From 071f7b6f4428b94d68ae060d89b2b097c8625a50 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Mon, 3 Jan 2011 16:53:59 +0100
Subject: [PATCH] implement ReducedPotential and ReducedStatistics for views
---
modules/qa/pymod/export_reduced.cc | 18 +++++--
modules/qa/src/impl/reduced_impl.cc | 74 +++++++++++++++++++---------
modules/qa/src/impl/reduced_impl.hh | 10 +++-
modules/qa/src/reduced_potential.cc | 13 ++++-
modules/qa/src/reduced_potential.hh | 2 +-
modules/qa/src/reduced_statistics.cc | 19 +++++++
modules/qa/src/reduced_statistics.hh | 5 +-
7 files changed, 109 insertions(+), 32 deletions(-)
diff --git a/modules/qa/pymod/export_reduced.cc b/modules/qa/pymod/export_reduced.cc
index 0c230fb7d..3384c4529 100644
--- a/modules/qa/pymod/export_reduced.cc
+++ b/modules/qa/pymod/export_reduced.cc
@@ -23,10 +23,17 @@
#include <ost/qa/reduced_potential.hh>
using namespace ost::qa;
-
+using namespace ost::mol;
using namespace boost::python;
-uint64_t (ReducedStatistics::*get_count)(AminoAcid,AminoAcid,int,int)=&ReducedStatistics::GetCount;
+uint64_t (ReducedStatistics::*get_count)(AminoAcid,
+ AminoAcid,
+ int,int)=&ReducedStatistics::GetCount;
+void (ReducedStatistics::*ex_h)(EntityHandle)=&ReducedStatistics::Extract;
+void (ReducedStatistics::*ex_v)(EntityView)=&ReducedStatistics::Extract;
+
+Real (ReducedPotential::*get_h)(EntityHandle,bool)=&ReducedPotential::GetTotalEnergy;
+Real (ReducedPotential::*get_v)(EntityView,bool)=&ReducedPotential::GetTotalEnergy;
void export_Reduced()
{
class_<ReducedStatOptions>("ReducedStatOptions", init<>())
@@ -43,7 +50,8 @@ void export_Reduced()
class_<ReducedStatistics, ReducedStatisticsPtr>("ReducedStatistics", no_init)
.def(init<Real,Real,uint,uint,uint>((arg("l_cutoff"), arg("u_cutoff"),
arg("num_ang_bins"), arg("num_dist_bins"), arg("sequence_sep"))))
- .def("Extract", &ReducedStatistics::Extract)
+ .def("Extract", ex_h, arg("ent"))
+ .def("Extract", ex_v, arg("ent"))
.add_property("options", make_function(&ReducedStatistics::GetOptions,
return_value_policy<copy_const_reference>()))
.def("Save", &ReducedStatistics::Save)
@@ -55,7 +63,9 @@ void export_Reduced()
.def("Create", &ReducedPotential::Create).staticmethod("Create")
.def("Save", &ReducedPotential::Save)
.def("GetEnergy", &ReducedPotential::GetEnergy)
- .def("GetTotalEnergy", &ReducedPotential::GetTotalEnergy,
+ .def("GetTotalEnergy", get_h,
+ (arg("ent"), arg("normalize")=true))
+ .def("GetTotalEnergy", get_v,
(arg("ent"), arg("normalize")=true))
.add_property("options", make_function(&ReducedPotential::GetOptions,
return_value_policy<copy_const_reference>()))
diff --git a/modules/qa/src/impl/reduced_impl.cc b/modules/qa/src/impl/reduced_impl.cc
index 8994fada4..a3778cb39 100644
--- a/modules/qa/src/impl/reduced_impl.cc
+++ b/modules/qa/src/impl/reduced_impl.cc
@@ -20,39 +20,65 @@ bool ReducedPotentialImpl::VisitResidue(const mol::ResidueHandle& res)
if (!this->GetCAlphaCBetaPos(res, ca_pos_one, cb_pos_one)) {
return false;
}
+
+ if (ent_) {
+ // we got a full entity handle.
+ mol::AtomHandleList within=ent_.FindWithin(ca_pos_one,
+ opts_.upper_cutoff-0.00001);
+ for (mol::AtomHandleList::const_iterator
+ i=within.begin(), e=within.end(); i!=e; ++i) {
+ if (i->GetName()=="CA") {
+ this->HandleResidue(aa_one, ca_pos_one, cb_pos_one, index, *i);
+ }
- mol::AtomHandleList within=ent_.FindWithin(ca_pos_one,
+ }
+ return false;
+ }
+ mol::AtomViewList within=view_.FindWithin(ca_pos_one,
opts_.upper_cutoff-0.00001);
- for (mol::AtomHandleList::const_iterator
+ for (mol::AtomViewList::const_iterator
i=within.begin(), e=within.end(); i!=e; ++i) {
- mol::ResidueHandle res_two=i->GetResidue();
- if (res_two.GetIndex()-index<opts_.sequence_sep) {
- continue;
- }
- if (i->GetName()!="CA" || !res_two.IsPeptideLinking()) {
- continue;
+ if (i->GetName()=="CA") {
+ this->HandleResidue(aa_one, ca_pos_one, cb_pos_one, index, i->GetHandle());
}
+ }
+ return false;
+}
- AminoAcid aa_two=OneLetterCodeToAminoAcid(res_two.GetOneLetterCode());
- if (aa_two==Xxx) {
- continue;
- }
- geom::Vec3 ca_pos_two;
- geom::Vec3 cb_pos_two;
- if (!this->GetCAlphaCBetaPos(res_two, ca_pos_two, cb_pos_two)) {
- continue;
- }
+void ReducedPotentialImpl::HandleResidue(AminoAcid aa_one,
+ const geom::Vec3& ca_pos_one,
+ const geom::Vec3& cb_pos_one,
+ uint index_one,
+ const mol::AtomHandle& ca_two)
+{
+
+ mol::ResidueHandle res_two=ca_two.GetResidue();
+ if (res_two.GetIndex()-index_one<opts_.sequence_sep) {
+ return;
+ }
+ if (!res_two.IsPeptideLinking()) {
+ return;
+ }
- Real dist=geom::Length(ca_pos_one-ca_pos_two);
- if (dist<opts_.lower_cutoff) {
- continue;
- }
- Real angle=geom::Angle(cb_pos_one-ca_pos_one, cb_pos_two-ca_pos_two);
- this->OnInteraction(aa_one, aa_two, dist, angle);
+ AminoAcid aa_two=OneLetterCodeToAminoAcid(res_two.GetOneLetterCode());
+ if (aa_two==Xxx) {
+ return;
}
- return false;
+ geom::Vec3 ca_pos_two;
+ geom::Vec3 cb_pos_two;
+ if (!this->GetCAlphaCBetaPos(res_two, ca_pos_two, cb_pos_two)) {
+ return;
+ }
+
+ Real dist=geom::Length(ca_pos_one-ca_pos_two);
+ if (dist<opts_.lower_cutoff) {
+ return;
+ }
+ Real angle=geom::Angle(cb_pos_one-ca_pos_one, cb_pos_two-ca_pos_two);
+
+ this->OnInteraction(aa_one, aa_two, dist, angle);
}
bool ReducedPotentialImpl::GetCAlphaCBetaPos(const mol::ResidueHandle& res,
diff --git a/modules/qa/src/impl/reduced_impl.hh b/modules/qa/src/impl/reduced_impl.hh
index 98651360b..43c312ea2 100644
--- a/modules/qa/src/impl/reduced_impl.hh
+++ b/modules/qa/src/impl/reduced_impl.hh
@@ -35,6 +35,10 @@ public:
ReducedPotentialImpl(const ReducedStatOptions& opts, mol::EntityHandle ent):
opts_(opts), ent_(ent)
{ }
+
+ ReducedPotentialImpl(const ReducedStatOptions& opts, mol::EntityView ent):
+ opts_(opts), view_(ent)
+ { }
virtual bool VisitResidue(const mol::ResidueHandle& res);
@@ -44,9 +48,13 @@ public:
virtual void OnInteraction(AminoAcid aa_one, AminoAcid aa_two,
Real dist, Real angle)=0;
-private:
+private:
+ void HandleResidue(AminoAcid aa_one, const geom::Vec3& ca_pos_one,
+ const geom::Vec3& cb_pos_one,
+ uint index_one, const mol::AtomHandle& ca_two);
ReducedStatOptions opts_;
mol::EntityHandle ent_;
+ mol::EntityView view_;
};
}}}
diff --git a/modules/qa/src/reduced_potential.cc b/modules/qa/src/reduced_potential.cc
index 78df5c902..1799c18e4 100644
--- a/modules/qa/src/reduced_potential.cc
+++ b/modules/qa/src/reduced_potential.cc
@@ -35,7 +35,11 @@ public:
impl::ReducedPotentialImpl(opts, ent),
energies_(energies), energy_(0.0), norm_(norm), count_(0)
{ }
-
+ ReducedEnergiesCalc(const ReducedStatOptions& opts, ReducedEnergies& energies,
+ mol::EntityView ent, bool norm):
+ impl::ReducedPotentialImpl(opts, ent),
+ energies_(energies), energy_(0.0), norm_(norm), count_(0)
+ { }
virtual void OnInteraction(AminoAcid aa_one, AminoAcid aa_two,
Real dist, Real angle)
{
@@ -138,5 +142,12 @@ Real ReducedPotential::GetTotalEnergy(ost::mol::EntityHandle ent, bool norm)
return calc.GetEnergy();
}
+Real ReducedPotential::GetTotalEnergy(ost::mol::EntityView ent, bool norm)
+{
+ ReducedEnergiesCalc calc(opts_, energies_, ent, norm);
+ ent.Apply(calc);
+ return calc.GetEnergy();
+}
+
}}
diff --git a/modules/qa/src/reduced_potential.hh b/modules/qa/src/reduced_potential.hh
index 534892678..0f90debce 100644
--- a/modules/qa/src/reduced_potential.hh
+++ b/modules/qa/src/reduced_potential.hh
@@ -49,7 +49,7 @@ public:
Real GetTotalEnergy(ost::mol::EntityHandle ent, bool normalize=true);
-
+ Real GetTotalEnergy(ost::mol::EntityView ent, bool normalize=true);
static bool GetCAlphaCBetaPos(const mol::ResidueHandle& res,
geom::Vec3& ca_pos,
geom::Vec3& cb_pos);
diff --git a/modules/qa/src/reduced_statistics.cc b/modules/qa/src/reduced_statistics.cc
index 9c20a9cd2..723fe29f9 100644
--- a/modules/qa/src/reduced_statistics.cc
+++ b/modules/qa/src/reduced_statistics.cc
@@ -41,6 +41,12 @@ public:
histo_(histo)
{ }
+ ReducedStatExtractor(const ReducedStatOptions& opts, ReducedHistogram& histo,
+ mol::EntityView ent):
+ impl::ReducedPotentialImpl(opts, ent),
+ histo_(histo)
+ { }
+
virtual void OnInteraction(AminoAcid aa_one, AminoAcid aa_two,
Real dist, Real angle)
{
@@ -130,4 +136,17 @@ void ReducedStatistics::Extract(mol::EntityHandle ent)
ent.Apply(extractor);
}
+void ReducedStatistics::Extract(mol::EntityView ent)
+{
+ if (ent.GetChainCount()!=1) {
+ std::stringstream ss;
+ ss << "Expected exactly one chain, but entity has "
+ << ent.GetChainCount() << "chains";
+ throw std::runtime_error(ss.str());
+ }
+ ReducedStatExtractor extractor(opts_, histo_, ent);
+ ent.Apply(extractor);
+}
+
+
}}
\ No newline at end of file
diff --git a/modules/qa/src/reduced_statistics.hh b/modules/qa/src/reduced_statistics.hh
index 419ac550f..7d1a24800 100644
--- a/modules/qa/src/reduced_statistics.hh
+++ b/modules/qa/src/reduced_statistics.hh
@@ -82,9 +82,12 @@ public:
const ReducedStatOptions& GetOptions() const { return opts_; }
- /// \brief extract the statistics from the given entity
+ /// \brief extract the statistics from the given entity (handle)
void Extract(mol::EntityHandle ent);
+ /// \brief extract statistics from given entity (view)
+ void Extract(mol::EntityView ent);
+
void Save(const String& filename);
--
GitLab