From 0f8c4f1938c5cca892da4dcc08bef3b890257411 Mon Sep 17 00:00:00 2001
From: Marco Biasini <mvbiasini@gmail.com>
Date: Tue, 11 Sep 2012 14:17:42 +0200
Subject: [PATCH] use rule-based processor for lddt
---
modules/mol/alg/src/lddt.cc | 60 +++++++++++++++++++++++++++++++++++++
1 file changed, 60 insertions(+)
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index 321ae803e..a2c5aedb9 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -30,19 +30,27 @@
#include <ost/io/mol/pdb_reader.hh>
#include <ost/io/io_exception.hh>
#include <ost/conop/conop.hh>
+#include <ost/conop/compound_lib.hh>
#include <ost/string_ref.hh>
#include <ost/conop/amino_acids.hh>
+#include <ost/conop/rule_based.hh>
#include <ost/mol/iterator.hh>
#include <ost/platform.hh>
#include <ost/log.hh>
+#if defined(__APPLE__)
+#include <mach-o/dyld.h>
+#endif
#include <ost/dyn_cast.hh>
using namespace ost;
using namespace ost::io;
+using namespace ost::conop;
using namespace ost::mol;
using namespace ost::mol::alg;
+
namespace po=boost::program_options;
+namespace fs=boost::filesystem;
// loads a file
EntityHandle load(const String& file, const IOProfile& profile)
@@ -108,6 +116,51 @@ std::pair<int,int> compute_coverage (const EntityView& v,const GlobalRDMap& glob
return std::make_pair<int,int>(first,second);
}
+CompoundLibPtr load_compound_lib(const String& custom_path)
+{
+ if (custom_path!="") {
+ if (fs::exists(custom_path)) {
+ return CompoundLib::Load(custom_path);
+ } else {
+ std::cerr << "Could not find compounds.chemlib at the provided location, trying other options" << std::endl;
+ }
+ }
+ if (fs::exists("compounds.chemlib")) {
+ return CompoundLib::Load("compounds.chemlib");
+ }
+ char result[ 1024 ];
+ CompoundLibPtr lib;
+ String exe_path;
+ #if defined(__APPLE__)
+ uint32_t size=1023;
+ if (!_NSGetExecutablePath(result, &size)) {
+ exe_path=String(result);
+ }
+ #else
+ ssize_t count = readlink( "/proc/self/exe", result, 1024 );
+ exe_path = std::string( result, (count > 0) ? count : 0 );
+ #endif
+ if (exe_path.empty()) {
+ std::cerr << "Could not determine the path of the molck executable. Will only "
+ "look for compounds.chemlib in the current working directory" << std::endl;
+ } else {
+ fs::path path_and_exe(exe_path);
+ fs::path path_only=path_and_exe.branch_path();
+ fs::path share_path = path_only.branch_path();
+ share_path = share_path / "share" / "openstructure" / "compounds.chemlib";
+
+ String share_path_string=BFPathToString(share_path);
+
+ if (fs::exists(share_path_string)) {
+ return CompoundLib::Load(share_path_string);
+ }
+ }
+ if (!lib) {
+ std::cerr << "Could not load compounds.chemlib" << std::endl;
+ exit(-1);
+ }
+ return CompoundLibPtr();
+}
int main (int argc, char **argv)
{
// sets some default values for parameters
@@ -124,6 +177,7 @@ int main (int argc, char **argv)
// parses options
String sel;
+ String custom_path;
bool structural_checks=false;
po::options_description desc("Options");
desc.add_options()
@@ -135,6 +189,7 @@ int main (int argc, char **argv)
("parameter-file,p", po::value<String>(), "stereo-chemical parameter file")
("verbosity,v", po::value<int>(), "verbosity level")
("bond_tolerance,b", po::value<Real>(), "tolerance in stddev for bonds")
+ ("complib", po::value<String>(&custom_path)->default_value(""),"location of the compound library file")
("angle_tolerance,a", po::value<Real>(), "tolerance in stddev for angles")
("inclusion_radius,r", po::value<Real>(), "distance inclusion radius")
("sequence_separation,i", po::value<int>(), "sequence separation")
@@ -153,6 +208,11 @@ int main (int argc, char **argv)
usage();
exit(-1);
}
+ conop::CompoundLibPtr lib = load_compound_lib(custom_path);
+ if (!lib) {
+ exit(0);
+ }
+ profile.processor = conop::RuleBasedProcessorPtr(new conop::RuleBasedProcessor(lib));
po::notify(vm);
if (vm.count("version")) {
std::cout << "Version: " << version << std::endl;
--
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