#include <devel/dna/ProteinDNA_Relax.hh>
#include <protocols/viewer/viewers.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/func/Func.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <utility/excn/Exceptions.hh>
#include <core/conformation/Residue.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pose/Pose.hh>
#include <basic/options/util.hh>
#include <basic/options/keys/dna.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/string.functions.hh>
#include <basic/Tracer.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/scoring/constraints/Constraint.hh>

Functions
void *	my_main (void *)

int	main (int argc, char *argv[])

Variables
static basic::Tracer	tt ("demo.phil.dimer_relax", basic::t_trace)

static basic::Tracer	td ("demo.phil.dimer_relax", basic::t_debug)

static basic::Tracer	ti ("demo.phil.dimer_relax", basic::t_info)

static basic::Tracer	tw ("demo.phil.dimer_relax", basic::t_warning)

Function Documentation

◆ main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, test.T009_Exceptions::e, basic::init(), my_main(), and viewer_main().

◆ my_main()

void* my_main ( void * )

void setup_dimer_relax_pose( Pose & pose ) { Pose const start_pose( pose );

foldtree: dont currently need dna-flexibility foldtree

choose jump points for DNA->protein jumps

requirements: >=4 chains total, 1st 2 protein and 1st 2 DNA taken as simulation chains

Size const nchains( pose.conformation().num_chains() ); assert( nchains >= 4 ); Size pchain1(0), pchain2(0), dchain1(0), dchain2(0); for ( Size i=1; i<= nchains; ++i ) { Residue const & rsd( pose.residue( pose.conformation().chain_begin(i) ) ); if ( rsd.is_protein() ) { if ( !pchain1 ) pchain1 = i; else if ( !pchain2 ) pchain2 = i; } else if ( rsd.is_DNA() ) { if ( !dchain1 ) dchain1 = i; else if ( !dchain2 ) dchain2 = i; } }

make a new pose pose.clear(); vector1< Size > chains; chains.push_back( dchain1 ); chains.push_back( dchain2 ); chains.push_back( pchain1 ); chains.push_back( pchain2 ); append_chains_from_pose( pose, start_pose, chains ); // in pose/util.cc

look for anchor points to the protein chains find_protein_DNA_anchor_point( setup_chain_mask( pose, 3 ), prot_root1, dna_anchor1 ); find_protein_DNA_anchor_point( setup_chain_mask( pose, 4 ), prot_root2, dna_anchor2 );

FoldTree f( pose.size() ); f.new_jump( dna_anchor1, prot_root1, pose.conformation().chain_end(2) ); f.new_jump( dna_anchor2, prot_root2, pose.conformation().chain_end(3) ); f.new_jump( dna_anchor1, dna_anchor2, pose.conformation().chain_end(1) ); f.reorder( dna_anchor1 ); pose.fold_tree(f);

}

References utility::io::oc::cout, lactamize::filename, create_a3b_hbs::i, ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, local::nstruct, option, options, drrafter_rna::output_tag, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::abinitio::relax, basic::options::OptionKeys::dna::specificity::score_function, oop_conformations::scorefxn, basic::options::start_file(), and utility_exit_with_message.