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 772a0c89c5963a7efb97004895c9736dfd29d206..b3fd346b6e87552242a509f853a0eb5ff093fd38 100644
--- a/modules/io/src/mol/CMakeLists.txt
+++ b/modules/io/src/mol/CMakeLists.txt
@@ -1,35 +1,32 @@
set(OST_IO_MOL_SOURCES
-dcd_io.cc
entity_io_crd_handler.cc
-entity_io_mae_handler.cc
+pdb_reader.cc
entity_io_pdb_handler.cc
+pdb_writer.cc
entity_io_sdf_handler.cc
+save_entity.cc
load_entity.cc
+surface_io_msms_handler.cc
load_surface.cc
-pdb_io.cc
-pdb_reader.cc
-pdb_writer.cc
-save_entity.cc
+dcd_io.cc
star_parser.cc
-surface_io_msms_handler.cc
PARENT_SCOPE
)
set(OST_IO_MOL_HEADERS
+star_parser.hh
dcd_io.hh
-entity_io_handler.hh
entity_io_crd_handler.hh
-entity_io_mae_handler.hh
-entity_io_pdb_handler.hh
-entity_io_sdf_handler.hh
-load_entity.hh
-load_surface.hh
pdb_io.hh
+entity_io_handler.hh
pdb_reader.hh
+entity_io_pdb_handler.hh
pdb_writer.hh
+entity_io_sdf_handler.hh
save_entity.hh
+load_entity.hh
surface_io_handler.hh
-star_parser.hh
+load_surface.hh
surface_io_msms_handler.hh
PARENT_SCOPE
)
diff --git a/modules/io/src/mol/dcd_io.cc b/modules/io/src/mol/dcd_io.cc
index 6fd936c42fc15ac93d6c3c753a3f76fcc0aeaf70..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>
@@ -60,20 +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);
@@ -131,7 +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");
@@ -146,8 +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) {
@@ -180,9 +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();
@@ -190,9 +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;
}
@@ -202,7 +188,6 @@ mol::CoordGroupHandle LoadCHARMMTraj(const String& crd_fn,
const String& trj_fn,
unsigned int stride)
{
- if(stride==0) stride=1;
boost::filesystem::path crd_f(crd_fn);
// first the coordinate reference file
@@ -212,18 +197,21 @@ mol::CoordGroupHandle LoadCHARMMTraj(const String& crd_fn,
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(ent.GetAtomList(),trj_fn,stride);
+ 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_mae_handler.cc b/modules/io/src/mol/entity_io_mae_handler.cc
deleted file mode 100755
index e41fa029c98e38c157b2c729de228f71aa5e7bbf..0000000000000000000000000000000000000000
--- a/modules/io/src/mol/entity_io_mae_handler.cc
+++ /dev/null
@@ -1,345 +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
-//------------------------------------------------------------------------------
-/*
- Author: Ansgar Philippsen
- */
-#include <iostream>
-#include <sstream>
-#include <iomanip>
-#include <vector>
-#include <string>
-
-#include <ctype.h>
-
-#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>
-
-#include <ost/log.hh>
-#include <ost/conop/conop.hh>
-#include <ost/mol/xcs_editor.hh>
-#include <ost/profile.hh>
-
-#include <ost/io/io_exception.hh>
-#include <ost/io/swap_util.hh>
-
-#include "entity_io_mae_handler.hh"
-
-namespace ost { namespace io {
-
-using boost::format;
-
- namespace {
-
- std::vector<std::string> tokenize(const std::string& line)
- {
- std::vector<std::string> nrvo;
- bool in_string=false;
- int p0=0;
- for(int p1=1;p1<line.size();++p1) {
- if(in_string) {
- if(line[p1]=='"') {
- in_string=false;
- nrvo.push_back(line.substr(p0,p1-p0));
- ++p1;
- p0=p1;
- while(isspace(line[p1]) and p1<line.size()) {++p0;++p1;}
- --p0; --p1;
- }
- } else {
- if(isspace(line[p1])) {
- nrvo.push_back(line.substr(p0+1,p1-p0-1));
- ++p1;
- p0=p1;
- while(isspace(line[p1]) and p1<line.size()) {++p0;++p1;}
- --p0; --p1;
- } else if(line[p1]=='"') {
- in_string=true;
- p0=p1+1;
- }
- }
- }
- return nrvo;
- }
-
- }
-
-MAEReader::MAEReader(const boost::filesystem::path& loc):
- curr_chain_(),
- curr_residue_(),
- chain_count_(0),
- residue_count_(0),
- atom_count_(0),
- infile_(loc),
- in_()
-{
- if (boost::iequals(".gz", boost::filesystem::extension(loc))) {
- in_.push(boost::iostreams::gzip_decompressor());
- }
- in_.push(infile_);
- if(!infile_) throw IOException("could not open "+loc.string());
-}
-
-void MAEReader::Import(mol::EntityHandle& ent)
-{
- Profile profile_import("MAEReader::Import");
-
- static const boost::regex r_ct_block("f_m_ct +\\{");
- static const boost::regex r_atom_block("m_atom\\[.*\\] +\\{");
- static const boost::regex r_delim(":::");
-
- String line;
- bool in_ct_block=false;
- bool in_atom_block=false;
- bool parsing_atoms=false;
- bool debug=true;
- std::vector<std::string> prop_list;
- int i_atom_name=-1;
- int i_atom_xpos=-1;
- int i_atom_ypos=-1;
- int i_atom_zpos=-1;
- int i_res_name=-1;
- int i_res_num=-1;
- int i_chain_name=-1;
-
- mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
-
- while(std::getline(in_,line)) {
- line = boost::trim_copy(line);
- if(in_ct_block) {
- if(in_atom_block) {
- if(parsing_atoms) {
- if(boost::regex_match(line,r_delim)) {
- std::cerr << "stopping atom parsing" << std::endl;
- parsing_atoms=false;
- } else {
- // parsing atom line
- std::vector<std::string> tokens=tokenize(line);
- add_atom(ent,editor,
- tokens[i_atom_name],
- tokens[i_atom_xpos],
- tokens[i_atom_ypos],
- tokens[i_atom_zpos],
- tokens[i_res_name],
- tokens[i_res_num],
- tokens[i_chain_name]);
- }
- } else { // not parsing atoms
- if(boost::regex_match(line,r_delim)) {
- if(i_atom_name==-1 ||
- i_atom_xpos==-1 ||
- i_atom_ypos==-1 ||
- i_atom_zpos==-1 ||
- i_res_name==-1 ||
- i_res_num==-1 ||
- i_chain_name==-1) {
- throw IOException("missing atom prop");
- }
- std::cerr << "starting atom parsing" << std::endl;
- parsing_atoms=true;
- } else if(line[0]=='}') {
- std::cerr << "exiting atom block" << std::endl;
- 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;
- }
- }
- } else { // not in atom block
- if(boost::regex_match(line,r_atom_block)) {
- std::cerr << "entering atom block" << std::endl;
- in_atom_block=true;
- } else if(line[0]=='}') {
- std::cerr << "exiting ct block" << std::endl;
- in_ct_block=false;
- }
- }
- } else { // not in ct block
- if(boost::regex_match(line,r_ct_block)) {
- std::cerr << "entering ct block" << std::endl;
- in_ct_block=true;
- }
- }
- }
-
- LOGN_MESSAGE("imported " << chain_count_ << " chains, " << residue_count_
- << " residues, " << atom_count_ << " atoms");
-}
-
-
-void MAEReader::add_atom(mol::EntityHandle ent,
- mol::XCSEditor& editor,
- const std::string& aname,
- const std::string& s_axpos,
- const std::string& s_aypos,
- const std::string& s_azpos,
- const std::string& rname,
- const std::string& s_rnum,
- const std::string& cname)
-{
- 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));
-
- mol::ResidueKey rkey(rname);
-
- // some postprocessing
- LOGN_TRACE( "cname: [" << cname << "]" );
-
- mol::ResNum rnum(irnum);
-
- // determine chain and residue update
- bool update_chain=false;
- bool update_residue=false;
- if(!curr_chain_) {
- update_chain=true;
- update_residue=true;
- } else if(curr_chain_.GetName()!=cname) {
- update_chain=true;
- update_residue=true;
- }
-
- if(!curr_residue_) {
- update_residue=true;
- } else if(curr_residue_.GetNumber()!=rnum) {
- update_residue=true;
- }
-
- if(update_chain) {
- if (!(curr_chain_=ent.FindChain(cname))) {
- LOGN_DUMP("new chain " << cname);
- curr_chain_=editor.InsertChain(cname);
- ++chain_count_;
- }
- }
-
- 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());
- ++residue_count_;
- }
- }
-
- // finally add atom
- LOGN_DUMP("adding atom " << aname << " (" << ele << ") @" << apos);
- mol::AtomProp aprop;
- aprop.element=ele;
- aprop.radius=conop::Conopology::Instance().GetDefaultAtomRadius(ele);
- aprop.is_hetatm=false;
- aprop.b_factor=0.0;
- aprop.occupancy=1.0;
- mol::AtomHandle ah = editor.InsertAtom(curr_residue_, aname, apos, aprop);
-}
-
-
-
-
-bool EntityIOMAEHandler::RequiresBuilder() const
-{
- return true;
-}
-
-void EntityIOMAEHandler::Import(mol::EntityHandle& ent,
- const boost::filesystem::path& loc)
-{
- MAEReader reader(loc);
- reader.Import(ent);
-}
-
-void EntityIOMAEHandler::Export(const mol::EntityView& ent,
- const boost::filesystem::path& loc) const
-{
-}
-
-namespace {
-
-bool mae_handler_is_responsible_for(const boost::filesystem::path& loc,
- const String& type) {
- if(type=="auto") {
- String match_suf_string=loc.string();
- std::transform(match_suf_string.begin(),match_suf_string.end(),match_suf_string.begin(),tolower);
- if( detail::FilenameEndsWith(match_suf_string,".mae") || detail::FilenameEndsWith(match_suf_string,".mae.gz") ) {
- return true;
- }
- } else if(type=="mae") {
- return true;
- }
-
- return false;
-}
-
-}
-
-bool EntityIOMAEHandler::ProvidesImport(const boost::filesystem::path& loc,
- const String& type)
-{
- return mae_handler_is_responsible_for(loc, type);
-}
-
-bool EntityIOMAEHandler::ProvidesExport(const boost::filesystem::path& loc,
- const String& type)
-{
- return false;
-}
-
-mol::EntityHandle LoadMAE(const String& file_name)
-{
- Profile profile_load("LoadMAE");
- conop::BuilderP builder = conop::Conopology::Instance().GetBuilder();
- MAEReader reader(file_name);
- mol::EntityHandle ent=mol::CreateEntity();
- mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
- reader.Import(ent);
- conop::Conopology::Instance().ConnectAll(builder,ent);
- return ent;
-}
-
-
-void EntityIOMAEHandler::Import(mol::EntityHandle& ent,
- std::istream& stream)
-{
- throw IOException("MAE format does not support import from stream");
-}
-
-
-void EntityIOMAEHandler::Export(const mol::EntityView& ent,
- std::ostream& stream) const
-{
- throw IOException("MAE format does not support export to stream");
-}
-
-}} // ns
-
-
diff --git a/modules/io/src/mol/entity_io_mae_handler.hh b/modules/io/src/mol/entity_io_mae_handler.hh
deleted file mode 100755
index 3924bd143a8930774276bbc2cb256df3821a51c5..0000000000000000000000000000000000000000
--- a/modules/io/src/mol/entity_io_mae_handler.hh
+++ /dev/null
@@ -1,83 +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_IO_ENTITY_IO_PLUGIN_MAE_H
-#define OST_IO_ENTITY_IO_PLUGIN_MAE_H
-
-#include <ost/io/mol/entity_io_handler.hh>
-
-#include <boost/iostreams/filtering_stream.hpp>
-#include <boost/filesystem/fstream.hpp>
-
-namespace ost { namespace io {
-
-class DLLEXPORT_OST_IO MAEReader {
-public:
- MAEReader(const boost::filesystem::path& loc);
-
- void Import(mol::EntityHandle& ent);
-
-private:
-
- void add_atom(mol::EntityHandle ent,
- mol::XCSEditor& editor,const std::string& s_aname,
- const std::string& s_axpos,
- const std::string& s_aypos,
- const std::string& s_azpos,
- const std::string& s_rname,
- const std::string& s_rnum,
- const std::string& s_cname);
-
- mol::ChainHandle curr_chain_;
- mol::ResidueHandle curr_residue_;
- int chain_count_;
- int residue_count_;
- int atom_count_;
- boost::filesystem::ifstream infile_;
- boost::iostreams::filtering_stream<boost::iostreams::input> in_;
-};
-
-class DLLEXPORT_OST_IO EntityIOMAEHandler: public EntityIOHandler {
-public:
- virtual void Import(mol::EntityHandle& ent, const boost::filesystem::path& loc);
-
- virtual void Export(const mol::EntityView& ent,
- const boost::filesystem::path& loc) const;
-
- virtual void Import(mol::EntityHandle& ent, std::istream& stream);
-
- virtual void Export(const mol::EntityView& ent, std::ostream& stream) const;
-
- static bool ProvidesImport(const boost::filesystem::path& loc,
- const String& format="auto");
- static bool ProvidesExport(const boost::filesystem::path& loc,
- const String& format="auto");
- virtual bool RequiresBuilder() const;
-
- static String GetFormatName() { return String("Mae"); }
- static String GetFormatDescription() { return String("MAEstro coordinate file format"); }
-};
-
-
-typedef EntityIOHandlerFactory<EntityIOMAEHandler> EntityIOMAEHandlerFactory;
-
-mol::EntityHandle DLLEXPORT_OST_IO LoadMAE(const String& file_name);
-
-}} // ns
-
-#endif
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 d9f3bc78ee50813cff776e1efa76452ae7a071be..140db87e3648055a3bff689f18657da8cceb820e 100644
--- a/modules/io/src/mol/pdb_io.hh
+++ b/modules/io/src/mol/pdb_io.hh
@@ -19,32 +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 {
-
- struct S {
- static S& I();
- std::stack<unsigned int> fstack;
- };
-
+ 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.
///
@@ -67,16 +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();
+ 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 1ea6f6da8e0c2456f6e4503cfe851e15bf17740d..ec0dbaccb37e140bd8227659455beee97f516ad3 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);
}
@@ -106,7 +106,7 @@ bool PDBReader::HasNext()
while (std::getline(in_, curr_line_) && ++line_num_) {
StringRef curr_line(curr_line_.c_str(), curr_line_.length());
if (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)) ||
@@ -123,8 +123,6 @@ 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...
@@ -173,7 +171,7 @@ 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,
@@ -252,6 +250,17 @@ 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,
@@ -267,7 +276,7 @@ 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));
@@ -277,7 +286,7 @@ 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));
@@ -302,7 +311,7 @@ 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));
@@ -311,7 +320,7 @@ 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";
@@ -319,7 +328,7 @@ 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";
@@ -358,7 +367,7 @@ 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));
@@ -423,31 +432,24 @@ 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());
}
@@ -491,22 +493,16 @@ 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 a6b32d39636d278386fada049323629d4346bbf1..9251f42b227ae6d8667724689f0b3a68d8dc81bd 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/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/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 4806c7cbd382511d9ffaea3fa0adb0c43a332208..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));
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);