From 9ffa67ae4e2a52f65978b5e34974d425b0d56f47 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 6 Feb 2012 17:33:46 +0100
Subject: [PATCH] Extended documentation of DSSP bindings
---
examples/dssp_sa.py | 7 +++++++
modules/bindings/doc/dssp.rst | 29 +++++++++++++++++++++++++----
modules/bindings/pymod/dssp.py | 5 ++++-
3 files changed, 36 insertions(+), 5 deletions(-)
create mode 100644 examples/dssp_sa.py
diff --git a/examples/dssp_sa.py b/examples/dssp_sa.py
new file mode 100644
index 000000000..23369a99e
--- /dev/null
+++ b/examples/dssp_sa.py
@@ -0,0 +1,7 @@
+from ost.bindings import dssp
+ent=io.LoadMMCIF('1ake.cif')
+dssp.AssignDSSP(ent, extract_burial_status=True)
+for chain in ent.chains:
+ if chain.is_polypeptide:
+ for res in chain.residues:
+ print res.GetFloatProp('relative_solvent_accessibility')
diff --git a/modules/bindings/doc/dssp.rst b/modules/bindings/doc/dssp.rst
index 61de495e3..bb9d2b57b 100644
--- a/modules/bindings/doc/dssp.rst
+++ b/modules/bindings/doc/dssp.rst
@@ -2,19 +2,22 @@
================================================================================
.. module:: ost.bindings.dssp
- :synopsis: Interface to the DSSP commandline utility
+ :synopsis: Interface to the DSSP command line utility
Introduction
--------------------------------------------------------------------------------
-DSSP is a program developed by Wolfgang Kabsch and Chris Sander to assign secondary structure states to protein structures. The assignment is based on hydrogen bonding patterns and geometric features.
+DSSP is a program developed by Wolfgang Kabsch and Chris Sander to assign
+secondary structure states to protein structures. The assignment is based on
+hydrogen bonding patterns and geometric features.
The program can be downloaded from `<http://swift.cmbi.ru.nl/gv/dssp/>`_.
-Example
+Examples
--------------------------------------------------------------------------------
-The following example assigns secondary structure states to an entity by using the DSSP program.
+The following example assigns secondary structure states to an entity by using
+the DSSP program.
.. code-block:: python
@@ -23,9 +26,27 @@ The following example assigns secondary structure states to an entity by using t
ent=io.LoadPDB('1ake.pdb')
dssp.AssignDSSP(ent)
+
+Now we fetch structure information plus solvent accessibility for an entity
+using the mmCIF interface.
+
+
+.. code-block:: python
+
+ from ost.bindings import dssp
+ ent=io.LoadMMCIF('1ake.cif')
+ dssp.AssignDSSP(ent, extract_burial_status=True)
+ for chain in ent.chains:
+ if chain.is_polypeptide:
+ for res in chain.residues:
+ print res.GetFloatProp('relative_solvent_accessibility')
+
+
DSSP bindings Usage
--------------------------------------------------------------------------------
.. autofunction:: ost.bindings.dssp.AssignDSSP
.. autofunction:: ost.bindings.dssp.LoadDSSP
+
+.. LocalWords: dssp AssignDSSP ent GetFloatProp autofunction
diff --git a/modules/bindings/pymod/dssp.py b/modules/bindings/pymod/dssp.py
index 1cb1db3aa..f27aa9db9 100644
--- a/modules/bindings/pymod/dssp.py
+++ b/modules/bindings/pymod/dssp.py
@@ -88,7 +88,10 @@ def AssignDSSP(ent, pdb_path="", extract_burial_status=False, tmp_dir=None,
:param ent: The entity for which the secondary structure should be calculated
:type ent: :class:`~ost.mol.EntityHandle` or :class:`~ost.mol.EntityView`
- :param extract_burial_status: If true, also extract burial status
+ :param extract_burial_status: If true, also extract burial status and store
+ as float-property
+ ``relative_solvent_accessibility`` at residue
+ level
:param tmp_dir: If set, overrides the default tmp directory of the
operating system
:param dssp_bin: The path to the DSSP executable
--
GitLab