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 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..."
)
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]))