def main():
"""
creates a resfile from an enzyme
"""
parser = OptionParser()
parser.add_option("-P", dest="pdblist", help="pdblist")
parser.add_option("-p", dest="pdbfile", help="pdbfile")
parser.add_option("-o", dest="outfile", help="outfile")
parser.add_option("-O", dest="outlist", help="outlist")
parser.add_option("--no_gly",
dest="no_gly",
help="no glycine at ss",
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()
outfiles = []
if options.outlist:
outfiles = files_from_list(options.outlist)
elif options.outfile:
outfiles.append(options.outfile)
else:
parser.print_help()
sys.exit()
nfiles = len(pdbfiles)
if len(outfiles) != nfiles:
print "number of files differ"
parser.print_help()
sys.exit()
enz = Enzyme()
resfile = Resfile()
for ifile in range(nfiles):
enz.clear()
resfile.clear()
enz.readPDB(pdbfiles[ifile])
resfile.setMolecule(enz)
if options.no_gly:
natss = getSecondaryStructure(pdbfiles[ifile])
if len(natss) < enz.protein.numResidues():
print "number of residues and secondary structure do no match"
sys.exit()
prot = enz.protein
lig = enz.ligand
nres = len(prot.residue)
designable = [False] * nres
repackable = [False] * nres
for i in range(nres):
res = prot.residue[i]
if enz.isCatalytic(res):
resfile.setCatalytic(i)
else:
if res.name == "GLY":
CB = res.getAtom(" CA ")
else:
CB = res.getAtom(" CB ")
#if options.only_cat:
# --- get distance to ligand --- #
distCB = closestApproachToResidue(CB, lig)
if distCB < 6.0:
designable[i] = True
elif distCB < 8.0:
if isResPointingToRes(res, lig, cutoff=60):
designable[i] = True
else:
repackable[i] = True
elif distCB < 10.0:
repackable[i] = True
# --- get distance to residue
focusedRes = None
mindist = 5000
for cres in enz.catalytic:
dist = closestApproachToResidue(CB, cres)
if dist < mindist:
focusedRes = cres
mindist = dist
if focusedRes != None:
if mindist < 5.5:
if isResPointingToRes(res, focusedRes, cutoff=60):
designable[i] = True
else:
repackable[i] = True
elif mindist < 7.0:
repackable[i] = True
for i in range(nres):
res = enz.protein.residue[i]
if designable[i]:
if options.no_gly and res.name != "GLY":
if natss[i] == "H" or natss[i] == "E":
resfile.designNoGly(i)
else:
resfile.designOnly(i)
else:
resfile.designOnly(i)
elif repackable[i]:
resfile.repackOnly(i)
resfile.write(outfiles[ifile])
def main():
"""
shows the clashes found in a rosetta pdbfile
"""
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("-x", dest="cutoff", help="cutoff", default=3.0)
parser.add_option("-v", dest="verbose", help="verbose", action="store_true")
parser.add_option("-c", dest="catalytic", help="catalytic", 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()
startline = re.compile("res aa Eatr")
endline = re.compile("totals")
if options.outfile:
try:
OUTFILE = open(options.outfile, 'w')
except:
print "unable to create outfile"
sys.exit()
enz = Enzyme()
for pdbfile in pdbfiles:
enz.readPDB(pdbfile)
first = False
try:
FILE = open(pdbfile)
except:
print "unable to open pdbfile"
sys.exit()
bRead = False
for line in FILE.readlines():
line = string.rstrip(line)
if startline.match(line):
bRead = True
continue
if bRead and endline.match(line):
bRead = False
if bRead:
cols = line.split()
Erep = float(cols[3])
if Erep > float(options.cutoff):
if enz.isCatalytic(resid=int(cols[0])):
if options.catalytic:
if options.verbose:
if not first:
print pdbfile + ":"
print " cat ",cols[0],cols[1],Erep
continue
else:
continue
if options.outfile:
if not first:
OUTFILE.write(pdbfile + ":\n")
OUTFILE.write(cols[0] + "\n")
if options.verbose:
if not first:
print pdbfile + ":"
print " ",cols[0],cols[1],Erep
else:
if not first:
print pdbfile
first = True
enz.clear()
if options.outfile:
OUTFILE.close()