diff --git a/modelling/pymod/_closegaps.py b/modelling/pymod/_closegaps.py
index b9b508565eb0519d225ecb86488986553280a56a..9b3776d322f18b8cac6f62e7a76363c062aafaa6 100644
--- a/modelling/pymod/_closegaps.py
+++ b/modelling/pymod/_closegaps.py
@@ -53,6 +53,7 @@ def _GetWeights():
weights["reduced"] = 2.13535565
weights["cbeta"] = 3.59177335
weights["cb_packing"] = 1.17280667
+ weights["constraint"] = -0.7
return weights
def _CloseLoopFrame(mhandle, scorer, gap_orig, actual_candidates,
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index 8b70c14d527742eca6bad5c2714fee59f7b4a8b5..0e0cd9cb41b6ab0ec31742c3d69b4a6c5544b598 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -403,7 +403,7 @@ def CheckFinalModel(mhandle):
ost.LogInfo("Stereo-chemical problem in sidechain " + \
"of residue " + str(res))
-def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list()):
+def BuildFromRawModel(mhandle, scorer = None, use_amber_ff=False, extra_force_fields=list()):
'''Build a model starting with a raw model (see :func:`BuildRawModel`).
This function implements a recommended pipeline to generate complete models
@@ -453,7 +453,8 @@ def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list()):
torsion_sampler = loop.LoadTorsionSamplerCoil()
merge_distance = 4
- scorer = SetupBackboneScorer(mhandle)
+ if scorer == None:
+ scorer = SetupBackboneScorer(mhandle)
# remove terminal gaps and close small deletions
RemoveTerminalGaps(mhandle)
diff --git a/modelling/src/setup_scorer.cc b/modelling/src/setup_scorer.cc
index 51703fcf8e8148ce29a2d361a10353cd54091e94..62376dd17ee1ed81642158016c9d0008c31b9983 100644
--- a/modelling/src/setup_scorer.cc
+++ b/modelling/src/setup_scorer.cc
@@ -114,7 +114,8 @@ void ExtractPositions(const ost::seq::AlignmentHandle& aln,
ost::seq::ConstSequenceHandle seqres = aln.GetSequence(0);
ost::seq::ConstSequenceHandle seq;
ost::mol::ResidueView res;
- ost::mol::AtomView ca;
+ ost::mol::AtomView cb;
+ geom::Vec3 pos;
for(int seq_idx = 1; seq_idx < aln.GetCount(); ++seq_idx){
@@ -133,15 +134,24 @@ void ExtractPositions(const ost::seq::AlignmentHandle& aln,
continue;
}
- ca = res.FindAtom("CA");
+ cb = res.FindAtom("CB");
- if(!ca.IsValid()){
- positions[seq_idx-1].push_back(geom::Vec3());
- valid_residues[seq_idx-1].push_back(false);
- continue;
+ if(cb.IsValid()){
+ pos = cb.GetPos();
+ }
+ else{
+ ost::mol::AtomView n = res.FindAtom("N");
+ ost::mol::AtomView ca = res.FindAtom("CA");
+ ost::mol::AtomView c = res.FindAtom("C");
+ if(! (n.IsValid() && ca.IsValid() && c.IsValid())){
+ positions[seq_idx-1].push_back(geom::Vec3());
+ valid_residues[seq_idx-1].push_back(false);
+ continue;
+ }
+ promod3::core::ConstructCBetaPos(n.GetPos(),ca.GetPos(),c.GetPos(),pos);
}
- positions[seq_idx-1].push_back(ca.GetPos());
+ positions[seq_idx-1].push_back(pos);
valid_residues[seq_idx-1].push_back(true);
}
}
@@ -154,7 +164,7 @@ bool GenerateDisCo(const std::vector<std::vector<bool> >& valid_residues,
uint resnum_one, uint resnum_two,
std::vector<Real>& disco){
- disco.assign(15, 0.0);
+ disco.assign(17, 0.0);
int idx_one = resnum_one - 1;
int idx_two = resnum_two - 1;
@@ -168,7 +178,7 @@ bool GenerateDisCo(const std::vector<std::vector<bool> >& valid_residues,
for(uint cluster_idx = 0; cluster_idx < clusters.size(); ++cluster_idx){
- std::vector<Real> cluster_function(15, 0.0);
+ std::vector<Real> cluster_function(17, 0.0);
int num_gaussians = 0;
for(uint cluster_ele_idx = 0; cluster_ele_idx < clusters[cluster_idx].size();
@@ -186,7 +196,7 @@ bool GenerateDisCo(const std::vector<std::vector<bool> >& valid_residues,
//check, whether positions are close in space
// (closer than 17 Angstrom)
- if(distance > Real(289.0)) continue;
+ if(distance > Real(225.0)) continue;
distance = std::sqrt(distance);
@@ -194,7 +204,7 @@ bool GenerateDisCo(const std::vector<std::vector<bool> >& valid_residues,
//Let's add a gausssian function at this position!
Real function_pos = 0.5;
Real temp;
- for(int i = 0; i < 15; ++i, function_pos += 1.0){
+ for(int i = 0; i < 17; ++i, function_pos += 1.0){
temp = function_pos - distance;
cluster_function[i] += std::exp(-Real(0.5) * temp * temp);
}
@@ -205,7 +215,7 @@ bool GenerateDisCo(const std::vector<std::vector<bool> >& valid_residues,
if(num_gaussians == 0) continue; // no signal for this cluster...
Real factor = Real(1.0) / num_gaussians;
- for(uint i = 0; i < 15; ++i){
+ for(uint i = 0; i < 17; ++i){
cluster_function[i] *= factor;
}
@@ -228,7 +238,7 @@ bool GenerateDisCo(const std::vector<std::vector<bool> >& valid_residues,
//let's smash everything together...
for(uint i = 0; i < cluster_functions.size(); ++i){
- for(uint j = 0; j < 15; ++j){
+ for(uint j = 0; j < 17; ++j){
disco[j] += (weights[i] * cluster_functions[i][j]);
}
}
@@ -273,6 +283,8 @@ void AttachDistanceConstraints(promod3::loop::BackboneLoopScorerPtr scorer,
blosum62->AssignPreset(ost::seq::alg::SubstWeightMatrix::BLOSUM62);
ClusterSequences(aln, blosum62, promod3::core::AVG_DIST_METRIC, cluster_thresh, clusters);
+ std::cout<<"num clusters:"<<clusters.size()<<std::endl;
+
//let's generate the cluster weights
std::vector<Real> cluster_weights;
GenerateClusterWeights(aln, clusters, blosum62, gamma, cluster_weights);
@@ -291,7 +303,12 @@ void AttachDistanceConstraints(promod3::loop::BackboneLoopScorerPtr scorer,
clusters, cluster_weights,
i + 1, j + 1, disco);
if(contains_info){
- uint f_idx = scorer->AddConstraintFunction(0.0, 15.0, disco);
+ std::cout<<"disco between "<< i+1 <<" and "<< j+1<<std::endl;
+ for(int pos = 0; pos < 17; ++pos){
+ std::cout<<disco[pos]<<" ";
+ }
+ std::cout<<std::endl;
+ uint f_idx = scorer->AddConstraintFunction(0.0, 17.0, disco);
for(std::vector<int>::const_iterator ch_it = indices.begin();
ch_it != indices.end(); ++ch_it){
scorer->AddConstraint(*ch_it, i + 1, *ch_it, j + 1, f_idx);
diff --git a/modelling/src/setup_scorer.hh b/modelling/src/setup_scorer.hh
index a72fe84a1067bfa61201880c573011bee217a2cb..6c5748a831f396f5b0ff291875c48fe04ceb996f 100644
--- a/modelling/src/setup_scorer.hh
+++ b/modelling/src/setup_scorer.hh
@@ -9,6 +9,7 @@
#include <promod3/modelling/model.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/cluster.hh>
+#include <promod3/core/geom_base.hh>
#include <vector>
#include <map>