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Interactions
================================================================================
.. currentmodule:: ost.mol.mm
The :class:`Interaction` object is intended to build a basic container that 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 15 possible values with
Invalid defining an unknown interaction:
HarmonicBond, HarmonicAngle, UreyBradleyAngle, PeriodicDihedral,
PeriodicImproper, HarmonicImproper, CMap, LJ, LJPair, GBSA,
DistanceConstraint, Exclusion, HarmonicPositionRestraint,
HarmonicDistanceRestraint, Invalid
The implementation guarantees that the parameter related to atom types,
names, parameters are checked regarding their dimension (e.g. 3 atoms and 2
parameters for a harmonic angle)
Interaction Parametrization
--------------------------------------------------------------------------------
* 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 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
The Interaction Class
--------------------------------------------------------------------------------
.. class:: Interaction (func_type)
:param func_type: :class:`FuncType` defining a particular interaction
.. method:: SetTypes(types)
Sets the forcefield specific atom types.
:param types: Strings describing the force field specific atom types.
:type types: :class:`list`
:raises: :class:`RuntimeError` when size of input is not consistent with
the interactions functype
.. method:: SetNames(names)
Sets atom names
:param names: Strings describing the atom names
:type names: :class:`list`
:raises: :class:`RuntimeError` when size of input is not
consistent with the interactions functype
.. method:: SetParam(param)
Sets interaction specific parameters.
:param param: Float values .
:type param: :class:`list`
:raises: :class:`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: :class:`list`
.. method:: GetAtoms(residue)
Returns an :class:`AtomHandleList` containing the atoms in residue matching
the atom names of the interaction
:param residue: Residue from which atoms are extracted
:type residue: :class:`ResidueHandle`
:returns: :class:`AtomHandleList`
:raises: :class:`RuntimeError` when an atom cannot be found in
**residue**
.. method:: GetFuncType()
Returns the functype enum of the interaction
:returns: :class:`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: Name of atom to be replaces
:param new_name: Its new name
:param new_type: Its new type
:type name: :class:`str`
:type new_name: :class:`str`
:type new_type: :class:`str`
:returns: :class:`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: Atom types to be matched
:type atom_types: :class:`list`
:returns: :class:`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: Atom names to be matched
:type atom_names: :class:`list`
:returns: :class:`bool`
.. method:: HasName(name)
Checks, whether the given name is present in the internal names
:param name: Name to be checked
:type name: :class:`str`
:returns: :class:`bool`
.. method:: HasType(type)
Checks, whether the given type is present in the internal types
:param type: Type to be checked
:type type: :class:`str`
:returns: :class:`bool`
.. method:: IsParametrized()
Checks, whether the parameters have been set
:returns: :class:`bool`
.. method:: HasTypeWildcard()
Checks, whether one of the types is a wildcard ('X')
:returns: :class:`bool`
.. method:: HasNameWildcard()
Checks, whether one of the names is a wildcard ('X')
:returns: :class:`bool`
|
