schrodinger.adapter module¶

schrodinger::adapter C++ wrappers

class schrodinger.adapter.Canonicalize¶

Enable = True¶

Disable = False¶

class schrodinger.adapter.CaptureRDErrorLog¶

schrodinger::rdkit_extensions::CaptureRDErrorLog

__init__(*args, **kwargs)¶

messages(self) → std::string¶

class schrodinger.adapter.Generate2DCoordinates¶

Enable = True¶

Disable = False¶

class schrodinger.adapter.Hydrogens¶

AS_INPUT = 0¶

IMPLICIT = 1¶

EXPLICIT = 2¶

exception schrodinger.adapter.InconsistentStructureError¶: The input structure for conversion is not internally consistent

class schrodinger.adapter.LabelAtoms¶

Enable = True¶

Disable = False¶

class schrodinger.adapter.Properties¶

Copy = True¶

Ignore = False¶

class schrodinger.adapter.RDKitOptions¶

schrodinger::adapter::RDKitOptions

__init__(*args, **kwargs)¶

hydrogens¶

labelatoms¶

properties¶

sanitize¶

stereochemistry¶

exception schrodinger.adapter.SMARTSParseError¶: SMARTS pattern could not be parsed

class schrodinger.adapter.Sanitize¶

Enable = True¶

Disable = False¶

class schrodinger.adapter.StereoChemistry¶

Copy = True¶

Ignore = False¶

class schrodinger.adapter.UniqueFilter¶

Enable = True¶

Disable = False¶

exception schrodinger.adapter.UnsupportedStructureError¶: For structures that can’t be translated between RDKit and Schrodinger yet

schrodinger.adapter.evaluate_smarts(st, smarts, unique_sets=False)¶

schrodinger.adapter.is_valid_smiles(smiles) → bool¶

schrodinger.adapter.smiles_to_3d_structure(smiles, *, require_stereo=True)¶: Convert a SMILES string to a 3D structure.

schrodinger.adapter.to_rdkit(st, options=schrodinger::adapter::RDKitOptions()) → boost::shared_ptr< RDKit::ROMol >¶

schrodinger.adapter.to_smarts(st, *, atoms=None, check_connectivity=True, stereo=True, hydrogens=1)¶: Convert an RDKit molecule to a SMARTS string.

schrodinger.adapter.to_smiles(st, *, strict=True, stereo=True)¶: Convert an RDKit molecule to a SMILES string

schrodinger.adapter.to_smiles_canonical_atom_order(st, *, strict=True, stereo=True)¶: Get a canonical ordering of atoms in a structure.

schrodinger.adapter.to_structure(mol, labelatoms=Enable, properties=Copy, conformer=None, stereochemistry=Copy, hydrogens=EXPLICIT) → Structure¶
schrodinger.adapter.to_structure(smiles, generate_coords=Disable, hydrogens=EXPLICIT) → Structure

schrodinger.adapter.validate_smarts(smarts)¶