From 37d97daf9474361d23ea6e3e91adc38a2aea3121 Mon Sep 17 00:00:00 2001
From: tobias <tobias@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 22 Apr 2010 11:32:47 +0000
Subject: [PATCH] allow export to CHARMM CRD file format
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2105 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/io/src/mol/entity_io_crd_handler.cc | 62 +++++++++++++++++++--
modules/io/src/mol/entity_io_crd_handler.hh | 17 ++++++
2 files changed, 73 insertions(+), 6 deletions(-)
diff --git a/modules/io/src/mol/entity_io_crd_handler.cc b/modules/io/src/mol/entity_io_crd_handler.cc
index cfbb7efcc..e89b294f9 100644
--- a/modules/io/src/mol/entity_io_crd_handler.cc
+++ b/modules/io/src/mol/entity_io_crd_handler.cc
@@ -154,7 +154,48 @@ void CRDReader::ParseAndAddAtom(const String& line, mol::EntityHandle& ent)
++atom_count_;
}
+CRDWriter::CRDWriter(std::ostream& ostream) :
+ outfile_(), outstream_(ostream), atom_count_(0)
+{}
+CRDWriter::CRDWriter(const boost::filesystem::path& filename) :
+ outfile_(filename.file_string().c_str()), outstream_(outfile_),
+ atom_count_(0)
+{}
+
+CRDWriter::CRDWriter(const String& filename) :
+ outfile_(filename.c_str()), outstream_(outfile_), atom_count_(0)
+{}
+
+void CRDWriter::WriteHeader(const mol::EntityView& ent)
+{
+ outstream_ << "* COOR FILE CREATED BY OPENSTRUCTURE" << std::endl;
+ outstream_ << "*" << std::endl;
+ outstream_ << ent.GetAtomCount() << std::endl;
+}
+
+bool CRDWriter::VisitAtom(const mol::AtomHandle& atom)
+{
+ atom_count_++;
+ String e_name=atom.GetEntity().GetName();
+ if (e_name=="") {
+ e_name="MOL";
+ }
+ mol::ResidueHandle res=atom.GetResidue();
+ outstream_ << format("%5i") % atom_count_
+ << format("%5i") % res.GetNumber() << " "
+ << format("%4s") % res.GetKey() << " "
+ << format("%-4s") % atom.GetName()
+ << format("%10.5f") % atom.GetPos().GetX()
+ << format("%10.5f") % atom.GetPos().GetY()
+ << format("%10.5f") % atom.GetPos().GetZ() << " "
+ << format("%-4s") % e_name << " "
+ << format("%-5i") % res.GetNumber() << " "
+ << format("%8.5f") % atom.GetProp().b_factor
+ << std::endl;
+
+ return true;
+}
bool EntityIOCRDHandler::RequiresBuilder() const
{
@@ -168,9 +209,22 @@ void EntityIOCRDHandler::Import(mol::EntityHandle& ent,
reader.Import(ent);
}
+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);
+}
+
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);
}
namespace {
@@ -201,7 +255,7 @@ bool EntityIOCRDHandler::ProvidesImport(const boost::filesystem::path& loc,
bool EntityIOCRDHandler::ProvidesExport(const boost::filesystem::path& loc,
const String& type)
{
- return false;
+ return crd_handler_is_responsible_for(loc, type);
}
mol::EntityHandle LoadCRD(const String& file_name)
@@ -224,11 +278,7 @@ void EntityIOCRDHandler::Import(mol::EntityHandle& ent,
}
-void EntityIOCRDHandler::Export(const mol::EntityView& ent,
- std::ostream& stream) const
-{
- throw IOException("CRD format does not support export to stream");
-}
+
}} // ns
diff --git a/modules/io/src/mol/entity_io_crd_handler.hh b/modules/io/src/mol/entity_io_crd_handler.hh
index ceb635f81..29ffa6705 100644
--- a/modules/io/src/mol/entity_io_crd_handler.hh
+++ b/modules/io/src/mol/entity_io_crd_handler.hh
@@ -52,6 +52,23 @@ private:
boost::iostreams::filtering_stream<boost::iostreams::input> in_;
};
+
+class DLLEXPORT_OST_IO CRDWriter : public mol::EntityVisitor {
+public:
+ CRDWriter(const String& filename);
+ CRDWriter(const boost::filesystem::path& filename);
+ CRDWriter(std::ostream& outstream);
+
+ virtual bool VisitAtom(const mol::AtomHandle& atom);
+
+ void WriteHeader(const mol::EntityView& ent);
+
+private:
+ std::ofstream outfile_;
+ std::ostream& outstream_;
+ int atom_count_;
+};
+
class DLLEXPORT_OST_IO EntityIOCRDHandler: public EntityIOHandler {
public:
virtual void Import(mol::EntityHandle& ent, const boost::filesystem::path& loc);
--
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