From c96834cccfd3c6193cb45179a323353c6218c058 Mon Sep 17 00:00:00 2001
From: ansgar <ansgar@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Wed, 28 Apr 2010 02:35:36 +0000
Subject: [PATCH] more functionality for coord group and coord source (pending
a considerable refactoring, however) some debug and fixes for mae io handler
added residue chemclass to python
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2125 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/io/src/mol/entity_io_mae_handler.cc | 74 ++++++++++++--------
modules/mol/base/pymod/export_coord_group.cc | 2 +
modules/mol/base/pymod/export_residue.cc | 5 ++
modules/mol/base/src/coord_group.cc | 12 +++-
modules/mol/base/src/coord_group.hh | 6 +-
modules/mol/base/src/coord_source.cc | 20 ++++--
modules/mol/base/src/coord_source.hh | 4 +-
modules/mol/base/src/in_mem_coord_source.cc | 9 ++-
modules/mol/base/src/in_mem_coord_source.hh | 1 +
9 files changed, 92 insertions(+), 41 deletions(-)
diff --git a/modules/io/src/mol/entity_io_mae_handler.cc b/modules/io/src/mol/entity_io_mae_handler.cc
index b8647c00a..03700f62a 100644
--- a/modules/io/src/mol/entity_io_mae_handler.cc
+++ b/modules/io/src/mol/entity_io_mae_handler.cc
@@ -30,7 +30,6 @@
#include <boost/iostreams/filter/gzip.hpp>
#include <boost/filesystem/convenience.hpp>
#include <boost/algorithm/string.hpp>
-#include <boost/lexical_cast.hpp>
#include <boost/format.hpp>
#include <boost/regex.hpp>
@@ -128,11 +127,16 @@ void MAEReader::Import(mol::EntityHandle& ent)
if(in_atom_block) {
if(parsing_atoms) {
if(boost::regex_match(line,r_delim)) {
- std::cerr << "stopping atom parsing" << std::endl;
+ LOGN_DUMP( "stopping atom parsing" );
parsing_atoms=false;
+ prop_list.clear();
} else {
// parsing atom line
std::vector<std::string> tokens=tokenize(line);
+ for(int i=0;i<tokens.size();++i) {
+ LOG_DUMP( "[" << tokens[i] << "] ");
+ }
+ LOGN_DUMP("");
add_atom(ent,editor,
tokens[i_atom_name],
tokens[i_atom_xpos],
@@ -153,37 +157,39 @@ void MAEReader::Import(mol::EntityHandle& ent)
i_chain_name==-1) {
throw IOException("missing atom prop");
}
- std::cerr << "starting atom parsing" << std::endl;
+ LOGN_DUMP( "starting atom parsing" );
parsing_atoms=true;
} else if(line[0]=='}') {
- std::cerr << "exiting atom block" << std::endl;
+ LOGN_DUMP( "exiting atom block" );
in_atom_block=false;
} else {
// parsing property line
- int pid=prop_list.size();
- prop_list.push_back(line);
- std::cerr << "found property '" << prop_list.back() << "'" << std::endl;
- if(line=="s_m_pdb_atom_name") i_atom_name=pid;
- else if(line=="r_m_x_coord") i_atom_xpos=pid;
- else if(line=="r_m_y_coord") i_atom_ypos=pid;
- else if(line=="r_m_z_coord") i_atom_zpos=pid;
- else if(line=="s_m_pdb_residue_name") i_res_name=pid;
- else if(line=="i_m_residue_number") i_res_num=pid;
- else if(line=="s_m_pdb_segment_name") i_chain_name=pid;
+ if(line[0]!='#') {
+ int pid=prop_list.size()+1;
+ prop_list.push_back(line);
+ LOGN_DUMP( "found property '" << prop_list.back() << "' id=" << pid );
+ if(line=="s_m_pdb_atom_name") i_atom_name=pid;
+ else if(line=="r_m_x_coord") i_atom_xpos=pid;
+ else if(line=="r_m_y_coord") i_atom_ypos=pid;
+ else if(line=="r_m_z_coord") i_atom_zpos=pid;
+ else if(line=="s_m_pdb_residue_name") i_res_name=pid;
+ else if(line=="i_m_residue_number") i_res_num=pid;
+ else if(line=="s_m_pdb_segment_name") i_chain_name=pid;
+ }
}
}
} else { // not in atom block
if(boost::regex_match(line,r_atom_block)) {
- std::cerr << "entering atom block" << std::endl;
+ LOGN_DUMP( "entering atom block" );
in_atom_block=true;
} else if(line[0]=='}') {
- std::cerr << "exiting ct block" << std::endl;
+ LOGN_DUMP( "exiting ct block" );
in_ct_block=false;
}
}
} else { // not in ct block
if(boost::regex_match(line,r_ct_block)) {
- std::cerr << "entering ct block" << std::endl;
+ LOGN_DUMP( "entering ct block" );
in_ct_block=true;
}
}
@@ -196,25 +202,27 @@ void MAEReader::Import(mol::EntityHandle& ent)
void MAEReader::add_atom(mol::EntityHandle ent,
mol::XCSEditor& editor,
- const std::string& aname,
+ const std::string& aname2,
const std::string& s_axpos,
const std::string& s_aypos,
const std::string& s_azpos,
- const std::string& rname,
+ const std::string& rname2,
const std::string& s_rnum,
- const std::string& cname)
+ const std::string& cname2)
{
- std::string ele = aname.substr(0,1);
- int irnum = boost::lexical_cast<int>(s_rnum);
- geom::Vec3 apos(boost::lexical_cast<Real>(s_axpos),
- boost::lexical_cast<Real>(s_aypos),
- boost::lexical_cast<Real>(s_azpos));
+ std::string aname=boost::trim_copy(aname2);
+ std::string rname=boost::trim_copy(rname2);
+ std::string cname=boost::trim_copy(cname2);
+ std::string ele=aname.substr(0,1);
+ if(isdigit(ele[0])) ele="H";
+
+ int irnum = atoi(s_rnum.c_str());
+ geom::Vec3 apos(atof(s_axpos.c_str()),
+ atof(s_aypos.c_str()),
+ atof(s_azpos.c_str()));
mol::ResidueKey rkey(rname);
- // some postprocessing
- LOGN_TRACE( "cname: [" << cname << "]" );
-
mol::ResNum rnum(irnum);
// determine chain and residue update
@@ -236,23 +244,27 @@ void MAEReader::add_atom(mol::EntityHandle ent,
if(update_chain) {
if (!(curr_chain_=ent.FindChain(cname))) {
- LOGN_DUMP("new chain " << cname);
curr_chain_=editor.InsertChain(cname);
+ LOGN_DUMP("new chain " << curr_chain_);
++chain_count_;
+ } else {
+ LOGN_DUMP("old chain " << curr_chain_);
}
}
if(update_residue) {
if (!(curr_residue_=curr_chain_.FindResidue(rnum))) {
- LOGN_DUMP("new residue " << rkey << " " << rnum);
curr_residue_=editor.AppendResidue(curr_chain_, rkey, rnum);
assert(curr_residue_.IsValid());
+ LOGN_DUMP(" new residue " << curr_residue_);
++residue_count_;
+ } else {
+ LOGN_DUMP(" old residue " << curr_residue_);
}
}
// finally add atom
- LOGN_DUMP("adding atom " << aname << " (" << ele << ") @" << apos);
+ LOGN_DUMP(" atom " << aname << " (" << ele << ") @" << apos);
mol::AtomProp aprop;
aprop.element=ele;
aprop.radius=conop::Conopology::Instance().GetDefaultAtomRadius(ele);
diff --git a/modules/mol/base/pymod/export_coord_group.cc b/modules/mol/base/pymod/export_coord_group.cc
index 28059f82b..90efa24de 100644
--- a/modules/mol/base/pymod/export_coord_group.cc
+++ b/modules/mol/base/pymod/export_coord_group.cc
@@ -54,6 +54,8 @@ void export_CoordGroup()
.def("IsValid", &CoordGroupHandle::IsValid)
.def("Capture", capture1)
.def("Capture", capture2)
+ .def("CaptureInto",&CoordGroupHandle::CaptureInto)
+ .def("GetAtomList",&CoordGroupHandle::GetAtomList)
.def("__getitem__",cg_getitem)
.def("__setitem__",cg_setitem)
;
diff --git a/modules/mol/base/pymod/export_residue.cc b/modules/mol/base/pymod/export_residue.cc
index 66214c7d4..688f81be8 100644
--- a/modules/mol/base/pymod/export_residue.cc
+++ b/modules/mol/base/pymod/export_residue.cc
@@ -36,6 +36,8 @@ namespace {
void set_sec_struct1(ResidueBase* b, const SecStructure& s) {b->SetSecStructure(s);}
void set_sec_struct2(ResidueBase* b, char c) {b->SetSecStructure(SecStructure(c));}
+ void set_chemclass1(ResidueBase* b, const ChemClass& cc) {b->SetChemClass(cc);}
+ void set_chemclass2(ResidueBase* b, char c) {b->SetChemClass(ChemClass(c));}
}
@@ -104,6 +106,9 @@ void export_Residue()
return_value_policy<copy_const_reference>())
.def("GetNumber", &ResidueBase::GetNumber,
return_value_policy<copy_const_reference>())
+ .def("GetChemClass", &ResidueBase::GetChemClass)
+ .def("SetChemClass", set_chemclass1)
+ .def("SetChemClass", set_chemclass2)
.add_property("number",
make_function(&ResidueBase::GetNumber,
return_value_policy<copy_const_reference>()))
diff --git a/modules/mol/base/src/coord_group.cc b/modules/mol/base/src/coord_group.cc
index 6675b5499..df0b1a5de 100644
--- a/modules/mol/base/src/coord_group.cc
+++ b/modules/mol/base/src/coord_group.cc
@@ -118,7 +118,7 @@ CoordFramePtr CoordGroupHandle::GetFrame(uint frame) const
return source_->GetFrame(frame);
}
-const AtomHandleList& CoordGroupHandle::GetAtomList() const
+AtomHandleList CoordGroupHandle::GetAtomList() const
{
this->CheckValidity();
return source_->GetAtomList();
@@ -134,6 +134,16 @@ void CoordGroupHandle::Capture()
}
}
+void CoordGroupHandle::CaptureInto(int pos)
+{
+ this->CheckValidity();
+ if (source_->IsMutable()) {
+ source_->CaptureInto(pos);
+ } else {
+ throw IntegrityError("Can't capture. CoordGroup is immutable");
+ }
+}
+
void CoordGroupHandle::Capture(uint frame)
{
this->CheckValidity();
diff --git a/modules/mol/base/src/coord_group.hh b/modules/mol/base/src/coord_group.hh
index 3b038e37b..38fa81d2e 100644
--- a/modules/mol/base/src/coord_group.hh
+++ b/modules/mol/base/src/coord_group.hh
@@ -62,6 +62,8 @@ public:
/// \brief store current atom positions in new frame
void Capture();
+ void CaptureInto(int pos);
+
/// \brief store current atom positions in given frame (must exist)
void Capture(uint frame);
@@ -80,7 +82,7 @@ public:
/// \brief whether the handle is valid
operator bool() const;
- const AtomHandleList& GetAtomList() const;
+ AtomHandleList GetAtomList() const;
CoordFramePtr GetFrame(uint frame) const;
private:
void CheckValidity() const;
@@ -91,7 +93,7 @@ private:
};
// factory method
-// create with a reference set of atoms and the number of frames
+// create with a reference set of atoms and zero frames
DLLEXPORT_OST_MOL CoordGroupHandle CreateCoordGroup(const AtomHandleList& atoms);
}} // ns
diff --git a/modules/mol/base/src/coord_source.cc b/modules/mol/base/src/coord_source.cc
index b25a91755..9b9f853e3 100644
--- a/modules/mol/base/src/coord_source.cc
+++ b/modules/mol/base/src/coord_source.cc
@@ -87,6 +87,21 @@ void CoordSource::Capture()
this->AddFrame(coords);
}
+void CoordSource::CaptureInto(int pos)
+{
+ std::vector<geom::Vec3> coords;
+ coords.reserve(atoms_.size());
+ for (AtomHandleList::const_iterator i=atoms_.begin(),
+ e=atoms_.end(); i!=e; ++i) {
+ coords.push_back(i->GetPos());
+ }
+ if(pos<0 || pos>=GetFrameCount()) {
+ this->AddFrame(coords);
+ } else {
+ this->InsertFrame(pos,coords);
+ }
+}
+
void CoordSource::Capture(uint f)
{
CoordFrame& fp=*(GetFrame(f));
@@ -124,11 +139,6 @@ bool CoordSource::IsMutable() const
return mutable_;
}
-void CoordSource::AddFrame(const std::vector<geom::Vec3>& coords)
-{
- assert(0 && "implement me");
-}
-
void CoordSource::SetMutable(bool flag)
{
mutable_=flag;
diff --git a/modules/mol/base/src/coord_source.hh b/modules/mol/base/src/coord_source.hh
index bc54b88a7..590ba8073 100644
--- a/modules/mol/base/src/coord_source.hh
+++ b/modules/mol/base/src/coord_source.hh
@@ -66,9 +66,11 @@ public:
bool IsMutable() const;
void Capture();
+ void CaptureInto(int pos);
void Capture(uint f);
- virtual void AddFrame(const std::vector<geom::Vec3>& coords);
+ virtual void AddFrame(const std::vector<geom::Vec3>& coords) = 0;
+ virtual void InsertFrame(int pos, const std::vector<geom::Vec3>& coords) = 0;
protected:
void SetMutable(bool flag);
private:
diff --git a/modules/mol/base/src/in_mem_coord_source.cc b/modules/mol/base/src/in_mem_coord_source.cc
index 089c667bd..1690c1104 100644
--- a/modules/mol/base/src/in_mem_coord_source.cc
+++ b/modules/mol/base/src/in_mem_coord_source.cc
@@ -16,7 +16,6 @@ uint InMemCoordSource::GetFrameCount()
CoordFramePtr InMemCoordSource::GetFrame(uint frame_id) const
{
-
return frame_id>=frames_.size() ? CoordFramePtr() : frames_[frame_id];
}
@@ -31,4 +30,12 @@ void InMemCoordSource::AddFrame(const std::vector<geom::Vec3>& coords)
frames_.push_back(fp);
}
+void InMemCoordSource::InsertFrame(int pos, const std::vector<geom::Vec3>& coords)
+{
+ CoordFrameList::iterator it = frames_.begin();
+ for(int i=0;i<pos;++i) ++it;
+ CoordFramePtr fp(new CoordFrame(coords));
+ frames_.insert(it,fp);
+}
+
}}
diff --git a/modules/mol/base/src/in_mem_coord_source.hh b/modules/mol/base/src/in_mem_coord_source.hh
index 08388f313..67b31e95f 100644
--- a/modules/mol/base/src/in_mem_coord_source.hh
+++ b/modules/mol/base/src/in_mem_coord_source.hh
@@ -44,6 +44,7 @@ public:
void AddFrame(const CoordFramePtr& frame);
virtual void AddFrame(const std::vector<geom::Vec3>& coords);
+ virtual void InsertFrame(int pos, const std::vector<geom::Vec3>& coords);
private:
CoordFrameList frames_;
--
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