def main():
"""
performs a simple clash check (hard spheres)
"""
parser = OptionParser()
parser.add_option("-p", dest="pdbfile", help="pdbfile")
parser.add_option("-P", dest="pdblist", help="pdblist")
parser.add_option("-s", dest="scale", help="scale (0.60)", default=0.60)
parser.add_option("-S", dest="sele", help="selection")
parser.set_description(main.__doc__)
(options, args) = parser.parse_args()
pdbfiles = []
if options.pdbfile:
pdbfiles.append(options.pdbfile)
elif options.pdblist:
pdbfiles = files_from_list(options.pdblist)
else:
parser.print_help()
sys.exit()
myscale = float(options.scale)
mymol = Enzyme()
sele = None
if options.sele:
sele = Selection()
sele.makeSelection(options.sele)
for pdbfile in pdbfiles:
mymol.readPDB(pdbfile)
if options.sele:
reslist = sele.apply_selection(mymol).residueList()
else:
reslist = mymol.residueList()
nres = len(reslist)
bFail = False
for i in range(nres):
for j in range(i + 1, nres):
if (bResidue_Residue_clash_check(reslist[i], reslist[j],
myscale)):
print pdbfile, reslist[i].file_id, reslist[
j].file_id, "FAIL"
bFail = True
break
if bFail:
break
mymol.clear()
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()