schrodinger.thirdparty.rdkit_adapter module

Conversions between Schrodinger structure objects (mmct) and RDKit mol objects.

There are some structural/philosophic differences between these two formats, stemming from their distinct origins (RDKit being originally used for chemiformatics, and schrodinger/mmct being originally used for molecular modeling.)

Notably: Schrodinger wants all atoms to have positions in space. RDKit allows unspecified position, or multiple conformers.

Schrodinger wants all Hydrogens to be fully specified (position and bonding). My understanding is that RDKit has three types of hydrogens:

* Implicit - calculated based on valence. These are not shown in SMILES.
* Explicit - as a property of the associated heavy atom. These are shown in
SMILES like [cH]
* Included in connectivity graph - (only these can have coordinates or
other properties). These are show in SMILES like c([H]).

There are other distinctions, for instance Schrodinger is aware of dative, or zero-order bonds, whereas RDKit is aware of aromatic and conjugated bonds.

exception schrodinger.thirdparty.rdkit_adapter.InconsistentStructureError

Bases: ValueError

__init__

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.thirdparty.rdkit_adapter.UnsupportedStructureError

Bases: NotImplementedError

For structures that can’t be translated between RDKit and Schrodinger yet

__init__

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.thirdparty.rdkit_adapter.to_rdkit(st, implicitH=False, include_properties=True, include_coordinates=True)

Create a RdKit molecule from a Schrodinger structure (aka mmct).

Parameters:
  • st (schrodinger.structure.Structure) – The schrodinger structure to be translated to RDKit. The input structure remains unmodified.
  • implicitH (bool) – Should hydrogens be listed implicitly? If False, hydrogens will be included in the connectivity graph, and 3D coordinates and properties of the hydrogens will be translated. Some pattern matching in RDKit requires implicit hydrogens, however.
  • include_properties (bool) – Should atom and structure level properties be copied from the schrodinger structure to the RDKit mol?
  • include_coordinates – Should the coordinates of the structure be copied to a conformer associated with the RDKit mol?
Returns:

An rdkit mol representing the same structure as the input st

Return type:

rdkit.Mol

Raises:

InconsistentStructureError – if the input structure has inconsistent or incorrect stereochemical labels.

schrodinger.thirdparty.rdkit_adapter.from_rdkit(mol, include_properties=True, generate_coordinates=False, conformer=None)

Create a Schrodinger structure from an RdKit molecule.

For correct behavoir, requires that the RdKit molecule be sanitized beforehand.

If the RDKit molecule does not have 3d structure, one can be generated using fast3d.

Parameters:
  • mol (rdkit.Mol) – RDKit mol to be converted to Schrodinger space. It will not be modified.
  • include_properties (bool) – Should atom and molecule properties be copied from the RDKit mol?
  • generate_coordinates (bool) – Should 3D coordinates be generated if the RDKit mol does not have associated coordinates? Uses fast3d.
  • conformer (NoneType or int) – If the RDKit mol has more than one associated conformer, choose one to turn into a Schrodinger structure.
Returns:

A schrodinger.Structure representing the same molecule as the input mol

Return type:

schrodinger.Structure

Raises:

ValueError – If there is more than one conformer associated with the structure or if a specific conformer is requested and is unavailable.

schrodinger.thirdparty.rdkit_adapter.translate_rdkit_props_dict(props)

Make a copy of a property dict like the one returned by mol.GetPropsAsDict, in which property names that don’t look like mmct properties are prefixed with <typechar>_rdkit_.

Parameters:props (dict) – property dictionary
Returns:new property dictionary
Return type:dict
schrodinger.thirdparty.rdkit_adapter.annotate(mol)

Annotate atoms with index to allow mapping back and forth.

schrodinger.thirdparty.rdkit_adapter.copy_lewis_structure_and_hydrogens(st, mol, kekulize=False)

Applies bond orders and charges from st to mol. Updates #implicitH to match

Assumes st includes all hydrogens. Adds no new explicit hydrogens to the mol. Assumes elements are the same, and that no bonds have been added or removed.

Basically, applies Schrodinger aromaticity model to the mol

schrodinger.thirdparty.rdkit_adapter.as_st(mol, kekulize=False, *args, **kwargs)

Create a structure representing a mol. At the end of the context, apply all changes in bond order and charge back to the original mol.