# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
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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)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# 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
#
"""RDKit molecule I/O --- :mod:`MDAnalysis.converters.RDKit`
================================================================
Read coordinates data from an `RDKit `__
:class:`rdkit.Chem.rdchem.Mol` with
:class:`RDKitReader` into an MDAnalysis Universe. Convert it back to a
:class:`rdkit.Chem.rdchem.Mol` with :class:`RDKitConverter`.
Example
-------
To read an RDKit molecule and then convert the AtomGroup back to an RDKit
molecule::
>>> from rdkit import Chem
>>> import MDAnalysis as mda
>>> mol = Chem.MolFromMol2File("docking_poses.mol2", removeHs=False)
>>> u = mda.Universe(mol)
>>> u
>>> u.trajectory
>>> u.atoms.convert_to("RDKIT")
.. warning::
The RDKit converter is currently *experimental* and may not work as
expected for all molecules. Currently the converter accurately
infers the structures of approximately 99% of the `ChEMBL27`_ dataset.
Work is currently ongoing on further improving this and updates to the
converter are expected in future releases of MDAnalysis.
Please see `Issue #3339`_ and the `RDKitConverter benchmark`_ for more
details.
Instead of using the default bond-order and charge inferring algorithm that
relies on the topology alone and the presence of explicit hydrogen atoms, you
can also use alternative builtin algorithms (see the
:mod:`~MDAnalysis.converters.RDKitInferring` module) or even your own function
to modify the RDKit molecule::
>>> template = Chem.MolFromSmiles("CC(=O)Oc1ccccc1C(=O)O")
>>> inferrer = mda.converters.RDKitInferring.TemplateInferrer(
... template=template
... )
>>> u.atoms.convert_to.rdkit(inferrer=inferrer)
>>> def dummy_inferrer(mol):
... # assign bond orders and do any other modification here
... return mol
>>> u.atoms.convert_to.rdkit(inferrer=dummy_inferrer)
Classes
-------
.. autoclass:: RDKitReader
:members:
.. autoclass:: RDKitConverter
:members:
.. Links
.. _`ChEMBL27`: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_27/
.. _`Issue #3339`: https://github.com/MDAnalysis/mdanalysis/issues/3339
.. _`RDKitConverter benchmark`: https://github.com/MDAnalysis/RDKitConverter-benchmark
"""
import copy
import warnings
from contextlib import suppress
from functools import lru_cache
from io import StringIO
import numpy as np
from ..coordinates import memory
from ..coordinates.PDB import PDBWriter
from ..core.topologyattrs import _TOPOLOGY_ATTRS
from ..exceptions import NoDataError
from . import base
from .RDKitInferring import RDBONDORDER, MDAnalysisInferrer
with suppress(ImportError):
from rdkit import Chem
RDATTRIBUTES = {
"altLocs": "AltLoc",
"chainIDs": "ChainId",
"icodes": "InsertionCode",
"names": "Name",
"occupancies": "Occupancy",
"resnames": "ResidueName",
"resids": "ResidueNumber",
"segindices": "SegmentNumber",
"tempfactors": "TempFactor",
}
DEFAULT_INFERER = MDAnalysisInferrer()
# only here for backwards compatibility
_infer_bo_and_charges = DEFAULT_INFERER._infer_bo_and_charges
_standardize_patterns = DEFAULT_INFERER._standardize_patterns
MONATOMIC_CATION_CHARGES = MDAnalysisInferrer.MONATOMIC_CATION_CHARGES
STANDARDIZATION_REACTIONS = MDAnalysisInferrer.STANDARDIZATION_REACTIONS
_deduce_PDB_atom_name = PDBWriter(StringIO())._deduce_PDB_atom_name
class RDKitReader(memory.MemoryReader):
"""Coordinate reader for RDKit.
.. versionadded:: 2.0.0
"""
format = "RDKIT"
# Structure.coordinates always in Angstrom
units = {"time": None, "length": "Angstrom"}
@staticmethod
def _format_hint(thing):
"""Can this reader read *thing*?"""
try:
from rdkit import Chem
except ImportError:
# if we can't import rdkit, it's probably not rdkit
return False
return isinstance(thing, Chem.Mol)
def __init__(self, filename, **kwargs):
"""Read coordinates from an RDKit molecule.
Each conformer in the original RDKit molecule will be read as a frame
in the resulting universe.
Parameters
----------
filename : rdkit.Chem.rdchem.Mol
RDKit molecule
"""
n_atoms = filename.GetNumAtoms()
coordinates = np.array(
[conf.GetPositions() for conf in filename.GetConformers()],
dtype=np.float32,
)
if coordinates.size == 0:
warnings.warn("No coordinates found in the RDKit molecule")
coordinates = np.empty((1, n_atoms, 3), dtype=np.float32)
coordinates[:] = np.nan
super(RDKitReader, self).__init__(coordinates, order="fac", **kwargs)
class RDKitConverter(base.ConverterBase):
"""Convert MDAnalysis :class:`~MDAnalysis.core.groups.AtomGroup` or
:class:`~MDAnalysis.core.universe.Universe` to RDKit
:class:`~rdkit.Chem.rdchem.Mol`
MDanalysis attributes are stored in each RDKit
:class:`~rdkit.Chem.rdchem.Atom` of the resulting molecule in two different
ways:
* in an :class:`~rdkit.Chem.rdchem.AtomPDBResidueInfo` object available
through the :meth:`~rdkit.Chem.rdchem.Atom.GetMonomerInfo` method if it's
an attribute that is typically found in a PDB file,
* directly as an atom property available through the
:meth:`~rdkit.Chem.rdchem.Atom.GetProp` methods for the others.
Supported attributes:
+-----------------------+-------------------------------------------+
| MDAnalysis attribute | RDKit |
+=======================+===========================================+
| altLocs | atom.GetMonomerInfo().GetAltLoc() |
+-----------------------+-------------------------------------------+
| chainIDs | atom.GetMonomerInfo().GetChainId() |
+-----------------------+-------------------------------------------+
| icodes | atom.GetMonomerInfo().GetInsertionCode() |
+-----------------------+-------------------------------------------+
| names | atom.GetMonomerInfo().GetName() |
| | atom.GetProp("_MDAnalysis_name") |
+-----------------------+-------------------------------------------+
| occupancies | atom.GetMonomerInfo().GetOccupancy() |
+-----------------------+-------------------------------------------+
| resnames | atom.GetMonomerInfo().GetResidueName() |
+-----------------------+-------------------------------------------+
| resids | atom.GetMonomerInfo().GetResidueNumber() |
+-----------------------+-------------------------------------------+
| segindices | atom.GetMonomerInfo().GetSegmentNumber() |
+-----------------------+-------------------------------------------+
| tempfactors | atom.GetMonomerInfo().GetTempFactor() |
+-----------------------+-------------------------------------------+
| charges | atom.GetDoubleProp("_MDAnalysis_charge") |
+-----------------------+-------------------------------------------+
| indices | atom.GetIntProp("_MDAnalysis_index") |
+-----------------------+-------------------------------------------+
| segids | atom.GetProp("_MDAnalysis_segid") |
+-----------------------+-------------------------------------------+
| types | atom.GetProp("_MDAnalysis_type") |
+-----------------------+-------------------------------------------+
Example
-------
To access MDAnalysis properties::
>>> import MDAnalysis as mda
>>> from MDAnalysis.tests.datafiles import PDB_full
>>> u = mda.Universe(PDB_full)
>>> mol = u.select_atoms('resname DMS').convert_to('RDKIT')
>>> mol.GetAtomWithIdx(0).GetMonomerInfo().GetResidueName()
'DMS'
To create a molecule for each frame of a trajectory::
from MDAnalysisTests.datafiles import PSF, DCD
from rdkit.Chem.Descriptors3D import Asphericity
u = mda.Universe(PSF, DCD, to_guess=['elements'])
ag = u.select_atoms("resid 1-10")
for ts in u.trajectory:
mol = ag.convert_to("RDKIT")
x = Asphericity(mol)
Notes
-----
The converter requires the :class:`~MDAnalysis.core.topologyattrs.Elements`
attribute to be present in the topology, else it will fail.
It also requires the `bonds` attribute, although they will be automatically
guessed if not present.
Hydrogens should be explicit in the topology file. If this is not the case,
use the parameter ``implicit_hydrogens=True`` when using the converter to
allow implicit hydrogens, and ``inferrer=None`` to disable inferring bond
orders and charges. You can also pass your own callable function to
``inferrer`` to assign bond orders and charges as you see fit::
>>> from rdkit import Chem
>>> from rdkit.Chem.AllChem import AssignBondOrdersFromTemplate
>>> template = Chem.MolFromSmiles("NC(Cc1ccccc1)C(=O)O")
>>> def infer_from_template(mol: Chem.Mol) -> Chem.Mol:
... return AssignBondOrdersFromTemplate(template, mol)
>>> mol = u.atoms.convert_to.rdkit(inferrer=infer_from_template)
Note that all builtin inferrer functions can be found in the
:mod:`RDKitInferring` module.
Since one of the main use case of the converter is converting trajectories
and not just a topology, creating a new molecule from scratch for every
frame would be too slow so the converter uses a caching system. The cache
only stores the 2 most recent AtomGroups that were converted, and is
sensitive to the arguments that were passed to the converter. The number of
objects cached can be changed with the function
:func:`set_converter_cache_size`. However, ``ag.convert_to("RDKIT")``
followed by ``ag.convert_to("RDKIT", implicit_hydrogens=False)`` will not
use the cache since the arguments given are different. You can pass a
``cache=False`` argument to the converter to bypass the caching system.
The ``_MDAnalysis_index`` property of the resulting molecule corresponds
to the index of the specific :class:`~MDAnalysis.core.groups.AtomGroup`
that was converted, which may not always match the ``index`` property.
To get a better understanding of how the converter works under the hood,
please refer to the following RDKit UGM presentation:
* `Video (4:55 to 8:05) `__
* `Slides `__
There are some molecules containing specific patterns that the default
inferrer cannot currently tackle correctly. See
`Issue #3339 `__ for
more info.
.. versionadded:: 2.0.0
.. versionchanged:: 2.2.0
Improved the accuracy of the converter. Atoms in the resulting molecule
now follow the same order as in the AtomGroup. The output of
``atom.GetMonomerInfo().GetName()`` now follows the guidelines for PDB
files while the original name is still available through
``atom.GetProp("_MDAnalysis_name")``
.. versionchanged:: 2.10.0
Added ``inferrer`` to specify a callable that can transform the
molecule (this operation is cached).
.. deprecated:: 2.10.0
Deprecated ``max_iter`` (moved to the inferrer class
:class:`~MDAnalysis.converters.RDKitInferring.MDAnalysisInferrer`) and
deprecated ``NoImplicit`` in favor of ``implicit_hydrogens``.
"""
lib = "RDKIT"
units = {"time": None, "length": "Angstrom"}
def convert(
self,
obj,
cache=True,
implicit_hydrogens=False,
force=False,
inferrer=DEFAULT_INFERER,
**kwargs,
):
"""Write selection at current trajectory frame to
:class:`~rdkit.Chem.rdchem.Mol`.
Parameters
-----------
obj : :class:`~MDAnalysis.core.groups.AtomGroup` or
:class:`~MDAnalysis.core.universe.Universe`
cache : bool
Use a cached copy of the molecule's topology when available. To be
used, the cached molecule and the new one have to be made from the
same AtomGroup selection and with the same arguments passed
to the converter
inferrer : Optional[Callable[[Chem.Mol], Chem.Mol]]
A callable to infer bond orders and charges for the RDKit molecule
created by the converter. If ``None``, inferring is skipped.
implicit_hydrogens : bool
Whether to allow implicit hydrogens on the molecule or not.
force : bool
Force the conversion when no hydrogens were detected but
``inferrer`` is not ``None``. Useful for inorganic molecules
mostly.
NoImplicit : bool
Opposite of ``implicit_hydrogens``.
.. deprecated:: 2.10.0
Use ``implicit_hydrogens`` instead (with an opposite value).
max_iter : int
Maximum number of iterations to standardize conjugated systems.
See :meth:`~MDAnalysis.converters.RDKitInferring.MDAnalysisInferrer._rebuild_conjugated_bonds`.
.. deprecated:: 2.10.0
Use ``inferrer=MDAnalysisInferrer(max_iter=...)`` instead.
"""
try:
from rdkit import Chem
except ImportError:
raise ImportError(
"RDKit is required for the RDKitConverter but "
"it's not installed. Try installing it with \n"
"`conda install -c conda-forge rdkit` or `pip install rdkit`"
) from None
try:
# make sure to use atoms (Issue 46)
ag = obj.atoms
except AttributeError:
raise TypeError(
f"No `atoms` attribute in object of type {type(obj)!r}, "
"please use a valid AtomGroup or Universe"
) from None
if (max_iter := kwargs.get("max_iter")) is not None:
warnings.warn(
"Using `max_iter` is deprecated, use "
"`inferrer=MDAnalysisInferrer(max_iter=...)` instead",
DeprecationWarning,
)
if isinstance(inferrer, MDAnalysisInferrer):
inferrer = MDAnalysisInferrer(max_iter=max_iter)
if (NoImplicit := kwargs.get("NoImplicit")) is not None:
warnings.warn(
"Using `NoImplicit` is deprecated, use `implicit_hydrogens` "
" instead. To disable bond order and formal charge inferring, "
"use `inferrer=None`",
DeprecationWarning,
)
implicit_hydrogens = not NoImplicit
# backwards compatibility
if implicit_hydrogens:
inferrer = None
# parameters passed to atomgroup_to_mol
params = dict(
implicit_hydrogens=implicit_hydrogens,
force=force,
inferrer=inferrer,
)
if cache:
mol = atomgroup_to_mol(ag, **params)
mol = copy.deepcopy(mol)
else:
mol = atomgroup_to_mol.__wrapped__(ag, **params)
# add a conformer for the current Timestep
if hasattr(ag, "positions"):
if np.isnan(ag.positions).any() or np.allclose(
ag.positions, 0.0, rtol=0.0, atol=1e-12
):
warnings.warn(
"NaN or empty coordinates detected in coordinates, "
"the output molecule will not have 3D coordinates "
"assigned"
)
else:
# assign coordinates
conf = Chem.Conformer(mol.GetNumAtoms())
for atom in mol.GetAtoms():
idx = atom.GetIdx()
xyz = ag.positions[idx].astype(float)
conf.SetAtomPosition(idx, xyz)
mol.AddConformer(conf)
# assign R/S to atoms and Z/E to bonds
Chem.AssignStereochemistryFrom3D(mol)
Chem.SetDoubleBondNeighborDirections(mol)
return mol
@lru_cache(maxsize=2)
def atomgroup_to_mol(
ag,
implicit_hydrogens=False,
force=False,
inferrer=DEFAULT_INFERER,
**kwargs,
):
"""Converts an AtomGroup to an RDKit molecule without coordinates.
Parameters
-----------
ag : MDAnalysis.core.groups.AtomGroup
The AtomGroup to convert
implicit_hydrogens : bool
Whether to allow implicit hydrogens on the molecule or not.
force : bool
Force the conversion when no hydrogens were detected but ``inferrer``
is not ``None``. Useful for inorganic molecules mostly.
inferrer : Optional[Callable[[rdkit.Chem.rdchem.Mol], rdkit.Chem.rdchem.Mol]]
A callable to infer bond orders and charges for the RDKit molecule
created by the converter. If ``None``, inferring is skipped.
NoImplicit : bool
Opposite of ``implicit_hydrogens``.
.. deprecated:: 2.10.0
Use ``implicit_hydrogens`` instead (with an opposite value).
max_iter : int
Maximum number of iterations to standardize conjugated systems.
See :meth:`~MDAnalysis.converters.RDKitInferring.MDAnalysisInferrer._rebuild_conjugated_bonds`.
.. deprecated:: 2.10.0
Use ``inferrer=MDAnalysisInferrer(max_iter=...)`` instead.
.. versionchanged:: 2.10.0
Added ``inferrer`` to specify a callable that can transform the
molecule (this operation is cached).
.. deprecated:: 2.10.0
Deprecated ``NoImplicit`` in favor of ``implicit_hydrogens``.
Deprecated ``max_iter``, replaced by
``inferrer=MDAnalysisInferrer(max_iter=...)``.
"""
try:
elements = ag.elements
except NoDataError:
raise AttributeError(
"The `elements` attribute is required for the RDKitConverter "
"but is not present in this AtomGroup. Please refer to the "
"documentation to guess elements from other attributes or "
"type `help(MDAnalysis.topology.guessers)`"
) from None
if "H" not in ag.elements:
if force:
warnings.warn(
"No hydrogen atom found in the topology. "
"Forcing to continue the conversion."
)
elif inferrer is not None:
raise AttributeError(
"No hydrogen atom could be found in the topology, but the "
"converter requires all hydrogens to be explicit. You can use "
"the parameter ``inferrer=None`` when using the converter "
"to disable inferring bond orders and charges. You can also "
"use ``force=True`` to ignore this error."
)
if (NoImplicit := kwargs.pop("NoImplicit", None)) is not None:
warnings.warn(
"Using `NoImplicit` is deprecated, use `implicit_hydrogens` "
"instead. To disable bond order and formal charge inferring, use "
"`inferrer=None`",
DeprecationWarning,
)
implicit_hydrogens = not NoImplicit
# backwards compatibility
if implicit_hydrogens:
inferrer = None
if kwargs:
raise ValueError(f"Found unexpected arguments: {kwargs}.")
# attributes accepted in PDBResidueInfo object
pdb_attrs = {}
for attr in RDATTRIBUTES:
if hasattr(ag, attr):
pdb_attrs[attr] = getattr(ag, attr)
resnames = pdb_attrs.get("resnames", None)
if resnames is None:
def get_resname(idx):
return ""
else:
def get_resname(idx):
return resnames[idx]
other_attrs = {}
for attr in ["charges", "segids", "types", "names"]:
if hasattr(ag, attr):
other_attrs[attr] = getattr(ag, attr)
mol = Chem.RWMol()
NoImplicit = not implicit_hydrogens
# map index in universe to index in mol
atom_mapper = {}
for i, (atom, element) in enumerate(zip(ag, elements)):
# create atom
rdatom = Chem.Atom(element.capitalize())
# enable/disable adding implicit H to the molecule
rdatom.SetNoImplicit(NoImplicit)
# add PDB-like properties
mi = Chem.AtomPDBResidueInfo()
for attr, values in pdb_attrs.items():
_add_mda_attr_to_rdkit(attr, values[i], mi, get_resname(i))
rdatom.SetMonomerInfo(mi)
# other properties
for attr, values in other_attrs.items():
attr = f"_MDAnalysis_{_TOPOLOGY_ATTRS[attr].singular}"
_set_atom_property(rdatom, attr, values[i])
_set_atom_property(rdatom, "_MDAnalysis_index", i)
# add atom
index = mol.AddAtom(rdatom)
atom_mapper[atom.ix] = index
try:
ag.bonds
except NoDataError:
warnings.warn(
"No `bonds` attribute in this AtomGroup. Guessing bonds based "
"on atoms coordinates"
)
ag.guess_bonds()
for bond in ag.bonds:
try:
bond_indices = [atom_mapper[i] for i in bond.indices]
except KeyError:
continue
bond_type = RDBONDORDER.get(bond.order, Chem.BondType.SINGLE)
mol.AddBond(*bond_indices, bond_type)
mol.UpdatePropertyCache(strict=False)
if inferrer is not None:
# infer bond orders and formal charges
mol = inferrer(mol)
return mol
def set_converter_cache_size(maxsize):
"""Set the maximum cache size of the RDKit converter
Parameters
----------
maxsize : int or None
If int, the cache will only keep the ``maxsize`` most recent
conversions in memory. Using ``maxsize=None`` will remove all limits
to the cache size, i.e. everything is cached.
"""
global atomgroup_to_mol # pylint: disable=global-statement
atomgroup_to_mol = lru_cache(maxsize=maxsize)(atomgroup_to_mol.__wrapped__)
def _add_mda_attr_to_rdkit(attr, value, mi, resname=""):
"""Converts an MDAnalysis atom attribute into the RDKit equivalent and
stores it into an RDKit :class:`~rdkit.Chem.rdchem.AtomPDBResidueInfo`.
Parameters
----------
attr : str
Name of the atom attribute in MDAnalysis in the singular form
value : object, np.int or np.float
Attribute value as found in the AtomGroup
mi : rdkit.Chem.rdchem.AtomPDBResidueInfo
MonomerInfo object that will store the relevant atom attributes
resname : str
Residue name of the atom, if available
"""
if isinstance(value, np.generic):
# convert numpy types to python standard types
value = value.item()
if attr == "names":
# RDKit needs the name to be properly formatted for a PDB file
value = _deduce_PDB_atom_name(value, resname)
# set attribute value in RDKit MonomerInfo
rdattr = RDATTRIBUTES[attr]
getattr(mi, f"Set{rdattr}")(value)
def _set_str_prop(atom, attr, value):
atom.SetProp(attr, value)
def _set_float_prop(atom, attr, value):
atom.SetDoubleProp(attr, value)
def _set_np_float_prop(atom, attr, value):
atom.SetDoubleProp(attr, float(value))
def _set_int_prop(atom, attr, value):
atom.SetIntProp(attr, value)
def _set_np_int_prop(atom, attr, value):
atom.SetIntProp(attr, int(value))
def _ignore_prop(atom, attr, value):
pass
_atom_property_dispatcher = {
str: _set_str_prop,
float: _set_float_prop,
np.float32: _set_np_float_prop,
np.float64: _set_np_float_prop,
int: _set_int_prop,
np.int8: _set_np_int_prop,
np.int16: _set_np_int_prop,
np.int32: _set_np_int_prop,
np.int64: _set_np_int_prop,
np.uint8: _set_np_int_prop,
np.uint16: _set_np_int_prop,
np.uint32: _set_np_int_prop,
np.uint64: _set_np_int_prop,
}
def _set_atom_property(atom, attr, value):
"""Saves any attribute and value into an RDKit atom property"""
_atom_property_dispatcher.get(type(value), _ignore_prop)(atom, attr, value)