SCHWED-1270: started doc for scoring module.

doc/tests/CMakeLists.txt

@@ -34,6 +34,8 @@ set (DOC_TEST_SCRIPTS
   scripts/loop_fragger.py
   scripts/loop_torsion_sampler.py
 
+  scripts/scoring_main.py
+
   scripts/modelling_all.py
   scripts/modelling_steps.py
   scripts/modelling_merge_gaps_by_distance.py

doc/tests/scripts/scoring_main.py

+from ost import io, seq
+from promod3 import loop, scoring
+
+# load data
+ent = io.LoadPDB("data/1CRN.pdb")
+ent_seq = seq.SequenceFromChain('A', ent.FindChain('A'))
+
+# setup score environment linked to entity
+score_env = scoring.BackboneScoreEnv(ent_seq)
+score_env.SetInitialEnvironment(ent)
+
+# setup scorers attached to that env.
+clash_scorer = scoring.ClashScorer()
+clash_scorer.AttachEnvironment(score_env)
+cbeta_scorer = scoring.LoadCBetaScorer()
+cbeta_scorer.AttachEnvironment(score_env)
+
+# get backbone list to be scored
+# (here extracted from the structure, but it could be anything)
+ev = ent.Select("rnum >= 23 and rnum <= 30")
+bb_seq = ''.join([r.one_letter_code for r in ev.residues])
+bb_res = [r.handle for r in ev.residues]
+bb_list = loop.BackboneList(bb_seq, bb_res)
+
+# score it (note that 23 is the starting res. num.)
+print "Clash-Score", clash_scorer.CalculateScore(bb_list, 23)
+print "CBeta-Score", cbeta_scorer.CalculateScore(bb_list, 23)

doc/tests/test_doctests.py

@@ -285,6 +285,12 @@ class DocTests(unittest.TestCase):
 
     ################################################################
 
+    def testScoringMain(self):
+        # just check that it doesn't crash
+        self.checkPMRun('scoring_main.py', [], 0)
+
+    ################################################################
+
     def testModellingAll(self):
         # run it
         self.checkPMRun('modelling_all.py', [], 0)

doc/users.rst

@@ -13,7 +13,8 @@ Contents:
    actions/index
    buildsystem
    modelling/index
-   loop/index
    sidechain/index
+   scoring/index
+   loop/index
    core/index
    core/setcompoundschemlib

loop/doc/CMakeLists.txt

 set(LOOP_RST
-index.rst
-torsion_sampler.rst
-loop_closing.rst
-backbone.rst
-backbone_loop_score.rst
-monte_carlo.rst
-structure_db.rst
-load_loop_objects.rst
-helper_classes.rst
+  index.rst
+  torsion_sampler.rst
+  loop_closing.rst
+  backbone.rst
+  backbone_loop_score.rst
+  monte_carlo.rst
+  structure_db.rst
+  load_loop_objects.rst
+  helper_classes.rst
 )
 
 add_doc_source(NAME loop RST ${LOOP_RST})
-

scoring/doc/CMakeLists.txt

+set(SCORING_RST
+  index.rst
+  backbone_score_env.rst
+  backbone_scorers.rst
+)
+
+add_doc_source(NAME scoring RST ${SCORING_RST})

scoring/doc/backbone_score_env.rst

+Backbone Score Environment
+================================================================================
+
+.. currentmodule:: promod3.scoring

scoring/doc/backbone_scorers.rst

+Backbone Scorers
+================================================================================
+
+.. currentmodule:: promod3.scoring

scoring/doc/index.rst

+:mod:`~promod3.scoring` - Loop Scoring
+================================================================================
+
+.. module:: promod3.scoring
+  :synopsis: Loop Scoring
+
+.. currentmodule:: promod3.scoring
+
+Tools and algorithms to score loops.
+The scoring system is split between an environment which contains positional
+information and a scorer which evaluates a loop.
+
+This example shows how we load a structure, setup a score environment and a few
+scorers. The scorers are then used to evaluate the quality of a loop.
+
+.. literalinclude:: ../../../tests/doc/scripts/scoring_main.py
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   Backbone Score Environment <backbone_score_env>
+   Backbone Scorers <backbone_scorers>