#! /usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function
import sys
# Local module
from .structure import Chain, Atom
from .PDB import PDB
# load MDAnalysis with limited support for Python 3
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
import MDAnalysis
# Create the __all__ keyword according to the conditional import
__all__ = ['chains_from_files', 'chains_from_trajectory']
[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
print("Read {0} chain(s) in {1}".format(pdb.nb_chains, pdb_name), file=sys.stderr)
[docs]def chains_from_trajectory(trajectory, topology):
universe = MDAnalysis.Universe(topology, trajectory)
selection = universe.select_atoms("backbone")
#Initialize structure with the selection
structure = Chain()
for atm in selection:
atom = Atom.read_from_xtc(atm)
# append structure with atom
structure.add_atom(atom)
nb_frames = len(universe.trajectory)
# Print the first frame
print("Frame {}/{}.".format(1, nb_frames), file=sys.stderr)
for ts in universe.trajectory:
#Update only with new coordinates
structure.set_coordinates(selection.positions)
# define structure comment
comment = "%s | frame %s" % (trajectory, ts.frame)
yield comment, structure
# Progress bar
# Print one frame every 100.
if ((ts.frame + 1) % 100 == 0):
print("Frame {}/{}.".format(ts.frame + 1, nb_frames), file=sys.stderr)
# Print the last frame
print("Frame {}/{}.".format(nb_frames, nb_frames), file=sys.stderr)