Source code for MDAnalysis.topology.tpr.obj
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# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
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#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
# TPR parser and tpr support module
# Copyright (c) 2011 Zhuyi Xue
# Released under the GNU Public Licence, v2
"""
Class definitions for the TPRParser
===================================
"""
from collections import namedtuple
from ..tables import Z2SYMB
TpxHeader = namedtuple(
"TpxHeader", [
"ver_str", "precision",
"fver", "fgen", "file_tag", "natoms", "ngtc", "fep_state", "lamb",
"bIr", "bTop", "bX", "bV", "bF", "bBox", "sizeOfTprBody"])
Box = namedtuple("Box", "size rel v")
Mtop = namedtuple("Mtop", "nmoltype moltypes nmolblock")
Params = namedtuple("Params", "atnr ntypes functype reppow fudgeQQ")
Atom = namedtuple("Atom", ["m", "q", "mB", "qB", "tp", "typeB", "ptype", "resind", "atomnumber"])
Atoms = namedtuple("Atoms", "atoms nr nres type typeB atomnames resnames")
Ilist = namedtuple("Ilist", "nr ik, iatoms")
Molblock = namedtuple("Molblock", [
"molb_type", "molb_nmol", "molb_natoms_mol",
"molb_nposres_xA", "molb_nposres_xB"])
[docs]class MoleculeKind(object):
def __init__(self, name, atomkinds, bonds=None, angles=None,
dihe=None, impr=None, donors=None, acceptors=None):
self.name = name # name of the molecule
self.atomkinds = atomkinds
self.bonds = bonds
self.angles = angles
self.dihe = dihe
self.impr = impr
self.donors = donors
self.acceptors = acceptors
def __repr__(self):
return (
f"Molecule: {self.name:<20s} "
f"#atoms: {self.number_of_atoms():<10d} "
f"#residues: {self.number_of_residues():<10d}"
)
# remap_ method returns [tuple(), tuple(), ..] or []
# Note: in MDAnalysis, bonds, angles, etc are represented as tuple and not as list
[docs] def remap_bonds(self, atom_start_ndx):
if self.bonds:
return [tuple(i + atom_start_ndx for i in b) for b in self.bonds]
else:
return []
[docs] def remap_angles(self, atom_start_ndx):
if self.angles:
return [tuple(i + atom_start_ndx for i in a) for a in self.angles]
else:
return []
[docs] def remap_dihe(self, atom_start_ndx):
if self.dihe:
return [tuple(i + atom_start_ndx for i in a) for a in self.dihe]
else:
return []
[docs] def remap_impr(self, atom_start_ndx):
# improper
if self.impr:
return [tuple(i + atom_start_ndx for i in a) for a in self.impr]
else:
return []
[docs]class AtomKind(object):
def __init__(
self, id, name, type, resid, resname, mass, charge, atomic_number):
# id is only within the scope of a single molecule, not the whole system
self.id = id
self.name = name
self.type = type
self.resid = resid
self.resname = resname
self.mass = mass
self.charge = charge
self.atomic_number = atomic_number
@property
def element_symbol(self):
"""
The symbol of the atom element.
The symbol corresponding to the atomic number. If the atomic number
is not recognized, which happens if a particle is not really an
atom (e.g a coarse-grained particle), an empty string is returned.
"""
return Z2SYMB.get(self.atomic_number, '')
def __repr__(self):
return (
f"< AtomKind: "
f"id {self.id:6d}, "
f"name {self.name:5s}, "
f"type {self.type:10s}, "
f"resid {self.resid:6d}, "
f"resname {self.resname:4s}, "
f"mass {self.mass:8.4f}, "
f"charge {6:12.3f} "
">"
)
[docs]class InteractionKind(object):
def __init__(self, name, long_name, natoms):
"""natoms: number of atoms involved in this type of interaction"""
self.name = name
self.long_name = long_name
self.natoms = natoms
[docs] def process(self, atom_ndx):
# The format for all record is (type, atom1, atom2, ...)
# but we are only interested in the atoms.
for cursor in range(0, len(atom_ndx), self.natoms + 1):
yield atom_ndx[cursor + 1: cursor + 1 + self.natoms]