def pdbidx1( pdbname ):
with open( pdbname, "r" ) as f:
outlines = pdb_util.pdb_idx1( pdbname )
outfn = pdb_util.get_uniq_outpdbname( pdbname, "_idx1")
buf = open( outfn, "w" )
buf.write( outlines )
buf.close()
def slice_pdb( arguments ):
pdb, resnum_to_slice_dict, save_hetatm = arguments
pdbline_dict = pdb_util.create_xyzDict_bychain( pdb, save_hetatm )[1]
outfn_lines = ""
for chain in pdb_util.chnids:
if chain in pdbline_dict.keys():
resnums = pdb_util.get_resnums_from_resnum_dict( resnum_to_slice_dict, pdbline_dict, chain )
if not resnums: continue
for resnum in resnums:
try:
outfn_lines += pdbline_dict[ chain ][ resnum ]
except KeyError:
if resnum <= max(pdbline_dict[chain]):
print "WARNING:", resnum, "is not present in the pdb"
continue
else:
print "NOT"
return False
outfn_lines += "TER\n" # end of a chain
outfn_lines += "END\n"
assert outfn_lines, "nothing is going to be sliced, check your chain definition while selecting residues"
outfn = pdb_util.get_uniq_outpdbname( pdb, "_sliced")
buf = open( outfn, "w" )
buf.write( outfn_lines )
buf.close()
def trim_pdb( arguments ):
pdb, resnum_to_trim_dict, save_hetatm = arguments
pdbline_dict = pdb_util.create_xyzDict_bychain( pdb, save_hetatm )[1]
trim_res_list = []
for chain in sorted( pdbline_dict.keys() ):
resnums = pdb_util.get_resnums_from_resnum_dict( resnum_to_trim_dict, pdbline_dict, chain )
if not resnums: continue
for resnum in resnums:
try:
del pdbline_dict[ chain ][ resnum ]
trim_res_list.append( str(resnum)+chain )
except KeyError:
if resnum <= max(pdbline_dict[chain]):
print "WARNING:", resnum, "not in pdb"
continue
else:
stderr.write("ERROR: residue %s not present in the file\n" %(str(resnum)+chain))
return False
outfn_lines = "REMARK trim residues: %s\n" % (" ".join( trim_res_list ))
#for chain in sorted(pdbline_dict.keys()):
for chain in pdb_util.chnids:
if chain in (pdbline_dict.keys()):
for rsn in sorted(pdbline_dict[ chain ].keys()):
outfn_lines += pdbline_dict[ chain ][ rsn ]
outfn_lines += "TER\n"
outfn_lines += "END\n"
outfn = pdb_util.get_uniq_outpdbname(pdb, "_trim")
'''
pdb = basename(pdb)
tag = "_trim"
outfn = pdb[:-4] + tag
while exists( outfn+".pdb" ):
outfn += tag
print outfn
outfn = outfn+".pdb"
'''
buf = open( outfn, "w" )
buf.write( outfn_lines )
buf.close()