Source code for MDAnalysis.topology.tpr.obj

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# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
# MDAnalysis ---
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# (see the file AUTHORS for the full list of names)
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# 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): = 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: {<20s} " f"#atoms: {self.number_of_atoms():<10d} " f"#residues: {self.number_of_residues():<10d}" )
[docs] def number_of_atoms(self): return len(self.atomkinds)
[docs] def number_of_residues(self): return len({a.resid for a in self.atomkinds})
# 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 = id = 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 {}, " f"name {}, " 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""" = 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]