From b40c7be8d4f31abb25a5231fb5a28e5e18492e02 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 1 Jun 2017 14:56:38 +0200
Subject: [PATCH] documentation for accessibility calculations
---
modules/mol/alg/doc/molalg.rst | 86 ++++++++++++++++++++++++++++++++++
1 file changed, 86 insertions(+)
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 4f81c318c..efc8daf7b 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -788,6 +788,92 @@ Superposing structures
of *view1*.
:type transformation: :class:`~ost.geom.Mat4`
+
+Algorithms on Structures
+--------------------------------------------------------------------------------
+
+.. method:: Accessibility(ent, [probe_radius=1.4, include_hydrogens=False,\
+ include_hetatm=False, include_water=False,\
+ oligo_mode=False, selection="", asa_abs="asaAbs",\
+ asa_rel="asaRel", asa_atom="asaAtom"])
+
+ Calculates the accesssible surface area for ever atom in *ent* according to
+ Lee & Richards by "rolling" a probe with given *probe_radius* over the atoms.
+
+ :param ent: Entity on which to calculate the surface
+ :type ent: :class:`~ost.mol.EntityView`/
+ :class:`~ost.mol.EntityHandle`
+
+ :param probe_radius: Radius of probe to determine accessible surface area
+ :type probe_radius: :class:`float`
+
+ :param include_hydrogens: Whether to include hydrogens in the solvent
+ accessibility calculations. By default,
+ every atom with ele=H,D is simply neglected.
+ :type include_hydrogens: :class:`bool`
+
+ :param include_hetatms: Whether to include atoms flagged as hetatms
+ , i.e. ligands, in the solvent
+ accessibility calculations. They are neglected
+ by default.
+ :type include_hetatms: :class:`bool`
+
+ :param include_water: Whether to include water in the solvent
+ accessibility calculations. By default,
+ every residue with name "HOH" is neglected.
+ :type include_water: :class:`bool`
+
+ :param oligo_mode: A typical used case of accessibility calculations is to
+ determine the solvent accessibility of a full complex
+ and then the accessibility of each chain individually.
+ Lots of calculations can be cached because only the
+ values of the atoms close to an interface change.
+ This is exactly what happens when you activate the
+ oligo mode. It returns exactly the same value but adds,
+ additionally to the values estimated in full complex,
+ the values from each individual chain as float
+ properties on every residue and atom. Example for atom
+ accessible surface if the according property name is set
+ to "asaAtom": Accessibility in the full complex is
+ stored as "asaAtom", the accessibility when only
+ considering that particular chain is stored as
+ "asaAtom_single_chain".
+ The other properties follow the same naming scheme.
+ :type oligo_mode: :class:`bool`
+
+ :param selection: Selection statement, that gets applied on *ent* before
+ doing anything. Everything that is not selected is
+ neglected. The default value of "" results in no
+ selection at all.
+ :type selection: :class:`str`
+
+ :param asa_abs: Float property name to assign the summed solvent
+ accessible surface from each atom to a residue.
+ :type asa_abs: :class:`str`
+
+ :param asa_rel: Float property name to assign the relative solvent
+ accessibility to a residue. This is the absolute
+ accessibility divided by the maximum solvent
+ accessibility of that particular residue. Only
+ residues of the 20 standarad amino acids can be handled.
+ Every non standard residue gets assigned a value of
+ -99.9.
+ :type asa_rel: :class:`str`
+
+ :param asa_atom: Float property name to assign the solvent accessible
+ area to each atom.
+ :type asa_atom: :class:`str`
+
+ :return: The summed solvent accessibilty of each atom in *ent*.
+
+
+
+
+
+
+
+
+
.. _traj-analysis:
Trajectory Analysis
--
GitLab