def main():
"""
program that checks to see if histidine binding to ligand is in the right place
if not it switches the tautomer
by default the proton is expected to be pointing AWAY from the ligand.
this behaviour is changed with the -inverse option
"""
parser = OptionParser()
parser.add_option("-p", dest="pdbfile", help="pdbfile")
parser.add_option("-P", dest="pdblist", help="pdblist")
parser.add_option("-o", dest="outfile", help="outfile")
parser.add_option("-O", dest="outlist", help="outlist")
parser.add_option("-r",
dest="replace",
help="replace",
action="store_true")
parser.add_option("-i",
dest="inverse",
help="inverse",
action="store_true")
parser.add_option("-v",
dest="virtual",
help="virtual",
action="store_true")
parser.add_option("-c", dest="catalytic", help="catalytic")
parser.set_description(main.__doc__)
(options, args) = parser.parse_args()
pdbfiles = []
if options.pdblist:
pdbfiles = files_from_list(options.pdblist)
elif options.pdbfile:
pdbfiles.append(options.pdbfile)
else:
parser.print_help()
sys.exit()
outfiles = []
if options.outlist:
outfiles = files_from_list(options.outlist)
elif options.outfile:
outfiles.append(options.outfile)
elif options.replace:
for file in pdbfiles:
outfiles.append(file)
else:
parser.print_help()
sys.exit()
if len(outfiles) != len(pdbfiles):
print "differing number of files"
sys.exit()
mycat = None
for i in range(len(pdbfiles)):
#protein = Molecule()
protein = Enzyme()
protein.readPDB(pdbfiles[i])
if options.catalytic:
icat = int(options.catalytic) - 1
if icat < 0 or icat >= len(protein.catalytic):
print "accessing catalytic out of bounds"
sys.exit()
mycat = protein.catalytic[icat]
chainB = extractCatResidues(protein)
if len(chainB) == 0:
print "NO CATALYTIC RESIDUES FOR", pdbfiles[i]
sys.exit()
hislist = []
for res in chainB:
if res == None:
print "missing catalytic residue"
continue
if res.name == "HIS":
if mycat == None:
hislist.append(res)
elif res == mycat:
hislist.append(res)
#his = res
if len(hislist) == 0:
print "cannot find histidine in catalytic residues"
sys.exit()
for his in hislist:
print his.file_id
NDstate = True
if his.atomExists(" HD1"):
proton = his.getAtom(" HD1")
elif his.atomExists(" HE2"):
proton = his.getAtom(" HE2")
NDstate = False
else:
print "histidine is not protonated"
hetlist = protein.getHeteroAtoms()
mind = 1000.0
for res in hetlist:
cpres = res.clone()
cpres.removeAtomsContaining("V")
dist = closestApproachToResidue(proton, cpres)
mind = min(mind, dist)
bPoint = False
if mind < 4.0:
bPoint = True
bChanged = False
# --- if pointing and we don't want that: --- #
if bPoint and not options.inverse:
switchHisTautomer(his)
bChanged = True
# --- if not pointing and we don't want that: --- #
if not bPoint and options.inverse:
switchHisTautomer(his)
bChanged = True
if bChanged:
print "changed", pdbfiles[i]
NDstate = not NDstate
if options.virtual:
hetatms = protein.getHeteroAtoms()
for myres in hetatms:
for atm in myres:
if atm == None:
break
if atm.name == "VHNE":
if not NDstate:
atm.name = "VHND"
continue
if atm.name == "VHND":
if NDstate:
atm.name = "VHNE"
continue
protein.writePDB(outfiles[i], resRenumber=False, atomRenumber=False)
def main():
"""
checks for hydrogen bonds to ligands. Ligands differ because we don't know
the acceptor antecedants
"""
parser = OptionParser()
parser.add_option("-p", dest="pdbfile", help="pdbfile")
parser.add_option("-P", dest="pdblist", help="pdblist")
parser.add_option("-a", dest="acceptors", help="ligand acceptors")
parser.add_option("-d", dest="donors", help="ligand donors")
parser.add_option("-c", dest="catalytic", help="catalytic")
parser.add_option("-x", dest="cutoff", help="cutoff", default=-0.3)
parser.set_description(main.__doc__)
(options, args) = parser.parse_args()
pdbfiles = []
if options.pdblist:
pdbfiles = files_from_list(options.pdblist)
elif options.pdbfile:
pdbfiles.append(options.pdbfile)
else:
parser.print_help()
sys.exit()
protein = Enzyme()
HBN = HBnetwork()
if options.donors:
donor_sel = Selection()
donor_sel.makeSelection(options.donors)
if options.acceptors:
acceptor_sel = Selection()
acceptor_sel.makeSelection(options.acceptors)
for pdbfile in pdbfiles:
protein.readPDB(pdbfile)
ligands = protein.getHeteroAtoms()
lig = ligands[0]
residues = []
if options.catalytic:
cres = protein.catalytic[int(options.catalytic) - 1]
#cres = getCatalyticResidue(protein,int(options.catalytic))
if cres == None:
print "unable to find catalytic residue!"
sys.exit()
residues.append(cres)
else:
residues = protein.residueList()
HBN.createNetwork(reslist=residues)
if options.donors:
donors = donor_sel.apply_selection(protein).atomList()
if options.acceptors:
acceptors = acceptor_sel.apply_selection(protein).atomList()
if len(acceptors) == 0:
print "unable to find acceptors"
sys.exit()
for a in acceptors:
HBN.newAcceptor(A=a, res=lig)
HBN.findHbonds(cutoff=float(options.cutoff), function=1)
hblist = HBN.getHbondsToResidue(lig)
if len(hblist) > 0:
for Hb in hblist:
print pdbfile, Hb
else:
print pdbfile, " none"
HBN.clear()
protein.clear()