Mol

Form adapter and capabilities for rdkit.Mol.

• Technical Form Name: rdkit.Mol

• Form Type: class

Added in version 1.0.0.

API documentation

• Form adapter module: molsysmt.form.rdkit_Mol

Overview

rdkit.Mol is a supported representation form in MolSysMT. Form adapter and capabilities for rdkit.Mol.

Supported attributes

The rdkit.Mol form container supports a total of 81 attributes:

Category	Subcategory / Level	Supported Attributes
Topological	Atom Level	atom_index, atom_name, atom_id, atom_type, isotope, formal_charge, atom_is_aromatic, n_unpaired_electrons, n_implicit_hydrogens, allows_implicit_hydrogens, atom_stereochemistry
Topological	Group Level	group_index, group_name, group_id, group_type
Topological	Component Level	component_completeness, component_evidence, component_index, component_name, component_id, component_type
Topological	Chain Level	chain_index, chain_name, chain_id, chain_type
Topological	Molecule Level	molecule_index, molecule_name, molecule_id, molecule_type
Topological	Entity Level	entity_index, entity_name, entity_id, entity_type
Topological	Bonds & Connectivity	connectivity_completeness, bond_index, bond_id, bond_type, bond_order, fractional_bond_order, bond_is_aromatic, bond_is_conjugated, bond_stereochemistry, bond_stereo_atom_indices, bond_donor_atom_index, bond_acceptor_atom_index, bond_joins_components, bond_evidence, bonded_atoms, bonded_atom_pairs, inner_bonded_atoms, inner_bonded_atom_pairs, inner_bond_index, n_bonds, n_inner_bonds
Topological	Chemical States	chemical_state_index, chemical_state_id, n_chemical_states, reference_chemical_state_index
Topological	Element Counts	n_atoms, n_groups, n_components, n_chains, n_molecules, n_entities, n_bonds, n_inner_bonds, n_amino_acids, n_nucleotides, n_ions, n_waters, n_small_molecules, n_peptides, n_proteins, n_dnas, n_rnas, n_lipids, n_polysaccharides, n_saccharides
Structural	Coordinates & Conformations	structure_index, structure_id, coordinates, n_structures
Structural	Other Attributes	atom_index, n_atoms
Mechanical	Force Field Parameters	partial_charge

Implemented operations

The form adapter module molsysmt.form.rdkit_Mol implements the following functions and modules:

Function / Module	Description
get_topological_attributes	Module containing getters for topological attributes.
get_structural_attributes	Module containing getters for structural attributes.
get_mechanical_attributes	Module containing getters for mechanical attributes.
has_attribute()	Checks whether a specific attribute name is supported by rdkit.Mol.
is_form()	Returns True if the provided object is an instance of rdkit.Mol.

Note

Each form adapter in MolSysMT implements only the specific functions that are meaningful for its data model.

Supported conversions

The following table lists all direct conversion functions implemented in molsysmt.form.rdkit_Mol:

Target Form	Form Type	API Documentation
file:smi	file	to_file_smi()
molsysmt.MolSys	class	to_molsysmt_MolSys()
molsysmt.Structures	class	to_molsysmt_Structures()
molsysmt.Topology	class	to_molsysmt_Topology()
openff.Molecule	class	to_openff_Molecule()
rdkit.Mol	class	to_rdkit_Mol()
string:smiles	string	to_string_smiles()

See also

Foundations & Object Architecture:

• The Molecular System: The fundamental definition of a molecular system, forms, and attributes in MolSysMT.

• MolSys: In-depth architectural guide on the native molsysmt.MolSys container.

• Topology: Architectural specification of the native Topology object.

• Structures: Architectural specification of the native Structures object.

Form Tools & Conversions:

• Convert: Converting between any molecular system representations with molsysmt.basic.convert().

• Get attributes: Querying all supported attributes for any form with molsysmt.form.get_attributes().

• Has attribute: Testing attribute availability for a form with molsysmt.form.has_attribute().