Add virtual templates

topology/core/virtualsite.py

@@ -0,0 +1,73 @@
+import warnings
+from topology.core.site import Site
+from topology.core.potential import Potential
+
+
+class VirtualSite(object):
+    """A virtual site construction
+
+    Partners
+    --------
+    virtual_site: topology.site
+        An instance of topology.site that is the virtual site
+    virtual_site_members: list of topology.Site
+        Should be length 2 or 3
+    virtual_site_type: topology.Potential
+        An instance of topology.Potential that describes
+        the virtual site function and parameters of this interaction
+    name: name of the virtual site
+    """
+
+    def __init__(self, virtual_site, virtual_site_members=[], virtual_site_type=None, name="VirtualSite"):
+        if virtual_site_members is None:
+            virtual_site_members = tuple()
+
+        # TODO: validate virtual site members
+        #self._virtual_site_members = _validate_virtual_site_members(virtual_site_members)
+        self._virtual_site = virtual_site
+        self._virtual_site_members = virtual_site_members
+        self._virtual_site_type = _validate_vs_type(virtual_site_type)
+        self._name = _validate_name(name)
+        # TODO: update members
+        #self._update_members()
+
+    @property
+    def virtual_site(self):
+        return self._virtual_site
+
+    @property
+    def virtual_site_members(self):
+        return self._virtual_site_members
+
+    @property
+    def virtual_site_type(self):
+        return self._virtual_site_type
+
+    @property
+    def name(self):
+        return self._name
+
+    @name.setter
+    def name(self, vsname):
+        self._name = _validate_name(vsname)
+
+    def __repr__(self):
+        descr = '<{} Virtual Site, id {}'.format(
+                self.virtual_site_type, id(self))
+        if self.name:
+            descr += ', name {}'.format(self.name)
+        descr += '>'
+
+        return descr
+
+def _validate_vs_type(c_type):
+    if c_type is None:
+        warnings.warn("Non-parametrized virtual site detected")
+    elif not isinstance(c_type, Potential):
+        raise TopologyError("Supplied non-Potential {}".format(c_type))
+    return c_type
+
+def _validate_name(conname):
+    if not isinstance(conname, str):
+        raise TopologyError("Supplied name {} is not a string".format(conname))
+    return conname

topology/core/virtualsite_type.py

@@ -0,0 +1,68 @@
+import warnings
+import unyt as u
+
+from topology.core.potential import Potential
+from topology.exceptions import TopologyError
+from topology.utils._constants import DIHEDRAL_TYPE_DICT
+
+class VirtualSiteType(Potential):
+    """A virtual site construction.
+
+    Parameters
+    ----------
+    name : str
+    expression : str or sympy.Expression
+        See `Potential` documentation for more information
+    parameters : dict {str, unyt.unyt_quantity}
+        See `Potential` documentation for more information
+    independent vars : set of str
+        See `Potential` documentation for more information
+    member_types : list of topology.AtomType.name (str)
+    topology: topology.core.Topology, the topology of which this virtual site type is a part of, default=None
+    set_ref: (str), the string name of the bookkeeping set in topology class.
+
+    Notes
+    ----
+    Inherits many functions from topology.Potential:
+        __eq__, _validate functions
+    """
+
+    def __init__(self,
+                 name='VirtualSiteType',
+                 expression='1 - a',
+                 parameters=None,
+                 independent_variables=None,
+                 member_types=None,
+                 topology=None,
+                 set_ref='virtualsite_type_set'):
+        if parameters is None:
+            parameters = {
+                'a': 0.35 * u.dimensionless
+            }
+
+        if member_types is None:
+            member_types = list()
+
+        super(VirtualSiteType, self).__init__(name=name, expression=expression,
+                                           parameters=parameters, independent_variables=independent_variables,
+                                           topology=topology)
+        #self._set_ref = VIRTUALSITE_TYPE_DICT
+        self._member_types = member_types
+
+    @property
+    def set_ref(self):
+        return self._set_ref
+
+    @property
+    def member_types(self):
+        return self._member_types
+
+    @member_types.setter
+    def member_types(self, val):
+        if self.member_types != val:
+            warnings.warn("Changing an VirtualSiteType's constituent "
+                          "member types: {} to {}".format(self.member_types, val))
+        self._member_types = _validate_four_member_type_names(val)
+
+    def __repr__(self):
+        return "<VirtualSiteType {}, id {}>".format(self.name, id(self))

topology/lib/virtual_templates.py

@@ -0,0 +1,40 @@
+from topology.core.potential import Potential
+
+
+class VirtualSiteTemplate(Potential):
+    def __init__(self,
+                 name='VirtualSiteTemplate',
+                 expression='1 - a',
+                 independent_variables=None,
+                 template=True):
+
+        super(VirtualSiteTemplate, self).__init__(
+            name=name,
+            expression=expression,
+            independent_variables=independent_variables,
+            template=template,
+        )
+
+class TwoSiteConstruction(VirtualSiteTemplate):
+    def __init__(self,
+                 name='TwoSiteConstruction',
+                 expression='1 - a)',
+                 independent_variables=None):
+        super(PotentialTemplate, self).__init__(
+            name=name,
+            expression=expression,
+            independent_variables=independent_variables,
+            template=True,
+        )
+
+class ThreeSiteConstruction(VirtualSiteTemplate):
+    def __init__(self,
+                 name='ThreeSiteConstruction',
+                 expression='1 - a - b)',
+                 independent_variables=None):
+        super(PotentialTemplate, self).__init__(
+            name=name,
+            expression=expression,
+            independent_variables=independent_variables,
+            template=True,
+        )