def main():
"""
reads a rosetta output pdbfile and reports residues that have a lig_dun > cutoff
"""
parser = OptionParser()
parser.add_option("-p", dest="pdbfile", help="pdbfile")
parser.add_option("-P", dest="pdblist", help="pdblist")
parser.add_option("-x", dest="cutoff", help="cutoff", default=3.0)
parser.add_option("-s",
dest="summary",
help="summary",
action="store_true")
parser.add_option("-c", dest="catalytic", help="catalytic residues")
parser.add_option("-l",
dest="ligand",
help="only ligand",
action="store_true")
parser.add_option("-n", dest="name", help="residue name (unique)")
parser.add_option("-C",
dest="catall",
help="catalytic and ligand",
action="store_true")
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()
cutoff = float(options.cutoff)
bCat = False
if options.catalytic or options.ligand or options.catall:
bCat = True
protein = Enzyme()
for pdbfile in pdbfiles:
protein.readPDB(pdbfile)
tot_value = 0
tot_atr = 0
max_val = -1
catres = []
if options.catall:
for cat in protein.catalytic:
catres.append(cat)
if options.catalytic:
icat = int(options.catalytic) - 1
if icat >= len(protein.catalytic):
print pdbfile, "catalytic out of bounds"
sys.exit()
catres.append(protein.catalytic[icat])
if options.ligand or options.catall:
catres.append(protein.ligand)
if options.name:
bCat = True
catres = protein.getResiduesByName(options.name)
if len(catres) != 1:
print "too many catalytic residues"
sys.exit()
for chn in protein.chain:
for res in chn.residue:
if bCat:
if not res in catres:
continue
edun = res.Edun
if edun > cutoff:
tot_value += edun
max_val = max(max_val, edun)
if options.summary:
print pdbfile
break
else:
print pdbfile, res.file_id, res.name, edun
#print pdbfile,tot_value,max_val
protein.clear()
def main():
"""
reads a rosetta output pdbfile and reports residues that have a lig_rep > cutoff
"""
parser = OptionParser()
parser.add_option("-p", dest="pdbfile", help="pdbfile")
parser.add_option("-P", dest="pdblist", help="pdblist")
parser.add_option("-x", dest="cutoff", help="cutoff", default=3.0)
parser.add_option("-s", dest="summary", help="summary", action="store_true")
parser.add_option("-c", dest="catalytic", help="catalytic residues", action="store_true")
parser.add_option("-l", dest="ligand", help="only ligand", action="store_true")
parser.add_option("-n", dest="name", help="residue name (unique)")
parser.add_option("-C", dest="catall", help="catalytic and ligand", action="store_true")
parser.add_option("-t", dest="total", help="total", action="store_true")
parser.add_option("-r", dest="radius", help="include residues within radius")
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()
cutoff = float(options.cutoff)
bCat = False
if options.catalytic or options.ligand or options.catall:
bCat = True
bRad = False
if options.radius:
bRad = True
rad_cutoff = float(options.radius)
protein = Enzyme()
for pdbfile in pdbfiles:
protein.readPDB(pdbfile)
tot_value = 0
tot_atr = 0
catres = []
if options.catalytic or options.catall:
for cat in protein.catalytic:
catres.append(cat)
if options.ligand or options.catall:
catres.append(protein.ligand)
if options.name:
bCat = True
catres = protein.getResiduesByName(options.name)
if len(catres) != 1:
print "too many catalytic residues"
sys.exit()
for chn in protein.chain:
if bRad:
ligAtms = protein.ligand.atom
near_res = residuesAroundAtoms(ligAtms, protein, rad_cutoff)
for res in chn.residue:
if bCat and not bRad:
if not res in catres:
continue
if bRad:
if not res in catres:
if not res in near_res:
continue
erep = res.Erep
if erep > cutoff:
tot_value += erep
tot_atr += res.Eatr
if options.summary:
print pdbfile
break
if not options.total:
myE = res.Erep + res.Eatr + res.EhbSC + res.Esol + res.Edun
print pdbfile,res.name,res.file_id,res.Erep,res.Eatr,res.EhbSC,res.Esol,res.Edun,myE
if options.total:
print pdbfile,tot_value,tot_atr
protein.clear()