From 1e709c334434c68386bb88dc29e79101fcf5824f Mon Sep 17 00:00:00 2001
From: tobias <tobias@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Tue, 11 May 2010 13:53:58 +0000
Subject: [PATCH] - added unit tests for sdf file reader/writer - moved
compare_files to base/test_utils - reorganized sdf file reader/writer
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2236 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/base/src/CMakeLists.txt | 3 +-
modules/base/src/test_utils/compare_files.cc | 52 +++
modules/base/src/test_utils/compare_files.hh | 27 ++
modules/gfx/tests/CMakeLists.txt | 6 +-
modules/gfx/tests/test_ent_pov_export.cc | 31 +-
modules/io/src/mol/CMakeLists.txt | 4 +
modules/io/src/mol/entity_io_sdf_handler.cc | 378 +-----------------
modules/io/src/mol/entity_io_sdf_handler.hh | 24 --
modules/io/src/mol/sdf_reader.cc | 275 +++++++++++++
modules/io/src/mol/sdf_reader.hh | 67 ++++
modules/io/src/mol/sdf_writer.cc | 158 ++++++++
modules/io/src/mol/sdf_writer.hh | 61 +++
modules/io/tests/test_io_pdb.cc | 31 +-
modules/io/tests/test_io_sdf.cc | 182 ++++++++-
.../{test_in.sdf => sdf/compound.sdf} | 264 ++++++------
.../tests/testfiles/sdf/empty_dataheader.sdf | 48 +++
modules/io/tests/testfiles/sdf/multiple.sdf | 72 ++++
modules/io/tests/testfiles/sdf/properties.sdf | 48 +++
modules/io/tests/testfiles/sdf/simple.sdf | 18 +
.../tests/testfiles/sdf/wrong_atomcount.sdf | 18 +
.../testfiles/sdf/wrong_atomlinelength.sdf | 18 +
.../io/tests/testfiles/sdf/wrong_atompos.sdf | 18 +
.../testfiles/sdf/wrong_bondatomnumber.sdf | 18 +
.../tests/testfiles/sdf/wrong_bondcount.sdf | 18 +
.../testfiles/sdf/wrong_bondlinelength.sdf | 18 +
.../io/tests/testfiles/sdf/wrong_bondtype.sdf | 18 +
.../io/tests/testfiles/sdf/wrong_charge.sdf | 18 +
.../tests/testfiles/sdf/wrong_dataheader.sdf | 48 +++
28 files changed, 1352 insertions(+), 589 deletions(-)
create mode 100644 modules/base/src/test_utils/compare_files.cc
create mode 100644 modules/base/src/test_utils/compare_files.hh
create mode 100644 modules/io/src/mol/sdf_reader.cc
create mode 100644 modules/io/src/mol/sdf_reader.hh
create mode 100644 modules/io/src/mol/sdf_writer.cc
create mode 100644 modules/io/src/mol/sdf_writer.hh
rename modules/io/tests/testfiles/{test_in.sdf => sdf/compound.sdf} (97%)
create mode 100644 modules/io/tests/testfiles/sdf/empty_dataheader.sdf
create mode 100644 modules/io/tests/testfiles/sdf/multiple.sdf
create mode 100644 modules/io/tests/testfiles/sdf/properties.sdf
create mode 100644 modules/io/tests/testfiles/sdf/simple.sdf
create mode 100644 modules/io/tests/testfiles/sdf/wrong_atomcount.sdf
create mode 100644 modules/io/tests/testfiles/sdf/wrong_atomlinelength.sdf
create mode 100644 modules/io/tests/testfiles/sdf/wrong_atompos.sdf
create mode 100644 modules/io/tests/testfiles/sdf/wrong_bondatomnumber.sdf
create mode 100644 modules/io/tests/testfiles/sdf/wrong_bondcount.sdf
create mode 100644 modules/io/tests/testfiles/sdf/wrong_bondlinelength.sdf
create mode 100644 modules/io/tests/testfiles/sdf/wrong_bondtype.sdf
create mode 100644 modules/io/tests/testfiles/sdf/wrong_charge.sdf
create mode 100644 modules/io/tests/testfiles/sdf/wrong_dataheader.sdf
diff --git a/modules/base/src/CMakeLists.txt b/modules/base/src/CMakeLists.txt
index ecdc389db..c2d698cf9 100644
--- a/modules/base/src/CMakeLists.txt
+++ b/modules/base/src/CMakeLists.txt
@@ -8,6 +8,7 @@ units.cc
string_ref.cc
platform.cc
message.cc
+test_utils/compare_files.cc
)
set(OST_BASE_HEADERS
@@ -32,7 +33,7 @@ tri_matrix.hh
)
module(NAME base SOURCES ${OST_BASE_SOURCES}
- HEADERS generic_property_def.hh IN_DIR export_helper ${OST_BASE_HEADERS}
+ HEADERS generic_property_def.hh IN_DIR export_helper compare_files.hh IN_DIR test_utils ${OST_BASE_HEADERS}
DEPENDS_ON geom
HEADER_OUTPUT_DIR ost)
diff --git a/modules/base/src/test_utils/compare_files.cc b/modules/base/src/test_utils/compare_files.cc
new file mode 100644
index 000000000..ff5578299
--- /dev/null
+++ b/modules/base/src/test_utils/compare_files.cc
@@ -0,0 +1,52 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <iostream>
+#include <fstream>
+#include "compare_files.hh"
+
+bool compare_files(const String& test, const String& gold_standard)
+{
+ std::ifstream test_stream(test.c_str());
+ std::ifstream gold_stream(gold_standard.c_str());
+ String test_line, gold_line;
+ while (true) {
+ bool test_end=std::getline(test_stream, test_line);
+ bool gold_end=std::getline(gold_stream, gold_line);
+ if (!(test_end || gold_end)) {
+ return true;
+ }
+ if (!test_end) {
+ std::cerr << gold_standard << " contains additional line(s):"
+ << std::endl << gold_line;
+ return false;
+ }
+ if (!gold_end) {
+ std::cerr << test << " contains additional line(s):"
+ << std::endl << test_line;
+ return false;
+ }
+ if (gold_line!=test_line) {
+ std::cerr << "line mismatch:" << std::endl << "test: " << test_line
+ << std::endl << "gold: " << gold_line;
+ return false;
+ }
+ }
+ return true;
+}
diff --git a/modules/base/src/test_utils/compare_files.hh b/modules/base/src/test_utils/compare_files.hh
new file mode 100644
index 000000000..7f441ae69
--- /dev/null
+++ b/modules/base/src/test_utils/compare_files.hh
@@ -0,0 +1,27 @@
+//------------------------------------------------------------------------------
+// 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_COMPARE_FILES_HH
+#define OST_COMPARE_FILES_HH
+
+#include <ost/base.hh>
+
+bool compare_files(const String& test, const String& gold_standard);
+
+#endif
diff --git a/modules/gfx/tests/CMakeLists.txt b/modules/gfx/tests/CMakeLists.txt
index a055e099e..fe6a3d670 100644
--- a/modules/gfx/tests/CMakeLists.txt
+++ b/modules/gfx/tests/CMakeLists.txt
@@ -4,10 +4,8 @@ set(OST_GFX_UNIT_TESTS
)
if (ENABLE_IMG)
list(APPEND OST_GFX_UNIT_TESTS test_map_octree.cc)
-
- ost_unittest(gfx "${OST_GFX_UNIT_TESTS}")
-
- target_link_libraries(gfx_tests ost_io)
endif()
+ost_unittest(gfx "${OST_GFX_UNIT_TESTS}")
+target_link_libraries(gfx_tests ost_io)
diff --git a/modules/gfx/tests/test_ent_pov_export.cc b/modules/gfx/tests/test_ent_pov_export.cc
index 450051dc7..bfb72ec79 100644
--- a/modules/gfx/tests/test_ent_pov_export.cc
+++ b/modules/gfx/tests/test_ent_pov_export.cc
@@ -26,6 +26,7 @@
#include <ost/io/load_entity.hh>
#include <ost/gfx/scene.hh>
#include <ost/gfx/entity.hh>
+#include <ost/test_utils/compare_files.hh>
using boost::unit_test_framework::test_suite;
using namespace ost;
@@ -42,36 +43,6 @@ boost::shared_ptr<Entity> prepare_object(gfx::RenderMode::Type mode)
return gfx_ent;
}
-bool compare_files(const String& test, const String& gold_standard)
-{
- std::ifstream test_stream(test.c_str());
- std::ifstream gold_stream(gold_standard.c_str());
- String test_line, gold_line;
- while (true) {
- bool test_end=std::getline(test_stream, test_line);
- bool gold_end=std::getline(gold_stream, gold_line);
- if (!(test_end || gold_end)) {
- return true;
- }
- if (!test_end) {
- std::cerr << gold_standard << " contains additional line(s):"
- << std::endl << gold_line;
- return false;
- }
- if (!gold_end) {
- std::cerr << test << " contains additional line(s):"
- << std::endl << test_line;
- return false;
- }
- if (gold_line!=test_line) {
- std::cerr << "line mismatch:" << std::endl << "test: " << test_line
- << std::endl << "gold: " << gold_line;
- return false;
- }
- }
- return true;
-}
-
// The GfxView uses a std::map for efficient access to atoms. This however has
// implications for the POV export. In general we can't assume that the atoms
// are written in any particular order. That's why we first filter out all
diff --git a/modules/io/src/mol/CMakeLists.txt b/modules/io/src/mol/CMakeLists.txt
index 5cdf0462b..860b4df0d 100644
--- a/modules/io/src/mol/CMakeLists.txt
+++ b/modules/io/src/mol/CMakeLists.txt
@@ -6,6 +6,8 @@ entity_io_pdb_handler.cc
pdb_io.cc
pdb_writer.cc
entity_io_sdf_handler.cc
+sdf_reader.cc
+sdf_writer.cc
save_entity.cc
load_entity.cc
surface_io_msms_handler.cc
@@ -26,6 +28,8 @@ pdb_reader.hh
entity_io_pdb_handler.hh
pdb_writer.hh
entity_io_sdf_handler.hh
+sdf_reader.hh
+sdf_writer.hh
save_entity.hh
load_entity.hh
surface_io_handler.hh
diff --git a/modules/io/src/mol/entity_io_sdf_handler.cc b/modules/io/src/mol/entity_io_sdf_handler.cc
index f9c49479f..72ec53cbc 100644
--- a/modules/io/src/mol/entity_io_sdf_handler.cc
+++ b/modules/io/src/mol/entity_io_sdf_handler.cc
@@ -16,392 +16,50 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
-#include <iostream>
-#include <sstream>
-#include <iomanip>
+/*
+ Author: Tobias Schmidt
+ */
-#include <boost/filesystem/fstream.hpp>
-#include <boost/filesystem/convenience.hpp>
-#include <boost/algorithm/string.hpp>
-#include <boost/lexical_cast.hpp>
-#include <boost/format.hpp>
#include <ost/log.hh>
-#include <ost/conop/conop.hh>
-#include <ost/io/io_exception.hh>
+#include <ost/io/sdf_writer.hh>
+#include <ost/io/sdf_reader.hh>
+
#include "entity_io_sdf_handler.hh"
namespace ost { namespace io {
-using boost::format;
bool EntityIOSDFHandler::RequiresBuilder() const
{
return false;
}
-// import data from provided stream
-void EntityIOSDFHandler::Import(mol::EntityHandle& ent, std::istream& instream)
+void EntityIOSDFHandler::Import(mol::EntityHandle& ent,
+ std::istream& instream)
{
- String line;
- mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
- while (std::getline(instream,line)) {
- ++line_num;
-
- if (line_num<=4) {
- ParseAndAddHeader(line, line_num, ent, editor);
- } else if (line_num<=atom_count_+4) {
- ParseAndAddAtom(line, line_num, ent, true, editor);
- } else if (line_num<=bond_count_+atom_count_+4) {
- ParseAndAddBond(line, line_num, ent, editor);
- } else if (boost::iequals(line.substr(0,2), "> ")) {
- // parse data items
- int data_header_start = line.find('<');
- String data_header = line.substr(data_header_start+1,line.rfind('>')-data_header_start-1);
- if(data_header.empty()) {
- String msg="Bad data line %d: Could not find data header";
- throw IOException(str(format(msg) % line_num));
- }
- String data_value="";
- while(std::getline(instream,line) && !boost::iequals(line, "")) {
- data_value.append(line);
- }
- curr_chain_.SetStringProp(data_header, data_value);
- } else if (boost::iequals(line, "$$$$")) {
- LOGN_MESSAGE("MOLECULE " << curr_chain_.GetName() << " (" << chain_count_ << ") added.")
- NextMolecule();
- }
- }
-
- LOGN_MESSAGE("imported " << chain_count_ << " chains, " << residue_count_
- << " residues, " << atom_count_ << " atoms");
+ SDFReader reader(instream);
+ reader.Import(ent);
}
-
-
void EntityIOSDFHandler::Import(mol::EntityHandle& ent,
const boost::filesystem::path& loc)
{
- ClearState();
- boost::filesystem::ifstream instream(loc);
- if(!instream) throw IOException("could not open "+loc.string());
- this->Import(ent, instream);
-}
-
-void EntityIOSDFHandler::ClearState()
-{
- curr_chain_=mol::ChainHandle();
- curr_residue_=mol::ResidueHandle();
- chain_count_=0;
- residue_count_=0;
- atom_count_=0;
- bond_count_=0;
- line_num=0;
-}
-
-void EntityIOSDFHandler::NextMolecule()
-{
- residue_count_=0;
- atom_count_=0;
- bond_count_=0;
- line_num=0;
-}
-
-void EntityIOSDFHandler::ParseAndAddHeader(const String& line, int line_num,
- mol::EntityHandle& ent, mol::XCSEditor& editor)
-{
- LOGN_TRACE( "line: [" << line << "]" );
- format chain_fmter("%05i_%s");
- switch(line_num)
- {
- case 1: // title line
- {
- ++chain_count_;
- String s_title=line;
- String s_chain;
- chain_fmter % chain_count_ % boost::trim_copy(s_title);
- s_chain=chain_fmter.str();
- if(s_chain.empty()) {
- String msg="Bad molecule name line %d: Line is empty";
- throw IOException(str(format(msg) % line_num));
- }
- curr_chain_=editor.InsertChain(s_chain);
- LOGN_DUMP("new chain " << s_chain);
-
- mol::ResidueKey rkey=boost::trim_copy(s_title);
- mol::ResNum rnum(++residue_count_);
- curr_residue_=editor.AppendResidue(curr_chain_, rkey, rnum);
- LOGN_DUMP("new residue " << rkey << "(" << rnum << ")");
- break;
- }
- case 2: // user information line
- break;
- case 3: // comments line
- break;
- case 4: // counts line
- {
- String s_anum=line.substr(0,3);
- try {
- atom_count_=boost::lexical_cast<int>(boost::trim_copy(s_anum));
- } catch(boost::bad_lexical_cast&) {
- String msg="Bad counts line %d: Can't convert number of atoms"
- " '%s' to integral constant.";
- throw IOException(str(format(msg) % line_num % s_anum));
- }
- String s_bnum=line.substr(3,3);
- try {
- bond_count_=boost::lexical_cast<int>(boost::trim_copy(s_bnum));
- } catch(boost::bad_lexical_cast&) {
- String msg="Bad counts line %d: Can't convert number of bonds"
- " '%s' to integral constant.";
- throw IOException(str(format(msg) % line_num % s_bnum));
- }
- break;
- }
- }
-}
-
-void EntityIOSDFHandler::ParseAndAddAtom(const String& line, int line_num,
- mol::EntityHandle& ent, bool hetatm,
- mol::XCSEditor& editor)
-{
-
- LOGN_TRACE( "line: [" << line << "]" );
-
- if(line.length()<48 || line.length()>69) {
- String msg="Bad atom line %d: Not correct number of characters on the"
- " line: %i (should be between 48 and 69)";
- throw IOException(str(format(msg) % line_num % line.length()));
- }
- int anum = line_num-4; // start at 1 on fifth line since first four lines are header
- String s_posx=line.substr(0,10);
- String s_posy=line.substr(10,10);
- String s_posz=line.substr(20,10);
- String s_ele=line.substr(31,3);
- String s_charge=line.substr(36,3);
-
- geom::Vec3 apos;
- try {
- apos=geom::Vec3(boost::lexical_cast<Real>(boost::trim_copy(s_posx)),
- boost::lexical_cast<Real>(boost::trim_copy(s_posy)),
- boost::lexical_cast<Real>(boost::trim_copy(s_posz)));
- } catch(boost::bad_lexical_cast&) {
- String msg="Bad atom line %d: Can't convert coordinates to "
- "floating point numbers";
- throw IOException(str(format(msg) % line_num));
- }
-
- String ele=boost::trim_copy(s_ele);
- String aname=boost::lexical_cast<String>(anum);
-
- mol::AtomProp aprop;
- aprop.element=ele;
- aprop.radius=conop::Conopology::Instance().GetDefaultAtomRadius(ele);
- aprop.mass=conop::Conopology::Instance().GetDefaultAtomMass(ele);
- aprop.is_hetatm=hetatm;
-
- try {
- aprop.charge=boost::lexical_cast<Real>(boost::trim_copy(s_charge));
- if(aprop.charge != 0) {
- aprop.charge=4-aprop.charge;
- } //4-sdf_charge=real_charge if not 0
- } catch(boost::bad_lexical_cast&) {
- String msg="Bad atom line %d: Can't convert charge"
- " '%s' to integral constant.";
- throw IOException(str(format(msg) % line_num % s_charge));
- }
-
- LOGN_DUMP("adding atom " << aname << " (" << s_ele << ") @" << apos);
-
- editor.InsertAtom(curr_residue_, aname,apos,aprop);
-}
-
-
-void EntityIOSDFHandler::ParseAndAddBond(const String& line, int line_num,
- mol::EntityHandle& ent, mol::XCSEditor& editor)
-{
-
- LOGN_TRACE( "line: [" << line << "]" );
-
- if(line.length()<18 || line.length()>21) {
- String msg="Bad bond line %d: Not correct number of characters on the"
- " line: %i (should be between 18 and 21)";
- throw IOException(str(format(msg) % line_num % line.length()));
- }
-
- String s_first_name=line.substr(0,3);
- String s_second_name=line.substr(3,3);
- String s_type=line.substr(6,3);
- String first_name, second_name;
- unsigned char type;
- mol::BondHandle bond;
-
- first_name=boost::trim_copy(s_first_name);
- second_name=boost::trim_copy(s_second_name);
-
- try {
- type=boost::lexical_cast<int>(boost::trim_copy(s_type));
- } catch(boost::bad_lexical_cast&) {
- String msg="Bad bond line %d: Can't convert bond type number"
- " '%s' to integral constant.";
- throw IOException(str(format(msg) % line_num % s_type));
- }
-
- mol::AtomHandle first,second;
-
- first = ent.FindAtom(curr_chain_.GetName(), mol::ResNum(residue_count_), first_name);
- second = ent.FindAtom(curr_chain_.GetName(), mol::ResNum(residue_count_), second_name);
-
- if(first.IsValid() && second.IsValid()) {
- bond = editor.Connect(first, second);
- bond.SetBondOrder(type);
- } else {
- String msg="Bad bond line %d: Can't find the atom names '%s', '%s'"
- " in entity.";
- throw IOException(str(format(msg) % line_num % first % second));
- }
-
- LOGN_DUMP("adding bond " << s_first_name << " " << s_second_name << " (" << s_type << ") ");
-}
-
-namespace {
-
- using boost::format;
-
- class SDFAtomWriter : public mol::EntityVisitor {
- public:
- SDFAtomWriter(std::ostream& ostream, std::map<long, int>& atom_indices)
- : ostr_(ostream), atom_indices_(atom_indices), counter_(0) {
- atom_indices_.clear();
- }
- private:
- public:
- virtual bool VisitAtom(const mol::AtomHandle& atom) {
- atom_indices_[atom.GetHashCode()] = ++counter_;
- ostr_ << format("%10.4f") % atom.GetPos()[0]
- << format("%10.4f") % atom.GetPos()[1]
- << format("%10.4f ") % atom.GetPos()[2]
- << format("%-3s") % atom.GetElement()
- << " 0 0 0 0 0 0"
- << std::endl;
- return true;
- }
- private:
- std::ostream& ostr_;
- std::map<long, int>& atom_indices_;
- int counter_;
- };
-
- class SDFBondWriter : public mol::EntityVisitor {
- public:
- SDFBondWriter(std::ostream& ostream, std::map<long, int>& atom_indices)
- : ostr_(ostream), atom_indices_(atom_indices), counter_(0) {
- }
- private:
- public:
- virtual bool VisitAtom(const mol::AtomHandle& atom) {
- counter_++;
- mol::AtomHandleList atoms = atom.GetBondPartners();
- mol::AtomHandleList::iterator atom_iter = atoms.begin();
- for(; atom_iter != atoms.end(); ++atom_iter) {
- int atom_index = atom_indices_.find((*atom_iter).GetHashCode())->second;
- if(atom_index > counter_) {
- int type = 1;
- mol::BondHandle bond = atom.FindBondToAtom(*atom_iter);
- if(bond.IsValid()) type = bond.GetBondOrder();
- ostr_ << format("%3i") % counter_
- << format("%3i") % atom_index
- << format("%3i") % type
- << " 0 0 0"
- << std::endl;
- }
- }
- return true;
- }
-
- private:
- std::ostream& ostr_;
- std::map<long, int>& atom_indices_;
- int counter_;
- };
-
- class SDFWriter : public mol::EntityVisitor {
- public:
- SDFWriter(std::ostream& ostream)
- : ostr_(ostream), counter_(0) {
- }
- private:
- public:
- virtual bool VisitChain(const mol::ChainHandle& chain) {
- // print end of molecule line
- if(counter_ != 0) {
- ostr_ << "$$$$" << std::endl;
- counter_ = 0;
- atom_indices_.clear();
- }
- // print header lines
- ostr_ << chain.GetName() << std::endl;
- ostr_ << std::endl;
- ostr_ << std::endl;
-
- // print counts line
- ostr_ << format("%3d") % chain.GetAtomCount()
- << format("%3d") % chain.GetBondCount()
- << " 0 0 0 0 0 0 0 0999 V2000"
- << std::endl;
-
- // write atom block
- SDFAtomWriter atom_writer(ostr_, atom_indices_);
- mol::ChainHandle non_const_chain = chain;
- non_const_chain.Apply(atom_writer);
-
- // write bond block
- SDFBondWriter bond_writer(ostr_, atom_indices_);
- non_const_chain.Apply(bond_writer);
-
- // write property block
- //TODO: wirte property block
- ostr_ << "M END" << std::endl;
-
- // write data block
- std::map<String,GenericPropValue> prop_map = non_const_chain.GetPropMap();
- std::map<String,GenericPropValue>::iterator iter;
- for(iter = prop_map.begin(); iter != prop_map.end(); ++iter) {
- ostr_ << "> <" << (*iter).first << ">" << std::endl;
- ostr_ << (*iter).second << std::endl;
- ostr_ << std::endl;
- }
-
- // write molecule endline
- ostr_ << "$$$$" << std::endl;
-
- return true;
- }
-
-
-
- private:
- std::ostream& ostr_;
- int counter_;
- std::map<long,int> atom_indices_;
- };
-
+ SDFReader reader(loc);
+ reader.Import(ent);
}
void EntityIOSDFHandler::Export(const mol::EntityView& ent,
const boost::filesystem::path& loc) const {
- boost::filesystem::ofstream outfile(loc);
- if(!outfile) throw IOException("could not open "+loc.string()+" for writing");
- this->Export(ent, outfile);
+ SDFWriter writer(loc);
+ writer.Write(ent);
}
-// export data from entity view to provided stream
void EntityIOSDFHandler::Export(const mol::EntityView& ent,
std::ostream& outstream) const
{
- SDFWriter writer(outstream);
- mol::EntityView non_const_view = ent;
- non_const_view.Apply(writer);
+ SDFWriter writer(outstream);
+ writer.Write(ent);
}
namespace {
@@ -436,16 +94,12 @@ bool EntityIOSDFHandler::ProvidesExport(const boost::filesystem::path& loc,
return sdf_handler_is_responsible_for(loc, type);
}
-
-
mol::EntityHandle LoadSDF(const String& file_name) {
mol::EntityHandle ent_handle=mol::CreateEntity();
EntityIOSDFHandler ent_io;
ent_io.Import(ent_handle,file_name);
- LOG_DUMP("running conopology" << std::endl);
-
return ent_handle;
}
diff --git a/modules/io/src/mol/entity_io_sdf_handler.hh b/modules/io/src/mol/entity_io_sdf_handler.hh
index 1baa629d4..cebf2fa5e 100644
--- a/modules/io/src/mol/entity_io_sdf_handler.hh
+++ b/modules/io/src/mol/entity_io_sdf_handler.hh
@@ -20,7 +20,6 @@
#define OST_IO_ENTITY_IO_PLUGIN_SDF_H
#include <ost/io/mol/entity_io_handler.hh>
-#include <ost//mol/xcs_editor.hh>
namespace ost { namespace io {
@@ -45,29 +44,6 @@ public:
static String GetFormatName() { return String("Sdf"); }
static String GetFormatDescription() { return String("Structure-data format from Molecular Design Limited"); }
-
-private:
- void ClearState();
-
- void NextMolecule();
-
- void ParseAndAddHeader(const String& line, int line_num, mol::EntityHandle& ent,
- mol::XCSEditor& editor);
-
- void ParseAndAddAtom(const String& line, int line_num, mol::EntityHandle& ent,
- bool hetatm, mol::XCSEditor& editor);
-
- void ParseAndAddBond(const String& line, int line_num, mol::EntityHandle& ent,
- mol::XCSEditor& editor);
-
- mol::ChainHandle curr_chain_;
- mol::ResidueHandle curr_residue_;
- int chain_count_;
- int residue_count_;
- int atom_count_;
- int bond_count_;
- int line_num;
-
};
typedef EntityIOHandlerFactory<EntityIOSDFHandler> EntityIOSDFHandlerFactory;
diff --git a/modules/io/src/mol/sdf_reader.cc b/modules/io/src/mol/sdf_reader.cc
new file mode 100644
index 000000000..e2f0fabd2
--- /dev/null
+++ b/modules/io/src/mol/sdf_reader.cc
@@ -0,0 +1,275 @@
+//------------------------------------------------------------------------------
+// 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: Tobias Schmidt
+ */
+
+#include <boost/algorithm/string.hpp>
+#include <boost/format.hpp>
+#include <boost/lexical_cast.hpp>
+
+#include <ost/conop/conop.hh>
+#include <ost/io/io_exception.hh>
+#include <ost/log.hh>
+#include <ost/mol/xcs_editor.hh>
+
+#include "sdf_reader.hh"
+
+namespace ost { namespace io {
+
+using boost::format;
+
+SDFReader::SDFReader(const String& filename)
+ : infile_(filename), instream_(infile_) {
+ this->ClearState();
+}
+
+SDFReader::SDFReader(const boost::filesystem::path& loc)
+ : infile_(loc), instream_(infile_) {
+ this->ClearState();
+}
+
+SDFReader::SDFReader(std::istream& instream)
+ : infile_(), instream_(instream) {
+ this->ClearState();
+}
+
+// import data from provided stream
+void SDFReader::Import(mol::EntityHandle& ent)
+{
+ String line;
+ mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
+ while (std::getline(instream_,line)) {
+ ++line_num;
+
+ if (line_num<=4) {
+ ParseAndAddHeader(line, line_num, ent, editor);
+ } else if (line_num<=atom_count_+4) {
+ ParseAndAddAtom(line, line_num, ent, true, editor);
+ } else if (line_num<=bond_count_+atom_count_+4) {
+ ParseAndAddBond(line, line_num, ent, editor);
+ } else if (boost::iequals(line.substr(0,2), "> ")) {
+ // parse data items
+ int data_header_start = line.find('<');
+ if(data_header_start==-1) {
+ String msg="Bad data line %d: Could not find start or end of header";
+ throw IOException(str(format(msg) % line_num));
+ }
+ String data_header = line.substr(data_header_start+1,line.rfind('>')-data_header_start-1);
+ if(data_header.empty()) {
+ String msg="Bad data line %d: Could not find data header";
+ throw IOException(str(format(msg) % line_num));
+ }
+ String data_value="";
+ while(std::getline(instream_,line) && !boost::iequals(line, "")) {
+ data_value.append(line);
+ }
+ curr_chain_.SetStringProp(data_header, data_value);
+ } else if (boost::iequals(line, "$$$$")) {
+ LOGN_MESSAGE("MOLECULE " << curr_chain_.GetName() << " (" << chain_count_ << ") added.")
+ NextMolecule();
+ }
+ }
+
+ LOGN_MESSAGE("imported " << chain_count_ << " chains, " << residue_count_
+ << " residues, " << atom_count_ << " atoms");
+}
+
+void SDFReader::ClearState()
+{
+ curr_chain_=mol::ChainHandle();
+ curr_residue_=mol::ResidueHandle();
+ chain_count_=0;
+ residue_count_=0;
+ atom_count_=0;
+ bond_count_=0;
+ line_num=0;
+}
+
+void SDFReader::NextMolecule()
+{
+ residue_count_=0;
+ atom_count_=0;
+ bond_count_=0;
+ line_num=0;
+}
+
+void SDFReader::ParseAndAddHeader(const String& line, int line_num,
+ mol::EntityHandle& ent, mol::XCSEditor& editor)
+{
+ LOGN_TRACE( "line: [" << line << "]" );
+ format chain_fmter("%05i_%s");
+ switch(line_num)
+ {
+ case 1: // title line
+ {
+ ++chain_count_;
+ String s_title=line;
+ String s_chain;
+ chain_fmter % chain_count_ % boost::trim_copy(s_title);
+ s_chain=chain_fmter.str();
+ if(s_chain.empty()) {
+ String msg="Bad molecule name line %d: Line is empty";
+ throw IOException(str(format(msg) % line_num));
+ }
+ curr_chain_=editor.InsertChain(s_chain);
+ LOGN_DUMP("new chain " << s_chain);
+
+ mol::ResidueKey rkey=boost::trim_copy(s_title);
+ mol::ResNum rnum(++residue_count_);
+ curr_residue_=editor.AppendResidue(curr_chain_, rkey, rnum);
+ LOGN_DUMP("new residue " << rkey << "(" << rnum << ")");
+ break;
+ }
+ case 2: // user information line
+ break;
+ case 3: // comments line
+ break;
+ case 4: // counts line
+ {
+ String s_anum=line.substr(0,3);
+ try {
+ atom_count_=boost::lexical_cast<int>(boost::trim_copy(s_anum));
+ } catch(boost::bad_lexical_cast&) {
+ String msg="Bad counts line %d: Can't convert number of atoms"
+ " '%s' to integral constant.";
+ throw IOException(str(format(msg) % line_num % s_anum));
+ }
+ String s_bnum=line.substr(3,3);
+ try {
+ bond_count_=boost::lexical_cast<int>(boost::trim_copy(s_bnum));
+ } catch(boost::bad_lexical_cast&) {
+ String msg="Bad counts line %d: Can't convert number of bonds"
+ " '%s' to integral constant.";
+ throw IOException(str(format(msg) % line_num % s_bnum));
+ }
+ break;
+ }
+ }
+}
+
+void SDFReader::ParseAndAddAtom(const String& line, int line_num,
+ mol::EntityHandle& ent, bool hetatm,
+ mol::XCSEditor& editor)
+{
+
+ LOGN_TRACE( "line: [" << line << "]" );
+
+ if(line.length()<48 || line.length()>69) {
+ String msg="Bad atom line %d: Not correct number of characters on the"
+ " line: %i (should be between 48 and 69)";
+ throw IOException(str(format(msg) % line_num % line.length()));
+ }
+ int anum = line_num-4; // start at 1 on fifth line since first four lines are header
+ String s_posx=line.substr(0,10);
+ String s_posy=line.substr(10,10);
+ String s_posz=line.substr(20,10);
+ String s_ele=line.substr(31,3);
+ String s_charge=line.substr(36,3);
+
+ geom::Vec3 apos;
+ try {
+ apos=geom::Vec3(boost::lexical_cast<Real>(boost::trim_copy(s_posx)),
+ boost::lexical_cast<Real>(boost::trim_copy(s_posy)),
+ boost::lexical_cast<Real>(boost::trim_copy(s_posz)));
+ } catch(boost::bad_lexical_cast&) {
+ String msg="Bad atom line %d: Can't convert coordinates to "
+ "floating point numbers";
+ throw IOException(str(format(msg) % line_num));
+ }
+
+ String ele=boost::trim_copy(s_ele);
+ String aname=boost::lexical_cast<String>(anum);
+
+ mol::AtomProp aprop;
+ aprop.element=ele;
+ aprop.radius=conop::Conopology::Instance().GetDefaultAtomRadius(ele);
+ aprop.mass=conop::Conopology::Instance().GetDefaultAtomMass(ele);
+ aprop.is_hetatm=hetatm;
+
+ try {
+ aprop.charge=boost::lexical_cast<Real>(boost::trim_copy(s_charge));
+ if(aprop.charge != 0) {
+ aprop.charge=4-aprop.charge;
+ } //4-sdf_charge=real_charge if not 0
+ } catch(boost::bad_lexical_cast&) {
+ String msg="Bad atom line %d: Can't convert charge"
+ " '%s' to integral constant.";
+ throw IOException(str(format(msg) % line_num % s_charge));
+ }
+
+ LOGN_DUMP("adding atom " << aname << " (" << s_ele << ") @" << apos);
+
+ editor.InsertAtom(curr_residue_, aname,apos,aprop);
+}
+
+
+void SDFReader::ParseAndAddBond(const String& line, int line_num,
+ mol::EntityHandle& ent, mol::XCSEditor& editor)
+{
+
+ LOGN_TRACE( "line: [" << line << "]" );
+
+ if(line.length()<18 || line.length()>21) {
+ String msg="Bad bond line %d: Not correct number of characters on the"
+ " line: %i (should be between 18 and 21)";
+ throw IOException(str(format(msg) % line_num % line.length()));
+ }
+
+ String s_first_name=line.substr(0,3);
+ String s_second_name=line.substr(3,3);
+ String s_type=line.substr(6,3);
+ String first_name, second_name;
+ unsigned char type;
+ mol::BondHandle bond;
+
+ first_name=boost::trim_copy(s_first_name);
+ second_name=boost::trim_copy(s_second_name);
+
+ try {
+ type=boost::lexical_cast<int>(boost::trim_copy(s_type));
+ if (type<1 || type>8) {
+ String msg="Bad bond line %d: Bond type number"
+ " '%s' not within accepted range (1-8).";
+ throw IOException(str(format(msg) % line_num % s_type));
+ }
+ } catch(boost::bad_lexical_cast&) {
+ String msg="Bad bond line %d: Can't convert bond type number"
+ " '%s' to integral constant.";
+ throw IOException(str(format(msg) % line_num % s_type));
+ }
+
+ mol::AtomHandle first,second;
+
+ first = ent.FindAtom(curr_chain_.GetName(), mol::ResNum(residue_count_), first_name);
+ second = ent.FindAtom(curr_chain_.GetName(), mol::ResNum(residue_count_), second_name);
+
+ if(first.IsValid() && second.IsValid()) {
+ bond = editor.Connect(first, second);
+ bond.SetBondOrder(type);
+ } else {
+ String msg="Bad bond line %d: Can't find the atom names '%s', '%s'"
+ " in entity.";
+ throw IOException(str(format(msg) % line_num % first % second));
+ }
+
+ LOGN_DUMP("adding bond " << s_first_name << " " << s_second_name << " (" << s_type << ") ");
+}
+
+}}
diff --git a/modules/io/src/mol/sdf_reader.hh b/modules/io/src/mol/sdf_reader.hh
new file mode 100644
index 000000000..0401e6ab7
--- /dev/null
+++ b/modules/io/src/mol/sdf_reader.hh
@@ -0,0 +1,67 @@
+//------------------------------------------------------------------------------
+// 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: Tobias Schmidt
+ */
+#ifndef OST_IO_SDF_READER_HH
+#define OST_IO_SDF_READER_HH
+
+#include <boost/filesystem/fstream.hpp>
+#include <ost/mol/mol.hh>
+#include <ost/io/module_config.hh>
+
+namespace ost { namespace io {
+
+class DLLEXPORT_OST_IO SDFReader {
+public:
+ SDFReader(const String& filename);
+ SDFReader(const boost::filesystem::path& loc);
+ SDFReader(std::istream& instream);
+
+ bool HasNext();
+
+ void Import(mol::EntityHandle& ent);
+
+private:
+ void ClearState();
+ void NextMolecule();
+
+ void ParseAndAddHeader(const String& line, int line_num, mol::EntityHandle& ent,
+ mol::XCSEditor& editor);
+
+ void ParseAndAddAtom(const String& line, int line_num, mol::EntityHandle& ent,
+ bool hetatm, mol::XCSEditor& editor);
+
+ void ParseAndAddBond(const String& line, int line_num, mol::EntityHandle& ent,
+ mol::XCSEditor& editor);
+
+ mol::ChainHandle curr_chain_;
+ mol::ResidueHandle curr_residue_;
+ int chain_count_;
+ int residue_count_;
+ int atom_count_;
+ int bond_count_;
+ int line_num;
+ boost::filesystem::ifstream infile_;
+ std::istream& instream_;
+};
+
+}}
+
+#endif
diff --git a/modules/io/src/mol/sdf_writer.cc b/modules/io/src/mol/sdf_writer.cc
new file mode 100644
index 000000000..b6243b4a6
--- /dev/null
+++ b/modules/io/src/mol/sdf_writer.cc
@@ -0,0 +1,158 @@
+//------------------------------------------------------------------------------
+// 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: Tobias Schmidt
+ */
+
+#include "sdf_writer.hh"
+
+namespace ost { namespace io {
+
+using boost::format;
+
+namespace {
+
+ class SDFAtomWriter : public mol::EntityVisitor {
+ public:
+ SDFAtomWriter(std::ostream& ostream, std::map<long, int>& atom_indices)
+ : ostr_(ostream), atom_indices_(atom_indices), counter_(0) {
+ atom_indices_.clear();
+ }
+ private:
+ public:
+ virtual bool VisitAtom(const mol::AtomHandle& atom) {
+ atom_indices_[atom.GetHashCode()] = ++counter_;
+ ostr_ << format("%10.4f") % atom.GetPos()[0]
+ << format("%10.4f") % atom.GetPos()[1]
+ << format("%10.4f ") % atom.GetPos()[2]
+ << format("%-3s") % atom.GetElement()
+ << " 0 0 0 0 0 0"
+ << std::endl;
+ return true;
+ }
+ private:
+ std::ostream& ostr_;
+ std::map<long, int>& atom_indices_;
+ int counter_;
+ };
+
+ class SDFBondWriter : public mol::EntityVisitor {
+ public:
+ SDFBondWriter(std::ostream& ostream, std::map<long, int>& atom_indices)
+ : ostr_(ostream), atom_indices_(atom_indices), counter_(0) {
+ }
+ private:
+ public:
+ virtual bool VisitAtom(const mol::AtomHandle& atom) {
+ counter_++;
+ mol::AtomHandleList atoms = atom.GetBondPartners();
+ mol::AtomHandleList::iterator atom_iter = atoms.begin();
+ for(; atom_iter != atoms.end(); ++atom_iter) {
+ int atom_index = atom_indices_.find((*atom_iter).GetHashCode())->second;
+ if(atom_index > counter_) {
+ int type = 1;
+ mol::BondHandle bond = atom.FindBondToAtom(*atom_iter);
+ if(bond.IsValid()) type = bond.GetBondOrder();
+ ostr_ << format("%3i") % counter_
+ << format("%3i") % atom_index
+ << format("%3i") % type
+ << " 0 0 0"
+ << std::endl;
+ }
+ }
+ return true;
+ }
+
+ private:
+ std::ostream& ostr_;
+ std::map<long, int>& atom_indices_;
+ int counter_;
+ };
+}
+
+SDFWriter::SDFWriter(std::ostream& ostream)
+ : outfile_(), ostr_(ostream), counter_(0) {
+}
+
+SDFWriter::SDFWriter(const String& filename)
+ : outfile_(filename.c_str()), ostr_(outfile_), counter_(0) {
+}
+
+SDFWriter::SDFWriter(const boost::filesystem::path& filename)
+ : outfile_(filename.file_string().c_str()), ostr_(outfile_), counter_(0) {
+}
+
+void SDFWriter::Write(const mol::EntityView& ent) {
+ mol::EntityView non_const_view = ent;
+ non_const_view.Apply(*this);
+}
+
+void SDFWriter::Write(const mol::EntityHandle& ent) {
+ mol::EntityHandle non_const_handle = ent;
+ non_const_handle.Apply(*this);
+}
+
+bool SDFWriter::VisitChain(const mol::ChainHandle& chain) {
+ // print end of molecule line
+ if(counter_ != 0) {
+ ostr_ << "$$$$" << std::endl;
+ counter_ = 0;
+ atom_indices_.clear();
+ }
+
+ // print header lines
+ ostr_ << chain.GetName().substr(6) << std::endl;
+ ostr_ << std::endl;
+ ostr_ << std::endl;
+
+ // print counts line
+ ostr_ << format("%3d") % chain.GetAtomCount()
+ << format("%3d") % chain.GetBondCount()
+ << " 0 0 0 0 999 V2000"
+ << std::endl;
+
+ // write atom block
+ SDFAtomWriter atom_writer(ostr_, atom_indices_);
+ mol::ChainHandle non_const_chain = chain;
+ non_const_chain.Apply(atom_writer);
+
+ // write bond block
+ SDFBondWriter bond_writer(ostr_, atom_indices_);
+ non_const_chain.Apply(bond_writer);
+
+ // write property block
+ //TODO: write property block
+ ostr_ << "M END" << std::endl;
+
+ // write data block
+ std::map<String,GenericPropValue> prop_map = non_const_chain.GetPropMap();
+ std::map<String,GenericPropValue>::iterator iter;
+ for(iter = prop_map.begin(); iter != prop_map.end(); ++iter) {
+ ostr_ << "> <" << (*iter).first << ">" << std::endl;
+ ostr_ << (*iter).second << std::endl;
+ ostr_ << std::endl;
+ }
+
+ // write molecule endline
+ ostr_ << "$$$$" << std::endl;
+
+ return true;
+}
+
+}}
diff --git a/modules/io/src/mol/sdf_writer.hh b/modules/io/src/mol/sdf_writer.hh
new file mode 100644
index 000000000..62a365d49
--- /dev/null
+++ b/modules/io/src/mol/sdf_writer.hh
@@ -0,0 +1,61 @@
+//------------------------------------------------------------------------------
+// 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: Tobias Schmidt
+ */
+#ifndef OST_IO_SDF_WRITER_HH
+#define OST_IO_SDF_WRITER_HH
+
+#include <iostream>
+#include <sstream>
+#include <iomanip>
+
+#include <boost/filesystem/fstream.hpp>
+#include <boost/filesystem/convenience.hpp>
+#include <boost/algorithm/string.hpp>
+#include <boost/lexical_cast.hpp>
+#include <boost/format.hpp>
+#include <ost/log.hh>
+#include <ost/conop/conop.hh>
+#include <ost/io/io_exception.hh>
+#include <ost/mol/mol.hh>
+
+namespace ost { namespace io {
+
+class DLLEXPORT_OST_IO SDFWriter : public mol::EntityVisitor {
+public:
+ SDFWriter(std::ostream& ostream);
+ SDFWriter(const String& filename);
+ SDFWriter(const boost::filesystem::path& filename);
+
+ void Write(const mol::EntityView& ent);
+ void Write(const mol::EntityHandle& ent);
+
+private:
+ virtual bool VisitChain(const mol::ChainHandle& chain);
+
+ std::ofstream outfile_;
+ std::ostream& ostr_;
+ int counter_;
+ std::map<long,int> atom_indices_;
+};
+
+}}
+
+#endif
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 9be98cdba..54d7d49a9 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -16,6 +16,7 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
+#include <ost/test_utils/compare_files.hh>
#include <ost/mol/mol.hh>
#include <ost/conop/conop.hh>
#include <ost/io/mol/entity_io_pdb_handler.hh>
@@ -29,36 +30,6 @@ using boost::unit_test_framework::test_suite;
using namespace ost;
using namespace ost::io;
-
-bool compare_files(const String& test, const String& gold_standard)
-{
- std::ifstream test_stream(test.c_str());
- std::ifstream gold_stream(gold_standard.c_str());
- String test_line, gold_line;
- while (true) {
- bool test_end=std::getline(test_stream, test_line);
- bool gold_end=std::getline(gold_stream, gold_line);
- if (!(test_end || gold_end)) {
- return true;
- }
- if (!test_end) {
- std::cerr << gold_standard << " contains additional line(s):"
- << std::endl << gold_line;
- return false;
- }
- if (!gold_end) {
- std::cerr << test << " contains additional line(s):"
- << std::endl << test_line;
- return false;
- }
- if (gold_line!=test_line) {
- std::cerr << "line mismatch:" << std::endl << "test: " << test_line
- << std::endl << "gold: " << gold_line;
- return false;
- }
- }
- return true;
-}
BOOST_AUTO_TEST_SUITE( io )
diff --git a/modules/io/tests/test_io_sdf.cc b/modules/io/tests/test_io_sdf.cc
index 71c773f39..19cdf7f49 100644
--- a/modules/io/tests/test_io_sdf.cc
+++ b/modules/io/tests/test_io_sdf.cc
@@ -16,33 +16,110 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
+#include <ost/test_utils/compare_files.hh>
#include <ost/mol/mol.hh>
#include <ost/io/mol/entity_io_sdf_handler.hh>
+#include <ost/io/save_entity.hh>
+#include <ost/io/io_exception.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
#include <boost/lexical_cast.hpp>
#include <boost/algorithm/string.hpp>
+using boost::unit_test_framework::test_suite;
using namespace ost;
using namespace ost::io;
BOOST_AUTO_TEST_SUITE( io )
-
-BOOST_AUTO_TEST_CASE(test_io_sdf)
+BOOST_AUTO_TEST_CASE(test_sdf_import_handler)
{
- const String fname("testfiles/test_in.sdf");
+ String fname("testfiles/sdf/compound.sdf");
mol::EntityHandle eh=mol::CreateEntity();
EntityIOSDFHandler sdfh;
- // check format
BOOST_CHECK(EntityIOSDFHandler::ProvidesImport("","sdf"));
BOOST_CHECK(EntityIOSDFHandler::ProvidesImport(fname));
BOOST_CHECK(EntityIOSDFHandler::ProvidesImport("test_in.SDF"));
+ BOOST_CHECK(EntityIOSDFHandler::ProvidesExport("","sdf"));
+ BOOST_CHECK(EntityIOSDFHandler::ProvidesExport(fname));
+ BOOST_CHECK(EntityIOSDFHandler::ProvidesExport("test_in.SDF"));
+
+ sdfh.Import(eh,"testfiles/sdf/compound.sdf");
+}
+
+BOOST_AUTO_TEST_CASE(simple_sdf)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+ sdfh.Import(eh,"testfiles/sdf/simple.sdf");
+
+ // check compounds/atoms/bonds count
+ BOOST_CHECK_EQUAL(eh.GetChainCount(), 1);
+ BOOST_CHECK_EQUAL(eh.GetAtomCount(), 6);
+ BOOST_CHECK_EQUAL(eh.GetBondCount(), 6);
+ BOOST_CHECK_CLOSE(eh.GetMass(), 121.545502, 1e-4);
+
+ // check atom/bond types
+ mol::AtomHandle ah=eh.GetAtomList()[0];
+ mol::AtomHandle ah2=eh.GetAtomList()[5];
+
+ BOOST_CHECK_EQUAL(ah.GetElement(), "N");
+ BOOST_CHECK_EQUAL(ah2.GetElement(), "Cl");
+ BOOST_CHECK_CLOSE(ah.GetRadius(), 1.55, 1e-2);
+ BOOST_CHECK_CLOSE(ah2.GetRadius(), 1.75, 1e-2);
+ BOOST_CHECK_CLOSE(ah.GetMass(), 14.0067, 1e-4);
+ BOOST_CHECK_CLOSE(ah2.GetMass(), 35.453, 1e-3);
+ BOOST_CHECK_EQUAL(ah.GetBondCount(), 3);
+ BOOST_CHECK_EQUAL(ah2.GetBondCount(), 1);
+ BOOST_CHECK_EQUAL(ah.GetCharge(), 1);
+ BOOST_CHECK_EQUAL(ah2.GetCharge(), 0);
+
+ mol::BondHandle bh=ah.GetBondList()[0];
+ BOOST_CHECK_EQUAL(bh.GetBondOrder(), 2);
+}
+
+BOOST_AUTO_TEST_CASE(multiple_sdf)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+ sdfh.Import(eh,"testfiles/sdf/multiple.sdf");
+
+ // check number of compounds
+ BOOST_CHECK_EQUAL(eh.GetChainCount(), 4);
+}
+
+BOOST_AUTO_TEST_CASE(properties_sdf)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+ sdfh.Import(eh,"testfiles/sdf/properties.sdf");
+
+ // check number of compounds
+ mol::ChainHandleList chl=eh.GetChainList();
+ int count=1;
+ for (mol::ChainHandleList::iterator i=chl.begin();i!=chl.end();++i,count++)
+ {
+ BOOST_REQUIRE(i->HasProp("prop_one"));
+ BOOST_REQUIRE(i->HasProp("prop_two"));
+ BOOST_CHECK_EQUAL(i->GetStringProp("prop_one"),
+ boost::lexical_cast<std::string>(count));
+ BOOST_CHECK_EQUAL(i->GetStringProp("prop_two"),
+ boost::lexical_cast<std::string>(count*(-2)));
+ }
+}
+
+BOOST_AUTO_TEST_CASE(read_sdf)
+{
+ const String fname("testfiles/sdf/compound.sdf");
+
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+
// check import
- sdfh.Import(eh,"testfiles/test_in.sdf");
+ sdfh.Import(eh,"testfiles/sdf/compound.sdf");
// check atoms/bonds
BOOST_CHECK_EQUAL(eh.GetChainCount(), 4);
@@ -50,7 +127,7 @@ BOOST_AUTO_TEST_CASE(test_io_sdf)
BOOST_CHECK_EQUAL(eh.GetBondCount(), 188);
// check molecule name
- mol::ChainHandle ch=eh.FindChain("00003_Displayed atoms");
+ mol::ChainHandle ch=eh.FindChain("00003_Test Ligand");
BOOST_CHECK(ch.IsValid());
// check properties
@@ -60,4 +137,97 @@ BOOST_AUTO_TEST_CASE(test_io_sdf)
0.543804f);
}
+BOOST_AUTO_TEST_CASE(write_sdf)
+{
+ // this scope is required to force the writer stream to be closed before
+ // opening the file again in compare_files. Avoids a race condition.
+ {
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+ sdfh.Import(eh,"testfiles/sdf/compound.sdf");
+ SaveEntity(eh, "testfiles/sdf/compound-out.sdf");
+ }
+ BOOST_CHECK(compare_files("testfiles/sdf/compound.sdf",
+ "testfiles/sdf/compound-out.sdf"));
+}
+
+BOOST_AUTO_TEST_CASE(wrong_atomcount_error_sdf)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+ BOOST_CHECK_THROW(sdfh.Import(eh,"testfiles/sdf/wrong_atomcount.sdf"), IOException);
+}
+
+BOOST_AUTO_TEST_CASE(wrong_bondcount_error_sdf)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+ BOOST_CHECK_THROW(sdfh.Import(eh,"testfiles/sdf/wrong_bondcount.sdf"), IOException);
+}
+
+BOOST_AUTO_TEST_CASE(wrong_atomlinelength_error_sdf)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+
+ BOOST_CHECK_THROW(sdfh.Import(eh,"testfiles/sdf/wrong_atomlinelength.sdf"), IOException);
+}
+
+BOOST_AUTO_TEST_CASE(wrong_atompos_error_sdf)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+
+ BOOST_CHECK_THROW(sdfh.Import(eh,"testfiles/sdf/wrong_atompos.sdf"), IOException);
+}
+
+BOOST_AUTO_TEST_CASE(wrong_charge_error_sdf)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+
+ BOOST_CHECK_THROW(sdfh.Import(eh,"testfiles/sdf/wrong_charge.sdf"), IOException);
+}
+
+BOOST_AUTO_TEST_CASE(wrong_bondlinelength_error_sdf)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+
+ BOOST_CHECK_THROW(sdfh.Import(eh,"testfiles/sdf/wrong_bondlinelength.sdf"), IOException);
+}
+
+BOOST_AUTO_TEST_CASE(wrong_bondtype_error_sdf)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+
+ BOOST_CHECK_THROW(sdfh.Import(eh,"testfiles/sdf/wrong_bondtype.sdf"), IOException);
+}
+
+BOOST_AUTO_TEST_CASE(wrong_bondatomnumber_error_sdf)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+
+ BOOST_CHECK_THROW(sdfh.Import(eh,"testfiles/sdf/wrong_bondatomnumber.sdf"), IOException);
+}
+
+BOOST_AUTO_TEST_CASE(wrong_dataheader_error_sdf)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+
+ BOOST_CHECK_THROW(sdfh.Import(eh,"testfiles/sdf/wrong_dataheader.sdf"), IOException);
+}
+
+BOOST_AUTO_TEST_CASE(empty_dataheader_error_sdf)
+{
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+
+ BOOST_CHECK_THROW(sdfh.Import(eh,"testfiles/sdf/empty_dataheader.sdf"), IOException);
+}
+
+
BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/io/tests/testfiles/test_in.sdf b/modules/io/tests/testfiles/sdf/compound.sdf
similarity index 97%
rename from modules/io/tests/testfiles/test_in.sdf
rename to modules/io/tests/testfiles/sdf/compound.sdf
index 9d7bdcfc1..66ddbb589 100644
--- a/modules/io/tests/testfiles/test_in.sdf
+++ b/modules/io/tests/testfiles/sdf/compound.sdf
@@ -1,7 +1,7 @@
-Displayed atoms
- 3D
- Structure written by MMmdl.
- 45 47 0 0 1 0 999 V2000
+Test Ligand
+
+
+ 45 47 0 0 0 0 999 V2000
35.9455 5.9021 22.1706 C 0 0 0 0 0 0
34.6074 5.5226 22.4445 O 0 0 0 0 0 0
33.9561 6.2475 23.4088 C 0 0 0 0 0 0
@@ -95,32 +95,29 @@ Displayed atoms
26 27 1 0 0 0
27 45 1 0 0 0
M END
+> <i_i_glide_confnum>
+2
+
> <i_i_glide_lignum>
1
-> <r_i_docking_score>
--8.84426
+> <i_i_glide_posenum>
+352
-> <r_i_glide_gscore>
+> <r_i_docking_score>
-8.84426
-> <r_i_glide_lipo>
--2.84534
-
-> <r_i_glide_hbond>
--0.960751
-
-> <r_i_glide_metal>
--0
+> <r_i_glide_ecoul>
+-16.1644
-> <r_i_glide_rewards>
--0.799851
+> <r_i_glide_einternal>
+6.78671
-> <r_i_glide_evdw>
--46.0502
+> <r_i_glide_emodel>
+-96.9661
-> <r_i_glide_ecoul>
--16.1644
+> <r_i_glide_energy>
+-62.2146
> <r_i_glide_erotb>
0.517993
@@ -128,38 +125,41 @@ M END
> <r_i_glide_esite>
-0.0291388
-> <r_i_glide_emodel>
--96.9661
+> <r_i_glide_evdw>
+-46.0502
-> <r_i_glide_energy>
--62.2146
+> <r_i_glide_gscore>
+-8.84426
-> <r_i_glide_einternal>
-6.78671
+> <r_i_glide_hbond>
+-0.960751
> <r_i_glide_ligand_efficiency>
-0.327565
+> <r_i_glide_ligand_efficiency_ln>
+-2.0588
+
> <r_i_glide_ligand_efficiency_sa>
-0.982695
-> <r_i_glide_ligand_efficiency_ln>
--2.0588
+> <r_i_glide_lipo>
+-2.84534
-> <i_i_glide_confnum>
-2
+> <r_i_glide_metal>
+-0
-> <i_i_glide_posenum>
-352
+> <r_i_glide_rewards>
+-0.799851
> <r_i_glide_rmsd>
0.6819
$$$$
-Displayed atoms
- 3D
- Structure written by MMmdl.
- 45 47 0 0 1 0 999 V2000
+Test Ligand
+
+
+ 45 47 0 0 0 0 999 V2000
34.3938 4.9895 21.4537 C 0 0 0 0 0 0
34.9786 5.7318 22.5298 O 0 0 0 0 0 0
34.1450 6.3862 23.4047 C 0 0 0 0 0 0
@@ -253,32 +253,29 @@ Displayed atoms
26 27 1 0 0 0
27 45 1 0 0 0
M END
+> <i_i_glide_confnum>
+14
+
> <i_i_glide_lignum>
1
-> <r_i_docking_score>
--8.79327
+> <i_i_glide_posenum>
+302
-> <r_i_glide_gscore>
+> <r_i_docking_score>
-8.79327
-> <r_i_glide_lipo>
--2.69167
-
-> <r_i_glide_hbond>
--0.966475
-
-> <r_i_glide_metal>
--0
+> <r_i_glide_ecoul>
+-16.9687
-> <r_i_glide_rewards>
--0.777126
+> <r_i_glide_einternal>
+5.76514
-> <r_i_glide_evdw>
--46.4187
+> <r_i_glide_emodel>
+-98.4298
-> <r_i_glide_ecoul>
--16.9687
+> <r_i_glide_energy>
+-63.3874
> <r_i_glide_erotb>
0.517993
@@ -286,38 +283,41 @@ M END
> <r_i_glide_esite>
-0.00975737
-> <r_i_glide_emodel>
--98.4298
+> <r_i_glide_evdw>
+-46.4187
-> <r_i_glide_energy>
--63.3874
+> <r_i_glide_gscore>
+-8.79327
-> <r_i_glide_einternal>
-5.76514
+> <r_i_glide_hbond>
+-0.966475
> <r_i_glide_ligand_efficiency>
-0.325677
+> <r_i_glide_ligand_efficiency_ln>
+-2.04693
+
> <r_i_glide_ligand_efficiency_sa>
-0.97703
-> <r_i_glide_ligand_efficiency_ln>
--2.04693
+> <r_i_glide_lipo>
+-2.69167
-> <i_i_glide_confnum>
-14
+> <r_i_glide_metal>
+-0
-> <i_i_glide_posenum>
-302
+> <r_i_glide_rewards>
+-0.777126
> <r_i_glide_rmsd>
0.605551
$$$$
-Displayed atoms
- 3D
- Structure written by MMmdl.
- 45 47 0 0 1 0 999 V2000
+Test Ligand
+
+
+ 45 47 0 0 0 0 999 V2000
36.2241 5.1749 22.8554 C 0 0 0 0 0 0
35.0609 5.8871 22.4479 O 0 0 0 0 0 0
34.2768 6.4601 23.4276 C 0 0 0 0 0 0
@@ -411,32 +411,29 @@ Displayed atoms
26 27 1 0 0 0
27 45 1 0 0 0
M END
+> <i_i_glide_confnum>
+1
+
> <i_i_glide_lignum>
1
-> <r_i_docking_score>
--8.70173
+> <i_i_glide_posenum>
+177
-> <r_i_glide_gscore>
+> <r_i_docking_score>
-8.70173
-> <r_i_glide_lipo>
--2.74283
-
-> <r_i_glide_hbond>
--0.97397
-
-> <r_i_glide_metal>
--0
+> <r_i_glide_ecoul>
+-15.8862
-> <r_i_glide_rewards>
--0.764823
+> <r_i_glide_einternal>
+1.84397
-> <r_i_glide_evdw>
--46.5538
+> <r_i_glide_emodel>
+-99.0481
-> <r_i_glide_ecoul>
--15.8862
+> <r_i_glide_energy>
+-62.44
> <r_i_glide_erotb>
0.517993
@@ -444,38 +441,41 @@ M END
> <r_i_glide_esite>
-0.0274759
-> <r_i_glide_emodel>
--99.0481
+> <r_i_glide_evdw>
+-46.5538
-> <r_i_glide_energy>
--62.44
+> <r_i_glide_gscore>
+-8.70173
-> <r_i_glide_einternal>
-1.84397
+> <r_i_glide_hbond>
+-0.97397
> <r_i_glide_ligand_efficiency>
-0.322286
+> <r_i_glide_ligand_efficiency_ln>
+-2.02562
+
> <r_i_glide_ligand_efficiency_sa>
-0.966858
-> <r_i_glide_ligand_efficiency_ln>
--2.02562
+> <r_i_glide_lipo>
+-2.74283
-> <i_i_glide_confnum>
-1
+> <r_i_glide_metal>
+-0
-> <i_i_glide_posenum>
-177
+> <r_i_glide_rewards>
+-0.764823
> <r_i_glide_rmsd>
0.543804
$$$$
-Displayed atoms
- 3D
- Structure written by MMmdl.
- 45 47 0 0 1 0 999 V2000
+Test Ligand
+
+
+ 45 47 0 0 0 0 999 V2000
36.1312 5.0238 22.8745 C 0 0 0 0 0 0
35.3492 6.1234 22.4285 O 0 0 0 0 0 0
34.5144 6.6833 23.3611 C 0 0 0 0 0 0
@@ -569,32 +569,29 @@ Displayed atoms
26 27 1 0 0 0
27 45 1 0 0 0
M END
+> <i_i_glide_confnum>
+9
+
> <i_i_glide_lignum>
1
-> <r_i_docking_score>
--8.69162
+> <i_i_glide_posenum>
+294
-> <r_i_glide_gscore>
+> <r_i_docking_score>
-8.69162
-> <r_i_glide_lipo>
--2.92829
-
-> <r_i_glide_hbond>
--0.870172
-
-> <r_i_glide_metal>
--0
+> <r_i_glide_ecoul>
+-14.7519
-> <r_i_glide_rewards>
--0.764823
+> <r_i_glide_einternal>
+5.89466
-> <r_i_glide_evdw>
--48.432
+> <r_i_glide_emodel>
+-97.7232
-> <r_i_glide_ecoul>
--14.7519
+> <r_i_glide_energy>
+-63.1839
> <r_i_glide_erotb>
0.517993
@@ -602,29 +599,32 @@ M END
> <r_i_glide_esite>
-0.0119369
-> <r_i_glide_emodel>
--97.7232
+> <r_i_glide_evdw>
+-48.432
-> <r_i_glide_energy>
--63.1839
+> <r_i_glide_gscore>
+-8.69162
-> <r_i_glide_einternal>
-5.89466
+> <r_i_glide_hbond>
+-0.870172
> <r_i_glide_ligand_efficiency>
-0.321912
+> <r_i_glide_ligand_efficiency_ln>
+-2.02327
+
> <r_i_glide_ligand_efficiency_sa>
-0.965735
-> <r_i_glide_ligand_efficiency_ln>
--2.02327
+> <r_i_glide_lipo>
+-2.92829
-> <i_i_glide_confnum>
-9
+> <r_i_glide_metal>
+-0
-> <i_i_glide_posenum>
-294
+> <r_i_glide_rewards>
+-0.764823
> <r_i_glide_rmsd>
0.463026
diff --git a/modules/io/tests/testfiles/sdf/empty_dataheader.sdf b/modules/io/tests/testfiles/sdf/empty_dataheader.sdf
new file mode 100644
index 000000000..9de4a7b63
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/empty_dataheader.sdf
@@ -0,0 +1,48 @@
+Simple Ligand 1
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+> <>
+1
+
+> <prop_two>
+-2
+
+$$$$
+Simple Ligand 2
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+> <prop_one>
+2
+
+> <prop_two>
+-4
+
+$$$$
diff --git a/modules/io/tests/testfiles/sdf/multiple.sdf b/modules/io/tests/testfiles/sdf/multiple.sdf
new file mode 100644
index 000000000..7570f2d4d
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/multiple.sdf
@@ -0,0 +1,72 @@
+Simple Ligand 1
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+$$$$
+Simple Ligand 2
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+$$$$
+Simple Ligand 3
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+$$$$
+Simple Ligand 4
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+$$$$
diff --git a/modules/io/tests/testfiles/sdf/properties.sdf b/modules/io/tests/testfiles/sdf/properties.sdf
new file mode 100644
index 000000000..edaf39129
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/properties.sdf
@@ -0,0 +1,48 @@
+Simple Ligand 1
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+> <prop_one>
+1
+
+> <prop_two>
+-2
+
+$$$$
+Simple Ligand 2
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+> <prop_one>
+2
+
+> <prop_two>
+-4
+
+$$$$
diff --git a/modules/io/tests/testfiles/sdf/simple.sdf b/modules/io/tests/testfiles/sdf/simple.sdf
new file mode 100644
index 000000000..beeb1acdd
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/simple.sdf
@@ -0,0 +1,18 @@
+Simple Ligand
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+$$$$
diff --git a/modules/io/tests/testfiles/sdf/wrong_atomcount.sdf b/modules/io/tests/testfiles/sdf/wrong_atomcount.sdf
new file mode 100644
index 000000000..ff9049fac
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/wrong_atomcount.sdf
@@ -0,0 +1,18 @@
+Simple Ligand
+
+ Teststructure
+ i 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+$$$$
diff --git a/modules/io/tests/testfiles/sdf/wrong_atomlinelength.sdf b/modules/io/tests/testfiles/sdf/wrong_atomlinelength.sdf
new file mode 100644
index 000000000..42f30f1a5
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/wrong_atomlinelength.sdf
@@ -0,0 +1,18 @@
+Simple Ligand
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+$$$$
diff --git a/modules/io/tests/testfiles/sdf/wrong_atompos.sdf b/modules/io/tests/testfiles/sdf/wrong_atompos.sdf
new file mode 100644
index 000000000..50d5268a0
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/wrong_atompos.sdf
@@ -0,0 +1,18 @@
+Simple Ligand
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+$$$$
diff --git a/modules/io/tests/testfiles/sdf/wrong_bondatomnumber.sdf b/modules/io/tests/testfiles/sdf/wrong_bondatomnumber.sdf
new file mode 100644
index 000000000..590827c4d
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/wrong_bondatomnumber.sdf
@@ -0,0 +1,18 @@
+Simple Ligand
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 8 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+$$$$
diff --git a/modules/io/tests/testfiles/sdf/wrong_bondcount.sdf b/modules/io/tests/testfiles/sdf/wrong_bondcount.sdf
new file mode 100644
index 000000000..3d6194d1b
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/wrong_bondcount.sdf
@@ -0,0 +1,18 @@
+Simple Ligand
+
+ Teststructure
+ 6 i 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+$$$$
diff --git a/modules/io/tests/testfiles/sdf/wrong_bondlinelength.sdf b/modules/io/tests/testfiles/sdf/wrong_bondlinelength.sdf
new file mode 100644
index 000000000..5be46a393
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/wrong_bondlinelength.sdf
@@ -0,0 +1,18 @@
+Simple Ligand
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+$$$$
diff --git a/modules/io/tests/testfiles/sdf/wrong_bondtype.sdf b/modules/io/tests/testfiles/sdf/wrong_bondtype.sdf
new file mode 100644
index 000000000..432c10464
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/wrong_bondtype.sdf
@@ -0,0 +1,18 @@
+Simple Ligand
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 -1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+$$$$
diff --git a/modules/io/tests/testfiles/sdf/wrong_charge.sdf b/modules/io/tests/testfiles/sdf/wrong_charge.sdf
new file mode 100644
index 000000000..01dba009e
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/wrong_charge.sdf
@@ -0,0 +1,18 @@
+Simple Ligand
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 i 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+$$$$
diff --git a/modules/io/tests/testfiles/sdf/wrong_dataheader.sdf b/modules/io/tests/testfiles/sdf/wrong_dataheader.sdf
new file mode 100644
index 000000000..b895448e6
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/wrong_dataheader.sdf
@@ -0,0 +1,48 @@
+Simple Ligand 1
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+> prop_one>
+1
+
+> <prop_two>
+-2
+
+$$$$
+Simple Ligand 2
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M END
+> <prop_one>
+2
+
+> <prop_two>
+-4
+
+$$$$
--
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