from Bio.PDB import PDBIO
from Bio.PDB.PDBParser import PDBParser
from optparse import OptionParser
parser = OptionParser()
parser.add_option(
"-f",
"--pdbfile",
default=None,
type="string",
help="pdb structure file for additional 3-coord cartesian per residue")
(options, args) = parser.parse_args()
parser = PDBParser()
structure = parser.get_structure("mystruct", options.pdbfile)
model = structure[0]
average_bfactors = {}
for residue in model["C"]:
average_bfactors[residue.get_id()[1]] = 0.0
for chain in model.get_list():
for residue in chain.get_list():
if residue.has_id("CA"):
ca = residue["CA"]
average_bfactors[residue.get_id()[1]] += float(
ca.get_bfactor()) / float(len(model.get_list()))
for chain in model.get_list():
pdb_text_file = open(args[0], 'r')
for line in pdb_text_file.readlines():
if line.strip() == "":
continue
elif line.strip().split()[0] == "ATOM":
continue
elif line.strip().split()[0] == "TER":
continue
else:
other_lines.append(line.strip())
pdb_text_file.close()
parser = PDBParser(PERMISSIVE=1)
warnings.simplefilter('ignore', PDBExceptions.PDBConstructionWarning)
input_pdb = parser.get_structure('X', args[0])
output_structure_builder = StructureBuilder.StructureBuilder()
output_structure_builder.init_structure(args[1])
output_structure_builder.init_model(0)
output_struct = output_structure_builder.get_structure()
for model in output_struct:
for new_order_id in new_chain_order:
model.add(input_pdb[0][new_order_id])
id_iterator = 0
for model in output_struct:
for chain in model:
chain.id = new_chain_ids[id_iterator]
id_iterator += 1
## opening file for dumping resolutions
sf = open('res.txt', 'w')
if options.path != None:
print ('Resolution', file=sf)
resolution = ''
pdb_path = []
parser = PDBParser()
for pdb in pdbid:
try:
pdb_dir = pdb[1:3]
pdb_dir = pdb_dir.lower()
pdb = pdb.lower() ## lower case, becuase last character fo pdbid from fasta file is in uppercase
#print (pdb)
pdb_path1 = str(options.path) + pdb_dir + '/pdb' + str(pdb) + '.ent' ## full path to the pdb.ent file
pdb_path.append(pdb_path1)
structure = parser.get_structure('PHA-L', pdb_path1)
resolution = str(structure.header['resolution'])
print ('for ', pdb)
print (resolution, file=sf)
#print (pdb_path)
except IOError:
print ('Can not find', pdb_path1, ' file')
#for pdb in pdb_path:
# try:
# #print (pdb)
# structure = parser.get_structure('PHA-L', pdb)
# resolution = str(structure.header['resolution'])
# print ('for ', pdb)
# print (resolution, file=sf)
# #print (resolution)
# except IOError:
parser.add_option("--output",dest="output",default="out", help="Output name for resfile")
parser.add_option("--native",dest="native",action='store_true',help='Just repack the residues on the side flagged "design side"', default=False)
parser.add_option("--design-side",dest="design_side",default='1',help="Side of interface to design - either 1 or 2. Defaults to 1.")
parser.add_option("--repack",dest="repack",action='store_true',default=False, help='Repack side of the interface not being designed')
(options,args)= parser.parse_args()
if len(args) < 1:
parser.error('specify a pdb file or use -h')
elif len(args) > 1:
print 'Warning: only the first pdb is considered by this script. The rest will be ignored'
warnings.simplefilter('ignore',PDBExceptions.PDBConstructionWarning)
print 'Processing',args[0]
parser = PDBParser()
structure = parser.get_structure( 'X', args[ 0 ] )
## As implemented thid script only considers side chain distances. Can easily
## be reconfigured for Ca or Cb distances though
side1, side2 = sc_distance_cutoff( structure[ 0 ],
list( options.side1 ),
list( options.side2 ),
float(options.nearby_atom_cutoff) )
side_dict = {
'1' : sorted( side1, key=lambda res: ( res[1], int(res[0]) ) ),
'2' : sorted( side2, key=lambda res: ( res[1], int(res[0]) ) )
}
opposing_side = '2' if options.design_side == '1' else '1'
packer_aas = 'NATAA' if options.native else 'ALLAA'
return antibody_residues
if __name__ == '__main__':
usage = "%prog [options] <pdb_file>"
parser=OptionParser(usage)
parser.add_option("--antibody",dest="antibody",help="the chains that make up antibody (as a string, e.g. 'AB')", default="")
parser.add_option("--output",dest="output",default="out", help="Output name for pivots file")
(options,args)= parser.parse_args()
if len(args) < 1:
parser.error('specify a pdb file or use -h')
elif len(args) > 1:
print('Warning: only the first pdb is considered by this script. The rest will be ignored')
warnings.simplefilter('ignore',PDBExceptions.PDBConstructionWarning)
print('Processing',args[0])
input_pdb = args[0]
output = options.output.strip()
antibody_chains=options.antibody
parser = PDBParser()
structure = parser.get_structure( 'X', input_pdb )
antibody_residues = get_antibody_residues(structure[0],antibody_chains)
with open(output+'.pivots', 'w') as out:
for seqpos, chain, resid in antibody_residues:
out.write( ''.join([ seqpos.strip(), chain.strip() ])+',' )
#!/usr/bin/python # Xavier Ambroggio, 2012 # [email protected] from Bio.PDB import PDBIO from Bio.PDB.PDBParser import PDBParser from optparse import OptionParser parser=OptionParser() parser.add_option("-f", "--pdbfile", default = None, type = "string", help="pdb structure file for additional 3-coord cartesian per residue") (options,args)=parser.parse_args() parser=PDBParser() structure=parser.get_structure("mystruct", options.pdbfile) model=structure[0] average_bfactors = {} for residue in model["X"] : average_bfactors[ residue.get_id()[1] ] = 0.0 for chain in model.get_list(): for residue in chain.get_list(): sum_over_natoms = 0 if residue.has_id("N"): ca=residue["N"] average_bfactors[ residue.get_id()[1] ] += float( ca.get_bfactor() ) sum_over_natoms += 1 if residue.has_id("H"): ca=residue["H"]
