* HarmonicBond, Interacting Particles: 2, Num Parameters: 2
#. :class:`float` bond length in nm
#. :class:`float` force constant in kJ/mol/nm^2
* HarmonicAngle, Interacting Particles: 3, Num Parameters: 2
#. :class:`float` angle in radians
#. :class:`float` force constant in kJ/mol/radian^2
* UreyBradleyAngle, Interacting Particles: 3, Num Parameters: 4
#. :class:`float` angle in radians
#. :class:`float` angle force constant in kJ/mol/radian^2
#. :class:`float` bond length in nm
#. :class:`float` bond force constant in kJ/mol/nm^2
* PeriodicDihedral, Interacting Particles: 4, Num Parameters: 3
#. :class:`int` multiplicity
#. :class:`float` phase in radians
#. :class:`float` force constant in kJ/mol/radian^2
* PeriodicImproper, Interacting Particles: 4, Num Parameters: 3
#. :class:`int` multiplicity
#. :class:`float` phase in radians
#. :class:`float` force constant in kJ/mol/radian^2
* HarmonicImproper, Interacting Particles: 4, Num Parameters: 2
#. :class:`float` angle in radians
#. :class:`float` force constant in
#. :class:`float` force constant in kJ/mol/radian^2
* CMap, Interacting Particles: 5, Num Parameters: n*n+1
#. :class:`list` of :class:`float` of size n*n+1, first value describes the dimension n of the cmap, the other n*n values describe the correction map in kJ/mol in the ordering (phi1,psi1),(phi1,psi2)... and torsion angles in [-pi,pi] (will be converted to the format OpenMM prefers)
* LJ, Interacting Particles: 1, Num Parameters: 2
#. :class:`float` sigma in nm
#. :class:`float` epsilon in kJ/mol
* LJPair, Interacting Particles: 2, Num Parameters: 2
#. :class:`float` sigma in nm
#. :class:`float` epsilon in kJ/mol
* GBSA, Interacting Particles: 1, Num Parameters: 2
#. :class:`float` GBSA radius in nm
#. :class:`float` OBC scaling factor
* DistanceConstraint, Interacting Particles: 2, Num Parameters: 1
#. :class:`float` constraint distance
* Exclusion, Interacting Particles: 2, Num Parameters: 0
* HarmonicPositionRestraint, Interacting Particles: 1, Num Parameters: 7
#. :class:`float` ref pos x
#. :class:`float` ref pos y
#. :class:`float` ref pos z
#. :class:`float` force constant
#. :class:`float` x_scale
#. :class:`float` y_scale
#. :class:`float` z_scale
* HarmonicDistanceRestraint, Interacting Particles: 2, Num Parameters: 2
#. :class:`float` restraint length
#. :class:`float` force constant
.. class:: Interaction(func_type)
.. class:: Interaction(func_type)
:param func_type: :class:`FuncType` defining a particular interaction
:param func_type: :class:`FuncType` defining a particular interaction
..method:: SetTypes(types)
Sets the forcefield specific atom types.
.. method:: SetTypes(types)
:param types: A list of strings describing the force field specific atom
Sets the forcefield specific atom types.
types.
:type types: :class:`list`
:param types: :class:`list` of :class:`str` A list of strings
describing the force field specific atom types.
:raises: :exc:`RuntimeError` when size of input is not consistent with
:raises: :class:`RuntimeError` when size of input is not consistent with
the interactions functype
the interactions functype
..method:: SetNames(names)
..method:: SetNames(names)
Sets atom names.
Sets atom names.
:param types: A list of strings describing the atom names.
:param types: :class:`list` of :class:`str` describing the atom names.
:type names: :class:`list`
:raises: :exc:`RuntimeError` when size of input is not consistent with
:raises: :class:`RuntimeError` when size of input is not
the interactions functype
consistent with the interactions functype
..method:: SetParam(names)
..method:: SetParam(names)
Sets interaction specific parameters.
Sets interaction specific parameters.
:param types: A list of real values .
:param types: A :class:`list` of :class:`float` values .
:type names: :class:`list`
:type names: :class:`list`
...
@@ -70,7 +146,7 @@ a harmonic angle)
...
@@ -70,7 +146,7 @@ a harmonic angle)
the interactions functype
the interactions functype
..method:: GetTypes()
..method:: GetTypes()
Get Previously set types
Get Previously set types
...
@@ -78,99 +154,101 @@ a harmonic angle)
...
@@ -78,99 +154,101 @@ a harmonic angle)
..method:: GetNames()
..method:: GetNames()
Get Previously set names
Get Previously set names
:returns: :class:`list`
:returns: :class:`list`
..method:: GetParam()
..method:: GetParam()
Get Previously set parameters
Get Previously set parameters
:returns: :wtf:`bool`
:returns: :class:`bool`
..method:: GetAtoms(residue)
..method:: GetAtoms(residue)
Returns an AtomHandleList containing the atoms in residue matching
Returns an AtomHandleList containing the atoms in residue matching
the atom names
the atom names of the interaction
:param residue: :class:`mol.ResidueHandle`
:param residue :class:`~mol.ResidueHandle`
:returns: :class:`mol.AtomHandleList`
:returns: :class:`~mol.AtomHandleList`
:raises: :exc:`RuntimeError` when atom cannot be found in residue
:raises: :class:`RuntimeError` when atom cannot be found in
residue
..method:: GetFuncType()
..method:: GetFuncType()
Returns the functype enum of the interaction
Returns the functype enum of the interaction
:returns: :enum:`mol.mm.FuncType`
:returns: :class:`FuncType`
..method:: ReplaceAtom(name, new_name, new_type)
..method:: ReplaceAtom(name, new_name, new_type)
Searches for given atom name. If found, this particular atom name
Searches for given atom name. If found, this particular atom name
gets changed to new_name. If the atom types are set as well, the
gets changed to new_name. If the atom types are set as well, the
associated atom type gets also reset to new_type.
associated atom type gets also reset to new_type.
:param name :class:`string`
:param name: class:`str`
:param new_name:class:`string`
:param new_name:class:`str`
:param new_type:class:`string`
:param new_type:class:`str`
:returns: :wtf:`bool` whether replacement was successful or not
:returns: :class:`bool` whether replacement was successful or not
..method::MatchTypes(atom_types)
..method::MatchTypes(atom_types)
Checks, whether the given types match the internal types. The match
Checks, whether the given types match the internal types. The match
can be "as is" or in reversed order
can be "as is" or in reversed order
:param atom_types :class:`list`
:param atom_types::class:`list` of :class:`str`
:returns: `:wtf:`bool`
:returns: :class:`bool`
..method::MatchNames(atom_names)
..method::MatchNames(atom_names)
Checks, whether the given names match the internal names. The match
Checks, whether the given names match the internal names. The match
can be "as is" or in reversed order
can be "as is" or in reversed order
:param atom_names :class:`list`
:param atom_names::class:`list` of :class:`str`
:returns: `:wtf:`bool`
:returns: :class:`bool`
..method::HasName(name)
..method::HasName(name)
Checks, whether the given name is present in the internal names
Checks, whether the given name is present in the internal names
:param name :class:`string`
:param name: :class:`string`
:returns: :wtf:`bool`
:returns: :class:`bool`
..method::HasType(type)
..method::HasType(type)
Checks, whether the given type is present in the internal types
Checks, whether the given type is present in the internal types
:param type :class:`string`
:param type: :class:`string`
:returns: :wtf:`bool`
:returns: :class:`bool`
..IsParametrized()
.. method:: IsParametrized()
Checks, whether the parameters have been set
Checks, whether the parameters have been set
:returns: :wtf:`bool`
:returns: :class:`bool`
..HasTypeWildcard()
.. method:: HasTypeWildcard()
Checks, whether one of the types is a wildcard (X)
Checks, whether one of the types is a wildcard ('X')
:returns: :wtf:`bool`
:returns: :class:`bool`
..HasNameWildcard()
.. method:: HasNameWildcard()
Checks, whether one of the names is a wildcard (X)
Checks, whether one of the names is a wildcard ('X')
