File size: 1,224 Bytes
10f2621 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | from Bio.PDB import *
# Exclude disordered atoms.
class NotDisordered(Select):
def accept_atom(self, atom):
return not atom.is_disordered() or atom.get_altloc() == 'A'
def extractHelix(helix, infilename, outfilename, chain_ids=None, includeWaters=False,\
invert=False):
parser = PDBParser(QUIET=True)
struct = parser.get_structure(infilename, infilename)
model = Selection.unfold_entities(struct, 'M')[0]
chains = Selection.unfold_entities(struct, 'C')
# Select residues to extract and build new structure
structBuild = StructureBuilder.StructureBuilder()
structBuild.init_structure("output")
structBuild.init_seg(" ")
structBuild.init_model(0)
outputStruct = structBuild.get_structure()
for chain in model:
if chain.get_id() in chain_ids:
structBuild.init_chain(chain.get_id())
for residue in chain:
het = residue.get_id()
if het[0] == ' ' and het in helix:
outputStruct[0][chain.get_id()].add(residue)
# Output the selected residues
pdbio = PDBIO()
pdbio.set_structure(outputStruct)
pdbio.save(outfilename, select=NotDisordered())
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