From 0dfc86836474b9bbcf98d4308dc18aa3a3236dfe Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Wed, 26 Jul 2017 14:10:55 +0200
Subject: [PATCH] Added doc for SecStructure.
---
modules/mol/base/doc/entity.rst | 50 ++++++++++++++++++++++++++++++++-
modules/mol/base/doc/query.rst | 2 +-
2 files changed, 50 insertions(+), 2 deletions(-)
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index 192d3e27a..6d036a70b 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -534,6 +534,8 @@ The Handle Classes
.. attribute:: sec_structure
The secondary structure of the residue.
+
+ :type: :class:`SecStructure`
.. attribute:: is_ligand
@@ -1755,7 +1757,7 @@ here.
``CHAINTYPE_POLY_PEPTIDE_D``, ``CHAINTYPE_POLY_PEPTIDE_L``,
``CHAINTYPE_POLY_DN``, ``CHAINTYPE_POLY_RN``, ``CHAINTYPE_POLY_SAC_D``,
``CHAINTYPE_POLY_SAC_L``, ``CHAINTYPE_POLY_DN_RN``,
- ``CHAINTYPE_UNKNOWN``, ``CHAINTYPE_N_CHAINTYPES``
+ ``CHAINTYPE_UNKNOWN``, ``CHAINTYPE_N_CHAINTYPES``
Where ``CHAINTYPE_N_CHAINTYPES`` holds the number of different types available.
@@ -1795,3 +1797,49 @@ ViewAddFlags
* ``CHECK_DUPLICATES`` - If set, it will be checked that no duplicates are
created when adding a new handle
+
+SecStructure
+--------------------------------------------------------------------------------
+
+.. class:: SecStructure(type)
+
+ Defines a secondary structure type following the types defined by DSSP.
+
+ :param type: Type to be set for this object.
+ :type type: :class:`SecStructure.Type` / :class:`str`
+
+ .. method:: IsHelical
+
+ :return: True, if the set type is any type of helix (i.e. ALPHA_HELIX,
+ PI_HELIX or THREE_TEN_HELIX)
+
+ .. method:: IsExtended
+
+ :return: True, if the set type is any type of beta sheet (i.e. EXTENDED,
+ BETA_BRIDGE)
+
+ .. method:: IsCoil
+
+ :return: True, if the set type is any type of coil (i.e. TURN, BEND or COIL)
+
+ .. method:: __str__
+
+ :return: The character corresponding to the set type (see
+ :class:`SecStructure.Type`)
+
+.. class:: SecStructure.Type
+
+ Enumerates all popssible secondary structure types distinguished by DSSP.
+ Their values with the corresponding character code are listed here:
+
+ .. hlist::
+ :columns: 2
+
+ * ALPHA_HELIX = 'H'
+ * PI_HELIX = 'I'
+ * THREE_TEN_HELIX = 'G'
+ * EXTENDED = 'E'
+ * BETA_BRIDGE = 'B'
+ * TURN = 'T'
+ * BEND = 'S'
+ * COIL = 'C'
diff --git a/modules/mol/base/doc/query.rst b/modules/mol/base/doc/query.rst
index d187296d4..8d5a63286 100644
--- a/modules/mol/base/doc/query.rst
+++ b/modules/mol/base/doc/query.rst
@@ -187,7 +187,7 @@ numeric part is honored.
**rtype** (str): Residue type as given by the DSSP code (e.g. "H" for alpha
helix, "E" for extended), "helix" for all helix types, "ext" or "strand" for
-all beta sheets or "coil" for any type of coil.
+all beta sheets or "coil" for any type of coil (see :class:`SecStructure`).
**rindex** (int): :attr:`Index<ResidueHandle.index>` of residue handle in chain.
This index is the same for views and handles.
--
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