diff --git a/.gitignore b/.gitignore
index f9b5a2f0ee6e680b33fc32ba135765c747db8041..c4c1b9add1cca6fb92c973b33b29748e8c3a46a8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -22,6 +22,7 @@ pov_*test.pov
pov_*test.inc
*-out.pdb
*-out.sdf
+*-out.crd
CMakeLists.txt.user
OpenStructure.cbp
DartConfiguration.tcl
@@ -51,4 +52,4 @@ Debug
/deployment/win/create_archive.bat
/install_manifest.txt
*_out.csv
-/modules/io/tests/temp_img.tmp
\ No newline at end of file
+/modules/io/tests/temp_img.tmp
diff --git a/modules/base/src/test_utils/compare_files.cc b/modules/base/src/test_utils/compare_files.cc
index f28821e686e4e7745d1de9b359f441ca3d99aea4..904b14a7fa75dde9bf4edcf3cab176966f312dc1 100644
--- a/modules/base/src/test_utils/compare_files.cc
+++ b/modules/base/src/test_utils/compare_files.cc
@@ -44,17 +44,17 @@ bool compare_files(const String& test, const String& gold_standard)
}
if (!test_end) {
std::cerr << gold_standard << " contains additional line(s):"
- << std::endl << gold_line;
+ << std::endl << gold_line << std::endl;
return false;
}
if (!gold_end) {
std::cerr << test << " contains additional line(s):"
- << std::endl << test_line;
+ << std::endl << test_line << std::endl;
return false;
}
if (gold_line!=test_line) {
std::cerr << "line mismatch:" << std::endl << "test: " << test_line
- << std::endl << "gold: " << gold_line;
+ << std::endl << "gold: " << gold_line << std::endl;
return false;
}
}
diff --git a/modules/io/src/mol/entity_io_crd_handler.cc b/modules/io/src/mol/entity_io_crd_handler.cc
index 8b0ceb837058b498a5cd21d7529f9590f7279aa8..58fdcb910d7346f8564be8dcc68fa3e64d34b8a2 100644
--- a/modules/io/src/mol/entity_io_crd_handler.cc
+++ b/modules/io/src/mol/entity_io_crd_handler.cc
@@ -43,6 +43,11 @@ namespace ost { namespace io {
using boost::format;
+
+/// \brief Reader for CHARMM crd file format
+///
+/// Standard and extended CHARMM format is supported, and file format is
+/// automatically detected based on file header or atom number
CRDReader::CRDReader(const boost::filesystem::path& loc):
sequential_atom_list_(),
curr_chain_(),
@@ -60,11 +65,14 @@ CRDReader::CRDReader(const boost::filesystem::path& loc):
if(!infile_) throw IOException("could not open "+loc.string());
}
+/// \brief Returns an vector containing all atom handles as observed in the file
std::vector<mol::AtomHandle> CRDReader::GetSequentialAtoms() const
{
return sequential_atom_list_;
}
+
+/// \brief Performes file import
void CRDReader::Import(mol::EntityHandle& ent)
{
Profile profile_import("CRDReader::Import");
@@ -79,21 +87,24 @@ void CRDReader::Import(mol::EntityHandle& ent)
std::vector<String> line_content;
boost::trim(line);
boost::split(line_content,line,boost::is_any_of(" "));
-
+
// expanded charmm CARD format check
if (line_content.size() > 1 || boost::lexical_cast<int>(line_content[0]) > 99999)
while(std::getline(in_,line)) {
- ParseAndAddAtomExpanded(line,ent);
+ if (!boost::trim_copy(line).empty())
+ ParseAndAddAtomExpanded(line,ent);
}
else
while(std::getline(in_,line)) {
- ParseAndAddAtom(line,ent);
+ if (!boost::trim_copy(line).empty())
+ ParseAndAddAtom(line,ent);
}
-
+
LOG_INFO("imported " << chain_count_ << " chains, " << residue_count_
<< " residues, " << atom_count_ << " atoms");
}
+/// \brief Parsing for standard format
void CRDReader::ParseAndAddAtom(const String& line, mol::EntityHandle& ent)
{
mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
@@ -103,7 +114,7 @@ void CRDReader::ParseAndAddAtom(const String& line, mol::EntityHandle& ent)
//int anum = boost::lexical_cast<int>(boost::trim_copy(line.substr(0,5)));
String aname = boost::trim_copy(line.substr(16,4));
String ele = aname.substr(0,1);
- String rname = boost::trim_copy(line.substr(11,3));
+ String rname = boost::trim_copy(line.substr(11,4));
int irnum = boost::lexical_cast<int>(boost::trim_copy(line.substr(55,4)));
String s_chain = boost::trim_copy(line.substr(51,4));
geom::Vec3 apos(boost::lexical_cast<Real>(boost::trim_copy(line.substr(21,9))),
@@ -155,7 +166,8 @@ void CRDReader::ParseAndAddAtom(const String& line, mol::EntityHandle& ent)
sequential_atom_list_.push_back(ah);
++atom_count_;
}
-
+
+/// \brief Parsing for extended format
void CRDReader::ParseAndAddAtomExpanded(const String& line, mol::EntityHandle& ent)
{
mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
@@ -167,10 +179,11 @@ void CRDReader::ParseAndAddAtomExpanded(const String& line, mol::EntityHandle& e
String ele = aname.substr(0,1);
String rname = boost::trim_copy(line.substr(22,8));
int irnum = boost::lexical_cast<int>(boost::trim_copy(line.substr(112,8)));
- String s_chain = boost::trim_copy(line.substr(102.8,8));
+ String s_chain = boost::trim_copy(line.substr(102,8));
geom::Vec3 apos(boost::lexical_cast<Real>(boost::trim_copy(line.substr(40,20))),
boost::lexical_cast<Real>(boost::trim_copy(line.substr(60,20))),
boost::lexical_cast<Real>(boost::trim_copy(line.substr(80,20))));
+ Real b_factor = boost::lexical_cast<Real>(boost::trim_copy(line.substr(128,12)));
mol::ResidueKey rkey(rname);
@@ -213,28 +226,38 @@ void CRDReader::ParseAndAddAtomExpanded(const String& line, mol::EntityHandle& e
// finally add atom
LOG_DEBUG("adding atom " << aname << " (" << ele << ") @" << apos);
- mol::AtomHandle ah = editor.InsertAtom(curr_residue_, aname, apos, ele);
+ mol::AtomHandle ah = editor.InsertAtom(curr_residue_, aname, apos, ele,
+ 1.0, b_factor);
sequential_atom_list_.push_back(ah);
++atom_count_;
}
-CRDWriter::CRDWriter(std::ostream& ostream) :
- outfile_(), outstream_(ostream), atom_count_(0)
+/// \brief CHARMM format writer
+///
+/// The charmm format writer supports both the standard and the extended
+/// format. Standard format supports at maximum 99999 atoms. If less atoms than
+/// that are present, the default format is standard format, otherwise the
+/// extended format is used. Extended format can be requested by setting the
+/// parameter ext to true.
+CRDWriter::CRDWriter(std::ostream& ostream, bool ext) :
+ outfile_(), outstream_(ostream), ext_(ext), atom_count_(0), res_count_(0)
{}
-CRDWriter::CRDWriter(const boost::filesystem::path& filename) :
+CRDWriter::CRDWriter(const boost::filesystem::path& filename, bool ext) :
#if BOOST_FILESYSTEM_VERSION==3
outfile_(filename.string().c_str()), outstream_(outfile_),
#else
outfile_(filename.file_string().c_str()), outstream_(outfile_),
#endif
- atom_count_(0)
+ ext_(ext), atom_count_(0), res_count_(0)
{}
-CRDWriter::CRDWriter(const String& filename) :
- outfile_(filename.c_str()), outstream_(outfile_), atom_count_(0)
+CRDWriter::CRDWriter(const String& filename, bool ext) :
+ outfile_(filename.c_str()), outstream_(outfile_), ext_(ext), atom_count_(0),
+ res_count_(0)
{}
+/// \brief Write header containing standard title and atom count/format row
void CRDWriter::WriteHeader(const mol::EntityView& ent)
{
outstream_ << "* COOR FILE CREATED BY OPENSTRUCTURE" << std::endl;
@@ -242,7 +265,7 @@ void CRDWriter::WriteHeader(const mol::EntityView& ent)
atom_total_ = ent.GetAtomCount();
- if (atom_total_ > 99999) {
+ if (atom_total_ > 99999 || ext_) {
outstream_ << format("%10i") % ent.GetAtomCount() << " EXT" << std::endl;
}
else {
@@ -250,6 +273,43 @@ void CRDWriter::WriteHeader(const mol::EntityView& ent)
}
}
+/// \brief Performs re-initialisation for writer
+///
+/// Currently, this only sets the residue count to zero
+void CRDWriter::Init()
+{
+ res_count_ = 0;
+}
+
+void CRDWriter::Write(const mol::EntityView& ent)
+{
+ if (!outstream_) {
+ throw IOException("Can't write CRD file. Bad output stream");
+ }
+ this->Init();
+ mol::EntityView non_const_view = ent;
+ this->WriteHeader(non_const_view);
+ non_const_view.Apply(*this);
+}
+
+void CRDWriter::Write(const mol::EntityHandle& ent)
+{
+ if (!outstream_) {
+ throw IOException("Can't write CRD file. Bad output stream");
+ }
+ this->Init();
+ mol::EntityView non_const_view = ent.CreateFullView();
+ this->WriteHeader(non_const_view);
+ non_const_view.Apply(*this);
+}
+
+
+bool CRDWriter::VisitResidue(const mol::ResidueHandle& r)
+{
+ res_count_++;
+ return true;
+}
+
bool CRDWriter::VisitAtom(const mol::AtomHandle& atom)
{
atom_count_++;
@@ -260,27 +320,27 @@ bool CRDWriter::VisitAtom(const mol::AtomHandle& atom)
mol::ResidueHandle res=atom.GetResidue();
- if (atom_total_ > 99999) {
+ if (atom_total_ > 99999 || ext_) {
outstream_ << format("%10i") % atom_count_
- << format("%10i") % res.GetNumber() << " "
+ << format("%10i") % res_count_ << " "
<< format("%-8s") % res.GetKey() << " "
<< format("%-8s") % atom.GetName()
<< format("%20.10f") % atom.GetPos().x
<< format("%20.10f") % atom.GetPos().y
<< format("%20.10f") % atom.GetPos().z << " "
- << format("%-8s") % e_name << " "
+ << format("%-8s") % res.GetChain().GetName() << " "
<< format("%-8i") % res.GetNumber()
<< format("%20.10f") % atom.GetBFactor()
<< std::endl;
} else {
outstream_ << format("%5i") % atom_count_
- << format("%5i") % res.GetNumber() << " "
- << format("%4s") % res.GetKey() << " "
+ << format("%5i") % res_count_ << " "
+ << format("%-4s") % res.GetKey() << " "
<< format("%-4s") % atom.GetName()
<< format("%10.5f") % atom.GetPos().x
<< format("%10.5f") % atom.GetPos().y
<< format("%10.5f") % atom.GetPos().z << " "
- << format("%-4s") % e_name << " "
+ << format("%-4s") % res.GetChain().GetName() << " "
<< format("%-5i") % res.GetNumber() << " "
<< format("%8.5f") % atom.GetBFactor()
<< std::endl;
@@ -288,6 +348,7 @@ bool CRDWriter::VisitAtom(const mol::AtomHandle& atom)
return true;
}
+/// \brief CHARMM file format requires builder
bool EntityIOCRDHandler::RequiresBuilder() const
{
return true;
@@ -304,18 +365,14 @@ void EntityIOCRDHandler::Export(const mol::EntityView& ent,
std::ostream& stream) const
{
CRDWriter writer(stream);
- writer.WriteHeader(ent);
- mol::EntityView non_const_view = ent;
- non_const_view.Apply(writer);
+ writer.Write(ent);
}
void EntityIOCRDHandler::Export(const mol::EntityView& ent,
const boost::filesystem::path& loc) const
{
CRDWriter writer(loc);
- writer.WriteHeader(ent);
- mol::EntityView non_const_view = ent;
- non_const_view.Apply(writer);
+ writer.Write(ent);
}
namespace {
diff --git a/modules/io/src/mol/entity_io_crd_handler.hh b/modules/io/src/mol/entity_io_crd_handler.hh
index 714a1d4019128264bd330e70468631772870e29c..c0d625a804258e7bd8b16d547d228bf5589ed6d2 100644
--- a/modules/io/src/mol/entity_io_crd_handler.hh
+++ b/modules/io/src/mol/entity_io_crd_handler.hh
@@ -16,14 +16,13 @@
// 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, Tobias Schmidt
+ */
+
#ifndef OST_IO_ENTITY_IO_PLUGIN_CRD_H
#define OST_IO_ENTITY_IO_PLUGIN_CRD_H
-/*
- CHARMM coordinate file import
- Author: Ansgar Philippsen
- */
-
#include <ost/mol/entity_handle.hh>
#include <ost/mol/chain_handle.hh>
#include <ost/mol/residue_handle.hh>
@@ -35,6 +34,7 @@
namespace ost { namespace io {
+/// \brief CHARMM coordinate file import
class DLLEXPORT_OST_IO CRDReader {
public:
CRDReader(const boost::filesystem::path& loc);
@@ -58,22 +58,30 @@ private:
boost::iostreams::filtering_stream<boost::iostreams::input> in_;
};
-
+/// \brief CHARMM coordinate file export
class DLLEXPORT_OST_IO CRDWriter : public mol::EntityVisitor {
public:
- CRDWriter(const String& filename);
- CRDWriter(const boost::filesystem::path& filename);
- CRDWriter(std::ostream& outstream);
+ CRDWriter(const String& filename, bool ext=false);
+ CRDWriter(const boost::filesystem::path& filename, bool ext=false);
+ CRDWriter(std::ostream& outstream, bool ext=false);
+
+ void Write(const mol::EntityView& ent);
+ void Write(const mol::EntityHandle& ent);
virtual bool VisitAtom(const mol::AtomHandle& atom);
+ virtual bool VisitResidue(const mol::ResidueHandle& r);
void WriteHeader(const mol::EntityView& ent);
private:
+ void Init();
+
std::ofstream outfile_;
std::ostream& outstream_;
+ bool ext_;
int atom_count_;
int atom_total_;
+ int res_count_;
};
class DLLEXPORT_OST_IO EntityIOCRDHandler: public EntityIOHandler {
diff --git a/modules/io/tests/test_io_crd.cc b/modules/io/tests/test_io_crd.cc
index 14400aed80c33c5c6e7865c71e45d540c8dbc7c6..82126d10f1fb9d9298e68a035340396df58dd57e 100644
--- a/modules/io/tests/test_io_crd.cc
+++ b/modules/io/tests/test_io_crd.cc
@@ -16,8 +16,10 @@
// 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_crd_handler.hh>
+#include <ost/io/save_entity.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
@@ -27,16 +29,129 @@ using namespace ost::io;
BOOST_AUTO_TEST_SUITE( io )
+BOOST_AUTO_TEST_CASE(test_io_crd_import_handler)
+{
+ String fname("testfiles/crd/test_in.crd");
+
+ mol::EntityHandle eh=mol::CreateEntity();
+ EntityIOCRDHandler crdh;
+
+ BOOST_CHECK(EntityIOCRDHandler::ProvidesImport("","crd"));
+ BOOST_CHECK(EntityIOCRDHandler::ProvidesImport(fname));
+ BOOST_CHECK(EntityIOCRDHandler::ProvidesImport("test_in.CRD"));
+
+ BOOST_CHECK(EntityIOCRDHandler::ProvidesExport("","crd"));
+ BOOST_CHECK(EntityIOCRDHandler::ProvidesExport(fname));
+ BOOST_CHECK(EntityIOCRDHandler::ProvidesExport("test_in.CRD"));
+}
+
+/// check standard format input
BOOST_AUTO_TEST_CASE(test_io_crd)
{
- const String fname("testfiles/test_in.crd");
+ const String fname("testfiles/crd/test_in.crd");
+
+ mol::EntityHandle eh=mol::CreateEntity();
+ CRDReader crdr(fname);
+
+ crdr.Import(eh);
+ std::vector<mol::AtomHandle> alist = crdr.GetSequentialAtoms();
+
+ BOOST_CHECK_EQUAL(eh.GetAtomCount(), 9);
+ BOOST_CHECK_EQUAL(eh.GetResidueCount(), 2);
+ BOOST_CHECK_EQUAL(eh.GetChainCount(), 2);
+ BOOST_CHECK_EQUAL(eh.GetResidueList()[0].GetNumber().GetNum(), 3);
+ BOOST_CHECK_EQUAL(eh.GetResidueList()[1].GetNumber().GetNum(), 4);
+ BOOST_CHECK_EQUAL(eh.GetResidueList()[0].GetName(), "ALA");
+ BOOST_CHECK_EQUAL(eh.GetResidueList()[1].GetName(), "P2AC");
+ BOOST_CHECK_EQUAL(eh.GetAtomList()[0].GetName(), "N");
+ BOOST_CHECK_EQUAL(eh.GetAtomList()[7].GetName(), "HA51");
+ BOOST_CHECK_EQUAL(eh.GetChainList()[0].GetName(), "PEPT");
+ BOOST_CHECK_EQUAL(eh.GetChainList()[1].GetName(), "RNA");
+}
+
+/// check extended format input
+BOOST_AUTO_TEST_CASE(test_io_crd_ext)
+{
+ const String fname("testfiles/crd/multisegment.crd");
mol::EntityHandle eh=mol::CreateEntity();
CRDReader crdr(fname);
crdr.Import(eh);
std::vector<mol::AtomHandle> alist = crdr.GetSequentialAtoms();
+
+ BOOST_CHECK_EQUAL(eh.GetAtomCount(), 43);
+ BOOST_CHECK_EQUAL(eh.GetResidueCount(), 6);
+ BOOST_CHECK_EQUAL(eh.GetChainCount(), 3);
+ BOOST_CHECK_EQUAL(eh.GetResidueList()[0].GetNumber().GetNum(), 1);
+ BOOST_CHECK_EQUAL(eh.GetResidueList()[1].GetNumber().GetNum(), 2);
+ BOOST_CHECK_EQUAL(eh.GetResidueList()[2].GetNumber().GetNum(), 1);
+ BOOST_CHECK_EQUAL(eh.GetResidueList()[0].GetName(), "GLY");
+ BOOST_CHECK_EQUAL(eh.GetResidueList()[1].GetName(), "GLU");
+ BOOST_CHECK_EQUAL(eh.GetResidueList()[2].GetName(), "G3AC");
+ BOOST_CHECK_EQUAL(eh.GetAtomList()[0].GetName(), "N");
+ BOOST_CHECK_EQUAL(eh.GetAtomList()[20].GetName(), "OE1");
+ BOOST_CHECK_EQUAL(eh.GetChainList()[0].GetName(), "PROTEIN");
+ BOOST_CHECK_EQUAL(eh.GetChainList()[1].GetName(), "RNA");
+ BOOST_CHECK_EQUAL(eh.GetChainList()[2].GetName(), "SAM");
}
-BOOST_AUTO_TEST_SUITE_END()
\ No newline at end of file
+/// check that empty lines at end of file are ignored
+BOOST_AUTO_TEST_CASE(test_io_crd_empty_line)
+{
+ const String fname("testfiles/crd/empty_line_at_end.crd");
+ mol::EntityHandle eh=mol::CreateEntity();
+ CRDReader reader(fname);
+ reader.Import(eh);
+}
+
+/// check extended format with multisegment file output
+BOOST_AUTO_TEST_CASE(test_io_crd_writer_ext)
+{
+ const String fname("testfiles/crd/multisegment.crd");
+ {
+ mol::EntityHandle eh=mol::CreateEntity();
+ CRDReader reader(fname);
+ reader.Import(eh);
+
+ CRDWriter writer(String("testfiles/crd/multisegment-out.crd"), true);
+ writer.Write(eh);
+ }
+ BOOST_CHECK(compare_files("testfiles/crd/multisegment-out.crd",
+ "testfiles/crd/multisegment.crd"));
+}
+
+/// check standard format output
+BOOST_AUTO_TEST_CASE(test_io_crd_writer_std)
+{
+ const String fname("testfiles/crd/test_in.crd");
+ {
+ mol::EntityHandle eh=mol::CreateEntity();
+ CRDReader reader(fname);
+ reader.Import(eh);
+
+ CRDWriter writer(String("testfiles/crd/test-out.crd"));
+ writer.Write(eh);
+ }
+ BOOST_CHECK(compare_files("testfiles/crd/test-out.crd",
+ "testfiles/crd/test_in.crd"));
+}
+
+/// check standard format is written by default
+BOOST_AUTO_TEST_CASE(test_io_crd_default_format)
+{
+ const String fname("testfiles/crd/test_in.crd");
+ {
+ mol::EntityHandle eh=mol::CreateEntity();
+ CRDReader reader(fname);
+ reader.Import(eh);
+
+ ost::io::SaveEntity(eh, "testfiles/crd/test-out.crd");
+ }
+ BOOST_CHECK(compare_files("testfiles/crd/test-out.crd",
+ "testfiles/crd/test_in.crd"));
+}
+
+
+BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/io/tests/testfiles/crd/empty_line_at_end.crd b/modules/io/tests/testfiles/crd/empty_line_at_end.crd
new file mode 100755
index 0000000000000000000000000000000000000000..c9903690b46caece44d905d77c94a9fa37a00c35
--- /dev/null
+++ b/modules/io/tests/testfiles/crd/empty_line_at_end.crd
@@ -0,0 +1,14 @@
+* COOR FILE CREATED BY OPENSTRUCTURE
+*
+ 9
+ 1 1 ALA N -2.53857 10.36006 28.21452 PEPT 3 0.00000
+ 2 1 ALA HT1 -2.09853 10.16934 29.15484 PEPT 3 0.00000
+ 3 1 ALA HT2 -3.19965 9.53958 28.27807 PEPT 3 0.00000
+ 4 1 ALA HT3 -3.03496 11.26844 28.29274 PEPT 3 0.00000
+ 5 1 ALA CA -1.58333 10.24913 27.09525 PEPT 3 0.00000
+ 6 1 ALA HA -0.74083 9.67002 27.43410 PEPT 3 0.00000
+ 7 1 ALA CB -2.26337 9.53603 25.91124 PEPT 3 0.00000
+ 8 2 P2AC HA51 -6.76933 80.69502 15.53886 RNA 4 0.00000
+ 9 2 P2AC HA52 -8.23100 81.32728 16.35343 RNA 4 0.00000
+
+
diff --git a/modules/io/tests/testfiles/crd/multisegment.crd b/modules/io/tests/testfiles/crd/multisegment.crd
new file mode 100644
index 0000000000000000000000000000000000000000..9b3e2e2870948fdbe62870224463e0ebaf6d46b1
--- /dev/null
+++ b/modules/io/tests/testfiles/crd/multisegment.crd
@@ -0,0 +1,46 @@
+* COOR FILE CREATED BY OPENSTRUCTURE
+*
+ 43 EXT
+ 1 1 GLY N -2.0000000000 -8.5000000000 -4.0000000000 PROTEIN 1 0.0000916632
+ 2 1 GLY HT1 -16.1250000000 -16.0009765625 -16.1259765625 PROTEIN 1 0.0000787743
+ 3 1 GLY HT2 -24.0502128601 -10.1571445465 -4.7282133102 PROTEIN 1 0.0000787526
+ 4 1 GLY HT3 -25.6165981293 -10.6957426071 -5.4588241577 PROTEIN 1 0.0000786720
+ 5 1 GLY CA -25.3130340576 -11.3211555481 -3.5009372234 PROTEIN 1 0.0000978857
+ 6 1 GLY HA1 -26.2965011597 -11.7470941544 -3.6310827732 PROTEIN 1 0.0000000000
+ 7 1 GLY HA2 -25.4361457825 -10.4118413925 -2.8764421940 PROTEIN 1 0.0000851970
+ 8 1 GLY C -24.4854793549 -12.3229217529 -2.9330530167 PROTEIN 1 0.0000944421
+ 9 1 GLY O -23.7718524933 -13.0324668884 -3.6388895512 PROTEIN 1 0.0000894775
+ 10 2 GLU N -24.5463562012 -12.6111087799 -1.6436747313 PROTEIN 2 0.0000000000
+ 11 2 GLU HN -23.9035968781 -13.3227586746 -1.3749105930 PROTEIN 2 0.0000000000
+ 12 2 GLU CA -25.4813365936 -12.0606479645 -0.6506563425 PROTEIN 2 0.0000000000
+ 13 2 GLU HA -26.1672992706 -11.3891696930 -1.1180906296 PROTEIN 2 0.0000000000
+ 14 2 GLU CB -26.2274837494 -13.2668724060 0.0429458581 PROTEIN 2 0.0000000000
+ 15 2 GLU HB1 -26.7839298248 -12.7876672745 0.9326843023 PROTEIN 2 0.0030197345
+ 16 2 GLU HB2 -25.4761943817 -13.9268684387 0.5624338984 PROTEIN 2 0.0000000000
+ 17 2 GLU CG -27.2343692780 -13.8997907639 -0.9133957624 PROTEIN 2 0.0166021846
+ 18 2 GLU HG1 -27.7255306244 -14.7208814621 -0.4454757869 PROTEIN 2 0.0368194766
+ 19 2 GLU HG2 -26.6897678375 -14.4738664627 -1.8157539368 PROTEIN 2 0.0017852589
+ 20 2 GLU CD -28.2506389618 -13.0106611252 -1.5168483257 PROTEIN 2 0.0774637908
+ 21 2 GLU OE1 -29.3007488251 -12.8661479950 -0.8537709117 PROTEIN 2 0.1687415987
+ 22 2 GLU OE2 -28.2000064850 -12.5138931274 -2.6356098652 PROTEIN 2 0.0706803948
+ 23 2 GLU C -24.6928653717 -11.2268772125 0.3724045455 PROTEIN 2 0.0000000000
+ 24 2 GLU O -25.2389545441 -10.7677593231 1.3376628160 PROTEIN 2 0.0000000000
+ 25 3 G3AC N9 -15.8120441437 6.0608630180 -6.6949663162 RNA 1 0.0000393577
+ 26 3 G3AC C4 -16.9207630157 6.8197221756 -7.0580096245 RNA 1 0.0000500576
+ 27 3 G3AC N2 -20.2281303406 7.6236495972 -6.4126434326 RNA 1 0.0000850955
+ 28 3 G3AC H21 -20.3844623566 6.9206910133 -5.6787233353 RNA 1 0.0000501027
+ 29 3 G3AC H22 -20.8750762939 8.3805465698 -6.5524845123 RNA 1 0.0000851209
+ 30 3 G3AC N3 -18.1747817993 6.6029930115 -6.5917358398 RNA 1 0.0000000000
+ 31 4 GUA P -1.5319050550 5.2959299088 -0.6717305183 RNA 2 0.0000786968
+ 32 4 GUA O1P -0.8520842195 4.0187578201 -0.6064184904 RNA 2 0.0000477555
+ 33 4 GUA O2P -1.8167773485 6.0385017395 0.5593457222 RNA 2 0.0000425713
+ 34 4 GUA O5' -0.7149851322 6.1814560890 -1.7396181822 RNA 2 0.0000425333
+ 35 5 CYT P 2.5655767918 10.5823450089 -2.4465763569 RNA 3 0.0000425641
+ 36 5 CYT O1P 3.6461751461 10.5359878540 -3.4340066910 RNA 3 0.0000000000
+ 37 5 CYT O2P 2.8808369637 11.1873378754 -1.1375198364 RNA 3 0.0000000000
+ 38 5 CYT O5' 1.2869589329 11.2338676453 -3.0263113976 RNA 3 0.0000917684
+ 39 6 SAM N 4.0659961700 1.8457804918 -0.2989104986 SAM 1 0.0001180591
+ 40 6 SAM HT1 4.6446375847 1.0045971870 -0.1713269502 SAM 1 0.0001002858
+ 41 6 SAM HT2 4.0898685455 2.4858167171 0.5328502059 SAM 1 0.0000425641
+ 42 6 SAM HT3 3.1142795086 1.6198593378 -0.4299965501 SAM 1 0.0000978186
+ 43 6 SAM CA 4.8570294380 2.6207458973 -1.2435295582 SAM 1 0.0000851861
diff --git a/modules/io/tests/testfiles/test_in.crd b/modules/io/tests/testfiles/crd/test_in.crd
similarity index 72%
rename from modules/io/tests/testfiles/test_in.crd
rename to modules/io/tests/testfiles/crd/test_in.crd
index 35353e12430e93f81c67b607bca8a78a9de8e880..ce552c3e191dc5d50d5434e6b8b9a7304309bd95 100755
--- a/modules/io/tests/testfiles/test_in.crd
+++ b/modules/io/tests/testfiles/crd/test_in.crd
@@ -1,12 +1,12 @@
-* FULL SYSTEM
-* AFTER MINIMIZATION AND 5 PSEC DYNAMICS
-* DATE: 4/ 5/ 5 8:46:31 CREATED BY USER: bernechs
-*
-45283
- 1 1 ALA N -2.53857 10.36006 28.21452 PEPT 3 0.00000
- 2 1 ALA HT1 -2.09853 10.16934 29.15484 PEPT 3 0.00000
- 3 1 ALA HT2 -3.19965 9.53958 28.27807 PEPT 3 0.00000
- 4 1 ALA HT3 -3.03496 11.26844 28.29274 PEPT 3 0.00000
- 5 1 ALA CA -1.58333 10.24913 27.09525 PEPT 3 0.00000
- 6 1 ALA HA -0.74083 9.67002 27.43410 PEPT 3 0.00000
- 7 1 ALA CB -2.26337 9.53603 25.91124 PEPT 3 0.00000
+* COOR FILE CREATED BY OPENSTRUCTURE
+*
+ 9
+ 1 1 ALA N -2.53857 10.36006 28.21452 PEPT 3 0.00000
+ 2 1 ALA HT1 -2.09853 10.16934 29.15484 PEPT 3 0.00000
+ 3 1 ALA HT2 -3.19965 9.53958 28.27807 PEPT 3 0.00000
+ 4 1 ALA HT3 -3.03496 11.26844 28.29274 PEPT 3 0.00000
+ 5 1 ALA CA -1.58333 10.24913 27.09525 PEPT 3 0.00000
+ 6 1 ALA HA -0.74083 9.67002 27.43410 PEPT 3 0.00000
+ 7 1 ALA CB -2.26337 9.53603 25.91124 PEPT 3 0.00000
+ 8 2 P2AC HA51 -6.76933 80.69502 15.53886 RNA 4 0.00000
+ 9 2 P2AC HA52 -8.23100 81.32728 16.35343 RNA 4 0.00000