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