From e755be7619f9ab9b62696195c533ee87972dd43a Mon Sep 17 00:00:00 2001
From: Rafal Gumienny <r.gumienny@unibas.ch>
Date: Thu, 26 Apr 2018 15:12:34 +0200
Subject: [PATCH] docs: SCHWED-3121 Add lDDTScorer documentation
---
modules/mol/alg/doc/molalg.rst | 72 ++++++++++++++++++++++++++++++++++
1 file changed, 72 insertions(+)
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 550c5d803..dfa77bc36 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -539,6 +539,78 @@ Local Distance Test scores (lDDT, DRMSD)
:return: String representation of the lDDTSettings object.
:rtype: :class:`str`
+.. class:: lDDTScorer(reference, model, settings)
+
+ Object to compute lDDT scores.
+
+ Example usage with pre-prepared references.
+
+ .. code:: python
+
+ import ost
+
+ :param references: Sets :attr:`references`
+ :param model: Sets :attr:`model`
+ :param settings: Sets :attr:`settings`
+
+ .. attribute:: references
+
+ A list of reference structures.
+
+ :type: list(:class:`~ost.mol.EntityView`)
+
+ .. attribute:: model
+
+ A model structure.
+
+ :type: :class:`~ost.mol.EntityView`
+
+ .. attribute:: settings
+
+ Settings used to calculate lDDT.
+
+ :type: :class:`~ost.mol.alg.lDDTSettings`
+
+ .. attribute:: global_dist_list
+
+ Global map of residue properties.
+
+ :type: :class:`~ost.mol.alg.GlobalRDMap`
+
+ .. attribute:: global_score
+
+ Global lDDT score.
+
+ :type: float
+
+ .. attribute:: conserved_contacts
+
+ Number of conserved distances.
+
+ :type: int
+
+ .. attribute:: total_contacts
+
+ Number of total distances.
+
+ :type:
+
+ .. attribute:: local_scores
+
+ Local scores.
+
+ :type: list(:class:`~ost.mol.alg.lDDTLocalScore`)
+
+ .. attribute:: is_valid
+
+ Is the calculated score valid?
+
+ :type: bool
+
+ .. method:: PrintPerResidueStats
+
+ Print per-residue statistics.
+
.. class:: UniqueAtomIdentifier(chain, residue_number, residue_name, atom_name)
--
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