diff --git a/modules/conop/pymod/CMakeLists.txt b/modules/conop/pymod/CMakeLists.txt
index 9c09906222fb97e1c935590ec22e81b536c94891..23dff26a0022fa9c312c9bfd1acda033d1c304b7 100644
--- a/modules/conop/pymod/CMakeLists.txt
+++ b/modules/conop/pymod/CMakeLists.txt
@@ -8,7 +8,6 @@ set(OST_CONOP_PYMOD_SOURCES
export_conop.cc
export_diag.cc
export_rule_based.cc
- export_non_standard.cc
export_ring_finder.cc
)
diff --git a/modules/conop/pymod/wrap_conop.cc b/modules/conop/pymod/wrap_conop.cc
index 119c86c325f3ce6fc48cf88298838f441cb04a36..04bcfce147b3ebf986cee454c2594e242ade7059 100644
--- a/modules/conop/pymod/wrap_conop.cc
+++ b/modules/conop/pymod/wrap_conop.cc
@@ -25,7 +25,6 @@ void export_Sanitizer();
void export_Conop();
void export_RingFinder();
void export_AminoAcids();
-void export_NonStandard();
void export_processor();
void export_rule_based();
void export_heuristic();
@@ -41,6 +40,5 @@ BOOST_PYTHON_MODULE(_ost_conop)
export_Compound();
export_RingFinder();
export_AminoAcids();
- export_NonStandard();
export_diag();
}
diff --git a/modules/conop/src/CMakeLists.txt b/modules/conop/src/CMakeLists.txt
index 0185618ea4a9ebb02d917393670ce3f401ed494c..c2f1f4c6d0148c62461be5852bd33872ad39f903 100644
--- a/modules/conop/src/CMakeLists.txt
+++ b/modules/conop/src/CMakeLists.txt
@@ -9,7 +9,6 @@ compound.hh
compound_lib.hh
module_config.hh
rule_based.hh
-nonstandard.hh
minimal_compound_lib.hh
compound_lib_base.hh
ring_finder.hh
@@ -27,12 +26,11 @@ rule_based.cc
model_check.cc
compound.cc
compound_lib.cc
-nonstandard.cc
ring_finder.cc
)
module(NAME conop SOURCES ${OST_CONOP_SOURCES}
- HEADERS ${OST_CONOP_HEADERS} DEPENDS_ON ost_mol ost_mol_alg ost_geom ost_db)
+ HEADERS ${OST_CONOP_HEADERS} DEPENDS_ON ost_mol ost_geom ost_db)
if (WIN32)
diff --git a/modules/mol/alg/pymod/CMakeLists.txt b/modules/mol/alg/pymod/CMakeLists.txt
index 612caccfb615c70f8ffefeffd567040da1eef630..5519c6adf2741e213eba44cb82fbaf559f4c19e8 100644
--- a/modules/mol/alg/pymod/CMakeLists.txt
+++ b/modules/mol/alg/pymod/CMakeLists.txt
@@ -7,6 +7,7 @@ set(OST_MOL_ALG_PYMOD_SOURCES
export_contact_overlap.cc
export_accessibility.cc
export_sec_structure.cc
+ export_non_standard.cc
export_molck.cc
)
diff --git a/modules/conop/pymod/export_non_standard.cc b/modules/mol/alg/pymod/export_non_standard.cc
similarity index 96%
rename from modules/conop/pymod/export_non_standard.cc
rename to modules/mol/alg/pymod/export_non_standard.cc
index 50b1fd2d6e169e31ff5e192e03b19b98541bf89d..8d485b169ecbd290483daf5f0ab5ca3e06e8da80 100644
--- a/modules/conop/pymod/export_non_standard.cc
+++ b/modules/mol/alg/pymod/export_non_standard.cc
@@ -18,11 +18,11 @@
//------------------------------------------------------------------------------
#include <boost/python.hpp>
#include <ost/mol/mol.hh>
-#include <ost/conop/nonstandard.hh>
+#include <ost/mol/alg/nonstandard.hh>
using namespace boost::python;
-using namespace ost::conop;
+using namespace ost::mol::alg;
using namespace ost::mol;
object copy_conserved_handle(ResidueHandle src_res, ResidueHandle dst_res,
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index b90ab2befa069e245c1c5f1c48027164c0117ef3..f32e3256f656586953ffa654c6617cb0377781cb 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -39,6 +39,7 @@ void export_svdSuperPose();
void export_TrajectoryAnalysis();
void export_StructureAnalysis();
void export_Clash();
+void export_NonStandard();
void export_Molck();
void export_contact_overlap();
void export_accessibility();
@@ -111,6 +112,7 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
export_TrajectoryAnalysis();
export_StructureAnalysis();
export_Clash();
+ export_NonStandard();
export_Molck();
export_contact_overlap();
export_accessibility();
diff --git a/modules/mol/alg/src/CMakeLists.txt b/modules/mol/alg/src/CMakeLists.txt
index 8049b99a9ac43b5545e6f12bdbe3650602c2addc..ef2ae22ae10ccc9172285b7d79e96b298c7d6fec 100644
--- a/modules/mol/alg/src/CMakeLists.txt
+++ b/modules/mol/alg/src/CMakeLists.txt
@@ -20,6 +20,7 @@ set(OST_MOL_ALG_HEADERS
similarity_matrix.hh
accessibility.hh
sec_struct.hh
+ nonstandard.hh
molck.hh
)
@@ -44,6 +45,7 @@ set(OST_MOL_ALG_SOURCES
similarity_matrix.cc
accessibility.cc
sec_struct.cc
+ nonstandard.cc
molck.cc
)
@@ -60,7 +62,7 @@ if (ENABLE_IMG)
entity_to_density.cc
)
- set(MOL_ALG_DEPS ${MOL_ALG_DEPS} ost_img ost_img_alg ost_seq_alg)
+ set(MOL_ALG_DEPS ${MOL_ALG_DEPS} ost_img ost_img_alg ost_seq_alg ost_conop)
endif()
executable(NAME lddt SOURCES lddt.cc
diff --git a/modules/mol/alg/src/molck.cc b/modules/mol/alg/src/molck.cc
index df931f8ed6474e4530711ba5bfb49ea13366d9e8..0667275af4a20db3500d68caf5136bc0c57fbb86 100644
--- a/modules/mol/alg/src/molck.cc
+++ b/modules/mol/alg/src/molck.cc
@@ -1,7 +1,7 @@
#include <ost/mol/xcs_editor.hh>
+#include <ost/mol/alg/nonstandard.hh>
#include <ost/conop/model_check.hh>
#include <ost/conop/amino_acids.hh>
-#include <ost/conop/nonstandard.hh>
#include <ost/mol/alg/molck.hh>
using namespace ost::conop;
@@ -36,7 +36,7 @@ EntityHandle ost::mol::alg::MapNonStandardResidues(EntityHandle& ent, CompoundLi
continue;
}
ResidueHandle dest_res = new_edi.AppendResidue(new_chain,OneLetterCodeToResidueName(compound->GetOneLetterCode()),r->GetNumber());
- CopyResidue(*r,dest_res,new_edi,lib);
+ ost::mol::alg::CopyResidue(*r,dest_res,new_edi,lib);
}
}
}
diff --git a/modules/mol/alg/src/molck.hh b/modules/mol/alg/src/molck.hh
index 1034602e7986498c0306a2577ef892cd688cab8c..d7e4b65d2975b8680c2f06ce44bd7b2f57fec5ee 100644
--- a/modules/mol/alg/src/molck.hh
+++ b/modules/mol/alg/src/molck.hh
@@ -27,7 +27,8 @@ struct MolckSettings{
};
-ost::mol::EntityHandle MapNonStandardResidues(ost::mol::EntityHandle& ent, ost::conop::CompoundLibPtr lib);
+ost::mol::EntityHandle MapNonStandardResidues(ost::mol::EntityHandle& ent,
+ ost::conop::CompoundLibPtr lib);
void RemoveAtoms(ost::mol::EntityHandle& ent,
ost::conop::CompoundLibPtr lib,
@@ -38,9 +39,12 @@ void RemoveAtoms(ost::mol::EntityHandle& ent,
bool rm_zero_occ_atoms,
bool colored=true);
-void CleanUpElementColumn(ost::mol::EntityHandle& ent, ost::conop::CompoundLibPtr lib);
+void CleanUpElementColumn(ost::mol::EntityHandle& ent,
+ ost::conop::CompoundLibPtr lib);
-void Molck(ost::mol::EntityHandle& ent, ost::conop::CompoundLibPtr lib, const MolckSettings& settings);
+void Molck(ost::mol::EntityHandle& ent,
+ ost::conop::CompoundLibPtr lib,
+ const MolckSettings& settings);
}}} // namespace
diff --git a/modules/mol/alg/src/nonstandard.cc b/modules/mol/alg/src/nonstandard.cc
index eaf06680d087c05080f0e578828c7bad3fd68c66..b51c582adcdd81fb5b02cff834c18c218b7b317d 100644
--- a/modules/mol/alg/src/nonstandard.cc
+++ b/modules/mol/alg/src/nonstandard.cc
@@ -32,7 +32,7 @@ using namespace ost::mol;
using namespace ost;
using namespace ost::conop;
-namespace ost { namespace conop {
+namespace ost { namespace mol { namespace alg {
bool CopyResidue(ResidueHandle src_res, ResidueHandle dst_res, XCSEditor& edi)
@@ -234,4 +234,4 @@ bool CopyNonConserved(ResidueHandle src_res, ResidueHandle dst_res,
-}}
+}}}
diff --git a/modules/mol/alg/src/nonstandard.hh b/modules/mol/alg/src/nonstandard.hh
index a57022def8ef7436889491c7ae6714c6e9a69d6e..b37ffd52bb16e2f77b12b03d2b182c106c073901 100644
--- a/modules/mol/alg/src/nonstandard.hh
+++ b/modules/mol/alg/src/nonstandard.hh
@@ -23,11 +23,11 @@
Author: Marco Biasini, Juergen Haas
*/
#include "module_config.hh"
-#include "compound_lib.hh"
+#include <ost/conop/compound_lib.hh>
-namespace ost { namespace conop {
+namespace ost { namespace mol { namespace alg {
/// \brief copies all atom of src_res to dst_res, gets compound lib from builder
@@ -40,7 +40,8 @@ bool DLLEXPORT_OST_CONOP CopyResidue(ost::mol::ResidueHandle src_res,
/// \brief copies all atom of src_res to dst_res, requires a compound lib
bool DLLEXPORT_OST_CONOP CopyResidue(ost::mol::ResidueHandle src_res,
ost::mol::ResidueHandle dst_res,
- ost::mol::XCSEditor& edi, CompoundLibPtr lib);
+ ost::mol::XCSEditor& edi,
+ ost::conop::CompoundLibPtr lib);
/// \brief copies all atom of src_res to dst_res
@@ -66,7 +67,8 @@ bool DLLEXPORT_OST_CONOP CopyIdentical(ost::mol::ResidueHandle src_res,
bool DLLEXPORT_OST_CONOP CopyConserved(ost::mol::ResidueHandle src_res,
ost::mol::ResidueHandle dst_res,
ost::mol::XCSEditor& edi,
- bool& has_cbeta, CompoundLibPtr lib);
+ bool& has_cbeta,
+ ost::conop::CompoundLibPtr lib);
/// \brief copies atoms of src_res to dst_res, requires compound lib
///
@@ -107,10 +109,11 @@ bool DLLEXPORT_OST_CONOP CopyMSE(ost::mol::ResidueHandle src_res,
bool DLLEXPORT_OST_CONOP CopyModified(ost::mol::ResidueHandle src_res,
ost::mol::ResidueHandle dst_res,
ost::mol::XCSEditor& edi,
- bool& has_cbeta, CompoundLibPtr lib);
+ bool& has_cbeta,
+ ost::conop::CompoundLibPtr lib);
-}}
+}}}
#endif
diff --git a/tools/molck/CMakeLists.txt b/tools/molck/CMakeLists.txt
index 4e1dc2fb79b73e90022dd2f546a5011c98eca118..c76f1fd71b4532bf32b2cfcfa5dc34a0b7fb00ff 100644
--- a/tools/molck/CMakeLists.txt
+++ b/tools/molck/CMakeLists.txt
@@ -1,4 +1,4 @@
if (NOT WIN32)
executable(NAME molck SOURCES main.cc
- DEPENDS_ON ost_io STATIC)
+ DEPENDS_ON ost_io ost_mol_alg STATIC)
endif(NOT WIN32)
diff --git a/tools/molck/main.cc b/tools/molck/main.cc
index 610c074bfbd6a3e6578b9abd2989ff3fe24e355c..ef2d77c207213957a20d2d2d460da74fa0280b73 100644
--- a/tools/molck/main.cc
+++ b/tools/molck/main.cc
@@ -15,10 +15,8 @@
#include <mach-o/dyld.h>
#endif
using namespace ost;
-using namespace ost::conop;
using namespace ost::mol;
using namespace ost::io;
-using namespace ost::mol::alg;
namespace po=boost::program_options;
namespace fs=boost::filesystem;
@@ -82,20 +80,20 @@ EntityHandle load_x(const String& file, const IOProfile& profile)
}
// load compound library, exiting if it could not be found...
-CompoundLibPtr load_compound_lib(const String& custom_path)
+ost::conop::CompoundLibPtr load_compound_lib(const String& custom_path)
{
if (custom_path!="") {
if (fs::exists(custom_path)) {
- return CompoundLib::Load(custom_path);
+ return ost::conop::CompoundLib::Load(custom_path);
} else {
std::cerr << "Could not find compounds.chemlib at the provided location, trying other options" << std::endl;
}
}
if (fs::exists("compounds.chemlib")) {
- return CompoundLib::Load("compounds.chemlib");
+ return ost::conop::CompoundLib::Load("compounds.chemlib");
}
char result[ 1024 ];
- CompoundLibPtr lib;
+ ost::conop::CompoundLibPtr lib;
String exe_path;
#if defined(__APPLE__)
uint32_t size=1023;
@@ -118,14 +116,14 @@ CompoundLibPtr load_compound_lib(const String& custom_path)
String share_path_string=BFPathToString(share_path);
if (fs::exists(share_path_string)) {
- return CompoundLib::Load(share_path_string);
+ return ost::conop::CompoundLib::Load(share_path_string);
}
}
if (!lib) {
std::cerr << "Could not load compounds.chemlib" << std::endl;
exit(-1);
}
- return CompoundLibPtr();
+ return ost::conop::CompoundLibPtr();
}
@@ -136,7 +134,7 @@ int main(int argc, char *argv[])
}
IOProfile prof;
prof.fault_tolerant=true;
- MolckSettings settings;
+ ost::mol::alg::MolckSettings settings;
String rm;
String color;
@@ -223,14 +221,14 @@ int main(int argc, char *argv[])
usage();
exit(-1);
}
- CompoundLibPtr lib=load_compound_lib(custom_path);
+ ost::conop::CompoundLibPtr lib=load_compound_lib(custom_path);
for (unsigned int i = 0; i < files.size(); ++i) {
EntityHandle ent=load_x(files[i], prof);
if (!ent.IsValid()) {
continue;
}
- Molck(ent, lib, settings);
+ ost::mol::alg::Molck(ent, lib, settings);
if (write_to_stdout) {
PDBWriter writer(std::cout, prof);