2079259884
Use python3 version of the print function when running under python2. Also added "from __future__ import division" to a few more module files.
396 lines
14 KiB
Python
396 lines
14 KiB
Python
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from __future__ import division
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from __future__ import print_function
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import sys
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import Source.lib
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def printHeader():
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"""
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prints the header section
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"""
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str = "%s\n" % ( getPropkaHeader() )
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str += "%s\n" % ( getReferencesHeader() )
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str += "%s\n" % ( getWarningHeader() )
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print(str)
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def writePDB(protein, file=None, filename=None, include_hydrogens=False, options=None):
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"""
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Write the residue to the new pdbfile
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"""
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if file == None:
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# opening file if not given
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if filename == None:
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filename = "%s.pdb" % (protein.name)
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file = open(filename, 'w')
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print("writing pdbfile %s" % (filename))
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close_file = True
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else:
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# don't close the file, it was opened in a different place
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close_file = False
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numb = 0
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for chain in protein.chains:
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for residue in chain.residues:
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if residue.resName not in ["N+ ", "C- "]:
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for atom in residue.atoms:
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if include_hydrogens == False and atom.name[0] == "H":
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""" don't print """
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else:
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numb += 1
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line = atom.makePDBLine(numb=numb)
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line += "\n"
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file.write(line)
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if close_file == True:
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file.close()
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def writePKA(protein, parameters, filename=None, conformation ='1A',reference="neutral", direction="folding", verbose=False, options=None):
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"""
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Write the pka-file based on the given protein
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"""
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verbose = True
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if filename == None:
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filename = "%s.pka" % (protein.name)
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file = open(filename, 'w')
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if verbose == True:
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print("Writing %s" % (filename))
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# writing propka header
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str = "%s\n" % ( getPropkaHeader() )
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str += "%s\n" % ( getReferencesHeader() )
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str += "%s\n" % ( getWarningHeader() )
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# writing pKa determinant section
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str += getDeterminantSection(protein,conformation, parameters)
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# writing pKa summary section
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str += getSummarySection(protein,conformation,parameters)
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str += "%s\n" % ( getTheLine() )
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# printing Folding Profile
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str += getFoldingProfileSection(protein, conformation=conformation, reference=reference, direction=direction, window=[0., 14., 1.0], options=options)
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# printing Protein Charge Profile
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str += getChargeProfileSection(protein, conformation=conformation)
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# now, writing the pka text to file
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file.write(str)
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file.close()
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def printTmProfile(protein, reference="neutral", window=[0., 14., 1.], Tm=[0.,0.], Tms=None, ref=None, verbose=False, options=None):
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"""
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prints Tm profile
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"""
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profile = protein.getTmProfile(reference=reference, grid=[0., 14., 0.1], Tms=Tms, ref=ref, options=options)
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if profile == None:
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str = "Could not determine Tm-profile\n"
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else:
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str = " suggested Tm-profile for %s\n" % (protein.name)
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for (pH, Tm) in profile:
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if pH >= window[0] and pH <= window[1] and (pH%window[2] < 0.01 or pH%window[2] > 0.99*window[2]):
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str += "%6.2lf%10.2lf\n" % (pH, Tm)
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print(str)
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def printResult(protein, conformation, parameters):
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"""
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prints all resulting output from determinants and down
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"""
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printPKASection(protein, conformation, parameters)
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def printPKASection(protein, conformation, parameters):
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"""
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prints out the pka-section of the result
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"""
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# geting the determinants section
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str = getDeterminantSection(protein, conformation, parameters)
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print(str)
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str = getSummarySection(protein,conformation,parameters)
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print(str)
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def getDeterminantSection(protein, conformation, parameters):
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"""
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prints out the pka-section of the result
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"""
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# getting the same order as in propka2.0
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str = "%s\n" % ( getDeterminantsHeader() )
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# printing determinants
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for chain in protein.conformations[conformation].chains:
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for residue_type in parameters.write_out_order:
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groups = [g for g in protein.conformations[conformation].groups if g.atom.chainID == chain]
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for group in groups:
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if group.residue_type == residue_type:
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str += "%s" % ( group.getDeterminantString(parameters.remove_penalised_group) )
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# Add a warning in case of coupled residues
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if protein.conformations[conformation].non_covalently_coupled_groups and not protein.options.display_coupled_residues:
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str += 'Coupled residues (marked *) were detected. Please rerun PropKa with the --display-coupled-residues \nor -d option for detailed information.\n'
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return str
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def getSummarySection(protein, conformation, parameters):
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"""
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prints out the pka-section of the result
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"""
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str = "%s\n" % ( getSummaryHeader() )
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# printing pKa summary
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for residue_type in parameters.write_out_order:
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for group in protein.conformations[conformation].groups:
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if group.residue_type == residue_type:
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str += "%s" % ( group.getSummaryString(parameters.remove_penalised_group) )
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return str
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def getFoldingProfileSection(protein, conformation='AVR', direction="folding", reference="neutral", window=[0., 14., 1.0], verbose=False, options=None):
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"""
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returns the protein-folding-profile section
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"""
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str = getTheLine()
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str += "\n"
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str += "Free energy of %9s (kcal/mol) as a function of pH (using %s reference)\n" % (direction, reference)
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profile, [pH_opt, dG_opt], [dG_min, dG_max], [pH_min, pH_max] = protein.getFoldingProfile(conformation=conformation,
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reference=reference,
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direction=direction, grid=[0., 14., 0.1], options=options)
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if profile == None:
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str += "Could not determine folding profile\n"
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else:
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for (pH, dG) in profile:
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if pH >= window[0] and pH <= window[1] and (pH%window[2] < 0.05 or pH%window[2] > 0.95):
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str += "%6.2lf%10.2lf\n" % (pH, dG)
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str += "\n"
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if pH_opt == None or dG_opt == None:
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str += "Could not determine pH optimum\n"
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else:
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str += "The pH of optimum stability is %4.1lf for which the free energy is%6.1lf kcal/mol at 298K\n" % (pH_opt, dG_opt)
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if dG_min == None or dG_max == None:
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str += "Could not determine pH values where the free energy is within 80 %s of minimum\n" % ("%")
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else:
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str += "The free energy is within 80 %s of maximum at pH %4.1lf to %4.1lf\n" % ("%", dG_min, dG_max)
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if pH_min == None or pH_max == None:
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str += "Could not determine the pH-range where the free energy is negative\n\n"
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else:
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str += "The free energy is negative in the range %4.1lf - %4.1lf\n\n" % (pH_min, pH_max)
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return str
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def getChargeProfileSection(protein, conformation='AVR', options=None):
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"""
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returns the protein-folding-profile section
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"""
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str = "Protein charge of folded and unfolded state as a function of pH\n"
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profile = protein.getChargeProfile(conformation=conformation,grid=[0., 14., 1.])
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if profile == None:
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str += "Could not determine charge profile\n"
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else:
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str += "%6s%10s%8s\n" % ("pH", "unfolded", "folded")
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for (pH, Q_mod, Q_pro) in profile:
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str += "%6.2lf%10.2lf%8.2lf\n" % (pH, Q_mod, Q_pro)
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pI_pro, pI_mod = protein.getPI(conformation=conformation)
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if pI_pro == None or pI_mod == None:
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str += "Could not determine the pI\n\n"
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else:
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str += "The pI is %5.2lf (folded) and %5.2lf (unfolded)\n" % (pI_pro, pI_mod)
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return str
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def writeJackalScapFile(mutationData=None, filename="1xxx_scap.list", options=None):
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"""
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writing a scap file for, i.e., generating a mutated protein
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"""
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file = open(filename, 'w')
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for chainID, code1, resNumb, code2 in mutationData:
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str = "%s, %d, %s\n" % (chainID, resNumb, code2)
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file.write(str)
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file.close()
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def writeScwrlSequenceFile(sequence, filename="x-ray.seq", options=None):
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"""
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writing a scwrl sequence file for, e.g., generating a mutated protein
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"""
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file = open(filename, 'w')
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start = 0
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while len(sequence[start:]) > 60:
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file.write( "%s\n" % (sequence[start:start+60]) )
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start += 60
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file.write( "%s\n" % (sequence[start:]) )
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file.close()
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# --- various header text --- #
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def getPropkaHeader():
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"""
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Creates the header
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"""
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from datetime import date
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today = date.today()
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str = "propka3.1 %93s\n" % (today)
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str += "-------------------------------------------------------------------------------------------------------\n"
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str += "-- --\n"
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str += "-- PROPKA: A PROTEIN PKA PREDICTOR --\n"
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str += "-- --\n"
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str += "-- VERSION 1.0, 04/25/2004, IOWA CITY --\n"
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str += "-- BY HUI LI --\n"
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str += "-- --\n"
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str += "-- VERSION 2.0, 11/05/2007, IOWA CITY/COPENHAGEN --\n"
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str += "-- BY DELPHINE C. BAS AND DAVID M. ROGERS --\n"
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str += "-- --\n"
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str += "-- VERSION 3.0, 01/06/2011, COPENHAGEN --\n"
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str += "-- BY MATS H.M. OLSSON AND CHRESTEN R. SONDERGARD --\n"
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str += "-- --\n"
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str += "-- VERSION 3.1, 07/01/2011, COPENHAGEN --\n"
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str += "-- BY CHRESTEN R. SONDERGARD AND MATS H.M. OLSSON --\n"
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str += "-------------------------------------------------------------------------------------------------------\n"
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str += "\n"
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return str
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def getReferencesHeader():
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"""
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Returns the 'references' part in output file
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"""
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str = ""
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str += "-------------------------------------------------------------------------------------------------------\n"
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str += " References:\n"
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str += "\n"
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str += " Very Fast Empirical Prediction and Rationalization of Protein pKa Values\n"
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str += " Hui Li, Andrew D. Robertson and Jan H. Jensen\n"
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str += " PROTEINS: Structure, Function, and Bioinformatics 61:704-721 (2005)\n"
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str += " \n"
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str += " Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes\n"
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str += " Delphine C. Bas, David M. Rogers and Jan H. Jensen\n"
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str += " PROTEINS: Structure, Function, and Bioinformatics 73:765-783 (2008)\n"
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str += " \n"
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str += " PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions\n"
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str += " Mats H.M. Olsson, Chresten R. Sondergard, Michal Rostkowski, and Jan H. Jensen\n"
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str += " Journal of Chemical Theory and Computation, 7(2):525-537 (2011)\n"
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str += " \n"
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str += " Improved Treatment of Ligands and Coupling Effects in Empirical Calculation\n"
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str += " and Rationalization of pKa Values\n"
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str += " Chresten R. Sondergaard, Mats H.M. Olsson, Michal Rostkowski, and Jan H. Jensen\n"
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str += " Journal of Chemical Theory and Computation, (2011)\n"
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str += " \n"
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str += "-------------------------------------------------------------------------------------------------------\n"
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return str
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def getWarningHeader():
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"""
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Returns the 'warning' part in output file
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"""
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str = ""
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return str
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def getDeterminantsHeader():
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"""
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Creates the Determinant header
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"""
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str = ""
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str += "--------- ----- ------ --------------------- -------------- -------------- --------------\n"
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str += " DESOLVATION EFFECTS SIDECHAIN BACKBONE COULOMBIC \n"
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str += " RESIDUE pKa BURIED REGULAR RE HYDROGEN BOND HYDROGEN BOND INTERACTION \n"
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str += "--------- ----- ------ --------- --------- -------------- -------------- --------------\n"
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return str
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def getSummaryHeader():
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"""
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returns the summary header
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"""
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str = getTheLine()
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str += "\n"
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str += "SUMMARY OF THIS PREDICTION\n"
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str += " Group pKa model-pKa ligand atom-type"
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return str
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def getTheLine():
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"""
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draw the line - Johnny Cash would have been proud - or actually Aerosmith!
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"""
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str = ""
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for i in range(0, 104):
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str += "-"
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return str
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# Interaction maps
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def make_interaction_map(name, list, interaction):
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""" Print out an interaction map named 'name' of the groups in 'list'
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based on the function 'interaction' """
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# return an empty string, if the list is empty
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if len(list)==0:
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return ''
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# for long list, use condensed formatting
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if len(list)>10:
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res = 'Condensed form:\n'
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for i in range(len(list)):
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for j in range(i,len(list)):
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if interaction(list[i],list[j]):
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res += 'Coupling: %9s - %9s\n'%(list[i].label,list[j].label)
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return res
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# Name and map header
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res = '%s\n%12s'%(name,'')
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for g in list:
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res += '%9s | '%g.label
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# do the map
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for g1 in list:
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res += '\n%-12s'%(g1.label)
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for g2 in list:
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tag = ''
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if interaction(g1, g2):
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tag = ' X '
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res += '%10s| '%tag
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return res
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