"""Module for working with mBuild Compounds."""
__all__ = ["clone", "Compound", "Particle"]
import itertools
import os
import tempfile
from collections import OrderedDict
from collections.abc import Iterable
from copy import deepcopy
from typing import Sequence
from warnings import warn
import ele
import numpy as np
from ele.element import Element, element_from_name, element_from_symbol
from ele.exceptions import ElementError
from mbuild import conversion
from mbuild.bond_graph import BondGraph
from mbuild.box import Box
from mbuild.coordinate_transform import _rotate, _translate
from mbuild.exceptions import MBuildError
from mbuild.periodic_kdtree import PeriodicKDTree
from mbuild.utils.decorators import experimental_feature
from mbuild.utils.exceptions import RemovedFuncError
from mbuild.utils.io import import_, run_from_ipython
from mbuild.utils.jsutils import overwrite_nglview_default
from mbuild.utils.orderedset import OrderedSet
def clone(existing_compound, clone_of=None, root_container=None):
"""Clone Compound.
A faster alternative to deepcopying. Does not resolve circular dependencies.
This should be safe provided you never try to add the top of a Compound
hierarchy to a sub-Compound.
Parameters
----------
existing_compound : mbuild.Compound
Existing Compound that will be copied
clone_of : dict, optional, default None,
root_container : mb.Compound, optional, default None,
"""
if clone_of is None:
clone_of = dict()
newone = existing_compound._clone(
clone_of=clone_of, root_container=root_container
)
existing_compound._clone_bonds(clone_of=clone_of)
return newone
[docs]class Compound(object):
"""A building block in the mBuild hierarchy.
Compound is the superclass of all composite building blocks in the mBuild
hierarchy. That is, all composite building blocks must inherit from
compound, either directly or indirectly. The design of Compound follows the
Composite design pattern::
@book{DesignPatterns,
author = "Gamma, Erich and Helm, Richard and Johnson, Ralph and
Vlissides, John M.",
title = "Design Patterns",
subtitle = "Elements of Reusable Object-Oriented Software",
year = "1995",
publisher = "Addison-Wesley",
note = "p. 395",
ISBN = "0-201-63361-2",
}
with Compound being the composite, and Particle playing the role of the
primitive (leaf) part, where Particle is in fact simply an alias to the
Compound class.
Compound maintains a list of children (other Compounds contained within),
and provides a means to tag the children with labels, so that the compounds
can be easily looked up later. Labels may also point to objects outside the
Compound's containment hierarchy. Compound has built-in support for copying
and deepcopying Compound hierarchies, enumerating particles or bonds in the
hierarchy, proximity based searches, visualization, I/O operations, and a
number of other convenience methods.
Parameters
----------
subcompounds : mb.Compound or list of mb.Compound, optional, default=None
One or more compounds to be added to self.
name : str, optional, default=self.__class__.__name__
The type of Compound.
pos : np.ndarray, shape=(3,), dtype=float, optional, default=[0, 0, 0]
The position of the Compound in Cartestian space
mass : float, optional, default=0.0
The mass of the compound. If none is set, then will try to
infer the mass from a compound's element attribute.
If neither `mass` or `element` are specified, then the
mass will be zero.
charge : float, optional, default=0.0
Currently not used. Likely removed in next release.
periodicity : tuple of bools, length=3, optional, default=None
Whether the Compound is periodic in the x, y, and z directions.
If None is provided, the periodicity is set to (False, False, False)
which is non-periodic in all directions.
port_particle : bool, optional, default=False
Whether or not this Compound is part of a Port
box : mb.Box, optional
The simulation box containing the compound. Also accounts for the
periodicity. Defaults to None which is treated as non-periodic.
element: str, optional, default=None
The one or two character element symbol
Attributes
----------
bond_graph : mb.BondGraph
Graph-like object that stores bond information for this Compound
children : OrderedSet
Contains all children (other Compounds).
labels : OrderedDict
Labels to Compound/Atom mappings. These do not necessarily need not be
in self.children.
parent : mb.Compound
The parent Compound that contains this part. Can be None if this
compound is the root of the containment hierarchy.
referrers : set
Other compounds that reference this part with labels.
rigid_id : int, default=None
The ID of the rigid body that this Compound belongs to. Only Particles
(the bottom of the containment hierarchy) can have integer values for
`rigid_id`. Compounds containing rigid particles will always have
`rigid_id == None`. See also `contains_rigid`.
boundingbox : mb.Box
The bounds (xmin, xmax, ymin, ymax, zmin, zmax) of particles in Compound
center
contains_rigid
mass
max_rigid_id
n_particles
n_bonds
root
xyz
xyz_with_ports
"""
def __init__(
self,
subcompounds=None,
name=None,
pos=None,
mass=0.0,
charge=0.0,
periodicity=None,
box=None,
element=None,
port_particle=False,
):
super(Compound, self).__init__()
if name:
if not isinstance(name, str):
raise ValueError(
f"Compound.name should be a string. You passed {name}."
)
self.name = name
else:
self.name = self.__class__.__name__
if pos is not None:
self._pos = np.asarray(pos, dtype=float)
else:
self._pos = np.zeros(3)
self.parent = None
self.children = OrderedSet()
self.labels = OrderedDict()
self.referrers = set()
self.bond_graph = None
self.port_particle = port_particle
self._rigid_id = None
self._contains_rigid = False
self._check_if_contains_rigid_bodies = False
self.element = element
if mass and float(mass) < 0.0:
raise ValueError("Cannot set a Compound mass value less than zero")
self._box = box
if periodicity is not None:
self.periodicity = periodicity
else:
self.periodicity = (False, False, False)
# self.add() must be called after labels and children are initialized.
if subcompounds:
if charge:
raise MBuildError(
"Can't set the charge of a Compound with subcompounds."
)
if mass:
raise MBuildError(
"Can't set the mass of a Compound with subcompounds. "
)
self._charge = 0.0
self._mass = mass
self.add(subcompounds)
else:
self._charge = charge
self._mass = mass
[docs] def particles(self, include_ports=False):
"""Return all Particles of the Compound.
Parameters
----------
include_ports : bool, optional, default=False
Include port particles
Yields
------
mb.Compound
The next Particle in the Compound
"""
if not self.children:
yield self
else:
for particle in self._particles(include_ports):
yield particle
def _particles(self, include_ports=False):
"""Return all Particles of the Compound."""
for child in self.successors():
if not child.children:
if include_ports or not child.port_particle:
yield child
[docs] def successors(self):
"""Yield Compounds below self in the hierarchy.
Yields
------
mb.Compound
The next Particle below self in the hierarchy
"""
if not self.children:
return
for part in self.children:
# Parts local to the current Compound.
yield part
# Parts further down the hierarchy.
for subpart in part.successors():
yield subpart
@property
def n_particles(self):
"""Return the number of Particles in the Compound.
Returns
-------
int,
The number of Particles in the Compound
"""
if not self.children:
return 1
else:
return self._n_particles(include_ports=False)
def _n_particles(self, include_ports=False):
"""Return the number of Particles in the Compound."""
return sum(1 for _ in self._particles(include_ports))
def _contains_only_ports(self):
for part in self.children:
if not part.port_particle:
return False
return True
[docs] def ancestors(self):
"""Generate all ancestors of the Compound recursively.
Yields
------
mb.Compound
The next Compound above self in the hierarchy
"""
if self.parent is not None:
yield self.parent
for ancestor in self.parent.ancestors():
yield ancestor
@property
def root(self):
"""Get the Compound at the top of self's hierarchy.
Returns
-------
mb.Compound
The Compound at the top of self's hierarchy
"""
parent = None
for parent in self.ancestors():
pass
if parent is None:
return self
return parent
[docs] def particles_by_name(self, name):
"""Return all Particles of the Compound with a specific name.
Parameters
----------
name : str
Only particles with this name are returned
Yields
------
mb.Compound
The next Particle in the Compound with the user-specified name
"""
for particle in self.particles():
if particle.name == name:
yield particle
[docs] def particles_by_element(self, element):
"""Return all Particles of the Compound with a specific element.
Parameters
----------
name : str or ele.Element
element abbreviation or element
Yields
------
mb.Compound
The next Particle in the Compound with the user-specified element
"""
if not isinstance(element, Element):
element = ele.element_from_symbol(element)
for particle in self.particles():
if particle.element == element:
yield particle
@property
def mass(self):
"""Return the total mass of a compound.
If the compound contains children compouds, the total mass of all
children compounds is returned.
If the compound contains element information (Compound.element) then
the mass is inferred from the elemental mass.
If Compound.mass has been set explicitly, then it will override the
mass inferred from Compound.element.
If neither of a Compound's element or mass attributes have been set,
then a mass of zero is returned.
"""
if self._contains_only_ports():
return self._particle_mass(self)
else:
return sum([self._particle_mass(p) for p in self.particles()])
@staticmethod
def _particle_mass(particle):
if particle._mass:
return particle._mass
else:
if particle.element:
return particle.element.mass
else:
return 0
@mass.setter
def mass(self, value):
if self._contains_only_ports() is False:
raise MBuildError(
"Cannot set the mass of a Compound containing "
"children compounds"
)
value = float(value)
if value < 0.0:
raise ValueError("Cannot set a mass value less than zero")
self._mass = value
@property
def charge(self):
"""Get the charge of the Compound."""
return sum([particle._charge for particle in self.particles()])
@charge.setter
def charge(self, value):
if self._contains_only_ports():
self._charge = value
else:
raise AttributeError(
"charge is immutable for Compounds that are "
"not at the bottom of the containment hierarchy."
)
@property
def rigid_id(self):
"""Get the rigid_id of the Compound."""
return self._rigid_id
@rigid_id.setter
def rigid_id(self, value):
if self._contains_only_ports():
self._rigid_id = value
for ancestor in self.ancestors():
ancestor._check_if_contains_rigid_bodies = True
else:
raise AttributeError(
"rigid_id is immutable for Compounds that are "
"not at the bottom of the containment hierarchy."
)
@property
def contains_rigid(self):
"""Return True if the Compound contains rigid bodies.
If the Compound contains any particle with a rigid_id != None
then contains_rigid will return True. If the Compound has no
children (i.e. the Compound resides at the bottom of the containment
hierarchy) then contains_rigid will return False.
Returns
-------
bool,
True if the Compound contains any particle with a rigid_id != None
Notes
-----
The private variable '_check_if_contains_rigid_bodies' is used to help
cache the status of 'contains_rigid'.
If '_check_if_contains_rigid_bodies' is False, then the rigid body
containment of the Compound has not changed, and the particle tree is
not traversed, boosting performance.
"""
if self._check_if_contains_rigid_bodies:
self._check_if_contains_rigid_bodies = False
if any(p.rigid_id is not None for p in self._particles()):
self._contains_rigid = True
else:
self._contains_rigid = False
return self._contains_rigid
@property
def max_rigid_id(self):
"""Return the maximum rigid body ID contained in the Compound.
This is usually used by compound.root to determine the maximum
rigid_id in the containment hierarchy.
Returns
-------
int or None
The maximum rigid body ID contained in the Compound. If no
rigid body IDs are found, None is returned
"""
try:
return max(
[p.rigid_id for p in self.particles() if p.rigid_id is not None]
)
except ValueError:
return
[docs] def rigid_particles(self, rigid_id=None):
"""Generate all particles in rigid bodies.
If a rigid_id is specified, then this function will only yield particles
with a matching rigid_id.
Parameters
----------
rigid_id : int, optional
Include only particles with this rigid body ID
Yields
------
mb.Compound
The next particle with a rigid_id that is not None, or the next
particle with a matching rigid_id if specified
"""
for particle in self.particles():
if rigid_id is not None:
if particle.rigid_id == rigid_id:
yield particle
else:
if particle.rigid_id is not None:
yield particle
[docs] def label_rigid_bodies(self, discrete_bodies=None, rigid_particles=None):
"""Designate which Compounds should be treated as rigid bodies.
If no arguments are provided, this function will treat the compound
as a single rigid body by providing all particles in `self` with the
same rigid_id. If `discrete_bodies` is not None, each instance of
a Compound with a name found in `discrete_bodies` will be treated as a
unique rigid body. If `rigid_particles` is not None, only Particles
(Compounds at the bottom of the containment hierarchy) matching this
name will be considered part of the rigid body.
Parameters
----------
discrete_bodies : str or list of str, optional, default=None
Name(s) of Compound instances to be treated as unique rigid bodies.
Compound instances matching this (these) name(s) will be provided
with unique rigid_ids
rigid_particles : str or list of str, optional, default=None
Name(s) of Compound instances at the bottom of the containment
hierarchy (Particles) to be included in rigid bodies. Only Particles
matching this (these) name(s) will have their rigid_ids altered to
match the rigid body number.
Examples
--------
Creating a rigid benzene
>>> import mbuild as mb
>>> from mbuild.utils.io import get_fn
>>> benzene = mb.load(get_fn('benzene.mol2'))
>>> benzene.label_rigid_bodies()
Creating a semi-rigid benzene, where only the carbons are treated as
a rigid body
>>> import mbuild as mb
>>> from mbuild.utils.io import get_fn
>>> benzene = mb.load(get_fn('benzene.mol2'))
>>> benzene.label_rigid_bodies(rigid_particles='C')
Create a box of rigid benzenes, where each benzene has a unique rigid
body ID.
>>> import mbuild as mb
>>> from mbuild.utils.io import get_fn
>>> benzene = mb.load(get_fn('benzene.mol2'))
>>> benzene.name = 'Benzene'
>>> filled = mb.fill_box(benzene,
... n_compounds=10,
... box=[0, 0, 0, 4, 4, 4])
>>> filled.label_rigid_bodies(distinct_bodies='Benzene')
Create a box of semi-rigid benzenes, where each benzene has a unique
rigid body ID and only the carbon portion is treated as rigid.
>>> import mbuild as mb
>>> from mbuild.utils.io import get_fn
>>> benzene = mb.load(get_fn('benzene.mol2'))
>>> benzene.name = 'Benzene'
>>> filled = mb.fill_box(benzene,
... n_compounds=10,
... box=[0, 0, 0, 4, 4, 4])
>>> filled.label_rigid_bodies(distinct_bodies='Benzene',
... rigid_particles='C')
"""
if discrete_bodies is not None:
if isinstance(discrete_bodies, str):
discrete_bodies = [discrete_bodies]
if rigid_particles is not None:
if isinstance(rigid_particles, str):
rigid_particles = [rigid_particles]
if self.root.max_rigid_id is not None:
rigid_id = self.root.max_rigid_id + 1
warn(
"{} rigid bodies already exist. Incrementing 'rigid_id'"
"starting from {}.".format(rigid_id, rigid_id)
)
else:
rigid_id = 0
for successor in self.successors():
if discrete_bodies and successor.name not in discrete_bodies:
continue
for particle in successor.particles():
if rigid_particles and particle.name not in rigid_particles:
continue
particle.rigid_id = rigid_id
if discrete_bodies:
rigid_id += 1
[docs] def unlabel_rigid_bodies(self):
"""Remove all rigid body labels from the Compound."""
self._check_if_contains_rigid_bodies = True
for child in self.children:
child._check_if_contains_rigid_bodies = True
for particle in self.particles():
particle.rigid_id = None
def _increment_rigid_ids(self, increment):
"""Increment the rigid_id of all rigid Particles in a Compound.
Adds `increment` to the rigid_id of all Particles in `self` that
already have an integer rigid_id.
"""
for particle in self.particles():
if particle.rigid_id is not None:
particle.rigid_id += increment
def _reorder_rigid_ids(self):
"""Reorder rigid body IDs ensuring consecutiveness.
Primarily used internally to ensure consecutive rigid_ids following
removal of a Compound.
"""
max_rigid = self.max_rigid_id
unique_rigid_ids = sorted(
set([p.rigid_id for p in self.rigid_particles()])
)
n_unique_rigid = len(unique_rigid_ids)
if max_rigid and n_unique_rigid != max_rigid + 1:
missing_rigid_id = (
unique_rigid_ids[-1] * (unique_rigid_ids[-1] + 1)
) / 2 - sum(unique_rigid_ids)
for successor in self.successors():
if successor.rigid_id is not None:
if successor.rigid_id > missing_rigid_id:
successor.rigid_id -= 1
if self.rigid_id:
if self.rigid_id > missing_rigid_id:
self.rigid_id -= 1
[docs] def add(
self,
new_child,
label=None,
containment=True,
replace=False,
inherit_periodicity=None,
inherit_box=False,
reset_rigid_ids=True,
):
"""Add a part to the Compound.
Note:
This does not necessarily add the part to self.children but may
instead be used to add a reference to the part to self.labels. See
'containment' argument.
Parameters
----------
new_child : mb.Compound or list-like of mb.Compound
The object(s) to be added to this Compound.
label : str, optional, default None
A descriptive string for the part.
containment : bool, optional, default=True
Add the part to self.children.
replace : bool, optional, default=True
Replace the label if it already exists.
inherit_periodicity : bool, optional, default=True
Replace the periodicity of self with the periodicity of the
Compound being added
inherit_box: bool, optional, default=False
Replace the box of self with the box of the Compound being added
reset_rigid_ids : bool, optional, default=True
If the Compound to be added contains rigid bodies, reset the
rigid_ids such that values remain distinct from rigid_ids
already present in `self`. Can be set to False if attempting
to add Compounds to an existing rigid body.
"""
# Support batch add via lists, tuples and sets.
from mbuild.port import Port
if isinstance(new_child, Iterable) and not isinstance(new_child, str):
for child in new_child:
self.add(child, reset_rigid_ids=reset_rigid_ids)
return
if not isinstance(new_child, Compound):
raise ValueError(
"Only objects that inherit from mbuild.Compound can be added "
f"to Compounds. You tried to add '{new_child}'."
)
if self._mass != 0.0 and not isinstance(new_child, Port):
warn(
f"{self} has a pre-defined mass of {self._mass}, "
"which will be reset to zero now that it contains children "
"compounds."
)
self._mass = 0
if new_child.contains_rigid or new_child.rigid_id is not None:
if self.contains_rigid and reset_rigid_ids:
new_child._increment_rigid_ids(increment=self.max_rigid_id + 1)
self._check_if_contains_rigid_bodies = True
if self.rigid_id is not None:
self.rigid_id = None
# Create children and labels on the first add operation
if self.children is None:
self.children = OrderedSet()
if self.labels is None:
self.labels = OrderedDict()
if containment:
if new_child.parent is not None:
raise MBuildError(
"Part {} already has a parent: {}".format(
new_child, new_child.parent
)
)
self.children.add(new_child)
new_child.parent = self
if new_child.bond_graph is not None:
if self.root.bond_graph is None:
self.root.bond_graph = new_child.bond_graph
else:
self.root.bond_graph.compose(new_child.bond_graph)
new_child.bond_graph = None
# Add new_part to labels. Does not currently support batch add.
if label is None:
label = "{0}[$]".format(new_child.__class__.__name__)
if label.endswith("[$]"):
label = label[:-3]
if label not in self.labels:
self.labels[label] = []
label_pattern = label + "[{}]"
count = len(self.labels[label])
self.labels[label].append(new_child)
label = label_pattern.format(count)
if not replace and label in self.labels:
raise MBuildError(f'Label "{label}" already exists in {self}.')
else:
self.labels[label] = new_child
new_child.referrers.add(self)
if inherit_periodicity and isinstance(new_child, Compound):
self.periodicity = new_child.periodicity
# If parent has no box --> inherit child box
# If parent has box --> keep unless inherit_box == True
# If inherit_box == True, parent box != None, child_box == None,
# keep parent box anyway and warn
if self.box is None:
if new_child.box is not None:
self.box = new_child.box
else:
if inherit_box:
if new_child.box is None:
warn(
"The Compound you are adding has no box but "
"inherit_box=True. The box of the original "
"Compound will remain unchanged."
)
else:
self.box = new_child.box
else:
if new_child.box is not None:
warn(
"The Compound you are adding has a box. "
"The box of the parent compound will be used. Use "
"inherit_box = True if you wish to replace the parent "
"compound box with that of Compound being added."
)
# Check that bounding box is within box after adding compound
if self.box:
if (
np.array(self.box.lengths)
< np.array(self.get_boundingbox().lengths)
).any():
warn(
"After adding new Compound, Compound.box.lengths < "
"Compound.boundingbox.lengths. There may be particles "
"outside of the defined simulation box"
)
[docs] def remove(self, objs_to_remove):
"""Remove children from the Compound cleanly.
Parameters
----------
objs_to_remove : mb.Compound or list of mb.Compound
The Compound(s) to be removed from self
"""
# Preprocessing and validating input type
from mbuild.port import Port
if not hasattr(objs_to_remove, "__iter__"):
objs_to_remove = [objs_to_remove]
objs_to_remove = set(objs_to_remove)
# If nothing is to be remove, do nothing
if len(objs_to_remove) == 0:
return
# Remove Port objects separately
ports_removed = set()
for obj in objs_to_remove:
if isinstance(obj, Port):
ports_removed.add(obj)
self._remove(obj)
obj.parent.children.remove(obj)
self._remove_references(obj)
objs_to_remove = objs_to_remove - ports_removed
# Get particles to remove
particles_to_remove = set(
[particle for obj in objs_to_remove for particle in obj.particles()]
)
# Recursively get container compounds to remove
to_remove = list()
def _check_if_empty(child):
if child in to_remove:
return
if set(child.particles()).issubset(particles_to_remove):
if child.parent:
to_remove.append(child)
_check_if_empty(child.parent)
else:
warn(f"This will remove all particles in {self}")
return
for particle in particles_to_remove:
_check_if_empty(particle)
# Fix rigid_ids and remove obj from bondgraph
for removed_part in to_remove:
self._remove(removed_part)
# Remove references to object
for removed_part in to_remove:
if removed_part.parent is not None:
removed_part.parent.children.remove(removed_part)
self._remove_references(removed_part)
# Remove ghost ports
all_ports_list = list(self.all_ports())
for port in all_ports_list:
if port.anchor not in [i for i in self.particles()]:
port.parent.children.remove(port)
# Check and reorder rigid id
for _ in particles_to_remove:
if self.contains_rigid:
self.root._reorder_rigid_ids()
def _remove(self, removed_part):
"""Worker for remove(). Fixes rigid IDs and removes bonds."""
if removed_part.rigid_id is not None:
for ancestor in removed_part.ancestors():
ancestor._check_if_contains_rigid_bodies = True
if self.root.bond_graph and self.root.bond_graph.has_node(removed_part):
for neighbor in self.root.bond_graph.neighbors(removed_part):
self.root.remove_bond((removed_part, neighbor))
self.root.bond_graph.remove_node(removed_part)
def _remove_references(self, removed_part):
"""Remove labels pointing to this part and vice versa."""
removed_part.parent = None
# Remove labels in the hierarchy pointing to this part.
referrers_to_remove = set()
for referrer in removed_part.referrers:
if removed_part not in referrer.ancestors():
for label, referred_part in list(referrer.labels.items()):
if referred_part is removed_part:
del referrer.labels[label]
referrers_to_remove.add(referrer)
removed_part.referrers -= referrers_to_remove
# Remove labels in this part pointing into the hierarchy.
labels_to_delete = []
if isinstance(removed_part, Compound):
for label, part in list(removed_part.labels.items()):
if not isinstance(part, Compound):
for p in part:
self._remove_references(p)
elif removed_part not in part.ancestors():
try:
part.referrers.discard(removed_part)
except KeyError:
pass
else:
labels_to_delete.append(label)
for label in labels_to_delete:
removed_part.labels.pop(label, None)
[docs] def referenced_ports(self):
"""Return all Ports referenced by this Compound.
Returns
-------
list of mb.Compound
A list of all ports referenced by the Compound
"""
from mbuild.port import Port
return [port for port in self.labels.values() if isinstance(port, Port)]
[docs] def all_ports(self):
"""Return all Ports referenced by this Compound and its successors.
Returns
-------
list of mb.Compound
A list of all Ports referenced by this Compound and its successors
"""
from mbuild.port import Port
return [s for s in self.successors() if isinstance(s, Port)]
[docs] def available_ports(self):
"""Return all unoccupied Ports referenced by this Compound.
Returns
-------
list of mb.Compound
A list of all unoccupied ports referenced by the Compound
"""
from mbuild.port import Port
return [
p
for p in self.labels.values()
if isinstance(p, Port) and not p.used
]
[docs] def bonds(self):
"""Return all bonds in the Compound and sub-Compounds.
Yields
------
tuple of mb.Compound
The next bond in the Compound
See Also
--------
bond_graph.edges_iter : Iterates over all edges in a BondGraph
"""
if self.root.bond_graph:
if self.root == self:
return self.root.bond_graph.edges_iter()
else:
return self.root.bond_graph.subgraph(
self.particles()
).edges_iter()
else:
return iter(())
@property
def n_bonds(self):
"""Return the number of bonds in the Compound.
Returns
-------
int
The number of bonds in the Compound
"""
return sum(1 for _ in self.bonds())
[docs] def add_bond(self, particle_pair):
"""Add a bond between two Particles.
Parameters
----------
particle_pair : indexable object, length=2, dtype=mb.Compound
The pair of Particles to add a bond between
"""
if self.root.bond_graph is None:
self.root.bond_graph = BondGraph()
self.root.bond_graph.add_edge(particle_pair[0], particle_pair[1])
[docs] def generate_bonds(self, name_a, name_b, dmin, dmax):
"""Add Bonds between all pairs of types a/b within [dmin, dmax].
Parameters
----------
name_a : str
The name of one of the Particles to be in each bond
name_b : str
The name of the other Particle to be in each bond
dmin : float
The minimum distance (in nm) between Particles for considering a bond
dmax : float
The maximum distance (in nm) between Particles for considering a bond
"""
if self.box is None:
self.box = self.get_boundingbox()
particle_kdtree = PeriodicKDTree.from_compound(
compound=self, leafsize=10
)
particle_array = np.array(list(self.particles()))
added_bonds = list()
for p1 in self.particles_by_name(name_a):
nearest = self.particles_in_range(
p1,
dmax,
max_particles=20,
particle_kdtree=particle_kdtree,
particle_array=particle_array,
)
for p2 in nearest:
if p2 == p1:
continue
bond_tuple = (p1, p2) if id(p1) < id(p2) else (p2, p1)
if bond_tuple in added_bonds:
continue
min_dist = self.min_periodic_distance(p2.pos, p1.pos)
if (p2.name == name_b) and (dmin <= min_dist <= dmax):
self.add_bond((p1, p2))
added_bonds.append(bond_tuple)
[docs] @experimental_feature()
def freud_generate_bonds(
self,
name_a,
name_b,
dmin,
dmax,
exclude_ii=True,
):
"""Add Bonds between all pairs of types a/b within [dmin, dmax].
Parameters
----------
name_a : str
The name of one of the Particles to be in each bond
name_b : str
The name of the other Particle to be in each bond
dmin : float
The minimum distance (in nm) between Particles for considering a bond
dmax : float
The maximum distance (in nm) between Particles for considering a bond
exclude_ii : bool, optional, default=True
Whether or not to include neighbors with the same index.
Notes
-----
This is an experimental feature and some behavior might change out of step of a standard development release.
"""
freud = import_("freud")
if self.box is None:
box = self.get_boundingbox()
else:
box = self.box
moved_positions = self.xyz - np.array(
[box.Lx / 2, box.Ly / 2, box.Lz / 2]
)
# quadruple box lengths for non-periodic dimensions
# since freud boxes are centered at the origin, extend box
# lengths 2x in the positive and negative direction
# we are periodic in all directions, no need to change anything
if all(self.periodicity):
freud_box = freud.box.Box.from_matrix(box.vectors.T)
# not periodic in some dimensions, lets make them pseudo-periodic
else:
tmp_lengths = [l for l in box.lengths]
max_tmp_length = max(tmp_lengths)
for i, is_periodic in enumerate(self.periodicity):
if is_periodic:
continue
else:
tmp_lengths[i] = tmp_lengths[i] + 4 * max_tmp_length
tmp_box = Box.from_lengths_angles(
lengths=tmp_lengths, angles=box.angles
)
freud_box = freud.box.Box.from_matrix(tmp_box.vectors.T)
freud_box.periodic = (True, True, True)
a_indices = []
b_indices = []
for i, part in enumerate(self.particles()):
if part.name == name_a:
a_indices.append(i)
if part.name == name_b:
b_indices.append(i)
aq = freud.locality.AABBQuery(freud_box, moved_positions[b_indices])
nlist = aq.query(
moved_positions[a_indices],
dict(
r_min=dmin,
r_max=dmax,
exclude_ii=exclude_ii,
),
).toNeighborList()
part_list = [part for part in self.particles(include_ports=False)]
for i, j in nlist[:]:
self.add_bond((part_list[a_indices[i]], part_list[b_indices[j]]))
[docs] def remove_bond(self, particle_pair):
"""Delete a bond between a pair of Particles.
Parameters
----------
particle_pair : indexable object, length=2, dtype=mb.Compound
The pair of Particles to remove the bond between
"""
from mbuild.port import Port
if self.root.bond_graph is None or not self.root.bond_graph.has_edge(
*particle_pair
):
warn("Bond between {} and {} doesn't exist!".format(*particle_pair))
return
self.root.bond_graph.remove_edge(*particle_pair)
bond_vector = particle_pair[0].pos - particle_pair[1].pos
if np.allclose(bond_vector, np.zeros(3)):
warn(
"Particles {} and {} overlap! Ports will not be added."
"".format(*particle_pair)
)
return
distance = np.linalg.norm(bond_vector)
particle_pair[0].parent.add(
Port(
anchor=particle_pair[0],
orientation=-bond_vector,
separation=distance / 2,
),
"port[$]",
)
particle_pair[1].parent.add(
Port(
anchor=particle_pair[1],
orientation=bond_vector,
separation=distance / 2,
),
"port[$]",
)
@property
def pos(self):
"""Get the position of the Compound.
If the Compound contains children, returns the center.
The position of a Compound containing children can't be set.
"""
if not self.children:
return self._pos
else:
return self.center
@pos.setter
def pos(self, value):
if not self.children:
self._pos = value
else:
raise MBuildError("Can't set position of Compound with children.")
@property
def periodicity(self):
"""Get the periodicity of the Compound."""
return self._periodicity
@periodicity.setter
def periodicity(self, periods):
if len(list(periods)) != 3:
raise ValueError("Periodicity must be of length 3")
if not all([isinstance(p, bool) for p in periods]):
raise TypeError(
"Periodicity values must be True/False; if you are trying to "
"set the dimensions, use Compound.box."
)
self._periodicity = tuple(periods)
@property
def box(self):
"""Get the box of the Compound.
Ports cannot have a box.
"""
return self._box
@box.setter
def box(self, box):
if box is not None and type(box) != Box:
raise TypeError("box must be specified as an mbuild.Box")
if self.port_particle and box is not None:
raise ValueError("Ports cannot have a box")
# Make sure the box is bigger than the bounding box
if box is not None:
if np.asarray((box.lengths < self.get_boundingbox().lengths)).any():
warn(
"Compound.box.lengths < Compound.boundingbox.lengths. "
"There may be particles outside of the defined "
"simulation box."
)
self._box = box
@property
def element(self):
"""Get the element of the Compound."""
return self._element
@element.setter
def element(self, element):
if element is None:
self._element = None
elif isinstance(element, Element):
self._element = element
else:
self._element = ele.element_from_symbol(element)
@property
def xyz(self):
"""Return all particle coordinates in this compound.
Returns
-------
pos : np.ndarray, shape=(n, 3), dtype=float
Array with the positions of all particles.
"""
if not self.children:
pos = np.expand_dims(self._pos, axis=0)
else:
arr = np.fromiter(
itertools.chain.from_iterable(p.pos for p in self.particles()),
dtype=float,
)
pos = arr.reshape((-1, 3))
return pos
@property
def xyz_with_ports(self):
"""Return all particle coordinates in this compound including ports.
Returns
-------
pos : np.ndarray, shape=(n, 3), dtype=float
Array with the positions of all particles and ports.
"""
if not self.children:
pos = self._pos
else:
arr = np.fromiter(
itertools.chain.from_iterable(
p.pos for p in self.particles(include_ports=True)
),
dtype=float,
)
pos = arr.reshape((-1, 3))
return pos
@xyz.setter
def xyz(self, arrnx3):
"""Set the positions of the particles in the Compound, excluding Ports.
This function does not set the position of the ports.
Parameters
----------
arrnx3 : np.ndarray, shape=(n,3), dtype=float
The new particle positions
"""
arrnx3 = np.array(arrnx3)
if not self.children:
if not arrnx3.shape[0] == 1:
raise ValueError(
"Trying to set position of {} with more than one"
"coordinate: {}".format(self, arrnx3)
)
self.pos = np.squeeze(arrnx3)
else:
for atom, coords in zip(
self._particles(include_ports=False), arrnx3
):
atom.pos = coords
@xyz_with_ports.setter
def xyz_with_ports(self, arrnx3):
"""Set the positions of the particles in the Compound, including Ports.
Parameters
----------
arrnx3 : np.ndarray, shape=(n,3), dtype=float
The new particle positions
"""
if not self.children:
if not arrnx3.shape[0] == 1:
raise ValueError(
"Trying to set position of {} with more than one"
"coordinate: {}".format(self, arrnx3)
)
self.pos = np.squeeze(arrnx3)
else:
for atom, coords in zip(
self._particles(include_ports=True), arrnx3
):
atom.pos = coords
@property
def center(self):
"""Get the cartesian center of the Compound based on its Particles.
Returns
-------
np.ndarray, shape=(3,), dtype=float
The cartesian center of the Compound based on its Particles
"""
if np.all(np.isfinite(self.xyz)):
return np.mean(self.xyz, axis=0)
@property
def mins(self):
"""Return the mimimum x, y, z coordinate of any particle in this compound."""
return self.xyz.min(axis=0)
@property
def maxs(self):
"""Return the maximum x, y, z coordinate of any particle in this compound."""
return self.xyz.max(axis=0)
[docs] def get_boundingbox(self, pad_box=None):
"""Compute the bounding box of the compound.
Compute and store the rectangular bounding box of the Compound.
Parameters
----------
pad_box: Sequence, optional, default=None
Pad all lengths or a list of lengths by a specified amount in nm.
Acceptable values are:
- A single float: apply this pad value to all 3 box lengths.
- A sequence of length 1: apply this pad value to all 3 box lengths.
- A sequence of length 3: apply these pad values to the a, b, c box lengths.
Returns
-------
mb.Box
The bounding box for this Compound.
Notes
-----
Triclinic bounding boxes are supported, but only for Compounds
that are generated from mb.Lattice's and the resulting
mb.Lattice.populate method
"""
# case where only 1 particle exists
is_one_particle = False
if self.xyz.shape[0] == 1:
is_one_particle = True
# are any columns all equalivalent values?
# an example of this would be a planar molecule
# example: all z values are 0.0
# from: https://stackoverflow.com/a/14860884
# steps: create mask array comparing first value in each column
# use np.all with axis=0 to do row columnar comparision
has_dimension = [True, True, True]
if not is_one_particle:
missing_dimensions = np.all(
np.isclose(self.xyz, self.xyz[0, :]), axis=0
)
for i, truthy in enumerate(missing_dimensions):
has_dimension[i] = not truthy
if is_one_particle:
v1 = np.asarray([[1.0, 0.0, 0.0]])
v2 = np.asarray([[0.0, 1.0, 0.0]])
v3 = np.asarray([[0.0, 0.0, 1.0]])
else:
v1 = np.asarray((self.maxs[0] - self.mins[0], 0.0, 0.0))
v2 = np.asarray((0.0, self.maxs[1] - self.mins[1], 0.0))
v3 = np.asarray((0.0, 0.0, self.maxs[2] - self.mins[2]))
vecs = [v1, v2, v3]
# handle any missing dimensions (planar molecules)
for i, dim in enumerate(has_dimension):
if not dim:
vecs[i][i] = 1.0
if pad_box is not None:
if isinstance(pad_box, (int, float, str, Sequence)):
if isinstance(pad_box, Sequence):
if len(pad_box) == 1:
padding = [float(pad_box[0])] * 3
elif len(pad_box) == 3:
padding = [float(val) for val in pad_box]
else:
raise TypeError(
f"Expected a Sequence of length 1 or 3 for pad_box. Provided: {len(pad_box)}"
)
else:
pad_box = float(pad_box)
padding = [pad_box] * 3
else:
raise TypeError(
f"Expected a value of type: int, float, str, or Sequence, was provided: {type(pad_box)}"
)
for dim, val in enumerate(padding):
vecs[dim][dim] = vecs[dim][dim] + val
bounding_box = Box.from_vectors(
vectors=np.asarray([vecs]).reshape(3, 3)
)
return bounding_box
[docs] def min_periodic_distance(self, xyz0, xyz1):
"""Vectorized distance calculation considering minimum image.
Only implemented for orthorhombic simulation boxes.
Parameters
----------
xyz0 : np.ndarray, shape=(3,), dtype=float
Coordinates of first point
xyz1 : np.ndarray, shape=(3,), dtype=float
Coordinates of second point
Returns
-------
float
Vectorized distance between the two points following minimum
image convention
"""
d = np.abs(xyz0 - xyz1)
if self.box is not None:
if np.allclose(self.box.angles, 90.0):
d = np.where(
d > 0.5 * np.array(self.box.lengths),
np.array(self.box.lengths) - d,
d,
)
else:
raise NotImplementedError(
"Periodic distance calculation is not implemented "
"for non-orthorhombic boxes"
)
else:
"""
raise MBuildError(f'Cannot calculate minimum periodic distance. '
f'No Box set for {self}')
"""
warn(
f"No Box object set for {self}, using rectangular bounding box"
)
self.box = self.get_boundingbox()
if np.allclose(self.box.angles, 90.0):
d = np.where(
d > 0.5 * np.array(self.box.lengths),
np.array(self.box.lengths) - d,
d,
)
else:
raise NotImplementedError(
"Periodic distance calculation is not implemented "
"for non-orthorhombic boxes"
)
return np.sqrt((d**2).sum(axis=-1))
[docs] def particles_in_range(
self,
compound,
dmax,
max_particles=20,
particle_kdtree=None,
particle_array=None,
):
"""Find particles within a specified range of another particle.
Parameters
----------
compound : mb.Compound
Reference particle to find other particles in range of
dmax : float
Maximum distance from 'compound' to look for Particles
max_particles : int, optional, default=20
Maximum number of Particles to return
particle_kdtree : mb.PeriodicKDTree, optional
KD-tree for looking up nearest neighbors. If not provided, a KD-
tree will be generated from all Particles in self
particle_array : np.ndarray, shape=(n,), dtype=mb.Compound, optional
Array of possible particles to consider for return. If not
provided, this defaults to all Particles in self
Returns
-------
np.ndarray, shape=(n,), dtype=mb.Compound
Particles in range of compound according to user-defined limits
See Also
--------
periodic_kdtree.PerioidicKDTree : mBuild implementation of kd-trees
scipy.spatial.kdtree : Further details on kd-trees
"""
if self.box is None:
self.box = self.get_boundingbox()
if particle_kdtree is None:
particle_kdtree = PeriodicKDTree.from_compound(self, leafsize=10)
_, idxs = particle_kdtree.query(
compound.pos, k=max_particles, distance_upper_bound=dmax
)
idxs = idxs[idxs != self.n_particles]
if particle_array is None:
particle_array = np.array(list(self.particles()))
return particle_array[idxs]
[docs] def visualize(
self, show_ports=False, backend="py3dmol", color_scheme={}
): # pragma: no cover
"""Visualize the Compound using py3dmol (default) or nglview.
Allows for visualization of a Compound within a Jupyter Notebook.
Parameters
----------
show_ports : bool, optional, default=False
Visualize Ports in addition to Particles
backend : str, optional, default='py3dmol'
Specify the backend package to visualize compounds
Currently supported: py3dmol, nglview
color_scheme : dict, optional
Specify coloring for non-elemental particles
keys are strings of the particle names
values are strings of the colors
i.e. {'_CGBEAD': 'blue'}
"""
viz_pkg = {
"nglview": self._visualize_nglview,
"py3dmol": self._visualize_py3dmol,
}
if run_from_ipython():
if backend.lower() in viz_pkg:
return viz_pkg[backend.lower()](
show_ports=show_ports, color_scheme=color_scheme
)
else:
raise RuntimeError(
f"Unsupported visualization backend ({backend}). "
"Currently supported backends include nglview and py3dmol"
)
else:
raise RuntimeError(
"Visualization is only supported in Jupyter Notebooks."
)
def _visualize_py3dmol(self, show_ports=False, color_scheme={}):
"""Visualize the Compound using py3Dmol.
Allows for visualization of a Compound within a Jupyter Notebook.
Parameters
----------
show_ports : bool, optional, default=False
Visualize Ports in addition to Particles
color_scheme : dict, optional
Specify coloring for non-elemental particles
keys are strings of the particle names
values are strings of the colors
i.e. {'_CGBEAD': 'blue'}
Returns
-------
view : py3Dmol.view
"""
py3Dmol = import_("py3Dmol")
cloned = clone(self)
modified_color_scheme = {}
for name, color in color_scheme.items():
# Py3dmol does some element string conversions,
# first character is as-is, rest of the characters are lowercase
new_name = name[0] + name[1:].lower()
modified_color_scheme[new_name] = color
modified_color_scheme[name] = color
for particle in cloned.particles():
if not particle.name:
particle.name = "UNK"
tmp_dir = tempfile.mkdtemp()
cloned.save(
os.path.join(tmp_dir, "tmp.mol2"),
show_ports=show_ports,
overwrite=True,
)
view = py3Dmol.view()
with open(os.path.join(tmp_dir, "tmp.mol2"), "r") as f:
view.addModel(f.read(), "mol2", keepH=True)
view.setStyle(
{
"stick": {"radius": 0.2, "color": "grey"},
"sphere": {"scale": 0.3, "colorscheme": modified_color_scheme},
}
)
view.zoomTo()
return view
def _visualize_nglview(self, show_ports=False, color_scheme={}):
"""Visualize the Compound using nglview.
Allows for visualization of a Compound within a Jupyter Notebook.
Parameters
----------
show_ports : bool, optional, default=False
Visualize Ports in addition to Particles
"""
nglview = import_("nglview")
mdtraj = import_("mdtraj")
from mdtraj.geometry.sasa import _ATOMIC_RADII
remove_digits = lambda x: "".join(
i for i in x if not i.isdigit() or i == "_"
)
for particle in self.particles():
particle.name = remove_digits(particle.name).upper()
if not particle.name:
particle.name = "UNK"
tmp_dir = tempfile.mkdtemp()
self.save(
os.path.join(tmp_dir, "tmp.mol2"),
show_ports=show_ports,
overwrite=True,
)
widget = nglview.show_file(os.path.join(tmp_dir, "tmp.mol2"))
widget.clear()
widget.add_ball_and_stick(cylinderOnly=True)
elements = set([particle.name for particle in self.particles()])
scale = 50.0
for element in elements:
try:
widget.add_ball_and_stick(
f"_{element.upper()}",
aspect_ratio=_ATOMIC_RADII[element.title()] ** 1.5 * scale,
)
except KeyError:
ids = [
str(i)
for i, particle in enumerate(self.particles())
if particle.name == element
]
widget.add_ball_and_stick(
f"@{','.join(ids)}",
aspect_ratio=0.17**1.5 * scale,
color="grey",
)
if show_ports:
widget.add_ball_and_stick("_VS", aspect_ratio=1.0, color="#991f00")
overwrite_nglview_default(widget)
return widget
[docs] def update_coordinates(self, filename, update_port_locations=True):
"""Update the coordinates of this Compound from a file.
Parameters
----------
filename : str
Name of file from which to load coordinates. Supported file types
are the same as those supported by load()
update_port_locations : bool, optional, default=True
Update the locations of Ports so that they are shifted along with
their anchor particles. Note: This conserves the location of
Ports with respect to the anchor Particle, but does not conserve
the orientation of Ports with respect to the molecule as a whole.
See Also
--------
load : Load coordinates from a file
"""
if update_port_locations:
xyz_init = self.xyz
self = conversion.load(filename, compound=self, coords_only=True)
self._update_port_locations(xyz_init)
else:
self = conversion.load(filename, compound=self, coords_only=True)
def _update_port_locations(self, initial_coordinates):
"""Adjust port locations after particles have moved.
Compares the locations of Particles between 'self' and an array of
reference coordinates. Shifts Ports in accordance with how far anchors
have been moved. This conserves the location of Ports with respect to
their anchor Particles, but does not conserve the orientation of Ports
with respect to the molecule as a whole.
Parameters
----------
initial_coordinates : np.ndarray, shape=(n, 3), dtype=float
Reference coordinates to use for comparing how far anchor Particles
have shifted.
"""
particles = list(self.particles())
for port in self.all_ports():
if port.anchor:
idx = particles.index(port.anchor)
shift = particles[idx].pos - initial_coordinates[idx]
port.translate(shift)
def _kick(self):
"""Slightly adjust all coordinates in a Compound.
Provides a slight adjustment to coordinates to kick them out of local
energy minima.
"""
xyz_init = self.xyz
for particle in self.particles():
particle.pos += (np.random.rand(3) - 0.5) / 100
self._update_port_locations(xyz_init)
[docs] def energy_minimize(self, forcefield="UFF", steps=1000, **kwargs):
"""Perform an energy minimization on a Compound.
Default behavior utilizes `Open Babel <http://openbabel.org/docs/dev/>`_
to perform an energy minimization/geometry optimization on a Compound by
applying a generic force field
Can also utilize `OpenMM <http://openmm.org/>`_ to energy minimize after
atomtyping a Compound using
`Foyer <https://github.com/mosdef-hub/foyer>`_ to apply a forcefield XML
file that contains valid SMARTS strings.
This function is primarily intended to be used on smaller components,
with sizes on the order of 10's to 100's of particles, as the energy
minimization scales poorly with the number of particles.
Parameters
----------
steps : int, optional, default=1000
The number of optimization iterations
forcefield : str, optional, default='UFF'
The generic force field to apply to the Compound for minimization.
Valid options are 'MMFF94', 'MMFF94s', ''UFF', 'GAFF', 'Ghemical'.
Please refer to the `Open Babel documentation
<http://open-babel.readthedocs.io/en/latest/Forcefields/Overview.html>`_
when considering your choice of force field.
Utilizing OpenMM for energy minimization requires a forcefield
XML file with valid SMARTS strings. Please refer to `OpenMM docs
<http://docs.openmm.org/7.0.0/userguide/application.html#creating-force-fields>`_
for more information.
Other Parameters
----------------
algorithm : str, optional, default='cg'
The energy minimization algorithm. Valid options are 'steep', 'cg',
and 'md', corresponding to steepest descent, conjugate gradient, and
equilibrium molecular dynamics respectively.
For _energy_minimize_openbabel
scale_bonds : float, optional, default=1
Scales the bond force constant (1 is completely on).
For _energy_minimize_openmm
scale_angles : float, optional, default=1
Scales the angle force constant (1 is completely on)
For _energy_minimize_openmm
scale_torsions : float, optional, default=1
Scales the torsional force constants (1 is completely on)
For _energy_minimize_openmm
Note: Only Ryckaert-Bellemans style torsions are currently supported
scale_nonbonded : float, optional, default=1
Scales epsilon (1 is completely on)
For _energy_minimize_openmm
constraints : str, optional, default="AllBonds"
Specify constraints on the molecule to minimize, options are:
None, "HBonds", "AllBonds", "HAngles"
For _energy_minimize_openmm
References
----------
If using _energy_minimize_openmm(), please cite:
.. [Eastman2013] P. Eastman, M. S. Friedrichs, J. D. Chodera,
R. J. Radmer, C. M. Bruns, J. P. Ku, K. A. Beauchamp, T. J. Lane,
L.-P. Wang, D. Shukla, T. Tye, M. Houston, T. Stich, C. Klein,
M. R. Shirts, and V. S. Pande. "OpenMM 4: A Reusable, Extensible,
Hardware Independent Library for High Performance Molecular
Simulation." J. Chem. Theor. Comput. 9(1): 461-469. (2013).
If using _energy_minimize_openbabel(), please cite:
.. [OBoyle2011] O'Boyle, N.M.; Banck, M.; James, C.A.; Morley, C.;
Vandermeersch, T.; Hutchison, G.R. "Open Babel: An open chemical
toolbox." (2011) J. Cheminf. 3, 33
.. [OpenBabel] Open Babel, version X.X.X http://openbabel.org,
(installed Month Year)
If using the 'MMFF94' force field please also cite the following:
.. [Halgren1996a] T.A. Halgren, "Merck molecular force field. I. Basis,
form, scope, parameterization, and performance of MMFF94." (1996)
J. Comput. Chem. 17, 490-519
.. [Halgren1996b] T.A. Halgren, "Merck molecular force field. II. MMFF94
van der Waals and electrostatic parameters for intermolecular
interactions." (1996) J. Comput. Chem. 17, 520-552
.. [Halgren1996c] T.A. Halgren, "Merck molecular force field. III.
Molecular geometries and vibrational frequencies for MMFF94." (1996)
J. Comput. Chem. 17, 553-586
.. [Halgren1996d] T.A. Halgren and R.B. Nachbar, "Merck molecular force
field. IV. Conformational energies and geometries for MMFF94." (1996)
J. Comput. Chem. 17, 587-615
.. [Halgren1996e] T.A. Halgren, "Merck molecular force field. V.
Extension of MMFF94 using experimental data, additional computational
data, and empirical rules." (1996) J. Comput. Chem. 17, 616-641
If using the 'MMFF94s' force field please cite the above along with:
.. [Halgren1999] T.A. Halgren, "MMFF VI. MMFF94s option for energy minimization
studies." (1999) J. Comput. Chem. 20, 720-729
If using the 'UFF' force field please cite the following:
.. [Rappe1992] Rappe, A.K., Casewit, C.J., Colwell, K.S., Goddard, W.A.
III, Skiff, W.M. "UFF, a full periodic table force field for
molecular mechanics and molecular dynamics simulations." (1992)
J. Am. Chem. Soc. 114, 10024-10039
If using the 'GAFF' force field please cite the following:
.. [Wang2004] Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A.,
Case, D.A. "Development and testing of a general AMBER force field"
(2004) J. Comput. Chem. 25, 1157-1174
If using the 'Ghemical' force field please cite the following:
.. [Hassinen2001] T. Hassinen and M. Perakyla, "New energy terms for
reduced protein models implemented in an off-lattice force field"
(2001) J. Comput. Chem. 22, 1229-1242
"""
tmp_dir = tempfile.mkdtemp()
original = clone(self)
self._kick()
self.save(os.path.join(tmp_dir, "un-minimized.mol2"))
extension = os.path.splitext(forcefield)[-1]
openbabel_ffs = ["MMFF94", "MMFF94s", "UFF", "GAFF", "Ghemical"]
if forcefield in openbabel_ffs:
self._energy_minimize_openbabel(
tmp_dir, forcefield=forcefield, steps=steps, **kwargs
)
elif extension == ".xml":
self._energy_minimize_openmm(
tmp_dir,
forcefield_files=forcefield,
forcefield_name=None,
steps=steps,
**kwargs,
)
else:
self._energy_minimize_openmm(
tmp_dir,
forcefield_files=None,
forcefield_name=forcefield,
steps=steps,
**kwargs,
)
self.update_coordinates(os.path.join(tmp_dir, "minimized.pdb"))
def _energy_minimize_openmm(
self,
tmp_dir,
forcefield_files=None,
forcefield_name=None,
steps=1000,
scale_bonds=1,
scale_angles=1,
scale_torsions=1,
scale_nonbonded=1,
constraints="AllBonds",
):
"""Perform energy minimization using OpenMM.
Converts an mBuild Compound to a ParmEd Structure,
applies a forcefield using Foyer, and creates an OpenMM System.
Parameters
----------
forcefield_files : str or list of str, optional, default=None
Forcefield files to load
forcefield_name : str, optional, default=None
Apply a named forcefield to the output file using the `foyer`
package, e.g. 'oplsaa'. `Foyer forcefields`
<https://github.com/mosdef-hub/foyer/tree/master/foyer/forcefields>_
steps : int, optional, default=1000
Number of energy minimization iterations
scale_bonds : float, optional, default=1
Scales the bond force constant (1 is completely on)
scale_angles : float, optiona, default=1
Scales the angle force constant (1 is completely on)
scale_torsions : float, optional, default=1
Scales the torsional force constants (1 is completely on)
scale_nonbonded : float, optional, default=1
Scales epsilon (1 is completely on)
constraints : str, optional, default="AllBonds"
Specify constraints on the molecule to minimize, options are:
None, "HBonds", "AllBonds", "HAngles"
Notes
-----
Assumes a particular organization for the force groups
(HarmonicBondForce, HarmonicAngleForce, RBTorsionForce, NonBondedForce)
References
----------
[Eastman2013]_
"""
foyer = import_("foyer")
to_parmed = self.to_parmed()
ff = foyer.Forcefield(
forcefield_files=forcefield_files, name=forcefield_name
)
to_parmed = ff.apply(to_parmed)
import openmm.unit as u
from openmm.app import AllBonds, HAngles, HBonds
from openmm.app.pdbreporter import PDBReporter
from openmm.app.simulation import Simulation
from openmm.openmm import LangevinIntegrator
if constraints:
if constraints == "AllBonds":
constraints = AllBonds
elif constraints == "HBonds":
constraints = HBonds
elif constraints == "HAngles":
constraints = HAngles
else:
raise ValueError(
f"Provided constraints value of: {constraints}.\n"
f'Expected "HAngles", "AllBonds" "HBonds".'
)
system = to_parmed.createSystem(
constraints=constraints
) # Create an OpenMM System
else:
system = to_parmed.createSystem() # Create an OpenMM System
# Create a Langenvin Integrator in OpenMM
integrator = LangevinIntegrator(
298 * u.kelvin, 1 / u.picosecond, 0.002 * u.picoseconds
)
# Create Simulation object in OpenMM
simulation = Simulation(to_parmed.topology, system, integrator)
# Loop through forces in OpenMM System and set parameters
for force in system.getForces():
if type(force).__name__ == "HarmonicBondForce":
for bond_index in range(force.getNumBonds()):
atom1, atom2, r0, k = force.getBondParameters(bond_index)
force.setBondParameters(
bond_index, atom1, atom2, r0, k * scale_bonds
)
force.updateParametersInContext(simulation.context)
elif type(force).__name__ == "HarmonicAngleForce":
for angle_index in range(force.getNumAngles()):
atom1, atom2, atom3, r0, k = force.getAngleParameters(
angle_index
)
force.setAngleParameters(
angle_index, atom1, atom2, atom3, r0, k * scale_angles
)
force.updateParametersInContext(simulation.context)
elif type(force).__name__ == "RBTorsionForce":
for torsion_index in range(force.getNumTorsions()):
(
atom1,
atom2,
atom3,
atom4,
c0,
c1,
c2,
c3,
c4,
c5,
) = force.getTorsionParameters(torsion_index)
force.setTorsionParameters(
torsion_index,
atom1,
atom2,
atom3,
atom4,
c0 * scale_torsions,
c1 * scale_torsions,
c2 * scale_torsions,
c3 * scale_torsions,
c4 * scale_torsions,
c5 * scale_torsions,
)
force.updateParametersInContext(simulation.context)
elif type(force).__name__ == "NonbondedForce":
for nb_index in range(force.getNumParticles()):
charge, sigma, epsilon = force.getParticleParameters(
nb_index
)
force.setParticleParameters(
nb_index, charge, sigma, epsilon * scale_nonbonded
)
force.updateParametersInContext(simulation.context)
elif type(force).__name__ == "CMMotionRemover":
pass
else:
warn(
"OpenMM Force {} is "
"not currently supported in _energy_minimize_openmm. "
"This Force will not be updated!".format(
type(force).__name__
)
)
simulation.context.setPositions(to_parmed.positions)
# Run energy minimization through OpenMM
simulation.minimizeEnergy(maxIterations=steps)
reporter = PDBReporter(os.path.join(tmp_dir, "minimized.pdb"), 1)
reporter.report(
simulation, simulation.context.getState(getPositions=True)
)
def _energy_minimize_openbabel(
self, tmp_dir, steps=1000, algorithm="cg", forcefield="UFF"
):
"""Perform an energy minimization on a Compound.
Utilizes Open Babel (http://openbabel.org/docs/dev/) to perform an
energy minimization/geometry optimization on a Compound by applying
a generic force field.
This function is primarily intended to be used on smaller components,
with sizes on the order of 10's to 100's of particles, as the energy
minimization scales poorly with the number of particles.
Parameters
----------
steps : int, optionl, default=1000
The number of optimization iterations
algorithm : str, optional, default='cg'
The energy minimization algorithm. Valid options are 'steep',
'cg', and 'md', corresponding to steepest descent, conjugate
gradient, and equilibrium molecular dynamics respectively.
forcefield : str, optional, default='UFF'
The generic force field to apply to the Compound for minimization.
Valid options are 'MMFF94', 'MMFF94s', ''UFF', 'GAFF', 'Ghemical'.
Please refer to the Open Babel documentation (http://open-babel.
readthedocs.io/en/latest/Forcefields/Overview.html) when considering
your choice of force field.
References
----------
[OBoyle2011]_
[OpenBabel]_
If using the 'MMFF94' force field please also cite the following:
[Halgren1996a]_
[Halgren1996b]_
[Halgren1996c]_
[Halgren1996d]_
[Halgren1996e]_
If using the 'MMFF94s' force field please cite the above along with:
[Halgren1999]_
If using the 'UFF' force field please cite the following:
[Rappe1992]_
If using the 'GAFF' force field please cite the following:
[Wang2001]_
If using the 'Ghemical' force field please cite the following:
[Hassinen2001]_
"""
openbabel = import_("openbabel")
for particle in self.particles():
if particle.element is None:
try:
element_from_symbol(particle.name)
except ElementError:
try:
element_from_name(particle.name)
except ElementError:
raise MBuildError(
"No element assigned to {}; element could not be"
"inferred from particle name {}. Cannot perform"
"an energy minimization.".format(
particle, particle.name
)
)
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("mol2", "pdb")
mol = openbabel.OBMol()
obConversion.ReadFile(mol, os.path.join(tmp_dir, "un-minimized.mol2"))
ff = openbabel.OBForceField.FindForceField(forcefield)
if ff is None:
raise MBuildError(
"Force field '{}' not supported for energy "
"minimization. Valid force fields are 'MMFF94', "
"'MMFF94s', 'UFF', 'GAFF', and 'Ghemical'."
"".format(forcefield)
)
warn(
"Performing energy minimization using the Open Babel package. "
"Please refer to the documentation to find the appropriate "
f"citations for Open Babel and the {forcefield} force field"
)
ff.Setup(mol)
if algorithm == "steep":
ff.SteepestDescent(steps)
elif algorithm == "md":
ff.MolecularDynamicsTakeNSteps(steps, 300)
elif algorithm == "cg":
ff.ConjugateGradients(steps)
else:
raise MBuildError(
"Invalid minimization algorithm. Valid options "
"are 'steep', 'cg', and 'md'."
)
ff.UpdateCoordinates(mol)
obConversion.WriteFile(mol, os.path.join(tmp_dir, "minimized.pdb"))
[docs] def save(
self,
filename,
show_ports=False,
forcefield_name=None,
forcefield_files=None,
forcefield_debug=False,
box=None,
overwrite=False,
residues=None,
combining_rule="lorentz",
foyer_kwargs=None,
**kwargs,
):
"""Save the Compound to a file.
Parameters
----------
filename : str
Filesystem path in which to save the trajectory. The extension or
prefix will be parsed and control the format. Supported extensions:
'hoomdxml', 'gsd', 'gro', 'top', 'lammps', 'lmp', 'mcf'
show_ports : bool, optional, default=False
Save ports contained within the compound.
forcefield_files : str, optional, default=None
Apply a forcefield to the output file using a forcefield provided
by the `foyer` package.
forcefield_name : str, optional, default=None
Apply a named forcefield to the output file using the `foyer`
package, e.g. 'oplsaa'. `Foyer forcefields
<https://github.com/mosdef-hub/foyer/tree/master/foyer/forcefields>`_
forcefield_debug : bool, optional, default=False
Choose verbosity level when applying a forcefield through `foyer`.
Specifically, when missing atom types in the forcefield xml file,
determine if the warning is condensed or verbose.
box : mb.Box, optional, default=self.boundingbox (with buffer)
Box information to be written to the output file. If 'None', a
bounding box is used with 0.25nm buffers at each face to avoid
overlapping atoms.
overwrite : bool, optional, default=False
Overwrite if the filename already exists
residues : str of list of str
Labels of residues in the Compound. Residues are assigned by
checking against Compound.name.
combining_rule : str, optional, default='lorentz'
Specify the combining rule for nonbonded interactions. Only relevant
when the `foyer` package is used to apply a forcefield. Valid
options are 'lorentz' and 'geometric', specifying Lorentz-Berthelot
and geometric combining rules respectively.
foyer_kwargs : dict, optional, default=None
Keyword arguments to provide to `foyer.Forcefield.apply`.
Depending on the file extension these will be passed to either
`write_gsd`, `write_hoomdxml`, `write_lammpsdata`,
`write_mcf`, or `parmed.Structure.save`.
See `parmed structure documentation
<https://parmed.github.io/ParmEd/html/structobj/parmed.structure.Structure.html#parmed.structure.Structure.save>`_
Other Parameters
----------------
ref_distance : float, optional, default=1.0
Normalization factor used when saving to .gsd and .hoomdxml formats
for converting distance values to reduced units.
ref_energy : float, optional, default=1.0
Normalization factor used when saving to .gsd and .hoomdxml formats
for converting energy values to reduced units.
ref_mass : float, optional, default=1.0
Normalization factor used when saving to .gsd and .hoomdxml formats
for converting mass values to reduced units.
atom_style: str, default='full'
Defines the style of atoms to be saved in a LAMMPS data file. The
following atom styles are currently supported:
'full', 'atomic', 'charge', 'molecular'
See `LAMMPS atom style documentation
<https://lammps.sandia.gov/doc/atom_style.html>`_ for more
information.
unit_style: str, default='real'
Defines to unit style to be save in a LAMMPS data file. Defaults
to 'real' units. Current styles are supported: 'real', 'lj'. See
`LAMMPS unit style documentation_
<https://lammps.sandia.gov/doc/units.html>`_ for more information.
Notes
-----
When saving the compound as a json, only the following arguments are
used:
* filename
* show_ports
See Also
--------
conversion.save : Main saver logic
formats.gsdwrite.write_gsd : Write to GSD format
formats.hoomdxml.write_hoomdxml : Write to Hoomd XML format
formats.xyzwriter.write_xyz : Write to XYZ format
formats.lammpsdata.write_lammpsdata : Write to LAMMPS data format
formats.cassandramcf.write_mcf : Write to Cassandra MCF format
formats.json_formats.compound_to_json : Write to a json file
"""
conversion.save(
self,
filename,
show_ports,
forcefield_name,
forcefield_files,
forcefield_debug,
box,
overwrite,
residues,
combining_rule,
foyer_kwargs,
**kwargs,
)
[docs] def translate(self, by):
"""Translate the Compound by a vector.
Parameters
----------
by : np.ndarray, shape=(3,), dtype=float
"""
new_positions = _translate(self.xyz_with_ports, by)
self.xyz_with_ports = new_positions
[docs] def translate_to(self, pos):
"""Translate the Compound to a specific position.
Parameters
----------
pos : np.ndarray, shape=3(,), dtype=float
"""
self.translate(pos - self.center)
[docs] def rotate(self, theta, around):
"""Rotate Compound around an arbitrary vector.
Parameters
----------
theta : float
The angle by which to rotate the Compound, in radians.
around : np.ndarray, shape=(3,), dtype=float
The vector about which to rotate the Compound.
"""
new_positions = _rotate(self.xyz_with_ports, theta, around)
self.xyz_with_ports = new_positions
[docs] def spin(self, theta, around):
"""Rotate Compound in place around an arbitrary vector.
Parameters
----------
theta : float
The angle by which to rotate the Compound, in radians.
around : np.ndarray, shape=(3,), dtype=float
The axis about which to spin the Compound.
"""
around = np.asarray(around).reshape(3)
center_pos = self.center
self.translate(-center_pos)
self.rotate(theta, around)
self.translate(center_pos)
# Interface to GMSO Topology for reading/writing mol2 files
[docs] def from_gmso(self, topology, coords_only=False, infer_hierarchy=True):
"""Convert a GMSO Topology to mBuild Compound.
Parameter
---------
topology : gmso.Topology
The GMSO Topology to be converted.
compound : mb.Compound, optional, default=None
Host mb.Compound that we are loading to.
coords_only : bool, optional, default=False
Set preexisting atoms in compound to coordinates given by Topology.
infer_hierarchy : bool, optional, default=True
If True, infer compound hierarchy from Topology residue, to be implemented.
Returns
-------
compound : mb.Compound
"""
return conversion.from_gmso(
topology=topology,
compound=self,
coords_only=coords_only,
infer_hierarchy=infer_hierarchy,
)
[docs] def to_gmso(self):
"""Create a GMSO Topology from a mBuild Compound.
Parameters
----------
compound : mb.Compound
The mb.Compound to be converted.
Returns
-------
topology : gmso.Topology
The converted gmso Topology
"""
return conversion.to_gmso(self)
# Interface to Trajectory for reading/writing .pdb and .mol2 files.
# -----------------------------------------------------------------
[docs] def from_trajectory(
self, traj, frame=-1, coords_only=False, infer_hierarchy=True
):
"""Extract atoms and bonds from a md.Trajectory.
Will create sub-compounds for every chain if there is more than one
and sub-sub-compounds for every residue.
Parameters
----------
traj : mdtraj.Trajectory
The trajectory to load.
frame : int, optional, default=-1 (last)
The frame to take coordinates from.
coords_only : bool, optional, default=False
Only read coordinate information
infer_hierarchy : bool, optional, default=True
If True, infer compound hierarchy from chains and residues
See Also
--------
mbuild.conversion.from_trajectory
"""
conversion.from_trajectory(
traj=traj,
compound=self,
frame=frame,
coords_only=coords_only,
infer_hierarchy=True,
)
[docs] def to_trajectory(
self, show_ports=False, chains=None, residues=None, box=None
):
"""Convert to an md.Trajectory and flatten the compound.
Parameters
----------
show_ports : bool, optional, default=False
Include all port atoms when converting to trajectory.
chains : mb.Compound or list of mb.Compound
Chain types to add to the topology
residues : str of list of str
Labels of residues in the Compound. Residues are assigned by
checking against Compound.name.
box : mb.Box, optional, default=self.boundingbox (with buffer)
Box information to be used when converting to a `Trajectory`.
If 'None', self.box is used. If self.box is None,
a bounding box is used with a 0.5 nm buffer in each
dimension to avoid overlapping atoms.
Returns
-------
trajectory : md.Trajectory
See Also
--------
_to_topology
"""
return conversion.to_trajectory(
compound=self,
show_ports=show_ports,
chains=chains,
residues=residues,
box=box,
)
[docs] def from_parmed(self, structure, coords_only=False, infer_hierarchy=True):
"""Extract atoms and bonds from a pmd.Structure.
Will create sub-compounds for every chain if there is more than one
and sub-sub-compounds for every residue.
Parameters
----------
structure : pmd.Structure
The structure to load.
coords_only : bool
Set preexisting atoms in compound to coordinates given by structure.
infer_hierarchy : bool, optional, default=True
If true, infer compound hierarchy from chains and residues
"""
conversion.from_parmed(
structure=structure,
compound=self,
coords_only=coords_only,
infer_hierarchy=infer_hierarchy,
)
[docs] def to_parmed(
self,
box=None,
title="",
residues=None,
show_ports=False,
infer_residues=False,
):
"""Create a ParmEd Structure from a Compound.
Parameters
----------
box : mb.Box, optional, default=self.boundingbox (with buffer)
Box information to be used when converting to a `Structure`.
If 'None', self.box is used. If self.box is None,
a bounding box is used with 0.5 nm buffer in each dimension
to avoid overlapping atoms.
title : str, optional, default=self.name
Title/name of the ParmEd Structure
residues : str of list of str
Labels of residues in the Compound. Residues are assigned by
checking against Compound.name.
show_ports : boolean, optional, default=False
Include all port atoms when converting to a `Structure`.
infer_residues : bool, optional, default=False
Attempt to assign residues based on names of children.
Returns
-------
parmed.structure.Structure
ParmEd Structure object converted from self
See Also
--------
mbuild.conversion.to_parmed
parmed.structure.Structure : Details on the ParmEd Structure object
"""
return conversion.to_parmed(
compound=self,
box=box,
title=title,
residues=residues,
show_ports=show_ports,
infer_residues=infer_residues,
)
[docs] def to_networkx(self, names_only=False):
"""Create a NetworkX graph representing the hierarchy of a Compound.
Parameters
----------
names_only : bool, optional, default=False
Store only the names of the compounds in the graph, appended with
their IDs, for distinction even if they have the same name. When
set to False, the default behavior, the nodes are the compounds
themselves.
Returns
-------
G : networkx.DiGraph
Notes
-----
This digraph is not the bondgraph of the compound.
See Also
--------
mbuild.conversion.to_networkx
mbuild.bond_graph
"""
return conversion.to_networkx(compound=self, names_only=names_only)
[docs] def to_pybel(
self,
box=None,
title="",
residues=None,
show_ports=False,
infer_residues=False,
):
"""Create a pybel.Molecule from a Compound.
Parameters
----------
box : mb.Box, def None
title : str, optional, default=self.name
Title/name of the ParmEd Structure
residues : str of list of str
Labels of residues in the Compound. Residues are assigned by
checking against Compound.name.
show_ports : boolean, optional, default=False
Include all port atoms when converting to a `Structure`.
infer_residues : bool, optional, default=False
Attempt to assign residues based on names of children
Returns
-------
pybel.Molecule
See Also
--------
mbuild.conversion.to_pybel
Notes
-----
Most of the mb.Compound is first converted to openbabel.OBMol
And then pybel creates a pybel.Molecule from the OBMol
Bond orders are assumed to be 1
OBMol atom indexing starts at 1, with spatial dimension Angstrom
"""
return conversion.to_pybel(
compound=self,
box=box,
title=title,
residues=residues,
show_ports=show_ports,
)
[docs] def from_pybel(
self,
pybel_mol,
use_element=True,
coords_only=False,
infer_hierarchy=True,
ignore_box_warn=False,
):
"""Create a Compound from a Pybel.Molecule.
Parameters
----------
pybel_mol: pybel.Molecule
use_element : bool, default True
If True, construct mb Particles based on the pybel Atom's element.
If False, construcs mb Particles based on the pybel Atom's type
coords_only : bool, default False
Set preexisting atoms in compound to coordinates given by
structure. Note: Not yet implemented, included only for parity
with other conversion functions
infer_hierarchy : bool, optional, default=True
If True, infer hierarchy from residues
ignore_box_warn : bool, optional, default=False
If True, ignore warning if no box is present.
See Also
--------
mbuild.conversion.from_pybel
"""
conversion.from_pybel(
pybel_mol=pybel_mol,
compound=self,
use_element=use_element,
coords_only=coords_only,
ignore_box_warn=ignore_box_warn,
)
[docs] def to_intermol(self, molecule_types=None): # pragma: no cover
"""Create an InterMol system from a Compound.
Parameters
----------
molecule_types : list or tuple of subclasses of Compound
Returns
-------
intermol_system : intermol.system.System
See Also
--------
mbuild.conversion.to_intermol
"""
return conversion.to_intermol(
compound=self, molecule_types=molecule_types
)
[docs] def get_smiles(self):
"""Get SMILES string for compound.
Bond order is guessed with pybel and may lead to incorrect SMILES
strings.
Returns
-------
smiles_string: str
"""
pybel_cmp = self.to_pybel()
pybel_cmp.OBMol.PerceiveBondOrders()
# we only need the smiles string
smiles = pybel_cmp.write().split()[0]
return smiles
def __getitem__(self, selection):
"""Get item from Compound."""
if isinstance(selection, int):
return list(self.particles())[selection]
if isinstance(selection, str):
if selection not in self.labels:
raise MBuildError(f"{self.name}['{selection}'] does not exist.")
return self.labels.get(selection)
def __repr__(self):
"""Compound representation."""
descr = list("<")
descr.append(self.name + " ")
if self.children:
descr.append("{:d} particles, ".format(self.n_particles))
if self.box is not None:
descr.append("System box: {}, ".format(self.box))
else:
descr.append("non-periodic, ")
else:
descr.append(
"pos=({}), ".format(np.array2string(self.pos, precision=4))
)
descr.append("{:d} bonds, ".format(self.n_bonds))
descr.append("id: {}>".format(id(self)))
return "".join(descr)
def _clone(self, clone_of=None, root_container=None):
"""Clones compound faster than deepcopying.
Does not resolve circular dependencies. This should be safe provided
you never try to add the top of a Compound hierarchy to a
sub-Compound. Clones compound hierarchy only, not the bonds.
"""
if root_container is None:
root_container = self
if clone_of is None:
clone_of = dict()
# If this compound has already been cloned, return that.
if self in clone_of:
return clone_of[self]
# Otherwise we make a new clone.
cls = self.__class__
newone = cls.__new__(cls)
# Remember that we're cloning the new one of self.
clone_of[self] = newone
newone.name = deepcopy(self.name)
newone._element = deepcopy(self.element)
newone._pos = deepcopy(self._pos)
newone.port_particle = deepcopy(self.port_particle)
newone._box = deepcopy(self._box)
newone._check_if_contains_rigid_bodies = deepcopy(
self._check_if_contains_rigid_bodies
)
newone._periodicity = deepcopy(self._periodicity)
newone._contains_rigid = deepcopy(self._contains_rigid)
newone._rigid_id = deepcopy(self._rigid_id)
newone._charge = deepcopy(self._charge)
newone._mass = deepcopy(self._mass)
if hasattr(self, "index"):
newone.index = deepcopy(self.index)
if self.children is None:
newone.children = None
else:
newone.children = OrderedSet()
# Parent should be None initially.
newone.parent = None
newone.labels = OrderedDict()
newone.referrers = set()
newone.bond_graph = None
# Add children to clone.
if self.children:
for child in self.children:
newchild = child._clone(clone_of, root_container)
newone.children.add(newchild)
newchild.parent = newone
# Copy labels, except bonds with atoms outside the hierarchy.
if self.labels:
for label, compound in self.labels.items():
if not isinstance(compound, list):
newone.labels[label] = compound._clone(
clone_of, root_container
)
compound.referrers.add(clone_of[compound])
else:
# compound is a list of compounds, so we create an empty
# list, and add the clones of the original list elements.
newone.labels[label] = []
for subpart in compound:
newone.labels[label].append(
subpart._clone(clone_of, root_container)
)
# Referrers must have been handled already, or the will
# be handled
return newone
def _clone_bonds(self, clone_of=None):
"""Clone the bond of the source compound to clone compound."""
newone = clone_of[self]
for c1, c2 in self.bonds():
try:
newone.add_bond((clone_of[c1], clone_of[c2]))
except KeyError:
raise MBuildError(
"Cloning failed. Compound contains bonds to "
"Particles outside of its containment hierarchy."
)
Particle = Compound