Source code for openforcefield.topology.molecule

#!/usr/bin/env python

#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Molecular chemical entity representation and routines to interface with cheminformatics toolkits

.. todo::

   * Our main philosophy here is to keep the object contents of topology objects easily serializable/deserializable

   * Have ``Molecule`` raise an exception if loading/creating molecules with unspecified stereochemistry?
   * Create ``FrozenMolecule`` to represent immutable molecule
   * Make ``Atom`` and ``Bond`` an inner class of Molecule?
   * Add ``Molecule.from_smarts()`` or ``.from_tagged_smiles()`` to allow a tagged SMARTS string
     (where tags are zero-indexed atom indices) to be used to create a molecule with the given atom numbering.
   * How can we make the ``Molecule`` API more useful to codes like perses that modify molecules on the fly?
   * Use `attrs <http://www.attrs.org/>`_ for convenient class initialization?
   * JSON/BSON representations of objects?
   * Generalize Molecule infrastructure to provide "plug-in" support for cheminformatics toolkits
   * Do we need a way to write a bunch of molecules to a file, or serialize a set of molecules to a file?
     We currently don't have a way to do that through the ``Molecule`` API, even though there is a way to
     read multiple molecules via ``Molecules.from_file()``.
   * Should we allow the removal of atoms too?
   * Should invalidation of cached properties be handled via something like a tracked list?
   * Refactor toolkit encapsulation to generalize and provide only a few major toolkit methods and toolkit objects that can be queried for features
   * Speed up overall import time by putting non-global imports only where they are needed

"""

#=============================================================================================
# GLOBAL IMPORTS
#=============================================================================================

import numpy as np
from collections import OrderedDict
from copy import deepcopy

from simtk import unit
from simtk.openmm.app import element

import openforcefield
from openforcefield.utils import serialize_numpy, deserialize_numpy, quantity_to_string, string_to_quantity
from openforcefield.utils.toolkits import ToolkitRegistry, ToolkitWrapper, RDKitToolkitWrapper, OpenEyeToolkitWrapper,\
    InvalidToolkitError, GLOBAL_TOOLKIT_REGISTRY
from openforcefield.utils.toolkits import DEFAULT_AROMATICITY_MODEL
from openforcefield.utils.serialization import Serializable



#=============================================================================================
# GLOBAL PARAMETERS
#=============================================================================================

# TODO: Can we have the `ALLOWED_*_MODELS` list automatically appear in the docstrings below?
# TODO: Should `ALLOWED_*_MODELS` be objects instead of strings?
# TODO: Should these be imported from `openforcefield.cheminformatics.aromaticity_models` and `.bondorder_models`?

# TODO: Allow all OpenEye aromaticity models to be used with OpenEye names?
#       Only support OEAroModel_MDL in RDKit version?

#=============================================================================================
# PRIVATE SUBROUTINES
#=============================================================================================

#=============================================================================================
# Particle
#=============================================================================================


[docs]class Particle(Serializable): """ Base class for all particles in a molecule. A particle object could be an ``Atom`` or a ``VirtualSite``. .. warning :: This API is experimental and subject to change. """ @property def molecule(self): """ The ``Molecule`` this atom is part of. .. todo:: * Should we have a single unique ``Molecule`` for each molecule type in the system, or if we have multiple copies of the same molecule, should we have multiple ``Molecule``s? """ return self._molecule @molecule.setter def molecule(self, molecule): """ Set the particle's molecule pointer. Note that this will only work if the particle currently doesn't have a molecule """ #TODO: Add informative exception here assert self._molecule is None self._molecule = molecule @property def molecule_particle_index(self): """ Returns the index of this particle in its molecule """ return self._molecule.particles.index(self) @property def name(self): """ The name of the particle """ return self._name
[docs] def to_dict(self): """Convert to dictionary representation.""" # Implement abstract method Serializable.to_dict() raise NotImplementedError() # TODO
[docs] @classmethod def from_dict(cls, d): """Static constructor from dictionary representation.""" # Implement abstract method Serializable.to_dict() raise NotImplementedError() # TODO
#============================================================================================= # Atom #=============================================================================================
[docs]class Atom(Particle): """ A particle representing a chemical atom. Note that non-chemical virtual sites are represented by the ``VirtualSite`` object. .. todo:: * Should ``Atom`` objects be immutable or mutable? * Do we want to support the addition of arbitrary additional properties, such as floating point quantities (e.g. ``charge``), integral quantities (such as ``id`` or ``serial`` index in a PDB file), or string labels (such as Lennard-Jones types)? .. todo :: Allow atoms to have associated properties. .. warning :: This API is experimental and subject to change. """
[docs] def __init__(self, atomic_number, formal_charge, is_aromatic, name=None, molecule=None, stereochemistry=None): """ Create an immutable Atom object. Object is serializable and immutable. .. todo :: Use attrs to validate? .. todo :: We can add setters if we need to. Parameters ---------- atomic_number : int Atomic number of the atom formal_charge : int Formal charge of the atom is_aromatic : bool If True, atom is aromatic; if False, not aromatic stereochemistry : str, optional, default=None Either 'R' or 'S' for specified stereochemistry, or None for ambiguous stereochemistry name : str, optional, default=None An optional name to be associated with the atom Examples -------- Create a non-aromatic carbon atom >>> atom = Atom(6, 0, False) Create a chiral carbon atom >>> atom = Atom(6, 0, False, stereochemistry='R', name='CT') """ self._atomic_number = atomic_number self._formal_charge = formal_charge self._is_aromatic = is_aromatic self._stereochemistry = stereochemistry if name is None: name = '' self._name = name self._molecule = molecule ## From Jeff: I'm going to assume that this is implicit in the parent Molecule's ordering of atoms #self._molecule_atom_index = molecule_atom_index self._bonds = list() self._virtual_sites = list()
# TODO: We can probably avoid an explicit call and determine this dynamically # from self._molecule (maybe caching the result) to get rid of some bookkeeping.
[docs] def add_bond(self, bond): """Adds a bond that this atom is involved in .. todo :: Is this how we want to keep records? Parameters ---------- bond: an openforcefield.topology.molecule.Bond A bond involving this atom """ self._bonds.append(bond)
#self._stereochemistry = None
[docs] def add_virtual_site(self, vsite): """Adds a bond that this atom is involved in .. todo :: Is this how we want to keep records? Parameters ---------- bond: an openforcefield.topology.molecule.Bond A bond involving this atom """ self._virtual_sites.append(vsite)
[docs] def to_dict(self): """Return a dict representation of the atom. """ # TODO atom_dict = OrderedDict() atom_dict['atomic_number'] = self._atomic_number atom_dict['formal_charge'] = self._formal_charge atom_dict['is_aromatic'] = self._is_aromatic atom_dict['stereochemistry'] = self._stereochemistry # TODO: Should we let atoms have names? atom_dict['name'] = self._name # TODO: Should this be implicit in the atom ordering when saved? #atom_dict['molecule_atom_index'] = self._molecule_atom_index return atom_dict
[docs] @classmethod def from_dict(cls, atom_dict): """Create an Atom from a dict representation. """ ## TODO: classmethod or static method? Classmethod is needed for Bond, so it have ## its _molecule set and then look up the Atom on each side of it by ID return cls.__init__(*atom_dict)
@property def formal_charge(self): """ The atom's formal charge """ return self._formal_charge @property def partial_charge(self): """ The partial charge of the atom, if any. Returns ------- float or None """ if self._molecule._partial_charges is None: return None else: index = self.molecule_atom_index return self._molecule._partial_charges[index] @property def is_aromatic(self): """ The atom's is_aromatic flag """ return self._is_aromatic @property def stereochemistry(self): """ The atom's stereochemistry (if defined, otherwise None) """ return self._stereochemistry @stereochemistry.setter def stereochemistry(self, value): """Set the atoms stereochemistry Parameters ---------- value : str The stereochemistry around this atom, allowed values are "CW", "CCW", or None, """ #if (value != 'CW') and (value != 'CCW') and not(value is None): # raise Exception("Atom stereochemistry setter expected 'CW', 'CCW', or None. Received {} (type {})".format(value, type(value))) self._stereochemistry = value @property def element(self): """ The element name """ return element.Element.getByAtomicNumber(self._atomic_number) @property def atomic_number(self): """ The integer atomic number of the atom. """ return self._atomic_number @property def mass(self): """ The standard atomic weight (abundance-weighted isotopic mass) of the atomic site. .. todo :: Should we discriminate between standard atomic weight and most abundant isotopic mass? TODO (from jeff): Are there atoms that have different chemical properties based on their isotopes? """ return self.element.mass @property def name(self): """ The name of this atom, if any """ return self._name @name.setter def name(self, other): """ Parameters ---------- other : string The new name for this atom """ if not (type(other) is str): raise Exception( "In setting atom name. Expected str, received {} (type {})". format(other, type(other))) self._name = other # TODO: How are we keeping track of bonds, angles, etc? @property def bonds(self): """ The list of ``Bond`` objects this atom is involved in. """ return self._bonds #for bond in self._bonds: # yield bond @property #def bonded_to(self): def bonded_atoms(self): """ The list of ``Atom`` objects this atom is involved in bonds with """ for bond in self._bonds: for atom in bond.atoms: if not (atom == self): # TODO: This seems dangerous. Ask John for a better way yield atom
[docs] def is_bonded_to(self, atom2): """ Determine whether this atom is bound to another atom Parameters ---------- atom2: openforcefield.topology.molecule.Atom a different atom in the same molecule Returns ------- bool Whether this atom is bound to atom2 """ #TODO: Sanity check (check for same molecule?) assert self != atom2 for bond in self._bonds: for bonded_atom in bond.atoms: if atom2 == bonded_atom: return True return False
@property def virtual_sites(self): """ The list of ``VirtualSite`` objects this atom is involved in. """ return self._virtual_sites #for vsite in self._vsites: # yield vsite @property def molecule_atom_index(self): """ The index of this Atom within the the list of atoms in ``Molecules``. Note that this can be different from ``molecule_particle_index``. """ if self._molecule is None: raise ValueError('This Atom does not belong to a Molecule object') return self._molecule.atoms.index(self) @property def molecule_particle_index(self): """ The index of this Atom within the the list of particles in the parent ``Molecule``. Note that this can be different from ``molecule_atom_index``. """ if self._molecule is None: raise ValueError('This Atom does not belong to a Molecule object') return self._molecule.particles.index(self) # ## From Jeff: Not sure if we actually need this # @property # def topology_atom_index(self): # """ # The index of this Atom within the the list of atoms in ``Topology``. # Note that this can be different from ``particle_index``. # # """ # if self._topology is None: # raise ValueError('This Atom does not belong to a Topology object') # # TODO: This will be slow; can we cache this and update it only when needed? # # Deleting atoms/molecules in the Topology would have to invalidate the cached index. # return self._topology.atoms.index(self) def __repr__(self): # TODO: Also include particle_index and which molecule this atom belongs to? return "Atom(name={}, atomic number={})".format( self._name, self._atomic_number) def __str__(self): # TODO: Also include particle_index and which molecule this atom belongs to? return "<Atom name='{}' atomic number='{}'>".format( self._name, self._atomic_number)
#============================================================================================= # VirtualSite #=============================================================================================
[docs]class VirtualSite(Particle): """ A particle representing a virtual site whose position is defined in terms of ``Atom`` positions. Note that chemical atoms are represented by the ``Atom``. .. warning :: This API is experimental and subject to change. .. todo:: * Should a virtual site be able to belong to more than one Topology? * Should virtual sites be immutable or mutable? """
[docs] def __init__(self, atoms, charge_increments=None, epsilon=None, sigma=None, rmin_half=None, name=None): """ Base class for VirtualSites .. todo :: * This will need to be generalized for virtual sites to allow out-of-plane sites, which are not simply a linear combination of atomic positions * Add checking for allowed virtual site types * How do we want users to specify virtual site types? Parameters ---------- atoms : list of Atom of shape [N] atoms[index] is the corresponding Atom for weights[index] charge_increments : list of floats of shape [N], optional, default=None The amount of charge to remove from the VirtualSite's atoms and put in the VirtualSite. Indexing in this list should match the ordering in the atoms list. Default is None. sigma : float, default=None Sigma term for VdW properties of virtual site. Default is None. epsilon : float Epsilon term for VdW properties of virtual site. Default is None. rmin_half : float Rmin_half term for VdW properties of virtual site. Default is None. name : string or None, default=None The name of this virtual site. Default is None. virtual_site_type : str Virtual site type. name : str or None, default=None The name of this virtual site. Default is None """ # Ensure we have as many charge_increments as we do atoms if not (charge_increments is None): if not (len(charge_increments) == len(atoms)): raise Exception( "VirtualSite definition must have same number of charge_increments ({}) and atoms({})" .format(len(charge_increments), len(atoms))) # VdW parameters can either be epsilon+rmin_half or epsilon+sigma, but not both if not (epsilon is None): if ((rmin_half != None) and (sigma != None)): raise Exception( "VirtualSite constructor given epsilon (value : {}), rmin_half (value : {}), and sigma (value : {}). If epsilon is nonzero, it should receive either rmin_half OR sigma" .format(epsilon, rmin_half, sigma)) if ((rmin_half is None) and (sigma is None)): raise Exception( "VirtualSite constructor given epsilon (value : {}) but not given rmin_half (value : {}) or sigma (value : {})" .format(epsilon, rmin_half, sigma)) if (sigma is None): # TODO: Save the 6th root of 2 if this starts being slow. sigma = (2. * rmin_half) / (2.**(1. / 6)) elif epsilon is None: if ((rmin_half != None) or (sigma != None)): raise Exception( "VirtualSite constructor given rmin_half (value : {}) or sigma (value : {}), but not epsilon (value : {})" .format(rmin_half, sigma, epsilon)) # Perform type-checking for atom in atoms: assert isinstance(atom, Atom) for atom_index in range(len(atoms) - 1): assert atoms[atom_index].molecule is atoms[atom_index + 1].molecule assert isinstance(atoms[1].molecule, FrozenMolecule) if sigma is None: self._sigma = None else: assert hasattr(sigma, 'unit') assert unit.angstrom.is_compatible(sigma.unit) self._sigma = sigma.in_units_of(unit.angstrom) if epsilon is None: self._epsilon = None else: assert hasattr(epsilon, 'unit') assert (unit.kilojoule_per_mole).is_compatible(epsilon.unit) self._epsilon = epsilon.in_units_of(unit.kilojoule_per_mole) if charge_increments is None: self._charge_increments = None else: assert hasattr(charge_increments, 'unit') assert unit.elementary_charges.is_compatible( charge_increments.unit) self._charge_increments = charge_increments.in_units_of( unit.elementary_charges) self._atoms = list() for atom in atoms: atom.add_virtual_site(self) self._atoms.append(atom) self._molecule = atoms[0].molecule self._name = name
# Subclassing makes _type unnecessary #self._type = None # TODO: Validate site types against allowed values #self._weights = np.array(weights) # make a copy and convert to array internally
[docs] def to_dict(self): """Return a dict representation of the virtual site. """ # Each subclass should have its own to_dict vsite_dict = OrderedDict() vsite_dict['name'] = self._name vsite_dict['atoms'] = tuple( [i.molecule_atom_index for i in self.atoms]) vsite_dict['charge_increments'] = quantity_to_string(self._charge_increments) vsite_dict['epsilon'] = quantity_to_string(self._epsilon) vsite_dict['sigma'] = quantity_to_string(self._sigma) return vsite_dict
[docs] @classmethod def from_dict(cls, vsite_dict): """Create a virtual site from a dict representation. """ # Each subclass needs to have its own from_dict # Make a copy of the vsite_dict, where we'll unit-wrap the appropriate values vsite_dict_units = deepcopy(vsite_dict) # Attach units to epsilon term vsite_dict_units['epsilon'] = string_to_quantity( vsite_dict['epsilon']) vsite_dict_units['sigma'] = string_to_quantity(vsite_dict['sigma']) vsite_dict_units['charge_increments'] = string_to_quantity( vsite_dict['charge_increments']) return VirtualSite(**vsite_dict_units)
@property def molecule_virtual_site_index(self): """ The index of this VirtualSite within the list of virtual sites within ``Molecule`` Note that this can be different from ``particle_index``. """ #if self._topology is None: # raise ValueError('This VirtualSite does not belong to a Topology object') # TODO: This will be slow; can we cache this and update it only when needed? # Deleting atoms/molecules in the Topology would have to invalidate the cached index. return self._molecule.virtual_sites.index(self) @property def molecule_particle_index(self): """ The index of this VirtualSite within the the list of particles in the parent ``Molecule``. Note that this can be different from ``molecule_virtual_site_index``. """ if self._molecule is None: raise ValueError( 'This VirtualSite does not belong to a Molecule object') return self._molecule.particles.index(self) @property def atoms(self): """ Atoms on whose position this VirtualSite depends. """ return self._atoms #for atom in self._atoms: # yield atom @property def charge_increments(self): """ Charges taken from this VirtualSite's atoms and given to the VirtualSite """ return self._charge_increments @property def epsilon(self): """ The VdW epsilon term of this VirtualSite """ return self._epsilon @property def sigma(self): """ The VdW sigma term of this VirtualSite """ return self._sigma @property def rmin_half(self): """ The VdW rmin_half term of this VirtualSite """ rmin = 2.**(1. / 6) * self._sigma rmin_half = rmin / 2 return rmin_half @property def name(self): """ The name of this VirtualSite """ return self._name @property def type(self): """The type of this VirtualSite (returns the class name as string)""" return self.__class__.__name__ def __repr__(self): # TODO: Also include particle_index, which molecule this atom belongs to? return "VirtualSite(name={}, type={}, atoms={})".format( self.name, self.type, self.atoms) def __str__(self): # TODO: Also include particle_index, which molecule this atom belongs to? return "<VirtualSite name={} type={} atoms={}>".format( self.name, self.type, self.atoms)
class BondChargeVirtualSite(VirtualSite): """ A particle representing a "Bond Charge"-type virtual site, in which the location of the charge is specified by the positions of two atoms. This supports placement of a virtual site S along a vector between two specified atoms, e.g. to allow for a sigma hole for halogens or similar contexts. With positive values of the distance, the virtual site lies outside the first indexed atom. .. warning :: This API is experimental and subject to change. """ def __init__(self, atoms, distance, charge_increments=None, weights=None, epsilon=None, sigma=None, rmin_half=None, name=None): """ Create a bond charge-type virtual site, in which the location of the charge is specified by the position of two atoms. This supports placement of a virtual site S along a vector between two specified atoms, e.g. to allow for a sigma hole for halogens or similar contexts. With positive values of the distance, the virtual site lies outside the first indexed atom. TODO: One of the examples on https://open-forcefield-toolkit.readthedocs.io/en/topology/smirnoff.html#virtualsites-virtual-sites-for-off-atom-charges has a BondCharge defined with three atoms -- How does that work? Parameters ---------- atoms : list of openforcefield.topology.molecule.Atom objects of shape [N] The atoms defining the virtual site's position distance : float weights : list of floats of shape [N] or None, optional, default=None weights[index] is the weight of particles[index] contributing to the position of the virtual site. Default is None charge_increments : list of floats of shape [N], optional, default=None The amount of charge to remove from the VirtualSite's atoms and put in the VirtualSite. Indexing in this list should match the ordering in the atoms list. Default is None. epsilon : float Epsilon term for VdW properties of virtual site. Default is None. sigma : float, default=None Sigma term for VdW properties of virtual site. Default is None. rmin_half : float Rmin_half term for VdW properties of virtual site. Default is None. name : string or None, default=None The name of this virtual site. Default is None. """ assert hasattr(distance, 'unit') assert unit.angstrom.is_compatible(distance.unit) super().__init__( atoms, charge_increments=charge_increments, epsilon=epsilon, sigma=sigma, rmin_half=rmin_half, name=name) self._distance = distance.in_units_of(unit.angstrom) def to_dict(self): vsite_dict = super().to_dict() vsite_dict['distance'] = quantity_to_string(self._distance) #type = self.type vsite_dict['vsite_type'] = self.type #vsite_dict['vsite_type'] = 'BondChargeVirtualSite' return vsite_dict @classmethod def from_dict(cls, vsite_dict): base_dict = deepcopy(vsite_dict) # Make sure it's the right type of virtual site assert vsite_dict['vsite_type'] == "BondChargeVirtualSite" base_dict.pop('vsite_type') base_dict.pop('distance') vsite = super().from_dict(**base_dict) vsite._distance = string_to_quantity(vsite_dict['distance']) return vsite @property def distance(self): """The distance parameter of the virtual site""" return self._distance class _LonePairVirtualSite(VirtualSite): """Private base class for mono/di/trivalent lone pair virtual sites.""" @classmethod def from_dict(cls, vsite_dict): base_dict = deepcopy(vsite_dict) # Make sure it's the right type of virtual site assert vsite_dict['vsite_type'] == cls.__name__ base_dict.pop('vsite_type') base_dict.pop('distance') base_dict.pop('out_of_plane_angle') base_dict.pop('in_plane_angle') vsite = super().from_dict(**base_dict) vsite._distance = string_to_quantity(vsite_dict['distance']) vsite._in_plane_angle = string_to_quantity( vsite_dict['in_plane_angle']) vsite._out_of_plane_angle = string_to_quantity( vsite_dict['out_of_plane_angle']) return vsite class MonovalentLonePairVirtualSite(VirtualSite): """ A particle representing a "Monovalent Lone Pair"-type virtual site, in which the location of the charge is specified by the positions of three atoms. This is originally intended for situations like a carbonyl, and allows placement of a virtual site S at a specified distance d, in_plane_angle, and out_of_plane_angle relative to a central atom and two connected atoms. .. warning :: This API is experimental and subject to change. """ def __init__(self, atoms, distance, out_of_plane_angle, in_plane_angle, charge_increments=None, weights=None, epsilon=None, sigma=None, rmin_half=None, name=None): """ Create a bond charge-type virtual site, in which the location of the charge is specified by the position of three atoms. TODO : Do "weights" have any meaning here? Parameters ---------- atoms : list of three openforcefield.topology.molecule.Atom objects The three atoms defining the virtual site's position distance : float out_of_plane_angle : float in_plane_angle : float epsilon : float Epsilon term for VdW properties of virtual site. Default is None. sigma : float, default=None Sigma term for VdW properties of virtual site. Default is None. rmin_half : float Rmin_half term for VdW properties of virtual site. Default is None. name : string or None, default=None The name of this virtual site. Default is None. """ #assert isinstance(distance, unit.Quantity) # TODO: Check for proper number of atoms assert hasattr(distance, 'unit') assert unit.angstrom.is_compatible(distance.unit) assert hasattr(in_plane_angle, 'unit') assert unit.degree.is_compatible(in_plane_angle.unit) assert hasattr(out_of_plane_angle, 'unit') assert unit.degree.is_compatible(out_of_plane_angle.unit) assert len(atoms) == 3 super().__init__( atoms, charge_increments=charge_increments, epsilon=epsilon, sigma=sigma, rmin_half=rmin_half, name=name) self._distance = distance.in_units_of(unit.angstrom) self._out_of_plane_angle = out_of_plane_angle.in_units_of(unit.degree) self._in_plane_angle = in_plane_angle.in_units_of(unit.degree) def to_dict(self): vsite_dict = super().to_dict() vsite_dict['distance'] = quantity_to_string(self._distance) vsite_dict['out_of_plane_angle'] = quantity_to_string( self._out_of_plane_angle) vsite_dict['in_plane_angle'] = quantity_to_string(self._in_plane_angle) #vsite_dict['vsite_type'] = self.type.fget() vsite_dict['vsite_type'] = self.type #vsite_dict['vsite_type'] = 'MonovalentLonePairVirtualSite' return vsite_dict @classmethod def from_dict(cls, vsite_dict): """ Construct a new MonovalentLonePairVirtualSite from an serialized dictionary representation. Parameters ---------- vsite_dict : dict The VirtualSite to deserialize. Returns ------- The newly created MonovalentLonePairVirtualSite """ # The function is overridden only to have a custom docstring. return super().from_dict(vsite_dict) @property def distance(self): """The distance parameter of the virtual site""" return self._distance @property def in_plane_angle(self): """The in_plane_angle parameter of the virtual site""" return self._in_plane_angle @property def out_of_plane_angle(self): """The out_of_plane_angle parameter of the virtual site""" return self._out_of_plane_angle class DivalentLonePairVirtualSite(VirtualSite): """ A particle representing a "Divalent Lone Pair"-type virtual site, in which the location of the charge is specified by the positions of three atoms. This is suitable for cases like four-point and five-point water models as well as pyrimidine; a charge site S lies a specified distance d from the central atom among three atoms along the bisector of the angle between the atoms (if out_of_plane_angle is zero) or out of the plane by the specified angle (if out_of_plane_angle is nonzero) with its projection along the bisector. For positive values of the distance d the virtual site lies outside the 2-1-3 angle and for negative values it lies inside. .. warning :: This API is experimental and subject to change. """ def __init__(self, atoms, distance, out_of_plane_angle, in_plane_angle, charge_increments=None, weights=None, epsilon=None, sigma=None, rmin_half=None, name=None): """ Create a divalent lone pair-type virtual site, in which the location of the charge is specified by the position of three atoms. TODO : Do "weights" have any meaning here? Parameters ---------- atoms : list of 3 openforcefield.topology.molecule.Atom objects The three atoms defining the virtual site's position distance : float out_of_plane_angle : float in_plane_angle : float epsilon : float Epsilon term for VdW properties of virtual site. Default is None. sigma : float, default=None Sigma term for VdW properties of virtual site. Default is None. rmin_half : float Rmin_half term for VdW properties of virtual site. Default is None. name : string or None, default=None The name of this virtual site. Default is None. """ #assert isinstance(distance, unit.Quantity) assert hasattr(distance, 'unit') assert unit.angstrom.is_compatible(distance.unit) assert hasattr(in_plane_angle, 'unit') assert unit.degree.is_compatible(in_plane_angle.unit) assert hasattr(out_of_plane_angle, 'unit') assert unit.degree.is_compatible(out_of_plane_angle.unit) assert len(atoms) == 3 super().__init__( atoms, charge_increments=charge_increments, epsilon=epsilon, sigma=sigma, rmin_half=rmin_half, name=name) self._distance = distance.in_units_of(unit.angstrom) self._out_of_plane_angle = out_of_plane_angle.in_units_of(unit.degree) self._in_plane_angle = in_plane_angle.in_units_of(unit.degree) def to_dict(self): vsite_dict = super().to_dict() vsite_dict['distance'] = quantity_to_string(self._distance) vsite_dict['out_of_plane_angle'] = quantity_to_string( self._out_of_plane_angle) vsite_dict['in_plane_angle'] = quantity_to_string(self._in_plane_angle) vsite_dict['vsite_type'] = self.type return vsite_dict @classmethod def from_dict(cls, vsite_dict): """ Construct a new DivalentLonePairVirtualSite from an serialized dictionary representation. Parameters ---------- vsite_dict : dict The VirtualSite to deserialize. Returns ------- The newly created DivalentLonePairVirtualSite """ # The function is overridden only to have a custom docstring. return super().from_dict(vsite_dict) @property def distance(self): """The distance parameter of the virtual site""" return self._distance @property def in_plane_angle(self): """The in_plane_angle parameter of the virtual site""" return self._in_plane_angle @property def out_of_plane_angle(self): """The out_of_plane_angle parameter of the virtual site""" return self._out_of_plane_angle class TrivalentLonePairVirtualSite(VirtualSite): """ A particle representing a "Trivalent Lone Pair"-type virtual site, in which the location of the charge is specified by the positions of four atoms. This is suitable for planar or tetrahedral nitrogen lone pairs; a charge site S lies above the central atom (e.g. nitrogen a distance d along the vector perpendicular to the plane of the three connected atoms (2,3,4). With positive values of d the site lies above the nitrogen and with negative values it lies below the nitrogen. .. warning :: This API is experimental and subject to change. """ def __init__(self, atoms, distance, out_of_plane_angle, in_plane_angle, charge_increments=None, weights=None, epsilon=None, sigma=None, rmin_half=None, name=None): """ Create a trivalent lone pair-type virtual site, in which the location of the charge is specified by the position of four atoms. TODO : Do "weights" have any meaning here? Parameters ---------- atoms : list of 4 openforcefield.topology.molecule.Atom objects The three atoms defining the virtual site's position distance : float out_of_plane_angle : float in_plane_angle : float epsilon : float Epsilon term for VdW properties of virtual site. Default is None. sigma : float, default=None Sigma term for VdW properties of virtual site. Default is None. rmin_half : float Rmin_half term for VdW properties of virtual site. Default is None. name : string or None, default=None The name of this virtual site. Default is None. """ assert len(atoms) == 4 assert hasattr(distance, 'unit') assert unit.angstrom.is_compatible(distance.unit) assert hasattr(in_plane_angle, 'unit') assert unit.degree.is_compatible(in_plane_angle.unit) assert hasattr(out_of_plane_angle, 'unit') assert unit.degree.is_compatible(out_of_plane_angle.unit) super().__init__( atoms, charge_increments=charge_increments, epsilon=epsilon, sigma=sigma, rmin_half=rmin_half, name=name) self._distance = distance.in_units_of(unit.angstrom) self._out_of_plane_angle = out_of_plane_angle.in_units_of(unit.degree) self._in_plane_angle = in_plane_angle.in_units_of(unit.degree) def to_dict(self): vsite_dict = super().to_dict() vsite_dict['distance'] = quantity_to_string(self._distance) vsite_dict['out_of_plane_angle'] = quantity_to_string( self._out_of_plane_angle) vsite_dict['in_plane_angle'] = quantity_to_string(self._in_plane_angle) vsite_dict['vsite_type'] = self.type return vsite_dict @classmethod def from_dict(cls, vsite_dict): """ Construct a new TrivalentPairVirtualSite from an serialized dictionary representation. Parameters ---------- vsite_dict : dict The VirtualSite to deserialize. Returns ------- The newly created TrivalentLonePairVirtualSite """ # The function is overridden only to have a custom docstring. return super().from_dict(vsite_dict) @property def distance(self): """The distance parameter of the virtual site""" return self._distance @property def in_plane_angle(self): """The in_plane_angle parameter of the virtual site""" return self._in_plane_angle @property def out_of_plane_angle(self): """The out_of_plane_angle parameter of the virtual site""" return self._out_of_plane_angle # ============================================================================================= # Bond Stereochemistry # ============================================================================================= #class BondStereochemistry(Serializable): #""" #Bond stereochemistry representation #""" #def __init__(self, stereo_type, neighbor1, neighbor2): # """ # # Parameters # ---------- # stereo_type # neighbor1 # neighbor2 # """ # assert isinstance(neighbor1, Atom) # assert isinstance(neighbor2, Atom) # # Use stereo_type @setter to check stereo type is a permitted value # self.stereo_type = stereo_type # self._neighbor1 = neighbor1 # self._neighbor2 = neighbor2 #def to_dict(self): # bs_dict = OrderedDict() # bs_dict['stereo_type'] = self._stereo_type # bs_dict['neighbor1_index'] = self._neighbor1.molecule_atom_index # bs_dict['neighbor2_index'] = self._neighbor2.molecule_atom_index # return bs_dict #classmethod #def from_dict(cls, molecule, bs_dict): # neighbor1 = molecule.atoms[bs_dict['neighbor1_index']] # neighbor2 = molecule.atoms[bs_dict['neighbor2_index']] # return cls.__init__(bs_dict['stereo_type'], neighbor1, neighbor2) #@property #def stereo_type(self): # return self._stereo_type #@stereo_type.setter #def stereo_type(self, value): # assert (value == 'CIS') or (value == 'TRANS') or (value is None) # self._stereo_type = value #@property #def neighbor1(self): # return self._neighbor1 #@property #def neighbor2(self): # return self._neighbor2 #@property #def neighbors(self): # return (self._neighbor1, self._neighbor2) # ============================================================================================= # Bond # =============================================================================================
[docs]class Bond(Serializable): """ Chemical bond representation. .. warning :: This API is experimental and subject to change. .. todo :: Allow bonds to have associated properties. Attributes ---------- atom1, atom2 : openforcefield.topology.Atom Atoms involved in the bond bondtype : int Discrete bond type representation for the Open Forcefield aromaticity model TODO: Do we want to pin ourselves to a single standard aromaticity model? type : str String based bond type order : int Integral bond order fractional_bond_order : float, optional Fractional bond order, or None. .. warning :: This API is experimental and subject to change. """
[docs] def __init__(self, atom1, atom2, bond_order, is_aromatic, fractional_bond_order=None, stereochemistry=None): """ Create a new chemical bond. """ assert type(atom1) == Atom assert type(atom2) == Atom assert atom1.molecule is atom2.molecule assert isinstance(atom1.molecule, FrozenMolecule) self._molecule = atom1.molecule self._atom1 = atom1 self._atom2 = atom2 atom1.add_bond(self) atom2.add_bond(self) # TODO: Check bondtype and fractional_bond_order are valid? # TODO: Dative bonds #self._type = bondtype self._fractional_bond_order = fractional_bond_order self._bond_order = bond_order self._is_aromatic = is_aromatic self._stereochemistry = stereochemistry
[docs] def to_dict(self): """ Return a dict representation of the bond. """ bond_dict = OrderedDict() bond_dict['atom1'] = self.atom1.molecule_atom_index bond_dict['atom2'] = self.atom2.molecule_atom_index bond_dict['bond_order'] = self._bond_order bond_dict['is_aromatic'] = self._is_aromatic bond_dict['stereochemistry'] = self._stereochemistry bond_dict['fractional_bond_order'] = self._fractional_bond_order return bond_dict
[docs] @classmethod def from_dict(cls, molecule, d): """Create a Bond from a dict representation.""" # TODO d['molecule'] = molecule d['atom1'] = molecule.atoms[d['atom1']] d['atom2'] = molecule.atoms[d['atom2']] return cls(*d)
@property def atom1(self): return self._atom1 @property def atom2(self): return self._atom2 @property def atom1_index(self): return self.molecule.atoms.index(self._atom1) @property def atom2_index(self): return self.molecule.atoms.index(self._atom2) @property def atoms(self): return (self._atom1, self._atom2) @property def bond_order(self): return self._bond_order @bond_order.setter def bond_order(self, value): self._bond_order = value @property def fractional_bond_order(self): return self._fractional_bond_order @fractional_bond_order.setter def fractional_bond_order(self, value): self._fractional_bond_order = value @property def stereochemistry(self): return self._stereochemistry @property def is_aromatic(self): return self._is_aromatic @property def molecule(self): return self._molecule @molecule.setter def molecule(self, value): """ Sets the Bond's parent molecule. Can not be changed after assignment """ assert self._molecule is None self._molecule = value @property def molecule_bond_index(self): """ The index of this Bond within the the list of bonds in ``Molecules``. """ if self._molecule is None: raise ValueError('This Atom does not belong to a Molecule object') return self._molecule.bonds.index(self)
#============================================================================================= # Molecule #============================================================================================= # TODO: How do we automatically trigger invalidation of cached properties if an ``Atom``, ``Bond``, or ``VirtualSite`` is modified, # rather than added/deleted via the API? The simplest resolution is simply to make them immutable.
[docs]class FrozenMolecule(Serializable): """ Immutable chemical representation of a molecule, such as a small molecule or biopolymer. .. todo :: What other API calls would be useful for supporting biopolymers as small molecules? Perhaps iterating over chains and residues? Examples -------- Create a molecule from a sdf file >>> from openforcefield.utils import get_data_file_path >>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf') >>> molecule = FrozenMolecule.from_file(sdf_filepath) Convert to OpenEye OEMol object >>> oemol = molecule.to_openeye() Create a molecule from an OpenEye molecule >>> molecule = FrozenMolecule.from_openeye(oemol) Convert to RDKit Mol object >>> rdmol = molecule.to_rdkit() Create a molecule from an RDKit molecule >>> molecule = FrozenMolecule.from_rdkit(rdmol) Create a molecule from IUPAC name (requires the OpenEye toolkit) >>> molecule = FrozenMolecule.from_iupac('imatinib') Create a molecule from SMILES >>> molecule = FrozenMolecule.from_smiles('Cc1ccccc1') .. warning :: This API is experimental and subject to change. """
[docs] def __init__(self, other=None, file_format=None, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, allow_undefined_stereo=False): """ Create a new FrozenMolecule object .. todo :: * If a filename or file-like object is specified but the file contains more than one molecule, what is the proper behavior? Read just the first molecule, or raise an exception if more than one molecule is found? * Should we also support SMILES strings or IUPAC names for ``other``? Parameters ---------- other : optional, default=None If specified, attempt to construct a copy of the Molecule from the specified object. This can be any one of the following: * a :class:`Molecule` object * a file that can be used to construct a :class:`Molecule` object * an ``openeye.oechem.OEMol`` * an ``rdkit.Chem.rdchem.Mol`` * a serialized :class:`Molecule` object file_format : str, optional, default=None If providing a file-like object, you must specify the format of the data. If providing a file, the file format will attempt to be guessed from the suffix. toolkit_registry : a :class:`ToolkitRegistry` or :class:`ToolkitWrapper` object, optional, default=GLOBAL_TOOLKIT_REGISTRY :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for I/O operations allow_undefined_stereo : bool, default=False If loaded from a file and ``False``, raises an exception if undefined stereochemistry is detected during the molecule's construction. Examples -------- Create an empty molecule: >>> empty_molecule = FrozenMolecule() Create a molecule from a file that can be used to construct a molecule, using either a filename or file-like object: >>> from openforcefield.utils import get_data_file_path >>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf') >>> molecule = FrozenMolecule(sdf_filepath) >>> molecule = FrozenMolecule(open(sdf_filepath, 'r'), file_format='sdf') >>> import gzip >>> mol2_gz_filepath = get_data_file_path('molecules/toluene.mol2.gz') >>> molecule = FrozenMolecule(gzip.GzipFile(mol2_gz_filepath, 'r'), file_format='mol2') Create a molecule from another molecule: >>> molecule_copy = FrozenMolecule(molecule) Convert to OpenEye OEMol object >>> oemol = molecule.to_openeye() Create a molecule from an OpenEye molecule: >>> molecule = FrozenMolecule(oemol) Convert to RDKit Mol object >>> rdmol = molecule.to_rdkit() Create a molecule from an RDKit molecule: >>> molecule = FrozenMolecule(rdmol) Create a molecule from a serialized molecule object: >>> serialized_molecule = molecule.__getstate__() >>> molecule_copy = Molecule(serialized_molecule) """ self._cached_smiles = None # Figure out if toolkit_registry is a whole registry, or just a single wrapper if isinstance(toolkit_registry, ToolkitRegistry): pass elif isinstance(toolkit_registry, ToolkitWrapper): toolkit = toolkit_registry toolkit_registry = ToolkitRegistry(toolkit_precedence=[]) toolkit_registry.add_toolkit(toolkit) else: raise ValueError( "'toolkit_registry' must be either a ToolkitRegistry or a ToolkitWrapper" ) if other is None: self._initialize() else: loaded = False if isinstance( other, openforcefield.topology.FrozenMolecule) and not (loaded): self._copy_initializer(other) loaded = True if isinstance(other, openforcefield.topology.Molecule) and not (loaded): # TODO: This will need to be updated once FrozenMolecules and Molecules are significantly different self._copy_initializer(other) loaded = True if isinstance(other, OrderedDict) and not (loaded): self.__setstate__(other) loaded = True # Check through the toolkit registry to find a compatible wrapper for loading if not loaded: try: result = toolkit_registry.call('from_object', other, allow_undefined_stereo=allow_undefined_stereo) except NotImplementedError: pass else: self._copy_initializer(result) loaded = True # TODO: Make this compatible with file-like objects (I couldn't figure out how to make an oemolistream # from a fileIO object) if (isinstance(other, str) or hasattr(other, 'read')) and not (loaded): mol = Molecule.from_file( other, file_format=file_format, toolkit_registry=toolkit_registry, allow_undefined_stereo=allow_undefined_stereo ) # returns a list only if multiple molecules are found if type(mol) == list: raise ValueError( 'Specified file or file-like object must contain exactly one molecule' ) self._copy_initializer(mol) loaded = True if not (loaded): msg = 'Cannot construct openforcefield.topology.Molecule from {}\n'.format( other) raise Exception(msg)
#################################################################################################### # Safe serialization ####################################################################################################
[docs] def to_dict(self): """ Return a dictionary representation of the molecule. .. todo :: * Document the representation standard. * How do we do version control with this standard? Returns ------- molecule_dict : OrderedDict A dictionary representation of the molecule. """ molecule_dict = OrderedDict() molecule_dict['name'] = self._name ## From Jeff: If we go the properties-as-dict route, then _properties should, at ## the top level, be a dict. Should we go through recursively and ensure all values are dicts too? molecule_dict['atoms'] = [atom.to_dict() for atom in self._atoms] molecule_dict['virtual_sites'] = [ vsite.to_dict() for vsite in self._virtual_sites ] molecule_dict['bonds'] = [bond.to_dict() for bond in self._bonds] # TODO: Charges # TODO: Properties # From Jeff: We could have the onerous requirement that all "properties" have to_dict() functions. # Or we could restrict properties to simple stuff (ints, strings, floats, and the like) # Or pickle anything unusual # Or not allow user-defined properties at all (just use our internal _cached_properties) #molecule_dict['properties'] = dict([(key, value._to_dict()) for key.value in self._properties]) # TODO: Assuming "simple stuff" properties right now, figure out a better standard molecule_dict['properties'] = self._properties if hasattr(self, '_cached_properties'): molecule_dict['cached_properties'] = self._cached_properties # TODO: Conformers if self._conformers is None: molecule_dict['conformers'] = None else: molecule_dict['conformers'] = [] molecule_dict[ 'conformers_unit'] = 'angstrom' # Have this defined as a class variable? for conf in self._conformers: conf_unitless = (conf / unit.angstrom) conf_serialized, conf_shape = serialize_numpy((conf_unitless)) molecule_dict['conformers'].append(conf_serialized) if self._partial_charges is None: molecule_dict['partial_charges'] = None molecule_dict['partial_charges_unit'] = None else: charges_unitless = self._partial_charges / unit.elementary_charge charges_serialized, charges_shape = serialize_numpy( charges_unitless) molecule_dict['partial_charges'] = charges_serialized molecule_dict['partial_charges_unit'] = 'elementary_charge' return molecule_dict
def __hash__(self): """ Returns a hash of this molecule. Used when checking molecule uniqueness in Topology creation. Returns ------- string """ return hash(self.to_smiles())
[docs] @classmethod def from_dict(cls, molecule_dict): """ Create a new Molecule from a dictionary representation Parameters ---------- molecule_dict : OrderedDict A dictionary representation of the molecule. Returns ------- molecule : Molecule A Molecule created from the dictionary representation """ # This implementation is a compromise to let this remain as a classmethod mol = cls() mol._initialize_from_dict(molecule_dict) return mol
def _initialize_from_dict(self, molecule_dict): """ Initialize this Molecule from a dictionary representation Parameters ---------- molecule_dict : OrderedDict A dictionary representation of the molecule. """ # TODO: Provide useful exception messages if there are any failures self._initialize() self.name = molecule_dict['name'] for atom_dict in molecule_dict['atoms']: self._add_atom(**atom_dict) # Handle virtual site unit reattachment and molecule tagging for vsite_dict in molecule_dict['virtual_sites']: vsite_dict_units = deepcopy(vsite_dict) # Attach units to epsilon term vsite_dict_units['epsilon'] = string_to_quantity( vsite_dict['epsilon']) vsite_dict_units['sigma'] = string_to_quantity( vsite_dict['sigma']) vsite_dict_units['charge_increments'] = string_to_quantity( vsite_dict['charge_increments']) # Call the correct molecule._add_X_virtual_site function, based on the stated type if vsite_dict_units['vsite_type'] == "BondChargeVirtualSite": del vsite_dict_units['vsite_type'] vsite_dict_units['distance'] = string_to_quantity( vsite_dict['distance']) self._add_bond_charge_virtual_site(**vsite_dict_units) elif vsite_dict_units[ 'vsite_type'] == "MonovalentLonePairVirtualSite": del vsite_dict_units['vsite_type'] vsite_dict_units['distance'] = string_to_quantity( vsite_dict['distance']) vsite_dict_units['in_plane_angle'] = string_to_quantity( vsite_dict['in_plane_angle']) vsite_dict_units['out_of_plane_angle'] = string_to_quantity( vsite_dict['out_of_plane_angle']) self._add_monovalent_lone_pair_virtual_site(**vsite_dict_units) elif vsite_dict_units[ 'vsite_type'] == "DivalentLonePairVirtualSite": del vsite_dict_units['vsite_type'] vsite_dict_units['distance'] = string_to_quantity( vsite_dict['distance']) vsite_dict_units['in_plane_angle'] = string_to_quantity( vsite_dict['in_plane_angle']) vsite_dict_units['out_of_plane_angle'] = string_to_quantity( vsite_dict['out_of_plane_angle']) self._add_divalent_lone_pair_virtual_site(**vsite_dict_units) elif vsite_dict_units[ 'vsite_type'] == "TrivalentLonePairVirtualSite": del vsite_dict_units['vsite_type'] vsite_dict_units['distance'] = string_to_quantity( vsite_dict['distance']) vsite_dict_units['in_plane_angle'] = string_to_quantity( vsite_dict['in_plane_angle']) vsite_dict_units['out_of_plane_angle'] = string_to_quantity( vsite_dict['out_of_plane_angle']) self._add_trivalent_lone_pair_virtual_site(**vsite_dict_units) else: raise Exception("Vsite type {} not recognized".format( vsite_dict['vsite_type'])) for bond_dict in molecule_dict['bonds']: bond_dict['atom1'] = int(bond_dict['atom1']) bond_dict['atom2'] = int(bond_dict['atom2']) self._add_bond(**bond_dict) if molecule_dict['partial_charges'] is None: self._partial_charges = None else: charges_shape = (self.n_atoms, ) partial_charges_unitless = deserialize_numpy( molecule_dict['partial_charges'], charges_shape) pc_unit = getattr(unit, molecule_dict['partial_charges_unit']) partial_charges = unit.Quantity(partial_charges_unitless, pc_unit) self._partial_charges = partial_charges if molecule_dict['conformers'] is None: self._conformers = None else: self._conformers = list() for ser_conf in molecule_dict['conformers']: # TODO: Update to use string_to_quantity conformers_shape = ((self.n_atoms, 3)) conformer_unitless = deserialize_numpy(ser_conf, conformers_shape) c_unit = getattr(unit, molecule_dict['conformers_unit']) conformer = unit.Quantity(conformer_unitless, c_unit) self._conformers.append(conformer) self._properties = molecule_dict['properties'] def __repr__(self): """Return the SMILES of this molecule""" return "Molecule with name '{}' and SMILES '{}'".format( self.name, self.to_smiles()) def __getstate__(self): return self.to_dict() def __setstate__(self, state): return self._initialize_from_dict(state) def _initialize(self): """ Clear the contents of the current molecule. """ self._name = '' self._atoms = list() self._virtual_sites = list() self._bonds = list() # List of bonds between Atom objects self._properties = {} # Attached properties to be preserved #self._cached_properties = None # Cached properties (such as partial charges) can be recomputed as needed self._partial_charges = None self._conformers = None # Optional conformers def _copy_initializer(self, other): """ Copy contents of the specified molecule .. todo :: Should this be a ``@staticmethod`` where we have an explicit copy constructor? Parameters ---------- other : optional Overwrite the state of this FrozenMolecule with the specified FrozenMolecule object. A deep copy is made. """ #assert isinstance(other, type(self)), "can only copy instances of {}".format(type(self)) other_dict = other.to_dict() self._initialize_from_dict(other_dict) def __eq__(self, other): """Test two molecules for equality to see if they are the chemical species, but do not check other annotated properties. .. note :: Note that this method simply tests whether two molecules are identical chemical species using equivalence of their canonical isomeric SMILES. No effort is made to ensure that the atoms are in the same order or that any annotated properties are preserved. """ return self.is_isomorphic(other)
[docs] def to_smiles(self, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): """ Return a canonical isomeric SMILES representation of the current molecule .. note :: RDKit and OpenEye versions will not necessarily return the same representation. Parameters ---------- toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for SMILES conversion Returns ------- smiles : str Canonical isomeric explicit-hydrogen SMILES Examples -------- >>> from openforcefield.utils import get_data_file_path >>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf') >>> molecule = Molecule(sdf_filepath) >>> smiles = molecule.to_smiles() """ # Initialize cached_smiles dict for this molecule if none exists if self._cached_smiles is None: self._cached_smiles = {} # Figure out which toolkit should be used to create the SMILES if isinstance(toolkit_registry, ToolkitRegistry): to_smiles_method = toolkit_registry.resolve('to_smiles') elif isinstance(toolkit_registry, ToolkitWrapper): to_smiles_method = toolkit_registry.to_smiles else: raise Exception( 'Invalid toolkit_registry passed to to_smiles. Expected ToolkitRegistry or ToolkitWrapper. Got {}' .format(type(toolkit_registry))) # Get a string representation of the function containing the toolkit name so we can check # if a SMILES was already cached for this molecule. This will return, for example # "RDKitToolkitWrapper.to_smiles" func_qualname = to_smiles_method.__qualname__ # Check to see if a SMILES for this molecule was already cached using this method if func_qualname in self._cached_smiles: return self._cached_smiles[func_qualname] else: smiles = to_smiles_method(self) self._cached_smiles[func_qualname] = smiles return smiles
[docs] @staticmethod def from_smiles(smiles, hydrogens_are_explicit=False, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, allow_undefined_stereo=False): """ Construct a Molecule from a SMILES representation Parameters ---------- smiles : str The SMILES representation of the molecule. hydrogens_are_explicit : bool, default = False If False, the cheminformatics toolkit will perform hydrogen addition toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for SMILES-to-molecule conversion allow_undefined_stereo : bool, default=False Whether to accept SMILES with undefined stereochemistry. If False, an exception will be raised if a SMILES with undefined stereochemistry is passed into this function. Returns ------- molecule : openforcefield.topology.Molecule Examples -------- >>> molecule = Molecule.from_smiles('Cc1ccccc1') """ if isinstance(toolkit_registry, ToolkitRegistry): return toolkit_registry.call('from_smiles', smiles, hydrogens_are_explicit=hydrogens_are_explicit, allow_undefined_stereo=allow_undefined_stereo) elif isinstance(toolkit_registry, ToolkitWrapper): toolkit = toolkit_registry return toolkit.from_smiles(smiles, hydrogens_are_explicit=hydrogens_are_explicit, allow_undefined_stereo=allow_undefined_stereo ) else: raise Exception( 'Invalid toolkit_registry passed to from_smiles. Expected ToolkitRegistry or ToolkitWrapper. Got {}' .format(type(toolkit_registry)))
[docs] def is_isomorphic( self, other, compare_atom_stereochemistry=True, compare_bond_stereochemistry=True, ): """ Determines whether the molecules are isomorphic by comparing their graphs. Parameters ---------- other : an openforcefield.topology.molecule.FrozenMolecule The molecule to test for isomorphism. compare_atom_stereochemistry : bool, optional If ``False``, atoms' stereochemistry is ignored for the purpose of determining equality. Default is ``True``. compare_bond_stereochemistry : bool, optional If ``False``, bonds' stereochemistry is ignored for the purpose of determining equality. Default is ``True``. Returns ------- molecules_are_isomorphic : bool """ import networkx as nx def node_match_func(x, y): is_equal = ( (x['atomic_number'] == y['atomic_number']) and (x['is_aromatic'] == y['is_aromatic']) and (x['formal_charge'] == y['formal_charge']) ) if compare_atom_stereochemistry: is_equal &= x['stereochemistry'] == y['stereochemistry'] return is_equal def edge_match_func(x, y): # We don't need to check the exact bond order (which is 1 or 2) # if the bond is aromatic. This way we avoid missing a match only # if the alternate bond orders 1 and 2 are assigned differently. is_equal = x['is_aromatic'] == y['is_aromatic'] or x['bond_order'] == y['bond_order'] if compare_bond_stereochemistry: is_equal &= x['stereochemistry'] == y['stereochemistry'] return is_equal return nx.is_isomorphic(self.to_networkx(), other.to_networkx(), node_match=node_match_func, edge_match=edge_match_func )
#if not (isinstance(other, FrozenMolecule)): # other_fm = FrozenMolecule(other) #else: # other_fm = other #self_smiles = self.to_smiles(toolkit_registry=toolkit_registry) #other_smiles = other_fm.to_smiles(toolkit_registry=toolkit_registry) #return self_smiles == other_smiles
[docs] def generate_conformers(self, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, n_conformers=10, clear_existing=True): """ Generate conformers for this molecule using an underlying toolkit Parameters ---------- toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for SMILES-to-molecule conversion n_conformers : int, default=1 The maximum number of conformers to produce clear_existing : bool, default=True Whether to overwrite existing conformers for the molecule Examples -------- >>> molecule = Molecule.from_smiles('CCCCCC') >>> molecule.generate_conformers() Raises ------ InvalidToolkitError If an invalid object is passed as the toolkit_registry parameter """ if isinstance(toolkit_registry, ToolkitRegistry): return toolkit_registry.call('generate_conformers', self, n_conformers=n_conformers, clear_existing=clear_existing) elif isinstance(toolkit_registry, ToolkitWrapper): toolkit = toolkit_registry return toolkit.generate_conformers(self, n_conformers=n_conformers, clear_existing=clear_existing) else: raise InvalidToolkitError( 'Invalid toolkit_registry passed to generate_conformers. Expected ToolkitRegistry or ToolkitWrapper. Got {}' .format(type(toolkit_registry)))
[docs] def compute_partial_charges_am1bcc(self, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): """ Calculate partial atomic charges for this molecule using AM1-BCC run by an underlying toolkit Parameters ---------- toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for the calculation Examples -------- >>> molecule = Molecule.from_smiles('CCCCCC') >>> molecule.generate_conformers() >>> molecule.compute_partial_charges_am1bcc() Raises ------ InvalidToolkitError If an invalid object is passed as the toolkit_registry parameter """ if isinstance(toolkit_registry, ToolkitRegistry): charges = toolkit_registry.call( 'compute_partial_charges_am1bcc', self ) elif isinstance(toolkit_registry, ToolkitWrapper): toolkit = toolkit_registry charges = toolkit.compute_partial_charges_am1bcc(self) else: raise InvalidToolkitError( 'Invalid toolkit_registry passed to compute_partial_charges_am1bcc. Expected ToolkitRegistry or ToolkitWrapper. Got {}' .format(type(toolkit_registry))) self.partial_charges = charges
[docs] def compute_partial_charges(self, #quantum_chemical_method='AM1-BCC', #partial_charge_method='None', toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): """ **Warning! Not Implemented!** Calculate partial atomic charges for this molecule using an underlying toolkit Parameters ---------- quantum_chemical_method : string, default='AM1-BCC' The quantum chemical method to use for partial charge calculation. partial_charge_method : string, default='None' The partial charge calculation method to use for partial charge calculation. toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for SMILES-to-molecule conversion Examples -------- >>> molecule = Molecule.from_smiles('CCCCCC') >>> molecule.generate_conformers() Raises ------ InvalidToolkitError If an invalid object is passed as the toolkit_registry parameter """ raise NotImplementedError
# TODO: Implement this in a way that's compliant with SMIRNOFF's <ChargeIncrementModel> tag when the spec gets finalized # if isinstance(toolkit_registry, ToolkitRegistry): # charges = toolkit_registry.call( # 'compute_partial_charges_am1bcc', # self, # ) # elif isinstance(toolkit_registry, ToolkitWrapper): # toolkit = toolkit_registry # charges = toolkit.compute_partial_charges_am1bcc( # self, # #quantum_chemical_method=quantum_chemical_method, # #partial_charge_method=partial_charge_method # ) # else: # raise InvalidToolkitError( # 'Invalid toolkit_registry passed to compute_partial_charges_am1bcc. Expected ToolkitRegistry or ToolkitWrapper. Got {}' # .format(type(toolkit_registry)))
[docs] def compute_wiberg_bond_orders(self, charge_model=None, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): """ Calculate wiberg bond orders for this molecule using an underlying toolkit Parameters ---------- toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for SMILES-to-molecule conversion charge_model : string, optional The charge model to use for partial charge calculation Examples -------- >>> molecule = Molecule.from_smiles('CCCCCC') >>> molecule.generate_conformers() >>> molecule.compute_wiberg_bond_orders() Raises ------ InvalidToolkitError If an invalid object is passed as the toolkit_registry parameter """ if isinstance(toolkit_registry, ToolkitRegistry): return toolkit_registry.call( 'compute_wiberg_bond_orders', self, charge_model=charge_model) elif isinstance(toolkit_registry, ToolkitWrapper): toolkit = toolkit_registry return toolkit.compute_wiberg_bond_orders( self, charge_model=charge_model) else: raise Exception( 'Invalid toolkit_registry passed to compute_wiberg_bond_orders. Expected ToolkitRegistry or ToolkitWrapper. Got {}' .format(type(toolkit_registry)))
def _invalidate_cached_properties(self): """ Indicate that the chemical entity has been altered. """ #if hasattr(self, '_cached_properties'): # delattr(self, '_cached_properties') self._conformers = None self._partial_charges = None self._propers = None self._impropers = None self._cached_smiles = None # TODO: Clear fractional bond orders
[docs] def to_networkx(self): """Generate a NetworkX undirected graph from the Molecule. Nodes are Atoms labeled with particle indices and atomic elements (via the ``element`` node atrribute). Edges denote chemical bonds between Atoms. Virtual sites are not included, since they lack a concept of chemical connectivity. .. todo :: * Do we need a ``from_networkx()`` method? If so, what would the Graph be required to provide? * Should edges be labeled with discrete bond types in some aromaticity model? * Should edges be labeled with fractional bond order if a method is specified? * Should we add other per-atom and per-bond properties (e.g. partial charges) if present? * Can this encode bond/atom chirality? Returns ------- graph : networkx.Graph The resulting graph, with nodes (atoms) labeled with atom indices, elements, stereochemistry and aromaticity flags and bonds with two atom indices, bond order, stereochemistry, and aromaticity flags Examples -------- Retrieve the bond graph for imatinib (OpenEye toolkit required) >>> molecule = Molecule.from_iupac('imatinib') >>> nxgraph = molecule.to_networkx() """ import networkx as nx G = nx.Graph() for atom in self.atoms: G.add_node( atom.molecule_atom_index, atomic_number=atom.atomic_number, is_aromatic=atom.is_aromatic, stereochemistry=atom.stereochemistry, formal_charge=atom.formal_charge) #G.add_node(atom.molecule_atom_index, attr_dict={'atomic_number': atom.atomic_number}) for bond in self.bonds: G.add_edge( bond.atom1_index, bond.atom2_index, bond_order=bond.bond_order, is_aromatic=bond.is_aromatic, stereochemistry = bond.stereochemistry) #G.add_edge(bond.atom1_index, bond.atom2_index, attr_dict={'order':bond.bond_order}) return G
def _add_atom(self, atomic_number, formal_charge, is_aromatic, stereochemistry=None, name=None): """ Add an atom Parameters ---------- atomic_number : int Atomic number of the atom formal_charge : int Formal charge of the atom is_aromatic : bool If True, atom is aromatic; if False, not aromatic stereochemistry : str, optional, default=None Either 'R' or 'S' for specified stereochemistry, or None if stereochemistry is irrelevant name : str, optional, default=None An optional name for the atom Returns ------- index : int The index of the atom in the molecule Examples -------- Define a methane molecule >>> molecule = Molecule() >>> molecule.name = 'methane' >>> C = molecule.add_atom(6, 0, False) >>> H1 = molecule.add_atom(1, 0, False) >>> H2 = molecule.add_atom(1, 0, False) >>> H3 = molecule.add_atom(1, 0, False) >>> H4 = molecule.add_atom(1, 0, False) >>> bond_idx = molecule.add_bond(C, H1, False, 1) >>> bond_idx = molecule.add_bond(C, H2, False, 1) >>> bond_idx = molecule.add_bond(C, H3, False, 1) >>> bond_idx = molecule.add_bond(C, H4, False, 1) """ # Create an atom atom = Atom( atomic_number, formal_charge, is_aromatic, stereochemistry=stereochemistry, name=name, molecule=self) self._atoms.append(atom) #self._particles.append(atom) self._invalidate_cached_properties() return self._atoms.index(atom) def _add_bond_charge_virtual_site(self, atoms, distance, **kwargs): """ Create a bond charge-type virtual site, in which the location of the charge is specified by the position of two atoms. This supports placement of a virtual site S along a vector between two specified atoms, e.g. to allow for a sigma hole for halogens or similar contexts. With positive values of the distance, the virtual site lies outside the first indexed atom. Parameters ---------- atoms : list of openforcefield.topology.molecule.Atom objects of shape [N] The atoms defining the virtual site's position distance : float weights : list of floats of shape [N] or None, optional, default=None weights[index] is the weight of particles[index] contributing to the position of the virtual site. Default is None charge_increments : list of floats of shape [N], optional, default=None The amount of charge to remove from the VirtualSite's atoms and put in the VirtualSite. Indexing in this list should match the ordering in the atoms list. Default is None. epsilon : float Epsilon term for VdW properties of virtual site. Default is None. sigma : float, default=None Sigma term for VdW properties of virtual site. Default is None. rmin_half : float Rmin_half term for VdW properties of virtual site. Default is None. name : string or None, default=None The name of this virtual site. Default is None. Returns ------- index : int The index of the newly-added virtual site in the molecule """ # Check if function was passed list of atoms or atom indices if all([isinstance(atom, int) for atom in atoms]): atom_list = [self.atoms[atom_index] for atom_index in atoms] elif all([isinstance(atom, Atom) for atom in atoms]): atom_list = atoms else: raise Exception( 'Invalid inputs to molecule._add_bond_charge_virtual_site.' ' Expected ints or Atoms. Received types {} '.format( [type(i) for i in atoms])) # TODO: Check to make sure bond does not already exist vsite = BondChargeVirtualSite(atom_list, distance, **kwargs) self._virtual_sites.append(vsite) self._invalidate_cached_properties() return self._virtual_sites.index(vsite) def _add_monovalent_lone_pair_virtual_site(self, atoms, distance, out_of_plane_angle, in_plane_angle, **kwargs): """ Create a bond charge-type virtual site, in which the location of the charge is specified by the position of three atoms. TODO : Do "weights" have any meaning here? Parameters ---------- atoms : list of three openforcefield.topology.molecule.Atom objects The three atoms defining the virtual site's position distance : float out_of_plane_angle : float in_plane_angle : float epsilon : float Epsilon term for VdW properties of virtual site. Default is None. sigma : float, default=None Sigma term for VdW properties of virtual site. Default is None. rmin_half : float Rmin_half term for VdW properties of virtual site. Default is None. name : string or None, default=None The name of this virtual site. Default is None. Returns ------- index : int The index of the newly-added virtual site in the molecule """ # Check if function was passed list of atoms or atom indices if all([isinstance(atom, int) for atom in atoms]): atom_list = [self.atoms[atom_index] for atom_index in atoms] elif all([isinstance(atom, Atom) for atom in atoms]): atom_list = atoms else: raise Exception( 'Invalid inputs to molecule._add_monovalent_lone_pair_virtual_site. Expected ints or Atoms.' ' Received types {} '.format([type(i) for i in atoms])) # TODO: Check to make sure bond does not already exist vsite = MonovalentLonePairVirtualSite( atom_list, distance, out_of_plane_angle, in_plane_angle, **kwargs) self._virtual_sites.append(vsite) self._invalidate_cached_properties() return self._virtual_sites.index(vsite) def _add_divalent_lone_pair_virtual_site(self, atoms, distance, out_of_plane_angle, in_plane_angle, **kwargs): """ Create a divalent lone pair-type virtual site, in which the location of the charge is specified by the position of three atoms. TODO : Do "weights" have any meaning here? Parameters ---------- atoms : list of 3 openforcefield.topology.molecule.Atom objects The three atoms defining the virtual site's position distance : float out_of_plane_angle : float in_plane_angle : float epsilon : float Epsilon term for VdW properties of virtual site. Default is None. sigma : float, default=None Sigma term for VdW properties of virtual site. Default is None. rmin_half : float Rmin_half term for VdW properties of virtual site. Default is None. name : string or None, default=None The name of this virtual site. Default is None. Returns ------- index : int The index of the newly-added virtual site in the molecule """ # Check if function was passed list of atoms or atom indices if all([isinstance(atom, int) for atom in atoms]): atom_list = [self.atoms[atom_index] for atom_index in atoms] elif all([isinstance(atom, Atom) for atom in atoms]): atom_list = atoms else: raise Exception( 'Invalid inputs to molecule._add_divalent_lone_pair_virtual_site. Expected ints or Atoms. ' 'Received types {} '.format([type(i) for i in atoms])) # TODO: Check to make sure bond does not already exist vsite = DivalentLonePairVirtualSite( atom_list, distance, out_of_plane_angle, in_plane_angle, **kwargs) self._virtual_sites.append(vsite) self._invalidate_cached_properties() return self._virtual_sites.index(vsite) def _add_trivalent_lone_pair_virtual_site(self, atoms, distance, out_of_plane_angle, in_plane_angle, **kwargs): """ Create a trivalent lone pair-type virtual site, in which the location of the charge is specified by the position of four atoms. TODO : Do "weights" have any meaning here? Parameters ---------- atoms : list of 4 openforcefield.topology.molecule.Atom objects or atom indices The three atoms defining the virtual site's position distance : float out_of_plane_angle : float in_plane_angle : float epsilon : float Epsilon term for VdW properties of virtual site. Default is None. sigma : float, default=None Sigma term for VdW properties of virtual site. Default is None. rmin_half : float Rmin_half term for VdW properties of virtual site. Default is None. name : string or None, default=None The name of this virtual site. Default is None. """ # Check if function was passed list of atoms or atom indices if all([isinstance(atom, int) for atom in atoms]): atom_list = [self.atoms[atom_index] for atom_index in atoms] elif all([isinstance(atom, Atom) for atom in atoms]): atom_list = atoms else: raise Exception( 'Invalid inputs to molecule._add_trivalent_lone_pair_virtual_site. Expected ints or Atoms. Received types {} ' .format([type(i) for i in atoms])) vsite = TrivalentLonePairVirtualSite( atom_list, distance, out_of_plane_angle, in_plane_angle, **kwargs) self._virtual_sites.append(vsite) self._invalidate_cached_properties() return self._virtual_sites.index(vsite) def _add_bond(self, atom1, atom2, bond_order, is_aromatic, stereochemistry=None, fractional_bond_order=None): """ Add a bond between two specified atom indices Parameters ---------- atom1 : int or openforcefield.topology.molecule.Atom Index of first atom or first atom atom2_index : int or openforcefield.topology.molecule.Atom Index of second atom or second atom bond_order : int Integral bond order of Kekulized form is_aromatic : bool True if this bond is aromatic, False otherwise stereochemistry : str, optional, default=None Either 'E' or 'Z' for specified stereochemistry, or None if stereochemistry is irrelevant fractional_bond_order : float, optional, default=None The fractional (eg. Wiberg) bond order Returns ------- index : int The index of the bond in the molecule """ if isinstance(atom1, int) and isinstance(atom2, int): atom1_atom = self.atoms[atom1] atom2_atom = self.atoms[atom2] elif isinstance(atom1, Atom) and isinstance(atom2, Atom): atom1_atom = atom1 atom2_atom = atom2 else: raise Exception( 'Invalid inputs to molecule._add_bond. Expected ints or Atoms. ' 'Received {} (type {}) and {} (type {}) '.format( atom1, type(atom1), atom2, type(atom2))) # TODO: Check to make sure bond does not already exist if atom1_atom.is_bonded_to(atom2_atom): raise Exception('Bond already exists between {} and {}'.format( atom1_atom, atom2_atom)) bond = Bond( atom1_atom, atom2_atom, bond_order, is_aromatic, stereochemistry=stereochemistry, fractional_bond_order=fractional_bond_order) self._bonds.append(bond) self._invalidate_cached_properties() # TODO: This is a bad way to get bond index return self._bonds.index(bond) def _add_conformer(self, coordinates): """ Add a conformation of the molecule Parameters ---------- coordinates: A simtk vector wrapped unit quantity The coordinates of the conformer to add. Returns ------- index: int The index of this conformer """ new_conf = unit.Quantity( np.zeros((self.n_atoms, 3), np.float), unit.angstrom) if not (new_conf.shape == coordinates.shape): raise Exception( "molecule.add_conformer given input of the wrong shape: " "Given {}, expected {}".format(coordinates.shape, new_conf.shape)) try: new_conf[:] = coordinates except AttributeError as e: print(e) raise Exception( 'Coordinates passed to Molecule._add_conformer without units. Ensure that coordinates are ' 'of type simtk.units.Quantity') if self._conformers is None: self._conformers = [] self._conformers.append(new_conf) return len(self._conformers) @property def partial_charges(self): """ Returns the partial charges (if present) on the molecule Returns ------- partial_charges : a simtk.unit.Quantity - wrapped numpy array [1 x n_atoms] The partial charges on this Molecule's atoms. """ return self._partial_charges @partial_charges.setter def partial_charges(self, charges): """ Set the atomic partial charges for this molecule Parameters ---------- charges : a simtk.unit.Quantity - wrapped numpy array [1 x n_atoms] The partial charges to assign to the molecule. Must be in units compatible with simtk.unit.elementary_charge """ assert hasattr(charges, 'unit') assert unit.elementary_charge.is_compatible(charges.unit) assert charges.shape == (self.n_atoms, ) charges_ec = charges.in_units_of(unit.elementary_charge) self._partial_charges = charges_ec @property def n_particles(self): """ The number of Particle objects, which corresponds to how many positions must be used. """ return len(self._atoms) + len(self._virtual_sites) @property def n_atoms(self): """ The number of Atom objects. """ return len(self._atoms) @property def n_virtual_sites(self): """ The number of VirtualSite objects. """ return sum([1 for virtual_site in self.virtual_sites]) @property def n_bonds(self): """ The number of Bond objects. """ return sum([1 for bond in self.bonds]) @property def n_angles(self): """int: number of angles in the Molecule.""" self._construct_angles() return len(self._angles) @property def n_propers(self): """int: number of proper torsions in the Molecule.""" self._construct_torsions() return len(self._propers) @property def n_impropers(self): """int: number of improper torsions in the Molecule.""" self._construct_torsions() return len(self._impropers) @property def particles(self): """ Iterate over all Particle objects. """ # TODO: Re-implement this when we see how it interfaces with Topology return self._atoms + self._virtual_sites @property def atoms(self): """ Iterate over all Atom objects. """ return self._atoms @property def conformers(self): """ Iterate over all conformers in this molecule. """ return self._conformers @property def n_conformers(self): """ Iterate over all Atom objects. """ if self._conformers is None: return 0 return len(self._conformers) @property def virtual_sites(self): """ Iterate over all VirtualSite objects. """ return self._virtual_sites @property def bonds(self): """ Iterate over all Bond objects. """ return self._bonds @property def angles(self): """ Get an iterator over all i-j-k angles. """ self._construct_angles() return self._angles @property def torsions(self): """ Get an iterator over all i-j-k-l torsions. Note that i-j-k-i torsions (cycles) are excluded. Returns ------- torsions : iterable of 4-Atom tuples """ self._construct_torsions() return self._torsions @property def propers(self): """ Iterate over all proper torsions in the molecule .. todo:: * Do we need to return a ``Torsion`` object that collects information about fractional bond orders? """ self._construct_torsions() return self._propers @property def impropers(self): """ Iterate over all proper torsions in the molecule .. todo:: * Do we need to return a ``Torsion`` object that collects information about fractional bond orders? """ self._construct_torsions() return self._impropers @property def total_charge(self): """ Return the total charge on the molecule """ return sum([atom.formal_charge for atom in self.atoms]) @property def name(self): """ The name (or title) of the molecule """ return self._name @name.setter def name(self, other): """ Set the name of this molecule """ if other is None: self._name = '' elif type(other) is str: self._name = other else: raise Exception("Molecule name must be a string") @property def properties(self): """ The properties dictionary of the molecule """ return self._properties
[docs] def chemical_environment_matches(self, query, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): """Retrieve all matches for a given chemical environment query. Parameters ---------- query : str or ChemicalEnvironment SMARTS string (with one or more tagged atoms) or ``ChemicalEnvironment`` query Query will internally be resolved to SMIRKS using ``query.asSMIRKS()`` if it has an ``.asSMIRKS`` method. toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=GLOBAL_TOOLKIT_REGISTRY :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for chemical environment matches Returns ------- matches : list of atom index tuples A list of tuples, containing the indices of the matching atoms. Examples -------- Retrieve all the carbon-carbon bond matches in a molecule >>> molecule = Molecule.from_iupac('imatinib') >>> matches = molecule.chemical_environment_matches('[#6X3:1]~[#6X3:2]') .. todo :: * Do we want to generalize ``query`` to allow other kinds of queries, such as mdtraj DSL, pymol selections, atom index slices, etc? We could call it ``topology.matches(query)`` instead of ``chemical_environment_matches`` """ # Resolve to SMIRKS if needed # TODO: Update this to use updated ChemicalEnvironment API if hasattr(query, 'asSMIRKS'): smirks = query.asSMIRKS() elif type(query) == str: smirks = query else: raise ValueError( "'query' must be either a string or a ChemicalEnvironment") # Use specified cheminformatics toolkit to determine matches with specified aromaticity model # TODO: Simplify this by requiring a toolkit registry for the molecule? # TODO: Do we have to pass along an aromaticity model? if isinstance(toolkit_registry, ToolkitRegistry): matches = toolkit_registry.call('find_smarts_matches', self, smirks) elif isinstance(toolkit_registry, ToolkitWrapper): matches = toolkit_registry.find_smarts_matches(self, smirks) else: raise ValueError( "'toolkit_registry' must be either a ToolkitRegistry or a ToolkitWrapper" ) return matches
# TODO: Move OE-dependent parts of this to toolkits.py
[docs] @classmethod @OpenEyeToolkitWrapper.requires_toolkit() def from_iupac(cls, iupac_name, **kwargs): """Generate a molecule from IUPAC or common name Parameters ---------- iupac_name : str IUPAC name of molecule to be generated allow_undefined_stereo : bool, default=False If false, raises an exception if molecule contains undefined stereochemistry. Returns ------- molecule : Molecule The resulting molecule with position .. note :: This method requires the OpenEye toolkit to be installed. Examples -------- Create a molecule from a common name >>> molecule = Molecule.from_iupac('4-[(4-methylpiperazin-1-yl)methyl]-N-(4-methyl-3-{[4-(pyridin-3-yl)pyrimidin-2-yl]amino}phenyl)benzamide') Create a molecule from a common name >>> molecule = Molecule.from_iupac('imatinib') """ from openeye import oechem, oeiupac oemol = oechem.OEMol() oeiupac.OEParseIUPACName(oemol, iupac_name) oechem.OETriposAtomNames(oemol) result = oechem.OEAddExplicitHydrogens(oemol) if result == False: raise Exception( "Addition of explicit hydrogens failed in from_iupac") return cls.from_openeye(oemol, **kwargs)
# TODO: Move OE-dependent parts of this to toolkits.py
[docs] @OpenEyeToolkitWrapper.requires_toolkit() def to_iupac(self): """Generate IUPAC name from Molecule Returns ------- iupac_name : str IUPAC name of the molecule .. note :: This method requires the OpenEye toolkit to be installed. Examples -------- >>> from openforcefield.utils import get_data_file_path >>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf') >>> molecule = Molecule(sdf_filepath) >>> iupac_name = molecule.to_iupac() """ from openeye import oeiupac return oeiupac.OECreateIUPACName(self.to_openeye())
[docs] @staticmethod def from_topology(topology): """Return a Molecule representation of an openforcefield Topology containing a single Molecule object. Parameters ---------- topology : openforcefield.topology.Topology The :class:`Topology` object containing a single :class:`Molecule` object. Note that OpenMM and MDTraj ``Topology`` objects are not supported. Returns ------- molecule : openforcefield.topology.Molecule The Molecule object in the topology Raises ------ ValueError If the topology does not contain exactly one molecule. Examples -------- Create a molecule from a Topology object that contains exactly one molecule >>> molecule = Molecule.from_topology(topology) # doctest: +SKIP """ # TODO: Ensure we are dealing with an openforcefield Topology object if topology.n_topology_molecules != 1: raise ValueError('Topology must contain exactly one molecule') molecule = [i for i in topology.reference_molecules][0] return Molecule(molecule)
[docs] def to_topology(self): """ Return an openforcefield Topology representation containing one copy of this molecule Returns ------- topology : openforcefield.topology.Topology A Topology representation of this molecule Examples -------- >>> molecule = Molecule.from_iupac('imatinib') >>> topology = molecule.to_topology() """ from openforcefield.topology import Topology return Topology.from_molecules(self)
[docs] @staticmethod def from_file(file_path, file_format=None, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, allow_undefined_stereo=False): """ Create one or more molecules from a file .. todo:: * Extend this to also include some form of .offmol Open Force Field Molecule format? * Generalize this to also include file-like objects? Parameters ---------- file_path : str or file-like object The path to the file or file-like object to stream one or more molecules from. file_format : str, optional, default=None Format specifier, usually file suffix (eg. 'MOL2', 'SMI') Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for your loaded toolkits for details. toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=GLOBAL_TOOLKIT_REGISTRY :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for file loading. If a Toolkit is passed, only the highest-precedence toolkit is used allow_undefined_stereo : bool, default=False If false, raises an exception if oemol contains undefined stereochemistry. Returns ------- molecules : Molecule or list of Molecules If there is a single molecule in the file, a Molecule is returned; otherwise, a list of Molecule objects is returned. Examples -------- >>> from openforcefield.tests.utils import get_monomer_mol2_file_path >>> mol2_file_path = get_monomer_mol2_file_path('cyclohexane') >>> molecule = Molecule.from_file(mol2_file_path) """ if file_format is None: if not (isinstance(file_path, str)): raise Exception( "If providing a file-like object for reading molecules, the format must be specified" ) # Assume that files ending in ".gz" should use their second-to-last suffix for compatibility check # TODO: Will all cheminformatics packages be OK with gzipped files? if file_path[-3:] == '.gz': file_format = file_path.split('.')[-2] else: file_format = file_path.split('.')[-1] file_format = file_format.upper() # Determine which toolkit to use (highest priority that's compatible with input type) if isinstance(toolkit_registry, ToolkitRegistry): # TODO: Encapsulate this logic into ToolkitRegistry.call()? toolkit = None supported_read_formats = {} for query_toolkit in toolkit_registry.registered_toolkits: if file_format in query_toolkit.toolkit_file_read_formats: toolkit = query_toolkit break supported_read_formats[ query_toolkit. toolkit_name] = query_toolkit.toolkit_file_read_formats if toolkit is None: raise NotImplementedError( "No toolkits in registry can read file {} (format {}). Supported formats in the " "provided ToolkitRegistry are {}".format( file_path, file_format, supported_read_formats)) elif isinstance(toolkit_registry, ToolkitWrapper): # TODO: Encapsulate this logic in ToolkitWrapper? toolkit = toolkit_registry if file_format not in toolkit.toolkit_file_read_formats: raise NotImplementedError( "Toolkit {} can not read file {} (format {}). Supported formats for this toolkit " "are {}".format(toolkit.toolkit_name, file_path, file_format, toolkit.toolkit_file_read_formats)) else: raise ValueError( "'toolkit_registry' must be either a ToolkitRegistry or a ToolkitWrapper" ) mols = list() if isinstance(file_path, str): mols = toolkit.from_file( file_path, file_format=file_format, allow_undefined_stereo=allow_undefined_stereo) elif hasattr(file_path, 'read'): file_obj = file_path mols = toolkit.from_file_obj( file_obj, file_format=file_format, allow_undefined_stereo=allow_undefined_stereo) if len(mols) == 0: raise Exception( 'Unable to read molecule from file: {}'.format(file_path)) elif len(mols) == 1: return mols[0] return mols
[docs] def to_file(self, file_path, file_format, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): """Write the current molecule to a file or file-like object Parameters ---------- file_path : str or file-like object A file-like object or the path to the file to be written. file_format : str Format specifier, one of ['MOL2', 'MOL2H', 'SDF', 'PDB', 'SMI', 'CAN', 'TDT'] Note that not all toolkits support all formats toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=GLOBAL_TOOLKIT_REGISTRY :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for file writing. If a Toolkit is passed, only the highest-precedence toolkit is used Raises ------ ValueError If the requested file_format is not supported by one of the installed cheminformatics toolkits Examples -------- >>> molecule = Molecule.from_iupac('imatinib') >>> molecule.to_file('imatinib.mol2', file_format='mol2') # doctest: +SKIP >>> molecule.to_file('imatinib.sdf', file_format='sdf') # doctest: +SKIP >>> molecule.to_file('imatinib.pdb', file_format='pdb') # doctest: +SKIP """ if isinstance(toolkit_registry, ToolkitRegistry): pass elif isinstance(toolkit_registry, ToolkitWrapper): toolkit = toolkit_registry toolkit_registry = ToolkitRegistry(toolkit_precedence=[]) toolkit_registry.add_toolkit(toolkit) else: raise ValueError( "'toolkit_registry' must be either a ToolkitRegistry or a ToolkitWrapper" ) file_format = file_format.upper() # Take the first toolkit that can write the desired output format toolkit = None for query_toolkit in toolkit_registry.registered_toolkits: if file_format in query_toolkit.toolkit_file_write_formats: toolkit = query_toolkit break # Raise an exception if no toolkit was found to provide the requested file_format if toolkit is None: supported_formats = {} for toolkit in toolkit_registry.registered_toolkits: supported_formats[ toolkit.toolkit_name] = toolkit.toolkit_file_write_formats raise ValueError( 'The requested file format ({}) is not available from any of the installed toolkits ' '(supported formats: {})'.format(file_format, supported_formats)) # Write file if type(file_path) == str: # Open file for writing toolkit.to_file(self, file_path, file_format) else: toolkit.to_file_obj(self, file_path, file_format)
[docs] @staticmethod @RDKitToolkitWrapper.requires_toolkit() def from_rdkit(rdmol, allow_undefined_stereo=False): """ Create a Molecule from an RDKit molecule. Requires the RDKit to be installed. Parameters ---------- rdmol : rkit.RDMol An RDKit molecule allow_undefined_stereo : bool, default=False If false, raises an exception if oemol contains undefined stereochemistry. Returns ------- molecule : openforcefield.Molecule An openforcefield molecule Examples -------- Create a molecule from an RDKit molecule >>> from rdkit import Chem >>> from openforcefield.tests.utils import get_data_file_path >>> rdmol = Chem.MolFromMolFile(get_data_file_path('systems/monomers/ethanol.sdf')) >>> molecule = Molecule.from_rdkit(rdmol) """ toolkit = RDKitToolkitWrapper() return toolkit.from_rdkit( rdmol, allow_undefined_stereo=allow_undefined_stereo)
[docs] @RDKitToolkitWrapper.requires_toolkit() def to_rdkit(self, aromaticity_model=DEFAULT_AROMATICITY_MODEL): """ Create an RDKit molecule Requires the RDKit to be installed. Parameters ---------- aromaticity_model : str, optional, default=DEFAULT_AROMATICITY_MODEL The aromaticity model to use Returns ------- rdmol : rkit.RDMol An RDKit molecule Examples -------- Convert a molecule to RDKit >>> from openforcefield.utils import get_data_file_path >>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf') >>> molecule = Molecule(sdf_filepath) >>> rdmol = molecule.to_rdkit() """ toolkit = RDKitToolkitWrapper() return toolkit.to_rdkit(self, aromaticity_model=aromaticity_model)
[docs] @staticmethod @OpenEyeToolkitWrapper.requires_toolkit() def from_openeye(oemol, allow_undefined_stereo=False): """ Create a Molecule from an OpenEye molecule. Requires the OpenEye toolkit to be installed. Parameters ---------- oemol : openeye.oechem.OEMol An OpenEye molecule allow_undefined_stereo : bool, default=False If false, raises an exception if oemol contains undefined stereochemistry. Returns ------- molecule : openforcefield.topology.Molecule An openforcefield molecule Examples -------- Create a Molecule from an OpenEye OEMol >>> from openeye import oechem >>> from openforcefield.tests.utils import get_data_file_path >>> ifs = oechem.oemolistream(get_data_file_path('systems/monomers/ethanol.mol2')) >>> oemols = list(ifs.GetOEGraphMols()) >>> molecule = Molecule.from_openeye(oemols[0]) """ toolkit = OpenEyeToolkitWrapper() return toolkit.from_openeye( oemol, allow_undefined_stereo=allow_undefined_stereo)
[docs] @OpenEyeToolkitWrapper.requires_toolkit() def to_openeye(self, aromaticity_model=DEFAULT_AROMATICITY_MODEL): """ Create an OpenEye molecule Requires the OpenEye toolkit to be installed. .. todo :: * Use stored conformer positions instead of an argument. * Should the aromaticity model be specified in some other way? Parameters ---------- aromaticity_model : str, optional, default=DEFAULT_AROMATICITY_MODEL The aromaticity model to use Returns ------- oemol : openeye.oechem.OEMol An OpenEye molecule Examples -------- Create an OpenEye molecule from a Molecule >>> molecule = Molecule.from_smiles('CC') >>> oemol = molecule.to_openeye() """ toolkit = OpenEyeToolkitWrapper() return toolkit.to_openeye(self, aromaticity_model=aromaticity_model)
[docs] def get_fractional_bond_orders(self, method='Wiberg', toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): """Get fractional bond orders. method : str, optional, default='Wiberg' The name of the charge method to use. Options are: * 'Wiberg' : Wiberg bond order toolkit_registry : openforcefield.utils.toolkits ToolkitRegistry The toolkit registry to use for molecule operations Examples -------- Get fractional Wiberg bond orders >>> molecule = Molecule.from_iupac('imatinib') >>> molecule.generate_conformers() >>> fractional_bond_orders = molecule.get_fractional_bond_orders(method='Wiberg') .. todo:: * Is it OK that the ``Molecule`` object does not store geometry, but will create it using ``openeye.omega`` or ``rdkit``? * Should this method assign fractional bond orders to the ``Bond``s in the molecule, a separate ``bond_orders`` molecule property, or just return the array of bond orders? * How do we add enough flexibility to specify the toolkit and optional parameters, such as: ``oequacpac.OEAssignPartialCharges(charged_copy, getattr(oequacpac, 'OECharges_AM1BCCSym'), False, False)`` * Generalize to allow user to specify both QM method and bond order computation approach (e.g. ``AM1`` and ``Wiberg``) """ # TODO: Let ToolkitRegistry handle this once compute_fractional_bond_orders will be added to the Wrappers API. if method != 'Wiberg': raise NotImplementedError('Only Wiberg bond order is currently implemented') # TODO: Use memoization to speed up subsequent calls; use decorator? fractional_bond_orders = toolkit_registry.call( 'compute_wiberg_bond_orders', molecule=self) return fractional_bond_orders
def _construct_angles(self): """ Get an iterator over all i-j-k angles. """ # TODO: Build Angle objects instead of tuple of atoms. if not hasattr(self, '_angles'): self._construct_bonded_atoms_list() self._angles = set() for atom1 in self._atoms: for atom2 in self._bondedAtoms[atom1]: for atom3 in self._bondedAtoms[atom2]: if atom1 == atom3: continue # TODO: Encapsulate this logic into an Angle class. if atom1.molecule_atom_index < atom3.molecule_atom_index: self._angles.add((atom1, atom2, atom3)) else: self._angles.add((atom3, atom2, atom1)) def _construct_torsions(self): """ Construct sets containing the atoms improper and proper torsions """ # TODO: Build Proper/ImproperTorsion objects instead of tuple of atoms. if not hasattr(self, '_torsions'): self._construct_bonded_atoms_list() #self._torsions = set() self._propers = set() self._impropers = set() for atom1 in self._atoms: for atom2 in self._bondedAtoms[atom1]: for atom3 in self._bondedAtoms[atom2]: if atom1 == atom3: continue for atom4 in self._bondedAtoms[atom3]: if atom4 == atom2: continue # Exclude i-j-k-i if atom1 == atom4: continue if atom1.molecule_atom_index < atom4.molecule_atom_index: torsion = (atom1, atom2, atom3, atom4) else: torsion = (atom4, atom3, atom2, atom1) self._propers.add(torsion) for atom3i in self._bondedAtoms[atom2]: if atom3i == atom3: continue if atom3i == atom1: continue improper = (atom1, atom2, atom3, atom3i) self._impropers.add(improper) self._torsions = self._propers | self._impropers #return iter(self._torsions) def _construct_bonded_atoms_list(self): """ Construct list of all atoms each atom is bonded to. """ # TODO: Add this to cached_properties if not hasattr(self, '_bondedAtoms'): #self._atoms = [ atom for atom in self.atoms() ] self._bondedAtoms = dict() for atom in self._atoms: self._bondedAtoms[atom] = set() for bond in self._bonds: atom1 = self.atoms[bond.atom1_index] atom2 = self.atoms[bond.atom2_index] self._bondedAtoms[atom1].add(atom2) self._bondedAtoms[atom2].add(atom1) def _is_bonded(self, atom_index_1, atom_index_2): """Return True if atoms are bonded, False if not. Parameters ---------- atom_index_1 : int atom_index_2 : int Atom indices Returns ------- is_bonded : bool True if atoms are bonded, False otherwise """ self._construct_bonded_atoms_list() atom1 = self._atoms[atom_index_1] atom2 = self._atoms[atom_index_2] return atom2 in self._bondedAtoms[atom1]
[docs] def get_bond_between(self, i, j): """Returns the bond between two atoms Parameters ---------- i, j : int or Atom Atoms or atom indices to check Returns ------- bond : Bond The bond between i and j. """ if isinstance(i, int) and isinstance(j, int): atom_i = self._atoms[i] atom_j = self._atoms[j] elif isinstance(i, Atom) and isinstance(j, Atom): atom_i = i atom_j = j else: raise TypeError( "Invalid input passed to is_bonded(). Expected ints or Atoms, " "got {} and {}".format(i, j)) for bond in atom_i.bonds: for atom in bond.atoms: if atom == atom_i: continue if atom == atom_j: return bond from openforcefield.topology import NotBondedError raise NotBondedError('No bond between atom {} and {}'.format(i, j))
[docs]class Molecule(FrozenMolecule): """ Mutable chemical representation of a molecule, such as a small molecule or biopolymer. .. todo :: What other API calls would be useful for supporting biopolymers as small molecules? Perhaps iterating over chains and residues? Examples -------- Create a molecule from an sdf file >>> from openforcefield.utils import get_data_file_path >>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf') >>> molecule = Molecule(sdf_filepath) Convert to OpenEye OEMol object >>> oemol = molecule.to_openeye() Create a molecule from an OpenEye molecule >>> molecule = Molecule.from_openeye(oemol) Convert to RDKit Mol object >>> rdmol = molecule.to_rdkit() Create a molecule from an RDKit molecule >>> molecule = Molecule.from_rdkit(rdmol) Create a molecule from IUPAC name (requires the OpenEye toolkit) >>> molecule = Molecule.from_iupac('imatinib') Create a molecule from SMILES >>> molecule = Molecule.from_smiles('Cc1ccccc1') .. warning :: This API is experimental and subject to change. """
[docs] def __init__(self, *args, **kwargs): """ Create a new Molecule object Parameters ---------- other : optional, default=None If specified, attempt to construct a copy of the Molecule from the specified object. This can be any one of the following: * a :class:`Molecule` object * a file that can be used to construct a :class:`Molecule` object * an ``openeye.oechem.OEMol`` * an ``rdkit.Chem.rdchem.Mol`` * a serialized :class:`Molecule` object Examples -------- Create an empty molecule: >>> empty_molecule = Molecule() Create a molecule from a file that can be used to construct a molecule, using either a filename or file-like object: >>> from openforcefield.utils import get_data_file_path >>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf') >>> molecule = Molecule(sdf_filepath) >>> molecule = Molecule(open(sdf_filepath, 'r'), file_format='sdf') >>> import gzip >>> mol2_gz_filepath = get_data_file_path('molecules/toluene.mol2.gz') >>> molecule = Molecule(gzip.GzipFile(mol2_gz_filepath, 'r'), file_format='mol2') Create a molecule from another molecule: >>> molecule_copy = Molecule(molecule) Convert to OpenEye OEMol object >>> oemol = molecule.to_openeye() Create a molecule from an OpenEye molecule: >>> molecule = Molecule(oemol) Convert to RDKit Mol object >>> rdmol = molecule.to_rdkit() Create a molecule from an RDKit molecule: >>> molecule = Molecule(rdmol) Create a molecule from a serialized molecule object: >>> serialized_molecule = molecule.__getstate__() >>> molecule_copy = Molecule(serialized_molecule) .. todo :: * If a filename or file-like object is specified but the file contains more than one molecule, what is the proper behavior? Read just the first molecule, or raise an exception if more than one molecule is found? * Should we also support SMILES strings or IUPAC names for ``other``? """ #super(self, Molecule).__init__(*args, **kwargs) super(Molecule, self).__init__(*args, **kwargs)
# TODO: Change this to add_atom(Atom) to improve encapsulation and extensibility?
[docs] def add_atom(self, atomic_number, formal_charge, is_aromatic, stereochemistry=None, name=None): """ Add an atom Parameters ---------- atomic_number : int Atomic number of the atom formal_charge : int Formal charge of the atom is_aromatic : bool If True, atom is aromatic; if False, not aromatic stereochemistry : str, optional, default=None Either 'R' or 'S' for specified stereochemistry, or None if stereochemistry is irrelevant name : str, optional, default=None An optional name for the atom Returns ------- index : int The index of the atom in the molecule Examples -------- Define a methane molecule >>> molecule = Molecule() >>> molecule.name = 'methane' >>> C = molecule.add_atom(6, 0, False) >>> H1 = molecule.add_atom(1, 0, False) >>> H2 = molecule.add_atom(1, 0, False) >>> H3 = molecule.add_atom(1, 0, False) >>> H4 = molecule.add_atom(1, 0, False) >>> bond_idx = molecule.add_bond(C, H1, False, 1) >>> bond_idx = molecule.add_bond(C, H2, False, 1) >>> bond_idx = molecule.add_bond(C, H3, False, 1) >>> bond_idx = molecule.add_bond(C, H4, False, 1) """ atom_index = self._add_atom( atomic_number, formal_charge, is_aromatic, stereochemistry=stereochemistry, name=name) return atom_index
[docs] def add_bond_charge_virtual_site(self, atoms, distance, charge_increments=None, weights=None, epsilon=None, sigma=None, rmin_half=None, name=''): """ Create a bond charge-type virtual site, in which the location of the charge is specified by the position of two atoms. This supports placement of a virtual site S along a vector between two specified atoms, e.g. to allow for a sigma hole for halogens or similar contexts. With positive values of the distance, the virtual site lies outside the first indexed atom. Parameters ---------- atoms : list of openforcefield.topology.molecule.Atom objects or ints of shape [N The atoms defining the virtual site's position or their indices distance : float weights : list of floats of shape [N] or None, optional, default=None weights[index] is the weight of particles[index] contributing to the position of the virtual site. Default is None charge_increments : list of floats of shape [N], optional, default=None The amount of charge to remove from the VirtualSite's atoms and put in the VirtualSite. Indexing in this list should match the ordering in the atoms list. Default is None. epsilon : float Epsilon term for VdW properties of virtual site. Default is None. sigma : float, default=None Sigma term for VdW properties of virtual site. Default is None. rmin_half : float Rmin_half term for VdW properties of virtual site. Default is None. name : string or None, default='' The name of this virtual site. Default is ''. Returns ------- index : int The index of the newly-added virtual site in the molecule """ vsite_index = self._add_bond_charge_virtual_site( atoms, distance, weights=weights, charge_increments=charge_increments, epsilon=epsilon, sigma=sigma, rmin_half=rmin_half, name=name) return vsite_index
[docs] def add_monovalent_lone_pair_virtual_site(self, atoms, distance, out_of_plane_angle, in_plane_angle, **kwargs): """ Create a bond charge-type virtual site, in which the location of the charge is specified by the position of three atoms. TODO : Do "weights" have any meaning here? Parameters ---------- atoms : list of three openforcefield.topology.molecule.Atom objects or ints The three atoms defining the virtual site's position or their molecule atom indices distance : float out_of_plane_angle : float in_plane_angle : float epsilon : float Epsilon term for VdW properties of virtual site. Default is None. sigma : float, default=None Sigma term for VdW properties of virtual site. Default is None. rmin_half : float Rmin_half term for VdW properties of virtual site. Default is None. name : string or None, default='' The name of this virtual site. Default is ''. Returns ------- index : int The index of the newly-added virtual site in the molecule """ #vsite_index = self._add_monovalent_lone_pair_virtual_site(self, atoms, distance, out_of_plane_angle, in_plane_angle, charge_increments=charge_increments, weights=weights, epsilon=epsilon, sigma=sigma, rmin_half=rmin_half, name=name) vsite_index = self._add_monovalent_lone_pair_virtual_site( atoms, distance, out_of_plane_angle, in_plane_angle, **kwargs) return vsite_index
#def add_divalent_lone_pair_virtual_site(self, atoms, distance, out_of_plane_angle, in_plane_angle, charge_increments=None, weights=None, epsilon=None, sigma=None, rmin_half=None, name=None):
[docs] def add_divalent_lone_pair_virtual_site(self, atoms, distance, out_of_plane_angle, in_plane_angle, **kwargs): """ Create a divalent lone pair-type virtual site, in which the location of the charge is specified by the position of three atoms. TODO : Do "weights" have any meaning here? Parameters ---------- atoms : list of 3 openforcefield.topology.molecule.Atom objects or ints The three atoms defining the virtual site's position or their molecule atom indices distance : float out_of_plane_angle : float in_plane_angle : float epsilon : float Epsilon term for VdW properties of virtual site. Default is None. sigma : float, default=None Sigma term for VdW properties of virtual site. Default is None. rmin_half : float Rmin_half term for VdW properties of virtual site. Default is None. name : string or None, default='' The name of this virtual site. Default is ''. Returns ------- index : int The index of the newly-added virtual site in the molecule """ #vsite_index = self._add_divalent_lone_pair_virtual_site(self, atoms, distance, out_of_plane_angle, in_plane_angle, charge_increments=charge_increments, weights=weights, epsilon=epsilon, sigma=sigma, rmin_half=rmin_half, name=name) vsite_index = self._add_divalent_lone_pair_virtual_site( atoms, distance, out_of_plane_angle, in_plane_angle, **kwargs) return vsite_index
[docs] def add_trivalent_lone_pair_virtual_site(self, atoms, distance, out_of_plane_angle, in_plane_angle, **kwargs): """ Create a trivalent lone pair-type virtual site, in which the location of the charge is specified by the position of four atoms. TODO : Do "weights" have any meaning here? Parameters ---------- atoms : list of 4 openforcefield.topology.molecule.Atom objects or ints The three atoms defining the virtual site's position or their molecule atom indices distance : float out_of_plane_angle : float in_plane_angle : float epsilon : float Epsilon term for VdW properties of virtual site. Default is None. sigma : float, default=None Sigma term for VdW properties of virtual site. Default is None. rmin_half : float Rmin_half term for VdW properties of virtual site. Default is None. name : string or None, default='' The name of this virtual site. Default is ''. Returns ------- index : int The index of the newly-added virtual site in the molecule """ vsite_index = self._add_trivalent_lone_pair_virtual_site( atoms, distance, out_of_plane_angle, in_plane_angle, **kwargs) return vsite_index
[docs] def add_bond(self, atom1, atom2, bond_order, is_aromatic, stereochemistry=None, fractional_bond_order=None): """ Add a bond between two specified atom indices Parameters ---------- atom1 : int or openforcefield.topology.molecule.Atom Index of first atom atom2 : int or openforcefield.topology.molecule.Atom Index of second atom bond_order : int Integral bond order of Kekulized form is_aromatic : bool True if this bond is aromatic, False otherwise stereochemistry : str, optional, default=None Either 'E' or 'Z' for specified stereochemistry, or None if stereochemistry is irrelevant fractional_bond_order : float, optional, default=None The fractional (eg. Wiberg) bond order Returns ------- index: int Index of the bond in this molecule """ bond_index = self._add_bond( atom1, atom2, bond_order, is_aromatic, stereochemistry=stereochemistry, fractional_bond_order=fractional_bond_order) return bond_index
[docs] def add_conformer(self, coordinates): """ # TODO: Should this not be public? Adds a conformer of the molecule Parameters ---------- coordinates: simtk.unit.Quantity(np.array) with shape (n_atoms, 3) Coordinates of the new conformer, with the first dimension of the array corresponding to the atom index in the Molecule's indexing system. Returns ------- index: int Index of the conformer in the Molecule """ return self._add_conformer(coordinates)