schrodinger.molutils.rgroups module¶

class schrodinger.molutils.rgroups.RGroup(smiles: str)¶

Bases: object

A class to represent an R-group, where attachment points are the atoms connected to a wildcard atom.

Each wildcard atom must be connected to only one other atom in the molecule by a single bond.

Example:

>>> RGroup('*C(O)C')
RGroup("*C(C)O")

__init__(smiles: str)¶

Parameters:: smiles – the SMILES for the R-group
Raises:: ValueError – if the SMILES is invalid, has no attachment atoms, or if any attachment atom is connected to more than one atom or not connected by a single bond

property smiles: str¶

Returns:: canonical SMILES of the R-group

property mol: Mol¶

Returns:: RDKit molecule for the R-group

attachmentCount() → int¶

Returns:: the number of attachments in the R-group

toSmarts() → str¶

Return a stereochemistry free SMARTS string with queries for atom type, implicit hydrogens, charges and connectivity.

Example:

>>> RGroup('*C(O)C').toSmarts()
'[#6&A&+0&X4;H1,H2]([C&H3&+0&X4])[O&H1&+0&X2]'

toTypedSmarts() → str¶

Return a stereochemistry free SMARTS string with queries for atom types, i.e, element and aromaticity.

Example:

>>> RGroup('*C(O)C').toTypedSmarts()
'[#6&A]([#6&A])[#8&A]'

toSingleAttachmentRGroups() → set[Self]¶

Return a set of RGroup objects that are equivalent to this RGroup but have just a single attachment point.

Example::

>>> rgroups = RGroup('*C(O)C*').toSingleAttachmentRGroups()
>>> rgroups == {RGroup("*C(C)O"), RGroup("*CCO")}
True
>>> RGroup('*C(*)N').toSingleAttachmentRGroups()
{RGroup("*CN")}

schrodinger.molutils.rgroups.smarts_from_smiles(smiles: str) → str¶

Generates a stereochemistry free SMARTS string with queries for the atom type, implicit hydrogens, charges and connectivity.

Wildcard atoms may be used to designate parts of the molecule that are not to be part of the SMARTS. The wildcard atoms may only have a single bond to only one atom in the molecule.

Example:

>>> smarts_from_smiles('CO')
'[C&H3&+0&X4][O&H1&+0&X2]'
>>> smarts_from_smiles('*CO')
'[#6&A&+0&X4;H2,H3][O&H1&+0&X2]'
>>> smarts_from_smiles('*C.O*')
'[#6&A&+0&X4;H3,H4].[#8&A&+0&X2;H1,H2]'
>>> smarts_from_smiles('*[C@@H](Cl)Br')
'[#6&A&+0&X4;H1,H2]([Cl&+0&X1])[Br&+0&X1]'

Parameters:: smiles – the RDKit SMILES string with wildcards for the R-groups
Raises:: ValueError – if the input SMILES is not valid, or if a wildcard atom is not bonded to exactly one atom by a single bond

schrodinger.molutils.rgroups.typed_smarts_from_smiles(smiles: str) → str¶

Return a stereochemistry free SMARTS string with queries for atom types, i.e, element and aromaticity.

Wild card atoms (R-groups) will be excluded from the result.

Example:

>>> typed_smarts_from_smiles('CO')
'[#6&A][#8&A]'
>>> typed_smarts_from_smiles('*C.O*')
'[#6&A].[#8&A]'
>>> typed_smarts_from_smiles('*[C@@H](Cl)Br')
'[#6&A]([#17&A])[#35&A]'

Parameters:: smiles – the RDKit SMILES string
Raises:: ValueError – if the input SMILES is not valid