From 619cfbda01612d557f06aafa3c6a3eb438c508b0 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 10 Aug 2016 20:47:26 +0200
Subject: [PATCH] directly connect OverallBackboneScorer with its
BackboneScoreEnv to the ModellingHandle
---
modelling/pymod/_pipeline.py | 2 +-
modelling/pymod/export_model.cc | 39 +++++++++++++++++++++++++++++++++
modelling/src/model.cc | 36 ++++++++++++++++++++++++++++++
modelling/src/model.hh | 7 ++++++
4 files changed, 83 insertions(+), 1 deletion(-)
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index 779ecc7a..ea3a0339 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -4,7 +4,7 @@ as argument.
'''
# internal
-from promod3 import loop, sidechain, core
+from promod3 import loop, sidechain, core, scoring
from _modelling import *
from _closegaps import *
from _ring_punches import *
diff --git a/modelling/pymod/export_model.cc b/modelling/pymod/export_model.cc
index 22b369ed..1de295e8 100644
--- a/modelling/pymod/export_model.cc
+++ b/modelling/pymod/export_model.cc
@@ -13,12 +13,45 @@ ModellingHandle (*BuildRawModelHandleList)(const ost::seq::AlignmentList&,
= &BuildRawModel;
namespace {
+
int WrapCountEnclosedGaps(ModellingHandle& mhandle, const StructuralGap& gap) {
return CountEnclosedGaps(mhandle, gap, false);
}
+
int WrapCountEnclosedIns(ModellingHandle& mhandle, const StructuralGap& gap) {
return CountEnclosedGaps(mhandle, gap, true);
}
+
+promod3::scoring::BackboneOverallScorerPtr
+WrapGetBackboneScorer(ModellingHandle& mhandle){
+ if(!mhandle.backbone_scorer){
+ String err = "backbone_scorer must first be properly initialized ";
+ err += "before it can be used!";
+ throw promod3::Error(err);
+ }
+ return mhandle.backbone_scorer;
+}
+
+void WrapSetBackboneScorer(ModellingHandle& mhandle,
+ promod3::scoring::BackboneOverallScorerPtr scorer){
+ mhandle.backbone_scorer = scorer;
+}
+
+promod3::scoring::BackboneScoreEnvPtr
+WrapGetBackboneScorerEnv(ModellingHandle& mhandle){
+ if(!mhandle.backbone_scorer_env){
+ String err = "backbone_scorer_env must first be properly initialized ";
+ err += "before it can be used!";
+ throw promod3::Error(err);
+ }
+ return mhandle.backbone_scorer_env;
+}
+
+void WrapSetBackboneScorerEnv(ModellingHandle& mhandle,
+ promod3::scoring::BackboneScoreEnvPtr env){
+ mhandle.backbone_scorer_env = env;
+}
+
} // anon ns
void export_model()
@@ -27,12 +60,18 @@ void export_model()
.def_readwrite("model", &ModellingHandle::model)
.def_readwrite("gaps", &ModellingHandle::gaps)
.def_readwrite("seqres", &ModellingHandle::seqres)
+ .add_property("backbone_scorer", &WrapGetBackboneScorer,
+ &WrapSetBackboneScorer)
+ .add_property("backbone_scorer_env", &WrapGetBackboneScorerEnv,
+ &WrapSetBackboneScorerEnv)
;
+
def("ClearGaps", ClearGaps, (arg("mhandle"),arg("gap")));
def("CountEnclosedGaps", WrapCountEnclosedGaps, (arg("mhandle"),arg("gap")));
def("CountEnclosedInsertions", WrapCountEnclosedIns, (arg("mhandle"),arg("gap")));
def("MergeGaps", MergeGaps, (arg("mhandle"),arg("index")));
def("RemoveTerminalGaps", RemoveTerminalGaps, (arg("mhandle")));
+ def("SetupDefaultBackboneScorer", &SetupDefaultBackboneScorer,(arg("mhandle")));
def("BuildRawModel", BuildRawModelHandle,
(arg("aln"),
arg("include_ligands")=false,
diff --git a/modelling/src/model.cc b/modelling/src/model.cc
index 23fb93f3..8d7b32f7 100644
--- a/modelling/src/model.cc
+++ b/modelling/src/model.cc
@@ -11,12 +11,17 @@
#include <ost/conop/compound_lib.hh>
#include <promod3/core/geom_base.hh>
#include <promod3/core/runtime_profiling.hh>
+#include <promod3/scoring/scoring_object_loader.hh>
+#include <promod3/scoring/pairwise_score.hh>
+#include <promod3/scoring/density_score.hh>
+#include <promod3/scoring/clash_score.hh>
#include "model.hh"
using namespace ost::mol;
using namespace ost;
using namespace ost::seq;
using namespace ost::conop;
+using namespace promod3::scoring;
namespace promod3 { namespace modelling {
@@ -202,6 +207,37 @@ int RemoveTerminalGaps(ModellingHandle& mhandle) {
return removed_gaps;
}
+template <typename ScorerPtr>
+void AttachScorer(BackboneOverallScorerPtr overall_scorer,
+ ScorerPtr scorer,
+ BackboneScoreEnvPtr env,
+ const String& score_name){
+ scorer->AttachEnvironment(*env);
+ (*overall_scorer)[score_name] = scorer;
+}
+
+void SetupDefaultBackboneScorer(ModellingHandle& mhandle){
+
+ //setup environment
+ BackboneScoreEnvPtr env(new BackboneScoreEnv(mhandle.seqres));
+ env->SetInitialEnvironment(mhandle.model);
+
+ BackboneOverallScorerPtr scorer(new BackboneOverallScorer);
+
+ AttachScorer(scorer, LoadCBPackingScorer(), env, "cb_packing");
+ AttachScorer(scorer, LoadCBetaScorer(), env, "cbeta");
+ AttachScorer(scorer, LoadReducedScorer(), env, "reduced");
+ AttachScorer(scorer, ClashScorerPtr(new ClashScorer), env, "clash");
+ AttachScorer(scorer, LoadHBondScorer(), env, "hbond");
+ AttachScorer(scorer, LoadSSAgreementScorer(), env, "ss_agreement");
+ AttachScorer(scorer, LoadTorsionScorer(), env, "torsion");
+ AttachScorer(scorer, PairwiseScorerPtr(new PairwiseScorer), env, "pairwise");
+ AttachScorer(scorer, DensityScorerPtr(new DensityScorer), env, "density");
+
+ mhandle.backbone_scorer_env = env;
+ mhandle.backbone_scorer = scorer;
+}
+
bool CopyConserved(ResidueView src_res, ResidueHandle dst_res, XCSEditor& edi,
bool& has_cbeta)
{
diff --git a/modelling/src/model.hh b/modelling/src/model.hh
index 31842714..bf2aaa8c 100644
--- a/modelling/src/model.hh
+++ b/modelling/src/model.hh
@@ -5,6 +5,8 @@
#include <ost/seq/sequence_list.hh>
#include <promod3/core/message.hh>
+#include <promod3/scoring/backbone_score_base.hh>
+#include <promod3/scoring/backbone_overall_scorer.hh>
#include "gap.hh"
@@ -30,6 +32,8 @@ struct ModellingHandle {
ost::mol::EntityHandle model;
StructuralGapList gaps;
ost::seq::SequenceList seqres;
+ promod3::scoring::BackboneScoreEnvPtr backbone_scorer_env;
+ promod3::scoring::BackboneOverallScorerPtr backbone_scorer;
};
// see Python doc
@@ -45,6 +49,9 @@ void MergeGaps(ModellingHandle& mhandle, uint index);
// see Python doc
int RemoveTerminalGaps(ModellingHandle& mhandle);
+//see Python doc
+void SetupDefaultBackboneScorer(ModellingHandle& mhandle);
+
/// \brief copies all atom of src_res to dst_res
/// \param has_cbeta will be set to true if the src_res has a cbeta and the
// dst_residue is not a glycine
--
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