"""Base data structure for GMSO chemical systems."""
import warnings
import numpy as np
import unyt as u
from boltons.setutils import IndexedSet
from gmso.core.angle import Angle
from gmso.core.angle_type import AngleType
from gmso.core.atom import Atom
from gmso.core.atom_type import AtomType
from gmso.core.bond import Bond
from gmso.core.bond_type import BondType
from gmso.core.dihedral import Dihedral
from gmso.core.dihedral_type import DihedralType
from gmso.core.improper import Improper
from gmso.core.improper_type import ImproperType
from gmso.core.parametric_potential import ParametricPotential
from gmso.exceptions import GMSOError
from gmso.utils._constants import (
ANGLE_TYPE_DICT,
ATOM_TYPE_DICT,
BOND_TYPE_DICT,
DIHEDRAL_TYPE_DICT,
IMPROPER_TYPE_DICT,
)
from gmso.utils.connectivity import (
identify_connections as _identify_connections,
)
[docs]class Topology(object):
"""A topology.
A topology represents a chemical structure wherein lie the collection
of sites which together form a chemical structure containing connections
(gmso.Bond, gmso.Angle and gmso.Dihedral (along with their associated types).
A topology is the fundamental data structure in GMSO, from which we can gather
various information about the chemical structure and apply a forcefield
before converting the structure into a format familiar to various simulation
engines.
Parameters
----------
name : str, optional, default='Topology'
A name for the Topology.
box : gmso.Box, optional, default=None
A gmso.Box object bounding the topology
Attributes
----------
typed : bool
True if the topology is typed
combining_rule : str, ['lorentz', 'geometric']
The combining rule for the topology, can be either 'lorentz' or 'geometric'
scaling_factors : dict
A collection of scaling factors used in the forcefield
n_sites : int
Number of sites in the topology
n_connections : int
Number of connections in the topology (Bonds, Angles, Dihedrals, Impropers)
n_bonds : int
Number of bonds in the topology
n_angles: int
Number of angles in the topology
n_dihedrals : int
Number of dihedrals in the topology
n_impropers : int
Number of impropers in the topology
n_subtops : int
Number of subtopolgies in the topology
connections : tuple of gmso.Connection objects
A collection of bonds, angles, dihedrals, and impropers in the topology
bonds : tuple of gmso.Bond objects
A collection of bonds in the topology
angles : tuple of gmso.Angle objects
A collection of angles in the topology
dihedrals : tuple of gmso.Dihedral objects
A collection of dihedrals in the topology
impropers : tuple of gmso.Improper objects
A collection of impropers in the topology
connection_types : tuple of gmso.Potential objects
A collection of BondTypes, AngleTypes, DihedralTypes, and ImproperTypes in the topology
atom_types : tuple of gmso.AtomType objects
A collection of AtomTypes in the topology
bond_types : tuple of gmso.BondType objects
A collection of BondTypes in the topology
angle_types : tuple of gmso.AngleType objects
A collection go AngleTypes in the topology
dihedral_types : tuple of gmso.DihedralType objects
A collection of DihedralTypes in the topology
improper_types : tuple of gmso.ImproperType objects
A collection of ImproperTypes in the topology
atom_type_expressions : list of gmso.AtomType.expression objects
A collection of all the expressions for the AtomTypes in topology
connection_type_expressions : list of gmso.Potential.expression objects
A collection of all the expressions for the Potential objects in the topology that represent a connection type
bond_type_expressions : list of gmso.BondType.expression objects
A collection of all the expressions for the BondTypes in topology
angle_type_expressions : list of gmso.AngleType.expression objects
A collection of all the expressions for the AngleTypes in topology
dihedral_type_expressions : list of gmso.DihedralType.expression objects
A collection of all the expression for the DihedralTypes in the topology
improper_type_expressions : list of gmso.ImproperType.expression objects
A collection of all the expression for the ImproperTypes in the topology
See Also
--------
gmso.SubTopology :
A topology within a topology
"""
def __init__(self, name="Topology", box=None):
self.name = name
self._box = box
self._sites = IndexedSet()
self._typed = False
self._connections = IndexedSet()
self._bonds = IndexedSet()
self._angles = IndexedSet()
self._dihedrals = IndexedSet()
self._impropers = IndexedSet()
self._subtops = IndexedSet()
self._atom_types = {}
self._atom_types_idx = {}
self._connection_types = {}
self._bond_types = {}
self._bond_types_idx = {}
self._angle_types = {}
self._angle_types_idx = {}
self._dihedral_types = {}
self._dihedral_types_idx = {}
self._improper_types = {}
self._improper_types_idx = {}
self._combining_rule = "lorentz"
self._scaling_factors = {
"vdw_12": 0.0,
"vdw_13": 0.0,
"vdw_14": 0.5,
"coul_12": 0.0,
"coul_13": 0.0,
"coul_14": 0.5,
}
self._set_refs = {
ATOM_TYPE_DICT: self._atom_types,
BOND_TYPE_DICT: self._bond_types,
ANGLE_TYPE_DICT: self._angle_types,
DIHEDRAL_TYPE_DICT: self._dihedral_types,
IMPROPER_TYPE_DICT: self._improper_types,
}
self._index_refs = {
ATOM_TYPE_DICT: self._atom_types_idx,
BOND_TYPE_DICT: self._bond_types_idx,
ANGLE_TYPE_DICT: self._angle_types_idx,
DIHEDRAL_TYPE_DICT: self._dihedral_types_idx,
IMPROPER_TYPE_DICT: self._improper_types_idx,
}
self._unique_connections = {}
@property
def name(self):
"""Return the name of the topology."""
return self._name
@name.setter
def name(self, name):
"""Set the name of the topology."""
self._name = str(name) if name else "Topology"
@property
def box(self):
"""Return the Box of the topology."""
return self._box
@box.setter
def box(self, box):
"""Set the box of the topology."""
self._box = box
@property
def typed(self):
"""Check if the system is parametrized."""
return self._typed
@typed.setter
def typed(self, typed):
"""Set the status of the topology if parametrized."""
self._typed = typed
@property
def combining_rule(self):
"""Return the combining rule for the topology."""
return self._combining_rule
@combining_rule.setter
def combining_rule(self, rule):
"""Set the combining rule for the topology."""
if rule not in ["lorentz", "geometric"]:
raise GMSOError("Combining rule must be `lorentz` or `geometric`")
self._combining_rule = rule
@property
def scaling_factors(self):
"""Return the scaling factors for the topology."""
return self._scaling_factors
@scaling_factors.setter
def scaling_factors(self, scaling_factors):
"""Set the scaling factors for the topology."""
expected_items = [
"vdw_12",
"vdw_13",
"vdw_14",
"coul_12",
"coul_13",
"coul_14",
]
if not isinstance(scaling_factors, dict):
raise GMSOError("Scaling factors should be a dictionary")
for item in expected_items:
if item not in scaling_factors.keys():
raise GMSOError(
f"Expected {expected_items} as keys in the scaling factors"
)
for val in scaling_factors.values():
if val < 0.0 or val > 1.0:
raise GMSOError("Scaling factors should be between 0.0 and 1.0")
self._scaling_factors = scaling_factors
@property
def positions(self):
"""Return the positions of the sites in the topology."""
xyz = np.empty(shape=(self.n_sites, 3)) * u.nm
for i, site in enumerate(self._sites):
xyz[i, :] = site.position
return xyz
@property
def n_sites(self):
"""Return the number of sites in the topology."""
return len(self.sites)
@property
def n_connections(self):
"""Return the number of connections in the topology."""
return len(self.connections)
@property
def n_bonds(self):
"""Return the number of bonds in the topology."""
return len(self.bonds)
@property
def n_angles(self):
"""Return the amount of angles in the topology."""
return len(self.angles)
@property
def n_dihedrals(self):
"""Return the amount of dihedrals in the topology."""
return len(self.dihedrals)
@property
def n_impropers(self):
"""Return the number of impropers in the topology."""
return len(self.impropers)
@property
def subtops(self):
"""Return the subtopologies in the topology."""
return self._subtops
@property
def n_subtops(self):
"""Return number of subtopolgies."""
return len(self._subtops)
@property
def sites(self):
"""Return all sites in the topology."""
return tuple(self._sites)
@property
def connections(self):
"""Return all connections in topology."""
return tuple(self._connections)
@property
def bonds(self):
"""Return all bonds in the topology."""
return tuple(self._bonds)
@property
def angles(self):
"""Return all angles in the topology."""
return tuple(self._angles)
@property
def dihedrals(self):
"""Return all dihedrals in the topology."""
return tuple(self._dihedrals)
@property
def impropers(self):
"""Return all impropers in the topology."""
return tuple(self._impropers)
@property
def atom_types(self):
"""Return all atom_types in the topology."""
return tuple(self._atom_types.values())
@property
def connection_types(self):
"""Return all connection_types in the topology."""
return tuple(self._connection_types.values())
@property
def bond_types(self):
"""Return all bond_types in the topology."""
return tuple(self._bond_types.values())
@property
def angle_types(self):
"""Return all angle_types in the topology."""
return tuple(self._angle_types.values())
@property
def dihedral_types(self):
"""Return all dihedral_types in the topology."""
return tuple(self._dihedral_types.values())
@property
def improper_types(self):
"""Return all improper_types in the topology."""
return tuple(self._improper_types.values())
@property
def atom_type_expressions(self):
"""Return all atom_type expressions in the topology."""
return list(set([atype.expression for atype in self.atom_types]))
@property
def connection_type_expressions(self):
"""Return all connection_type expressions in the topology."""
return list(
set([contype.expression for contype in self.connection_types])
)
@property
def bond_type_expressions(self):
"""Return all bond_type expressions in the topology."""
return list(set([btype.expression for btype in self.bond_types]))
@property
def angle_type_expressions(self):
"""Return all angle_type expressions in the topology."""
return list(set([atype.expression for atype in self.angle_types]))
@property
def dihedral_type_expressions(self):
"""Return all dihedral_type expressions in the topology."""
return list(set([atype.expression for atype in self.dihedral_types]))
@property
def improper_type_expressions(self):
"""Return all improper_type expressions in the topology."""
return list(set([atype.expression for atype in self.improper_types]))
[docs] def add_site(self, site, update_types=True):
"""Add a site to the topology.
This method will add a site to the existing topology, since
sites are stored in an indexed set, adding redundant site
will have no effect. If the update_types parameter is set to
true (default behavior), this method will also check if there
is an gmso.AtomType associated with the site and it to the
topology's AtomTypes collection.
Parameters
----------
site : gmso.core.Site
Site to be added to this topology
update_types : (bool), default=True
If true, add this site's atom type to the topology's set of AtomTypes
"""
self._sites.add(site)
if update_types and site.atom_type:
site.atom_type.topology = self
if site.atom_type in self._atom_types:
site.atom_type = self._atom_types[site.atom_type]
else:
self._atom_types[site.atom_type] = site.atom_type
self._atom_types_idx[site.atom_type] = len(self._atom_types) - 1
self.is_typed(updated=False)
def update_sites(self):
"""Update the sites of the topology.
This method will update the sites in the topology
based on the connection members, For example- if you
add a bond to a topology, without adding the constituent
sites, this method can be called to add the sites which are the
connection members of the bond as shown below.
>>> import gmso
>>> site1 = gmso.Site(name='MySite1')
>>> site2 = gmso.Site(name='MySite2')
>>> bond1 = gmso.Bond(name='site1-site2', connection_members=[site1, site2])
>>> this_topology = gmso.Topology('TwoSitesTopology')
>>> this_topology.add_connection(bond1)
>>> this_topology.update_sites()
See Also
--------
gmso.Topology.add_site : Add a site to the topology.
gmso.Topology.add_connection : Add a Bond, an Angle or a Dihedral to the topology.
gmso.Topology.update_topology : Update the entire topology.
"""
for connection in self.connections:
for member in connection.connection_members:
if member not in self._sites:
self.add_site(member)
[docs] def add_connection(self, connection, update_types=True):
"""Add a gmso.Connection object to the topology.
This method will add a gmso.Connection object to the
topology, it can be used to generically include any
Connection object i.e. Bond or Angle or Dihedral to
the topology. According to the type of object added,
the equivalent collection in the topology is updated.
For example- If you add a Bond, this method will update
topology.connections and topology.bonds object. Additionally,
if update_types is True (default behavior), it will also
update any Potential objects associated with the connection.
Parameters
----------
connection : one of gmso.Connection, gmso.Bond, gmso.Angle, gmso.Dihedral, or gmso.Improper object
update_types : bool, default=True
If True also add any Potential object associated with connection to the
topology.
Returns
-------
gmso.Connection
The Connection object or equivalent Connection object that
is in the topology
"""
# Check if an equivalent connection is in the topology
equivalent_members = connection._equivalent_members_hash()
if equivalent_members in self._unique_connections:
warnings.warn(
"An equivalent connection already exists. "
"Providing the existing equivalent Connection."
)
connection = self._unique_connections[equivalent_members]
for conn_member in connection.connection_members:
if conn_member not in self.sites:
self.add_site(conn_member)
self._connections.add(connection)
self._unique_connections.update({equivalent_members: connection})
if isinstance(connection, Bond):
self._bonds.add(connection)
if isinstance(connection, Angle):
self._angles.add(connection)
if isinstance(connection, Dihedral):
self._dihedrals.add(connection)
if isinstance(connection, Improper):
self._impropers.add(connection)
if update_types:
self.update_connection_types()
return connection
def identify_connections(self):
"""Identify all connections in the topology."""
_identify_connections(self)
def update_connection_types(self):
"""Update the connection types based on the connection collection in the topology.
This method looks into all the connection objects (Bonds, Angles, Dihedrals, Impropers) to
check if any Potential object (BondType, AngleType, DihedralType, ImproperType) is not in the
topology's respective collection and will add those objects there.
See Also
--------
gmso.Topology.update_atom_types : Update atom types in the topology.
"""
for c in self.connections:
if c.connection_type is None:
warnings.warn(
"Non-parametrized Connection {} detected".format(c)
)
elif not isinstance(c.connection_type, ParametricPotential):
raise GMSOError(
"Non-Potential {} found"
"in Connection {}".format(c.connection_type, c)
)
elif c.connection_type not in self._connection_types:
c.connection_type.topology = self
self._connection_types[c.connection_type] = c.connection_type
if isinstance(c.connection_type, BondType):
self._bond_types[c.connection_type] = c.connection_type
self._bond_types_idx[c.connection_type] = (
len(self._bond_types) - 1
)
if isinstance(c.connection_type, AngleType):
self._angle_types[c.connection_type] = c.connection_type
self._angle_types_idx[c.connection_type] = (
len(self._angle_types) - 1
)
if isinstance(c.connection_type, DihedralType):
self._dihedral_types[c.connection_type] = c.connection_type
self._dihedral_types_idx[c.connection_type] = (
len(self._dihedral_types) - 1
)
if isinstance(c.connection_type, ImproperType):
self._improper_types[c.connection_type] = c.connection_type
self._improper_types_idx[c.connection_type] = (
len(self._improper_types) - 1
)
elif c.connection_type in self.connection_types:
if isinstance(c.connection_type, BondType):
c.connection_type = self._bond_types[c.connection_type]
if isinstance(c.connection_type, AngleType):
c.connection_type = self._angle_types[c.connection_type]
if isinstance(c.connection_type, DihedralType):
c.connection_type = self._dihedral_types[c.connection_type]
if isinstance(c.connection_type, ImproperType):
c.connection_type = self._improper_types[c.connection_type]
def update_atom_types(self):
"""Update atom types in the topology.
This method checks all the sites in the topology which have an
associated AtomType and if that AtomType is not in the topology's
AtomTypes collection, it will add it there.
See Also
--------
gmso.Topology.update_connection_types :
Update the connection types based on the connection collection in the topology
"""
for site in self._sites:
if site.atom_type is None:
warnings.warn("Non-parametrized site detected {}".format(site))
elif not isinstance(site.atom_type, AtomType):
raise GMSOError(
"Non AtomType instance found in site {}".format(site)
)
elif site.atom_type not in self._atom_types:
site.atom_type.topology = self
self._atom_types[site.atom_type] = site.atom_type
self._atom_types_idx[site.atom_type] = len(self._atom_types) - 1
elif site.atom_type in self._atom_types:
site.atom_type = self._atom_types[site.atom_type]
self.is_typed(updated=True)
def add_subtopology(self, subtop, update=True):
"""Add a sub-topology to this topology.
This methods adds a gmso.Core.SubTopology object to the topology
All the sites in this sub-topology are added to the collection of current
sites in this topology.
Parameters
----------
subtop : gmso.SubTopology
The sub-topology object to be added.
update : bool, default=True
See Also
--------
gmso.SubTopology : A topology within a topology
"""
self._subtops.add(subtop)
subtop.parent = self
self._sites.union(subtop.sites)
if update:
self.update_topology()
def is_typed(self, updated=False):
"""Verify if the topology is parametrized."""
if not updated:
self.update_connection_types()
self.update_atom_types()
if len(self.atom_types) > 0 or len(self.connection_types) > 0:
self._typed = True
else:
self._typed = False
return self._typed
def update_angle_types(self):
"""Use gmso.Topology.update_connection_types to update AngleTypes in the topology.
This method is an alias for gmso.Topology.update_connection_types.
See Also
--------
gmso.Topology.update_connection_types :
Update the connection types based on the connection collection in the topology.
"""
self.update_connection_types()
def update_bond_types(self):
"""Use gmso.Topology.update_connection_types to update BondTypes in the topology.
This method is an alias for gmso.Topology.update_connection_types.
See Also
--------
gmso.Topology.update_connection_types :
Update the connection types based on the connection collection in the topology.
"""
self.update_connection_types()
def update_dihedral_types(self):
"""Use gmso.Topology.update_connection_types to update DihedralTypes in the topology.
This method is an alias for gmso.Topology.update_connection_types.
See Also
--------
gmso.Topology.update_connection_types :
Update the connection types based on the connection collection in the topology.
"""
self.update_connection_types()
def update_improper_types(self):
"""Use gmso.Topology.update_connection_types to update ImproperTypes in the topology.
This method is an alias for gmso.Topology.update_connection_types.
See Also
--------
gmso.Topology.update_connection_types :
Update the connection types based on the connection collection in the topology.
"""
self.update_connection_types()
[docs] def update_topology(self):
"""Update the entire topology."""
self.update_sites()
self.update_atom_types()
self.update_connection_types()
self.is_typed(updated=True)
def _get_bonds_for(self, site):
"""Return a list of bonds in this Topology that the site is a part of."""
bonds = []
for bond in self.bonds:
if site in bond.connection_members:
bonds.append(bond)
return bonds
def _get_angles_for(self, site):
"""Return a list of angles in this Topology that the site is a part of."""
angles = []
for angle in self.angles:
if site in angle.connection_members:
angles.append(angle)
return angles
def _get_dihedrals_for(self, site):
"""Return a list of dihedrals in this Topology that the site is a part of."""
dihedrals = []
for dihedral in self.dihedrals:
if site in dihedral.connection_members:
dihedrals.append(dihedral)
return dihedrals
def get_index(self, member):
"""Get index of a member in the topology.
Parameters
----------
member : gmso Topology objects
The member to for which to return index for.
`member` can be of type gmso.Site, gmso.Bond, gmso.Angle, gmso.Dihedral, gmso.Improper,
gmso.AtomType, gmso.BondType, gmso.AngleType, gmso.DihedralType or gmso.ImproperType.
Returns
-------
int
The index of the member in the topology's collection objects
"""
refs = {
Atom: self._sites,
Bond: self._bonds,
Angle: self._angles,
Dihedral: self._dihedrals,
Improper: self._impropers,
AtomType: self._atom_types_idx,
BondType: self._bond_types_idx,
AngleType: self._angle_types_idx,
DihedralType: self._dihedral_types_idx,
ImproperType: self._improper_types_idx,
}
member_type = type(member)
if member_type not in refs.keys():
raise TypeError(
f"Cannot index member of type {member_type.__name__}"
)
try:
index = refs[member_type].index(member)
except AttributeError:
index = refs[member_type][member]
return index
def _reindex_connection_types(self, ref):
"""Re-generate the indices of the connection types in the topology."""
if ref not in self._index_refs:
raise GMSOError(
f"cannot reindex {ref}. It should be one of "
f"{ANGLE_TYPE_DICT}, {BOND_TYPE_DICT}, "
f"{ANGLE_TYPE_DICT}, {DIHEDRAL_TYPE_DICT}, {IMPROPER_TYPE_DICT}"
)
for i, ref_member in enumerate(self._set_refs[ref].keys()):
self._index_refs[ref][ref_member] = i
def __repr__(self):
"""Return custom format to represent topology."""
return (
f"<Topology {self.name}, {self.n_sites} sites,\n "
f"{self.n_connections} connections,\n "
f"{len(self.connection_types)} potentials,\n "
f"id: {id(self)}>"
)
def __str__(self):
"""Return custom format to represent topology as a string."""
return f"<Topology {self.name}, {self.n_sites} sites, id: {id(self)}>"