diff --git a/modules/io/pymod/export_pdb_io.cc b/modules/io/pymod/export_pdb_io.cc
index fe2a3a75f0635e36dbab85cc4157bacb696151d6..1aec7e6fe5415aea60d813955b924b271c3159db 100644
--- a/modules/io/pymod/export_pdb_io.cc
+++ b/modules/io/pymod/export_pdb_io.cc
@@ -53,6 +53,7 @@ void export_pdb_io()
pdb_scope.attr("SKIP_FAULTY_RECORDS")=PDB::SKIP_FAULTY_RECORDS;
pdb_scope.attr("WRITE_MULTIPLE_MODELS")=PDB::WRITE_MULTIPLE_MODELS;
pdb_scope.attr("JOIN_SPREAD_ATOM_RECORDS")=PDB::JOIN_SPREAD_ATOM_RECORDS;
+ pdb_scope.attr("CALPHA_ONLY")=PDB::CALPHA_ONLY;
}
class_<PDBReader, boost::noncopyable>("PDBReader", init<String>())
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index a2ce79cd12998a98f8e4cccb139cd967bebd5455..c8e1136526d786b8daf971f99c586b29350db34d 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -283,8 +283,18 @@ bool PDBReader::ParseAtomIdent(const StringRef& line, int line_num,
}
throw IOException(str(format("invalid res number on line %d") % line_num));
}
+
char ins_c=line[26];
resnum=to_res_num(res_num.second, ins_c);
+ if (PDB::Flags() & PDB::CALPHA_ONLY) {
+ if (record_type[0]=='H' || record_type[0]=='h') {
+ return false;
+ }
+ if (atom_name!=StringRef("CA", 2)) {
+ return false;
+ }
+ return true;
+ }
return true;
}
@@ -301,7 +311,7 @@ void PDBReader::ParseAnisou(const StringRef& line, int line_num,
}
double anisou[6]={0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
for (int i=0;i<6; ++i) {
- std::pair<bool, int> result=line.substr(29+i*7, 6).to_int();
+ std::pair<bool, int> result=line.substr(29+i*7, 6).ltrim().to_int();
if (!result.first) {
if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS) {
return;
@@ -312,7 +322,8 @@ void PDBReader::ParseAnisou(const StringRef& line, int line_num,
}
String aname(atom_name.str());
if (!curr_residue_.IsValid()) {
- if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS) {
+ if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS ||
+ PDB::Flags() & PDB::CALPHA_ONLY) {
return;
}
const char* fmt_str="invalid ANISOU record for inexistent atom on line %d";
@@ -320,7 +331,8 @@ void PDBReader::ParseAnisou(const StringRef& line, int line_num,
}
mol::AtomHandle atom=curr_residue_.FindAtom(aname);
if (!atom.IsValid()) {
- if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS) {
+ if (PDB::Flags() & PDB::SKIP_FAULTY_RECORDS ||
+ PDB::Flags() & PDB::CALPHA_ONLY) {
return;
}
const char* fmt_str="invalid ANISOU record for inexistent atom on line %d";
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 7866377c2056932e99732b36d60fcdaceff3041d..fe5c51f3af93f401554f6e4ec356180d75a69e08 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -56,7 +56,8 @@ BOOST_AUTO_TEST_CASE(atom_record)
BOOST_REQUIRE_EQUAL(ent.GetChainCount(), 2);
BOOST_REQUIRE_EQUAL(ent.GetResidueCount(), 2);
BOOST_REQUIRE_EQUAL(ent.GetAtomCount(), 2);
- mol::AtomHandle a1=ent.FindChain("A").GetAtomList()[0];
+ mol::AtomHandle a1=ent.FindAtom("A", mol::ResNum(1), "N");
+ BOOST_REQUIRE(a1.IsValid());
BOOST_CHECK_EQUAL(a1.GetName(), "N");
BOOST_CHECK_EQUAL(a1.GetResidue().GetName(), "MET");
BOOST_CHECK_EQUAL(a1.GetResidue().GetChain().GetName(), "A");
@@ -66,7 +67,8 @@ BOOST_AUTO_TEST_CASE(atom_record)
BOOST_CHECK_EQUAL(a1.GetProp().occupancy, 0.5);
BOOST_CHECK_EQUAL(a1.GetProp().element, "N");
BOOST_CHECK_EQUAL(a1.GetProp().is_hetatm, false);
- mol::AtomHandle a2=ent.FindChain(" ").GetAtomList()[0];
+ mol::AtomHandle a2=ent.FindAtom(" ", mol::ResNum(1), "CA");
+ BOOST_REQUIRE(a2.IsValid());
BOOST_CHECK_EQUAL(a2.GetName(), "CA");
BOOST_CHECK_EQUAL(a2.GetResidue().GetName(), "MET");
BOOST_CHECK_EQUAL(a2.GetResidue().GetChain().GetName(), " ");
@@ -120,9 +122,53 @@ BOOST_AUTO_TEST_CASE(join_spread_records_off)
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_REQUIRE(res2.IsValid());
BOOST_CHECK_EQUAL(res2.GetAtomCount(), 1);
BOOST_CHECK(res2.FindAtom("N"));
}
+BOOST_AUTO_TEST_CASE(calpha_only_import_on)
+{
+ String fname("testfiles/pdb/calpha.pdb");
+ PDBReader reader(fname);
+ PDB::PushFlags(PDB::CALPHA_ONLY);
+ mol::EntityHandle ent=mol::CreateEntity();
+ reader.Import(ent);
+ PDB::PopFlags();
+ BOOST_CHECK_EQUAL(ent.GetResidueCount(), 1);
+ BOOST_CHECK_EQUAL(ent.GetAtomCount(), 1);
+}
+
+BOOST_AUTO_TEST_CASE(calpha_only_import_off)
+{
+ String fname("testfiles/pdb/calpha.pdb");
+ PDBReader reader(fname);
+ mol::EntityHandle ent=mol::CreateEntity();
+ reader.Import(ent);
+ BOOST_CHECK_EQUAL(ent.GetResidueCount(), 2);
+ BOOST_CHECK_EQUAL(ent.GetAtomCount(), 4);
+}
+
+BOOST_AUTO_TEST_CASE(anisou_record)
+{
+ String fname("testfiles/pdb/anisou.pdb");
+ PDBReader reader(fname);
+ mol::EntityHandle ent=mol::CreateEntity();
+ reader.Import(ent);
+ BOOST_REQUIRE(ent.GetAtomCount()==1);
+ mol::AtomHandle a1=ent.FindAtom("A", mol::ResNum(7), "N");
+ BOOST_REQUIRE(a1.IsValid());
+ mol::AtomProp props=a1.GetProp();
+ BOOST_CHECK_CLOSE( 0.0100, props.anisou(0, 0), 1e-4);
+ BOOST_CHECK_CLOSE(-0.0016, props.anisou(1, 0), 1e-4);
+ BOOST_CHECK_CLOSE(-0.0026, props.anisou(2, 0), 1e-4);
+ BOOST_CHECK_CLOSE(-0.0016, props.anisou(0, 1), 1e-4);
+ BOOST_CHECK_CLOSE( 0.0110, props.anisou(1, 1), 1e-4);
+ BOOST_CHECK_CLOSE(-0.0054, props.anisou(2, 1), 1e-4);
+ BOOST_CHECK_CLOSE(-0.0026, props.anisou(0, 2), 1e-4);
+ BOOST_CHECK_CLOSE(-0.0054, props.anisou(1, 2), 1e-4);
+ BOOST_CHECK_CLOSE( 0.0120, props.anisou(2, 2), 1e-4);
+}
+
+
BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/io/tests/testfiles/pdb/anisou.pdb b/modules/io/tests/testfiles/pdb/anisou.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..55692976ebb41d2288dac08652f7083967c03434
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/anisou.pdb
@@ -0,0 +1,2 @@
+ATOM 134 N GLU A 7 -3.391 15.554 9.400 1.00 3.46 C
+ANISOU 133 N GLU A 7 100 110 120 -16 -26 -54 N
diff --git a/modules/io/tests/testfiles/pdb/calpha.pdb b/modules/io/tests/testfiles/pdb/calpha.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..9e30b5c6b2c971639b95235b35784b84f07cec7f
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/calpha.pdb
@@ -0,0 +1,6 @@
+ATOM 134 CA GLU A 7 -3.391 15.554 9.400 1.00 3.46 C
+ANISOU 134 CA GLU A 7 443 511 361 -28 -37 -88 C
+ATOM 135 C GLU A 7 -3.799 15.410 10.865 1.00 3.42 C
+ANISOU 135 C GLU A 7 419 507 375 -14 -45 -103 C
+ATOM 136 O GLU A 7 -4.948 15.082 11.188 1.00 4.00 O
+HETATM 1469 CA CA A1000 46.224 7.128 -8.698 1.00 7.59 CA
\ No newline at end of file