Module rdkit_adapter
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.
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rdkit.Mol
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to_rdkit(st,
implicitH=False,
include_properties=True,
include_coordinates=True)
Create a RdKit molecule from a Schrodinger structure (aka mmct). |
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schrodinger.Structure
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from_rdkit(mol,
include_properties=True,
generate_coordinates=False,
conformer=None)
Create a Schrodinger structure from an RdKit molecule. |
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_rdkit_parity_from_chirality(schro_st,
rdkmol,
index_mapping)
Use Schrodinger chirality to assign RDKit parity. |
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_get_parity(unsorted)
Use a basic bubble sort to get the parity of a list. |
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_copy_props_mmct_to_rdk(mmct_st_or_atom,
rdk_mol_or_atom)
Copy the properties from an MMCT st or atom to a RDKit mol or atom. |
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_copy_props_rdk_to_mmct(rdk_mol_or_atom,
mmct_st_or_atom)
Copy the properties from a RDKit mol or atom to an MMCT st or atom. |
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CT_PROP_FORMAT = re.compile(r'[birs]_[^_ ]+_\w*')
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RDKIT_PROP_FORMAT = re.compile(r'[birs]_rdkit_(\w+)')
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BOND_TYPES_S2R = {<BondType.Double: 3>: rdkit.Chem.rdchem.Bond... |
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BOND_TYPES_R2S = {rdkit.Chem.rdchem.BondType.SINGLE: <BondType... |
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MMMDL_ATOM_PARITY_PROP = 'i_sd_original_parity' |
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__package__ = 'schrodinger.thirdparty' |
to_rdkit(st,
implicitH=False,
include_properties=True,
include_coordinates=True)
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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: rdkit.Mol
- An rdkit mol representing the same structure as the input st
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from_rdkit(mol,
include_properties=True,
generate_coordinates=False,
conformer=None)
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Create a Schrodinger structure from an RdKit molecule.
If the RDKit molecule does not have a 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: schrodinger.Structure
- A schrodinger.Structure representing the same molecule as the
input mol
- Raises:
ValueError - If there is more than one conformer associated with the structure
or if a specific conformer is requested and is unavailable.
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_chirality_from_rdkit_parity(rdkmol,
schro_st)
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Turn the atom parity (clockwise vs counterclockwise) into an R/S
chirality.
Cribbed from ChmMmctAdapter.
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BOND_TYPES_S2R
- Value:
{<BondType.Double: 3>: rdkit.Chem.rdchem.BondType.DOUBLE,
<BondType.Single: 2>: rdkit.Chem.rdchem.BondType.SINGLE,
<BondType.Triple: 4>: rdkit.Chem.rdchem.BondType.TRIPLE}
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BOND_TYPES_R2S
- Value:
{rdkit.Chem.rdchem.BondType.SINGLE: <BondType.Single: 2>,
rdkit.Chem.rdchem.BondType.DOUBLE: <BondType.Double: 3>,
rdkit.Chem.rdchem.BondType.TRIPLE: <BondType.Triple: 4>}
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