Updated Ligand Motifs Code

source/src/apps.src.settings

@@ -184,8 +184,10 @@ sources = {
 		"enzyme_design",
 	],
 	"public/motif_ligand_discovery": [
+		"determine_real_motifs",
 		"identify_ligand_motifs",
 		"ligand_discovery_search_protocol",
+		"remove_duplicate_motifs",
 	],
 	"public/pose_sewing": [
 		"MakeSegmentFile"

source/src/apps/public/motif_ligand_discovery/determine_real_motifs.cc

@@ -0,0 +1,151 @@
+// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
+// vi: set ts=2 noet:
+//
+// (c) Copyright Rosetta Commons Member Institutions.
+// (c) This file is part of the Rosetta software suite and is made available under license.
+// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
+// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
+// (c) addressed to University of Washington CoMotion, email: [email protected].
+
+/// @file
+/// @brief
+
+// libRosetta headers
+#include <basic/options/keys/in.OptionKeys.gen.hh>
+
+#include <sstream>
+#include <string>
+
+#include <devel/init.hh>
+#include <utility/excn/Exceptions.hh>
+#include <utility/string_util.hh>
+
+#include <protocols/motifs/IdentifyLigandMotifs.fwd.hh>
+#include <protocols/motifs/IdentifyLigandMotifs.hh>
+#include <protocols/motifs/Motif.hh>
+#include <protocols/motifs/MotifLibrary.hh>
+#include <protocols/motifs/motif_utils.hh>
+
+#include <core/io/pdb/pdb_writer.hh> // pose_from_pdb
+#include <core/pose/Pose.hh>
+
+#include <basic/Tracer.hh>
+
+#include <core/import_pose/import_pose.hh> // Need since refactor
+
+#include <basic/options/option.hh>
+
+// C++ headers
+//#include <cstdlib>
+#include <fstream>
+#include <iostream>
+#include <string>
+#include <algorithm>
+#include <utility/io/ozstream.hh>
+#include <utility/file/FileName.hh>
+#include <utility/file/file_sys_util.hh> // file_exists
+#include <utility/vector1.hh>
+
+// Time profiling header
+#include <time.h>
+
+using namespace core;
+//using namespace ObjexxFCL;
+using namespace pose;
+//using namespace chemical;
+using namespace scoring;
+//using namespace optimization;
+using namespace basic;
+using namespace options;
+using namespace OptionKeys;
+
+using utility::string_split;
+using utility::vector1;
+
+int
+main( int argc, char * argv [] )
+{
+	try {
+		static basic::Tracer ms_tr( "determine_real_motifs", basic::t_info );
+
+
+
+		devel::init( argc, argv ); // reading options--name should be more descriptive
+
+		//load in pdb(s)
+
+		ms_tr << "Making Pose of input pdb file(s)" << std::endl;
+
+		typedef vector1< utility::file::FileName > Filenames;
+		Filenames pdbnames;
+
+		//borrowing code from motif_ligand_packer_design.cc to take in a single or multiple pdb files (using -l or -s flags), and be able to iterate discovery upon all files
+		if ( option[ in::file::l ].user() ) {
+			Filenames listnames( option[ in::file::l ]().vector() );
+			for ( Filenames::const_iterator filename( listnames.begin() );
+					filename != listnames.end(); ++filename ) {
+				std::ifstream list( (*filename).name().c_str() );
+				while ( list ) {
+					std::string pdbname;
+					list >> pdbname;
+					pdbnames.push_back( pdbname );
+				}
+			}
+
+		} else if ( option[ in::file::s ].user() ) {
+			pdbnames = option[ in::file::s ]().vector();
+
+		} else {
+			std::cerr << "No files given: Use either -file:s or -file:l "
+				<< "to designate a single pdb or a list of pdbs"
+				<< std::endl;
+		}
+
+		//read in the compare library of motifs (presummably real motifs)
+		//create a vector that only stores the identity of the atoms  in the ligand (not their index  value); this vector will be empty, but is necessary to call wanted versions of overloaded  function to loading in the library
+		//version if we don't use this empty vector has potential to terminate the read of motifs early if a single bad motif is  read in, this version ditches the bad motif and keeps reading
+		utility::vector1< std::string > ligand_atom_names;
+		bool check_for_bad_motifs = true;
+		protocols::motifs::MotifLibrary real_motifs( protocols::motifs::get_LigandMotifLibrary_user(check_for_bad_motifs, ligand_atom_names) );
+		protocols::motifs::MotifCOPs real_motifcops = real_motifs.library();
+		ms_tr << "Collected motifs library with " << real_motifcops.size() << " motifs. " << std::endl;
+
+		//hash the library by residue and atoms
+		std::map<protocols::motifs::motif_atoms,protocols::motifs::MotifCOPs> hashed_real_library;
+		protocols::motifs::hash_motif_library_into_map(real_motifcops,hashed_real_library);
+
+		//create and use IdentifyLigandMotifs
+		IdentifyLigandMotifs ilm;
+
+		//iterate through all pdb files and run the real motif check
+		for ( Filenames::const_iterator filename( pdbnames.begin() ); filename != pdbnames.end(); ++filename ) {
+
+			if ( !utility::file::file_exists( *filename ) ) {
+				ms_tr << "WARNING! " << *filename << " does not exist!" << std::endl;
+				continue;
+			}
+
+			//get pdb name prefix for outputs:
+			//strip path and file type
+			std::string pdbprefix( string_split( string_split( *filename, '/' ).back(), '.' ).front() );
+
+			ms_tr << "On file " << *filename << " with pdb prefix of " << pdbprefix << std::endl;
+
+			//import pose from pdb
+			pose::Pose pose_pointer_helper;
+			core::import_pose::pose_from_file( pose_pointer_helper, *filename , core::import_pose::PDB_file);
+			pose::PoseOP pose(new pose::Pose(pose_pointer_helper));
+
+			//run evaluate_motifs_of_pose() on the pose
+			ilm.evaluate_motifs_of_pose(pose, hashed_real_library, pdbprefix);
+
+			//dump the pose to a pdb file and append _real_motif_data to the name so that the original is not overwriten
+			core::io::pdb::dump_pdb(*pose, pdbprefix + "_real_motif_data.pdb");
+		}
+
+	} catch (utility::excn::Exception const & e ) {
+		e.display();
+		return -1;
+	}
+	return 0;
+}

source/src/apps/public/motif_ligand_discovery/identify_ligand_motifs.cc

@@ -57,7 +57,7 @@ main( int argc, char * argv [] )
 		//create and use IdentifyLigandMotifs
 		IdentifyLigandMotifs ilm;
 		//create MotifLibrary to hold motif library that ILM will generate
-		//protocols::motifs::MotifLibrary motifs = ilm.process_file_list();
+
 		ilm.process_file_list();
 		ilm.write_motifs_to_disk();
 	} catch (utility::excn::Exception const & e ) {

source/src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc

@@ -62,7 +62,6 @@ using namespace protocols::dna;
 
 #include <basic/prof.hh>
 #include <basic/Tracer.hh>
-static basic::Tracer TR( "apps.pilot.motif_dna_packer_design" );
 
 #include <core/import_pose/import_pose.hh> // Need since refactor
 
@@ -73,10 +72,8 @@ static basic::Tracer TR( "apps.pilot.motif_dna_packer_design" );
 #include <utility/file/file_sys_util.hh> // file_exists
 #include <utility/file/FileName.hh>
 #include <utility/vector1.hh>
-using utility::vector1;
 #include <utility/string_util.hh>
 #include <utility/excn/Exceptions.hh>
-using utility::string_split;
 
 // c++ headers
 #include <fstream>
@@ -137,6 +134,8 @@ using namespace chemical;
 using namespace pack;
 using namespace task;
 using namespace scoring;
+using utility::string_split;
+using utility::vector1;
 
 ////////////////////////////////////////////////////////////////////////////////
 
@@ -240,7 +239,18 @@ main( int argc, char * argv [] )
 			pose::PoseOP pose(new pose::Pose(pose_pointer_helper));
 
 			//get discovery position
-			core::Size discovery_position = option[ OptionKeys::motifs::protein_discovery_locus ];
+			//core::Size discovery_position = option[ OptionKeys::motifs::protein_discovery_locus ];
+			//now using a vector instead of a single core::Size value
+			//read as int and then convert to core::Size
+			//utility::vector1<int> discovery_position_int = option[ OptionKeys::motifs::protein_discovery_locus ];
+			utility::vector1<core::Size> discovery_position;
+
+			utility::vector1<core::Size> discovery_positions_int = option[ OptionKeys::motifs::protein_discovery_locus ]();
+
+			//iteratively append discovery positions to the discovery_position vector
+			for ( const auto & position : discovery_positions_int ) {
+				discovery_position.push_back(position);
+			}
 
 			//declare LigandDiscoverySearch object
 			ms_tr << "Making LigandDiscoverySearch object" << std::endl;