From 15c7c64d74bec45769a3525fd79315ee2a1622e3 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 5 May 2015 09:22:40 +0200
Subject: [PATCH] modification of interaction docu
---
modules/mol/mm/doc/interaction.rst | 184 ++++++++++++++++++++---------
1 file changed, 131 insertions(+), 53 deletions(-)
diff --git a/modules/mol/mm/doc/interaction.rst b/modules/mol/mm/doc/interaction.rst
index 8687fd7d5..a1eff84d1 100644
--- a/modules/mol/mm/doc/interaction.rst
+++ b/modules/mol/mm/doc/interaction.rst
@@ -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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