From 62402fd732867bb4372f0dda2afb60be22ab5978 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 30 Apr 2015 15:50:15 +0200
Subject: [PATCH] some updates on documentation
---
modules/mol/mm/doc/forcefield.rst | 26 +++++++---
modules/mol/mm/doc/simulation.rst | 81 ++++++++++++++++++++++++++++++-
modules/mol/mm/doc/topology.rst | 28 ++++++++++-
3 files changed, 123 insertions(+), 12 deletions(-)
diff --git a/modules/mol/mm/doc/forcefield.rst b/modules/mol/mm/doc/forcefield.rst
index 13cc06b5a..ffb80d522 100644
--- a/modules/mol/mm/doc/forcefield.rst
+++ b/modules/mol/mm/doc/forcefield.rst
@@ -40,7 +40,17 @@ gromacs format. The reader is capable of resolving the preprocessor statements
as they are used in GROMACS.
-.. class:: FFReader
+.. class:: FFReader(base_dir)
+
+ :param base_dir: :class:`str` defining the base_path of the reader.
+ All loaded files must be defined relative to this base
+ path.
+
+ The :class:`FFReader` builds up a :class:`Forcefield`, that gets updated with
+ every call to the read functions. If the read files contain preprocessor
+ statements as they are used in Gromacs, they will be applied to all
+ subsequent lines read in. Parsed preprocessor statements are:
+ #include, #define, #ifdef, #ifndef, #else and #endif
.. method:: ReadGromacsForcefield()
@@ -67,7 +77,8 @@ as they are used in GROMACS.
.. method:: SetForcefield(forcefield)
- Resets reader internal forcefield. Everything read so far is lost.
+ Resets reader internal forcefield. Everything read so far is lost,
+ except the already read preprocessor statements.
:param forcefield: :class:`Forcefield`
@@ -238,8 +249,7 @@ as they are used in GROMACS.
used otherwise.
- .. method:: AddResidueRenamingRule(name, ff_main_name, ff_n_ter_name,
- ff_c_ter_name, ff_two_ter_name)
+ .. method:: AddResidueRenamingRule(name, ff_main_name, ff_n_ter_name, ff_c_ter_name, ff_two_ter_name)
:param name: :class:`str` original name or the residue
(e.g. pdb/gromacs standard)
@@ -319,7 +329,7 @@ as they are used in GROMACS.
modifier for this residue
- .. method:: AssignFFSpecificNames(ent, reverse = False)
+ .. method:: AssignFFSpecificNames(ent,[,reverse = False])
This function does the forcefield specific renaming magic. It takes
the given :class:`EntityHandle` and applies the rules set in
@@ -444,7 +454,7 @@ as they are used in GROMACS.
matching given type can be found
- .. method:: GetLJ(type1, type2, pair=False)
+ .. method:: GetLJ(type1, type2,[,pair=False])
:param type1: :class:`str`
@@ -538,7 +548,7 @@ as they are used in GROMACS.
be found
- .. method:: GetNTerModifier(res_name, ter_name="")
+ .. method:: GetNTerModifier(res_name,[,ter_name=""])
:param res_name: :class:`str`
@@ -549,7 +559,7 @@ as they are used in GROMACS.
be found
- .. method:: GetCTerModifier(name, ter_name="")
+ .. method:: GetCTerModifier(name,[,ter_name=""])
:param res_name: :class:`str`
diff --git a/modules/mol/mm/doc/simulation.rst b/modules/mol/mm/doc/simulation.rst
index 0a7176133..9073856de 100644
--- a/modules/mol/mm/doc/simulation.rst
+++ b/modules/mol/mm/doc/simulation.rst
@@ -42,6 +42,10 @@ mapped back to the attached structure at any time.
:param settings: :class:`Settings` to control the parametrization of
the :class:`Simulation`
+ :raises: :class:`RuntimeException` when number of atoms in
+ **entity** is not equal the number of particles
+ in **topology**
+
.. method:: Save(filename)
@@ -154,95 +158,168 @@ mapped back to the attached structure at any time.
.. method:: ResetHarmonicBond(index,bond_length, force_constant)
+ Update of the harmonic bond parameters in the simulation **and**
+ in the attached :class:`Topology`
+
:param index: :class:`int`
:param bond_length: :class:`float`
:param force_constant: :class:`float`
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of harmonic bonds
+
.. method:: ResetHarmonicAngle()
+ Update of the harmonic angle parameters in the simulation **and**
+ in the attached :class:`Topology`
+
:param index: :class:`int`
:param angle: :class:`float`
:param force_constant: :class:`float`
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of harmonic angles
.. method:: ResetUreyBradleyAngle(index, angle, angle_force_constant, bond_length, bond_force_constant)
+ Update of the urey-bradley angle parameters in the simulation **and**
+ in the attached :class:`Topology`
+
:param index: :class:`int`
:param angle: :class:`float`
:param force_constant: :class:`float`
:param bond_length: :class:`float`
:param force_constant: :class:`float`
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of urey-bradley angles
.. method:: ResetPeriodicDihedral(index, multiplicity, phase, force_constant)
+ Update of the periodic dihedral parameters in the simulation **and**
+ in the attached :class:`Topology`
+
:param index: :class:`int`
:param multiplicity: :class:`int`
:param phase: :class:`float`
:param force_constant: :class:`float`
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of periodic dihedrals
+
.. method:: ResetPeriodicImproper(index, multiplicity, phase, force_constant)
+ Update of the periodic improper parameters in the simulation **and**
+ in the attached :class:`Topology`
+
:param index: :class:`int`
:param multiplicity: :class:`int`
:param phase: :class:`float`
:param force_constant: :class:`float`
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of periodic impropers
.. method:: ResetHarmonicImproper(index, phase, force_constant)
+ Update of the harmonic improper parameters in the simulation **and**
+ in the attached :class:`Topology`
+
:param index: :class:`int`
:param phase: :class:`float`
:param force_constant: :class:`float`
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of harmonic impropers
.. method:: ResetLJPair(index,sigma,epsilon)
+ Update of the harmonic improper parameters in the simulation **and**
+ in the attached :class:`Topology`
+
:param index: :class:`int`
:param sigma: :class:`float`
:param epsilon: :class:`float`
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of lj-pairs
.. method:: ResetDistanceConstraint(index, constraint_length)
+
+ Update of the distance constraint parameters in the simulation **and**
+ in the attached :class:`Topology`
:param index: :class:`int`
- :param constraint_length: :class:`float`
+ :param constraint_length: :class:`float`
+
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of distance constraints
.. method:: ResetHarmonicPositionRestraint(index,ref_position, force_constant,x_scale,y_scale,z_scale)
+ Update of the harmonic position restraint parameters in the simulation **and**
+ in the attached :class:`Topology`
+
:param index: :class:`int`
:param ref_position: :class:`~ost.geom.Vec3`
:param force_constant: :class:`float`
:param x_scale: :class:`float`
:param y_scale: :class:`float`
:param z_scale: :class:`float`
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of harmonic position restraints
.. method:: ResetHarmonicDistanceRestraint(index,bond_length, force_constant)
+ Update of the harmonic distance restraint parameters in the simulation **and**
+ in the attached :class:`Topology`
+
:param index: :class:`int`
:param bond_length: :class:`float`
:param force_constant: :class:`float`
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of harmonic distance restraints
.. method:: ResetLJ(index,sigma,epsilon)
+ Update of the lj parameters in the simulation **and**
+ in the attached :class:`Topology`
+
:param index: :class:`int`
:param sigma: :class:`float`
:param epsilon: :class:`float`
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of particles
+
.. method:: ResetGBSA(index,radius,scaling)
+ Update of the GBSA parameters in the simulation **and**
+ in the attached :class:`Topology`
+
:param index: :class:`int`
:param radius: :class:`float`
:param scaling: :class:`float`
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of particles
.. method:: ResetCharge(index,charge)
+ Update of the charge in the simulation **and**
+ in the attached :class:`Topology`
+
:param index: :class:`int`
:param charge: :class:`float`
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of particles
.. method:: ResetMass(index,mass)
+ Update of the mass in the simulation **and**
+ in the attached :class:`Topology`
+
:param index: :class:`int`
:param mass: :class:`float`
-
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of particles
diff --git a/modules/mol/mm/doc/topology.rst b/modules/mol/mm/doc/topology.rst
index 2a4f63604..6988f1e10 100644
--- a/modules/mol/mm/doc/topology.rst
+++ b/modules/mol/mm/doc/topology.rst
@@ -19,8 +19,32 @@ that should suffice most needs.
Creates a topology given an :class:`EntityHandle` and a :class:`Settings`
object. Note, that the :class:`EntityHandle` is passed by reference
- and gets altered by adding hydrogens and modification of terminal residues
- based on the information given by the :class:`Settings`/:class:`Forcefield`.
+ and gets altered by rebuilding bonds, adding hydrogens and modification of
+ terminal residues based on the information given by the
+ :class:`Settings`/:class:`Forcefield`.
+ The Topology Creation process consists of:
+
+ #. Rename to the gromacs standard
+
+ #. Kill all bonds
+
+ #. Build difulfid bonds if flag is set in **settings**
+
+ #. Rename to the standard defined in the forcefield
+
+ #. Extract the building blocks from the forcefield for every residue
+
+ #. Apply BlockModifiers on termini and reconstruct hydrogens with HydrogenConstructors
+
+ #. Reconnect based on the connectivity definitions in the building blocks
+
+ #. Check, whether the residues match with the building blocks
+
+ #. Extract bonds/angles etc. based on the flags in the **settings**
+
+ #. Add Parametrization from forcefield to the Topology
+
+ #. Rename entity back to PDB naming if according flag is set in **settings**
:param entity: :class:`EntityHandle`
--
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