InterfaceMutMaker.cc File Reference

Makes a mutation from a command line flag and outputs wt and mut complex and separated structures. More...

#include <utility/io/izstream.hh>
#include <devel/init.hh>
#include <core/chemical/AA.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Edge.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBPoseMap.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionInfo.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/conformation/Conformation.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/simple_moves/SetReturningPackRotamersMover.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/pose_metric_calculators/NeighborhoodByDistanceCalculator.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <basic/MetricValue.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <ObjexxFCL/format.hh>
#include <sstream>
#include <iostream>
#include <string>
#include <stdlib.h>
#include <core/import_pose/import_pose.hh>

Namespaces
	InterfaceMutMaker

Enumerations
enum	Index {   chain_index = 1 , wt_index = 2 , res_index = 3 , mut_index = 4 ,   chain_index = 1 , start_index = 2 , end_index = 3 , max_neighbors = 16 ,   trans = 1 , rot = 2 }

Functions
void	tokenize_string (const vector1< std::string > &str_vector, utility::vector1< utility::vector1< std::string > > &tokens, const std::string &delimiters=" ")
pose::Pose	reorder_foldtree (core::pose::Pose &pose, utility::vector1< std::string > &mobile_chains_string, core::Size &mobile_jump)
pose::Pose	split_chains (core::pose::Pose &pose, scoring::ScoreFunctionOP &scorefxn, Size &jump)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("InterfaceMutMaker")
BooleanOptionKey const	InterfaceMutMaker::allow_rbmin ("InterfaceMutMaker::allow_rbmin")
BooleanOptionKey const	InterfaceMutMaker::output_all_packruns ("InterfaceMutMaker::output_all_packruns")
StringVectorOptionKey const	InterfaceMutMaker::mutation ("InterfaceMutMaker::mutation")
StringOptionKey const	InterfaceMutMaker::mutation_file ("InterfaceMutMaker::mutation_file")
StringVectorOptionKey const	InterfaceMutMaker::movechains ("InterfaceMutMaker::movechains")

Detailed Description

Makes a mutation from a command line flag and outputs wt and mut complex and separated structures.

Author

Ben Stranges

Enumeration Type Documentation

Index

enum Index

Enumerator
chain_index
wt_index
res_index
mut_index
chain_index
start_index
end_index
max_neighbors
trans
rot

Function Documentation

main()

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

References InterfaceMutMaker::allow_rbmin, argv, utility::file::FileName::base(), chain_index, utility::io::oc::cout, test.T009_Exceptions::e, end, getline(), ObjexxFCL::format::I(), create_a3b_hbs::ii, basic::init(), beta_nonlocal::jj, make_symmdef_file_denovo::jump_num, oop_conformations::length, line, vancomycin::min_mover, basic::options::OptionKeys::dna::specificity::min_type, InterfaceMutMaker::movechains, basic::options::OptionKeys::in::file::movemap, mut_index, InterfaceMutMaker::mutation, InterfaceMutMaker::mutation_file, utility::file::FileName::name(), in::file::native(), docking::native_pose, packing::ndruns(), num_chains(), basic::options::option, option, basic::options::OptionKeys::frags::contacts::output_all, InterfaceMutMaker::output_all_packruns, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, reorder_foldtree(), res_index, predPRE::resnum, in::file::s(), oop_conformations::scorefxn, split_chains(), challenge::ss, basic::options::start_file(), tokenize_string(), TR, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, utility_exit_with_message_status, basic::MetricValue< T >::value(), value, and wt_index.

reorder_foldtree()

pose::Pose reorder_foldtree	(	core::pose::Pose &	pose,
		utility::vector1< std::string > &	mobile_chains_string,
		core::Size &	mobile_jump
	)

References create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::pose, TR, and utility_exit_with_message_status.

Referenced by main().

split_chains()

pose::Pose split_chains	(	core::pose::Pose &	pose,
		scoring::ScoreFunctionOP &	scorefxn,
		Size &	jump
	)

References erraser_util::copy(), beta_nonlocal::pose, and beta_nonlocal::translate.

Referenced by main().

tokenize_string()

void tokenize_string	(	const vector1< std::string > &	str_vector,
		utility::vector1< utility::vector1< std::string > > &	tokens,
		const std::string &	delimiters = " "
	)

References create_a3b_hbs::ii, make_symmdef_file_denovo::pos, and str().

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("InterfaceMutMaker") ( "InterfaceMutMaker"  )

static

Referenced by main(), and reorder_foldtree().