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

# Conditional import
try:
    import MDAnalysis
except ImportError:
    IS_MDANALYSIS = False
else:
    IS_MDANALYSIS = True


# Create the __all__ keyword according to the conditional import
__all__ = ['chains_from_files']
if IS_MDANALYSIS:
    __all__ += ['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
[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) 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