From 12f78739ed742a4daeeeafe6c410b8ff8ff96ad3 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Fri, 5 Nov 2010 09:45:54 +0100
Subject: [PATCH] fix pdb output for alt atom locations
---
modules/io/src/mol/pdb_writer.cc | 3 ++-
modules/io/tests/test_io_pdb.cc | 25 +++++++++++++++++++++++++
2 files changed, 27 insertions(+), 1 deletion(-)
diff --git a/modules/io/src/mol/pdb_writer.cc b/modules/io/src/mol/pdb_writer.cc
index 8b16c2cce..94a6e8564 100644
--- a/modules/io/src/mol/pdb_writer.cc
+++ b/modules/io/src/mol/pdb_writer.cc
@@ -136,7 +136,8 @@ void write_atom(std::ostream& ostr, FormattedLine& line,
} else {
for (std::vector<String>::const_iterator
i=names.begin(), e=names.end(); i!=e; ++i) {
- p=atom.GetAltPos(*i);
+ geom::Mat4 tf=atom.GetEntity().GetTransformationMatrix();
+ p=geom::Vec3(tf*geom::Vec4(atom.GetAltPos(*i)));
line(30, 50).Clear();
if (i->size()>1) {
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index df8ff5295..5d78e6984 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -364,6 +364,31 @@ BOOST_AUTO_TEST_CASE(write_conect)
"testfiles/pdb/conect-out.pdb"));
}
+BOOST_AUTO_TEST_CASE(alt_loc_tf)
+{
+ String fname("testfiles/pdb/alt-loc.pdb");
+ // 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 ent=mol::CreateEntity();
+ PDBReader reader(fname);
+ reader.Import(ent);
+ String out_name("testfiles/pdb/alt-loc-tf-out.pdb");
+ {
+ PDBWriter writer(out_name);
+ geom::Mat4 shift;
+ shift.PasteTranslation(geom::Vec3(10,20,30));
+ ent.RequestXCSEditor().ApplyTransform(shift);
+ writer.Write(ent);
+ }
+ PDBReader r2(out_name);
+ mol::EntityHandle ent2=mol::CreateEntity();
+ r2.Import(ent2);
+ mol::ResidueHandle res1=ent2.FindResidue("A", mol::ResNum(1));
+ mol::AtomHandle a1=res1.FindAtom("N");
+ BOOST_CHECK_EQUAL(res1.GetAltAtomPos(a1, "A"), geom::Vec3(26,84,30));
+ BOOST_CHECK_EQUAL(res1.GetAltAtomPos(a1, "B"), geom::Vec3(18,-108,30));
+}
+
BOOST_AUTO_TEST_CASE(res_name_too_long)
{
std::stringstream out;
--
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