From 7cba23a2a3c9f5326e1a99964c730a8eb3a8f62c Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Wed, 5 Jul 2017 15:23:33 +0200
Subject: [PATCH] SCHWED-1786: improved example for QSscorer.
---
modules/mol/alg/pymod/qsscoring.py | 18 ++++++++++--------
1 file changed, 10 insertions(+), 8 deletions(-)
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index 95e25df8a..c37178e82 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -27,20 +27,22 @@ class QSscorer:
.. code-block:: python
- from ost import io, LogScript
+ import ost
from ost.mol.alg import qsscoring
- # load two structures
- ent_1 = io.LoadPDB('4ux8', remote=True)
- ent_2 = io.LoadPDB('3fub', remote=True)
+ # load two biounits to compare
+ ent_full = ost.io.LoadPDB('3ia3', remote=True)
+ ent_1 = ent_full.Select('cname=A,D')
+ ent_2 = ent_full.Select('cname=B,C')
# get score
+ ost.PushVerbosityLevel(3)
try:
qs_scorer = qsscoring.QSscorer(ent_1, ent_2)
- LogScript('QSscore:', str(qs_scorer.global_score))
- LogScript('Chain mapping used:', str(qs_scorer.chain_mapping))
+ ost.LogScript('QSscore:', str(qs_scorer.global_score))
+ ost.LogScript('Chain mapping used:', str(qs_scorer.chain_mapping))
except qsscoring.QSscoreError as ex:
- # default handling: QS score failed!
- LogError('QSscore failed: ...')
+ # default handling: report failure and set score to 0
+ ost.LogError('QSscore failed:', str(ex))
qs_score = 0
For maximal performance when computing QS scores of the same entity with many
--
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