def main():
"""
uses Will's packing 'holes' and reports the number of holes near a given selection
"""
parser = OptionParser()
parser.add_option("-p", dest="pdbfile", help="pdbfile")
parser.add_option("-P", dest="pdblist", help="pdblist")
parser.add_option("-s", dest="selection", help="selection")
parser.add_option("-c", dest="catalytic", help="catalytic")
parser.add_option("-x",
dest="cutoff",
help="hole radius cuotoff",
default="1.4")
parser.add_option("-r",
dest="radius",
help="radius around selection",
default="4.0")
parser.add_option("-v",
dest="verbose",
help="print holes",
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()
sele = Selection()
if options.selection:
sele.makeSelection(options.selection)
hole_sele = Selection()
hole_sele.makeSelection("resn=WSS")
hole_radius = float(options.cutoff)
protein = Enzyme()
for pdbfile in pdbfiles:
protein.readPDB(pdbfile)
holes = hole_sele.apply_selection(protein).atomList()
if len(holes) == 0:
print pdbfile, "no packing information found"
protein.clear()
continue
catres = []
if options.selection:
protein = sele.apply_selection(protein)
elif options.catalytic:
if len(protein.catalytic) == 0:
print "no catalytic information found!"
sys.exit()
catindex = int(options.catalytic) - 1
if catindex < 0 or catindex >= len(protein.catalytic):
print "accessing catalytic residue out of bounds: ", catindex
sys.exit()
catres = protein.catalytic[catindex]
if options.catalytic:
protList = catres.atom
else:
protList = protein.atomList()
surrounding = atomsAroundAtoms(atms=protList,
atomList=holes,
cutoff=float(options.radius))
# filter based on radius of sphere
outholes_b = []
outholes = []
for atm in surrounding:
if atm.bfactor > hole_radius:
if not atm.occupancy in outholes_b:
outholes.append(atm)
outholes_b.append(atm.occupancy)
print pdbfile, len(outholes)
if options.verbose:
for atm in outholes:
print atm
print "------------------------------------------------------"
protein.clear()
def main():
"""
prints the number of atoms that are near atoms in a given selection
default does not include ligand atoms
"""
parser = OptionParser()
parser.add_option("-p", dest="pdbfile", help="pdbfile")
parser.add_option("-P", dest="pdblist", help="pdblist")
parser.add_option("-c", dest="catalytic", help="catalytic sidechain")
parser.add_option("-l", dest="ligand", help="ligand")
parser.add_option("-s", dest="selection", help="selection")
parser.add_option("-S",
dest="neighbor_selection",
help="neighbor selection")
parser.add_option("-x",
dest="cutoff",
help="distance cutoff (default 4.5)",
default=4.5)
parser.add_option("--include_ligand",
dest="use_ligand",
help="include ligand atoms",
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()
if not options.selection and not options.catalytic:
parser.print_help()
sys.exit()
sele1 = Selection()
if options.selection:
sele1.makeSelection(options.selection)
sele2 = Selection()
if options.neighbor_selection:
sele2.makeSelection(options.neighbor_selection)
if options.catalytic:
cres = int(options.catalytic)
cres -= 1
cutoff = float(options.cutoff)
protein = Enzyme()
for pdbfile in pdbfiles:
protein.readPDB(pdbfile)
atmlist = []
alllist = []
if options.catalytic:
if cres >= len(protein.catalytic):
print "accessing catalytic residue out of bounds"
sys.exit()
# just grab sidechain
for mya in protein.catalytic[cres].atom:
nm = mya.name
if nm != " N " and nm != " CA " and nm != " C " and nm != " H " and nm != " O ":
atmlist.append(mya)
if options.selection:
mol1 = sele1.apply_selection(protein)
atmlist = mol1.atomList()
if len(atmlist) == 0:
print "selection does not specify any atoms"
sys.exit()
if options.neighbor_selection:
mol2 = sele2.apply_selection(protein)
alllist = mol2.atomList()
else:
if options.use_ligand:
alllist = protein.atomList()
else:
alllist = protein.protein.atomList()
taken = {}
for atm in atmlist:
for atm2 in alllist:
if (atm2.resi == atm.resi):
continue
icb = int(atm2.file_id)
if icb in taken.keys():
continue
dist = atm.distance(atm2)
if dist < cutoff:
taken[icb] = 1
# subtract 1 from taken as it includes self
print pdbfile, len(taken) - 1
protein.clear()