__all__ = ['load', 'clone', 'Compound', 'Particle']
from collections import OrderedDict, defaultdict, Iterable
from copy import deepcopy
import itertools
import os
import sys
import tempfile
from warnings import warn
import mdtraj as md
from mdtraj.core.element import get_by_symbol
import numpy as np
from oset import oset as OrderedSet
import parmed as pmd
from parmed.periodic_table import AtomicNum, element_by_name, Mass, Element
from mbuild.bond_graph import BondGraph
from mbuild.box import Box
from mbuild.exceptions import MBuildError
from mbuild.utils.decorators import deprecated
from mbuild.formats.xyz import read_xyz, write_xyz
from mbuild.formats.json_formats import compound_to_json, compound_from_json
from mbuild.formats.hoomdxml import write_hoomdxml
from mbuild.formats.lammpsdata import write_lammpsdata
from mbuild.formats.gsdwriter import write_gsd
from mbuild.formats.par_writer import write_par
from mbuild.periodic_kdtree import PeriodicCKDTree
from mbuild.utils.io import run_from_ipython, import_, has_networkx
from mbuild.utils.jsutils import overwrite_nglview_default
from mbuild.coordinate_transform import _translate, _rotate
def load(filename_or_object, relative_to_module=None, compound=None, coords_only=False,
rigid=False, use_parmed=False, smiles=False,
infer_hierarchy=True, **kwargs):
"""Load a file or an existing topology into an mbuild compound.
Files are read using the MDTraj package unless the `use_parmed` argument is
specified as True. Please refer to http://mdtraj.org/1.8.0/load_functions.html
for formats supported by MDTraj and https://parmed.github.io/ParmEd/html/
readwrite.html for formats supported by ParmEd.
Parameters
----------
filename_or_object : str, mdtraj.Trajectory, parmed.Structure, mbuild.Compound,
pybel.Molecule
Name of the file or topology from which to load atom and bond information.
relative_to_module : str, optional, default=None
Instead of looking in the current working directory, look for the file
where this module is defined. This is typically used in Compound
classes that will be instantiated from a different directory
(such as the Compounds located in mbuild.lib).
compound : mb.Compound, optional, default=None
Existing compound to load atom and bond information into.
coords_only : bool, optional, default=False
Only load the coordinates into an existing compound.
rigid : bool, optional, default=False
Treat the compound as a rigid body
use_parmed : bool, optional, default=False
Use readers from ParmEd instead of MDTraj.
smiles: bool, optional, default=False
Use Open Babel to parse filename as a SMILES string
or file containing a SMILES string.
infer_hierarchy : bool, optional, default=True
If True, infer hierarchy from chains and residues
**kwargs : keyword arguments
Key word arguments passed to mdTraj for loading.
Returns
-------
compound : mb.Compound
"""
# If compound doesn't exist, we will initialize one
if compound is None:
compound = Compound()
# First check if we are loading from an existing parmed or trajectory structure
type_dict = {
pmd.Structure:compound.from_parmed,
md.Trajectory:compound.from_trajectory,
}
try:
pybel = import_('pybel')
type_dict.update({pybel.Molecule:compound.from_pybel})
except ImportError:
pass
if isinstance(filename_or_object, Compound):
return filename_or_object
for type in type_dict:
if isinstance(filename_or_object, type):
type_dict[type](filename_or_object,coords_only=coords_only,
infer_hierarchy=infer_hierarchy, **kwargs)
return compound
if not isinstance(filename_or_object, str):
raise ValueError('Input not supported.')
# Handle mbuild *.py files containing a class that wraps a structure file
# in its own folder. E.g., you build a system from ~/foo.py and it imports
# from ~/bar/baz.py where baz.py loads ~/bar/baz.pdb.
if relative_to_module:
script_path = os.path.realpath(
sys.modules[relative_to_module].__file__)
file_dir = os.path.dirname(script_path)
filename_or_object = os.path.join(file_dir, filename_or_object)
# Handle the case of a xyz and json file, which must use an internal reader
extension = os.path.splitext(filename_or_object)[-1]
if extension == '.json':
compound = compound_from_json(filename_or_object)
return compound
if extension == '.xyz' and not 'top' in kwargs:
if coords_only:
tmp = read_xyz(filename_or_object)
if tmp.n_particles != compound.n_particles:
raise ValueError('Number of atoms in {filename_or_object} does not match'
' {compound}'.format(**locals()))
ref_and_compound = zip(tmp._particles(include_ports=False),
compound.particles(include_ports=False))
for ref_particle, particle in ref_and_compound:
particle.pos = ref_particle.pos
else:
compound = read_xyz(filename_or_object, compound=compound)
return compound
if extension == '.sdf':
pybel = import_('pybel')
pybel_mol = pybel.readfile('sdf', filename_or_object)
# pybel returns a generator, so we grab the first molecule of a list of len 1
# Raise ValueError user if there are more molecules
pybel_mol = [i for i in pybel_mol]
if len(pybel_mol) == 1:
compound.from_pybel(pybel_mol[0])
else:
compound.from_pybel(pybel_mol[0])
raise ValueError("More than one pybel molecule in file, more than one pybel "
"molecule is not supported, using {}".format(filename_or_object))
return compound
if use_parmed:
warn(
"use_parmed set to True. Bonds may be inferred from inter-particle "
"distances and standard residue templates!")
structure = pmd.load_file(filename_or_object, structure=True, **kwargs)
compound.from_parmed(structure, coords_only=coords_only,
infer_hierarchy=infer_hierarchy)
elif smiles:
pybel = import_('pybel')
# First we try treating filename_or_object as a SMILES string
try:
mymol = pybel.readstring("smi", filename_or_object)
# Now we treat it as a filename
except(OSError, IOError):
# For now, we only support reading in a single smiles molecule,
# but pybel returns a generator, so we get the first molecule
# and warn the user if there is more
mymol_generator = pybel.readfile("smi", filename_or_object)
mymol_list = list(mymol_generator)
if len(mymol_list) == 1:
mymol = mymol_list[0]
else:
mymol = mymol_list[0]
warn("More than one SMILES string in file, more than one SMILES "
"string is not supported, using {}".format(mymol.write("smi")))
# We create a temporary directory and mol2 file that will created from the smiles string
# A ParmEd structure and subsequenc mBuild compound will be created from this mol2 file
tmp_dir = tempfile.mkdtemp()
temp_file = os.path.join(tmp_dir, 'smiles_to_mol2_intermediate.mol2')
mymol.make3D()
compound = Compound()
compound.from_pybel(mymol, infer_hierarchy=infer_hierarchy)
else:
traj = md.load(filename_or_object, **kwargs)
compound.from_trajectory(traj, frame=-1, coords_only=coords_only,
infer_hierarchy=infer_hierarchy)
if rigid:
compound.label_rigid_bodies()
return compound
def clone(existing_compound, clone_of=None, root_container=None):
"""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 : mb.Compound
Existing Compound that will be copied
Other Parameters
----------------
clone_of : dict, optional
root_container : mb.Compound, optional
"""
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 (Gamma, Erich; Richard Helm; Ralph Johnson; John
M. Vlissides (1995). Design Patterns: Elements of Reusable Object-Oriented
Software. Addison-Wesley. 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
charge : float, optional, default=0.0
Currently not used. Likely removed in next release.
periodicity : np.ndarray, shape=(3,), dtype=float, optional, default=[0, 0, 0]
The periodic lengths of the Compound in the x, y and z directions.
Defaults to zeros which is treated as non-periodic.
port_particle : bool, optional, default=False
Whether or not this Compound is part of a Port
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
center
contains_rigid
max_rigid_id
n_particles
n_bonds
root
xyz
xyz_with_ports
"""
def __init__(self, subcompounds=None, name=None, pos=None, charge=0.0,
periodicity=None, port_particle=False):
super(Compound, self).__init__()
if name:
if not isinstance(name, str):
raise ValueError(
'Compound.name should be a string. You passed '
'{}'.format(name))
self.name = name
else:
self.name = self.__class__.__name__
# A periodicity of zero in any direction is treated as non-periodic.
if periodicity is None:
self._periodicity = np.array([0.0, 0.0, 0.0])
else:
self._periodicity = np.asarray(periodicity)
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.add() must be called after labels and children are initialized.
if subcompounds:
if charge:
raise MBuildError(
'Cannot set the charge of a Compound containing '
'subcompounds.')
self.add(subcompounds)
self._charge = 0.0
else:
self._charge = charge
[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):
"""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
@property
def charge(self):
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):
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):
"""Returns 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(particle.rigid_id is not None for particle in self._particles()):
self._contains_rigid = True
else:
self._contains_rigid = False
return self._contains_rigid
@property
def max_rigid_id(self):
"""Returns 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([particle.rigid_id for particle in self.particles()
if particle.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=True, 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
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
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.
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 to Compounds. You tried to add '
'"{}".'.format(new_child))
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('Label "{0}" already exists in {1}.'.format(
label, self))
else:
self.labels[label] = new_child
new_child.referrers.add(self)
if (inherit_periodicity and isinstance(new_child, Compound) and
new_child.periodicity.any()):
self.periodicity = new_child.periodicity
[docs] def remove(self, objs_to_remove):
""" Cleanly remove children from the Compound.
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("This will remove all particles in "
"compound {}".format(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 [successor for successor in self.successors()
if isinstance(successor, 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 [port for port in self.labels.values()
if isinstance(port, Port) and not port.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 between Particles for considering a bond
dmax : float
The maximum distance between Particles for considering a bond
"""
particle_kdtree = PeriodicCKDTree(
data=self.xyz, bounds=self.periodicity)
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] def remove_bond(self, particle_pair):
"""Deletes 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):
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('Cannot set position on a Compound that has'
' children.')
@property
def periodicity(self):
return self._periodicity
@periodicity.setter
def periodicity(self, periods):
self._periodicity = np.array(periods)
@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(
particle.pos for particle 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(
particle.pos for particle 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 the Ports.
This function does not set the position of the 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=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 the 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):
"""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 boundingbox(self):
"""Compute the bounding box of the compound.
Returns
-------
mb.Box
The bounding box for this Compound
"""
xyz = self.xyz
return Box(mins=xyz.min(axis=0), maxs=xyz.max(axis=0))
[docs] def min_periodic_distance(self, xyz0, xyz1):
"""Vectorized distance calculation considering minimum image.
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)
d = np.where(d > 0.5 * self.periodicity, self.periodicity - d, d)
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.PeriodicCKDTree, 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.PerioidicCKDTree : mBuild implementation of kd-trees
scipy.spatial.ckdtree : Further details on kd-trees
"""
if particle_kdtree is None:
particle_kdtree = PeriodicCKDTree(
data=self.xyz, bounds=self.periodicity)
_, 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("Unsupported visualization " +
"backend ({}). ".format(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')
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('_{}'.format(
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(
'@{}'.format(
','.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 = load(filename, compound=self, coords_only=True)
self._update_port_locations(xyz_init)
else:
self = 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)
warning_message = 'Please use Compound.energy_minimize()'
@deprecated(warning_message)
def energy_minimization(self, forcefield='UFF', steps=1000, **kwargs):
self.energy_minimize(forcefield=forcefield, steps=steps, **kwargs)
[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', and '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 (http://docs.
openmm.org/7.0.0/userguide/application.html#creating-force-fields)
for more information.
Keyword Arguments
------------
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
References
----------
If using _energy_minimize_openmm(), please cite:
.. [1] 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:
.. [1] 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
.. [2] Open Babel, version X.X.X http://openbabel.org, (installed
Month Year)
If using the 'MMFF94' force field please also cite the following:
.. [3] T.A. Halgren, "Merck molecular force field. I. Basis, form,
scope, parameterization, and performance of MMFF94." (1996)
J. Comput. Chem. 17, 490-519
.. [4] 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
.. [5] T.A. Halgren, "Merck molecular force field. III. Molecular
geometries and vibrational frequencies for MMFF94." (1996)
J. Comput. Chem. 17, 553-586
.. [6] 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
.. [7] 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:
.. [8] 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:
.. [3] 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:
.. [3] 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:
.. [3] 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):
""" 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'. Forcefields listed here:
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)
Notes
-----
Assumes a particular organization for the force groups
(HarmonicBondForce, HarmonicAngleForce, RBTorsionForce, NonBondedForce)
References
----------
.. [1] 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).
"""
foyer = import_('foyer')
to_parmed = self.to_parmed()
ff = foyer.Forcefield(forcefield_files=forcefield_files, name=forcefield_name)
to_parmed = ff.apply(to_parmed)
from simtk.openmm.app.simulation import Simulation
from simtk.openmm.app.pdbreporter import PDBReporter
from simtk.openmm.openmm import LangevinIntegrator
import simtk.unit as u
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', and '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
----------
.. [1] 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
.. [2] Open Babel, version X.X.X http://openbabel.org, (installed
Month Year)
If using the 'MMFF94' force field please also cite the following:
.. [3] T.A. Halgren, "Merck molecular force field. I. Basis, form,
scope, parameterization, and performance of MMFF94." (1996)
J. Comput. Chem. 17, 490-519
.. [4] 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
.. [5] T.A. Halgren, "Merck molecular force field. III. Molecular
geometries and vibrational frequencies for MMFF94." (1996)
J. Comput. Chem. 17, 553-586
.. [6] 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
.. [7] 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:
.. [8] 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:
.. [3] 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:
.. [3] 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:
.. [3] 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
"""
openbabel = import_('openbabel')
for particle in self.particles():
try:
get_by_symbol(particle.name)
except KeyError:
raise MBuildError("Element name {} not recognized. Cannot "
"perform minimization."
"".format(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 citations for "
"Open Babel and the {} force field".format(forcefield))
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 are: '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'. Forcefields listed here:
https://github.com/mosdef-hub/foyer/tree/master/foyer/forcefields
forcefield_debug : bool, optional, default=False
Choose level of verbosity 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`.
**kwargs
Depending on the file extension these will be passed to either
`write_gsd`, `write_hoomdxml`, `write_lammpsdata`,
`write_mcf`, or `parmed.Structure.save`.
See 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 http://lammps.sandia.gov/doc/atom_style.html for more
information on atom styles.
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 https://lammps.sandia.gov/doc/99/units.html for more information
on unit styles
Notes
------
When saving the compound as a json, only the following arguments are used:
- filename
- show_ports
See Also
--------
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
"""
extension = os.path.splitext(filename)[-1]
if extension == '.json':
compound_to_json(self,
file_path=filename,
include_ports=show_ports)
return
# Savers supported by mbuild.formats
savers = {'.hoomdxml': write_hoomdxml,
'.gsd': write_gsd,
'.xyz': write_xyz,
'.lammps': write_lammpsdata,
'.lmp': write_lammpsdata,
'.par': write_par,}
if has_networkx:
from mbuild.formats.cassandramcf import write_mcf
savers.update({'.mcf': write_mcf})
try:
saver = savers[extension]
except KeyError:
saver = None
if os.path.exists(filename) and not overwrite:
raise IOError('{0} exists; not overwriting'.format(filename))
structure = self.to_parmed(box=box, residues=residues,
show_ports=show_ports)
# Apply a force field with foyer if specified
if forcefield_name or forcefield_files:
foyer = import_('foyer')
ff = foyer.Forcefield(forcefield_files=forcefield_files,
name=forcefield_name, debug=forcefield_debug)
if not foyer_kwargs:
foyer_kwargs = {}
structure = ff.apply(structure, **foyer_kwargs)
structure.combining_rule = combining_rule
total_charge = sum([atom.charge for atom in structure])
if round(total_charge, 4) != 0.0:
warn('System is not charge neutral. Total charge is {}.'
''.format(total_charge))
# Provide a warning if rigid_ids are not sequential from 0
if self.contains_rigid:
unique_rigid_ids = sorted(set([
p.rigid_id for p in self.rigid_particles()]))
if max(unique_rigid_ids) != len(unique_rigid_ids) - 1:
warn("Unique rigid body IDs are not sequential starting from zero.")
if saver: # mBuild supported saver.
if extension in ['.gsd', '.hoomdxml']:
kwargs['rigid_bodies'] = [
p.rigid_id for p in self.particles()]
saver(filename=filename, structure=structure, **kwargs)
elif extension == '.sdf':
pybel = import_('pybel')
new_compound = Compound()
# Convert pmd.Structure to mb.Compound
new_compound.from_parmed(structure)
# Convert mb.Compound to pybel molecule
pybel_molecule = new_compound.to_pybel()
# Write out pybel molecule to SDF file
output_sdf = pybel.Outputfile("sdf", filename,
overwrite=overwrite)
output_sdf.write(pybel_molecule)
output_sdf.close()
else: # ParmEd supported saver.
structure.save(filename, overwrite=overwrite, **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 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
"""
if coords_only:
if traj.n_atoms != self.n_particles:
raise ValueError('Number of atoms in {traj} does not match'
' {self}'.format(**locals()))
atoms_particles = zip(traj.topology.atoms,
self.particles(include_ports=False))
if None in self._particles(include_ports=False):
raise ValueError('Some particles are None')
for mdtraj_atom, particle in atoms_particles:
particle.pos = traj.xyz[frame, mdtraj_atom.index]
return
atom_mapping = dict()
for chain in traj.topology.chains:
if traj.topology.n_chains > 1:
chain_compound = Compound()
self.add(chain_compound, 'chain[$]')
else:
chain_compound = self
for res in chain.residues:
if infer_hierarchy:
res_compound = Compound(name=res.name)
chain_compound.add(res_compound)
parent_cmpd = res_compound
else:
parent_cmpd = chain_compound
for atom in res.atoms:
new_atom = Particle(name=str(atom.name),
pos=traj.xyz[frame, atom.index])
parent_cmpd.add(
new_atom, label='{0}[$]'.format(
atom.name))
atom_mapping[atom] = new_atom
for mdtraj_atom1, mdtraj_atom2 in traj.topology.bonds:
atom1 = atom_mapping[mdtraj_atom1]
atom2 = atom_mapping[mdtraj_atom2]
self.add_bond((atom1, atom2))
if np.any(traj.unitcell_lengths) and np.any(traj.unitcell_lengths[0]):
self.periodicity = traj.unitcell_lengths[0]
else:
self.periodicity = np.array([0., 0., 0.])
[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', a bounding box is used with a 0.5nm buffer in each
dimension. to avoid overlapping atoms, unless `self.periodicity`
is not None, in which case those values are used for the
box lengths.
Returns
-------
trajectory : md.Trajectory
See also
--------
_to_topology
"""
atom_list = [particle for particle in self.particles(show_ports)]
top = self._to_topology(atom_list, chains, residues)
# Coordinates.
xyz = np.ndarray(shape=(1, top.n_atoms, 3), dtype='float')
for idx, atom in enumerate(atom_list):
xyz[0, idx] = atom.pos
# Unitcell information.
unitcell_angles = [90.0, 90.0, 90.0]
if box is None:
unitcell_lengths = np.empty(3)
for dim, val in enumerate(self.periodicity):
if val:
unitcell_lengths[dim] = val
else:
unitcell_lengths[dim] = self.boundingbox.lengths[dim] + 0.5
else:
unitcell_lengths = box.lengths
unitcell_angles = box.angles
return md.Trajectory(xyz, top, unitcell_lengths=unitcell_lengths,
unitcell_angles=unitcell_angles)
def _to_topology(self, atom_list, chains=None, residues=None):
"""Create a mdtraj.Topology from a Compound.
Parameters
----------
atom_list : list of mb.Compound
Atoms to include in the topology
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.
Returns
-------
top : mdtraj.Topology
See Also
--------
mdtraj.Topology : Details on the mdtraj Topology object
"""
from mdtraj.core.topology import Topology
if isinstance(chains, str):
chains = [chains]
if isinstance(chains, (list, set)):
chains = tuple(chains)
if isinstance(residues, str):
residues = [residues]
if isinstance(residues, (list, set)):
residues = tuple(residues)
top = Topology()
atom_mapping = {}
default_chain = top.add_chain()
default_residue = top.add_residue('RES', default_chain)
compound_residue_map = dict()
atom_residue_map = dict()
compound_chain_map = dict()
atom_chain_map = dict()
for atom in atom_list:
# Chains
if chains:
if atom.name in chains:
current_chain = top.add_chain()
compound_chain_map[atom] = current_chain
else:
for parent in atom.ancestors():
if chains and parent.name in chains:
if parent not in compound_chain_map:
current_chain = top.add_chain()
compound_chain_map[parent] = current_chain
current_residue = top.add_residue(
'RES', current_chain)
break
else:
current_chain = default_chain
else:
current_chain = default_chain
atom_chain_map[atom] = current_chain
# Residues
if residues:
if atom.name in residues:
current_residue = top.add_residue(atom.name, current_chain)
compound_residue_map[atom] = current_residue
else:
for parent in atom.ancestors():
if residues and parent.name in residues:
if parent not in compound_residue_map:
current_residue = top.add_residue(
parent.name, current_chain)
compound_residue_map[parent] = current_residue
break
else:
current_residue = default_residue
else:
if chains:
try: # Grab the default residue from the custom chain.
current_residue = next(current_chain.residues)
except StopIteration: # Add the residue to the current chain
current_residue = top.add_residue('RES', current_chain)
else: # Grab the default chain's default residue
current_residue = default_residue
atom_residue_map[atom] = current_residue
# Add the actual atoms
try:
elem = get_by_symbol(atom.name)
except KeyError:
elem = get_by_symbol("VS")
at = top.add_atom(atom.name, elem, atom_residue_map[atom])
at.charge = atom.charge
atom_mapping[atom] = at
# Remove empty default residues.
chains_to_remove = [
chain for chain in top.chains if chain.n_atoms == 0]
residues_to_remove = [res for res in top.residues if res.n_atoms == 0]
for chain in chains_to_remove:
top._chains.remove(chain)
for res in residues_to_remove:
for chain in top.chains:
try:
chain._residues.remove(res)
except ValueError: # Already gone.
pass
for atom1, atom2 in self.bonds():
# Ensure that both atoms are part of the compound. This becomes an
# issue if you try to convert a sub-compound to a topology which is
# bonded to a different subcompound.
if all(a in atom_mapping.keys() for a in [atom1, atom2]):
top.add_bond(atom_mapping[atom1], atom_mapping[atom2])
return top
[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
"""
if coords_only:
if len(structure.atoms) != self.n_particles:
raise ValueError(
'Number of atoms in {structure} does not match'
' {self}'.format(
**locals()))
atoms_particles = zip(structure.atoms,
self.particles(include_ports=False))
if None in self._particles(include_ports=False):
raise ValueError('Some particles are None')
for parmed_atom, particle in atoms_particles:
particle.pos = np.array([parmed_atom.xx,
parmed_atom.xy,
parmed_atom.xz]) / 10
return
atom_mapping = dict()
chain_id = None
chains = defaultdict(list)
for residue in structure.residues:
chains[residue.chain].append(residue)
for chain, residues in chains.items():
if len(chains) > 1:
chain_compound = Compound()
self.add(chain_compound, chain_id)
else:
chain_compound = self
for residue in residues:
if infer_hierarchy:
residue_compound = Compound(name=residue.name)
chain_compound.add(residue_compound)
parent_cmpd = residue_compound
else:
parent_cmpd = chain_compound
for atom in residue.atoms:
pos = np.array([atom.xx, atom.xy, atom.xz]) / 10
new_atom = Particle(name=str(atom.name), pos=pos)
parent_cmpd.add(
new_atom, label='{0}[$]'.format(
atom.name))
atom_mapping[atom] = new_atom
for bond in structure.bonds:
atom1 = atom_mapping[bond.atom1]
atom2 = atom_mapping[bond.atom2]
self.add_bond((atom1, atom2))
if structure.box is not None:
# Convert from A to nm
self.periodicity = 0.1 * structure.box[0:3]
else:
self.periodicity = np.array([0., 0., 0.])
[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', a bounding box is used with 0.25nm buffers at
each face to avoid overlapping atoms, unless `self.periodicity`
is not None, in which case those values are used for the
box lengths.
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
--------
parmed.structure.Structure : Details on the ParmEd Structure object
"""
structure = pmd.Structure()
structure.title = title if title else self.name
atom_mapping = {} # For creating bonds below
guessed_elements = set()
# Attempt to grab residue names based on names of children
if not residues and infer_residues:
residues = list(set([child.name for child in self.children]))
if isinstance(residues, str):
residues = [residues]
if isinstance(residues, (list, set)):
residues = tuple(residues)
default_residue = pmd.Residue('RES')
port_residue = pmd.Residue('PRT')
compound_residue_map = dict()
atom_residue_map = dict()
# Loop through particles and add initialize ParmEd atoms
for atom in self.particles(include_ports=show_ports):
if atom.port_particle:
current_residue = port_residue
atom_residue_map[atom] = current_residue
if current_residue not in structure.residues:
structure.residues.append(current_residue)
pmd_atom = pmd.Atom(atomic_number=0, name='VS',
mass=0, charge=0)
pmd_atom.xx, pmd_atom.xy, pmd_atom.xz = atom.pos * 10 # Angstroms
else:
if residues and atom.name in residues:
current_residue = pmd.Residue(atom.name)
atom_residue_map[atom] = current_residue
compound_residue_map[atom] = current_residue
elif residues:
for parent in atom.ancestors():
if residues and parent.name in residues:
if parent not in compound_residue_map:
current_residue = pmd.Residue(parent.name)
compound_residue_map[parent] = current_residue
atom_residue_map[atom] = current_residue
break
else: # Did not find specified residues in ancestors.
current_residue = default_residue
atom_residue_map[atom] = current_residue
else:
current_residue = default_residue
atom_residue_map[atom] = current_residue
if current_residue not in structure.residues:
structure.residues.append(current_residue)
atomic_number = None
name = ''.join(char for char in atom.name if not char.isdigit())
try:
atomic_number = AtomicNum[atom.name.capitalize()]
except KeyError:
element = element_by_name(atom.name.capitalize())
if name not in guessed_elements:
warn(
'Guessing that "{}" is element: "{}"'.format(
atom, element))
guessed_elements.add(name)
else:
element = atom.name.capitalize()
atomic_number = atomic_number or AtomicNum[element]
mass = Mass[element]
pmd_atom = pmd.Atom(atomic_number=atomic_number, name=atom.name,
mass=mass, charge=atom.charge)
pmd_atom.xx, pmd_atom.xy, pmd_atom.xz = atom.pos * 10 # Angstroms
residue = atom_residue_map[atom]
structure.add_atom(pmd_atom, resname=residue.name,
resnum=residue.idx)
atom_mapping[atom] = pmd_atom
# "Claim" all of the items it contains and subsequently index all of its items
structure.residues.claim()
# Create and add bonds to ParmEd Structure
for atom1, atom2 in self.bonds():
bond = pmd.Bond(atom_mapping[atom1], atom_mapping[atom2])
structure.bonds.append(bond)
# pad box with .25nm buffers
if box is None:
box = self.boundingbox
box_vec_max = box.maxs.tolist()
box_vec_min = box.mins.tolist()
for dim, val in enumerate(self.periodicity):
if val:
box_vec_max[dim] = val
box_vec_min[dim] = 0.0
if not val:
box_vec_max[dim] += 0.25
box_vec_min[dim] -= 0.25
# In rare cases `AssertionError` will be raised if `mins` is set before `maxs`
# As a result, set `maxs` before `mins`
box.maxs = np.asarray(box_vec_max)
box.mins = np.asarray(box_vec_min)
box_vector = np.empty(6)
if box.angles is not None:
box_vector[3:6] = box.angles
else:
box_vector[3] = box_vector[4] = box_vector[5] = 90.0
for dim in range(3):
box_vector[dim] = box.lengths[dim] * 10
structure.box = box_vector
return structure
[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.bond_graph
"""
nx = import_('networkx')
nodes = list()
edges = list()
if names_only:
nodes.append(self.name + '_' + str(id(self)))
else:
nodes.append(self)
nodes, edges = self._iterate_children(nodes, edges, names_only=names_only)
graph = nx.DiGraph()
graph.add_nodes_from(nodes)
graph.add_edges_from(edges)
return graph
def _iterate_children(self, nodes, edges, names_only=False):
""" Create nodes and edges that connect parents and their corresponding children"""
if not self.children:
return nodes, edges
for child in self.children:
if names_only:
unique_name = child.name + '_' + str(id(child))
unique_name_parent = child.parent.name + '_' + str((id(child.parent)))
nodes.append(unique_name)
edges.append([unique_name_parent, unique_name])
else:
nodes.append(child)
edges.append([child.parent, child])
nodes, edges = child._iterate_children(nodes, edges, names_only=names_only)
return nodes, edges
[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
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
"""
openbabel = import_('openbabel')
pybel = import_('pybel')
mol = openbabel.OBMol()
particle_to_atom_index = {}
if not residues and infer_residues:
residues = list(set([child.name for child in self.children]))
if isinstance(residues, str):
residues = [residues]
if isinstance(residues, (list, set)):
residues = tuple(residues)
compound_residue_map = dict()
atom_residue_map = dict()
for i, part in enumerate(self.particles(include_ports=show_ports)):
if residues and part.name in residues:
current_residue = mol.NewResidue()
current_residue.SetName(part.name)
atom_residue_map[part] = current_residue
compound_residue_map[part] = current_residue
elif residues:
for parent in part.ancestors():
if residues and parent.name in residues:
if parent not in compound_residue_map:
current_residue = mol.NewResidue()
current_residue.SetName(parent.name)
compound_residue_map[parent] = current_residue
atom_residue_map[part] = current_residue
break
else: # Did not find specified residues in ancestors.
current_residue = mol.NewResidue()
current_residue.SetName("RES")
atom_residue_map[part] = current_residue
else:
current_residue = mol.NewResidue()
current_residue.SetName("RES")
atom_residue_map[part] = current_residue
temp = mol.NewAtom()
residue = atom_residue_map[part]
temp.SetResidue(residue)
if part.port_particle:
temp.SetAtomicNum(0)
else:
try:
temp.SetAtomicNum(AtomicNum[part.name.capitalize()])
except KeyError:
warn("Could not infer atomic number from "
"{}, setting to 0".format(part.name))
temp.SetAtomicNum(0)
temp.SetVector(*(part.xyz[0]*10))
particle_to_atom_index[part] = i
ucell = openbabel.OBUnitCell()
if box is None:
box = self.boundingbox
a, b, c = 10.0 * box.lengths
alpha, beta, gamma = np.radians(box.angles)
cosa = np.cos(alpha)
cosb = np.cos(beta)
sinb = np.sin(beta)
cosg = np.cos(gamma)
sing = np.sin(gamma)
mat_coef_y = (cosa - cosb * cosg) / sing
mat_coef_z = np.power(sinb, 2, dtype=float) - \
np.power(mat_coef_y, 2, dtype=float)
if mat_coef_z > 0.:
mat_coef_z = np.sqrt(mat_coef_z)
else:
raise Warning('Non-positive z-vector. Angles {} '
'do not generate a box with the z-vector in the'
'positive z direction'.format(box.angles))
box_vec = [[1, 0, 0],
[cosg, sing, 0],
[cosb, mat_coef_y, mat_coef_z]]
box_vec = np.asarray(box_vec)
box_mat = (np.array([a,b,c])* box_vec.T).T
first_vector = openbabel.vector3(*box_mat[0])
second_vector = openbabel.vector3(*box_mat[1])
third_vector = openbabel.vector3(*box_mat[2])
ucell.SetData(first_vector, second_vector, third_vector)
mol.CloneData(ucell)
for bond in self.bonds():
bond_order = 1
mol.AddBond(particle_to_atom_index[bond[0]]+1,
particle_to_atom_index[bond[1]]+1,
bond_order)
pybelmol = pybel.Molecule(mol)
pybelmol.title = title if title else self.name
return pybelmol
[docs] def from_pybel(self, pybel_mol, use_element=True, coords_only=False,
infer_hierarchy=True):
"""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
"""
openbabel = import_("openbabel")
self.name = pybel_mol.title.split('.')[0]
resindex_to_cmpd = {}
if coords_only:
raise Warning('coords_only=True not yet implemented for '
'conversion from pybel')
# Iterating through pybel_mol for atom/residue information
# This could just as easily be implemented by
# an OBMolAtomIter from the openbabel library,
# but this seemed more convenient at time of writing
# pybel atoms are 1-indexed, coordinates in Angstrom
for atom in pybel_mol.atoms:
xyz = np.array(atom.coords)/10
if use_element:
try:
temp_name = Element[atom.atomicnum]
except KeyError:
warn("No element detected for atom at index "
"{} with number {}, type {}".format(
atom.idx, atom.atomicnum, atom.type))
temp_name = atom.type
else:
temp_name = atom.type
temp = Particle(name=temp_name, pos=xyz)
if infer_hierarchy and hasattr(atom, 'residue'):
# Is there a safer way to check for res?
if atom.residue.idx not in resindex_to_cmpd:
res_cmpd = Compound(name=atom.residue.name)
resindex_to_cmpd[atom.residue.idx] = res_cmpd
self.add(res_cmpd)
resindex_to_cmpd[atom.residue.idx].add(temp)
else:
self.add(temp)
# Iterating through pybel_mol.OBMol for bond information
# Bonds are 0-indexed, but the atoms are 1-indexed
# Bond information doesn't appear stored in pybel_mol,
# so we need to look into the OBMol object,
# using an iterator from the openbabel library
for bond in openbabel.OBMolBondIter(pybel_mol.OBMol):
self.add_bond([self[bond.GetBeginAtomIdx()-1],
self[bond.GetEndAtomIdx()-1]])
if hasattr(pybel_mol, 'unitcell'):
box = Box(lengths=[pybel_mol.unitcell.GetA()/10,
pybel_mol.unitcell.GetB()/10,
pybel_mol.unitcell.GetC()/10],
angles=[pybel_mol.unitcell.GetAlpha(),
pybel_mol.unitcell.GetBeta(),
pybel_mol.unitcell.GetGamma()])
self.periodicity = box.lengths
else:
warn("No unitcell detected for pybel.Molecule {}".format(pybel_mol))
# TODO: Decide how to gather PBC information from openbabel. Options may
# include storing it in .periodicity or writing a separate function
# that returns the box.
[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
"""
from intermol.atom import Atom as InterMolAtom
from intermol.molecule import Molecule
from intermol.system import System
import simtk.unit as u
if isinstance(molecule_types, list):
molecule_types = tuple(molecule_types)
elif molecule_types is None:
molecule_types = (type(self),)
intermol_system = System()
last_molecule_compound = None
for atom_index, atom in enumerate(self.particles()):
for parent in atom.ancestors():
# Don't want inheritance via isinstance().
if type(parent) in molecule_types:
# Check if we have encountered this molecule type before.
if parent.name not in intermol_system.molecule_types:
self._add_intermol_molecule_type(
intermol_system, parent)
if parent != last_molecule_compound:
last_molecule_compound = parent
last_molecule = Molecule(name=parent.name)
intermol_system.add_molecule(last_molecule)
break
else:
# Should never happen if molecule_types only contains
# type(self)
raise ValueError(
'Found an atom {} that is not part of any of '
'the specified molecule types {}'.format(
atom, molecule_types))
# Add the actual intermol atoms.
intermol_atom = InterMolAtom(atom_index + 1, name=atom.name,
residue_index=1, residue_name='RES')
intermol_atom.position = atom.pos * u.nanometers
last_molecule.add_atom(intermol_atom)
return intermol_system
[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
@staticmethod
def _add_intermol_molecule_type(intermol_system, parent): # pragma: no cover
"""Create a molecule type for the parent and add bonds.
This method takes an intermol system and adds a
parent compound, including its particles and bonds, to it.
"""
from intermol.moleculetype import MoleculeType
from intermol.forces.bond import Bond as InterMolBond
molecule_type = MoleculeType(name=parent.name)
intermol_system.add_molecule_type(molecule_type)
for index, parent_atom in enumerate(parent.particles()):
parent_atom.index = index + 1
for atom1, atom2 in parent.bonds():
intermol_bond = InterMolBond(atom1.index, atom2.index)
molecule_type.bonds.add(intermol_bond)
def __getitem__(self, selection):
if isinstance(selection, int):
return list(self.particles())[selection]
if isinstance(selection, str):
if selection not in self.labels:
raise MBuildError('{}[\'{}\'] does not exist.'.format(self.name,selection))
return self.labels.get(selection)
def __repr__(self):
descr = list('<')
descr.append(self.name + ' ')
if self.children:
descr.append('{:d} particles, '.format(self.n_particles))
if any(self.periodicity):
descr.append('periodicity: {}, '.format(self.periodicity))
else:
descr.append('non-periodic, ')
else:
descr.append('pos=({: .4f},{: .4f},{: .4f}), '.format(*self.pos))
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):
"""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. 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.periodicity = deepcopy(self.periodicity)
newone._pos = deepcopy(self._pos)
newone.port_particle = deepcopy(self.port_particle)
newone._check_if_contains_rigid_bodies = deepcopy(
self._check_if_contains_rigid_bodies)
newone._contains_rigid = deepcopy(self._contains_rigid)
newone._rigid_id = deepcopy(self._rigid_id)
newone._charge = deepcopy(self._charge)
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):
"""While cloning, 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