diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index f96926070f83b8c7a0047a6d1872e4cf5b3db1dc..5df0433cf8cbbe4551e681b1fe0d9f020316fce2 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -567,6 +567,7 @@ The Handle Classes
The residue name is usually a str of 3 characters, e.g. `GLY` for
glycine or `ALA` for alanine, but may be shorter, e.g. `G` for guanosine,
or longer for structures loaded from formats other than PDB.
+ Also available as :meth:`GetName`.
This property is read-only. To change the name of the residue, use
:meth:`~EditorBase.RenameResidue`.
@@ -626,12 +627,6 @@ The Handle Classes
The total mass of this residue in Dalton. Also available as :meth:`GetMass`.
:type: float
-
- .. attribute:: center_of_mass
-
- Center of mass. Also available as :meth:`GetCenterOfMass`
-
- :type: :class:`~ost.geom.Vec3`
.. attribute:: center_of_atoms
@@ -640,6 +635,12 @@ The Handle Classes
:type: :class:`~ost.geom.Vec3`
+ .. attribute:: center_of_mass
+
+ Center of mass. Also available as :meth:`GetCenterOfMass`
+
+ :type: :class:`~ost.geom.Vec3`
+
.. attribute:: chain
The chain this residue belongs to. Read-only. Also available as
@@ -814,46 +815,83 @@ The Handle Classes
:returns: Whether the switch was successful (e.g. False if no such
group exists)
+ .. method:: GetName()
+
+ See :attr:`name`
+
.. method:: GetQualifiedName()
See :attr:`qualified_name`
+ .. method:: GetNumber()
+
+ See :attr:`number`
+
+ .. method:: GetOneLetterCode()
+
+ See :attr:`one_letter_code`
+
.. method:: GetAtomList()
See :attr:`atoms`
- .. method:: IsPeptideLinking()
+ .. method:: GetBounds()
- See :attr:`peptide_linking`
+ See :attr:`bounds`
- .. method:: IsNucleotideLinking()
+ .. method:: GetMass()
+
+ See :attr:`mass`
- See :attr:`nucleotide_linking`
-
- .. method:: GetChain()
-
- See :attr:`chain`
-
.. method:: GetCenterOfAtoms()
-
+
See :attr:`center_of_atoms`
-
+
.. method:: GetCenterOfMass()
-
+
See :attr:`center_of_mass`
-
+
+ .. method:: GetChain()
+
+ See :attr:`chain`
+
.. method:: GetPhiTorsion()
-
+
See :attr:`phi_torsion`
-
+
.. method:: GetPsiTorsion()
-
+
See :attr:`psi_torsion`
-
+
+ .. method:: GetChemClass()
+
+ See :attr:`chem_class`
+
.. method:: GetChemType()
-
+
See :attr:`chem_type`
+ .. method:: GetSecStructure()
+
+ See :attr:`sec_structure`
+
+ .. method:: IsLigand()
+ SetIsLigand()
+
+ See :attr:`is_ligand`
+
+ .. method:: IsProtein()
+
+ See :attr:`is_protein`
+
+ .. method:: IsPeptideLinking()
+
+ See :attr:`peptide_linking`
+
+ .. method:: IsNucleotideLinking()
+
+ See :attr:`nucleotide_linking`
+
.. method:: GetIndex()
See :attr:`index`
@@ -871,6 +909,14 @@ The Handle Classes
See :attr:`valid`
+ .. method:: GetNext()
+
+ See :attr:`next`
+
+ .. method:: GetPrev()
+
+ See :attr:`next`
+
.. class:: AtomHandle
@@ -1808,68 +1854,39 @@ The View Classes
:type: :class:`ResidueHandle`
.. attribute:: name
+ qualified_name
+ number
+ one_letter_code
+ bounds
+ mass
+ center_of_atoms
+ center_of_mass
+ phi_torsion
+ psi_torsion
+ chem_class
+ chem_type
+ sec_structure
+ is_ligand
+ is_protein
+ peptide_linking
+ nucleotide_linking
+ central_atom
+ central_normal
+ valid
+ next
+ prev
+
+ See the respective attributes in :class:`ResidueHandle`.
- The residue name is usually a str of 3 characters, e.g. `GLY` for
- glycine or `ALA` for alanine, but may be shorter, e.g. `G` for guanosine,
- or longer for structures loaded from formats other than PDB.
-
- This property is read-only. To change the name of the residue, use
- :meth:`~EditorBase.RenameResidue`.
-
- .. attribute:: qualified_name
-
- See :meth:`~ResidueHandle.qualified_name`.
- Also available as :meth:`GetQualifiedName`.
-
- .. attribute:: number
-
- The number of this residue. The residue number has a numeric part and an
- insertion-code. This property is read-only. Also available as
- :meth:`GetNumber`.
-
- :type: :class:`ResNum`
-
- .. attribute:: one_letter_code
-
- For amino acids, and nucleotides the `one_letter_code` is an alpha-numeric
- character. For unknown or more *exotic* residues, the one letter code is set
- to '?'.
-
- **Example**
-
- This code-snippet shows how to get the sequence string from a list of
- residues.
-
- .. code-block:: python
-
- print(''.join([r.one_letter_code for r in chain.residues]))
-
- :type: str
-
- .. attribute:: bounds
-
- Axis-aligned bounding box of the residue view. Read-only
-
- :type: :class:`ost.geom.AlignedCuboid`
-
- .. attribute:: mass
-
- The total mass of this residue in Dalton. Also available as :meth:`GetMass`.
-
- :type: float
-
- .. attribute:: center_of_mass
+ .. attribute:: atoms
- Center of mass. Also available as :meth:`GetCenterOfMass`
+ Get list of all atoms of this residue included in the view.
+ To access a single atom, use
+ :meth:`FindAtom`.
- :type: :class:`~ost.geom.Vec3`
+ This property is read-only. Also available as :meth:`GetAtomList`
- .. attribute:: center_of_atoms
-
- Center of atoms (not mass weighted). Also available as
- :meth:`GetCenterOfAtoms`.
-
- :type: :class:`~ost.geom.Vec3`
+ :type: :class:`AtomViewList` (list of :class:`AtomView`)
.. attribute:: chain
@@ -1878,15 +1895,6 @@ The View Classes
:type: :class:`ChainView`
- .. attribute:: atoms
-
- Get list of all atoms of this residue. To access a single atom, use
- :meth:`FindAtom`.
-
- This property is read-only. Also available as :meth:`GetAtomList`
-
- :type: :class:`AtomHandleList` (list of :class:`AtomHandle`)
-
.. attribute:: index
Residue index (starting at 0) within chain view.
@@ -1904,13 +1912,32 @@ The View Classes
See :attr:`handle`
- .. method:: GetQualifiedName()
-
- See :attr:`qualified_name`
-
- .. method:: GetMass()
-
- See :attr:`mass`
+ .. method:: GetName
+ GetQualifiedName
+ GetNumber
+ GetOneLetterCode
+ GetBounds
+ GetMass
+ GetCenterOfAtoms
+ GetCenterOfMass
+ GetPhiTorsion
+ GetPsiTorsion
+ GetChemClass
+ GetChemType
+ GetSecStructure
+ IsLigand
+ SetIsLigand
+ IsProtein
+ IsPeptideLinking
+ IsNucleotideLinking
+ GetCentralAtom
+ SetCentralAtom
+ GetCentralNormal
+ IsValid
+ GetNext
+ GetPrev
+
+ See the respective methods in :class:`ResidueHandle`.
.. method:: GetChain()
@@ -1925,14 +1952,6 @@ The View Classes
:type atom_name: str
:rtype: :class:`AtomView`
- .. method:: GetIndex()
-
- See :attr:`index`
-
- .. method:: GetCenterOfMass()
-
- See :attr:`center_of_mass`
-
.. method:: IsAtomIncluded(atom_handle)
Returns true if the given atom is part of the view, false if not.
@@ -1941,10 +1960,6 @@ The View Classes
:type atom_handle: :class:`AtomHandle`
:rtype: bool
- .. method:: GetGeometricCenter()
-
- See :attr:`geometric_center`
-
.. method:: AddAtom(atom_handle[, flags])
Add atom to the view.
@@ -1955,13 +1970,17 @@ The View Classes
:type flags: :class:`int` / :class:`ViewAddFlag`
:rtype: :class:`AtomView`
- .. method:: GetCenterOfAtoms()
-
- See :attr:`center_of_atoms`
-
.. method:: GetAtomList()
See :attr:`atoms`
+
+ .. method:: GetIndex()
+
+ See :attr:`index`
+
+ .. method:: GetGeometricCenter()
+
+ See :attr:`geometric_center`
.. method:: Select(query, flags=0)