Mol Toolkits¶

chemper wraps around existing cheminformatics packages to extract information about atoms and bonds stored in molecules. These are accessed through chemper.mol_toolks.mol_toolkit which accesses the source code for only the installed cheminformatics package. Right now we support OpenEye Toolkits

These and any future packge support follow the template laid out as adapters.

adapters.py

This script contains adapters or the structure for molecules, atoms, and bonds. Our chemical perception code is designed to be independent of the users cheminformatics packages. For each cheminformatics package we support we will provide classes following the structure in these adapters.

class chemper.mol_toolkits.adapters.AtomAdapter[source]¶

This is a ChemPer wrapper for an atom from one of the cheminformatics toolkits. ChemPer Atoms are initiated from the reference package object. Currently we support OpenEye and RDKit toolkits.

atom¶

Type: Atom from reference toolkit

abstract atomic_number()[source]¶

Returns: atomic_number – atomic number for the atom
Return type: int

abstract connectivity()[source]¶

Returns: connectivity – connectivity or total number of bonds (regardless of order) around the atom
Return type: int

abstract degree()[source]¶

Returns: degree – degree or number of explicit bond orders around the atom
Return type: int

abstract formal_charge()[source]¶

Returns: formal_charge – the atom’s formal charge
Return type: int

abstract get_bonds()[source]¶

Returns: bonds – Bonds connected to this atom
Return type: list[ChemPer Bonds]

abstract get_index()[source]¶

Returns: index – atom index in its molecule
Return type: int

abstract get_molecule()[source]¶

Extracts the parent molecule this atom is from.

Returns: mol – Molecule this atom is stored in
Return type: ChemPer Mol

abstract get_neighbors()[source]¶

Returns: neighbors – Atoms that are one bond away from this atom
Return type: list[ChemPer Atoms]

abstract hydrogen_count()[source]¶

Returns: H_count – total number of hydrogen atoms connected to this Atom
Return type: int

abstract is_aromatic()[source]¶

Returns: is_aromatic – True if the atom is aromatic otherwise False
Return type: boolean

abstract is_connected_to(atom2)[source]¶

Parameters: atom2 (ChemPer Atom) – Atom to check if it is bonded to this atom
Returns: connected – True if atom2 is a bonded to atom1
Return type: boolean

abstract min_ring_size()[source]¶

Returns: min_ring_size – size of the smallest ring this atom is a part of
Return type: int

abstract ring_connectivity()[source]¶

Returns: ring_connectivity – number of bonds on the atom that are a part of a ring
Return type: int

abstract valence()[source]¶

Returns: valence – the atoms valence (equivalent to degree when all bonds are explicit)
Return type: int

class chemper.mol_toolkits.adapters.BondAdapter[source]¶

This is a ChemPer wrapper for a bond from one of the cheminformatics toolkits. ChemPer Bonds are initiated from the reference package object. Currently we support OpenEye and RDKit toolkits.

bond¶

Type: Bond from reference class

abstract get_atoms()[source]¶

Returns: atoms – The two atoms connected by this bond
Return type: list[ChemPer Atoms]

abstract get_index()[source]¶

Returns: index – index of this bond in its parent molecule
Return type: int

abstract get_molecule()[source]¶

Extracts the parent molecule this bond is from

Returns: mol – Molecule this bond is stored in
Return type: ChemPer Mol

abstract get_order()[source]¶

Returns: order – This is the absolute order, returns 1.5 if bond is aromatic
Return type: int or float

abstract is_aromatic()[source]¶

Returns: is_aromatic – True if it is an aromatic bond
Return type: boolean

abstract is_double()[source]¶

Returns: is_double – True if it is a double bond
Return type: boolean

abstract is_ring()[source]¶

Returns: is_ring – True if bond is a part of a ring, otherwise False
Return type: boolean

abstract is_single()[source]¶

Returns: is_single – True if it is a single bond
Return type: boolean

abstract is_triple()[source]¶

Returns: is_triple – True if it is a triple bond
Return type: boolean

class chemper.mol_toolkits.adapters.MolAdapter[source]¶

This is a ChemPer wrapper for a molecule from one of the cheminformatics toolkits. ChemPer molecules are initiated from the reference package molecule object. Currently we support OpenEye and RDKit toolkits.

mol¶

Mol object from the reference cheminformatics toolkit

Type: toolkit Mol

abstract classmethod from_smiles(smiles)[source]¶

Creates a ChemPer Mol form a SMILES string

Parameters: smiles (str) – SMILES used to create molecule with wrapped toolkit
Returns: Mol
Return type: ChemPer Mol

abstract get_atom_by_index(idx)[source]¶

Parameters: idx (int) – atom index
Returns: atom – atom with index idx
Return type: ChemPer Atom

abstract get_atoms()[source]¶

Returns: atom_list – list of all atoms in the molecule
Return type: list[ChemPer Atoms]

abstract get_bond_by_atoms(atom1, atom2)[source]¶

Finds a bond between two atoms

Parameters

atom1 (ChemPer Atom) –
atom2 (ChemPer Atom) –

Returns

bond – If atoms are connected returns bond otherwise None

Return type

ChemPer Bond or None

abstract get_bond_by_index(idx)[source]¶

Parameters: idx (int) – bond index
Returns: bond – bond with index idx
Return type: ChemPer Bond

abstract get_bonds()[source]¶

Returns: bond_list – list of all bonds in the molecule
Return type: list[ChemPer Bonds]

abstract get_smiles()[source]¶

Returns: smiles – SMILES string for the molecule
Return type: str

abstract set_aromaticity_mdl()[source]¶: Sets the aromaticity flags in this molecule to use the MDL model

abstract smirks_search(smirks)[source]¶

Performs a substructure search on the molecule with the provided SMIRKS pattern. Note - this function expects SMIRKS patterns with indexed atoms that is with :n for at least some atoms.

Parameters: smirks (str) – SMIRKS pattern with indexed atoms (:n)
Returns: matches – match dictionaries have the form {smirks index: atom index}
Return type: list[match dictionary]