schrodinger.comparison.chirality module¶
- schrodinger.comparison.chirality.get_chirality(st, ignore_annotations=True)¶
Make list of the chiralities and stereo chemistry.
- Parameters
st (Structure instance) – Use the atoms in this structure
ignore_annotations (boolean) – If True then structure level properties defining the stereochemistry will be ignored and stereochemistry is computed only from geometries and current Lewis structure
- Return type
list(str or None)
- Returns
list of chirality/stereochemistry labels
- schrodinger.comparison.chirality.get_atom_numbering_chirality(st)¶
Make list of the chiralities and stereo chemistry due to atom number for the atoms in st.
- Parameters
st (Structure instance) – Use the atoms in this structure
- Return type
list(str or None)
- Returns
list of atom-numbering chirality/stereochemistry labels
- schrodinger.comparison.chirality.get_pseudochirality(st)¶
Use RDKit to obtain pseudo-chirality labels (see SHARED-6352).
We will turn any dummy atoms in the structure into Lr because RDKit doesn’t handle dummy atoms properly for CIP labels.
- Parameters
st (Structure instance) – Use the atoms in this structure
- Return type
list(str or None)
- Returns
list of pseudochirality/stereochemistry labels
- schrodinger.comparison.chirality.get_chiral_centers(st)¶
Return indices of CIP chiral centers in structure.
- Parameters
st (Structure instance) – Use the atoms in this structure
- schrodinger.comparison.chirality.valid_chiral_comp(ch1, ch2)¶
Maestro’s chirality checker returns both E/Z double bond isomer labels and R/S chirality labels. If a reaction (e.g. and addition or elimination reaction) changes a molecule from a double bond to a single bond, merely checking if the chirality labels match will always lead to an apparent mismatch, even though there is no actual problem. This function returns True if the chirality types can be correctly compared and False if not.
- Parameters
ch1 (string) – chirality label of atom 1
ch2 (string) – chirality label of atom 2
- Returns
True if chiralities are comparable else False