OpenEye¶

Following the template outlined, chemper Mol, Atom, and Bond objects can be created from OpenEye tools.

cp_openeye.py

Cheminformatics tools using OpenEye Toolkits

The classes provided here follow the structure in adapters. This is a wrapper allowing our actual package to use openeye toolkits

class chemper.mol_toolkits.cp_openeye.Atom(atom)[source]¶

atomic_number()[source]¶

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

connectivity()[source]¶

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

degree()[source]¶

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

formal_charge()[source]¶

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

get_bonds()[source]¶

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

get_index()[source]¶

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

get_molecule()[source]¶

Extracts the parent molecule this atom is from.

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

get_neighbors()[source]¶

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

hydrogen_count()[source]¶

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

is_aromatic()[source]¶

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

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

min_ring_size()[source]¶

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

ring_connectivity()[source]¶

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

valence()[source]¶

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

class chemper.mol_toolkits.cp_openeye.Bond(bond)[source]¶

get_atoms()[source]¶

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

get_index()[source]¶

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

get_molecule()[source]¶

Extracts the parent molecule this bond is from

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

get_order()[source]¶

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

is_aromatic()[source]¶

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

is_double()[source]¶

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

is_ring()[source]¶

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

is_single()[source]¶

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

is_triple()[source]¶

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

class chemper.mol_toolkits.cp_openeye.Mol(mol)[source]¶

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

get_atom_by_index(idx)[source]¶

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

get_atoms()[source]¶

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

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

get_bond_by_index(idx)[source]¶

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

get_bonds()[source]¶

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

get_smiles()[source]¶

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

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

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]

chemper.mol_toolkits.cp_openeye.mols_from_file(mol_file)[source]¶

Parses a standard molecule file into ChemPer molecules using OpenEye toolkits

Parameters: mol_file (str) – relative or full path to molecule containing the molecule file that is accessible from the current working directory
Returns: mols – list of molecules in the mol2 file as ChemPer Mols
Return type: list[ChemPer Mol]