# Source code for MDAnalysis.topology.guessers

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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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#
# 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
#
"""
Guessing unknown Topology information --- :mod:MDAnalysis.topology.guessers
=============================================================================

In general guess_atom_X returns the guessed value for a single value,
while guess_Xs will work on an array of many atoms.

"""
from __future__ import absolute_import

import numpy as np
import warnings
import re

from ..lib import distances
from . import tables

[docs]def guess_masses(atom_types): """Guess the mass of many atoms based upon their type Parameters ---------- atom_types Type of each atom Returns ------- atom_masses : np.ndarray dtype float64 """ validate_atom_types(atom_types) masses = np.array([get_atom_mass(atom_t) for atom_t in atom_types], dtype=np.float64) return masses
[docs]def validate_atom_types(atom_types): """Vaildates the atom types based on whether they are available in our tables Parameters ---------- atom_types Type of each atom Returns ------- None .. versionchanged:: 0.20.0 Try uppercase atom type name as well """ for atom_type in np.unique(atom_types): try: tables.masses[atom_type] except KeyError: try: tables.masses[atom_type.upper()] except KeyError: warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
[docs]def guess_types(atom_names): """Guess the atom type of many atoms based on atom name Parameters ---------- atom_names Name of each atom Returns ------- atom_types : np.ndarray dtype object """ return np.array([guess_atom_element(name) for name in atom_names], dtype=object)
[docs]def guess_atom_type(atomname): """Guess atom type from the name. At the moment, this function simply returns the element, as guessed by :func:guess_atom_element. See Also -------- :func:guess_atom_element :mod:MDAnalysis.topology.tables """ return guess_atom_element(atomname)
NUMBERS = re.compile(r'[0-9]') # match numbers SYMBOLS = re.compile(r'[\*\+\-]') # match *, +, -
[docs]def guess_atom_element(atomname): """Guess the element of the atom from the name. Looks in dict to see if element is found, otherwise it uses the first character in the atomname. The table comes from CHARMM and AMBER atom types, where the first character is not sufficient to determine the atom type. Some GROMOS ions have also been added. .. Warning: The translation table is incomplete. This will probably result in some mistakes, but it still better than nothing! See Also -------- :func:guess_atom_type :mod:MDAnalysis.topology.tables """ if atomname == '': return '' try: return tables.atomelements[atomname.upper()] except KeyError: # strip symbols and numbers no_symbols = re.sub(SYMBOLS, '', atomname) name = re.sub(NUMBERS, '', no_symbols).upper() # just in case if name in tables.atomelements: return tables.atomelements[name] while name: if name in tables.elements: return name if name[:-1] in tables.elements: return name[:-1] if name[1:] in tables.elements: return name[1:] if len(name) <= 2: return name[0] name = name[:-1] # probably element is on left not right # if it's numbers return no_symbols
[docs]def guess_bonds(atoms, coords, box=None, **kwargs): r"""Guess if bonds exist between two atoms based on their distance. Bond between two atoms is created, if the two atoms are within .. math:: d < f \cdot (R_1 + R_2) of each other, where :math:R_1 and :math:R_2 are the VdW radii of the atoms and :math:f is an ad-hoc *fudge_factor*. This is the same algorithm that VMD uses_. Parameters ---------- atoms : AtomGroup atoms for which bonds should be guessed coords : array coordinates of the atoms (i.e., AtomGroup.positions)) fudge_factor : float, optional The factor by which atoms must overlap eachother to be considered a bond. Larger values will increase the number of bonds found. [0.55] vdwradii : dict, optional To supply custom vdwradii for atoms in the algorithm. Must be a dict of format {type:radii}. The default table of van der Waals radii is hard-coded as :data:MDAnalysis.topology.tables.vdwradii. Any user defined vdwradii passed as an argument will supercede the table values. [None] lower_bound : float, optional The minimum bond length. All bonds found shorter than this length will be ignored. This is useful for parsing PDB with altloc records where atoms with altloc A and B maybe very close together and there should be no chemical bond between them. [0.1] box : array_like, optional Bonds are found using a distance search, if unit cell information is given, periodic boundary conditions will be considered in the distance search. [None] Returns ------- list List of tuples suitable for use in Universe topology building. Warnings -------- No check is done after the bonds are guessed to see if Lewis structure is correct. This is wrong and will burn somebody. Raises ------ :exc:ValueError if inputs are malformed or vdwradii data is missing. .. _same algorithm that VMD uses: http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node26.html .. versionadded:: 0.7.7 .. versionchanged:: 0.9.0 Updated method internally to use more :mod:numpy, should work faster. Should also use less memory, previously scaled as :math:O(n^2). *vdwradii* argument now augments table list rather than replacing entirely. """ # why not just use atom.positions? if len(atoms) != len(coords): raise ValueError("'atoms' and 'coord' must be the same length") fudge_factor = kwargs.get('fudge_factor', 0.55) vdwradii = tables.vdwradii.copy() # so I don't permanently change it user_vdwradii = kwargs.get('vdwradii', None) if user_vdwradii: # this should make algo use their values over defaults vdwradii.update(user_vdwradii) # Try using types, then elements atomtypes = atoms.types # check that all types have a defined vdw if not all(val in vdwradii for val in set(atomtypes)): raise ValueError(("vdw radii for types: " + ", ".join([t for t in set(atomtypes) if not t in vdwradii]) + ". These can be defined manually using the" + " keyword 'vdwradii'")) lower_bound = kwargs.get('lower_bound', 0.1) if box is not None: box = np.asarray(box) # to speed up checking, calculate what the largest possible bond # atom that would warrant attention. # then use this to quickly mask distance results later max_vdw = max([vdwradii[t] for t in atomtypes]) bonds = [] pairs, dist = distances.self_capped_distance(coords, max_cutoff=2.0*max_vdw, min_cutoff=lower_bound, box=box) for idx, (i, j) in enumerate(pairs): d = (vdwradii[atomtypes[i]] + vdwradii[atomtypes[j]])*fudge_factor if (dist[idx] < d): bonds.append((atoms[i].index, atoms[j].index)) return tuple(bonds)
[docs]def guess_angles(bonds): """Given a list of Bonds, find all angles that exist between atoms. Works by assuming that if atoms 1 & 2 are bonded, and 2 & 3 are bonded, then (1,2,3) must be an angle. Returns ------- list of tuples List of tuples defining the angles. Suitable for use in u._topology See Also -------- :meth:guess_bonds .. versionadded 0.9.0 """ angles_found = set() for b in bonds: for atom in b: other_a = b.partner(atom) # who's my friend currently in Bond for other_b in atom.bonds: if other_b != b: # if not the same bond I start as third_a = other_b.partner(atom) desc = tuple([other_a.index, atom.index, third_a.index]) if desc[0] > desc[-1]: # first index always less than last desc = desc[::-1] angles_found.add(desc) return tuple(angles_found)
[docs]def guess_dihedrals(angles): """Given a list of Angles, find all dihedrals that exist between atoms. Works by assuming that if (1,2,3) is an angle, and 3 & 4 are bonded, then (1,2,3,4) must be a dihedral. Returns ------- list of tuples List of tuples defining the dihedrals. Suitable for use in u._topology .. versionadded 0.9.0 """ dihedrals_found = set() for b in angles: a_tup = tuple([a.index for a in b]) # angle as tuple of numbers # if searching with b[0], want tuple of (b[2], b[1], b[0], +new) # search the first and last atom of each angle for atom, prefix in zip([b.atoms[0], b.atoms[-1]], [a_tup[::-1], a_tup]): for other_b in atom.bonds: if not other_b.partner(atom) in b: third_a = other_b.partner(atom) desc = prefix + (third_a.index,) if desc[0] > desc[-1]: desc = desc[::-1] dihedrals_found.add(desc) return tuple(dihedrals_found)
[docs]def guess_improper_dihedrals(angles): """Given a list of Angles, find all improper dihedrals that exist between atoms. Works by assuming that if (1,2,3) is an angle, and 2 & 4 are bonded, then (2, 1, 3, 4) must be an improper dihedral. ie the improper dihedral is the angle between the planes formed by (1, 2, 3) and (1, 3, 4) Returns ------- List of tuples defining the improper dihedrals. Suitable for use in u._topology .. versionadded 0.9.0 """ dihedrals_found = set() for b in angles: atom = b[1] # select middle atom in angle # start of improper tuple a_tup = tuple([b[a].index for a in [1, 2, 0]]) # if searching with b[1], want tuple of (b[1], b[2], b[0], +new) # search the first and last atom of each angle for other_b in atom.bonds: other_atom = other_b.partner(atom) # if this atom isn't in the angle I started with if not other_atom in b: desc = a_tup + (other_atom.index,) if desc[0] > desc[-1]: desc = desc[::-1] dihedrals_found.add(desc) return tuple(dihedrals_found)
[docs]def get_atom_mass(element): """Return the atomic mass in u for *element*. Masses are looked up in :data:MDAnalysis.topology.tables.masses. .. Warning:: Unknown masses are set to 0.0 .. versionchanged:: 0.20.0 Try uppercase atom type name as well """ try: return tables.masses[element] except KeyError: try: return tables.masses[element.upper()] except KeyError: return 0.0
[docs]def guess_atom_mass(atomname): """Guess a mass based on the atom name. :func:guess_atom_element is used to determine the kind of atom. .. warning:: Anything not recognized is simply set to 0; if you rely on the masses you might want to double check. """ return get_atom_mass(guess_atom_element(atomname))
[docs]def guess_atom_charge(atomname): """Guess atom charge from the name. .. Warning:: Not implemented; simply returns 0. """ # TODO: do something slightly smarter, at least use name/element return 0.0