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 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)