from enum import Enum, unique
from rdkit.Chem import Atom as RDAtom
from rdkit.Chem import Mol as RDMol
from rdkit.Chem import Bond as RDBond
from rdkit.Chem import BondType as RDBondType
from rdkit.Chem import MolFromSmiles, MolToSmiles, MolToPDBBlock, MolToMolBlock, GetPeriodicTable
from openbabel import openbabel as ob
from openbabel.pybel import Molecule as PybelMol
from openbabel.pybel import readstring
from luna.wrappers.rdkit import new_mol_from_block
from luna.util.exceptions import (AtomObjectTypeError, BondObjectTypeError, MoleculeObjectTypeError,
IllegalArgumentError, MoleculeObjectError)
import logging
logger = logging.getLogger()
[docs]@unique
class BondType(Enum):
"""An enumeration of bond types available at RDKit."""
# Same values and bond types available at RDKit.
UNSPECIFIED = 0
SINGLE = 1
DOUBLE = 2
TRIPLE = 3
QUADRUPLE = 4
QUINTUPLE = 5
HEXTUPLE = 6
ONEANDAHALF = 7
TWOANDAHALF = 8
THREEANDAHALF = 9
FOURANDAHALF = 10
FIVEANDAHALF = 11
AROMATIC = 12
IONIC = 13
HYDROGEN = 14
THREECENTER = 15
DATIVEONE = 16
DATIVE = 17
DATIVEL = 18
DATIVER = 19
OTHER = 20
ZERO = 21
[docs]class OBBondType(Enum):
"""An enumeration of bond types available at Open Babel."""
# Same values and bond types available at OpenBabel.
SINGLE = 1
DOUBLE = 2
TRIPLE = 3
AROMATIC = 5
[docs]class AtomWrapper:
"""This class provides util functions to access atomic properties and
other information from RDKit and Open Babel objects.
Parameters
----------
atm_obj : :class:`AtomWrapper`, :class:`rdkit.Chem.rdchem.Atom`, or :class:`openbabel.OBAtom`
An atom to wrap.
mol_obj : `MolWrapper`, :class:`rdkit.Chem.rdchem.Mol`, :class:`openbabel.pybel.Molecule`, or None
The molecule that contains the atom ``atom``. If None, the molecule is recovered directly from the atom object.
Raises
------
AtomObjectTypeError
If the atom object is not an instance
of `MolWrapper`, :class:`rdkit.Chem.rdchem.Mol`, or :class:`openbabel.pybel.Molecule`.
"""
def __init__(self, atm_obj, mol_obj=None):
if isinstance(atm_obj, self.__class__):
atm_obj = atm_obj.unwrap()
if not isinstance(atm_obj, RDAtom) and not isinstance(atm_obj, ob.OBAtom):
logger.exception("Objects of type '%s' are not currently accepted." % atm_obj.__class__)
raise AtomObjectTypeError("Objects of type '%s' are not currently accepted." % atm_obj.__class__)
self._atm_obj = atm_obj
self._parent = None
if mol_obj is None:
mol_obj = self.get_parent()
self._parent = MolWrapper(mol_obj)
@property
def atm_obj(self):
""":class:`rdkit.Chem.rdchem.Atom` or :class:`openbabel.OBAtom`: The wrapped atom object."""
return self._atm_obj
@atm_obj.setter
def atm_obj(self, atm_obj):
if not isinstance(atm_obj, RDAtom) and not isinstance(atm_obj, ob.OBAtom):
logger.exception("Objects of type '%s' are not currently accepted." % atm_obj.__class__)
raise AtomObjectTypeError("Objects of type '%s' are not currently accepted." % atm_obj.__class__)
else:
self._atm_obj = atm_obj
@property
def parent(self):
"""`MolWrapper`, :class:`rdkit.Chem.rdchem.Mol`, or :class:`openbabel.pybel.Molecule`: The molecule that contains this atom."""
return self.get_parent()
@parent.setter
def parent(self, mol_obj):
self._parent = MolWrapper(mol_obj)
[docs] def get_idx(self):
"""Get this atom's internal index within a molecule.
Returns
-------
: int
"""
return self._atm_obj.GetIdx() # Both RDKit and Open Babel have the same function name.
[docs] def get_id(self):
"""Get this atom's unique id.
When using RDKit, :py:meth:`get_id` and :py:meth:`get_idx` returns the same value.
Returns
-------
: int
"""
if self.is_rdkit_obj():
return self._atm_obj.GetIdx()
elif self.is_openbabel_obj():
return self._atm_obj.GetId()
[docs] def get_parent(self, wrapped=True):
"""Get the molecule that contains this atom.
Parameters
----------
wrapped : bool
If True, wrap the molecule with :class:`~luna.wrappers.base.MolWrapper`.
Returns
-------
: `MolWrapper`, :class:`rdkit.Chem.rdchem.Mol`, or :class:`openbabel.pybel.Molecule`
"""
if self._parent is None:
if self.is_rdkit_obj():
mol_obj = self._atm_obj.GetOwningMol()
elif self.is_openbabel_obj():
mol_obj = self._atm_obj.GetParent()
self._parent = mol_obj
if wrapped:
return MolWrapper(self._parent)
return self._parent
[docs] def get_atomic_num(self):
"""Get this atom's atomic number.
Returns
-------
: int
"""
return self._atm_obj.GetAtomicNum() # Both RDKit and Open Babel have the same function name.
[docs] def get_symbol(self):
"""Get the element symbol of this atom.
Returns
-------
: str
"""
if self.is_rdkit_obj():
return self._atm_obj.GetSymbol()
elif self.is_openbabel_obj():
return ob.GetSymbol(self._atm_obj.GetAtomicNum())
[docs] def get_charge(self):
"""Get this atom's formal charge.
Returns
-------
: int
"""
return self._atm_obj.GetFormalCharge() # Both RDKit and Open Babel have the same function name.
[docs] def get_isotope(self):
"""Get this atom's isotope number.
Returns
-------
: int
"""
if self.is_rdkit_obj():
return int(round(self._atm_obj.GetMass()))
elif self.is_openbabel_obj():
return int(round(self._atm_obj.GetExactMass()))
[docs] def get_mass(self):
"""Get this atom's exact atomic mass, which can vary given the isotope.
Returns
-------
: float
"""
if self.is_rdkit_obj():
return self._atm_obj.GetMass()
elif self.is_openbabel_obj():
return self._atm_obj.GetExactMass()
[docs] def get_atomic_mass(self):
"""Get this atom's atomic mass given by standard IUPAC average molar mass.
Returns
-------
: float
"""
if self.is_rdkit_obj():
return GetPeriodicTable().GetAtomicWeight(self.get_atomic_num())
elif self.is_openbabel_obj():
return self._atm_obj.GetAtomicMass()
[docs] def get_neighbors_number(self, only_heavy_atoms=False):
"""Get the number of atoms bound to this atom.
Parameters
----------
only_heavy_atoms : bool
If True, count only heavy atoms.
Returns
-------
: int
"""
# Subtract the number of hydrogens from the degree if only heavy atoms must be considered.
penalty = 0 if only_heavy_atoms is False else self.get_h_count()
return self.get_degree() - penalty
[docs] def get_neighbors(self, wrapped=True):
"""Get all atoms that are bound to this atom.
Parameters
----------
wrapped : bool
If True, wrap each atom with :class:`~luna.wrappers.base.AtomWrapper`.
Returns
-------
: iterable of `AtomWrapper`, :py:class:`rdkit.Chem.rdchem.Atom`, or :class:`openbabel.OBAtom`
"""
atoms = []
if self.is_rdkit_obj():
atoms = self._atm_obj.GetNeighbors()
elif self.is_openbabel_obj():
atoms = ob.OBAtomAtomIter(self._atm_obj)
if atoms and wrapped:
return [AtomWrapper(atom) for atom in atoms]
return atoms
[docs] def get_degree(self):
"""Get this atom's total degree.
Returns
-------
: int
"""
if self.is_rdkit_obj():
return self._atm_obj.GetTotalDegree()
elif self.is_openbabel_obj():
return self._atm_obj.GetTotalDegree()
[docs] def get_valence(self):
"""Get this atom's total valence (implicit and explicit)."""
if self.is_rdkit_obj():
return self._atm_obj.GetExplicitValence() + self._atm_obj.GetImplicitValence()
elif self.is_openbabel_obj():
return self._atm_obj.GetTotalValence()
bonds = [b.GetBondOrder() for b in ob.OBAtomBondIter(self._atm_obj)]
return sum(bonds) + self._atm_obj.ImplicitHydrogenCount()
[docs] def get_h_count(self):
"""Get the total number of hydrogens (implicit and explicit) bound to this atom.
Returns
-------
: int
"""
if self.is_rdkit_obj():
return self._atm_obj.GetTotalNumHs(includeNeighbors=True)
elif self.is_openbabel_obj():
return self._atm_obj.GetImplicitHCount() + self._atm_obj.ExplicitHydrogenCount()
[docs] def get_bonds(self, wrapped=True):
"""Get this atom’s bonds.
Parameters
----------
wrapped : bool
If True, wrap each bond with :class:`~luna.wrappers.base.BondWrapper`.
Returns
-------
: iterable of `BondWrapper`, :class:`rdkit.Chem.rdchem.Bond`, or :class:`openbabel.OBBond`
"""
bonds = []
if self.is_rdkit_obj():
bonds = self._atm_obj.GetBonds()
elif self.is_openbabel_obj():
bonds = ob.OBAtomBondIter(self._atm_obj)
if bonds and wrapped:
return [BondWrapper(bond) for bond in bonds]
return bonds
[docs] def get_atomic_invariants(self):
"""Get the atomic invariants of this atom.
Atomic invariants are derived from ECFP [1]_ and E3FP [2]_ and consists of seven fields:
* Number of heavy atoms;
* Valence - Number of hydrogens;
* Atomic number;
* Isotope number;
* Formal charge;
* Number of hydrogens;
* If the atom belongs to a ring or not.
Returns
-------
: list
"""
return [self.get_neighbors_number(only_heavy_atoms=True), # Number of heavy atoms
(self.get_valence() - self.get_h_count()), # Valence - Num. Hs
self.get_atomic_num(), # Atomic number
self.get_isotope(), # Isotope number
self.get_charge(), # Formal charge
self.get_h_count(), # Num. Hs
int(self.is_in_ring())] # If the atom belongs to a ring or not
[docs] def is_in_ring(self):
"""Check if this atom is in a ring."""
return self._atm_obj.IsInRing() # Both RDKit and Open Babel have the same function name.
[docs] def is_aromatic(self):
"""Check if this atom is aromatic."""
if self.is_rdkit_obj():
return self._atm_obj.GetIsAromatic()
elif self.is_openbabel_obj():
return self._atm_obj.IsAromatic()
[docs] def has_bond_type(self, bond_type):
"""Check if this atom has a bond of type ``bond_type``.
Parameters
----------
bond_type : `BondType`
Raises
------
IllegalArgumentError
If the informed bond type is not an instance of `BondType`.
"""
if isinstance(bond_type, BondType):
return any([bond_obj.get_bond_type() == bond_type for bond_obj in self.get_bonds()])
else:
raise IllegalArgumentError("The informed bond type must be an instance of '%s'." % BondType)
[docs] def has_only_bond_type(self, bond_type):
"""Check if this atom has only bonds of type ``bond_type``.
Parameters
----------
bond_type : `BondType`
Raises
------
IllegalArgumentError
If the informed bond type is not an instance of `BondType`.
"""
if isinstance(bond_type, BondType):
return all([bond_obj.get_bond_type() == bond_type for bond_obj in self.get_bonds()])
else:
raise IllegalArgumentError("The informed bond type must be an instance of '%s'." % BondType)
[docs] def set_charge(self, charge):
"""Set the formal charge of this atom.
Parameters
----------
charge : int
"""
self._atm_obj.SetFormalCharge(charge) # Both RDKit and Open Babel have the same function name.
[docs] def set_as_aromatic(self, is_aromatic):
"""Set whether this atom is aromatic or not.
Parameters
----------
is_aromatic : bool
"""
if self.is_rdkit_obj():
self._atm_obj.SetIsAromatic(is_aromatic)
elif self.is_openbabel_obj():
self._atm_obj.SetAromatic(is_aromatic)
[docs] def set_in_ring(self, in_ring):
"""Set whether this atom belongs to a ring or not.
Parameters
----------
in_ring : bool
"""
if self.is_rdkit_obj():
# TODO
raise NotImplementedError("Currently, there is no function in RDKit to define if an atom belongs to a ring or not. "
"Please, use Open Babel instead.")
elif self.is_openbabel_obj():
self._atm_obj.SetInRing(in_ring)
[docs] def matches_smarts(self, smarts):
"""Check if this atom matches the substructure through a SMARTS substructure search.
**Note:** currently, this function only works with molecules read with Open Babel.
Parameters
----------
smarts : str
A substructure defined as SMARTS.
Returns
-------
: bool or None
Whether matches occurred. Return None if the molecule was read with RDKit.
Examples
--------
First, let's read a molecule (glutamine) using Open Babel.
>>> from luna.wrappers.base import MolWrapper
>>> mol_obj = MolWrapper.from_smiles("N[C@@H](CCC(N)=O)C(O)=O", mol_obj_type="openbabel")
Now, we'll loop over the list of atoms in the glutamine and check which atom is the amide's carbon.
To do so, we can call the function :py:meth:`MolWrapper.get_atoms`, which, by default,
returns `AtomWrapper` objects and then call :py:meth:`matches_smarts`.
>>> for atm in mol_obj.get_atoms():
>>> print("%d\t%s\t%s" % (atm.get_idx(), atm.get_symbol(), atm.matches_smarts("C(N)(C)=O")))
1 N False
2 C False
3 C False
4 C False
5 C True
6 N False
7 O False
8 C False
9 O False
10 O False
"""
if self.is_rdkit_obj():
# TODO: Implement
raise NotImplementedError("Currently, matches_smarts() does not support RDKit objects. "
"Please, use Open Babel objects instead.")
elif self.is_openbabel_obj():
ob_smart = ob.OBSmartsPattern()
ob_smart.Init(smarts)
if ob_smart.Match(self.parent):
for match in ob_smart.GetMapList():
if match[0] == self.get_idx():
return True
return False
[docs] def unwrap(self):
"""Return the original atomic object.
Returns
-------
: :class:`rdkit.Chem.rdchem.Atom` or :class:`openbabel.OBAtom`
"""
return self._atm_obj
[docs] def is_rdkit_obj(self):
"""Check if this atom is an RDKit object."""
if isinstance(self._atm_obj, RDAtom):
return True
return False
[docs] def is_openbabel_obj(self):
"""Check if this atom is an Open Babel object."""
if isinstance(self._atm_obj, ob.OBAtom):
return True
return False
def __getattr__(self, attr):
return getattr(self._atm_obj, attr)
[docs]class BondWrapper:
"""This class provides util functions to access bond properties and
other information from RDKit and Open Babel objects.
Parameters
----------
bond_obj : `BondWrapper`, :py:class:`rdkit.Chem.rdchem.Bond`, or :py:class:`openbabel.OBBond`
A bond to wrap.
Raises
------
BondObjectTypeError
If the bond object is not an instance
of `BondWrapper`, :class:`rdkit.Chem.rdchem.Bond`, or :class:`openbabel.pybel.OBBond`.
"""
def __init__(self, bond_obj):
if isinstance(bond_obj, self.__class__):
bond_obj = bond_obj.unwrap()
if not isinstance(bond_obj, RDBond) and not isinstance(bond_obj, ob.OBBond):
logger.exception("Objects of type '%s' are not currently accepted." % bond_obj.__class__)
raise BondObjectTypeError("Objects of type '%s' are not currently accepted." % bond_obj.__class__)
self._bond_obj = bond_obj
@property
def bond_obj(self):
""":class:`rdkit.Chem.rdchem.Bond` or :class:`openbabel.OBBond`: The wrapped bond object."""
return self._bond_obj
@bond_obj.setter
def bond_obj(self, bond_obj):
if not isinstance(bond_obj, RDBond) and not isinstance(bond_obj, ob.OBBond):
logger.exception("Objects of type '%s' are not currently accepted." % bond_obj.__class__)
raise AtomObjectTypeError("Objects of type '%s' are not currently accepted." % bond_obj.__class__)
else:
self._bond_obj = bond_obj
[docs] def get_partner_atom(self, atm, wrapped=True):
"""Get the partner atom that forms this bond with ``atm``.
Parameters
----------
atm : `AtomWrapper`, :py:class:`rdkit.Chem.rdchem.Atom`, or :class:`openbabel.OBAtom`
Get the partner of this atom.
wrapped : bool
If True, wrap the partner atom with `AtomWrapper`.
Returns
-------
: `AtomWrapper`, :py:class:`rdkit.Chem.rdchem.Atom`, or :class:`openbabel.OBAtom`
"""
if isinstance(atm, AtomWrapper):
atm = atm.unwrap()
partner = None
if atm == self._bond_obj.GetBeginAtom():
partner = self._bond_obj.GetEndAtom()
elif atm == self._bond_obj.GetEndAtom():
partner = self._bond_obj.GetBeginAtom()
if partner and wrapped:
return AtomWrapper(partner)
return partner
[docs] def get_begin_atom(self, wrapped=True):
"""Return the bond’s first atom.
Parameters
----------
wrapped : bool
If True, wrap the atom with `AtomWrapper`.
Returns
-------
: `AtomWrapper`, :py:class:`rdkit.Chem.rdchem.Atom`, or :class:`openbabel.OBAtom`
"""
# Both RDKit and Open Babel have the same function name.
if wrapped:
return AtomWrapper(self._bond_obj.GetBeginAtom())
return self._bond_obj.GetBeginAtom()
[docs] def get_end_atom(self, wrapped=True):
"""Return the bond’s second atom.
Parameters
----------
wrapped : bool
If True, wrap the atom with `AtomWrapper`.
Returns
-------
: `AtomWrapper`, :py:class:`rdkit.Chem.rdchem.Atom`, or :class:`openbabel.OBAtom`
"""
# Both RDKit and Open Babel have the same function name.
if wrapped:
return AtomWrapper(self._bond_obj.GetEndAtom())
return self._bond_obj.GetEndAtom()
[docs] def get_bond_type(self):
"""Get the bond type (e.g., single bond).
Returns
-------
: `BondType`
"""
if self.is_rdkit_obj():
return BondType[self._bond_obj.GetBondType().name]
elif self.is_openbabel_obj():
# Map Open Babel bonds to BondType.
return BondType[OBBondType(self._bond_obj.GetBondOrder()).name]
[docs] def is_aromatic(self):
"""Check if this bond is aromatic or not."""
if self.is_rdkit_obj():
return self._bond_obj.GetIsAromatic()
elif self.is_openbabel_obj():
return self._bond_obj.IsAromatic()
[docs] def set_bond_type(self, bond_type):
"""Set the type of the bond as a ``bond_type``.
Parameters
----------
bond_type : `BondType`
"""
# Convert BondType to a valid type accepted by Open Babel or RDKit.
if isinstance(bond_type, BondType):
try:
if self.is_rdkit_obj():
bond_type = RDBondType.values[bond_type.value]
elif self.is_openbabel_obj():
bond_type = OBBondType[bond_type.name].value
except KeyError as e:
logger.exception(e)
tool = "Open Babel" if self.is_openbabel_obj() else "RDKit"
raise KeyError("The bond type '%s' is not a valid %s bond type." % (bond_type.name, tool))
else:
raise IllegalArgumentError("The informed bond type must be an instance of '%s'." % BondType)
if self.is_rdkit_obj():
try:
self._bond_obj.SetBondType(bond_type)
except Exception as e:
logger.exception(e)
raise
elif self.is_openbabel_obj():
self._bond_obj.SetBondOrder(bond_type)
[docs] def set_as_aromatic(self, is_aromatic):
"""Set if this bond is aromatic or not.
Parameters
----------
is_aromatic : bool
"""
if self.is_rdkit_obj():
self._bond_obj.SetIsAromatic(is_aromatic)
elif self.is_openbabel_obj():
self._bond_obj.SetAromatic(is_aromatic)
[docs] def unwrap(self):
"""Return the original bond object.
Returns
-------
: :class:`rdkit.Chem.rdchem.Bond` or :class:`openbabel.OBBond`
"""
return self._bond_obj
[docs] def is_rdkit_obj(self):
"""Check if this bond is an RDKit object."""
if isinstance(self._bond_obj, RDBond):
return True
return False
[docs] def is_openbabel_obj(self):
"""Check if this bond is an Open Babel object."""
if isinstance(self._bond_obj, ob.OBBond):
return True
return False
def __getattr__(self, attr):
return getattr(self._bond_obj, attr)
[docs]class MolWrapper:
"""This class provides util functions to access molecule properties and
other information from RDKit and Open Babel objects.
Parameters
----------
mol_obj : `MolWrapper`, :class:`rdkit.Chem.rdchem.Mol`, or :class:`openbabel.pybel.Molecule`
A molecule to wrap.
Raises
------
MoleculeObjectTypeError
If the molecular object is not an instance
of `MolWrapper`, :class:`rdkit.Chem.rdchem.Mol`, or :class:`openbabel.pybel.Molecule`.
"""
def __init__(self, mol_obj):
if isinstance(mol_obj, self.__class__):
mol_obj = mol_obj.unwrap()
elif isinstance(mol_obj, PybelMol):
mol_obj = mol_obj.OBMol
if not isinstance(mol_obj, RDMol) and not isinstance(mol_obj, ob.OBMol):
logger.exception("Objects of type '%s' are not currently accepted." % mol_obj.__class__)
raise MoleculeObjectTypeError("Objects of type '%s' are not currently accepted." % mol_obj.__class__)
self._mol_obj = mol_obj
[docs] @classmethod
def from_mol_block(cls, block, mol_format, mol_obj_type="rdkit"):
"""Initialize a molecule from a string block.
Parameters
----------
block : str
The molecular string block.
mol_format : str
Define the format in which the molecule is represented (e.g., 'mol2' or 'mol').
mol_obj_type : {'rdkit', 'openbabel'}
Define which library (RDKit or Open Babel) to use to parse the molecular block.
The default value is RDKit.
Returns
-------
: `MolWrapper`
"""
if mol_obj_type == "rdkit":
return cls(new_mol_from_block(block, mol_format))
elif mol_obj_type == "openbabel":
return cls(readstring(mol_format, block))
[docs] @classmethod
def from_smiles(cls, smiles, mol_obj_type="rdkit", name=None):
"""Initialize a molecule from a SMILES string.
Parameters
----------
smiles : str
The SMILES string.
Define the format in which the molecule is represented (e.g., 'mol2' or 'mol').
mol_obj_type : {'rdkit', 'openbabel'}
Define which library (RDKit or Open Babel) to use to parse the molecular block.
The default value is RDKit.
name : str, optional
A name to identify the molecule.
Returns
-------
: `MolWrapper`
Raises
------
MoleculeObjectError
If it could not create a molecule from the provided SMILES.
Examples
--------
>>> from luna.wrappers.base import MolWrapper
>>> mol_obj = MolWrapper.from_smiles("N[C@@H](CCC(N)=O)C(O)=O", mol_obj_type="openbabel", name="Glutamine")
"""
if mol_obj_type == "rdkit":
mol = MolFromSmiles(smiles)
elif mol_obj_type == "openbabel":
mol = readstring("smi", smiles)
# Raise an error if the molecule could not be created.
if mol is None:
raise MoleculeObjectError("It could not create a molecule from the provided SMILES '%s'." % smiles)
mol = cls(mol)
mol.set_name(name or smiles)
return mol
@property
def mol_obj(self):
""":class:`rdkit.Chem.rdchem.Mol` or :class:`openbabel.pybel.Molecule`: The wrapped molecular object."""
return self._mol_obj
@mol_obj.setter
def mol_obj(self, mol_obj):
if isinstance(mol_obj, PybelMol):
mol_obj = mol_obj.OBMol
if not isinstance(mol_obj, RDMol) and not isinstance(mol_obj, ob.OBMol):
logger.exception("Objects of type '%s' are not currently accepted." % mol_obj.__class__)
raise MoleculeObjectTypeError("Objects of type '%s' are not currently accepted." % mol_obj.__class__)
self._mol_obj = mol_obj
[docs] def as_rdkit(self):
"""If the molecule is an Open Babel object, convert it to an RDKit object."""
if self.is_rdkit_obj():
return self._mol_obj
elif self.is_openbabel_obj():
new_mol = MolWrapper.from_smiles(self.to_smiles(), mol_obj_type="rdkit")
new_mol.set_name(self.get_name())
return new_mol.unwrap()
[docs] def as_openbabel(self):
"""If the molecule is an RDKit object, convert it to an Open Babel object."""
if self.is_openbabel_obj():
return self._mol_obj
elif self.is_rdkit_obj():
new_mol = MolWrapper.from_smiles(self.to_smiles(), mol_obj_type="openbabel")
new_mol.set_name(self.get_name())
return new_mol.unwrap()
[docs] def get_name(self):
"""Get the molecule name.
Returns
-------
: str
"""
if self.is_rdkit_obj():
if self._mol_obj.HasProp("_Name"):
return self._mol_obj.GetProp("_Name")
return ""
elif self.is_openbabel_obj():
return self._mol_obj.GetTitle()
[docs] def get_atoms(self, wrapped=True):
"""Get all molecule's atoms.
Parameters
----------
wrapped : bool
If True, wrap all atoms with `AtomWrapper`.
Returns
-------
: iterable of `AtomWrapper`, :py:class:`rdkit.Chem.rdchem.Atom`, or :class:`openbabel.OBAtom`
"""
atoms = []
if self.is_rdkit_obj():
atoms = self._mol_obj.GetAtoms()
elif self.is_openbabel_obj():
atoms = ob.OBMolAtomIter(self._mol_obj)
if atoms and wrapped:
return [AtomWrapper(atm, self) for atm in atoms]
return atoms
[docs] def get_bonds(self, wrapped=True):
"""Get all molecule's bonds.
Parameters
----------
wrapped : bool
If True, wrap all bonds with `BondWrapper`.
Returns
-------
: iterable of `BondWrapper`, :class:`rdkit.Chem.rdchem.Bond`, or :class:`openbabel.OBBond`
"""
bonds = []
if self.is_rdkit_obj():
bonds = self._mol_obj.GetBonds()
elif self.is_openbabel_obj():
bonds = ob.OBMolBondIter(self._mol_obj)
if bonds and wrapped:
return [BondWrapper(bond) for bond in bonds]
return bonds
[docs] def get_num_heavy_atoms(self):
"""Get the number of heavy atoms in this molecule."""
if self.is_rdkit_obj():
return self._mol_obj.GetNumHeavyAtoms()
elif self.is_openbabel_obj():
return self._mol_obj.NumHvyAtoms()
[docs] def get_atom_coord_by_id(self, atm_id):
"""Get the coordinates of an atom given by its id.
Returns
-------
: array_like of float (size 3)
Atomic coordinates (x, y, z).
"""
if self.is_rdkit_obj():
return list(self._mol_obj.GetConformer().GetAtomPosition(atm_id))
elif self.is_openbabel_obj():
atm = self._mol_obj.GetAtomById(atm_id)
return [atm.GetX(), atm.GetY(), atm.GetZ()]
[docs] def get_obj_type(self):
"""Get the object type ("rdkit" or "openbabel")."""
if self.is_rdkit_obj():
return "rdkit"
elif self.is_openbabel_obj():
return "openbabel"
[docs] def has_name(self):
"""Check if this molecule has a name."""
if self.get_name():
return True
return False
[docs] def set_name(self, name):
"""Set a name to this molecule.
Parameters
----------
name : str
"""
if self.is_rdkit_obj():
self._mol_obj.SetProp("_Name", name)
elif self.is_openbabel_obj():
self._mol_obj.SetTitle(name)
[docs] def to_smiles(self):
"""Return the canonical SMILES string for this molecule."""
if self.is_rdkit_obj():
return MolToSmiles(self._mol_obj)
elif self.is_openbabel_obj():
return PybelMol(self._mol_obj).write("smi").split("\t")[0]
[docs] def to_pdb_block(self):
"""Return the PDB string block for this molecule."""
if self.is_rdkit_obj():
return MolToPDBBlock(self._mol_obj)
elif self.is_openbabel_obj():
return PybelMol(self._mol_obj).write("pdb")
[docs] def to_mol_block(self):
"""Return the MOL string block for this molecule."""
if self.is_rdkit_obj():
return MolToMolBlock(self._mol_obj)
elif self.is_openbabel_obj():
return PybelMol(self._mol_obj).write("mol")
[docs] def unwrap(self):
"""Return the original molecular object.
Returns
-------
: :class:`rdkit.Chem.rdchem.Mol` or :class:`openbabel.pybel.Molecule`.
"""
return self._mol_obj
[docs] def is_rdkit_obj(self):
"""Check if this molecule is an RDKit object."""
if isinstance(self._mol_obj, RDMol):
return True
return False
[docs] def is_openbabel_obj(self):
"""Check if this molecule is an Open Babel object."""
if isinstance(self._mol_obj, ob.OBMol):
return True
elif isinstance(self._mol_obj, PybelMol):
return True
return False
[docs] def is_pybel_obj(self):
"""Check if this molecule is a Pybel object."""
if isinstance(self._mol_obj, PybelMol):
return True
return False
def __getattr__(self, attr):
if self.mol_obj is None:
return None
return getattr(self._mol_obj, attr)
def __getstate__(self):
# Creates a copy of the class' dictionary in case we need to modify the molecular object to pickle it.
my_dict = self.__dict__.copy()
if self.is_openbabel_obj():
my_dict["_mol_block"] = self.to_mol_block()
my_dict["_mol_obj_type"] = self.get_obj_type()
my_dict["_mol_obj"] = None
return my_dict
def __setstate__(self, state):
if "_mol_obj_type" in state and "_mol_block" in state:
state["_mol_obj"] = self.from_mol_block(state["_mol_block"], "mol", "openbabel").unwrap()
del state["_mol_obj_type"]
del state["_mol_block"]
self.__dict__.update(state)