interaction.rst



Interactions
The interaction object is intended to build a basic container tat can be used
in various scenarios. At the initialization a FuncType has to be defined.
Whenever names, types or parameters are set, the number of parameters
gets checked according to the FuncType. A name or type can also consist of
a wildcard expressed as X.

The FuncType enum
Every Interaction is linked to one particular FuncType describing the types
of interactions supported by OpenStructure. There are a 15 possible values with
Invalid defining an unknown interaction:

HarmonicBond, HarmonicAngle, UreyBradleyAngle, PeriodicDihedral,
PeriodicImproper, HarmonicImproper, CMap, LJ, LJPair, GBSA,
DistanceConstraint, Exclusion, HarmonicPositionRestraint,
HarmonicPositionRestraint, Invalid
The implementation guarantees, that the parameter related to atom types,
names, parameters are checked regarding their dimension (e.g. 3 atoms for
a harmonic angle)

..method:: SetTypes(types)

Sets the forcefield specific atom types.


param types:
A list of strings describing the force field specific atom
types.


type types:
:class:`list`


raises:
:exc:` RuntimeError` when size of input is not consistent with
the interactions functype


..method:: SetNames(names)

Sets atom names.


param types:
A list of strings describing the atom names.


type names:
:class:`list`


raises:
:exc:` RuntimeError` when size of input is not consistent with
the interactions functype


..method:: SetParam(names)

Sets interaction specific parameters.


param types:
A list of real values .


type names:
:class:`list`


raises:
:exc:`RuntimeError` when size of input is not consistent with
the interactions functype


..method:: GetTypes()

Get Previously set types


returns:
:class:`list`


..method:: GetNames()

Get Previously set names


returns:
:class:`list`


..method:: GetParam()

Get Previously set parameters


returns:
:wtf:`bool`


..method:: GetAtoms(residue)

Returns an AtomHandleList containing the atoms in residue matching
the atom names
:param residue :class:`~mol.ResidueHandle`
:returns:      :class:`~mol.AtomHandleList`
:raises: :exc:`RuntimeError` when atom cannot be found in residue

..method:: GetFuncType()

Returns the functype enum of the interaction


returns:
:enum:`~mol.mm.FuncType`


..method:: ReplaceAtom(name, new_name, new_type)

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
associated atom type gets also reset to new_type.
:param name    :class:`string`
:param new_name:class:string
:param new_type:class:string
:returns:      :wtf:`bool` whether replacement was successful or not

..method::MatchTypes(atom_types)

Checks, whether the given types match the internal types. The match
can be "as is" or in reversed order
:param atom_types    :class:`list`
:returns:     :wtf:`bool

..method::MatchNames(atom_names)

Checks, whether the given names match the internal names. The match
can be "as is" or in reversed order
:param atom_names    :class:`list`
:returns:     :wtf:`bool

..method::HasName(name)

Checks, whether the given name is present in the internal names
:param name    :class:`string`
:returns:      :wtf:`bool`

..method::HasType(type)

Checks, whether the given type is present in the internal types
:param type    :class:`string`
:returns:      :wtf:`bool`

..IsParametrized()

Checks, whether the parameters have been set


returns:
:wtf:`bool`


..HasTypeWildcard()

Checks, whether one of the types is a wildcard (X)


returns:
:wtf:`bool`


..HasNameWildcard()

Checks, whether one of the names is a wildcard (X)


returns:
:wtf:`bool`