documentation update for entity and related classes

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2395 5a81b35b-ba03-0410-adc8-b2c5c5119f08

doc/conf/conf.py

@@ -164,7 +164,6 @@ html_static_path = ['_static']
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'openstructure-doc'
 
-
 # -- Options for LaTeX output --------------------------------------------------
 
 # The paper size ('letter' or 'a4').

modules/base/doc/generic.rst

@@ -4,7 +4,10 @@ Storing Custom Data
 Introduction
 --------------------------------------------------------------------------------
 
-It is often very convenient to store any arbitrary data inside an Entity. A few examples are: 
+.. currentmodule:: ost
+
+It is often very convenient to store any arbitrary data inside an Entity. A few 
+examples are: 
 
   * calculated properties of atoms
   * sequence conservation of a residue
@@ -12,27 +15,29 @@ It is often very convenient to store any arbitrary data inside an Entity. A few
   * fit of a fragment inside an electron density map
 
 In OpenStructure this is supported by the use of generic properties. Most 
-building blocks are derived from :class:`GenericPropertyContainer`, meaning that 
-arbitrary key-value pairs can be stored in them. In essence, the following 
+building blocks are derived from :class:`~ost.GenericPropertyContainer`, meaning 
+that arbitrary key-value pairs can be stored in them. In essence, the following 
 classes support generic properties:
 
-  * :class:`~mol.EntityHandle` and :class:`~mol.EntityView`
-  * :class:`~mol.ChainHandle` and :class:`~mol.ChainView`
-  * :class:`~ResidueHandle` and :class:`~mol.ResidueView`
-  * :class:`~mol.AtomHandle` and :class:`~mol.AtomView`
-  * :class:`~mol.BondHandle`
-  * :class:`~seq.SequenceHandle` and :class:`~seq.AlignmentHandle`
+  * :class:`~ost.mol.EntityHandle` and :class:`~ost.mol.EntityView`
+  * :class:`~ost.mol.ChainHandle` and :class:`~ost.mol.ChainView`
+  * :class:`~ost.mol.ResidueHandle` and :class:`~ost.mol.ResidueView`
+  * :class:`~ost.mol.AtomHandle` and :class:`~ost.mol.AtomView`
+  * :class:`~ost.mol.BondHandle`
+  * :class:`~ost.seq.SequenceHandle` and :class:`~ost.seq.AlignmentHandle`
 
 The view variants will reflect the generic properties of the handle variants.
 
-A generic property key is always a string, and a value can be one of string, float, int or bool. For each of these data types, methods to retrieve and store values are available both in Python and C++.
+A generic property key is always a string, and a value can be one of string, 
+float, int or bool. For each of these data types, methods to retrieve and store 
+values are available both in Python and C++.
 
 Storing and Accessing Data
 --------------------------------------------------------------------------------
 
-All OpenStructure building blocks that are :class:`GenericPropContainers`, have 
-four different methods to store generic data, depending on the data type (i.e. 
-string, float, int or bool).
+All OpenStructure building blocks that are :class:`~ost.GenericPropContainers`, 
+have four different methods to store generic data, depending on the data type 
+(i.e. string, float, int or bool).
 
 To store a float value with the key 'myfloatprop' in all atoms of an entity:
 
@@ -53,7 +58,7 @@ already exists, it will be overwritten. To check if it exists, use:
     
 To access the value of a generic property, we first check if the property exists
 and then access it, using the method suitable for the data type of the property. 
-For the previously set property "myfloatprop" of the data type real, at the atom 
+For the previously set property `myfloatprop` of the data type real, at the atom 
 level:
 
 .. code-block:: python
@@ -82,12 +87,12 @@ to access a property of a different data type, e.g.:
 Use of Generic Properties in Queries
 --------------------------------------------------------------------------------
 
-The :doc:`../mol/base/query` can also be used for numeric generic properties (i.e. bool, 
-int, float), but the syntax is slightly different. To access any generic 
-properties, it needs to be specified that they are generic and at which level 
-they are defined. Therefore, all generic properties start with a 'g', followed 
-by an 'a', 'r' or 'c' for atom, residue or chain level respectively. For more 
-details see :doc:`../mol/base/query`. 
+The :doc:`../mol/base/query` can also be used for numeric generic properties 
+(i.e. bool, int, float), but the syntax is slightly different. To access any 
+generic properties, it needs to be specified that they are generic and at which 
+level (chain, residue, atom) they are defined. Therefore, all generic properties 
+start with a 'g', followed by an 'a', 'r' or 'c' for atom, residue or chain 
+level respectively. For more details see :doc:`../mol/base/query`. 
 
 
 API documentation

modules/mol/base/pymod/export_atom.cc

@@ -79,6 +79,7 @@ void export_Atom()
     .def("Apply", &AtomHandle::Apply, args("visitor"))
     .def("GetBondList", &AtomHandle::GetBondList)
     .def("GetBondCount", &AtomHandle::GetBondCount)
+    .add_property("valid", &AtomHandle::IsValid)    
     .def("GetEntity", &AtomHandle::GetEntity)
     .def("GetHandle", &AtomHandle::GetHandle)
     .add_property("handle", &AtomHandle::GetHandle)

modules/mol/base/pymod/export_atom_view.cc

@@ -42,6 +42,7 @@ void export_AtomView()
     .def("RemoveBonds", &AtomView::RemoveBonds)
     .def("GetHandle", &AtomView::GetHandle)
     .def("GetBondCount", &AtomView::GetBondCount)
+    .add_property("valid", &AtomView::IsValid)    
     .def("GetBondList", &AtomView::GetBondList)
     .def("GetHashCode", &AtomView::GetHashCode)
     .def("__hash__", &AtomView::GetHashCode)

modules/mol/base/pymod/export_chain.cc

@@ -86,6 +86,11 @@ void export_Chain()
     .def("GetCenterOfAtoms", &ChainHandle::GetCenterOfAtoms)
     .def("GetGeometricCenter", &ChainHandle::GetGeometricCenter)
     .add_property("geometric_center", &ChainHandle::GetGeometricCenter)
+    .add_property("mass", &ChainHandle::GetMass)
+    .add_property("center_of_mass", &ChainHandle::GetCenterOfMass)
+    .add_property("center_of_atoms", &ChainHandle::GetCenterOfAtoms)  
+    .add_property("in_sequence", &ChainHandle::InSequence)  
+    .add_property("valid", &ChainHandle::IsValid)    
     .def("GetGeometricStart", &ChainHandle::GetGeometricStart)
     .def("GetGeometricEnd", &ChainHandle::GetGeometricEnd)
   ;

modules/mol/base/pymod/export_chain_view.cc

@@ -99,6 +99,11 @@ void export_ChainView()
     .def("GetCenterOfAtoms", &ChainView::GetCenterOfAtoms)
     .def("GetGeometricCenter", &ChainView::GetGeometricCenter)
     .add_property("geometric_center", &ChainView::GetGeometricCenter)
+    .add_property("mass", &ChainView::GetMass)
+    .add_property("center_of_mass", &ChainView::GetCenterOfMass)
+    .add_property("center_of_atoms", &ChainView::GetCenterOfAtoms)
+    .add_property("valid", &ChainView::IsValid)      
+    .add_property("in_sequence", &ChainView::InSequence)    
     .def("GetGeometricStart", &ChainView::GetGeometricStart)
     .def("GetGeometricEnd", &ChainView::GetGeometricEnd)
   ;

modules/mol/base/pymod/export_entity.cc

@@ -95,6 +95,9 @@ void export_Entity()
     .add_property("chain_count", &EntityHandle::GetChainCount)
     .add_property("residue_count", &EntityHandle::GetResidueCount)
     .add_property("atom_count", &EntityHandle::GetAtomCount)
+    .add_property("mass", &EntityHandle::GetMass)
+    .add_property("center_of_mass", &EntityHandle::GetCenterOfMass)
+    .add_property("center_of_atoms", &EntityHandle::GetCenterOfAtoms)
     .def("FindWithin", &EntityHandle::FindWithin)
     .def("GetAngle", get_angle1)
     .def("GetAngle", get_angle2)
@@ -108,6 +111,7 @@ void export_Entity()
     .add_property("atoms", &EntityHandle::GetAtomList)
     .add_property("chains", &EntityHandle::GetChainList)
     .add_property("bonds", &EntityHandle::GetBondList)
+    .add_property("valid", &EntityHandle::IsValid)
     .def("GetTransformationMatrix", &EntityHandle::GetTransformationMatrix,
          return_value_policy<copy_const_reference>())
     .add_property("transform", 

modules/mol/base/pymod/export_entity_view.cc

@@ -119,6 +119,10 @@ void export_EntityView()
     .add_property("residue_count", &EntityView::GetResidueCount)
     .add_property("atom_count", &EntityView::GetAtomCount)
     .add_property("bond_count", &EntityView::GetBondCount)
+    .add_property("mass", &EntityView::GetMass)
+    .add_property("center_of_mass", &EntityView::GetCenterOfMass)
+    .add_property("center_of_atoms", &EntityView::GetCenterOfAtoms)
+    .add_property("valid", &EntityView::IsValid)    
     .def("GetResidueList", &EntityView::GetResidueList)
     .def("GetAtomList", &EntityView::GetAtomList)
     .add_property("atoms", &EntityView::GetAtomList)

modules/mol/base/pymod/export_residue.cc

@@ -109,6 +109,8 @@ void export_Residue()
                  &ResidueBase::SetOneLetterCode)  
     .def("GetQualifedName", &ResidueBase::GetQualifiedName)
     .def("IsPeptideLinking", &ResidueBase::IsPeptideLinking)
+    .add_property("peptide_linking", &ResidueBase::IsPeptideLinking)
+    
     .def("GetKey", &ResidueBase::GetKey,
          return_value_policy<copy_const_reference>())
      .def("GetName", &ResidueBase::GetName,
@@ -165,7 +167,14 @@ void export_Residue()
     .def("GetCenterOfMass", &ResidueHandle::GetCenterOfMass)
     .def("GetCenterOfAtoms", &ResidueHandle::GetCenterOfAtoms)
     .def("GetGeometricCenter", &ResidueHandle::GetGeometricCenter)
+    .add_property("mass", &ResidueHandle::GetMass)
+    .add_property("center_of_mass", &ResidueHandle::GetCenterOfMass)
+    .add_property("center_of_atoms", &ResidueHandle::GetCenterOfAtoms)  
     .add_property("geometric_center", &ResidueHandle::GetGeometricCenter)
+    .add_property("phi_torsion", &ResidueHandle::GetPhiTorsion)
+    .add_property("psi_torsion", &ResidueHandle::GetPsiTorsion)
+    .add_property("omega_torsion", &ResidueHandle::GetOmegaTorsion)
+    .add_property("valid", &ResidueHandle::IsValid) 
     .def("GetGeometricStart", &ResidueHandle::GetGeometricStart)
     .def("GetGeometricEnd", &ResidueHandle::GetGeometricEnd)
     .def(self==self)

modules/mol/base/pymod/export_residue_view.cc

@@ -69,7 +69,7 @@ void export_ResidueView()
     .def("IsAtomIncluded", &ResidueView::IsAtomIncluded, args("atom_handle"))
     .def("Apply", apply1, args("visitor"))
     .def("Apply", apply2, args("visitor"))
-    .def("GetIndex", &ResidueView::GetIndex)
+    .def("GetIndex", &ResidueView::GetIndex)  
     .add_property("chain", &ResidueView::GetChain)
     .add_property("entity", &ResidueView::GetEntity)
     .add_property("index", &ResidueView::GetIndex)
@@ -85,7 +85,11 @@ void export_ResidueView()
     .def("GetCenterOfMass", &ResidueView::GetCenterOfMass)
     .def("GetCenterOfAtoms", &ResidueView::GetCenterOfAtoms)
     .def("GetGeometricCenter", &ResidueView::GetGeometricCenter)
+    .add_property("mass", &ResidueView::GetMass)
+    .add_property("center_of_mass", &ResidueView::GetCenterOfMass)
+    .add_property("center_of_atoms", &ResidueView::GetCenterOfAtoms)    
     .add_property("geometric_center", &ResidueView::GetGeometricCenter)
+    .add_property("valid", &ResidueView::IsValid)    
     .def("GetGeometricStart", &ResidueView::GetGeometricStart)
     .def("GetGeometricEnd", &ResidueView::GetGeometricEnd) 
   ;