diff --git a/modules/io/src/img/map_io_tiff_handler.cc b/modules/io/src/img/map_io_tiff_handler.cc
index 233a43c2d4b0069df0b4543c930ac3f174984463..10c1a5c3f754a2a9b70cfd9da68f704b8e43cb45 100644
--- a/modules/io/src/img/map_io_tiff_handler.cc
+++ b/modules/io/src/img/map_io_tiff_handler.cc
@@ -40,6 +40,7 @@
#include <ost/io/io_exception.hh>
#include "map_io_tiff_handler.hh"
+#include "tiff_util.hh"
namespace ost { namespace io {
diff --git a/modules/io/src/img/map_io_tiff_handler.hh b/modules/io/src/img/map_io_tiff_handler.hh
index 7fbfb901e8b44cc6d6616648a70abf842ec26505..4fced407477c08c4ab62f28f7169cbe34408894f 100644
--- a/modules/io/src/img/map_io_tiff_handler.hh
+++ b/modules/io/src/img/map_io_tiff_handler.hh
@@ -17,21 +17,21 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
-#ifndef DX_IO_TIFF_IO_PLUGIN_OST_HH
-#define DX_IO_TIFF_IO_PLUGIN_OST_HH
+#ifndef DX_IO_tiff_IO_PLUGIN_OST_HH
+#define DX_IO_tiff_IO_PLUGIN_OST_HH
/*
Authors: Ansgar Philippsen, Andreas Schenk
*/
#include <boost/logic/tribool.hpp>
-#include "tiff_util.hh"
#include "map_io_handler.hh"
-
+struct tiff;
+
namespace ost { namespace io {
class DLLEXPORT_OST_IO TIF: public ImageFormatBase
@@ -65,7 +65,7 @@ class DLLEXPORT_OST_IO TIF: public ImageFormatBase
protected:
TIF(String format_string, boost::logic::tribool normalize_on_save = boost::logic::indeterminate, Format bit_depth = OST_DEFAULT_FORMAT, bool sign = false, bool phasecolor = false, int subimage = -1);
- void do_export(const img::MapHandle& image,TIFF* tfile,const TIF& formattif) const;
+ void do_export(const img::MapHandle& image,tiff* tfile,const TIF& formattif) const;
private:
@@ -84,10 +84,15 @@ class DLLEXPORT_OST_IO MapIOTiffHandler: public MapIOHandler
/// \brief Map IO handler to read/write Tiff files
///
/// This map IO handler reads and writes tiff-formatted files.
- virtual void Import(img::MapHandle& sh, const boost::filesystem::path& loc,const ImageFormatBase& formatstruct);
- virtual void Import(img::MapHandle& sh, std::istream& loc,const ImageFormatBase& formatstruct);
- virtual void Export(const img::MapHandle& sh, const boost::filesystem::path& loc,const ImageFormatBase& formatstruct) const;
- virtual void Export(const img::MapHandle& sh, std::ostream& loc,const ImageFormatBase& formatstruct) const;
+ virtual void Import(img::MapHandle& sh, const boost::filesystem::path& loc,
+ const ImageFormatBase& formatstruct);
+ virtual void Import(img::MapHandle& sh, std::istream& loc,
+ const ImageFormatBase& formatstruct);
+ virtual void Export(const img::MapHandle& sh,
+ const boost::filesystem::path& loc,
+ const ImageFormatBase& formatstruct) const;
+ virtual void Export(const img::MapHandle& sh, std::ostream& loc,
+ const ImageFormatBase& formatstruct) const;
static bool MatchContent(unsigned char* header);
static bool MatchType(const ImageFormatBase& type);
static bool MatchSuffix(const String& loc);
@@ -96,10 +101,13 @@ class DLLEXPORT_OST_IO MapIOTiffHandler: public MapIOHandler
protected:
- TIFF* open_subimage_file(const boost::filesystem::path& location,const TIF& formattif);
- TIFF* open_subimage_stream(std::istream& location,const TIF& formattif);
- void load_image_data(TIFF* tfile, img::ImageHandle& image, const TIF& formattif);
- virtual void do_export(const img::MapHandle& sh,TIFF* tfile,TIF& formatstruct) const;
+ tiff* open_subimage_file(const boost::filesystem::path& location,
+ const TIF& formattif);
+ tiff* open_subimage_stream(std::istream& location,const TIF& formattif);
+ void load_image_data(tiff* tfile, img::ImageHandle& image,
+ const TIF& formattif);
+ virtual void do_export(const img::MapHandle& sh,tiff* tfile,
+ TIF& formatstruct) const;
};
diff --git a/modules/mol/alg/src/svd_superpose.cc b/modules/mol/alg/src/svd_superpose.cc
index 6608372c13a2372196041a0d6dfee8f2e312e647..2f770167f236fa5c1a7dc02aef7016c77823fc90 100644
--- a/modules/mol/alg/src/svd_superpose.cc
+++ b/modules/mol/alg/src/svd_superpose.cc
@@ -21,13 +21,15 @@
* Author Juergen Haas
*/
#include <stdexcept>
-
+#include <iostream>
#include <boost/bind.hpp>
+#include <Eigen/Core>
+#include <Eigen/Array>
#include <Eigen/SVD>
#include <Eigen/LU>
-#include <iostream>
+
#include <ost/base.hh>
#include <ost/geom/vec3.hh>
#include <ost/mol/alg/svd_superpose.hh>
@@ -36,7 +38,13 @@
namespace ost { namespace mol { namespace alg {
+
using boost::bind;
+typedef Eigen::Matrix<Real,3,1> EVec3;
+typedef Eigen::Matrix<Real,3,3> EMat3;
+typedef Eigen::Matrix<Real,1,3> ERVec3;
+typedef Eigen::Matrix<Real,Eigen::Dynamic,Eigen::Dynamic> EMatX;
+typedef Eigen::Matrix<Real,1,Eigen::Dynamic> ERVecX;
Real CalculateRMSD(const mol::EntityView& ev1,
const mol::EntityView& ev2,
@@ -93,22 +101,55 @@ Real calc_rmsd_for_atom_lists(const mol::AtomViewList& atoms1,
return rmsd;
}
+class SuperposerSVDImpl {
+public:
+ SuperposerSVDImpl(int natoms, bool alloc_atoms):
+ natoms_(natoms), alloc_atoms_(alloc_atoms)
+ {
-SuperposerSVD::SuperposerSVD(int natoms, bool alloc_atoms):
- natoms_(natoms), alloc_atoms_(alloc_atoms)
-{
+ ERVec3 avg1_=EVec3::Zero();
+ ERVec3 avg2_=EVec3::Zero();
- ERVec3 avg1_=EVec3::Zero();
- ERVec3 avg2_=EVec3::Zero();
+ if (alloc_atoms_) {
+ atoms1_=EMatX::Zero(natoms,3);
+ atoms2_=EMatX::Zero(natoms,3);
+ }
- if (alloc_atoms_) {
- atoms1_=EMatX::Zero(natoms,3);
- atoms2_=EMatX::Zero(natoms,3);
}
+private:
+ int natoms_;
+ bool alloc_atoms_;
+ EMatX atoms1_;
+ EMatX atoms2_;
+public:
+ void EntToMatrices(const mol::EntityView& ev1, const mol::EntityView& ev2);
+ geom::Vec3 EigenVec3ToVec3(const EVec3 &vec);
+ geom::Mat3 EigenMat3ToMat3(const EMat3 &mat);
+ EVec3 Vec3ToEigenRVec(const geom::Vec3 &vec);
+ EVec3 Vec3ToEigenVec(const geom::Vec3 &vec);
+ EMatX SubtractVecFromMatrixRows(EMatX Mat,
+ ERVecX Vec);
+ SuperpositionResult Run(const mol::AtomViewList& atoms1,
+ const mol::AtomViewList& atoms2);
+ SuperpositionResult DoSuperposition();
+ EIGEN_MAKE_ALIGNED_OPERATOR_NEW //needed only if *fixed* sized matrices are
+ //members of classes
+};
+
+SuperposerSVD::~SuperposerSVD()
+{
+ assert(impl_);
+ delete impl_;
+}
+
+SuperposerSVD::SuperposerSVD(int natoms, bool alloc_atoms):
+ impl_(new SuperposerSVDImpl(natoms, alloc_atoms))
+{
+
}
-geom::Vec3 SuperposerSVD::EigenVec3ToVec3(const EVec3 &vec){
+geom::Vec3 SuperposerSVDImpl::EigenVec3ToVec3(const EVec3 &vec){
#if defined _MSC_VER
geom::Vec3 myvec3;
for (int i=0; i<3; ++i) {
@@ -120,7 +161,8 @@ geom::Vec3 SuperposerSVD::EigenVec3ToVec3(const EVec3 &vec){
#endif
}
-geom::Mat3 SuperposerSVD::EigenMat3ToMat3(const EMat3 &mat){
+geom::Mat3 SuperposerSVDImpl::EigenMat3ToMat3(const EMat3 &mat)
+{
#if defined _MSC_VER
geom::Mat3 mymat3;
for (int i=0; i<3; ++i) {
@@ -135,7 +177,8 @@ geom::Mat3 SuperposerSVD::EigenMat3ToMat3(const EMat3 &mat){
}
-EVec3 SuperposerSVD::Vec3ToEigenRVec(const geom::Vec3 &vec){
+EVec3 SuperposerSVDImpl::Vec3ToEigenRVec(const geom::Vec3 &vec)
+{
#if defined _MSC_VER
EVec3 myvec3=EVec3::Zero();
for (int counter=0; counter<3; ++counter) {
@@ -147,7 +190,8 @@ EVec3 SuperposerSVD::Vec3ToEigenRVec(const geom::Vec3 &vec){
#endif
}
-EVec3 SuperposerSVD::Vec3ToEigenVec(const geom::Vec3 &vec){
+EVec3 SuperposerSVDImpl::Vec3ToEigenVec(const geom::Vec3 &vec)
+{
#if defined _MSC_VER
EVec3 myvec3=EVec3::Zero();
for (int counter=0; counter<3; ++counter) {
@@ -159,8 +203,9 @@ EVec3 SuperposerSVD::Vec3ToEigenVec(const geom::Vec3 &vec){
#endif
}
-EMatX SuperposerSVD::SubtractVecFromMatrixRows(EMatX Mat,
- ERVecX Vec){
+EMatX SuperposerSVDImpl::SubtractVecFromMatrixRows(EMatX Mat,
+ ERVecX Vec)
+{
for (int row=0; row<Mat.rows();++row) {
Mat.row(row)-=Vec;
@@ -168,8 +213,8 @@ EMatX SuperposerSVD::SubtractVecFromMatrixRows(EMatX Mat,
return Mat;
}
-void SuperposerSVD::EntToMatrices(const mol::EntityView& ev1,
- const mol::EntityView& ev2)
+void SuperposerSVDImpl::EntToMatrices(const mol::EntityView& ev1,
+ const mol::EntityView& ev2)
{
//Now iterate over atoms in entities and extract coords into Nx3 matrices
//for superposition
@@ -183,23 +228,23 @@ void SuperposerSVD::EntToMatrices(const mol::EntityView& ev1,
for (int counter=0; a_ev1_end!=a_ev1; ++a_ev1, ++a_ev2, ++counter) {
av1=*a_ev1;
pos=av1.GetPos();
- e=SuperposerSVD::Vec3ToEigenVec(pos);
+ e=SuperposerSVDImpl::Vec3ToEigenVec(pos);
atoms1_.row(counter)=e ;
av2=*a_ev2;
pos=av2.GetPos();
- e=SuperposerSVD::Vec3ToEigenVec(pos);
+ e=SuperposerSVDImpl::Vec3ToEigenVec(pos);
atoms2_.row(counter)=e;
}
}
-SuperpositionResult SuperposerSVD::DoSuperposition()
+SuperpositionResult SuperposerSVDImpl::DoSuperposition()
{
ERVec3 avg1_=atoms1_.colwise().sum()/atoms1_.rows();
ERVec3 avg2_=atoms2_.colwise().sum()/atoms2_.rows();
//center the structures
- atoms1_=this->SuperposerSVD::SubtractVecFromMatrixRows(atoms1_, avg1_);
- atoms2_=this->SuperposerSVD::SubtractVecFromMatrixRows(atoms2_, avg2_);
+ atoms1_=this->SubtractVecFromMatrixRows(atoms1_, avg1_);
+ atoms2_=this->SubtractVecFromMatrixRows(atoms2_, avg2_);
EMatX atoms2=atoms2_.transpose();
//single value decomposition
@@ -221,9 +266,9 @@ SuperpositionResult SuperposerSVD::DoSuperposition()
SuperpositionResult res;
// prepare rmsd calculation
- geom::Vec3 shift=SuperposerSVD::EigenVec3ToVec3(avg2_);
- geom::Vec3 com_vec=-SuperposerSVD::EigenVec3ToVec3(avg1_);
- geom::Mat3 rot=SuperposerSVD::EigenMat3ToMat3(ERot.transpose());
+ geom::Vec3 shift=SuperposerSVDImpl::EigenVec3ToVec3(avg2_);
+ geom::Vec3 com_vec=-SuperposerSVDImpl::EigenVec3ToVec3(avg1_);
+ geom::Mat3 rot=SuperposerSVDImpl::EigenMat3ToMat3(ERot.transpose());
geom::Mat4 mat4_com, mat4_rot, mat4_shift;
mat4_rot.PasteRotation(rot);
mat4_shift.PasteTranslation(shift);
@@ -238,14 +283,20 @@ SuperpositionResult SuperposerSVD::DoSuperposition()
SuperpositionResult SuperposerSVD::Run(const mol::EntityView& ev1,
const mol::EntityView& ev2)
{
- this->EntToMatrices(ev1, ev2);
- SuperpositionResult r=this->DoSuperposition();
+ impl_->EntToMatrices(ev1, ev2);
+ SuperpositionResult r=impl_->DoSuperposition();
r.rmsd=CalculateRMSD(ev1, ev2, r.transformation);
return r;
}
SuperpositionResult SuperposerSVD::Run(const mol::AtomViewList& atoms1,
const mol::AtomViewList& atoms2)
+{
+ return impl_->Run(atoms1, atoms2);
+}
+
+SuperpositionResult SuperposerSVDImpl::Run(const mol::AtomViewList& atoms1,
+ const mol::AtomViewList& atoms2)
{
mol::AtomViewList::const_iterator a_ev1=atoms1.begin();
mol::AtomViewList::const_iterator a_ev1_end=atoms1.end();
@@ -254,23 +305,17 @@ SuperpositionResult SuperposerSVD::Run(const mol::AtomViewList& atoms1,
for (int counter=0; a_ev1_end!=a_ev1; ++a_ev1, ++a_ev2, ++counter) {
mol::AtomView av=*a_ev1;
geom::Vec3 pos=av.GetPos();
- ERVec3 e=SuperposerSVD::Vec3ToEigenVec(pos);
+ ERVec3 e=SuperposerSVDImpl::Vec3ToEigenVec(pos);
atoms1_.row(counter)=e ;
av=*a_ev2;
pos=av.GetPos();
- e=SuperposerSVD::Vec3ToEigenVec(pos);
+ e=SuperposerSVDImpl::Vec3ToEigenVec(pos);
atoms2_.row(counter)=e;
}
return this->DoSuperposition();
}
-SuperpositionResult SuperposerSVD::Run(EMatX atoms1,
- EMatX atoms2)
-{
- atoms1_=atoms1;
- atoms2_=atoms2;
- return this->DoSuperposition();
-}
+
SuperpositionResult SuperposeAtoms(const mol::AtomViewList& atoms1,
const mol::AtomViewList& atoms2,
diff --git a/modules/mol/alg/src/svd_superpose.hh b/modules/mol/alg/src/svd_superpose.hh
index de7403bc1c83658da4c3a2eb196256cff63630b3..80f0762785df0d71bbd90a588c14ed79f30f37e1 100644
--- a/modules/mol/alg/src/svd_superpose.hh
+++ b/modules/mol/alg/src/svd_superpose.hh
@@ -23,9 +23,6 @@
#ifndef OST_SUPERPOSITION_HH
#define OST_SUPERPOSITION_HH
-#include <Eigen/Core>
-#include <Eigen/Array>
-
#include <ost/base.hh>
#include <ost/geom/geom.hh>
#include <ost/mol/mol.hh>
@@ -48,46 +45,22 @@ struct DLLEXPORT_OST_MOL_ALG SuperpositionResult {
mol::EntityView entity_view2;
};
-
-typedef Eigen::Matrix<Real,3,1> EVec3;
-typedef Eigen::Matrix<Real,3,3> EMat3;
-typedef Eigen::Matrix<Real,1,3> ERVec3;
-typedef Eigen::Matrix<Real,Eigen::Dynamic,Eigen::Dynamic> EMatX;
-typedef Eigen::Matrix<Real,1,Eigen::Dynamic> ERVecX;
+class SuperposerSVDImpl;
/// \brief effiently superpose a bunch of models with the same number of atoms
-/// Choose either two EntityViews, two AtomViewLists or two EigenMatrices of the
-/// same size to superpose.
+/// Choose either two EntityViews or two AtomViewLists.
class DLLEXPORT_OST_MOL_ALG SuperposerSVD {
public:
SuperposerSVD(int natoms, bool alloc_atoms);
-
+ ~SuperposerSVD();
SuperpositionResult Run(const mol::EntityView& ev1,
const mol::EntityView& ev2);
SuperpositionResult Run(const mol::AtomViewList& atoms1,
const mol::AtomViewList& atoms2);
- SuperpositionResult Run(const EMatX atoms1,
- const EMatX atoms2);
private:
-
-
- int natoms_;
- bool alloc_atoms_;
- EMatX atoms1_;
- EMatX atoms2_;
- void EntToMatrices(const mol::EntityView& ev1, const mol::EntityView& ev2);
- geom::Vec3 EigenVec3ToVec3(const EVec3 &vec);
- geom::Mat3 EigenMat3ToMat3(const EMat3 &mat);
- EVec3 Vec3ToEigenRVec(const geom::Vec3 &vec);
- EVec3 Vec3ToEigenVec(const geom::Vec3 &vec);
- EMatX SubtractVecFromMatrixRows(EMatX Mat,
- ERVecX Vec);
- EIGEN_MAKE_ALIGNED_OPERATOR_NEW //needed only if *fixed* sized matrices are
- //members of classes
- SuperpositionResult DoSuperposition();
-
+ SuperposerSVDImpl* impl_;
};
/// \brief takes the corresponding atoms and superposes them
diff --git a/modules/qa/pymod/CMakeLists.txt b/modules/qa/pymod/CMakeLists.txt
index 5923ef71e1869586fbd6c9ca121a385783b75c52..c4fff8b16c9a6f8fc579717f9d2ccd988c59002c 100644
--- a/modules/qa/pymod/CMakeLists.txt
+++ b/modules/qa/pymod/CMakeLists.txt
@@ -1,5 +1,4 @@
set(OST_QA_PYMOD_SOURCES
- export_ca_distance.cc
export_interaction.cc
export_torsion.cc
export_packing.cc
diff --git a/modules/qa/pymod/export_ca_distance.cc b/modules/qa/pymod/export_ca_distance.cc
deleted file mode 100644
index ef6bd2846dd5ad617f7c3af9ee8496ed4571bd7c..0000000000000000000000000000000000000000
--- a/modules/qa/pymod/export_ca_distance.cc
+++ /dev/null
@@ -1,71 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include <boost/python.hpp>
-
-
-#include <ost/qa/ca_distance.hh>
-
-using namespace ost::qa;
-using namespace ost;
-
-///\todo put this into a header? seems like other might need this as well.
-namespace boost{
-
- template<class T>
- inline T* get_pointer( boost::shared_ptr<const T> const& p ){
- return const_cast< T* >( p.get() );
- }
-
-}
-
-namespace boost{ namespace python{
-
- template<class T>
- struct pointee< boost::shared_ptr<T const> >{
- typedef T type;
- };
-
-} } //boost::python
-
-namespace utils{
-
- template< class T >
- void register_shared_ptrs_to_python(){
- namespace bpl = boost::python;
- bpl::register_ptr_to_python< boost::shared_ptr< T > >();
- bpl::register_ptr_to_python< boost::shared_ptr< const T > >();
- bpl::implicitly_convertible< boost::shared_ptr< T >,
- boost::shared_ptr< const T > >();
- }
-
-}
-using namespace boost::python;
-
-void export_CaDistance()
-{
- def("CalculateCalphaDistance", &CalculateCalphaDistance);
-
- class_<CalphaDistance, boost::noncopyable>("CalphaDistance", no_init)
- .def("IsDistanceDefined", &CalphaDistance::IsDistanceDefined,
- args("number_a", "number_b"))
- .def("GetDistance", &CalphaDistance::GetDistance,
- args("number_a", "number_b"))
- ;
- utils::register_shared_ptrs_to_python<CalphaDistance>();
-}
diff --git a/modules/qa/pymod/wrap_qa.cc b/modules/qa/pymod/wrap_qa.cc
index 543ccc9f518d46b58f5352273643ac737eb69628..bb6519155ef12476d31c1e1fac7752069ca182d2 100644
--- a/modules/qa/pymod/wrap_qa.cc
+++ b/modules/qa/pymod/wrap_qa.cc
@@ -21,13 +21,11 @@
void export_Torsion();
void export_Interaction();
void export_Packing();
-void export_CaDistance();
void export_Clash();
BOOST_PYTHON_MODULE(_qa)
{
export_Torsion();
export_Interaction();
- export_Packing();
- export_CaDistance();
+ export_Packing();
export_Clash();
}
diff --git a/modules/qa/src/CMakeLists.txt b/modules/qa/src/CMakeLists.txt
index 088906a2f1b57d6e972a6e4e90f5928e9fb3e3db..cc75ea3b85e8c3a6de3f98aeb75732ccf14f0849 100644
--- a/modules/qa/src/CMakeLists.txt
+++ b/modules/qa/src/CMakeLists.txt
@@ -10,7 +10,6 @@ solis_torsion_potential.hh
interaction_statistics.hh
all_atom_potential.hh
packing_statistics.hh
-ca_distance.hh
atom_types.hh
packing_potential.hh
clash_score.hh
@@ -24,7 +23,6 @@ solis_torsion_statistics.cc
solis_torsion_potential.cc
interaction_statistics.cc
packing_statistics.cc
-ca_distance.cc
amino_acids.cc
atom_types.cc
all_atom_potential.cc
diff --git a/modules/qa/src/ca_distance.cc b/modules/qa/src/ca_distance.cc
deleted file mode 100644
index 1b9da37ed6de0046a88866eddbe7ce5f1a074d12..0000000000000000000000000000000000000000
--- a/modules/qa/src/ca_distance.cc
+++ /dev/null
@@ -1,103 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include "ca_distance.hh"
-#include <ost/geom/geom.hh>
-#include <Eigen/Array>
-/*
- Author: Marco Biasini
- */
-
-namespace ost { namespace qa {
-
-namespace {
-class DistanceCalculator : public mol::EntityVisitor {
-public:
- DistanceCalculator(const mol::AtomHandle& atom_handle,
- Eigen::MatrixXd mat)
- : atom_a_(atom_handle), distance_mat_(mat) {
-
- }
- virtual bool VisitAtom(const mol::AtomHandle& atom) {
- Real d=geom::Length(atom_a_.GetPos()-atom.GetPos());
- int i=atom_a_.GetResidue().GetNumber().GetNum();
- int j=atom.GetResidue().GetNumber().GetNum();
- distance_mat_(i-1, j-1)= d;
- return true;
- }
-private:
- mol::AtomHandle atom_a_;
- Eigen::MatrixXd distance_mat_;
-};
-
-}
-
-mol::ResNum CalphaDistance::GetBiggestResNumber(const mol::EntityView& e) const {
- assert(e.GetChainCount()==1);
- return e.GetChainList().front().GetResidueList().back().GetNumber();
-}
-
-CalphaDistancePtr CalculateCalphaDistance(const mol::EntityView& a,
- const mol::EntityView& b) {
- if (a.GetChainCount()!=1 || b.GetChainCount()!=1) {
- throw Error("One or more views have chain count not equal to 1");
- }
- return CalphaDistancePtr(new CalphaDistance(a, b));
-}
-
-CalphaDistance::CalphaDistance(const mol::EntityView& a, const mol::EntityView& b)
- : a_(a), b_(b), distance_mat_() {
- assert(a_.GetChainCount()==1);
- assert(b_.GetChainCount()==1);
- mol::ResNum last_a=this->GetBiggestResNumber(a_);
- mol::ResNum last_b=this->GetBiggestResNumber(b_);
- distance_mat_=Eigen::MatrixXd::Constant(last_a.GetNum(), last_b.GetNum(), -1);
- this->CalculateDistances();
-}
-
-void CalphaDistance::CalculateDistances() {
- a_.Apply(*this);
-}
-
-bool CalphaDistance::IsDistanceDefined(const mol::ResNum& number_a,
- const mol::ResNum& number_b) const {
- int i=number_a.GetNum();
- int j=number_b.GetNum();
- return (1<=i && 1<=j && static_cast<int>(distance_mat_.cols())>=i &&
- static_cast<int>(distance_mat_.rows())>=j &&
- distance_mat_(i-1, j-1)>=0.0);
-
-}
-
-
-bool CalphaDistance::VisitAtom(const mol::AtomHandle& atom) {
- DistanceCalculator dist_calc(atom, distance_mat_);
- b_.Apply(dist_calc);
- return true;
-}
-
-Real CalphaDistance::GetDistance(const mol::ResNum& number_a,
- const mol::ResNum& number_b) const {
- if (this->IsDistanceDefined(number_a, number_b))
- return distance_mat_(number_a.GetNum()-1,
- number_b.GetNum()-1);
- throw Error("distance between C-alpha atoms is undefined");
-}
-
-}}
-
diff --git a/modules/qa/src/ca_distance.hh b/modules/qa/src/ca_distance.hh
deleted file mode 100644
index 4690ad934848cdeef098c872be3cc678f285b312..0000000000000000000000000000000000000000
--- a/modules/qa/src/ca_distance.hh
+++ /dev/null
@@ -1,92 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2010 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_CA_DISTANCE_HH
-#define OST_QA_CA_DISTANCE_HH
-
-/*
- Author: Marco Biasini
- */
-
-#include <ost/mol/mol.hh>
-#include <ost/message.hh>
-#include <Eigen/Core>
-#include <boost/scoped_ptr.hpp>
-#include <ost/qa/module_config.hh>
-
-namespace ost { namespace qa {
-
-class CalphaDistance;
-
-typedef boost::shared_ptr<CalphaDistance> CalphaDistancePtr;
-
-/// \brief calculate C-alpha distance matrix
-///
-/// \param a first entity view. The entity view is required to contain only
-/// C-alpha atoms.
-///
-/// \param b second entity view. The entity view is required to contain only
-/// C-alpha atoms.
-///
-/// \throws Error, if one or both of the two views do not
-/// contain exactly one chain
-CalphaDistancePtr DLLEXPORT_OST_QA CalculateCalphaDistance(const mol::EntityView& a,
- const mol::EntityView& b);
-
-
-class DLLEXPORT_OST_QA CalphaDistance : public mol::EntityVisitor {
-public:
- CalphaDistance(const mol::EntityView& a, const mol::EntityView& b);
-
- virtual bool VisitAtom(const mol::AtomHandle& atom);
-
- /// \brief Check if distance between two C-alpha is defined
- ///
- /// Check whether the distance between C-alpha of residue with \c number_a
- /// in the first entity and residue with \c number_b in the second entity is
- /// defined, i.e. if both C-alphas are part of the view.
- ///
- /// \param number_a residue number in first entity view.
- ///
- /// \param number_b residue number in second entity view.
- bool IsDistanceDefined(const mol::ResNum& number_a,
- const mol::ResNum& number_b) const;
-
- /// \brief Get distance between two C-alpha atoms.
- ///
- /// \throws Error when distance between the two C-alpha atoms is
- /// not defined.
- ///
- /// \sa IsDistanceDefined
- Real GetDistance(const mol::ResNum& number_a,
- const mol::ResNum& number_b) const;
-
-
-private:
- CalphaDistance(const CalphaDistance&);
- mol::ResNum GetBiggestResNumber(const mol::EntityView& e) const;
- void CalculateDistances();
-
- mol::EntityView a_;
- mol::EntityView b_;
- Eigen::MatrixXd distance_mat_;
-};
-
-}}
-
-#endif