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Commit 15c7c64d authored by Studer Gabriel's avatar Studer Gabriel
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modification of interaction docu

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......@@ -20,49 +20,125 @@ Invalid defining an unknown interaction:
HarmonicBond, HarmonicAngle, UreyBradleyAngle, PeriodicDihedral,
PeriodicImproper, HarmonicImproper, CMap, LJ, LJPair, GBSA,
DistanceConstraint, Exclusion, HarmonicPositionRestraint,
HarmonicPositionRestraint, Invalid
HarmonicDistanceRestraint, 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)
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
#. :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)
: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
types.
Sets the forcefield specific atom 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
..method:: SetNames(names)
.. method:: SetNames(names)
Sets atom names.
:param types: A list of strings describing the atom names.
:type names: :class:`list`
:param types: :class:`list` of :class:`str` describing the atom names.
:raises: :exc:` RuntimeError` when size of input is not consistent with
the interactions functype
:raises: :class:`RuntimeError` when size of input is not
consistent with the interactions functype
..method:: SetParam(names)
.. method:: SetParam(names)
Sets interaction specific parameters.
:param types: A list of real values .
:param types: A :class:`list` of :class:`float` values .
:type names: :class:`list`
......@@ -70,7 +146,7 @@ a harmonic angle)
the interactions functype
..method:: GetTypes()
.. method:: GetTypes()
Get Previously set types
......@@ -78,99 +154,101 @@ a harmonic angle)
..method:: GetNames()
.. method:: GetNames()
Get Previously set names
:returns: :class:`list`
..method:: GetParam()
.. method:: GetParam()
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
the atom names
the atom names of the interaction
:param residue: :class:`mol.ResidueHandle`
:param residue :class:`~mol.ResidueHandle`
:returns: :class:`~mol.AtomHandleList`
:raises: :exc:`RuntimeError` when atom cannot be found in residue
:returns: :class:`mol.AtomHandleList`
:raises: :class:`RuntimeError` when atom cannot be found in
residue
..method:: GetFuncType()
.. method:: GetFuncType()
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
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
:param name: class:`str`
:param new_name: class:`str`
:param new_type: class:`str`
: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
can be "as is" or in reversed order
:param atom_types :class:`list`
:returns: `:wtf:`bool`
:param atom_types: :class:`list` of :class:`str`
:returns: :class:`bool`
..method::MatchNames(atom_names)
.. 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`
:param atom_names: :class:`list` of :class:`str`
:returns: :class:`bool`
..method::HasName(name)
.. method:: HasName(name)
Checks, whether the given name is present in the internal names
:param name :class:`string`
:returns: :wtf:`bool`
:param name: :class:`string`
:returns: :class:`bool`
..method::HasType(type)
.. method:: HasType(type)
Checks, whether the given type is present in the internal types
:param type :class:`string`
:returns: :wtf:`bool`
:param type: :class:`string`
:returns: :class:`bool`
..IsParametrized()
.. method:: IsParametrized()
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')
:returns: :wtf:`bool`
:returns: :class:`bool`
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