igd d Z ddlZddlZddlmZ ddlmZ ddlmZ ddl Z
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lmZmZ ee 5 ddlmZ ddd n # 1 swxY w Y dddddddddd Z e Z e j Z e j Z ej Z ej Z e e j! Z! G d de j" Z# G d d ej$ Z% ed d d e fd a&d Z'd*d"Z(d# Z)d$ Z*d% Z+d& Z,d' Z-d( Z.e/e)e0e*e
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Z`__
: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
N)suppress) lru_cache)StringIO )memory) PDBWriter)_TOPOLOGY_ATTRS) NoDataError )base) RDBONDORDERMDAnalysisInferrerChemAltLocChainId
InsertionCodeName Occupancy ResidueName
ResidueNumber
SegmentNumber
TempFactor) altLocschainIDsicodesnames occupanciesresnamesresids
segindices tempfactorsc F e Zd ZdZdZdddZed Z fdZ xZ S ) RDKitReaderz>Coordinate reader for RDKit.
.. versionadded:: 2.0.0
RDKITNAngstromtimelengthc ^ ddl m} n# t $ r Y dS w xY wt | |j S )z Can this reader read *thing*?r r F)rdkitr ImportError
isinstanceMol)thingr s e/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/converters/RDKit.py _format_hintzRDKitReader._format_hint sR " " " " " " " 55 %***s
c | }t j d | D t j }|j dk rHt
j d t j d|dft j }t j |dd< t t | j |fdd i| dS )
a
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
c 6 g | ]}| S ) GetPositions).0confs r0
z(RDKitReader.__init__.. s$ F F FTT
F F F )dtyper z*No coordinates found in the RDKit moleculer Norderfac)
GetNumAtomsnparray
GetConformersfloat32sizewarningswarnemptynansuperr$ __init__)selffilenamekwargsn_atoms coordinates __class__s r0 rI zRDKitReader.__init__ s &&((h F FX-C-C-E-E F F F*
q MF G G G (Aw?"*EEEK VKN)k4 )+MMUMfMMMMMr9 )
__name__
__module__ __qualname____doc__formatunits staticmethodr1 rI
__classcell__)rO s @r0 r$ r$ sz
F Z 0 0E+ + \+N N N N N N N N Nr9 r$ c 0 e Zd ZdZdZdddZdddefdZdS ) RDKitConvertera 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``.
r% Nr& r' TFc ddl m} n # t $ r t d dw xY w |j }n/# t $ r" t dt
| d dw xY w| d x} ?t j dt t |t rt | }| d
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}|rd}t ||| } |r"t |fi | } t j | } nt j |fi | } t% |d
rt' j |j s t' j |j ddd rt j d n |j | }
| D ]Q}| }|j | t: }|
|| R| |
|j | |j! | | S )a 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.
r r zRDKit is required for the RDKitConverter but it's not installed. Try installing it with
`conda install -c conda-forge rdkit` or `pip install rdkit`Nz'No `atoms` attribute in object of type z*, please use a valid AtomGroup or Universemax_iterzWUsing `max_iter` is deprecated, use `inferrer=MDAnalysisInferrer(max_iter=...)` instead)r[
NoImplicitzUsing `NoImplicit` is deprecated, use `implicit_hydrogens` instead. To disable bond order and formal charge inferring, use `inferrer=None`)implicit_hydrogensforceinferrer positionsg g-q=)rtolatolzkNaN or empty coordinates detected in coordinates, the output molecule will not have 3D coordinates assigned)"r+ r r, atomsAttributeError TypeErrortypegetrD rE DeprecationWarningr- r dictatomgroup_to_molcopydeepcopy __wrapped__hasattrr? isnanr` anyallclose Conformerr> GetAtomsGetIdxastypefloatSetAtomPosition AddConformerAssignStereochemistryFrom3D SetDoubleBondNeighborDirections)rJ objcacher] r^ r_ rL r agr[ r\ paramsmolr7 atomidxxyzs r0 convertzRDKitConverter.convertF s V " " " " " " " N
BB ;$s)) ; ; ;
:.. .H ; MF"
($677
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1
="20000C-$$CC".r< $ r Y #w xY wtA j |j! t j" j# } | j$ g ||R `| % d | || } | S )a 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=...)``.
zThe `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)`NHzKNo hydrogen atom found in the topology. Forcing to continue the conversion.a 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.r\ zUsing `NoImplicit` is deprecated, use `implicit_hydrogens` instead. To disable bond order and formal charge inferring, use `inferrer=None`z Found unexpected arguments: .r c dS )N r4 )r s r0 get_resnamez%atomgroup_to_mol..get_resname s 2r9 c | S Nr4 )r r s r0 r z%atomgroup_to_mol..get_resname s
C= r9 )chargessegidstypesr _MDAnalysis__MDAnalysis_indexzQNo `bonds` attribute in this AtomGroup. Guessing bonds based on atoms coordinatesc g | ]
}| S r4 r4 )r6 i atom_mappers r0 r8 z$atomgroup_to_mol..G s AAAqKNAAAr9 F)strict)&elementsr
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8
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K#"K#c L t | t j adS )a7 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.
r N)r rj rm r s r0 set_converter_cache_sizer V s) 2y1112B2NOOr9 r c t |t j r| }| dk rt || }t
| } t
|d| | dS )a 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
r SetN)r- r? genericitem_deduce_PDB_atom_namer r )r valuer resnamerdattrs r0 r r d so %$$
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_set_int_propr s OOD% r9 c L | |t | d S r )r intr s r0 _set_np_int_propr s" OOD#e**%%%%%r9 c d S r r4 r s r0 _ignore_propr s Dr9 c t t t | t | || dS )z9Saves any attribute and value into an RDKit atom propertyN)_atom_property_dispatcherrg rf r r s r0 r r s0 !!$u++|<rS rk rD
contextlibr functoolsr ior numpyr? rN r coordinates.PDBr core.topologyattrsr
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r r, r+ r r r _infer_bo_and_charges_standardize_patternsMONATOMIC_CATION_CHARGESSTANDARDIZATION_REACTIONSr MemoryReaderr$
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