Source code for MDAnalysis.topology.guessers
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# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
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"""
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