Support chain designations of multiple letters.

source/src/apps/pilot/ameya/mixedMC.cc

@@ -72,7 +72,7 @@ get_movable_jumps(
 	using namespace core;
 	using namespace protocols;
 	pose::PDBInfoCOP pdb_info = pose.pdb_info();
-	char second_chain = '_';
+	std::string second_chain = "_";
 	Size cutpoint = 0;
 	utility::vector1_int movable_jumps_;
 	kinematics::FoldTree f( pose.fold_tree() );

source/src/apps/pilot/delucasl/generate_ligand_start_position_file.cc

@@ -38,7 +38,7 @@ int main(int argc, char*argv[])
 		devel::init(argc,argv);
 
 
-		char ligand_id = basic::options::option[basic::options::OptionKeys::ligand_chain]()[0];
+		std::string ligand_id = basic::options::option[basic::options::OptionKeys::ligand_chain]();
 		std::string outfile_path =  basic::options::option[basic::options::OptionKeys::start_position_file]();
 
 		utility::vector1<std::string> file_names = basic::options::start_files();

source/src/apps/pilot/jkleman/interface_statistics.cc

@@ -42,6 +42,7 @@
 #include <core/pose/util.hh>
 #include <core/pose/chains_util.hh>
 #include <core/pose/subpose_manipulation_util.hh>
+#include <core/pose/DockingPartners.hh>
 #include <core/types.hh>
 #include <protocols/jd2/JobDistributor.hh>
 #include <protocols/jd2/Job.hh>
@@ -194,10 +195,7 @@ class MPInterfaceStatistics : public Mover {
 	core::scoring::ScoreFunctionOP sfxn_;
 
 	/// @brief Partners;
-	std::string partner_;
-
-	/// @brief Partners split up
-	utility::vector1< std::string > partners_;
+	core::pose::DockingPartners partner_;
 
 	/// @brief jumps
 	utility::vector1< core::Size > jumps_;
@@ -206,7 +204,7 @@ class MPInterfaceStatistics : public Mover {
 	utility::vector1< Interface > interfaces_;
 
 	/// @brief Chains to consider for computing statistics
-	std::string chains_;
+	utility::vector1< std::string > chains_;
 
 	/// @brief Unique chains to minimize bias from multiple counts
 	utility::vector1< bool > uniq_;
@@ -231,8 +229,6 @@ class MPInterfaceStatistics : public Mover {
 MPInterfaceStatistics::MPInterfaceStatistics() :
 	Mover(),
 	sfxn_(),
-	partner_(),
-	partners_(),
 	jumps_(),
 	interfaces_(),
 	chains_(),
@@ -296,9 +292,9 @@ void MPInterfaceStatistics::apply( Pose & pose ) {
 		// writing a scorefile anyway, we might as well...
 		sfxn_ = core::scoring::ScoreFunctionFactory::create_score_function( "mpframework_smooth_fa_2012.wts" );
 
-		// get foldtree from partners and movable jumps
 		// see ASCII art in protocols/membrane/util for how the foldtree is set up
-		jumps_ = create_membrane_multi_partner_foldtree_anchor_tmcom( pose, partner_ );
+		utility::vector1< utility::vector1< std::string > > partner_chains( {partner_.partner1, partner_.partner2} );
+		jumps_ = create_membrane_multi_partner_foldtree_anchor_tmcom( pose, partner_chains );
 		TR << "membrane interface jumps_ from foldtree: " << std::endl;
 		for ( core::Size i = 1; i <= jumps_.size(); ++i ) {
 			TR << jumps_[ i ] << " ";
@@ -389,7 +385,7 @@ void MPInterfaceStatistics::init_from_cmd() {
 	// docking partners
 	// requires all chains in the PDB file and is only for setting up the foldtree!!!
 	if ( option[ OptionKeys::docking::partners ].user() ) {
-		partner_ = option[ OptionKeys::docking::partners ]();
+		partner_ = core::pose::DockingPartners::docking_partners_from_string( option[ OptionKeys::docking::partners ]() );
 	} else {
 		utility_exit_with_message( "Please provide -docking:partners flag!" );
 	}
@@ -401,7 +397,10 @@ void MPInterfaceStatistics::init_from_cmd() {
 
 	// which chains to consider for getting statistics
 	if ( option[ OptionKeys::intf::chains ].user() ) {
-		chains_ = option[ OptionKeys::intf::chains ]();
+		chains_.clear();
+		for ( char c: option[ OptionKeys::intf::chains ]() ) {
+			chains_.push_back( std::string{c} );
+		}
 	}
 
 } // init from commandline
@@ -418,8 +417,7 @@ utility::vector1< bool > MPInterfaceStatistics::get_chains_from_cmd( Pose & pose
 		// get chain
 		core::Size res_chain = pose.residue( r ).chain();
 
-		// go through chains in string, 0-indexed
-		for ( char c : chains_ ) {
+		for ( std::string const & c : chains_ ) {
 
 			// get chain
 			core::Size chain = get_chain_id_from_chain( c, pose );
@@ -499,31 +497,20 @@ Real MPInterfaceStatistics::get_size( Pose & pose ) {
 	utility::vector1< core::Size > chains( get_chains( pose ) );
 	utility::vector1< Pose > pose_partners;
 
-	// go through partners and append the chains into subposes to fit the partners
-	for ( core::Size p = 1; p <= partners_.size(); ++p ) {
-
+	for ( auto const & p: { partner_.partner1, partner_.partner2 } ) {
 		Pose subpose;
-
-		// go through chains in partner, string indexes from 0
-		for ( char c : partners_[ p ] ) {
-
-			// get chainID from chain
+		for ( std::string const & c: p ) {
 			core::Size chainid( get_chain_id_from_chain( c, pose ) );
-
-			// go through pose chains to find pose chain in vector
 			for ( core::Size i = 1; i <= pose_chains.size(); ++i ) {
-
 				// if the chainids match, append chain to subpose
 				if ( chainid == chains[ i ] ) {
 					append_pose_to_pose( subpose, *pose_chains[ i ], true );
 				}
-
-			} // chains
+			} // pose chains
 		} // chains in partner
 
 		// add subpose to vector
 		pose_partners.push_back( subpose );
-
 	} // partners
 
 	// get total SASA
@@ -968,11 +955,6 @@ Size MPInterfaceStatistics::get_number_hbonds( Pose & pose ) {
 	using namespace core::scoring;
 	using namespace core::scoring::hbonds;
 
-	// get the partners
-	utility::vector1< std::string > partners( utility::string_split( partner_, '_' ) );
-	utility::vector1< std::string > partner1( utility::split( partners[1] ) );
-	utility::vector1< std::string > partner2( utility::split( partners[2] ) );
-
 	// get the Hbonds
 	hbonds::HBondDatabaseCOP hb_database(hbonds::HBondDatabase::get_database());
 	hbonds::HBondSet hb_set;
@@ -996,13 +978,13 @@ Size MPInterfaceStatistics::get_number_hbonds( Pose & pose ) {
 		bool acc_in_1( false );
 
 		// donor in partner1?
-		for ( Size j = 1; j <= partner1.size(); ++j ) {
-			don_in_1 = res_in_chain( pose, don, partner1[ j ] );
+		for ( Size j = 1; j <= partner_.partner1.size(); ++j ) {
+			don_in_1 = res_in_chain( pose, don, partner_.partner1[ j ] );
 		}
 
 		// acceptor in partner1?
-		for ( Size j = 1; j <= partner1.size(); ++j ) {
-			acc_in_1 = res_in_chain( pose, acc, partner1[ j ] );
+		for ( Size j = 1; j <= partner_.partner1.size(); ++j ) {
+			acc_in_1 = res_in_chain( pose, acc, partner_.partner1[ j ] );
 		}
 
 		//  TR << "hbond: don " << don << ", acc " << acc;
@@ -1352,9 +1334,6 @@ void MPInterfaceStatistics::fill_vectors_with_data( Pose & pose ) {
 /// @detail This is for 2-body docking
 void MPInterfaceStatistics::calculate_interfaces( Pose & pose ) {
 
-	// fill partners_ vector
-	partners_ = utility::string_split( partner_, '_' );
-
 	// initialize intf_ vector with false for each residue
 	utility::vector1< bool > tmp( pose.size(), false );
 	intf_ = tmp;

source/src/apps/pilot/jtseffer/SID_rescore.cc

@@ -121,7 +121,7 @@ void calc_RF( const utility::vector1<core::pose::PoseOP> &pose_by_chain, core::R
 
 }
 
-void predict_AE( const core::pose::PoseOP &pose, core::Real &AE_pred, const std::string &interface, const core::Real &HSA_weight, const core::Real &NR_weight, const core::Real &RF_weight, const core::Real &RF, const core::Real &n_ints ) {
+void predict_AE( const core::pose::PoseOP &pose, core::Real &AE_pred, const core::pose::DockingPartners &interface, const core::Real &HSA_weight, const core::Real &NR_weight, const core::Real &RF_weight, const core::Real &RF, const core::Real &n_ints ) {
 	protocols::analysis::InterfaceAnalyzerMoverOP IAM = utility::pointer::make_shared< protocols::analysis::InterfaceAnalyzerMover >(interface, true, core::scoring::ScoreFunctionFactory::create_score_function("ref2015")/*scorefxn_*/, false/*compute_packstat_*/, false/*pack_together_*/, false/*pack_separated_*/);
 
 	core::scoring::ScoreFunctionOP sfxn = core::scoring::get_score_function();
@@ -195,7 +195,7 @@ main( int argc, char * argv [] )
 		core::Real AE_exp( option[ AE ].value() );
 		core::Real ints( option[ n_ints ].value() );
 		AE_exp = AE_exp / ints;
-		std::string intf( option[ interface ].value() );
+		core::pose::DockingPartners intf = core::pose::DockingPartners::docking_partners_from_string( option[ interface ].value() );
 
 		//SID weights
 		core::Real HSA_weight = 0.121422027;

source/src/apps/pilot/kdrew/ld_converter.cc

@@ -171,7 +171,7 @@ LDConverterMover::apply(
 	core::pose::PDBPoseMap const & pose_map(pose.pdb_info()->pdb2pose());
 	//kdrew: chain and res numbers are a pair so increment by 2
 	for ( Size i = 1; i <= l_pdb_positions.size(); i=i+2 ) {
-		core::Size respos = pose_map.find( *l_pdb_positions[i].c_str(), atoi(l_pdb_positions[i+1].c_str()) );
+		core::Size respos = pose_map.find( l_pdb_positions[i], atoi(l_pdb_positions[i+1].c_str()) );
 		l_positions.push_back(respos);
 	}
 
@@ -192,7 +192,7 @@ LDConverterMover::apply(
 	//kdrew: parse pdb numbering in convert_pdb_position options
 	//kdrew: chain and res numbers are a pair so increment by 2
 	for ( Size i = 1; i <= d_pdb_positions.size(); i=i+2 ) {
-		core::Size respos = pose_map.find( *d_pdb_positions[i].c_str(), std::atoi(d_pdb_positions[i+1].c_str()) );
+		core::Size respos = pose_map.find( d_pdb_positions[i], std::atoi(d_pdb_positions[i+1].c_str()) );
 		d_positions.push_back(respos);
 
 	}

source/src/apps/pilot/will/sym_multicomp_test.cc

@@ -56,9 +56,9 @@ bool check_coords_match(
 
 
 vector1<Vec>
-chain_coords(Pose const & pose, char chain, core::Size nres) {
+chain_coords(Pose const & pose, std::string const & chain, core::Size nres) {
 	vector1<Vec> result;
-	std::map<core::Size,char> conf2chain = core::pose::conf2pdb_chain(pose);
+	std::map<core::Size,std::string> conf2chain = core::pose::conf2pdb_chain(pose);
 	for ( core::Size i = 1; i <= nres; ++i ) {
 		if ( conf2chain[pose.chain(i)] == chain ) {
 			result.push_back(pose.xyz(AtomID(2,i)));
@@ -67,9 +67,9 @@ chain_coords(Pose const & pose, char chain, core::Size nres) {
 	return result;
 }
 vector1<Vec>
-non_chain_coords(Pose const & pose, char chain, core::Size nres) {
+non_chain_coords(Pose const & pose, std::string const & chain, core::Size nres) {
 	vector1<Vec> result;
-	std::map<core::Size,char> conf2chain = core::pose::conf2pdb_chain(pose);
+	std::map<core::Size,std::string> conf2chain = core::pose::conf2pdb_chain(pose);
 	for ( core::Size i = 1; i <= nres; ++i ) {
 		if ( conf2chain[pose.chain(i)] != chain ) {
 			result.push_back(pose.xyz(AtomID(2,i)));
@@ -109,7 +109,7 @@ int main (int argc, char *argv[]) {
 			std::map<core::Size,core::conformation::symmetry::SymDof> dofs( syminfo->get_dofs() );
 			for ( std::map<core::Size,core::conformation::symmetry::SymDof>::const_iterator i = dofs.begin(); i != dofs.end(); ++i ) {
 				std::string jname = syminfo->get_jump_name(i->first);
-				char chain = jname[jname.size()-1];
+				std::string chain{ jname[jname.size()-1] };
 				vector1<Vec> preC   =     chain_coords(pose,chain,nres);
 				vector1<Vec> preNoC = non_chain_coords(pose,chain,nres);
 				move_jump(pose,i->first);

source/src/apps/public/analysis/InterfaceAnalyzer.cc

@@ -25,6 +25,7 @@
 #include <core/scoring/ScoreFunctionFactory.hh>
 
 #include <core/pose/Pose.hh>
+#include <core/pose/DockingPartners.hh>
 #include <core/pose/PDBInfo.hh>
 
 // Utility Headers
@@ -114,7 +115,7 @@ void IAMover::assign_IA_mover(core::pose::Pose & pose){
 		std::set< int > fixed_chains; //This is a set of the CHAIN IDs, not residue ids
 		TR << "Fixed chains are: " ;
 		for ( core::Size j = 1; j <= fixed_chains_string.size(); ++j ) {
-			char this_chain (fixed_chains_string[ j ][0]);
+			std::string this_chain = fixed_chains_string[ j ];
 			for ( core::Size i = 1; i<=pose.size(); ++i ) {
 				if ( pose.pdb_info()->chain( i ) == this_chain ) {
 					fixed_chains.insert( pose.chain(i) );
@@ -135,7 +136,7 @@ void IAMover::assign_IA_mover(core::pose::Pose & pose){
 			jobname
 		);
 	} else if ( basic::options::option[interface].active() ) {
-		std::string dock_chains = basic::options::option[interface].value();
+		core::pose::DockingPartners dock_chains = core::pose::DockingPartners::docking_partners_from_string( basic::options::option[interface].value() );
 		TR << "Using interface definition: "<<dock_chains <<std::endl;
 		IAM_ = utility::pointer::make_shared< protocols::analysis::InterfaceAnalyzerMover >(
 			dock_chains,