From 9d5a38b0f474048b755feb628b26c337adf01b35 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Wed, 4 Apr 2018 16:08:58 +0200
Subject: [PATCH] Doc update for residue validity and connectivity.
---
modules/mol/base/doc/entity.rst | 97 ++++++++++++++++++++++++++++++---
1 file changed, 88 insertions(+), 9 deletions(-)
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index 41945d534..3b0aa5c9f 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -118,7 +118,13 @@ The Handle Classes
an enabled ``USE_NUMPY`` flag (see :ref:`here <cmake-flags>` for details).
:type: :class:`numpy.array`
-
+
+ .. attribute:: valid
+
+ Validity of handle.
+
+ :type: bool
+
.. method:: GetName()
:returns: Name associated to this entity.
@@ -327,6 +333,10 @@ The Handle Classes
:type radius: float
:returns: :class:`AtomHandleList` (list of :class:`AtomHandle`)
+
+ .. method:: IsValid()
+
+ See :attr:`valid`
.. class:: ChainHandle
@@ -424,6 +434,12 @@ The Handle Classes
:meth:`GetCenterOfAtoms`.
:type: :class:`~ost.geom.Vec3`
+
+ .. attribute:: valid
+
+ Validity of handle.
+
+ :type: bool
.. method:: FindResidue(res_num)
@@ -469,6 +485,10 @@ The Handle Classes
See :attr:`description`
+ .. method:: IsValid()
+
+ See :attr:`valid`
+
.. class:: ResidueHandle
The residue is either used to represent complete molecules or building blocks
@@ -625,8 +645,6 @@ The Handle Classes
Central atom used for rendering traces. For peptides, this is usually
the CA atom. For nucleotides, this is usually the P atom.
- Also available as :meth:`GetCentralAtom` and :meth:`SetCentralAtom`.
-
:type: :class:`AtomHandle`
.. attribute:: central_normal
@@ -635,10 +653,30 @@ The Handle Classes
nucleotides if all required atoms available. Otherwise, the (1,0,0) vector
is returned.
- Read-only. Also available as :meth:`GetCentralNormal`.
-
:type: :class:`~ost.geom.Vec3`
+ .. attribute:: valid
+
+ Validity of handle.
+
+ :type: bool
+
+ .. attribute:: next
+
+ Residue after this one in the same chain. Invalid handle returned if there
+ is no next residue. Residues are ordered as in :attr:`ChainHandle.residues`
+ independently on whether they are connected or not (see
+ :func:`InSequence` to check for connected residues).
+
+ :type: :class:`ResidueHandle`
+
+ .. attribute:: prev
+
+ Residue before this one in the same chain. Otherwise same behaviour as
+ :attr:`next`.
+
+ :type: :class:`ResidueHandle`
+
.. method:: FindAtom(atom_name)
Get atom by atom name. See also :attr:`atoms`
@@ -693,8 +731,12 @@ The Handle Classes
.. method:: GetCentralNormal()
- See :attr:`index`
+ See :attr:`central_normal`
+
+ .. method:: IsValid()
+ See :attr:`valid`
+
.. class:: AtomHandle
@@ -811,6 +853,12 @@ The Handle Classes
:type: int
+ .. attribute:: valid
+
+ Validity of handle.
+
+ :type: bool
+
.. method:: FindBondToAtom(other_atom)
Finds and returns the bond formed between this atom and `other_atom`. If no
@@ -928,8 +976,7 @@ The Handle Classes
.. method:: IsValid()
See :attr:`valid`
-
- :rtype: bool
+
The View Classes
--------------------------------------------------------------------------------
@@ -1010,6 +1057,12 @@ The View Classes
:type: :class:`EntityHandle`
+ .. attribute:: valid
+
+ Validity of view.
+
+ :type: bool
+
.. method:: GetName()
:returns: :func:`~EntityHandle.GetName` of entity :attr:`handle`.
@@ -1271,6 +1324,10 @@ The View Classes
See :attr:`atom_count`
+ .. method:: IsValid()
+
+ See :attr:`valid`
+
.. class:: ChainView
A view representation of a :class:`ChainHandle`. Mostly, the same
@@ -1380,7 +1437,7 @@ The View Classes
.. attribute:: valid
- Validity of handle.
+ Validity of view.
:type: bool
@@ -1782,6 +1839,28 @@ Other Entity-Related Functions
:returns: :class:`EntityHandle`
+.. function:: InSequence(res, res_next)
+
+ :return: True, if both *res* and *res_next* are :attr:`~ResidueHandle.valid`,
+ *res_next* is the residue following *res* (see
+ :attr:`ResidueHandle.next`), both residues are linking (i.e.
+ :attr:`~ChemClass.IsPeptideLinking` or
+ :attr:`~ChemClass.IsNucleotideLinking`) and are connected by an
+ appropriate bond.
+ :rtype: :class:`bool`
+ :param res: First residue to check.
+ :type res: :class:`ResidueHandle`
+ :param res_next: Second residue to check.
+ :type res_next: :class:`ResidueHandle`
+
+.. function:: BondExists(atom_a, atom_b)
+
+ :return: True, if *atom_a* and *atom_b* are connected by a bond.
+ :rtype: :class:`bool`
+ :param atom_a: First atom to check.
+ :type atom_a: :class:`AtomHandle`
+ :param atom_b: Second atom to check.
+ :type atom_b: :class:`AtomHandle`
Residue Numbering
--------------------------------------------------------------------------------
--
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