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"""Hydrogen Bond Analysis --- :mod:`MDAnalysis.analysis.hydrogenbonds.hbond_analysis`
=====================================================================================
:Author: Paul Smith
:Year: 2019
:Copyright: GNU Public License v3
.. versionadded:: 1.0.0
This module provides methods to find and analyse hydrogen bonds in a Universe.
The :class:`HydrogenBondAnalysis` class is a new version of the original
:class:`MDAnalysis.analysis.hbonds.HydrogenBondAnalysis` class from the module
:mod:`MDAnalysis.analysis.hbonds.hbond_analysis`, which itself was modeled after the `VMD
HBONDS plugin`_.
.. _`VMD HBONDS plugin`: http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/
Input
------
Required:
- *universe* : an MDAnalysis Universe object
Options:
- *donors_sel* [None] : Atom selection for donors. If `None`, then will be identified via the topology.
- *hydrogens_sel* [None] : Atom selection for hydrogens. If `None`, then will be identified via charge and mass.
- *acceptors_sel* [None] : Atom selection for acceptors. If `None`, then will be identified via charge.
- *d_h_cutoff* (Å) [1.2] : Distance cutoff used for finding donor-hydrogen pairs
- *d_a_cutoff* (Å) [3.0] : Distance cutoff for hydrogen bonds. This cutoff refers to the D-A distance.
- *d_h_a_angle_cutoff* (degrees) [150] : D-H-A angle cutoff for hydrogen bonds.
- *update_selections* [True] : If true, will update atom selections at each frame.
Output
------
- *frame* : frame at which a hydrogen bond was found
- *donor id* : atom id of the hydrogen bond donor atom
- *hydrogen id* : atom id of the hydrogen bond hydrogen atom
- *acceptor id* : atom id of the hydrogen bond acceptor atom
- *distance* (Å): length of the hydrogen bond
- *angle* (degrees): angle of the hydrogen bond
Hydrogen bond data are returned in a :class:`numpy.ndarray` on a "one line, one observation" basis
and can be accessed via :attr:`HydrogenBondAnalysis.hbonds`::
results = [
[
<frame>,
<donor index (0-based)>,
<hydrogen index (0-based)>,
<acceptor index (0-based)>,
<distance>,
<angle>
],
...
]
Example use of :class:`HydrogenBondAnalysis`
--------------------------------------------
The simplest use case is to allow :class:`HydrogenBondAnalysis` to guess the acceptor and hydrogen atoms, and to
identify donor-hydrogen pairs via the bonding information in the topology::
import MDAnalysis
from MDAnalysis.analysis.hydrogenbonds.hbond_analysis import HydrogenBondAnalysis as HBA
u = MDAnalysis.Universe(psf, trajectory)
hbonds = HBA(universe=u)
hbonds.run()
It is also possible to specify which hydrogens and acceptors to use in the analysis. For example, to find all hydrogen
bonds in water::
import MDAnalysis
from MDAnalysis.analysis.hydrogenbonds.hbond_analysis import HydrogenBondAnalysis as HBA
u = MDAnalysis.Universe(psf, trajectory)
hbonds = HBA(universe=u, hydrogens_sel='resname TIP3 and name H1 H2', acceptors_sel='resname TIP3 and name OH2')
hbonds.run()
Alternatively, :attr:`hydrogens_sel` and :attr:`acceptors_sel` may be generated via the :attr:`guess_hydrogens` and
:attr:`guess_acceptors`. This selection strings may then be modified prior to calling :attr:`run`, or a subset of
the universe may be used to guess the atoms. For example, find hydrogens and acceptors belonging to a protein::
import MDAnalysis
from MDAnalysis.analysis.hydrogenbonds.hbond_analysis import HydrogenBondAnalysis as HBA
u = MDAnalysis.Universe(psf, trajectory)
hbonds = HBA(universe=u)
hbonds.hydrogens_sel = hbonds.guess_hydrogens("protein")
hbonds.acceptors_sel = hbonds.guess_acceptors("protein")
hbonds.run()
Slightly more complex selection strings are also possible. For example, to find hydrogen bonds involving a protein and
any water molecules within 10 Å of the protein (which may be useful for subsequently finding the lifetime of
protein-water hydrogen bonds or finding water-bridging hydrogen bond paths)::
import MDAnalysis
from MDAnalysis.analysis.hydrogenbonds.hbond_analysis import HydrogenBondAnalysis as HBA
u = MDAnalysis.Universe(psf, trajectory)
hbonds = HBA(universe=u)
protein_hydrogens_sel = hbonds.guess_hydrogens("protein")
protein_acceptors_sel = hbonds.guess_acceptors("protein")
water_hydrogens_sel = "resname TIP3 and name H1 H2"
water_acceptors_sel = "resname TIP3 and name OH2"
hbonds.hydrogens_sel = f"({protein_hydrogens_sel}) or ({water_hydrogens_sel} and around 10 not resname TIP3})"
hbonds.acceptors_sel = f"({protein_acceptors_sel}) or ({water_acceptors_sel} and around 10 not resname TIP3})"
hbonds.run()
It is highly recommended that a topology with bonding information is used to generate the universe, e.g `PSF`, `TPR`, or
`PRMTOP` files. This is the only method by which it can be guaranteed that donor-hydrogen pairs are correctly identified.
However, if, for example, a `PDB` file is used instead, a :attr:`donors_sel` may be provided along with a
:attr:`hydrogens_sel` and the donor-hydrogen pairs will be identified via a distance cutoff, :attr:`d_h_cutoff`::
import MDAnalysis
from MDAnalysis.analysis.hydrogenbonds.hbond_analysis import HydrogenBondAnalysis as HBA
u = MDAnalysis.Universe(pdb, trajectory)
hbonds = HBA(
universe=u,
donors_sel='resname TIP3 and name OH2',
hydrogens_sel='resname TIP3 and name H1 H2',
acceptors_sel='resname TIP3 and name OH2',
d_h_cutoff=1.2
)
hbonds.run()
The class and its methods
-------------------------
.. autoclass:: HydrogenBondAnalysis
:members:
"""
from __future__ import absolute_import, division
import warnings
import numpy as np
from .. import base
from MDAnalysis.lib.distances import capped_distance, calc_angles
from MDAnalysis.exceptions import NoDataError
from MDAnalysis.core.groups import AtomGroup
from ...due import due, Doi
due.cite(Doi("10.1039/C9CP01532A"),
description="Hydrogen bond analysis implementation",
path="MDAnalysis.analysis.hydrogenbonds.hbond_analysis",
cite_module=True)
del Doi
[docs]class HydrogenBondAnalysis(base.AnalysisBase):
"""
Perform an analysis of hydrogen bonds in a Universe.
"""
def __init__(self, universe, donors_sel=None, hydrogens_sel=None, acceptors_sel=None,
d_h_cutoff=1.2, d_a_cutoff=3.0, d_h_a_angle_cutoff=150, update_selections=True):
"""Set up atom selections and geometric criteria for finding hydrogen bonds in a Universe.
Parameters
----------
universe : Universe
MDAnalysis Universe object
donors_sel : str
Selection string for the hydrogen bond donor atoms. If the universe topology contains bonding information,
leave :attr:`donors_sel` as `None` so that donor-hydrogen pairs can be correctly identified.
hydrogens_sel : str
Selection string for the hydrogen bond hydrogen atoms. Leave as `None` to guess which hydrogens to use in
the analysis using :attr:`guess_hydrogens`. If :attr:`hydrogens_sel` is left as `None`, also leave
:attr:`donors_sel` as None so that donor-hydrogen pairs can be correctly identified.
acceptors_sel : str
Selection string for the hydrogen bond acceptor atoms. Leave as `None` to guess which atoms to use in the
analysis using :attr:`guess_acceptors`
d_h_cutoff : float (optional)
Distance cutoff used for finding donor-hydrogen pairs [1.2]. Only used to find donor-hydrogen pairs if the
universe topology does not contain bonding information
d_a_cutoff : float (optional)
Distance cutoff for hydrogen bonds. This cutoff refers to the D-A distance. [3.0]
d_h_a_angle_cutoff: float (optional)
D-H-A angle cutoff for hydrogen bonds, in degrees. [150]
update_selections: bool (optional)
Whether or not to update the acceptor, donor and hydrogen lists at each frame. [True]
Note
----
It is highly recommended that a universe topology with bonding information is used, as this is the only way
that guarantees the correct identification of donor-hydrogen pairs.
"""
self.u = universe
self._trajectory = self.u.trajectory
self.donors_sel = donors_sel
self.hydrogens_sel = hydrogens_sel
self.acceptors_sel = acceptors_sel
self.d_h_cutoff = d_h_cutoff
self.d_a_cutoff = d_a_cutoff
self.d_h_a_angle = d_h_a_angle_cutoff
self.update_selections = update_selections
[docs] def guess_hydrogens(self,
select='all',
max_mass=1.1,
min_charge=0.3,
min_mass=0.9
):
"""Guesses which hydrogen atoms should be used in the analysis.
Parameters
----------
select: str (optional)
Selection string for atom group from which hydrogens will be identified.
max_mass: float (optional)
Maximum allowed mass of a hydrogen atom.
min_charge: float (optional)
Minimum allowed charge of a hydrogen atom.
Returns
-------
potential_hydrogens: str
String containing the :attr:`resname` and :attr:`name` of all hydrogen atoms potentially capable of forming
hydrogen bonds.
Notes
-----
This function makes use of atomic masses and atomic charges to identify which atoms are hydrogen atoms that are
capable of participating in hydrogen bonding. If an atom has a mass less than :attr:`max_mass` and an atomic
charge greater than :attr:`min_charge` then it is considered capable of participating in hydrogen bonds.
If :attr:`hydrogens_sel` is `None`, this function is called to guess the selection.
Alternatively, this function may be used to quickly generate a :class:`str` of potential hydrogen atoms involved
in hydrogen bonding. This str may then be modified before being used to set the attribute
:attr:`hydrogens_sel`.
"""
if min_mass > max_mass:
raise ValueError("min_mass is higher than (or equal to) max_mass")
ag = self.u.select_atoms(select)
hydrogens_ag = ag[
np.logical_and.reduce((
ag.masses < max_mass,
ag.charges > min_charge,
ag.masses > min_mass,
))
]
hydrogens_list = np.unique(
[
'(resname {} and name {})'.format(r, p) for r, p in zip(hydrogens_ag.resnames, hydrogens_ag.names)
]
)
return " or ".join(hydrogens_list)
[docs] def guess_donors(self, select='all', max_charge=-0.5):
"""Guesses which atoms could be considered donors in the analysis. Only use if the universe topology does not
contain bonding information, otherwise donor-hydrogen pairs may be incorrectly assigned.
Parameters
----------
select: str (optional)
Selection string for atom group from which donors will be identified.
max_charge: float (optional)
Maximum allowed charge of a donor atom.
Returns
-------
potential_donors: str
String containing the :attr:`resname` and :attr:`name` of all atoms that potentially capable of forming
hydrogen bonds.
Notes
-----
This function makes use of and atomic charges to identify which atoms could be considered donor atoms in the
hydrogen bond analysis. If an atom has an atomic charge less than :attr:`max_charge`, and it is within
:attr:`d_h_cutoff` of a hydrogen atom, then it is considered capable of participating in hydrogen bonds.
If :attr:`donors_sel` is `None`, and the universe topology does not have bonding information, this function is
called to guess the selection.
Alternatively, this function may be used to quickly generate a :class:`str` of potential donor atoms involved
in hydrogen bonding. This :class:`str` may then be modified before being used to set the attribute
:attr:`donors_sel`.
"""
# We need to know `hydrogens_sel` before we can find donors
# Use a new variable `hydrogens_sel` so that we do not set `self.hydrogens_sel` if it is currently `None`
if not self.hydrogens_sel:
hydrogens_sel = self.guess_hydrogens()
else:
hydrogens_sel = self.hydrogens_sel
hydrogens_ag = self.u.select_atoms(hydrogens_sel)
ag = hydrogens_ag.residues.atoms.select_atoms(
"({donors_sel}) and around {d_h_cutoff} {hydrogens_sel}".format(
donors_sel=select,
d_h_cutoff=self.d_h_cutoff,
hydrogens_sel=hydrogens_sel
)
)
donors_ag = ag[ag.charges < max_charge]
donors_list = np.unique(
[
'(resname {} and name {})'.format(r, p) for r, p in zip(donors_ag.resnames, donors_ag.names)
]
)
return " or ".join(donors_list)
[docs] def guess_acceptors(self, select='all', max_charge=-0.5):
"""Guesses which atoms could be considered acceptors in the analysis.
Parameters
----------
select: str (optional)
Selection string for atom group from which acceptors will be identified.
max_charge: float (optional)
Maximum allowed charge of an acceptor atom.
Returns
-------
potential_acceptors: str
String containing the :attr:`resname` and :attr:`name` of all atoms that potentially capable of forming
hydrogen bonds.
Notes
-----
This function makes use of and atomic charges to identify which atoms could be considered acceptor atoms in the
hydrogen bond analysis. If an atom has an atomic charge less than :attr:`max_charge` then it is considered
capable of participating in hydrogen bonds.
If :attr:`acceptors_sel` is `None`, this function is called to guess the selection.
Alternatively, this function may be used to quickly generate a :class:`str` of potential acceptor atoms involved
in hydrogen bonding. This :class:`str` may then be modified before being used to set the attribute
:attr:`acceptors_sel`.
"""
ag = self.u.select_atoms(select)
acceptors_ag = ag[ag.charges < max_charge]
acceptors_list = np.unique(
[
'(resname {} and name {})'.format(r, p) for r, p in zip(acceptors_ag.resnames, acceptors_ag.names)
]
)
return " or ".join(acceptors_list)
def _get_dh_pairs(self):
"""Finds donor-hydrogen pairs.
Returns
-------
donors, hydrogens: AtomGroup, AtomGroup
AtomGroups corresponding to all donors and all hydrogens. AtomGroups are ordered such that, if zipped, will
produce a list of donor-hydrogen pairs.
"""
# If donors_sel is not provided, use topology to find d-h pairs
if not self.donors_sel:
# We're using u._topology.bonds rather than u.bonds as it is a million times faster to access.
# This is because u.bonds also calculates properties of each bond (e.g bond length).
# See https://github.com/MDAnalysis/mdanalysis/issues/2396#issuecomment-596251787
if not (hasattr(self.u._topology, 'bonds') and len(self.u._topology.bonds.values) != 0):
raise NoDataError('Cannot assign donor-hydrogen pairs via topology as no bond information is present. '
'Please either: load a topology file with bond information; use the guess_bonds() '
'topology guesser; or set HydrogenBondAnalysis.donors_sel so that a distance cutoff '
'can be used.')
hydrogens = self.u.select_atoms(self.hydrogens_sel)
donors = sum(h.bonded_atoms[0] for h in hydrogens) if hydrogens \
else AtomGroup([], self.u)
# Otherwise, use d_h_cutoff as a cutoff distance
else:
hydrogens = self.u.select_atoms(self.hydrogens_sel)
donors = self.u.select_atoms(self.donors_sel)
donors_indices, hydrogen_indices = capped_distance(
donors.positions,
hydrogens.positions,
max_cutoff=self.d_h_cutoff,
box=self.u.dimensions,
return_distances=False
).T
donors = donors[donors_indices]
hydrogens = hydrogens[hydrogen_indices]
return donors, hydrogens
def _prepare(self):
self.hbonds = [[], [], [], [], [], []]
# Set atom selections if they have not been provided
if not self.acceptors_sel:
self.acceptors_sel = self.guess_acceptors()
if not self.hydrogens_sel:
self.hydrogens_sel = self.guess_hydrogens()
# Select atom groups
self._acceptors = self.u.select_atoms(self.acceptors_sel,
updating=self.update_selections)
self._donors, self._hydrogens = self._get_dh_pairs()
def _single_frame(self):
box = self._ts.dimensions
# Update donor-hydrogen pairs if necessary
if self.update_selections:
self._donors, self._hydrogens = self._get_dh_pairs()
# find D and A within cutoff distance of one another
# min_cutoff = 1.0 as an atom cannot form a hydrogen bond with itself
d_a_indices, d_a_distances = capped_distance(
self._donors.positions,
self._acceptors.positions,
max_cutoff=self.d_a_cutoff,
min_cutoff=1.0,
box=box,
return_distances=True,
)
# Remove D-A pairs more than d_a_cutoff away from one another
tmp_donors = self._donors[d_a_indices.T[0]]
tmp_hydrogens = self._hydrogens[d_a_indices.T[0]]
tmp_acceptors = self._acceptors[d_a_indices.T[1]]
# Find D-H-A angles greater than d_h_a_angle_cutoff
d_h_a_angles = np.rad2deg(
calc_angles(
tmp_donors.positions,
tmp_hydrogens.positions,
tmp_acceptors.positions,
box=box
)
)
hbond_indices = np.where(d_h_a_angles > self.d_h_a_angle)[0]
# Retrieve atoms, distances and angles of hydrogen bonds
hbond_donors = tmp_donors[hbond_indices]
hbond_hydrogens = tmp_hydrogens[hbond_indices]
hbond_acceptors = tmp_acceptors[hbond_indices]
hbond_distances = d_a_distances[hbond_indices]
hbond_angles = d_h_a_angles[hbond_indices]
# Store data on hydrogen bonds found at this frame
self.hbonds[0].extend(np.full_like(hbond_donors, self._ts.frame))
self.hbonds[1].extend(hbond_donors.indices)
self.hbonds[2].extend(hbond_hydrogens.indices)
self.hbonds[3].extend(hbond_acceptors.indices)
self.hbonds[4].extend(hbond_distances)
self.hbonds[5].extend(hbond_angles)
def _conclude(self):
self.hbonds = np.asarray(self.hbonds).T
[docs] def count_by_time(self):
"""Counts the number of hydrogen bonds per timestep.
Returns
-------
counts : numpy.ndarray
Contains the total number of hydrogen bonds found at each timestep.
Can be used along with :attr:`HydrogenBondAnalysis.times` to plot
the number of hydrogen bonds over time.
"""
indices, tmp_counts = np.unique(self.hbonds[:, 0], axis=0,
return_counts=True)
indices -= self.start
indices /= self.step
counts = np.zeros_like(self.frames)
counts[indices.astype(np.intp)] = tmp_counts
return counts
[docs] def count_by_type(self):
"""Counts the total number of each unique type of hydrogen bond.
Returns
-------
counts : numpy.ndarray
Each row of the array contains the donor resname, donor atom type, acceptor resname, acceptor atom type and
the total number of times the hydrogen bond was found.
Note
----
Unique hydrogen bonds are determined through a consideration of the resname and atom type of the donor and
acceptor atoms in a hydrogen bond.
"""
d = self.u.atoms[self.hbonds[:, 1].astype(np.intp)]
a = self.u.atoms[self.hbonds[:, 3].astype(np.intp)]
tmp_hbonds = np.array([d.resnames, d.types, a.resnames, a.types],
dtype=str).T
hbond_type, type_counts = np.unique(
tmp_hbonds, axis=0, return_counts=True)
hbond_type_list = []
for hb_type, hb_count in zip(hbond_type, type_counts):
hbond_type_list.append([":".join(hb_type[:2]),
":".join(hb_type[2:4]), hb_count])
return np.array(hbond_type_list)
[docs] def count_by_ids(self):
"""Counts the total number hydrogen bonds formed by unique combinations of donor, hydrogen and acceptor atoms.
Returns
-------
counts : numpy.ndarray
Each row of the array contains the donor atom id, hydrogen atom id, acceptor atom id and the total number
of times the hydrogen bond was observed. The array is sorted by frequency of occurrence.
Note
----
Unique hydrogen bonds are determined through a consideration of the hydrogen atom id and acceptor atom id
in a hydrogen bond.
"""
d = self.u.atoms[self.hbonds[:, 1].astype(np.intp)]
h = self.u.atoms[self.hbonds[:, 2].astype(np.intp)]
a = self.u.atoms[self.hbonds[:, 3].astype(np.intp)]
tmp_hbonds = np.array([d.ids, h.ids, a.ids]).T
hbond_ids, ids_counts = np.unique(tmp_hbonds, axis=0,
return_counts=True)
# Find unique hbonds and sort rows so that most frequent observed bonds are at the top of the array
unique_hbonds = np.concatenate((hbond_ids, ids_counts[:, None]),
axis=1)
unique_hbonds = unique_hbonds[unique_hbonds[:, 3].argsort()[::-1]]
return unique_hbonds