diff --git a/examples/harmony/harmony b/examples/harmony/harmony
index 4abd9d73dc2ac9b4a3b0beec87662cd27271cd67..f55eec9e481880eec721632ef05d67346d628c30 100755
--- a/examples/harmony/harmony
+++ b/examples/harmony/harmony
@@ -1,2 +1,2 @@
#!/bin/sh
-cat harmony.py | gosty Harmony $@
\ No newline at end of file
+gosty harmony.py Harmony $@
\ No newline at end of file
diff --git a/modules/gfx/pymod/export_render_options.cc b/modules/gfx/pymod/export_render_options.cc
index 51e9829c7ca6fa7ae4d2d80fce7d2bf430c072fd..113d364cb3a3b5573353077c040822bd0b603c86 100644
--- a/modules/gfx/pymod/export_render_options.cc
+++ b/modules/gfx/pymod/export_render_options.cc
@@ -123,8 +123,6 @@ void export_RenderOptions()
.def("GetNormalSmoothFactor", &TraceRenderOptions::GetNormalSmoothFactor)
.def("SetTubeRadius", &TraceRenderOptions::SetTubeRadius)
.def("GetTubeRadius", &TraceRenderOptions::GetTubeRadius)
- .def("SetRadius", &TraceRenderOptions::SetTubeRadius)
- .def("GetRadius", &TraceRenderOptions::GetTubeRadius)
;
}
diff --git a/modules/gfx/pymod/export_scene.cc b/modules/gfx/pymod/export_scene.cc
index 267c07e01fa76d2ff39f1996b8273b537ac5db8b..e39c87232410d7fb0d2d82a4c2b4b189e40f64a0 100644
--- a/modules/gfx/pymod/export_scene.cc
+++ b/modules/gfx/pymod/export_scene.cc
@@ -124,8 +124,6 @@ void export_Scene()
.def("SetShadow",&Scene::SetShadow)
.def("SetShadowQuality",&Scene::SetShadowQuality)
.def("AttachObserver",&Scene::AttachObserver)
- .def("StartOffscreenMode",&Scene::StartOffscreenMode)
- .def("StopOffscreenMode",&Scene::StopOffscreenMode)
.def("__getitem__",scene_getitem)
.add_property("bg",
&Scene::GetBackground,
diff --git a/modules/gfx/pymod/wrap_gfx.cc b/modules/gfx/pymod/wrap_gfx.cc
index 1c8ca00655a03830eaed53a3e6c9f1a407395956..dd2049702cb4ca0d643517dce0de21917630ae6c 100644
--- a/modules/gfx/pymod/wrap_gfx.cc
+++ b/modules/gfx/pymod/wrap_gfx.cc
@@ -23,9 +23,7 @@ using namespace boost::python;
#include <ost/gfx/prim_list.hh>
#include <ost/gfx/gradient.hh>
#include <ost/gfx/gfx_test_object.hh>
-#if OST_SHADER_SUPPORT_ENABLED
-#include <ost/gfx/shader.hh>
-#endif
+
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
extern void export_Scene();
@@ -172,15 +170,6 @@ BOOST_PYTHON_MODULE(_gfx)
.def("GetRel", &Stop::GetRel)
;
-#if OST_SHADER_SUPPORT_ENABLED
- class_<Shader, boost::noncopyable>("Shader", no_init)
- .def("Instance",&Shader::Instance,
- return_value_policy<reference_existing_object>()).staticmethod("Instance")
- .def("PushProgram",&Shader::PushProgram)
- .def("PopProgram",&Shader::PopProgram)
- .def("Activate",&Shader::Activate)
- ;
-#endif
export_primitives();
}
diff --git a/modules/gfx/src/scene.cc b/modules/gfx/src/scene.cc
index e6cd329a4a2fd08b5f8b80f51098893f92db8de1..4a315636d76f722136485e79f5c1e40f24a0bd39 100644
--- a/modules/gfx/src/scene.cc
+++ b/modules/gfx/src/scene.cc
@@ -293,7 +293,7 @@ void Scene::InitGL()
void Scene::RequestRedraw()
{
- if (win_ && !offscreen_flag_) {
+ if (win_) {
win_->DoRefresh();
}
}
@@ -545,37 +545,6 @@ namespace {
GfxObjP node;
};
-#if 0
- struct RegexFindObj: public GfxNodeVisitor {
- RegexFindObj(const String& rs): reg(), valid(false), node() {
- try {
- reg = boost::regex(rs);
- valid = true;
- } catch (boost::regex_error& e) {
- LOGN_ERROR("invalid regex");
- }
- }
-
- virtual bool VisitNode(GfxNode* n, const Stack& st) {
- return true;
- }
-
- virtual void VisitObject(GfxObj* o, const Stack& st) {
- if(boost::regex_match(o->GetName(),reg)) {
- GfxNodeP nn = o->shared_from_this();
- GfxObjP oo = dyn_cast<GfxObj>(nn);
- if(oo) {
- olist.push_back(oo);
- }
- }
- }
-
- boost::regex reg;
- bool valid;
- std::vector<GfxObjP> olist;
- };
-#endif
-
struct FindNode2: public GfxNodeVisitor {
FindNode2(GfxNodeP n): node(n), found(false) {}
virtual bool VisitNode(GfxNode* n, const Stack& st) {
@@ -615,14 +584,6 @@ void Scene::Add(const GfxNodeP& n, bool redraw)
}
LOG_DEBUG("scene: graphical object added @" << n.get() << std::endl);
-
- if(root_node_->GetChildCount()==0) {
- GfxObjP go = boost::dynamic_pointer_cast<GfxObj>(n);
- if(go) {
- SetCenter(go->GetCenter());
- }
- }
-
root_node_->Add(n);
if (redraw) {
this->RequestRedraw();
@@ -1201,55 +1162,6 @@ uint Scene::GetSelectionMode() const
return selection_mode_;
}
-void Scene::StartOffscreenMode(unsigned int width, unsigned int height)
-{
- if(main_offscreen_buffer_) return;
- main_offscreen_buffer_ = new OffscreenBuffer(width,height,OffscreenBufferFormat(),true);
-
- if(!main_offscreen_buffer_->IsValid()) {
- LOGN_ERROR("error during offscreen buffer creation");
- delete main_offscreen_buffer_;
- main_offscreen_buffer_=0;
- return;
- }
- old_vp_[0]=vp_width_;
- old_vp_[1]=vp_height_;
- main_offscreen_buffer_->MakeActive();
- offscreen_flag_=true;
- root_node_->ContextSwitch();
-
-#if OST_SHADER_SUPPORT_ENABLED
- String shader_name = Shader::Instance().GetCurrentName();
-#endif
- LOGN_DEBUG("initializing GL");
- this->InitGL();
- LOGN_DEBUG("setting viewport");
- Resize(width,height);
- LOGN_DEBUG("updating fog settings");
- update_fog();
- glDrawBuffer(GL_FRONT);
-#if OST_SHADER_SUPPORT_ENABLED
- LOGN_DEBUG("activating shader");
- Shader::Instance().Activate(shader_name);
-#endif
-}
-
-void Scene::StopOffscreenMode()
-{
- if(main_offscreen_buffer_) {
- if (win_) {
- win_->MakeActive();
- }
- delete main_offscreen_buffer_;
- main_offscreen_buffer_=0;
- Scene::Instance().SetViewport(old_vp_[0],old_vp_[1]);
- offscreen_flag_=false;
- root_node_->ContextSwitch();
- glDrawBuffer(GL_BACK);
- update_fog();
- }
-}
-
void Scene::Export(const String& fname, unsigned int width,
unsigned int height, bool transparent)
{
@@ -1264,94 +1176,80 @@ void Scene::Export(const String& fname, unsigned int width,
return;
}
+ LOGN_DEBUG("switching to offscreen rendering");
+ bool old_flag=offscreen_flag_;
GLint old_vp[4];
glGetIntegerv(GL_VIEWPORT,old_vp);
- bool old_flag=offscreen_flag_;
- if(!main_offscreen_buffer_) {
- LOGN_DEBUG("switching to offscreen rendering");
- glGetIntegerv(GL_VIEWPORT,old_vp);
- try {
- OffscreenBuffer ob(width,height,OffscreenBufferFormat(),true);
-
- if(!ob.IsValid()) {
- LOGN_ERROR("error during offscreen buffer creation");
- return;
- }
-
- ob.MakeActive();
- offscreen_flag_=true;
- root_node_->ContextSwitch();
+ try {
+ OffscreenBuffer ob(width,height,OffscreenBufferFormat(),true);
+
+ if(!ob.IsValid()) {
+ LOGN_ERROR("error during offscreen buffer creation");
+ return;
+ }
+
+ ob.MakeActive();
+ offscreen_flag_=true;
+ root_node_->ContextSwitch();
#if 1
#if OST_SHADER_SUPPORT_ENABLED
- String shader_name = Shader::Instance().GetCurrentName();
+ String shader_name = Shader::Instance().GetCurrentName();
#endif
- LOGN_DEBUG("initializing GL");
- this->InitGL();
- LOGN_DEBUG("setting viewport");
- SetViewport(width,height);
- LOGN_DEBUG("reseting projection");
- ResetProjection();
- LOGN_DEBUG("updating fog settings");
- update_fog();
- glDrawBuffer(GL_FRONT);
- //this->flag_all_dirty();
+ LOGN_DEBUG("initializing GL");
+ this->InitGL();
+ LOGN_DEBUG("setting viewport");
+ SetViewport(width,height);
+ LOGN_DEBUG("reseting projection");
+ ResetProjection();
+ LOGN_DEBUG("updating fog settings");
+ update_fog();
+ glDrawBuffer(GL_FRONT);
+ //this->flag_all_dirty();
#if OST_SHADER_SUPPORT_ENABLED
- LOGN_DEBUG("activating shader");
- Shader::Instance().Activate(shader_name);
+ LOGN_DEBUG("activating shader");
+ Shader::Instance().Activate(shader_name);
#endif
#endif
- } catch (std::exception& e) {
- LOGN_ERROR("exception during offscreen rendering: " << e.what());
- throw;
- // noop
+ LOGN_DEBUG("doing rendering");
+ this->RenderGL();
+ // make sure drawing operations are finished
+ glFinish();
+ boost::shared_array<uchar> img_data(new uchar[width*height*4]);
+
+ LOGN_DEBUG("setting background transparency");
+ if (transparent) {
+ glPixelTransferf(GL_ALPHA_BIAS, 0.0);
+ } else {
+ // shift alpha channel by one to make sure pixels are read out as opaque
+ glPixelTransferf(GL_ALPHA_BIAS, 1.0);
}
- }
- LOGN_DEBUG("doing rendering");
- this->RenderGL();
- // make sure drawing operations are finished
- glFinish();
- unsigned int width2=width;
- unsigned int height2=height;
- if(!main_offscreen_buffer_) {
- width2=old_vp[2];
- height2=old_vp[3];
+ LOGN_DEBUG("reading framebuffer pixels");
+ glReadBuffer(GL_FRONT);
+ glReadPixels(0,0,width,height,GL_RGBA,GL_UNSIGNED_BYTE,img_data.get());
+
+ LOGN_DEBUG("calling bitmap export");
+ BitmapExport(fname,ext,width,height,img_data.get());
+ } catch (std::exception& e) {
+ LOGN_ERROR("exception during offscreen rendering: " << e.what());
+ throw;
+ // noop
}
- boost::shared_array<uchar> img_data(new uchar[width2*height2*4]);
-
- LOGN_DEBUG("setting background transparency");
- if (transparent) {
- glPixelTransferf(GL_ALPHA_BIAS, 0.0);
+ LOGN_DEBUG("switching back to main context");
+ if(main_offscreen_buffer_) {
+ main_offscreen_buffer_->MakeActive();
+ } else if (win_) {
+ win_->MakeActive();
} else {
- // shift alpha channel by one to make sure pixels are read out as opaque
- glPixelTransferf(GL_ALPHA_BIAS, 1.0);
- }
-
- LOGN_DEBUG("reading framebuffer pixels");
- glReadBuffer(GL_FRONT);
- glReadPixels(0,0,width2,height2,GL_RGBA,GL_UNSIGNED_BYTE,img_data.get());
-
- LOGN_DEBUG("calling bitmap export");
- BitmapExport(fname,ext,width2,height2,img_data.get());
-
-
- if(!main_offscreen_buffer_) {
- LOGN_DEBUG("switching back to main context");
- if(main_offscreen_buffer_) {
- main_offscreen_buffer_->MakeActive();
- } else if (win_) {
- win_->MakeActive();
- } else {
- LOGN_ERROR("erm, no context to fall back to");
- return;
- }
- Scene::Instance().SetViewport(old_vp[2],old_vp[3]);
- offscreen_flag_=old_flag;
- root_node_->ContextSwitch();
- glDrawBuffer(GL_BACK);
- LOGN_DEBUG("updating fog");
- update_fog();
+ LOGN_ERROR("erm, no context to fall back to");
+ return;
}
+ Scene::Instance().SetViewport(old_vp[2],old_vp[3]);
+ offscreen_flag_=old_flag;
+ root_node_->ContextSwitch();
+ glDrawBuffer(GL_BACK);
+ LOGN_DEBUG("updating fog");
+ update_fog();
}
void Scene::Export(const String& fname, bool transparent)
diff --git a/modules/gfx/src/scene.hh b/modules/gfx/src/scene.hh
index e4ea2c5e99b2fffacd1f25b5a74b8cf24d4d334f..abcd7a9483bc2676033a3d0033b11c77ad421df0 100644
--- a/modules/gfx/src/scene.hh
+++ b/modules/gfx/src/scene.hh
@@ -330,9 +330,6 @@ class DLLEXPORT_OST_GFX Scene {
float ElapsedTime() const;
Viewport GetViewport() const;
-
- void StartOffscreenMode(unsigned int w, unsigned int h);
- void StopOffscreenMode();
// temporary interface
void ActivateShader(const String& name);
@@ -397,7 +394,6 @@ private:
bool offscreen_flag_;
OffscreenBuffer* main_offscreen_buffer_;
- uint old_vp_[2];
uint selection_mode_;
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 996ff1ffcb76a3dddbd6b8b08bbee7e73b72fbe3..82ab97c27b96400ea16d1bf5db285af1fea57c5b 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -52,27 +52,21 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=False,
flags|=PDB.NO_HETATMS
if join_spread_atom_records:
flags|=PDB.JOIN_SPREAD_ATOM_RECORDS
- try:
- PDB.PushFlags(PDB.Flags() | flags)
- if load_multi:
- ent_list=[]
- while reader.HasNext():
- ent=mol.CreateEntity()
- reader.Import(ent, restrict_chains)
- conop_inst.ConnectAll(builder, ent, 0)
- ent_list.append(ent)
- PDB.PopFlags()
- return ent_list
- else:
- ent=mol.CreateEntity()
- if reader.HasNext():
- reader.Import(ent, restrict_chains)
- conop_inst.ConnectAll(builder, ent, 0)
- PDB.PopFlags()
- return ent
- except:
- PDB.PopFlags()
- raise
+ reader.SetFlags(flags)
+ if load_multi:
+ ent_list=[]
+ while reader.HasNext():
+ ent=mol.CreateEntity()
+ reader.Import(ent, restrict_chains)
+ conop_inst.ConnectAll(builder, ent, 0)
+ ent_list.append(ent)
+ return ent_list
+ else:
+ ent=mol.CreateEntity()
+ if reader.HasNext():
+ reader.Import(ent, restrict_chains)
+ conop_inst.ConnectAll(builder, ent, 0)
+ return ent
def SavePDB(models, filename):
"""
diff --git a/modules/io/pymod/export_pdb_io.cc b/modules/io/pymod/export_pdb_io.cc
index fe2a3a75f0635e36dbab85cc4157bacb696151d6..6cc80b813ca1c95fca26604b91f93012684390e4 100644
--- a/modules/io/pymod/export_pdb_io.cc
+++ b/modules/io/pymod/export_pdb_io.cc
@@ -31,38 +31,26 @@ BOOST_PYTHON_FUNCTION_OVERLOADS(load_PDB_ov, LoadPDB, 1, 2)
void (PDBWriter::*write_a)(const mol::EntityHandle&)=&PDBWriter::Write;
void (PDBWriter::*write_b)(const mol::EntityView&)=&PDBWriter::Write;
-
-namespace {
- void push_flags(unsigned int x) {PDB::PushFlags(x);}
- unsigned int flags() {return PDB::Flags();}
- void pop_flags() {PDB::PopFlags();}
-}
-
void export_pdb_io()
{
- {
- scope pdb_scope=class_<PDB>("PDB",no_init)
- .def("PushFlags",&PDB::PushFlags)
- .staticmethod("PushFlags")
- .def("Flags",&PDB::Flags)
- .staticmethod("Flags")
- .def("PopFlags",&PDB::PopFlags)
- .staticmethod("PopFlags")
- ;
- pdb_scope.attr("NO_HETATMS")=PDB::NO_HETATMS;
- pdb_scope.attr("SKIP_FAULTY_RECORDS")=PDB::SKIP_FAULTY_RECORDS;
- pdb_scope.attr("WRITE_MULTIPLE_MODELS")=PDB::WRITE_MULTIPLE_MODELS;
- pdb_scope.attr("JOIN_SPREAD_ATOM_RECORDS")=PDB::JOIN_SPREAD_ATOM_RECORDS;
- }
-
+ enum_<PDB::Type>("PDB")
+ .value("NO_HETATMS", PDB::NO_HETATMS)
+ .value("SKIP_FAULTY_RECORDS", PDB::SKIP_FAULTY_RECORDS)
+ .value("WRITE_MULTIPLE_MODELS", PDB::WRITE_MULTIPLE_MODELS)
+ .value("JOIN_SPREAD_ATOM_RECORDS", PDB::JOIN_SPREAD_ATOM_RECORDS)
+ .value("SEQUENTIAL_ATOM_IMPORT", PDB::SEQUENTIAL_ATOM_IMPORT)
+ ;
class_<PDBReader, boost::noncopyable>("PDBReader", init<String>())
.def("HasNext", &PDBReader::HasNext)
.def("Import", &PDBReader::Import,
X_import(args("entity", "restrict_chains")))
+ .def("SetFlags", &PDBReader::SetFlags)
+ .def("GetSequentialAtoms", &PDBReader::GetSequentialAtoms)
;
class_<PDBWriter, boost::noncopyable>("PDBWriter", init<String>())
.def("Write", write_a)
.def("Write", write_b)
+ .def("SetFlags", &PDBWriter::SetFlags)
;
}
diff --git a/modules/io/pymod/wrap_io.cc b/modules/io/pymod/wrap_io.cc
index b04d3ac78ab729a8125fd258f9b7de89c2f15653..79920189ef60ba1cb71c122bb566907291646bef 100644
--- a/modules/io/pymod/wrap_io.cc
+++ b/modules/io/pymod/wrap_io.cc
@@ -28,7 +28,6 @@ using namespace boost::python;
#include <ost/io/seq/save.hh>
#include <ost/io/mol/entity_io_pdb_handler.hh>
#include <ost/io/mol/entity_io_crd_handler.hh>
-#include <ost/io/mol/entity_io_mae_handler.hh>
#include <ost/io/mol/entity_io_sdf_handler.hh>
#include <ost/io/mol/pdb_reader.hh>
#include <ost/io/mol/dcd_io.hh>
@@ -121,9 +120,6 @@ BOOST_PYTHON_MODULE(_io)
def("LoadCHARMMTraj",load_dcd3);
def("LoadCHARMMTraj",load_dcd4);
def("SaveCHARMMTraj",SaveCHARMMTraj,save_charmm_trj_ov());
-
- def("LoadMAE", &LoadMAE);
-
export_pdb_io();
#if OST_IMG_ENABLED
export_map_io();
diff --git a/modules/io/src/io_manager.cc b/modules/io/src/io_manager.cc
index b03169d8c84e49f80a7af74c23cf2780d20928b3..23ab54bd29a2bc3efe72085ac9f9242b80c7a69f 100644
--- a/modules/io/src/io_manager.cc
+++ b/modules/io/src/io_manager.cc
@@ -20,7 +20,6 @@
#include <ost/io/mol/entity_io_pdb_handler.hh>
#include <ost/io/mol/entity_io_crd_handler.hh>
#include <ost/io/mol/entity_io_sdf_handler.hh>
-#include <ost/io/mol/entity_io_mae_handler.hh>
#include <ost/io/seq/fasta_io_handler.hh>
#include <ost/io/seq/promod_io_handler.hh>
#include <ost/io/mol/surface_io_msms_handler.hh>
@@ -44,7 +43,6 @@ IOManager::IOManager()
RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOPDBHandlerFactory));
RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOCRDHandlerFactory));
RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOSDFHandlerFactory));
- RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOMAEHandlerFactory));
RegisterFactory(SequenceIOHandlerFactoryBasePtr(new FastaIOHandlerFactory));
RegisterFactory(SequenceIOHandlerFactoryBasePtr(new ClustalIOHandlerFactory));
RegisterFactory(SequenceIOHandlerFactoryBasePtr(new PromodIOHandlerFactory));
diff --git a/modules/io/src/mol/CMakeLists.txt b/modules/io/src/mol/CMakeLists.txt
index 5cdf0462bb889d48a63a4d64092b0297d5270102..b3fd346b6e87552242a509f853a0eb5ff093fd38 100644
--- a/modules/io/src/mol/CMakeLists.txt
+++ b/modules/io/src/mol/CMakeLists.txt
@@ -1,9 +1,7 @@
set(OST_IO_MOL_SOURCES
entity_io_crd_handler.cc
-entity_io_mae_handler.cc
pdb_reader.cc
entity_io_pdb_handler.cc
-pdb_io.cc
pdb_writer.cc
entity_io_sdf_handler.cc
save_entity.cc
@@ -19,7 +17,6 @@ set(OST_IO_MOL_HEADERS
star_parser.hh
dcd_io.hh
entity_io_crd_handler.hh
-entity_io_mae_handler.hh
pdb_io.hh
entity_io_handler.hh
pdb_reader.hh
diff --git a/modules/io/src/mol/dcd_io.cc b/modules/io/src/mol/dcd_io.cc
index c580ce1b244361b28e85199f2c206f3d8c61c1be..efe9f1dfb368cc888c5785279af00ee8510a3fb7 100644
--- a/modules/io/src/mol/dcd_io.cc
+++ b/modules/io/src/mol/dcd_io.cc
@@ -22,8 +22,6 @@
*/
#include <fstream>
-#include <algorithm>
-
#include <boost/iostreams/filter/gzip.hpp>
#include <boost/filesystem/convenience.hpp>
@@ -33,13 +31,12 @@
#include <ost/conop/conop.hh>
#include <ost/mol/xcs_editor.hh>
-#include <ost/io/io_exception.hh>
-#include <ost/io/swap_util.hh>
-#include "load_entity.hh"
#include "dcd_io.hh"
#include "pdb_reader.hh"
#include "pdb_writer.hh"
#include "entity_io_crd_handler.hh"
+#include <ost/io/io_exception.hh>
+#include <ost/io/swap_util.hh>
namespace ost { namespace io {
@@ -61,20 +58,12 @@ struct DCDHeader {
int t_atom_count,f_atom_count, atom_count;
};
-bool less_index(const mol::AtomHandle& a1, const mol::AtomHandle& a2)
-{
- return a1.GetIndex()<a2.GetIndex();
-}
-
-mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
+mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist,
const String& trj_fn,
unsigned int stride)
{
Profile profile_load("LoadCHARMMTraj");
- mol::AtomHandleList alist(alist2);
- std::sort(alist.begin(),alist.end(),less_index);
-
bool gap_flag = true;
boost::filesystem::path trj_f(trj_fn);
@@ -132,7 +121,7 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
header.f_atom_count=header.icntrl[8];
header.atom_count=header.t_atom_count-header.f_atom_count;
- LOGN_DEBUG("LoadCHARMMTraj: " << header.num << " trajectories with "
+ LOGN_MESSAGE("LoadCHARMMTraj: " << header.num << " trajectories with "
<< header.atom_count << " atoms (" << header.f_atom_count
<< " fixed) each");
@@ -147,8 +136,7 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
std::vector<geom::Vec3> clist(header.t_atom_count);
std::vector<float> xlist(header.t_atom_count);
- int i=0;
- for(;i<header.num;++i) {
+ for(int i=0;i<header.num;++i) {
if(skip_flag) ff.seekg(14*4,std::ios_base::cur);
// read each frame
if(!ff) {
@@ -181,9 +169,9 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
for(uint j=0;j<clist.size();++j) {
clist[j].SetZ(xlist[j]);
}
-
- cg.AddFrame(clist);
-
+ if(i%stride) {
+ cg.AddFrame(clist);
+ }
}
ff.get();
@@ -191,9 +179,6 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
LOGN_VERBOSE("LoadCHARMMTraj: unexpected trailing file data, bytes read: "
<< ff.tellg());
}
-
- LOGN_VERBOSE("Loaded " << cg.GetFrameCount() << " frames with " << cg.GetAtomCount() << " atoms each");
-
return cg;
}
@@ -203,8 +188,30 @@ mol::CoordGroupHandle LoadCHARMMTraj(const String& crd_fn,
const String& trj_fn,
unsigned int stride)
{
- mol::EntityHandle ent=LoadEntity(crd_fn);
- return load_dcd(ent.GetAtomList(),trj_fn,stride);
+ boost::filesystem::path crd_f(crd_fn);
+
+ // first the coordinate reference file
+ conop::BuilderP builder = conop::Conopology::Instance().GetBuilder();
+ mol::EntityHandle ent=mol::CreateEntity();
+ mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
+ std::vector<mol::AtomHandle> alist;
+ if(boost::filesystem::extension(crd_f)==".pdb") {
+ PDBReader reader(crd_f);
+ reader.SetFlags(PDB::SEQUENTIAL_ATOM_IMPORT);
+ LOGN_MESSAGE("importing coordinate data");
+ reader.Import(ent);
+ alist = reader.GetSequentialAtoms();
+ } else if (boost::filesystem::extension(crd_f)==".crd") {
+ CRDReader reader(crd_f);
+ LOGN_MESSAGE("importing coordinate data");
+ reader.Import(ent);
+ alist = reader.GetSequentialAtoms();
+ } else {
+ throw(IOException("unsupported coordinate file format"));
+ }
+ conop::Conopology::Instance().ConnectAll(builder,ent);
+
+ return load_dcd(alist,trj_fn,stride);
}
diff --git a/modules/io/src/mol/entity_io_crd_handler.cc b/modules/io/src/mol/entity_io_crd_handler.cc
index cfbb7efccbc7986a61b903409c90755b4fe17a1f..ce4a1679b765cc8aa13fbddb873b82c33f427871 100644
--- a/modules/io/src/mol/entity_io_crd_handler.cc
+++ b/modules/io/src/mol/entity_io_crd_handler.cc
@@ -43,6 +43,9 @@ namespace ost { namespace io {
using boost::format;
+String FORMAT_NAME_STRING;
+String FORMAT_DESCRIPTION_STRING;
+
CRDReader::CRDReader(const boost::filesystem::path& loc):
sequential_atom_list_(),
curr_chain_(),
diff --git a/modules/io/src/mol/entity_io_pdb_handler.cc b/modules/io/src/mol/entity_io_pdb_handler.cc
index 99b8ea49560a7dbe9ef2ca79ab9dbbc855c94dbe..ca64835e7372b51d8b7089d0197ce47cb04c6f96 100644
--- a/modules/io/src/mol/entity_io_pdb_handler.cc
+++ b/modules/io/src/mol/entity_io_pdb_handler.cc
@@ -50,12 +50,9 @@ void EntityIOPDBHandler::Export(const mol::EntityView& ent,
{
PDBWriter writer(loc);
if (boost::iequals(boost::filesystem::extension(loc), ".pqr")) {
- PDB::PushFlags(PDB::Flags() | PDB::PQR_FORMAT);
- writer.Write(ent);
- PDB::PopFlags();
- } else {
- writer.Write(ent);
+ writer.SetFlags(PDB::PQR_FORMAT);
}
+ writer.Write(ent);
}
void EntityIOPDBHandler::Import(mol::EntityHandle& ent,
diff --git a/modules/io/src/mol/pdb_io.hh b/modules/io/src/mol/pdb_io.hh
index bc295a84688878b8ff97b3e71854a423512fea06..140db87e3648055a3bff689f18657da8cceb820e 100644
--- a/modules/io/src/mol/pdb_io.hh
+++ b/modules/io/src/mol/pdb_io.hh
@@ -19,28 +19,22 @@
#ifndef OST_IO_PDB_IO_HH
#define OST_IO_PDB_IO_HH
-#include <stack>
-
namespace ost { namespace io {
-
/// \brief flags that incluence the behaviour of the PDBReader and PDBWriter
struct PDB {
-
+ typedef enum {
/// \brief skip faulty records
+ ///
/// This flag tells the PDB loader to ignore faulty records. By default,
/// faulty records abort import.
- static const unsigned int SKIP_FAULTY_RECORDS;
-
+ SKIP_FAULTY_RECORDS=1,
/// \brief do not import HETATM records
- static const unsigned int NO_HETATMS;
-
+ NO_HETATMS=2,
/// \brief enable writing of multiple models
- static const unsigned int WRITE_MULTIPLE_MODELS;
-
+ WRITE_MULTIPLE_MODELS=4,
/// \brief enable for PQR
- static const unsigned int PQR_FORMAT;
-
+ PQR_FORMAT=8,
/// \brief Join atom records into one residue, even if the atom records
/// are not sequential.
///
@@ -63,20 +57,21 @@ struct PDB {
///
/// By default, the atom 550 will start a new residue instead of being
/// joined with atoms 43-48 into one residue.
- static const unsigned int JOIN_SPREAD_ATOM_RECORDS;
-
+ JOIN_SPREAD_ATOM_RECORDS=16,
+ //// \brief keep track of the order of atom records
+ ///
+ /// This option is mostly useful in combination with
+ /// PDB::JOIN_SPREAD_ATOM_RECORDS and CoordGroups.
+ ///
+ /// The atoms are accessible via PDBReader::GetSequentialAtoms()
+ SEQUENTIAL_ATOM_IMPORT=32,
/// \brief only import C-alpha atoms
- static const unsigned int CALPHA_ONLY;
-
- static void PushFlags(unsigned int flags);
- static unsigned int Flags();
- static void PopFlags();
-
- static PDB& Instance();
-
- std::stack<unsigned int> fstack;
+ CALPHA_ONLY=64
+ } Type;
};
+typedef unsigned int PDBFlags;
+
}}
#endif
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index a2ce79cd12998a98f8e4cccb139cd967bebd5455..fa0357bedd93f340e62e393803b5c19af8ff2a78 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -62,19 +62,19 @@ mol::ResNum to_res_num(int num, char ins_code)
}
PDBReader::PDBReader(std::istream& instream):
- infile_(), instream_(instream)
+ infile_(), instream_(instream), flags_(0)
{
this->Init(boost::filesystem::path(""));
}
PDBReader::PDBReader(const String& filename)
- : infile_(filename), instream_(infile_)
+ : infile_(filename), instream_(infile_), flags_(0)
{
this->Init(boost::filesystem::path(filename));
}
PDBReader::PDBReader(const boost::filesystem::path& loc):
- infile_(loc), instream_(infile_)
+ infile_(loc), instream_(infile_), flags_(0)
{
this->Init(loc);
}
@@ -107,7 +107,7 @@ bool PDBReader::HasNext()
StringRef curr_line(curr_line_.c_str(), curr_line_.length());
if (curr_line.size()>5 &&
(IEquals(curr_line.substr(0, 6), StringRef("ATOM ", 6)) ||
- (!(PDB::Flags() & PDB::NO_HETATMS) &&
+ (!(flags_ & PDB::NO_HETATMS) &&
IEquals(curr_line.substr(0, 6),StringRef("HETATM ", 6))) ||
IEquals(curr_line.substr(0, 6),StringRef("ANISOU ", 6)) ||
IEquals(curr_line.substr(0, 6), StringRef("SHEET ", 6)) ||
@@ -124,8 +124,6 @@ bool PDBReader::HasNext()
void PDBReader::Import(mol::EntityHandle& ent,
const String& restrict_chains)
{
- LOGN_DEBUG("PDBReader: current flags: " << PDB::Flags());
-
Profile profile_import("PDBReader::Import");
this->ClearState();
// first read curr_line and then read next...
@@ -174,7 +172,7 @@ void PDBReader::Import(mol::EntityHandle& ent,
continue;
}
if (IEquals(curr_line.substr(0, 6), StringRef("HETATM", 6))) {
- if (PDB::Flags() & PDB::NO_HETATMS)
+ if (flags_ & PDB::NO_HETATMS)
continue;
LOGN_TRACE("processing HETATM entry");
this->ParseAndAddAtom(curr_line, line_num_, ent,
@@ -253,6 +251,17 @@ void PDBReader::ClearState()
hard_end_=false;
helix_list_.clear();
strand_list_.clear();
+ sequential_atom_list_.clear();
+}
+
+std::vector<mol::AtomHandle> PDBReader::GetSequentialAtoms() const
+{
+ return sequential_atom_list_;
+}
+
+void PDBReader::SetFlags(PDBFlags flags)
+{
+ flags_=flags;
}
bool PDBReader::ParseAtomIdent(const StringRef& line, int line_num,
@@ -268,7 +277,7 @@ bool PDBReader::ParseAtomIdent(const StringRef& line, int line_num,
std::pair<bool, int> a_num=line.substr(6, 5).ltrim().to_int();
if (!a_num.first) {
- if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS) {
+ if (flags_ & PDB::SKIP_FAULTY_RECORDS) {
return false;
}
throw IOException(str(format("invalid atom number on line %d") %line_num));
@@ -278,7 +287,7 @@ bool PDBReader::ParseAtomIdent(const StringRef& line, int line_num,
res_name=line.substr(17, 3).trim();
std::pair<bool, int> res_num=line.substr(22, 4).ltrim().to_int();;
if (!res_num.first) {
- if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS) {
+ if (flags_ & PDB::SKIP_FAULTY_RECORDS) {
return false;
}
throw IOException(str(format("invalid res number on line %d") % line_num));
@@ -303,7 +312,7 @@ void PDBReader::ParseAnisou(const StringRef& line, int line_num,
for (int i=0;i<6; ++i) {
std::pair<bool, int> result=line.substr(29+i*7, 6).to_int();
if (!result.first) {
- if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS) {
+ if (flags_ & PDB::SKIP_FAULTY_RECORDS) {
return;
}
throw IOException(str(format("invalid ANISOU record on line %d")%line_num));
@@ -312,7 +321,7 @@ void PDBReader::ParseAnisou(const StringRef& line, int line_num,
}
String aname(atom_name.str());
if (!curr_residue_.IsValid()) {
- if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS) {
+ if (flags_ & PDB::SKIP_FAULTY_RECORDS) {
return;
}
const char* fmt_str="invalid ANISOU record for inexistent atom on line %d";
@@ -320,7 +329,7 @@ void PDBReader::ParseAnisou(const StringRef& line, int line_num,
}
mol::AtomHandle atom=curr_residue_.FindAtom(aname);
if (!atom.IsValid()) {
- if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS) {
+ if (flags_ & PDB::SKIP_FAULTY_RECORDS) {
return;
}
const char* fmt_str="invalid ANISOU record for inexistent atom on line %d";
@@ -359,7 +368,7 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
for (int i=0;i<3; ++i) {
std::pair<bool, float> result=line.substr(30+i*8, 8).ltrim().to_float();
if (!result.first) {
- if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS) {
+ if (flags_ & PDB::SKIP_FAULTY_RECORDS) {
return;
}
throw IOException(str(format("invalid coordinate on line %d")%line_num));
@@ -424,31 +433,24 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
}
if(update_chain) {
- curr_chain_=mol::ChainHandle();
-#if 0
- // TODO: should this depend on JOIN_SPREAD as well?
- if (PDB::Flags() & PDB::JOIN_SPREAD_ATOM_RECORDS) {
- curr_chain_=ent.FindChain(s_chain);
- }
-#else
- curr_chain_=ent.FindChain(s_chain);
-#endif
- if(!curr_chain_.IsValid()) {
+ if (!(curr_chain_=ent.FindChain(s_chain))) {
LOGN_DUMP("new chain " << s_chain);
curr_chain_=editor.InsertChain(s_chain);
++chain_count_;
}
- assert(curr_chain_.IsValid());
}
if(update_residue) {
- curr_residue_=mol::ResidueHandle();
- if (PDB::Flags() & PDB::JOIN_SPREAD_ATOM_RECORDS) {
+ if (flags_ & PDB::JOIN_SPREAD_ATOM_RECORDS) {
curr_residue_=curr_chain_.FindResidue(res_num);
- }
- if (!curr_residue_.IsValid()) {
+ if (!curr_residue_.IsValid()) {
+ LOGN_DUMP("new residue " << res_name << " " << res_num);
+ curr_residue_=editor.AppendResidue(curr_chain_, res_name.str(), res_num);
+ ++residue_count_;
+ }
+ } else {
LOGN_DUMP("new residue " << res_name << " " << res_num);
curr_residue_=editor.AppendResidue(curr_chain_, res_name.str(), res_num);
- ++residue_count_;
+ ++residue_count_;
}
assert(curr_residue_.IsValid());
}
@@ -492,22 +494,16 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
} else {
mol::AtomHandle ah=editor.InsertAltAtom(curr_residue_, aname,
String(1, alt_loc), apos, aprop);
- /*
- for now, this is not needed - the cg will use an global atom id sorted
- list insteadx
- if (PDB::Flags() & PDB::SEQUENTIAL_ATOM_IMPORT) {
+ if (flags_ & PDB::SEQUENTIAL_ATOM_IMPORT) {
sequential_atom_list_.push_back(ah);
}
- */
++atom_count_;
}
} else {
mol::AtomHandle ah = editor.InsertAtom(curr_residue_, aname, apos, aprop);
- /*
- if (PDB::Flags() & PDB::SEQUENTIAL_ATOM_IMPORT) {
+ if (flags_ & PDB::SEQUENTIAL_ATOM_IMPORT) {
sequential_atom_list_.push_back(ah);
}
- */
++atom_count_;
}
}
diff --git a/modules/io/src/mol/pdb_reader.hh b/modules/io/src/mol/pdb_reader.hh
index 6d9f715c6cd9071a471d33427464533bb6b29294..5c85e23a14a88e80d6229f728171914b9deaa6b9 100644
--- a/modules/io/src/mol/pdb_reader.hh
+++ b/modules/io/src/mol/pdb_reader.hh
@@ -47,7 +47,17 @@ public:
bool HasNext();
void Import(mol::EntityHandle& ent,
- const String& restrict_chains="");
+ const String& restrict_chains="");
+ void SetFlags(PDBFlags flags);
+
+ /// \brief get list of atoms
+ ///
+ /// The atom handles reflect the order of atom records in the PDb files. This
+ /// is used to synchronize PDB and coordgroup io.
+ ///
+ /// By default, the atom list is empty, The PDB::SEQUENTIAL_ATOM_IMPORT flag
+ /// must be set.
+ std::vector<mol::AtomHandle> GetSequentialAtoms() const;
private:
void ClearState();
@@ -80,7 +90,8 @@ private:
std::istream& instream_;
boost::iostreams::filtering_stream<boost::iostreams::input> in_;
String curr_line_;
-
+ std::vector<mol::AtomHandle> sequential_atom_list_;
+ PDBFlags flags_;
// this needs to be set to true for reading pqr
// file (i.e. pdb formatted file with charges in occupacy
// column, and radii in b-factor column)
diff --git a/modules/io/src/mol/pdb_writer.cc b/modules/io/src/mol/pdb_writer.cc
index 36f9ce9e2f8fae5081204e6546f4077022313b54..8e461a56e95da8aa00b28ed6ef44b1be660b3745 100644
--- a/modules/io/src/mol/pdb_writer.cc
+++ b/modules/io/src/mol/pdb_writer.cc
@@ -123,20 +123,27 @@ private:
PDBWriter::PDBWriter(std::ostream& stream):
outfile_(), outstream_(stream)
-{}
+{
+
+}
PDBWriter::PDBWriter(const boost::filesystem::path& filename):
- outfile_(filename.file_string().c_str()), outstream_(outfile_), mol_count_(0)
-{}
+ outfile_(filename.file_string().c_str()), outstream_(outfile_), mol_count_(0),
+ flags_(0)
+{
+
+}
PDBWriter::PDBWriter(const String& filename):
- outfile_(filename.c_str()), outstream_(outfile_), mol_count_(0)
-{}
+ outfile_(filename.c_str()), outstream_(outfile_), mol_count_(0), flags_(0)
+{
+
+}
void PDBWriter::WriteModelLeader()
{
++mol_count_;
- if (PDB::Flags() & PDB::WRITE_MULTIPLE_MODELS) {
+ if (flags_ & PDB::WRITE_MULTIPLE_MODELS) {
outstream_ << "MODEL " << mol_count_ << std::endl;
} else if (mol_count_>1) {
throw IOException("Please enable the PDB::WRITE_MULTIPLE_MODELS flag to "
@@ -146,7 +153,7 @@ void PDBWriter::WriteModelLeader()
void PDBWriter::WriteModelTrailer()
{
- if (PDB::Flags() & PDB::WRITE_MULTIPLE_MODELS) {
+ if (flags_ & PDB::WRITE_MULTIPLE_MODELS) {
outstream_ << "ENDMDL" << std::endl;
}
}
@@ -156,13 +163,18 @@ void PDBWriter::WriteModel(H ent)
{
this->WriteModelLeader();
PDBWriterImpl writer(outstream_);
- if (PDB::Flags() & PDB::PQR_FORMAT) {
+ if (flags_ & PDB::PQR_FORMAT) {
writer.SetIsPQR(true);
}
ent.Apply(writer);
this->WriteModelTrailer();
}
+void PDBWriter::SetFlags(PDBFlags flags)
+{
+ flags_=flags;
+}
+
void PDBWriter::Write(const mol::EntityView& ent)
{
this->WriteModel(ent);
@@ -187,7 +199,7 @@ void PDBWriter::Write(const mol::AtomHandleList& atoms)
}
last_chain=(*i).GetResidue().GetChain();
}
- write_atom(outstream_, *i, counter, PDB::Flags() & PDB::PQR_FORMAT);
+ write_atom(outstream_, *i, counter, flags_ & PDB::PQR_FORMAT);
}
this->WriteModelTrailer();
}
diff --git a/modules/io/src/mol/pdb_writer.hh b/modules/io/src/mol/pdb_writer.hh
index 971890eeb66d75cba69453e1782a185b84a51d24..83f2f923e38ede6435bda01ab860a1421d907ec4 100644
--- a/modules/io/src/mol/pdb_writer.hh
+++ b/modules/io/src/mol/pdb_writer.hh
@@ -42,6 +42,8 @@ public:
PDBWriter(const boost::filesystem::path& filename);
PDBWriter(std::ostream& outstream);
+ void SetFlags(PDBFlags flags);
+
void Write(const mol::EntityView& ent);
void Write(const mol::EntityHandle& ent);
@@ -57,6 +59,7 @@ private:
std::ofstream outfile_;
std::ostream& outstream_;
int mol_count_;
+ PDBFlags flags_;
};
}}
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 7866377c2056932e99732b36d60fcdaceff3041d..64f46c26b62a2bc508afe0d84a67376597b9fba8 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -91,11 +91,10 @@ BOOST_AUTO_TEST_CASE(join_spread_records_on)
{
String fname("testfiles/pdb/join-spread-records.pdb");
PDBReader reader(fname);
+ reader.SetFlags(PDB::JOIN_SPREAD_ATOM_RECORDS);
mol::EntityHandle ent=mol::CreateEntity();
- PDB::PushFlags(PDB::JOIN_SPREAD_ATOM_RECORDS);
reader.Import(ent);
- PDB::PopFlags();
BOOST_CHECK_EQUAL(ent.GetResidueCount(), 2);
mol::ResidueHandle res1=ent.FindResidue("A", mol::ResNum(1));
BOOST_CHECK(res1.IsValid());
@@ -125,4 +124,4 @@ BOOST_AUTO_TEST_CASE(join_spread_records_off)
BOOST_CHECK(res2.FindAtom("N"));
}
-BOOST_AUTO_TEST_SUITE_END()
+BOOST_AUTO_TEST_SUITE_END()
\ No newline at end of file
diff --git a/modules/mol/base/pymod/export_atom.cc b/modules/mol/base/pymod/export_atom.cc
index ccebbfb0adf0f9b7eb3aba0f10ba914ef68e987c..52983f3ae26775d4014f16028925230a4cc31420 100644
--- a/modules/mol/base/pymod/export_atom.cc
+++ b/modules/mol/base/pymod/export_atom.cc
@@ -46,7 +46,6 @@ void export_Atom()
.def("GetProp", &AtomBase::GetProp,
return_value_policy<copy_const_reference>())
.def("SetProp", &AtomBase::SetProp, args("prop"))
- .def("GetIndex", &AtomBase::GetIndex)
.add_property("prop",
make_function(&AtomBase::GetProp,
return_value_policy<copy_const_reference>()))
@@ -57,7 +56,6 @@ void export_Atom()
make_function(&AtomBase::GetName,
return_value_policy<copy_const_reference>()),
&AtomBase::SetName)
- .add_property("index",&AtomBase::GetIndex)
;
generic_prop_def<AtomBase>(atom_base);
diff --git a/modules/mol/base/pymod/export_residue.cc b/modules/mol/base/pymod/export_residue.cc
index 1ff735cf642d3ca604a54d3dd5c45dca7517b3da..615c6bc3d0b39551ab4a3c6e91279bdd04b7a3c1 100644
--- a/modules/mol/base/pymod/export_residue.cc
+++ b/modules/mol/base/pymod/export_residue.cc
@@ -34,10 +34,6 @@ namespace {
typedef EntityView (ResidueHandle::*StringMethod)(const String&, uint) const;
QueryMethod select_query=&ResidueHandle::Select;
StringMethod select_string=&ResidueHandle::Select;
-
- void set_sec_struct1(ResidueBase* b, const SecStructure& s) {b->SetSecStructure(s);}
- void set_sec_struct2(ResidueBase* b, char c) {b->SetSecStructure(SecStructure(c));}
-
}
//BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_insert_overloads,
@@ -86,8 +82,7 @@ void export_Residue()
class_<ResidueBase> residue_base("ResidueBase", no_init);
residue_base
.def("GetSecStructure", &ResidueBase::GetSecStructure)
- .def("SetSecStructure", set_sec_struct1)
- .def("SetSecStructure", set_sec_struct2)
+ .def("SetSecStructure", &ResidueBase::SetSecStructure)
.def("GetPhiTorsion", &ResidueBase::GetPhiTorsion)
.def("GetPsiTorsion", &ResidueBase::GetPsiTorsion)
.def("GetOmegaTorsion", &ResidueBase::GetOmegaTorsion)
diff --git a/modules/mol/base/src/atom_base.cc b/modules/mol/base/src/atom_base.cc
index 9a8cfb1fc0ce1438612555e2909c7be900fc7558..95141733ff27a4ab798e67d9aa814b1d7201aa58 100644
--- a/modules/mol/base/src/atom_base.cc
+++ b/modules/mol/base/src/atom_base.cc
@@ -156,11 +156,5 @@ int AtomBase::GetIntProperty(Prop::ID prop_id) const
return Impl()->GetIntProperty(prop_id);
}
-unsigned long AtomBase::GetIndex() const
-{
- this->CheckValidity();
- return Impl()->GetIndex();
-}
-
}} // ns
diff --git a/modules/mol/base/src/atom_base.hh b/modules/mol/base/src/atom_base.hh
index 3b10fb8ca241ff4aa5c452d0b86a63c2bb848127..0a17ce2508b7a904e92e738de0fe72fbf4a7249b 100644
--- a/modules/mol/base/src/atom_base.hh
+++ b/modules/mol/base/src/atom_base.hh
@@ -116,10 +116,7 @@ public:
/// \brief Get int property by id
int GetIntProperty(Prop::ID prop_id) const;
-
- /// \brief Get the internal index
- unsigned long GetIndex() const;
-
+public:
/// \brief get atom implementation.
///
/// Intended for internal use.
diff --git a/modules/mol/base/src/coord_frame.hh b/modules/mol/base/src/coord_frame.hh
index 017a58865a239a10bc7869ab4a2380047a528c85..4a04ca4e45ef0be5a7785e72c6198f046a960e42 100644
--- a/modules/mol/base/src/coord_frame.hh
+++ b/modules/mol/base/src/coord_frame.hh
@@ -29,10 +29,17 @@
namespace ost { namespace mol {
-typedef std::vector<geom::Vec3> CoordFrame;
+class CoordFrame;
+
typedef boost::shared_ptr<CoordFrame> CoordFramePtr;
typedef std::vector<CoordFramePtr> CoordFrameList;
+class DLLEXPORT_OST_MOL CoordFrame : public std::vector<geom::Vec3> {
+public:
+ CoordFrame() {}
+ CoordFrame(Real ts) {}
+};
+
}}
#endif
diff --git a/modules/mol/base/src/coord_source.cc b/modules/mol/base/src/coord_source.cc
index b25a91755d461be23870de214a5e592c038ece6a..a8d95ff1a9828a56663539407aa7df11ccf7b546 100644
--- a/modules/mol/base/src/coord_source.cc
+++ b/modules/mol/base/src/coord_source.cc
@@ -20,7 +20,6 @@
/*
Author: Marco Biasini
*/
-#include <ost/log.hh>
#include <ost/mol/atom_handle.hh>
#include <ost/mol/xcs_editor.hh>
#include <ost/mol/in_mem_coord_source.hh>
@@ -54,12 +53,10 @@ CoordSource::~CoordSource()
void CoordSource::CopyFrame(uint frame_id)
{
if (atoms_.empty()) {
- LOGN_DEBUG("atom list empty, ignored");
return;
}
CoordFramePtr frame=this->GetFrame(frame_id);
if (!frame) {
- LOGN_DEBUG("invalid frame given, ignored");
return;
}
assert(frame->size()==atoms_.size());
@@ -67,7 +64,7 @@ void CoordSource::CopyFrame(uint frame_id)
CoordFrame::const_iterator c=frame->begin();
for (AtomHandleList::iterator i=atoms_.begin(),
e=atoms_.end(); i!=e; ++i, ++c) {
- edi.SetAtomPos(*i, *c);
+ edi.SetAtomPos(*i, *c);
}
}
diff --git a/modules/mol/base/src/impl/atom_impl.cc b/modules/mol/base/src/impl/atom_impl.cc
index cb3ecf87a290166e78a14329655b9ff7a733698c..d8e37b25c38fd459f6e9d1c41d940f9247dd5852 100644
--- a/modules/mol/base/src/impl/atom_impl.cc
+++ b/modules/mol/base/src/impl/atom_impl.cc
@@ -40,8 +40,7 @@ AtomImpl::AtomImpl(const EntityImplPtr& e,
const ResidueImplPtr& r,
const String& n,
const geom::Vec3& p,
- const AtomProp& prop,
- unsigned long index):
+ const AtomProp& prop):
res_(r),
name_(n),
pos_(p),
@@ -49,8 +48,7 @@ AtomImpl::AtomImpl(const EntityImplPtr& e,
prim_connector_(),
connector_list_(),
fragment_(),
- state_(0),
- index_(index)
+ state_(0)
{
EntityHandle ent = this->GetEntity();
geom::Mat4 transf_matrix = ent.GetTransformationMatrix();
diff --git a/modules/mol/base/src/impl/atom_impl.hh b/modules/mol/base/src/impl/atom_impl.hh
index f3c2cc1c03db42b317b49606c326979e5b473d46..3db9ff520d4cf7ce0bb03f540e8fa8687fc14339 100644
--- a/modules/mol/base/src/impl/atom_impl.hh
+++ b/modules/mol/base/src/impl/atom_impl.hh
@@ -50,8 +50,7 @@ class AtomImpl: public GenericPropertyContainerImpl,
public boost::enable_shared_from_this<AtomImpl> {
public:
AtomImpl(const EntityImplPtr& ent, const ResidueImplPtr& res,
- const String& name, const geom::Vec3& pos, const AtomProp& prop,
- unsigned long index);
+ const String& name, const geom::Vec3& pos, const AtomProp& prop);
~AtomImpl();
void Apply(EntityVisitor& h);
@@ -138,9 +137,6 @@ public:
Real GetFloatProperty(Prop::ID prop_id) const;
int GetIntProperty(Prop::ID prop_id) const;
-
- unsigned long GetIndex() const {return index_;}
- void SetIndex(unsigned long index) {index_=index;}
private:
ResidueImplW res_;
@@ -175,8 +171,6 @@ private:
unsigned int mask = 0x1<<bit;
return (state_ & mask)!=0;
}
-
- unsigned long index_;
};
/// \internal
diff --git a/modules/mol/base/src/impl/entity_impl.cc b/modules/mol/base/src/impl/entity_impl.cc
index 2a271f341946116568f34fb9fff8ca1a96e481d9..e17a5a76dbcd2b23047cd34df54ed6ac3a5dff61 100644
--- a/modules/mol/base/src/impl/entity_impl.cc
+++ b/modules/mol/base/src/impl/entity_impl.cc
@@ -76,8 +76,7 @@ EntityImpl::EntityImpl():
xcs_editor_count_(0),
ics_editor_count_(0),
dirty_flags_(DisableICS),
- name_(""),
- next_index_(0L)
+ name_("")
{
}
@@ -351,9 +350,9 @@ AtomImplPtr EntityImpl::CreateAtom(const ResidueImplPtr& rp,
{
#if MAKE_SHARED_AVAILABLE
AtomImplPtr ap=boost::make_shared<AtomImpl>(shared_from_this(), rp, name,
- pos, prop,next_index_++);
+ pos, prop);
#else
- AtomImplPtr ap(new AtomImpl(shared_from_this(), rp, name, pos, prop,next_index_++));
+ AtomImplPtr ap(new AtomImpl(shared_from_this(), rp, name, pos, prop));
#endif
if (identity_transf_ == false) {
geom::Vec3 transformed_pos = geom::Vec3(transformation_matrix_*geom::Vec4(pos));
@@ -1166,7 +1165,7 @@ void EntityImpl::DecXCSEditorCount()
void EntityImpl::UpdateOrganizerIfNeeded()
{
if (dirty_flags_ & DirtyOrganizer) {
- LOGN_DEBUG("atom organizer marked as dirty. updating");
+ LOGN_VERBOSE("atom organizer marked as dirty. updating");
this->UpdateOrganizer();
dirty_flags_&=~DirtyOrganizer;
}
diff --git a/modules/mol/base/src/impl/entity_impl.hh b/modules/mol/base/src/impl/entity_impl.hh
index ebe32704b8309441f87898b52d37bbbaf7fbbe43..4042e92975df4ad29d2b8c327d6f113aa0d8b0aa 100644
--- a/modules/mol/base/src/impl/entity_impl.hh
+++ b/modules/mol/base/src/impl/entity_impl.hh
@@ -268,9 +268,6 @@ private:
int ics_editor_count_;
int dirty_flags_;
String name_;
-
- unsigned long next_index_;
-
template <bool always_true>
EntityView do_selection(const EntityHandle&, const Query&, QueryFlags) const;
};
diff --git a/modules/mol/base/src/in_mem_coord_source.cc b/modules/mol/base/src/in_mem_coord_source.cc
index 089c667bd1971f1a7ea6ee7c77d807deaeeb3d8e..98417d1594aa55ba4f26a0a9cfaa208c1fe2ad3f 100644
--- a/modules/mol/base/src/in_mem_coord_source.cc
+++ b/modules/mol/base/src/in_mem_coord_source.cc
@@ -27,8 +27,8 @@ void InMemCoordSource::AddFrame(const CoordFramePtr& frame)
void InMemCoordSource::AddFrame(const std::vector<geom::Vec3>& coords)
{
- CoordFramePtr fp(new CoordFrame(coords));
- frames_.push_back(fp);
+ frames_.push_back(CoordFramePtr(new CoordFrame(0.0)));
+ frames_.back()->insert(frames_.back()->end(), coords.begin(), coords.end());
}
}}
diff --git a/modules/mol/base/tests/test_entity.cc b/modules/mol/base/tests/test_entity.cc
index 0504422946e34546f0c3dee532bb05de4fbd232a..8deba9b01bad9b3a814daee98736ef1e8d0b465f 100644
--- a/modules/mol/base/tests/test_entity.cc
+++ b/modules/mol/base/tests/test_entity.cc
@@ -95,12 +95,10 @@ BOOST_AUTO_TEST_CASE(entity_creator)
AtomHandle atom1 = e.InsertAtom(res, "X1",geom::Vec3());
BOOST_CHECK(res==atom1.GetResidue());
BOOST_CHECK(atom1.GetName()=="X1");
- BOOST_CHECK(atom1.GetIndex()==0);
AtomHandle atom2 = e.InsertAtom(res, "X2",geom::Vec3());
BOOST_CHECK(res==atom2.GetResidue());
BOOST_CHECK(atom2.GetName()=="X2");
- BOOST_CHECK(atom2.GetIndex()==1);
BondHandle bond = e.Connect(atom1, atom2);