diff --git a/modules/io/pymod/export_pdb_io.cc b/modules/io/pymod/export_pdb_io.cc
index 5f252d31897a86ac906566f55f91e552d80cfff5..6cc80b813ca1c95fca26604b91f93012684390e4 100644
--- a/modules/io/pymod/export_pdb_io.cc
+++ b/modules/io/pymod/export_pdb_io.cc
@@ -38,12 +38,14 @@ void export_pdb_io()
.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>())
diff --git a/modules/io/src/mol/entity_io_crd_handler.cc b/modules/io/src/mol/entity_io_crd_handler.cc
index 8cd61e3e9ee486ad7520b88c71db42d35eeef7f6..a7870b33ed239d98bee19519cdfbabb7a73fa7ca 100644
--- a/modules/io/src/mol/entity_io_crd_handler.cc
+++ b/modules/io/src/mol/entity_io_crd_handler.cc
@@ -259,7 +259,7 @@ mol::CoordGroupHandle LoadCHARMMTraj(const String& crd_fn,
std::vector<mol::AtomHandle> alist;
if(boost::filesystem::extension(crd_f)==".pdb") {
PDBReader reader(crd_f);
- reader.CollectSequentialAtoms(true);
+ reader.SetFlags(PDB::SEQUENTIAL_ATOM_IMPORT);
LOGN_MESSAGE("importing coordinate data");
reader.Import(ent);
alist = reader.GetSequentialAtoms();
diff --git a/modules/io/src/mol/pdb_io.hh b/modules/io/src/mol/pdb_io.hh
index e14cfb2d44fa37f282f30cd802d3f9abeca39286..54edc8a1320cf57f697bb44b2d8ac4d2a13e603c 100644
--- a/modules/io/src/mol/pdb_io.hh
+++ b/modules/io/src/mol/pdb_io.hh
@@ -57,7 +57,14 @@ struct PDB {
///
/// By default, the atom 550 will start a new residue instead of being
/// joined with atoms 43-48 into one residue.
- JOIN_SPREAD_ATOM_RECORDS=16
+ 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
} Type;
};
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index c59be53a623e88ad163a94086cfb486fe62b9c57..5ad97901e4ebc4da64db7b957177f0564ee9f8a4 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -146,8 +146,6 @@ void PDBReader::Init(const boost::filesystem::path& loc)
in_.push(instream_);
if(!infile_) throw IOException("could not open "+loc.string());
line_num_=0;
- collect_sequential_atoms_=false;
-
if(boost::iequals(boost::filesystem::extension(loc), ".pqr")) {
is_pqr_=true;
} else {
@@ -261,11 +259,6 @@ void PDBReader::ClearState()
sequential_atom_list_.clear();
}
-void PDBReader::CollectSequentialAtoms(bool f)
-{
- collect_sequential_atoms_=f;
-}
-
std::vector<mol::AtomHandle> PDBReader::GetSequentialAtoms() const
{
return sequential_atom_list_;
@@ -501,14 +494,14 @@ void PDBReader::ParseAndAddAtom(const String& line, int line_num,
} else {
mol::AtomHandle ah=editor.InsertAltAtom(curr_residue_, aname,
String(1, alt_loc), apos, aprop);
- if (collect_sequential_atoms_) {
+ 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 (collect_sequential_atoms_) {
+ 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 a3581510f89996248c1084cb6a914a43d029d200..b41eef65a1444e07fa151201bab7ee790adaca8a 100644
--- a/modules/io/src/mol/pdb_reader.hh
+++ b/modules/io/src/mol/pdb_reader.hh
@@ -49,8 +49,14 @@ public:
void Import(mol::EntityHandle& ent,
const String& restrict_chains="");
void SetFlags(PDBFlags flags);
- // these two are needed for synchronizing with a traj import
- void CollectSequentialAtoms(bool f);
+
+ /// \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:
@@ -76,7 +82,6 @@ private:
std::istream& instream_;
boost::iostreams::filtering_stream<boost::iostreams::input> in_;
String curr_line_;
- bool collect_sequential_atoms_;
std::vector<mol::AtomHandle> sequential_atom_list_;
PDBFlags flags_;
// this needs to be set to true for reading pqr
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 5bc9f8e4c7c9cae6968ed20359d32972b32e76ed..44b7f3db415e838848633ae7d656f5d7b59efaf7 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -18,6 +18,7 @@
//------------------------------------------------------------------------------
#include <ost/mol/mol.hh>
#include <ost/io/mol/entity_io_pdb_handler.hh>
+#include <ost/io/pdb_reader.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
using boost::unit_test_framework::test_suite;
@@ -29,7 +30,7 @@ BOOST_AUTO_TEST_SUITE( io )
BOOST_AUTO_TEST_CASE(test_io_pdb)
{
- const String fname("testfiles/test_in.pdb");
+ String fname("testfiles/test_in.pdb");
mol::EntityHandle eh=mol::CreateEntity();
EntityIOPDBHandler pdbh;
@@ -42,7 +43,44 @@ BOOST_AUTO_TEST_CASE(test_io_pdb)
BOOST_CHECK(EntityIOPDBHandler::ProvidesExport(fname));
BOOST_CHECK(EntityIOPDBHandler::ProvidesExport("test_in.PDB"));
- pdbh.Import(eh,"testfiles/test_in.pdb");
+ pdbh.Import(eh,"testfiles/pdb/simple.pdb");
+}
+
+BOOST_AUTO_TEST_CASE(join_spread_records_on)
+{
+ String fname("testfiles/pdb/join-spread-records.pdb");
+ PDBReader reader(fname);
+ reader.SetFlags(PDB::JOIN_SPREAD_ATOM_RECORDS);
+
+ mol::EntityHandle ent=mol::CreateEntity();
+ reader.Import(ent);
+ BOOST_CHECK_EQUAL(ent.GetResidueCount(), 2);
+ mol::ResidueHandle res1=ent.FindResidue("A", mol::ResNum(1));
+ BOOST_CHECK(res1.IsValid());
+ BOOST_CHECK_EQUAL(res1.GetAtomCount(), 2);
+ BOOST_CHECK(res1.FindAtom("N"));
+ BOOST_CHECK(res1.FindAtom("CE"));
+ mol::ResidueHandle res2=ent.FindResidue("A", mol::ResNum(2));
+ BOOST_CHECK(res2.IsValid());
+ BOOST_CHECK_EQUAL(res2.GetAtomCount(), 1);
+ BOOST_CHECK(res2.FindAtom("N"));
+}
+
+BOOST_AUTO_TEST_CASE(join_spread_records_off)
+{
+ String fname("testfiles/pdb/join-spread-records.pdb");
+ PDBReader reader(fname);
+ mol::EntityHandle ent=mol::CreateEntity();
+ reader.Import(ent);
+ BOOST_CHECK_EQUAL(ent.GetResidueCount(), 2);
+ mol::ResidueHandle res1=ent.FindResidue("A", mol::ResNum(1));
+ BOOST_CHECK(res1.IsValid());
+ BOOST_CHECK_EQUAL(res1.GetAtomCount(), 1);
+ BOOST_CHECK(res1.FindAtom("N"));
+ mol::ResidueHandle res2=ent.FindResidue("A", mol::ResNum(2));
+ BOOST_CHECK(res2.IsValid());
+ BOOST_CHECK_EQUAL(res2.GetAtomCount(), 1);
+ BOOST_CHECK(res2.FindAtom("N"));
}
BOOST_AUTO_TEST_SUITE_END()
\ No newline at end of file
diff --git a/modules/io/tests/testfiles/pdb/join-spread-records.pdb b/modules/io/tests/testfiles/pdb/join-spread-records.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..e87adc9748fbd6446648b00f04a0b98a2e0f8166
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/join-spread-records.pdb
@@ -0,0 +1,3 @@
+ATOM 1 N MET A 1 21.609 35.384 56.705 1.00 41.48 N
+ATOM 9 N ARG A 2 20.202 33.112 58.011 1.00 36.39 N
+ATOM 8 CE MET A 1 23.233 37.697 58.529 1.00 54.59 C
diff --git a/modules/io/tests/testfiles/test_in.pdb b/modules/io/tests/testfiles/pdb/simple.pdb
similarity index 100%
rename from modules/io/tests/testfiles/test_in.pdb
rename to modules/io/tests/testfiles/pdb/simple.pdb