Source code for mdtraj.formats.prmtop

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# MDTraj: A Python Library for Loading, Saving, and Manipulating
#         Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: TJ Lane
# Contributors: Robert McGibbon, Jason Swails
#
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
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# This library is distributed in the hope that it will be useful,
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
#
# Portions of this code originate from the OpenMM molecular simulation
# toolkit, copyright (c) 2012 Stanford University and Peter Eastman. Those
# portions are distributed under the following terms:
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
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##############################################################################
"""Load an md.Topology from AMBER PRMTOP files"""

# Written by: TJ Lane <tjlane@stanford.edu> 2/25/14
# This code was mostly stolen/stripped down from OpenMM code, specifically
# the files amber_file_parser.py and amberprmtopfile.py


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# Imports
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import re

from mdtraj.core import element as elem
from mdtraj.core import topology
from mdtraj.formats import pdb

FORMAT_RE_PATTERN = re.compile(r"([0-9]+)([a-zA-Z]+)([0-9]+)\.?([0-9]*)")

__all__ = ["load_prmtop"]

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# Functions
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def _get_pointer_value(pointer_label, raw_data):
    POINTER_LABELS = """
    NATOM, NTYPES, NBONH, MBONA, NTHETH, MTHETA,
    NPHIH, MPHIA, NHPARM, NPARM, NEXT, NRES,
    NBONA, NTHETA, NPHIA, NUMBND, NUMANG, NPTRA,
    NATYP, NPHB, IFPERT, NBPER, NGPER, NDPER,
    MBPER, MGPER, MDPER, IFBOX, NMXRS, IFCAP
    """

    POINTER_LABEL_LIST = POINTER_LABELS.replace(",", "").split()

    index = POINTER_LABEL_LIST.index(pointer_label)
    return float(raw_data["POINTERS"][index])


[docs] def load_prmtop(filename, **kwargs): """Load an AMBER prmtop topology file from disk. Parameters ---------- filename : path-like Path to the prmtop file on disk. Returns ------- top : md.Topology The resulting topology, as an md.Topology object. Notes ----- Deprecated fields in the prmtop file are not loaded. This includes the BOX dimensions, which should be stored in trajectory files instead of the prmtop for systems with periodic boundary conditions. Because '.binpos' files do not store box dimensions, this means that unitcell information will be lost if you use .binpos + .prmtop files with MDTraj. Examples -------- >>> topology = md.load_prmtop('mysystem.prmtop') >>> # or >>> trajectory = md.load('trajectory.mdcrd', top='system.prmtop') """ top = topology.Topology() prmtop_version = None flags = [] raw_format = {} raw_data = {} ignoring = False with open(filename) as f: for line in f: if line[0] == "%": if line.startswith("%VERSION"): tag, prmtop_version = line.rstrip().split(None, 1) elif line.startswith("%FLAG"): tag, flag = line.rstrip().split(None, 1) flags.append(flag) raw_data[flag] = [] ignoring = flag in ("TITLE", "CTITLE") elif line.startswith("%FORMAT"): format = line.rstrip() index0 = format.index("(") index1 = format.index(")") format = format[index0 + 1 : index1] m = FORMAT_RE_PATTERN.search(format) if m is None: ignoring = True else: raw_format[flags[-1]] = ( format, m.group(1), m.group(2), m.group(3), m.group(4), ) elif line.startswith("%COMMENT"): continue elif not ignoring: flag = flags[-1] format, numItems, itemType, itemLength, itemPrecision = raw_format[flag] iLength = int(itemLength) line = line.rstrip() for index in range(0, len(line), iLength): item = line[index : index + iLength] if item: raw_data[flag].append(item.strip()) # Add atoms to the topology pdb.PDBTrajectoryFile._loadNameReplacementTables() previous_residue = None c = top.add_chain() n_atoms = int(_get_pointer_value("NATOM", raw_data)) # built a dictionary telling us which atom belongs to which residue residue_pointer_dict = {} res_pointers = raw_data["RESIDUE_POINTER"] first_atom = [int(p) - 1 for p in res_pointers] # minus 1 necessary first_atom.append(n_atoms) res = 0 for i in range(n_atoms): while first_atom[res + 1] <= i: res += 1 residue_pointer_dict[i] = res # add each residue/atom to the topology object for index in range(n_atoms): res_number = residue_pointer_dict[index] if res_number != previous_residue: previous_residue = res_number # check res_name = raw_data["RESIDUE_LABEL"][residue_pointer_dict[index]].strip() if res_name in pdb.PDBTrajectoryFile._residueNameReplacements: res_name = pdb.PDBTrajectoryFile._residueNameReplacements[res_name] r = top.add_residue(res_name, c) if res_name in pdb.PDBTrajectoryFile._atomNameReplacements: atom_replacements = pdb.PDBTrajectoryFile._atomNameReplacements[res_name] else: atom_replacements = {} atom_name = raw_data["ATOM_NAME"][index].strip() if atom_name in atom_replacements: atom_name = atom_replacements[atom_name] # Get the element from the prmtop file if available if "ATOMIC_NUMBER" in raw_data: try: element = elem.Element.getByAtomicNumber( int(raw_data["ATOMIC_NUMBER"][index]), ) except KeyError: element = elem.virtual else: # Try to guess the element from the atom name. upper = atom_name.upper() if upper.startswith("CL"): element = elem.chlorine elif upper.startswith("NA"): element = elem.sodium elif upper.startswith("MG"): element = elem.magnesium elif upper.startswith("ZN"): element = elem.zinc else: try: element = elem.get_by_symbol(atom_name[0]) except KeyError: element = elem.virtual top.add_atom(atom_name, element, r) # Add bonds to the topology bond_pointers = raw_data["BONDS_INC_HYDROGEN"] + raw_data["BONDS_WITHOUT_HYDROGEN"] atoms = list(top.atoms) bond_list = [] for ii in range(0, len(bond_pointers), 3): if int(bond_pointers[ii]) < 0 or int(bond_pointers[ii + 1]) < 0: raise Exception( "Found negative bonded atom pointers {}".format( ( bond_pointers[ii], bond_pointers[ii + 1], ), ), ) else: bond_list.append( (int(bond_pointers[ii]) // 3, int(bond_pointers[ii + 1]) // 3), ) for bond in bond_list: top.add_bond(atoms[bond[0]], atoms[bond[1]]) return top