Source code for pbxplore.structure.loader
#! /usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import absolute_import
# Local module
from .structure import Chain, Atom
from .PDB import PDB
try:
import MDAnalysis
except ImportError:
pass
[docs]def chains_from_files(path_list):
for pdb_name in path_list:
pdb = PDB(pdb_name)
for chain in pdb.get_chains():
# build comment
comment = pdb_name
if chain.model:
comment += " | model %s" % (chain.model)
if chain.name:
comment += " | chain %s" % (chain.name)
yield comment, chain
[docs]def chains_from_trajectory(trajectory, topology):
comment = ""
universe = MDAnalysis.Universe(topology, trajectory)
for ts in universe.trajectory:
structure = Chain()
selection = universe.select_atoms("backbone")
for atm in selection:
atom = Atom()
atom.read_from_xtc(atm)
# append structure with atom
structure.add_atom(atom)
# define structure comment
# when the structure contains 1 atom
if structure.size() == 1:
comment = "%s | frame %s" % (trajectory, ts.frame)
yield comment, structure