From 9a6ea8e71c68b8b4f6d82b919527015845f874cc Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Wed, 17 Nov 2010 09:38:09 +0100
Subject: [PATCH] added executable to calculate LDT score
---
modules/mol/alg/src/CMakeLists.txt | 3 +
modules/mol/alg/src/ldt.cc | 94 ++++++++++++++++++++++++++++++
2 files changed, 97 insertions(+)
create mode 100644 modules/mol/alg/src/ldt.cc
diff --git a/modules/mol/alg/src/CMakeLists.txt b/modules/mol/alg/src/CMakeLists.txt
index e613a9c73..fef02349e 100644
--- a/modules/mol/alg/src/CMakeLists.txt
+++ b/modules/mol/alg/src/CMakeLists.txt
@@ -29,6 +29,9 @@ if (ENABLE_IMG)
set(MOL_ALG_DEPS ${MOL_ALG_DEPS} img img_alg)
endif()
+executable(NAME ldt SOURCES ldt.cc
+ DEPENDS_ON io mol_alg STATIC)
+
module(NAME mol_alg SOURCES ${OST_MOL_ALG_SOURCES}
HEADERS ${OST_MOL_ALG_HEADERS}
HEADER_OUTPUT_DIR ost/mol/alg
diff --git a/modules/mol/alg/src/ldt.cc b/modules/mol/alg/src/ldt.cc
new file mode 100644
index 000000000..589bd125f
--- /dev/null
+++ b/modules/mol/alg/src/ldt.cc
@@ -0,0 +1,94 @@
+#include <ost/mol/alg/local_dist_test.hh>
+#include <ost/io/mol/pdb_reader.hh>
+#include <ost/io/io_exception.hh>
+using namespace ost;
+using namespace ost::io;
+using namespace ost::mol;
+
+EntityHandle load(const String& file)
+{
+ try {
+ PDBReader reader(file);
+ if (reader.HasNext()) {
+ EntityHandle ent=CreateEntity();
+ reader.Import(ent);
+ return ent;
+ }
+ std::cerr << "ERROR: '" << file << "' does not contain any ATOM records. "
+ << "Are you sure this is a PDB file?" << std::endl;
+ return EntityHandle();
+ } catch (io::IOException& e) {
+ std::cerr << "ERROR: " << e.what() << std::endl;
+ return EntityHandle();
+ }
+}
+
+void usage()
+{
+ std::cerr << "usage: ldt [options] <mod1> [mod1 [mod2]] <ref>" << std::endl;
+ std::cerr << " -s selection performed on ref" << std::endl;
+ std::cerr << " -c use Calphas only" << std::endl;
+ std::cerr << " -f filter clashes (not implemented yet)" << std::endl;
+ std::cerr << " -t fault tolerant parsing" << std::endl;
+}
+
+int main (int argc, char* const *argv)
+{
+ // parse options
+ String sel;
+ int flags=0;
+ bool filter_clashes=false;
+ char ch=0;
+ while((ch=getopt(argc, argv, "ftcs:"))!=-1) {
+ switch (ch) {
+ case 'c':
+ flags|=PDB::CALPHA_ONLY;
+ break;
+ case 't':
+ flags|=PDB::SKIP_FAULTY_RECORDS;
+ break;
+ case 'f':
+ filter_clashes=true;
+ break;
+ case 's':
+ sel=optarg;
+ break;
+ case '?':
+ default:
+ usage();
+ return -1;
+ }
+ }
+ argc-=optind;
+ argv+=optind;
+ if (argc<2) {
+ usage();
+ return -1;
+ }
+ PDB::PushFlags(flags);
+
+ String ref_file=argv[argc-1];
+ EntityHandle ref=load(ref_file);
+ if (!ref) {
+ return -1;
+ }
+ EntityView ref_view=ref.Select(sel);
+ for (int i=0; i<argc-1; ++i) {
+ EntityHandle model=load(argv[i]);
+ if (!model) {
+ if (!(flags&PDB::SKIP_FAULTY_RECORDS)) {
+ return -1;
+ }
+ continue;
+ }
+ EntityView v=model.CreateFullView();
+ float cutoffs[]={0.5,1,2,4};
+ float ldt=0.0;
+ for (int n=0; n<4; ++n) {
+ ldt+=alg::LocalDistTest(v, ref_view, cutoffs[n], 8.0);
+ }
+ ldt/=4.0;
+ std::cout << argv[i] << " " << ldt << std::endl;
+ }
+ return 0;
+}
\ No newline at end of file
--
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