rdkit.Chem.rdDepictor module

Module containing the functionality to compute 2D coordinates for a molecule

class rdkit.Chem.rdDepictor.ConstrainedDepictionParams(self)

Bases: object

Parameters controlling constrained depiction

property acceptFailure

if False (default), a DepictException is thrown if the molecule does not have a substructure match to the reference; if True, an unconstrained depiction will be generated

property adjustMolBlockWedging

if True (default), existing wedging information will be updated or cleared as required; if False, existing molblock wedging information will always be preserved

property alignOnly

if False (default), a part of the molecule is hard-constrained to have the same coordinates as the reference, and the rest of the molecule is built around it; if True, coordinates from conformation existingConfId are preserved (if they exist) or generated without constraints (if they do not exist), then the conformation is rigid-body aligned to the reference

property allowRGroups

if True, terminal dummy atoms in the reference are ignored if they match an implicit hydrogen in the molecule or if they are attached top a query atom; defaults to False

property existingConfId

conformation id whose 2D coordinates should be rigid-body aligned to the reference (if alignOnly is True), or used to determine whether existing molblock wedging information can be preserved following the constrained depiction (if adjustMolBlockWedging is True

property forceRDKit

if True, use RDKit to generate coordinates even if preferCoordGen is set to True; defaults to False

property useRingTemplates

use templates to generate coordinates of complex ring systems

exception rdkit.Chem.rdDepictor.DepictException

Bases: ValueError

class rdkit.Chem.rdDepictor.UsingCoordGen(self, temp_state: bool)

Bases: object

Context manager to temporarily set CoordGen library preference in RDKit depiction.

Constructor