some updates on documentation

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`
 

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
 
 
 

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`