From 30aadd066794667273ca5e2e01f6855927b78905 Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Sat, 3 Apr 2010 08:20:17 +0000
Subject: [PATCH] minor tweaks to PDBReader interface
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1917 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/io/pymod/export_pdb_io.cc | 2 +
modules/io/src/mol/entity_io_crd_handler.cc | 2 +-
modules/io/src/mol/pdb_io.hh | 9 +++-
modules/io/src/mol/pdb_reader.cc | 11 +----
modules/io/src/mol/pdb_reader.hh | 11 +++--
modules/io/tests/test_io_pdb.cc | 42 ++++++++++++++++++-
.../testfiles/pdb/join-spread-records.pdb | 3 ++
.../testfiles/{test_in.pdb => pdb/simple.pdb} | 0
8 files changed, 64 insertions(+), 16 deletions(-)
create mode 100644 modules/io/tests/testfiles/pdb/join-spread-records.pdb
rename modules/io/tests/testfiles/{test_in.pdb => pdb/simple.pdb} (100%)
diff --git a/modules/io/pymod/export_pdb_io.cc b/modules/io/pymod/export_pdb_io.cc
index 5f252d318..6cc80b813 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 8cd61e3e9..a7870b33e 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 e14cfb2d4..54edc8a13 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 c59be53a6..5ad97901e 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 a3581510f..b41eef65a 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 5bc9f8e4c..44b7f3db4 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 000000000..e87adc974
--- /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
--
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