def GetInterfaceChainsAndResiduesInfo(MolName1, ChainIDs1, MolName2, ChainIDs2,
Method, Cutoff):
"""Get interface chains and residues info for chains using a specified methodology."""
InterfaceChainsResiduesInfo1 = None
InterfaceChainsResiduesInfo2 = None
ChainNames1 = ",".join(ChainIDs1)
ChainNames2 = ",".join(ChainIDs2)
if re.match("^BySASAChange$", Method, re.I):
InterfaceChainsResiduesInfo1, InterfaceChainsResiduesInfo2 = PyMOLUtil.GetInterfaceChainsResiduesBySASAChange(
MolName1, ChainNames1, MolName2, ChainNames2, Cutoff)
elif re.match("^ByHeavyAtomsDistance$", Method, re.I):
InterfaceChainsResiduesInfo1, InterfaceChainsResiduesInfo2 = PyMOLUtil.GetnterfaceChainsResiduesByHeavyAtomsDistance(
MolName1, ChainNames1, MolName2, ChainNames2, Cutoff)
elif re.match("^ByCAlphaAtomsDistance$", Method, re.I):
InterfaceChainsResiduesInfo1, InterfaceChainsResiduesInfo2 = PyMOLUtil.GetInterfaceChainsResiduesByCAlphaAtomsDistance(
MolName1, ChainNames1, MolName2, ChainNames2, Cutoff)
else:
MiscUtil.PrintError(
"Failed to retrieve interface residues information: Method %s is not valid..."
% Method)
return InterfaceChainsResiduesInfo1, InterfaceChainsResiduesInfo2
def GetPocketSelectionResiduesInfo(MolName, ChainID, LigandResName,
LigandResNum, PocketDistanceCutoff,
SelectionType):
"""Get pocket residues info for a specified selection type. """
SelectionInfo = None
if re.match("^Pockets$", SelectionType, re.I):
SelectionInfo = PyMOLUtil.GetPocketPolymerResiduesInfo(
MolName, ChainID, LigandResName, LigandResNum,
PocketDistanceCutoff)
elif re.match("^PocketSolvents$", SelectionType, re.I):
SelectionInfo = PyMOLUtil.GetPocketSolventResiduesInfo(
MolName, ChainID, LigandResName, LigandResNum,
PocketDistanceCutoff)
elif re.match("^PocketInorganics$", SelectionType, re.I):
SelectionInfo = PyMOLUtil.GetPocketInorganicResiduesInfo(
MolName, ChainID, LigandResName, LigandResNum,
PocketDistanceCutoff)
else:
MiscUtil.PrintError(
"Failed to retrieve pocket residues information: Selection type %s is not valid..."
% SelectionType)
return SelectionInfo
def GetSelectionResiduesInfo(MolName, ChainID, SelectionType):
"""Get residues info for a specified selection type. """
SelectionInfo = None
SelectionLabel = None
if re.match("^Ligands$", SelectionType, re.I):
SelectionLabel = "ligand"
SelectionInfo = PyMOLUtil.GetLigandResiduesInfo(
MolName, ChainID) if ChainID is not None else None
elif re.match("^Solvents$", SelectionType, re.I):
SelectionLabel = "solvent"
SelectionInfo = PyMOLUtil.GetSolventResiduesInfo(
MolName, ChainID) if ChainID is not None else None
elif re.match("^Inorganics$", SelectionType, re.I):
SelectionLabel = "inorganic"
SelectionInfo = PyMOLUtil.GetInorganicResiduesInfo(
MolName, ChainID) if ChainID is not None else None
elif re.match("^Chains$", SelectionType, re.I):
SelectionLabel = "polymer chain"
SelectionInfo = PyMOLUtil.GetPolymerResiduesInfo(
MolName, ChainID) if ChainID is not None else None
elif re.match("^NonStandardAminoAcids$", SelectionType, re.I):
SelectionLabel = "non-standard amino acids"
SelectionInfo = PyMOLUtil.GetAminoAcidResiduesInfo(
MolName, ChainID, "NonStandard") if ChainID is not None else None
else:
MiscUtil.PrintError(
"Failed to retrieve residues information: Selection type %s is not valid..."
% SelectionType)
return SelectionInfo, SelectionLabel
def ProcessChainIDs():
"""Process specified chain IDs for infiles."""
OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"] = []
OptionsInfo["InfilesInfo"]["ChainSelections"] = []
for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
MiscUtil.PrintInfo("\nProcessing specified chain IDs for input file %s..." % OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex])
ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
SpecifiedChainsAndLigandsInfo = PyMOLUtil.ProcessChainsAndLigandsOptionsInfo(ChainsAndLigandsInfo, "-c, --chainIDs", OptionsInfo["ChainIDs"], None, None)
# Setup chain selections...
ChainSelections = None
if not OptionsInfo["AllChains"]:
Chains = []
for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
Chains.append("chain %s" % ChainID)
ChainSelections = " or ".join(Chains)
ChainSelections = "(%s)" % ChainSelections
OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"].append(SpecifiedChainsAndLigandsInfo)
OptionsInfo["InfilesInfo"]["ChainSelections"].append(ChainSelections)
MiscUtil.PrintInfo("Specified chain IDs: %s" % (", ".join(SpecifiedChainsAndLigandsInfo["ChainIDs"])))
def GetFormattedPropertyValue(Selection, Name):
"""Calculate and return a formatted property value. """
Quiet = OptionsInfo["Quiet"]
Precision = OptionsInfo["Precision"]
Value = None
if re.match("^CenterOfMass$", Name, re.I):
Value = PyMOLUtil.CalculateCenterOfMass(Selection, Quiet)
elif re.match("^MolecularWeight$", Name, re.I):
Value = pymol.util.compute_mass(Selection, implicit = False, quiet = Quiet)
elif re.match("^MolecularSurfaceArea$", Name, re.I):
Value = pymol.util.get_area(Selection, -1, 0, quiet = Quiet)
elif re.match("^SumOfFormalCharges$", Name, re.I):
Value = pymol.util.sum_formal_charges(Selection, quiet = Quiet)
elif re.match("^SumOfPartialCharges$", Name, re.I):
Value = pymol.util.sum_partial_charges(Selection, quiet = Quiet)
elif re.match("^SolventAccessibleSurfaceArea$", Name, re.I):
Value = pymol.util.get_sasa(Selection, quiet = Quiet)
else:
MiscUtil.PrintError("The property name specified, %s, using \"-m, --mode\" option is not a valid name." % Name)
if Value is None:
FormattedValue = "NA"
else:
if type(Value) is list:
FormattedValues = []
for ListElement in Value:
FormattedListElement = "%.*f" % (Precision, ListElement)
FormattedValues.append(FormattedListElement)
FormattedValue = " ".join(FormattedValues)
else:
FormattedValue = "%.*f" % (Precision, Value)
return FormattedValue
def ListFileInfo(Infile):
"""List information for macromolecules in a file."""
FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
MolName = FileName
# Load infile...
pymol.cmd.load(Infile, MolName)
ChainIDs = PyMOLUtil.GetChains(MolName)
ListHeaderInfo(Infile)
ListChainsInfo(MolName, ChainIDs)
ListChainsResiduesInfo(MolName, ChainIDs)
ListLigandsInfo(MolName, ChainIDs)
ListSolventsInfo(MolName, ChainIDs)
ListInorganicsInfo(MolName, ChainIDs)
ListPocketsInfo(MolName, ChainIDs)
ListInterfaceResiduesInfo(MolName, ChainIDs)
ListSurfaceResiduesInfo(MolName, ChainIDs)
ListPhiPsiAnglesInfo(MolName, ChainIDs)
ListBoundingBoxInfo(MolName)
# Delete infile object...
pymol.cmd.delete(MolName)
ListFileSizeAndModificationInfo(Infile)
def ListPocketsInfo(MolName, ChainIDs):
"""List pockect residues information across all chains."""
if not (OptionsInfo["All"] or OptionsInfo["PocketLigands"] or
OptionsInfo["PocketSolvents"] or OptionsInfo["PocketInorganics"]):
return
for ChainID in ChainIDs:
MiscUtil.PrintInfo(
"\nListing ligand pockets information for chain %s..." % (ChainID))
LigandsInfo = PyMOLUtil.GetLigandResiduesInfo(MolName, ChainID)
if not len(LigandsInfo["ResNames"]):
MiscUtil.PrintInfo("\nNumber of residues in ligand pocket: None")
MiscUtil.PrintInfo("Chain ID: %s; Ligands: None" % (ChainID))
continue
for LigandResName in sorted(LigandsInfo["ResNames"]):
for LigandResNum in LigandsInfo["ResNum"][LigandResName]:
ListPocketsPolymerInfo(MolName, ChainID, LigandResName,
LigandResNum)
ListPocketsSolventsInfo(MolName, ChainID, LigandResName,
LigandResNum)
ListPocketsInorganicsInfo(MolName, ChainID, LigandResName,
LigandResNum)
def RetrieveInfileInfo():
"""Retrieve information for input file."""
Infile = OptionsInfo["Infile"]
InfileRoot = OptionsInfo["InfileRoot"]
ChainsAndLigandsInfo = PyMOLUtil.GetChainsAndLigandsInfo(Infile, InfileRoot)
OptionsInfo["ChainsAndLigandsInfo"] = ChainsAndLigandsInfo
def ProcessChainIDs():
"""Process specified chain IDs for infile."""
MiscUtil.PrintInfo("\nProcessing specified chain IDs for input file %s..." % OptionsInfo["Infile"])
ChainsAndLigandsInfo = OptionsInfo["ChainsAndLigandsInfo"]
SpecifiedChainsAndLigandsInfo = PyMOLUtil.ProcessChainsAndLigandsOptionsInfo(ChainsAndLigandsInfo, "-c, --chainIDs", OptionsInfo["ChainIDs"], None, None)
OptionsInfo["SpecifiedChainsAndLigandsInfo"] = SpecifiedChainsAndLigandsInfo
MiscUtil.PrintInfo("Specified chain IDs: %s" % (", ".join(SpecifiedChainsAndLigandsInfo["ChainIDs"])))
def ProcessChainAndLigandIDs():
"""Process chain and ligand IDs"""
MolName = OptionsInfo["InfileRoot"]
ChainsAndLigandsInfo = PyMOLUtil.GetChainsAndLigandsInfo(
OptionsInfo["Infile"], MolName)
OptionsInfo["ChainsAndLigandsInfo"] = ChainsAndLigandsInfo
MiscUtil.PrintInfo(
"\nProcessing specified chain and ligand IDs for input file %s..." %
OptionsInfo["Infile"])
SpecifiedChainsAndLigandsInfo = PyMOLUtil.ProcessChainsAndLigandsOptionsInfo(
ChainsAndLigandsInfo, "-c, --chainIDs", OptionsInfo["ChainIDs"],
"-l, --ligandIDs", OptionsInfo["LigandIDs"])
OptionsInfo[
"SpecifiedChainsAndLigandsInfo"] = SpecifiedChainsAndLigandsInfo
CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo,
SpecifiedChainsAndLigandsInfo)
def ConvertLigandFileFormat():
"""Comvert ligand file format."""
Infile = OptionsInfo["Infile"]
Outfile = OptionsInfo["Outfile"]
MiscUtil.PrintInfo("\nGenerating file %s..." % Outfile)
PyMOLUtil.ConvertFileFormat(Infile, Outfile)
if not os.path.exists(Outfile):
MiscUtil.PrintWarning("Failed to generate Outfile file, %s..." %
(Outfile))
def GeneratePSEFile():
"""Comvert PML file to PSE file."""
PMLFile = OptionsInfo["Infile"]
PSEFile = OptionsInfo["Outfile"]
MiscUtil.PrintInfo("\nGenerating file %s..." % PSEFile)
PyMOLUtil.ConvertPMLFileToPSEFile(PMLFile,
PSEFile,
OutputFeedback=OptionsInfo["Feedback"])
if not os.path.exists(PSEFile):
MiscUtil.PrintWarning("Failed to generate PSE file, %s..." % (PSEFile))
def ListPhiPsiAnglesInfo(MolName, ChainIDs):
"""List phi and psi torsion angles for polymer chains with in a molecule."""
if not (OptionsInfo["All"] or OptionsInfo["PhiPsi"]):
return
MiscUtil.PrintInfo("\nListing phi and psi angles information...")
if not len(ChainIDs):
MiscUtil.PrintInfo("\nNumber of phi and psi angles: None\n")
return
for ChainID in ChainIDs:
if re.match("^Categories$", OptionsInfo["PhiPsiMode"], re.I):
# Retrieve phi and psi angles by categories used for Ramachandran plots
GeneralPhiPsiInfo, GlyPhiPsiInfo, ProPhiPsiInfo, PreProPhiPsiInfo = PyMOLUtil.GetPhiPsiCategoriesResiduesInfo(
MolName, ChainID)
SetupAndListPhiPsiResiduesInfo(
GeneralPhiPsiInfo,
"General (All residues except glycine, proline, or pre-proline)",
ChainID)
SetupAndListPhiPsiResiduesInfo(GlyPhiPsiInfo,
"Glycine (Only glycine residues)",
ChainID)
SetupAndListPhiPsiResiduesInfo(ProPhiPsiInfo,
"Proline (Only proline residues)",
ChainID)
SetupAndListPhiPsiResiduesInfo(
PreProPhiPsiInfo,
"Pre-Proline (Only residues before proline not including glycine or proline)",
ChainID)
else:
PhiPsiResiduesInfo = PyMOLUtil.GetPhiPsiResiduesInfo(
MolName, ChainID, Categorize=True)
SetupAndListPhiPsiResiduesInfo(PhiPsiResiduesInfo, "All", ChainID)
def CalculatePhiPsiAngles():
"""Calculate phi and psi angles for macromolecules containing amino acids."""
SetupOutputFiles()
WriteColumnLabels()
Infile = OptionsInfo["Infile"]
MolName = OptionsInfo["InfileRoot"]
MiscUtil.PrintInfo("\nCalculating phi and psi torsion angles for input file %s..." % Infile)
# Load infile
pymol.cmd.load(Infile, MolName)
OutDelim = OptionsInfo["OutDelim"]
Precision = OptionsInfo["Precision"]
# Go over specified chain IDs..
for ChainID in OptionsInfo["SpecifiedChainsAndLigandsInfo"]["ChainIDs"]:
# Write out information for combined file...
PhiPsiInfo = PyMOLUtil.GetPhiPsiResiduesInfo(MolName, ChainID, Categorize = True)
OptionsInfo["OutfileResCount"] += len(PhiPsiInfo["ResNums"])
WritePhiPsiInfo(OptionsInfo["OutFH"], MolName, ChainID, PhiPsiInfo, OutDelim, Precision)
# Write out information for category fies...
if OptionsInfo["MultipleOutFiles"]:
PhiPsiInfoList = []
GeneralPhiPsiInfo, GlycinePhiPsiInfo, ProlinePhiPsiInfo, PreProlinePhiPsiInfo = PyMOLUtil.GetPhiPsiCategoriesResiduesInfo(MolName, ChainID)
PhiPsiInfoList.extend([GeneralPhiPsiInfo, GlycinePhiPsiInfo, ProlinePhiPsiInfo, PreProlinePhiPsiInfo])
for Index, Category in enumerate(OptionsInfo["Categories"]):
OptionsInfo["CategoriesResCount"][Category] += len(PhiPsiInfoList[Index]["ResNums"])
WritePhiPsiInfo(OptionsInfo["CategoriesOutFHs"][Category], MolName, ChainID, PhiPsiInfoList[Index], OutDelim, Precision)
# Delete MolName object
pymol.cmd.delete(MolName)
# Close all files...
CloseOutputFiles()
# List number of phi and psi angles in output files...
MiscUtil.PrintInfo("\nNumber of phi and psi angles in output file %s: %d" % (OptionsInfo["Outfile"], OptionsInfo["OutfileResCount"]))
if OptionsInfo["MultipleOutFiles"]:
MiscUtil.PrintInfo("")
for Index, Category in enumerate(OptionsInfo["Categories"]):
MiscUtil.PrintInfo("Number of phi and psi angles in output file %s: %d" % (OptionsInfo["CategoriesOutfiles"][Category], OptionsInfo["CategoriesResCount"][Category]))
def RetrieveChainIDs(Infile, InfileRoot):
"""Retrieve chains IDs for an input file."""
pymol.cmd.reinitialize()
MolName = InfileRoot
pymol.cmd.load(Infile, MolName)
ChainIDs = PyMOLUtil.GetChains(MolName)
pymol.cmd.delete(MolName)
if ChainIDs is None:
ChainIDs = []
# Print out chain and ligand IDs...
ChainInfo = ", ".join(ChainIDs) if len(ChainIDs) else "None"
MiscUtil.PrintInfo("Chain IDs: %s" % ChainInfo)
return ChainIDs
def ListSurfaceResiduesInfo(MolName, ChainIDs):
"""List surface and buried residues for polymer chains with in a molecule."""
if not (OptionsInfo["All"] or OptionsInfo["SurfaceResidues"]):
return
MiscUtil.PrintInfo("\nListing surface and buried residues information...")
if not len(ChainIDs):
MiscUtil.PrintInfo(
"\nNumber of surface residues: None\nNumber of buried residues: None"
)
return
TotalSurfaceResidues, TotalBuriedResidues = [0] * 2
for ChainID in ChainIDs:
SurfaceResiduesSelectionInfo, BuriedResiduesSelectionInfo = PyMOLUtil.GetSurfaceAndBuriedResiduesInfo(
MolName, ChainID, OptionsInfo["SurfaceResiduesCutoff"])
SurfaceResiduesCount, SurfaceResiduesDistribution, SurfaceResiduesIDs = SetupSelectionResiduesInfo(
SurfaceResiduesSelectionInfo)
BuriedResiduesCount, BuriedResiduesDistribution, BuriedResiduesIDs = SetupSelectionResiduesInfo(
BuriedResiduesSelectionInfo)
TotalSurfaceResidues += SurfaceResiduesCount
MiscUtil.PrintInfo("\nChainID: %s; Number of surface residues: %d" %
(ChainID, SurfaceResiduesCount))
MiscUtil.PrintInfo("Residue distribution: %s" %
(SurfaceResiduesDistribution))
if OptionsInfo["SurfaceResiduesIDs"]:
MiscUtil.PrintInfo("Residue IDs: %s" % (SurfaceResiduesIDs))
TotalBuriedResidues += BuriedResiduesCount
MiscUtil.PrintInfo("\nChainID: %s; Number of buried residues: %d" %
(ChainID, BuriedResiduesCount))
MiscUtil.PrintInfo("Residue distribution: %s" %
(BuriedResiduesDistribution))
if OptionsInfo["SurfaceResiduesIDs"]:
MiscUtil.PrintInfo("Residue IDs: %s" % (BuriedResiduesIDs))
MiscUtil.PrintInfo(
"\nTotal number of surface residues: %d\nTotal number of buried residues: %s"
% (TotalSurfaceResidues, TotalBuriedResidues))
def RetrieveInfilesInfo():
"""Retrieve information for input files."""
InfilesInfo = {}
InfilesInfo["InfilesNames"] = []
InfilesInfo["InfilesRoots"] = []
InfilesInfo["ChainsAndLigandsInfo"] = []
for Infile in OptionsInfo["InfilesNames"]:
FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
InfileRoot = FileName
ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(Infile, InfileRoot)
InfilesInfo["InfilesNames"].append(Infile)
InfilesInfo["InfilesRoots"].append(InfileRoot)
InfilesInfo["ChainsAndLigandsInfo"].append(ChainsAndLigandInfo)
OptionsInfo["InfilesInfo"] = InfilesInfo
def RetrieveChainsIDs():
"""Retrieve chain IDs. """
MolName = OptionsInfo["InfileRoot"]
Infile = OptionsInfo["Infile"]
MiscUtil.PrintInfo("\nRetrieving chains information for input file %s..." % Infile)
LoadMolecule(Infile, MolName)
ChainIDs = PyMOLUtil.GetChains(MolName)
DeleteMolecule(MolName)
if ChainIDs is None:
ChainIDs = []
# Print out chain and ligand IDs...
ChainInfo = ", ".join(ChainIDs) if len(ChainIDs) else "None"
MiscUtil.PrintInfo("Chain IDs: %s" % ChainInfo)
OptionsInfo["ChainIDs"] = ChainIDs
def ProcessSpecifiedMutations():
"""Process specified mutations"""
MiscUtil.PrintInfo("\nProcessing specified mutations...")
SpecifiedMutationsInfo = []
Mutations = re.sub(" ", "", OptionsInfo["Mutations"])
MutationsWords = Mutations.split(",")
if not len(MutationsWords):
MiscUtil.PrintError("The number of comma delimited mutations specified using \"-m, --mutations\" option, \"%s\", must be > 0." % (OptionsInfo["Mutations"]))
# Load macromolecule from input file...
MolName = OptionsInfo["InfileRoot"]
LoadMolecule(OptionsInfo["Infile"], MolName)
FirstMutation = True
CurrentChainID = None
CanonicalMutationMap = {}
MutationsCount, ValidMutationsCount = [0] * 2
for Mutation in MutationsWords:
MutationsCount += 1
if not len(Mutation):
MiscUtil.PrintWarning("The mutation, \"%s\", specified using \"-m, --mutations\" option is empty.\nIgnoring mutation..." % (Mutation))
continue
CanonicalMutation = Mutation.lower()
if CanonicalMutation in CanonicalMutationMap:
MiscUtil.PrintWarning("The mutation, \"%s\", specified using \"-m, --mutations\" option already exist.\nIgnoring mutation..." % (Mutation))
continue
CanonicalMutationMap[CanonicalMutation] = Mutation
# Match with a chain ID...
MatchedResults = re.match(r"^([a-z0-9]+):([a-z]+)([0-9]+)([a-z]+)$", Mutation, re.I)
if not MatchedResults:
# Match without a chain ID...
MatchedResults = re.match(r"^([a-z]+)([0-9]+)([a-z]+)$", Mutation, re.I)
if not MatchedResults:
MiscUtil.PrintWarning("The format of mutation, \"%s\", specified using \"-m, --mutations\" option is not valid. Supported format: <ChainID>:<ResName><ResNum><ResName> or <ResName><ResNum><ResName>\nIgnoring mutation..." % (Mutation))
continue
NumOfMatchedGroups = len(MatchedResults.groups())
if NumOfMatchedGroups == 3:
ResName, ResNum, NewResName = MatchedResults.groups()
elif NumOfMatchedGroups == 4:
CurrentChainID, ResName, ResNum, NewResName = MatchedResults.groups()
else:
MiscUtil.PrintWarning("The format of mutation, \"%s\", specified using \"-m, --mutations\" option is not valid. Supported format: <ChainID>:<ResName><ResNum><ResName> or <ResName><ResNum><ResName>\nIgnoring mutation..." % (Mutation))
continue
if FirstMutation:
FirstMutation = False
if CurrentChainID is None:
MiscUtil.PrintError("The first mutation, \"%s\", specified using \"-m, --mutations\" option must be colon delimited and contain only two values, the first value corresponding to chain ID" % (Mutation))
ResName = ResName.upper()
NewResName = NewResName.upper()
# Is ResNum and ResName present in input file?
SelectionCmd = "%s and chain %s and resi %s and resn %s" % (MolName, CurrentChainID, ResNum, ResName)
ResiduesInfo = PyMOLUtil.GetSelectionResiduesInfo(SelectionCmd)
if (ResiduesInfo is None) or (not len(ResiduesInfo["ResNames"])):
MiscUtil.PrintWarning("The residue name, %s, and residue number, %s, in mutation, \"%s\", specified using \"-m, --mutations\" option appears to be missing in input file.\nIgnoring mutation..." % (ResName, ResNum, Mutation))
continue
ValidMutationsCount += 1
# Track mutation information...
SpecifiedMutationsInfo.append([Mutation, CurrentChainID, ResName, ResNum, NewResName])
# Delete macromolecule...
DeleteMolecule(MolName)
MiscUtil.PrintInfo("\nTotal number of mutations: %d" % MutationsCount)
MiscUtil.PrintInfo("Number of valid mutations: %d" % ValidMutationsCount)
MiscUtil.PrintInfo("Number of ignored mutations: %d" % (MutationsCount - ValidMutationsCount))
if not len(SpecifiedMutationsInfo):
MiscUtil.PrintError("No valid mutations, \"%s\" specified using \"-m, --mutations\" option." % (OptionsInfo["Mutations"]))
OptionsInfo["SpecifiedMutationsInfo"] = SpecifiedMutationsInfo
def CalculatePhiPsiAngles():
"""Calculate phi and psi angles for scatter plots."""
Infile = OptionsInfo["Infile"]
MolName = OptionsInfo["InfileRoot"]
# Load molecule...
pymol.cmd.reinitialize()
pymol.cmd.load(Infile, MolName)
MiscUtil.PrintInfo(
"\nCalculating phi and psi torsion angles for input file %s..." %
Infile)
# Initialize...
OptionsInfo["PlotTypesInfo"]["PhiAngles"] = {}
OptionsInfo["PlotTypesInfo"]["PsiAngles"] = {}
OptionsInfo["PlotTypesInfo"]["ResCount"] = {}
for PlotType in OptionsInfo["PlotTypesInfo"]["Types"]:
OptionsInfo["PlotTypesInfo"]["PhiAngles"][PlotType] = []
OptionsInfo["PlotTypesInfo"]["PsiAngles"][PlotType] = []
OptionsInfo["PlotTypesInfo"]["ResCount"][PlotType] = 0
Precision = OptionsInfo["Precision"]
TotalResCount = 0
# Go over specified chain IDs..
for ChainID in OptionsInfo["SpecifiedChainsAndLigandsInfo"]["ChainIDs"]:
PhiPsiInfoList = []
GeneralPhiPsiInfo, GlycinePhiPsiInfo, ProlinePhiPsiInfo, PreProlinePhiPsiInfo = PyMOLUtil.GetPhiPsiCategoriesResiduesInfo(
MolName, ChainID)
PhiPsiInfoList.extend([
GeneralPhiPsiInfo, GlycinePhiPsiInfo, ProlinePhiPsiInfo,
PreProlinePhiPsiInfo
])
for Index, PlotType in enumerate(
OptionsInfo["PlotTypesInfo"]["Types"]):
PhiPsiInfo = PhiPsiInfoList[Index]
ResCount = len(PhiPsiInfo["ResNums"])
if not ResCount:
continue
TotalResCount += ResCount
OptionsInfo["PlotTypesInfo"]["ResCount"][PlotType] += ResCount
PhiAngles, PsiAngles = ProcessPsiInfo(PhiPsiInfo, Precision)
OptionsInfo["PlotTypesInfo"]["PhiAngles"][PlotType].extend(
PhiAngles)
OptionsInfo["PlotTypesInfo"]["PsiAngles"][PlotType].extend(
PsiAngles)
# Delete MolName object
pymol.cmd.delete(MolName)
MiscUtil.PrintInfo("\nTotal number of phi and psi angles: %d" %
TotalResCount)
MiscUtil.PrintInfo("")
for PlotType in OptionsInfo["PlotTypesInfo"]["Types"]:
MiscUtil.PrintInfo(
"Number of \"%s\" phi and psi angles: %s" %
(PlotType, OptionsInfo["PlotTypesInfo"]["ResCount"][PlotType]))
if not TotalResCount:
MiscUtil.PrintInfo("")
MiscUtil.PrintWarning(
"No valid phi and psi angles found in input file. Ramachandran plots will be generated without phi and psi scatter plots..."
)
