.dataloaded = False FILE = open(datapath, 'r') try: for line in FILE: if line.find('%') > -1: continue if len(line.rstrip()) >= 50: ## resnum1=line[5:10].strip() ## resnum2=line[15:20].strip() ## ETpair=float(line[25:37].strip()) ## L=float(line[37:49].strip()) #Angela computed coverage #### self.network[(resnum1,resnum2)]=ETpair ## self.network[(resnum1,resnum2)]=L resnum1 = line[19:25].strip() resnum2 = line[33:39].strip() L = float(line[5:19].strip()) # cvg(ETP/Ave) self.network[(resnum1, resnum2)] = L try: tmpL = self.resnumsMaxL[resnum1] if tmpL > L: self.resnumsMaxL[resnum1] = L except KeyError: self.resnumsMaxL[resnum1] = L try: tmpL = self.resnumsMaxL[resnum2] if tmpL > L: self.resnumsMaxL[resnum2] = L except KeyError: self.resnumsMaxL[resnum2] = L finally: FILE.close() if len(self.network) > 0: self.dataloaded = True # This control group preceded InterproteinPairRankControlGroup class PairETControlGroup: def __init__(self, page, groupname='Pair ET Ranks Network', defaultstructurename='(pdb)', defaultrankspath='.ranks', etcolor='red', noetcolor='white'): self.etcolor = etcolor self.noetcolor = noetcolor group = Pmw.Group(page, tag_text=groupname) group.pack(fill='both', expand=1, padx=10, pady=5) # Field for entering name of structure or model self.structure = Pmw.EntryField(group.interior(), labelpos='w', label_text='structure to use: ', value=defaultstructurename, ) def quickFileValidation(s): if s == '': return Pmw.PARTIAL elif os.path.isfile(s): return Pmw.OK elif os.path.exists(s): return Pmw.PARTIAL else: return Pmw.PARTIAL # Button for assigning ranks to structure self.map_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.map_buttonbox.add('Map pair ranks to structure', command=self.mapRanks) # Field for entering ranks file self.ranksfile = Pmw.EntryField(group.interior(), labelpos='w', label_pyclass=FileDialogButtonClassFactory.get(self.setRanksFileLocation, '*.dat'), validate={'validator': quickFileValidation, }, value=defaultrankspath, label_text='pair ranks file path:') # Tkinter Slider Tkinterfor changing ET residue coverage. # TODO: Use a Pmw implementation? self.slider = Scale(group.interior(), # from_=self.min, to=self.max, from_=0, to=2, showvalue=1, length=200, orient=HORIZONTAL, resolution=0.01, tickinterval=0, # repeatinterval=500, #Dunno what repeatinterval is for... repeatdelay=500 ) self.slider.set(0.01) # self.slider.grid() self.slider.bind("", self.slider_button_release) # self.slider.bind("", self.slider_button_release) # Field for displaying ET coverage ## self.percentcoverage = Pmw.EntryField(group.interior(), ## labelpos='w', ## label_text='Percent coverage: ', ## value='', ## ) self.rankvalue = Pmw.EntryField(group.interior(), labelpos='w', label_text='pair percent coverage: ', value='', ) self.et_options_tuple = ('Colors only(' + self.etcolor + ')', 'as Spheres', 'as Spheres (C-alpha only)', 'cvg(ETP/Ave) clusters') self.show_et_options = Pmw.OptionMenu(group.interior(), labelpos='w', label_text='Show ET residues', items=self.et_options_tuple, initialitem=self.et_options_tuple[0], command=self.slider_button_release ) ## self.show_et_var=IntVar() ## self.show_et_var.set(0) ## self.show_et_checkbutton = Checkbutton(group.interior(), ## text = "Show conductivity network residues (as spheres)", ## variable = self.show_et_var) for entry in (self.structure, self.ranksfile, self.map_buttonbox, self.slider, ## self.percentcoverage, self.rankvalue, # self.show_et_checkbutton self.show_et_options): entry.pack(fill='x', padx=4, pady=1) # vertical self.dataObj = PairETRanks() self.ranksStructureOK = False def mapRanks(self): structurename = self.structure.getvalue().strip() self.ranksStructureOK = False if len(structurename) < 1: print('Provide structure name!') return try: model = cmd.get_model(structurename) except Exception: print("Structure \'%s\' does not exist!" % structurename) return rankspath = self.ranksfile.getvalue().strip() if len(rankspath) < 1: print('Provide path to pair ranks file!') return self.dataObj.readData(rankspath) if self.dataObj.dataLoaded(): print("Pair ranks file \'%s\' loaded" % rankspath) else: print("Error loading pair ranks file \'%s\'!" % rankspath) return # Check that the residue numbers in the model # and in the ranks file are identical ## resnumDict={} ## for i in range(len(model.atom)): ## resnumDict[model.atom[i].resi]=1 ## if len(resnumDict)<1: ## print 'Structure \'%s\' has no residues!' % structurename ## return ## if len(resnumDict)!=self.ranksObj.getSize(): ## print "Residue numbers in \'%s\' and \'%s\' are not the same!" % (structurename, rankspath) ## return ## for i in range(self.ranksObj.getSize()): ## try: ## r=resnumDict[self.ranksObj.getResnum(i)] ## except KeyError: ## print "Residue numbers in \'%s\' and \'%s\' do not match!" % (structurename, rankspath) ## return self.structurename = structurename self.ranksStructureOK = True ## print 'Residue numbers checked with structure \'%s\'' % structurename self.slider_button_release(None) def slider_button_release(self, event): if self.ranksStructureOK: # reslist=[] maxcov = 0 slideval = self.slider.get() if self.show_et_options.getvalue() == self.et_options_tuple[3]: # clusters = self.dataObj.clusters(slideval) if clusters: print(clusters) print("Number of cvg(ETP/Ave) clusters", len(clusters)) cmd.hide('spheres', self.structurename) # Get largest cluster cluster1 = [] size1 = 0 for clust in clusters: if len(clust) > size1: size1 = len(clust) cluster1 = clust if len(cluster1) > 0: clusters.remove(cluster1) # Get second largest cluster cluster2 = [] size2 = 0 for clust in clusters: if len(clust) > size2: size2 = len(clust) cluster2 = clust if len(cluster2) > 0: clusters.remove(cluster2) # Get third largest cluster cluster3 = [] size3 = 0 for clust in clusters: if len(clust) > size3: size3 = len(clust) cluster3 = clust cmd.hide('spheres', self.structurename) cmd.color('white', self.structurename) for r in cluster1: cmd.color('red', '%s and resi %s' % (self.structurename, r)) cmd.show('spheres', '%s and resi %s' % (self.structurename, r)) for r in cluster2: cmd.color('green', '%s and resi %s' % (self.structurename, r)) cmd.show('spheres', '%s and resi %s' % (self.structurename, r)) for r in cluster3: cmd.color('blue', '%s and resi %s' % (self.structurename, r)) cmd.show('spheres', '%s and resi %s' % (self.structurename, r)) else: cmd.hide('spheres', self.structurename) cmd.color('white', self.structurename) elif self.show_et_options.getvalue() == self.et_options_tuple[2]: cmd.hide('spheres', self.structurename) for resnum, cov in list(self.dataObj.resnumsMaxL.items()): if slideval >= cov: # reslist.append(resnum) if cov > maxcov: maxcov = cov cmd.color(self.etcolor, '%s and resi %s' % (self.structurename, resnum)) cmd.show('spheres', '%s and resi %s and name CA' % (self.structurename, resnum)) else: # TODO: Color only the spheres? cmd.color(self.noetcolor, '%s and resi %s' % (self.structurename, resnum)) cmd.hide('spheres', '%s and resi %s' % (self.structurename, resnum)) # if self.show_et_var.get()==1: elif self.show_et_options.getvalue() == self.et_options_tuple[1]: for resnum, cov in list(self.dataObj.resnumsMaxL.items()): if slideval >= cov: # reslist.append(resnum) if cov > maxcov: maxcov = cov cmd.color(self.etcolor, '%s and resi %s' % (self.structurename, resnum)) cmd.show('spheres', '%s and resi %s' % (self.structurename, resnum)) else: # TODO: Color only the spheres? cmd.color(self.noetcolor, '%s and resi %s' % (self.structurename, resnum)) cmd.hide('spheres', '%s and resi %s' % (self.structurename, resnum)) else: # print self.dataObj.resnumsMaxL for resnum, cov in list(self.dataObj.resnumsMaxL.items()): if slideval >= cov: # reslist.append(resnum) if cov > maxcov: maxcov = cov cmd.color(self.etcolor, '%s and resi %s' % (self.structurename, resnum)) else: cmd.color(self.noetcolor, '%s and resi %s' % (self.structurename, resnum)) ## self.percentcoverage.setvalue(maxcov) self.rankvalue.setvalue(maxcov) # print "Residues with L>%f:" % (slideval) # print reslist def setRanksFileLocation(self, value): self.ranksfile.setvalue(value) ################################################################### class ConductivityNetwork: def __init__(self): self.dataloaded = False def dataLoaded(self): return self.dataloaded def readData(self, datapath): self.network = {} # (resnum1,resnum2): L value (resnum1= 27: resnum1 = line[0:5].strip() resnum2 = line[5:11].strip() # Conductivity values between residues # next to each other in sequence are usually # large, so ignore these. if int(resnum2) == int(resnum1) + 1 or \ int(resnum1) == int(resnum2) + 1: continue L = float(line[11:27].strip()) self.network[(resnum1, resnum2)] = L try: tmpL = self.resnumsMaxL[resnum1] if tmpL < L: self.resnumsMaxL[resnum1] = L except KeyError: self.resnumsMaxL[resnum1] = L try: tmpL = self.resnumsMaxL[resnum2] if tmpL < L: self.resnumsMaxL[resnum2] = L except KeyError: self.resnumsMaxL[resnum2] = L finally: FILE.close() if len(self.network) > 0: self.dataloaded = True # A residue is part of the conductivity network if one of its # links passes the conductivity threshold # (rankspath -> datapath) class ConductivityViewerGroup: def __init__(self, page, groupname='Conductivity Network', defaultstructurename='(pdb)', defaultrankspath='.dat', etcolor='red', noetcolor='white'): self.etcolor = etcolor self.noetcolor = noetcolor group = Pmw.Group(page, tag_text=groupname) group.pack(fill='both', expand=1, padx=10, pady=5) # Field for entering name of structure or model self.structure = Pmw.EntryField(group.interior(), labelpos='w', label_text='structure to use: ', value=defaultstructurename, ) def quickFileValidation(s): if s == '': return Pmw.PARTIAL elif os.path.isfile(s): return Pmw.OK elif os.path.exists(s): return Pmw.PARTIAL else: return Pmw.PARTIAL # Button for assigning ranks to structure self.map_buttonbox = Pmw.ButtonBox(group.interior(), padx=0) self.map_buttonbox.add('Map conductivity to structure', command=self.mapRanks) # Field for entering ranks file self.ranksfile = Pmw.EntryField(group.interior(), labelpos='w', label_pyclass=FileDialogButtonClassFactory.get(self.setRanksFileLocation, '*.dat'), validate={'validator': quickFileValidation, }, value=defaultrankspath, label_text='Conductivity data file path:') # Tkinter Slider Tkinterfor changing ET residue coverage. # TODO: Use a Pmw implementation? self.slider = Scale(group.interior(), # from_=self.min, to=self.max, from_=0, to=2, showvalue=1, length=200, orient=HORIZONTAL, resolution=0.01, tickinterval=0, # repeatinterval=500, #Dunno what repeatinterval is for... repeatdelay=500 ) self.slider.set(0.01) # self.slider.grid() self.slider.bind("", self.slider_button_release) # self.slider.bind("", self.slider_button_release) # Field for displaying ET coverage ## self.percentcoverage = Pmw.EntryField(group.interior(), ## labelpos='w', ## label_text='Percent coverage: ', ## value='', ## ) self.rankvalue = Pmw.EntryField(group.interior(), labelpos='w', label_text='Minimum conductivity: ', value='', ) self.et_options_tuple = ('Colors only(' + self.etcolor + ')', 'as Spheres', 'as Spheres (C-alpha only)') self.show_et_options = Pmw.OptionMenu(group.interior(), labelpos='w', label_text='Show network residues', items=self.et_options_tuple, initialitem=self.et_options_tuple[0], command=self.slider_button_release ) ## self.show_et_var=IntVar() ## self.show_et_var.set(0) ## self.show_et_checkbutton = Checkbutton(group.interior(), ## text = "Show conductivity network residues (as spheres)", ## variable = self.show_et_var) for entry in (self.structure, self.ranksfile, self.map_buttonbox, self.slider, ## self.percentcoverage, self.rankvalue, # self.show_et_checkbutton self.show_et_options): entry.pack(fill='x', padx=4, pady=1) # vertical self.dataObj = ConductivityNetwork() self.ranksStructureOK = False def mapRanks(self): structurename = self.structure.getvalue().strip() self.ranksStructureOK = False if len(structurename) < 1: print('Provide structure name!') return try: model = cmd.get_model(structurename) except Exception: print("Structure \'%s\' does not exist!" % structurename) return rankspath = self.ranksfile.getvalue().strip() if len(rankspath) < 1: print('Provide path to conductivity data file!') return self.dataObj.readData(rankspath) if self.dataObj.dataLoaded(): print("Conductivity data file \'%s\' loaded" % rankspath) else: print("Error loading conductivity data file \'%s\'!" % rankspath) return # Check that the residue numbers in the model # and in the ranks file are identical ## resnumDict={} ## for i in range(len(model.atom)): ## resnumDict[model.atom[i].resi]=1 ## if len(resnumDict)<1: ## print 'Structure \'%s\' has no residues!' % structurename ## return ## if len(resnumDict)!=self.ranksObj.getSize(): ## print "Residue numbers in \'%s\' and \'%s\' are not the same!" % (structurename, rankspath) ## return ## for i in range(self.ranksObj.getSize()): ## try: ## r=resnumDict[self.ranksObj.getResnum(i)] ## except KeyError: ## print "Residue numbers in \'%s\' and \'%s\' do not match!" % (structurename, rankspath) ## return self.structurename = structurename self.ranksStructureOK = True ## print 'Residue numbers checked with structure \'%s\'' % structurename self.slider_button_release(None) def slider_button_release(self, event): if self.ranksStructureOK: reslist = [] ## maxcov=0 minL = 100 slideval = self.slider.get() if self.show_et_options.getvalue() == self.et_options_tuple[2]: cmd.hide('spheres', self.structurename) for resnum, L in list(self.dataObj.resnumsMaxL.items()): if slideval < L: reslist.append(resnum) if L < minL: minL = L cmd.color(self.etcolor, '%s and resi %s' % (self.structurename, resnum)) cmd.show('spheres', '%s and resi %s and name CA' % (self.structurename, resnum)) else: # TODO: Color only the spheres? cmd.color(self.noetcolor, '%s and resi %s' % (self.structurename, resnum)) cmd.hide('spheres', '%s and resi %s' % (self.structurename, resnum)) # if self.show_et_var.get()==1: elif self.show_et_options.getvalue() == self.et_options_tuple[1]: for resnum, L in list(self.dataObj.resnumsMaxL.items()): if slideval < L: reslist.append(resnum) if L < minL: minL = L cmd.color(self.etcolor, '%s and resi %s' % (self.structurename, resnum)) cmd.show('spheres', '%s and resi %s' % (self.structurename, resnum)) else: # TODO: Color only the spheres? cmd.color(self.noetcolor, '%s and resi %s' % (self.structurename, resnum)) cmd.hide('spheres', '%s and resi %s' % (self.structurename, resnum)) else: # print self.dataObj.resnumsMaxL for resnum, L in list(self.dataObj.resnumsMaxL.items()): if slideval < L: reslist.append(resnum) if L < minL: minL = L cmd.color(self.etcolor, '%s and resi %s' % (self.structurename, resnum)) else: cmd.color(self.noetcolor, '%s and resi %s' % (self.structurename, resnum)) ## self.percentcoverage.setvalue(maxcov) self.rankvalue.setvalue(minL) print("Residues with L>%f:" % (slideval)) print(reslist) def setRanksFileLocation(self, value): self.ranksfile.setvalue(value) ################################################################### class ETTools: def __init__(self, app): showmode = 1 # 0 - simple interface, for public. 1 - show (everything) more. if '_et_tools_pyetv_opened' not in cmd.__dict__: cmd._et_tools_pyetv_opened = False # Value tells the plugin if it has been opened before numPrismColors = 100 self.createPrismColors(numPrismColors) # 100 is hardcoded into the Prismatic options above self.createRedGreenColors(numPrismColors) # 100 is hardcoded into the Prismatic options above self.createGreyscaleColors(numPrismColors) # 100 is hardcoded into the Prismatic options above self.createDiffETColors(10) # Check if these members have been defined previously (e.g. by a .pml file) # These are used in the first Difference ET control group to load # structures and ranks files from a URL. if '_et_tools_structurename' not in cmd.__dict__: # cmd._et_tools_structurename='(pdb)' cmd._et_tools_structurename = '' if '_et_tools_structureurl' not in cmd.__dict__: cmd._et_tools_structureurl = '' if '_et_tools_rankspath1' not in cmd.__dict__: cmd._et_tools_rankspath1 = '' if '_et_tools_rankspath2' not in cmd.__dict__: cmd._et_tools_rankspath2 = '.ranks' if '_et_tools_ranksurl1' not in cmd.__dict__: cmd._et_tools_ranksurl1 = '' if '_et_tools_ranksurl2' not in cmd.__dict__: cmd._et_tools_ranksurl2 = '' # New options if '_et_tools_selectpage' not in cmd.__dict__: # This flag tells the plugin to select a particular page cmd._et_tools_selectpage = 'ET' if '_et_tools_structurename2' not in cmd.__dict__: cmd._et_tools_structurename2 = '' if len(cmd._et_tools_ranksurl1.strip()) > 0 and \ len(cmd._et_tools_ranksurl2.strip()) > 0: # import urllib tmprankspath1 = urllib.request.urlretrieve(cmd._et_tools_ranksurl1)[0] tmprankspath2 = urllib.request.urlretrieve(cmd._et_tools_ranksurl2)[0] if os.path.getsize(tmprankspath1) > 0 and \ os.path.getsize(tmprankspath2) > 0: cmd._et_tools_rankspath1 = tmprankspath1 cmd._et_tools_rankspath2 = tmprankspath2 cmd._et_tools_ranksurl1 = '' cmd._et_tools_ranksurl2 = '' parent = app.root self.parent = parent self.dialog3 = Pmw.Dialog(parent, buttons=('Close',), title='PyETV: Processing, please wait...', command=self.close3) self.dialog3.withdraw() msg = tkinter.Label(self.dialog3.interior(), text=' PyETV processing your request, please wait... Done ', # background = 'black', # foreground = 'white', # pady = 20, ) msg.pack() # Create another window for displaying Red_to_Green color ramp as legend self.dialog2 = Pmw.Dialog(parent, buttons=('Close',), title='PyETV Red_to_Green scale', command=self.close2) self.dialog2.withdraw() ramplength = 400 rampthick = 40 canvas = tkinter.Canvas(self.dialog2.interior(), width=ramplength, height=rampthick) canvas.pack() rampstripthick = ramplength / 100 for i in range(numPrismColors): canvas.create_rectangle(i * rampstripthick, 0, (i + 1) * rampstripthick, rampthick / 2, outline='grey', fill=("#%02x%02x%02x" % cmd._et_tools_prism_rg[i])) canvas.create_text(rampstripthick, 3 * rampthick / 4, text='Important (low ET score)', anchor='w') canvas.create_text(ramplength - rampstripthick, 3 * rampthick / 4, text='Unimportant', anchor='e') # Create another window for displaying gobstopper/prismatic color ramp as legend self.dialog1 = Pmw.Dialog(parent, buttons=('Close',), title='PyETV Prismatic/Gobstopper legend', command=self.close1) self.dialog1.withdraw() ramplength = 600 rampthick = 40 canvas = tkinter.Canvas(self.dialog1.interior(), width=ramplength, height=rampthick) canvas.pack() rampstripthick = ramplength / 100 for i in range(numPrismColors): canvas.create_rectangle(i * rampstripthick, 0, (i + 1) * rampstripthick, rampthick / 2, outline='grey', fill=("#%02x%02x%02x" % cmd._et_tools_prism_rgb[i])) canvas.create_text(rampstripthick, 3 * rampthick / 4, text='Important (low ET percent coverage)', anchor='w') canvas.create_text(ramplength - rampstripthick, 3 * rampthick / 4, text='Unimportant', anchor='e') # Create the main dialog. self.dialog = Pmw.Dialog(parent, buttons=('Exit PyETV',), title='PyETV PyMOL Evolutionary Trace Viewer 1.3', command=self.close) self.dialog.withdraw() Pmw.setbusycursorattributes(self.dialog.component('hull')) self.notebook = Pmw.NoteBook(self.dialog.interior()) # self.notebook.pack(fill='both',expand=1,padx=10,pady=10) ##################################################################### # Create as many ETControlGroup's as unique chains in a pdb structure # e.g. 1gotA, 1gotB, 1gotG ##################################################################### # # First option: # Expect a list of structurenames # cmd._et_tools_structurenamelist # and URLs of ranks files # cmd._et_tools_ranksurllist ## if cmd.__dict__.has_key('_et_tools_structurenamelist'): ## import urllib ## self.tracelist=[] ## numstructures=len(cmd._et_tools_structurenamelist) ## for i in range(numstructures): ## structurename=cmd._et_tools_structurenamelist[i] ## page=self.notebook.add(structurename) ## try: ## rankspath=urllib.urlretrieve(cmd._et_tools_ranksurllist[i])[0] ## except KeyError: ## rankspath='' ## self.tracelist.append(ETControlGroup(page, ## groupname=structurename, ## defaultstructurename=structurename, ## defaultrankspath=rankspath, ## etcolor='red', ## noetcolor='salmon')) ## self.tracelist[-1].mapRanks() # Second option: # Expect a python list of structure names # cmd._et_tools_structurenamelist # and the URL of the directory containing the .zip of the trace results # cmd._et_tools_zipurl # Third option: # Expect a python list of structure names # cmd._et_tools_structurenamelist # and a list of URL's of etvx files # cmd._et_tools_etvxurllist # the ranks section will be extracted from the etvx file # We want the structure to show up immediately # after launching PyMOL. This can't be done using plugins. # The pdb structures may be loaded from the etvx files, or by # loading the full structure and selecting and creating objects # representing the required chains # if '_et_tools_structurenamelist' in cmd.__dict__: # import urllib self.tracelist = [] numstructures = len(cmd._et_tools_structurenamelist) # Create a control group that controls all sliders if numstructures > 1: first_structure = cmd._et_tools_structurenamelist[0] last_structure = cmd._et_tools_structurenamelist[-1] if type(first_structure) == tuple: firsttabname = first_structure[0] + first_structure[1] # structure + chain indicator else: firsttabname = first_structure if type(last_structure) == tuple: lasttabname = last_structure[0] + last_structure[1] # structure + chain indicator else: lasttabname = last_structure # Sometimes, we get a name that ends with an '_', e.g. '1tem_'. # Underscores are not allowed in tab names for a notebook, so we have to get rid of it. mastergroupname = 'Control sliders from %s to %s' % ( firsttabname.replace('_', ' '), lasttabname.replace('_', ' ')) page = self.notebook.add('Complex') self.mastercontrol = ETMasterControlGroup(page, groupname=mastergroupname, slavelist=self.tracelist, defaultetoption=3, defaultslidercoverage=100) cmd._et_tools_selectpage = 'Complex' for i in range(numstructures): # This could be either a name of a PyMOL object ('1finA'), or a tuple of a PyMOL object and a chain indicator (('1fin','A')) structure_chain = cmd._et_tools_structurenamelist[i] if type(structure_chain) == tuple: structurenameonly = structure_chain[0] structurechain = structure_chain[1] tabname = structurenameonly + structurechain else: structurenameonly = structure_chain # Assume a string structurechain = '' tabname = structurenameonly if numstructures > 1: page = self.mastercontrol.notebook.add(tabname.replace('_', ' ')) else: page = self.notebook.add(tabname.replace('_', ' ')) rankspath = '' try: filepath = cmd._et_tools_etvxurllist[i].strip() # Consider loading from URL or local file if filepath.find('http') == 0: # Check if file is .etvx or .ranks if filepath[-5:] == '.etvx': tmpetvxpath = urllib.request.urlretrieve(filepath)[0] if os.path.getsize(tmpetvxpath) > 0: rankspath = self.extractRanks(tmpetvxpath, tabname) else: # Assume file is in .ranks format tmprankspath = urllib.request.urlretrieve(filepath)[0] if os.path.getsize(tmprankspath) > 0: rankspath = os.path.dirname(tmprankspath) + os.sep + tabname + '.ranks' try: os.rename(tmprankspath, rankspath) except OSError: # rankspath exists, try removing it first os.remove(rankspath) os.rename(tmprankspath, rankspath) else: # Check if file is .etvx or .ranks if filepath[-5:] == '.etvx': rankspath = self.extractRanks(filepath, tabname) else: # Assume file is in .ranks format rankspath = filepath except KeyError: pass if '_et_tools_colors' in cmd.__dict__: try: (etcolor_, noetcolor_) = cmd._et_tools_colors[cmd._et_tools_structurenamelist[i]] except KeyError: etcolor_ = 'red' noetcolor_ = 'salmon' else: etcolor_ = 'red' noetcolor_ = 'salmon' # cmd.load(pdbpath,object=structurename) self.tracelist.append(ETControlGroup(page, groupname=tabname, defaultstructurename=structurenameonly, defaultchain=structurechain, defaultrankspath=rankspath, defaultetoption=3, defaultslidercoverage=100, etcolor=etcolor_, noetcolor=noetcolor_, et_loader_on=False, et_colorramp=self.dialog2, et_colorPrism=self.dialog1, et_messagebox=self.dialog3 )) self.tracelist[-1].mapRanks() # TODO: Next time the plugin is opened, should the etvx/ranks files be downloaded again? if numstructures > 1: page = self.mastercontrol.notebook.add('Zcoupling') self.couplingCalculatorComplex = CouplingGroup2(page, groupname='Compute ET coupling z-score', tracelist=self.tracelist, et_messagebox=self.dialog3 ) self.InterfaceGroupComplex = InterfaceControlGroup2(page, groupname='Mark interface between structures 1 and 2', tracelist=self.tracelist, defaultinterfaceoption1=1, defaultinterfaceoption2=1, et_messagebox=self.dialog3 ) self.mastercontrol.notebook.pack(fill='both', padx=4, pady=1) # Set up a page (aka tab or folder) page = self.notebook.add('ET') self.traceA = ETControlGroup(page, groupname='View Evolutionary Trace', defaultstructurename=cmd._et_tools_structurename, defaultrankspath=cmd._et_tools_rankspath1, etcolor='red', noetcolor='salmon', # interface_on=False et_colorramp=self.dialog2, et_colorPrism=self.dialog1, et_messagebox=self.dialog3 ) # self.traceA._group.grid(column=0,row=0) # commented by Hari '''if 1: # showmode==1: page = self.notebook.add('ET2') self.traceB = ETControlGroup(page, groupname='View Evolutionary Trace 2', defaultstructurename=cmd._et_tools_structurename2, defaultrankspath=cmd._et_tools_rankspath2, etcolor='blue', noetcolor='lightblue', # interface_on=False, et_colorramp=self.dialog2, et_messagebox=self.dialog3 ) # self.traceB._group.grid(column=1,row=0)''' # Suggested to me and Panos by OL, 08/XX/12 page = self.notebook.add('EA') try: # TODO self.EvoAct = EAControlGroup(page, groupname='View Evolutionary Action', # defaultstructurename=cmd._et_tools_structurename, # defaultrankspath=cmd._et_tools_rankspath1, etcolor='red', noetcolor='green', # interface_on=False et_colorramp=self.dialog2, et_colorPrism=self.dialog1, et_messagebox=self.dialog3 ) except Exception as e: print(e) # commented by Hari '''if 1: # showmode==1: page = self.notebook.add('Zcoupling') self.couplingCalculator1 = CouplingGroup(page, groupname='Compute ET coupling z-score between Trace 1 and Trace 2', trace1=self.traceA, trace2=self.traceB, et_messagebox=self.dialog3 ) self.InterfaceGroup = InterfaceControlGroup(page, groupname='Mark interface between structures 1 and 2', defaultinterfaceoption1=0, defaultinterfaceoption2=0, et_messagebox=self.dialog3 ) page = self.notebook.add('Assembly') self.AssemblyControl = ETAssemblyControlGroup(page, groupname='Load Biological Unit from PISA', defaultetoption=3, defaultslidercoverage=100, et_colorramp=self.dialog2, et_messagebox=self.dialog3 )''' ## page = self.notebook.add('More ET') ## #Make as many of these as you like ## self.traceC=ETControlGroup(page, ## groupname='Trace C', ## #defaultstructurename='query_1finA', ## #defaultrankspath='ET_1finA.ranks', ## etcolor='magenta', ## noetcolor='pink') ## self.traceD=ETControlGroup(page, ## groupname='Trace D', ## #defaultstructurename='query_1finB', ## #defaultrankspath='ET_1finB.ranks', ## etcolor='green', ## noetcolor='palegreen') if showmode == 1: # Make as many of these as you like page = self.notebook.add('Diff ET') self.difftrace1 = DiffETControlGroup(page, groupname='Difference trace', defaultstructurename=cmd._et_tools_structurename, defaultrankspath1=cmd._et_tools_rankspath1, defaultrankspath2=cmd._et_tools_rankspath2, et_messagebox=self.dialog3 ) ## page = self.notebook.add('Diff ET 2') ## #Make as many of these as you like ## self.difftrace2=DiffETControlGroup(page, ## groupname='Diff trace', ## ) ## page = self.notebook.add('Conductivity') ## #Make as many of these as you like ## self.network1=ConductivityViewerGroup(page, ## groupname='Conductivity Network 1', ## defaultstructurename='query_2phyA', ## defaultrankspath='pyp-conductivity.dat', ## etcolor='orange', ## noetcolor='white') ## self.network2=ConductivityViewerGroup(page, ## groupname='Conductivity Network 2', ## defaultstructurename='query_2phyA', ## defaultrankspath='2phy_MI.dat', ## etcolor='cyan', ## noetcolor='white') ## page = self.notebook.add('Pair ET') ## #Make as many of these as you like ## self.pairET=PairETControlGroup(page, ## groupname='Pair ET', ## defaultstructurename='query_2phyA', ## defaultrankspath='2phyA.cvg_change', ## etcolor='red', ## noetcolor='white') # commented by Hari '''if showmode == 2: page = self.notebook.add('Interprotein ET') # Make as many of these as you like self.interproteintrace = InterproteinPairRankControlGroup(page, groupname='Interprotein ET Pair Network', defaultstructurename1='query_1f6mF', defaultstructurename2='query_1f6mH', defaultrankspath='1f6mFH.pp_rank_sorted') ## defaultstructurename1='query_1finA', ## defaultstructurename2='query_1finB', ## defaultrankspath='1finAB.pp_rank_sorted') if showmode == 1: # Possibly need this for EA work (09/01/14) page = self.notebook.add('Compute') # Make as many of these as you like self.SCWGroup = SCWGroup(page, groupname='Clustering z-score', # defaultstructurename='query_2phyA' )''' page = self.notebook.add('Credits') group = Pmw.Group(page, tag_text='Credits') group.pack(fill='both', expand=1, padx=10, pady=5) creditstext = ''' PyETV PyMOL Evolutionary Trace Viewer Created by Rhonald Lua Modified by Harikumar Govindarajan Lichtarge Lab, Baylor College of Medicine Houston, Texas Protein interfaces, surfaces and assemblies service PISA at European Bioinformatics Institute (http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html), authored by E. Krissinel and K. Henrick The code for creating a file selection dialog box was taken from apbs_tools.py of M. Lerner. Thank you to W. L. DeLano for PyMOL, and to the developers of apbs_tools.py and remote_pdb_load.py for providing these examples on how to write a PyMOL plugin, and to others who made their python scripts available on the Web. ''' credits = tkinter.Label(group.interior(), text=creditstext, background='black', foreground='white', # pady = 20, ) credits.pack(expand=1, fill='both', padx=4, pady=4) # Test # cmd.load('query_1finA.pdb') # cmd.load('query_1finB.pdb') # if cmd._et_tools_selectpage=='Diff ET 1': # self.notebook.selectpage('Diff ET 1') # elif cmd._et_tools_selectpage=='ET': # self.notebook.selectpage('ET') if cmd._et_tools_selectpage == 'Diff ET 1': # Backward compatibility self.notebook.selectpage('Diff ET') # Sometimes, we get a name that ends with an '_', e.g. '1tem_'. # Underscores are not allowed in tab names for a notebook, so we have to get rid of it. if cmd._et_tools_selectpage.replace('_', ' ') in self.notebook.pagenames(): self.notebook.selectpage(cmd._et_tools_selectpage.replace('_', ' ')) self.notebook.pack(fill='both', expand=1, padx=10, pady=10) self.notebook.setnaturalsize() self.dialog.show() cmd._et_tools_pyetv_opened = True def close(self, result): if 1: # if result=='Exit ET tools': if __name__ == '__main__': # # dies with traceback, but who cares # self.parent.destroy() else: # self.dialog.deactivate(result) self.dialog.withdraw() # This just hides the window, does not destroy and free resources? self.dialog1.withdraw() self.dialog2.withdraw() self.dialog3.withdraw() def close1(self, result): if 1: if 0: # __name__ == '__main__': # # dies with traceback, but who cares # self.parent.destroy() else: # self.dialog.deactivate(result) self.dialog1.withdraw() # This just hides the window, does not destroy and free resources? def close2(self, result): if 1: if 0: # __name__ == '__main__': # # dies with traceback, but who cares # self.parent.destroy() else: # self.dialog.deactivate(result) self.dialog2.withdraw() # This just hides the window, does not destroy and free resources? def close3(self, result): if 1: if 0: # __name__ == '__main__': # # dies with traceback, but who cares # self.parent.destroy() else: # self.dialog.deactivate(result) self.dialog3.withdraw() # This just hides the window, does not destroy and free resources? def createPrismColors(self, numcolors): if cmd._et_tools_pyetv_opened: return # Do the following only once cmd._et_tools_prism_rgb = [] # hexlist=[] for i in range(numcolors): hsv = (i * 0.8 / numcolors, 1.0, 1.0) # David's color scheme # reversegray=False #True or False # if reversegray: # hsv=(0,0,(i+1)*1.0/numcolors) # else: # hsv=(0,0,(numcolors-i)*1.0/numcolors) rgb = colorsys.hsv_to_rgb(hsv[0], hsv[1], hsv[2]) cmd._et_tools_prism_rgb.append((int(255 * rgb[0]), int(255 * rgb[1]), int(255 * rgb[2]))) # For creating a color ramp in Tkinter.Canvas # Make a perl list of prismatic colors in hex # hexlist.append("\"%.2x%.2x%.2x\"" % (int(255*rgb[0]), int(255*rgb[1]), int(255*rgb[2]))) cmd.set_color('_et_prism_color%d' % i, rgb) # print string.join(hexlist,',') def createRedGreenColors(self, numcolors): if cmd._et_tools_pyetv_opened: return # Do the following only once cmd._et_tools_prism_rg = [] # hexlist=[] for i in range(numcolors): hsv = (i * 0.33 / numcolors, 1.0, 1.0) # reversegray=False #True or False # if reversegray: # hsv=(0,1,(i+1)*1.0/numcolors) # else: # hsv=(0,1,(numcolors-i)*1.0/numcolors) rg = colorsys.hsv_to_rgb(hsv[0], hsv[1], hsv[2]) cmd._et_tools_prism_rg.append((int(255 * rg[0]), int(255 * rg[1]), int(255 * rg[2]))) # For creating a color ramp in Tkinter.Canvas # Make a perl list of prismatic colors in hex # hexlist.append("\"%.2x%.2x%.2x\"" % (int(255*rgb[0]), int(255*rgb[1]), int(255*rgb[2]))) cmd.set_color('_et_rg_color%d' % i, rg) # print string.join(hexlist,',') def createGreyscaleColors(self, numcolors): if cmd._et_tools_pyetv_opened: return # Do the following only once cmd._et_tools_greyscale_rgb = [] # David's color scheme reversegray = False # True or False for i in range(numcolors): if reversegray: hsv = (0, 0, (i + 1) * 1.0 / numcolors) # hsv=(1,1,(i+1)*1.0/numcolors) #Hue=0 or 1 for red # hsv=(0.33,1,(i+1)*1.0/numcolors) # hsv=(0.66,1,(i+1)*1.0/numcolors) else: hsv = (0, 0, (numcolors - i) * 1.0 / numcolors) # hsv=(1,1,(numcolors-i)*1.0/numcolors) # hsv=(0.33,1,(numcolors-i)*1.0/numcolors) # hsv=(0.66,1,(numcolors-i)*1.0/numcolors) rgb = colorsys.hsv_to_rgb(hsv[0], hsv[1], hsv[2]) cmd._et_tools_greyscale_rgb.append((int(255 * rgb[0]), int(255 * rgb[1]), int(255 * rgb[2]))) # For creating a color ramp in Tkinter.Canvas cmd.set_color('_et_greyscale_color%d' % i, rgb) def createDiffETColors(self, numcolors): # Make red and blue spectrum of colors for difference ET for i in range(numcolors): # hsv=(0.0,(i+1)*1.0/numcolors,1.0) #red hsv = (0.3, (i + 1) * 1.0 / numcolors, 1.0) # red rgb = colorsys.hsv_to_rgb(hsv[0], hsv[1], hsv[2]) cmd.set_color('_et_red_color%d' % i, rgb) hsv = (0.6, (i + 1) * 1.0 / numcolors, 1.0) # blue(ish) rgb = colorsys.hsv_to_rgb(hsv[0], hsv[1], hsv[2]) cmd.set_color('_et_blue_color%d' % i, rgb) def extractRanks(self, etvxpath, pdb_chain): # Get the ranks section FILE = open(etvxpath, 'r') data = '' ready = False try: for line in FILE: if line[:5] == '~tree': break if ready: data += line if line[:9] == '~ET_ranks': ready = True finally: FILE.close() # Write ranks section to file ranksfilename = os.path.dirname(etvxpath) + os.sep + pdb_chain + '.ranks' FILE_RANKS = open(ranksfilename, 'w') FILE_RANKS.write(data) FILE_RANKS.close() return ranksfilename # Create demo in root window for testing. if __name__ == '__main__': class App: def my_show(self, *args, **kwargs): pass app = App() app.root = Tk() Pmw.initialise(app.root) app.root.title('Exit button for __main__') widget = ETTools(app) exitButton = Button(app.root, text='Exit', command=app.root.destroy) exitButton.pack() app.root.mainloop() # Problem: command line scripts (e.g. pymol xxx.pml) are executed # before this plugin file is fully read. ##def Set_Diff_ET_Input(structurename,rankspath1,rankspath2): ## cmd._et_tools_structurename=structurename ## cmd._et_tools_rankspath1=rankspath1 ## cmd._et_tools_rankspath2=rankspath2 ##def Set_Diff_ET_Input_URL(structurename,ranksurl1,ranksurl2): ## import urllib #Learned this trick from remove_pdb ## rankspath1 = urllib.urlretrieve(ranksurl1)[0] ## rankspath2 = urllib.urlretrieve(ranksurl2)[0] ## cmd._et_tools_structurename=structurename ## cmd._et_tools_rankspath1=rankspath1 ## cmd._et_tools_rankspath2=rankspath2 # cmd.extend('Set_Diff_ET_Input', Set_Diff_ET_Input) # cmd.extend('Set_Diff_ET_Input_URL', Set_Diff_ET_Input_URL)