minimalCstHomology.cc File Reference

: Generates the minimal coordinate constraints necessary for fixing homology model. Also creates fasta with virtual. @usage: -in::file::alignment alignment.filt -in::file::template_pdb <pdb names from within the alignment> -in:file:coordCsts <pdb names from within the alignment> -in:file:fasta <fasta name> More...

#include <utility/exit.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <core/types.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <basic/Tracer.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/import_pose/import_pose.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/sequence/util.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/id/SequenceMapping.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/relax/cst_util.hh>
#include <utility/options/keys/FileOptionKey.fwd.hh>
#include <utility/options/keys/FileOptionKey.hh>
#include <utility/options/keys/FileVectorOptionKey.fwd.hh>
#include <utility/options/keys/FileVectorOptionKey.hh>
#include <utility/options/keys/BooleanOptionKey.fwd.hh>
#include <utility/options/keys/BooleanOptionKey.hh>
#include <devel/init.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/relax.OptionKeys.gen.hh>
#include <ObjexxFCL/format.hh>
#include <fstream>
#include <map>
#include <set>
#include <sstream>
#include <devel/cstEnergyBalance/minimalCstRelaxUtil.hh>

Namespaces
	minimalCstHomology

Functions
void	output_alignments (vector1< SequenceAlignment > alns, std::ostream &out)
map< string, std::set< Size > >	input_coordCstsMapped (vector1< std::string >const &fn_list)
std::map< std::string, core::pose::Pose >	poses_from_cmd_line (utility::vector1< std::string > const &fn_list)
std::set< Size >	removeConstraintsNearGap (std::set< Size > caAtomsToConstrainAll, SequenceAlignment aln, Size gapSize)
bool	calc_outputCoordCsts (SequenceOP fastaSequenceOP, map< string, SequenceAlignment > alnData, map< string, Pose > poseData, map< string, set< Size > > coordCstsData, Size nResFromGapExclude, Size minNumCoordCsts, bool only_res_out)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	tr ("minimalCstHomology")
basic::options::FileVectorOptionKey	minimalCstHomology::coordCstFiles ("minimalCstHomology:coordCstFiles")
basic::options::BooleanOptionKey	minimalCstHomology::only_res_out ("minimalCstHomology:only_res_out")

Detailed Description

: Generates the minimal coordinate constraints necessary for fixing homology model. Also creates fasta with virtual. @usage: -in::file::alignment alignment.filt -in::file::template_pdb <pdb names from within the alignment> -in:file:coordCsts <pdb names from within the alignment> -in:file:fasta <fasta name>

Author

TJ Brunette {tjbru.nosp@m.nett.nosp@m.e@gma.nosp@m.il.c.nosp@m.om}

Function Documentation

calc_outputCoordCsts()

bool calc_outputCoordCsts	(	SequenceOP	fastaSequenceOP,
		map< string, SequenceAlignment >	alnData,
		map< string, Pose >	poseData,
		map< string, set< Size > >	coordCstsData,
		Size	nResFromGapExclude,
		Size	minNumCoordCsts,
		bool	only_res_out
	)

References subloop_histogram::iterator, minimalCstHomology::only_res_out, output_alignments(), removeConstraintsNearGap(), and utility_exit_with_message.

Referenced by main().

input_coordCstsMapped()

map<string,std::set<Size> > input_coordCstsMapped

(

vector1< std::string >const &

fn_list

)

References end, utility::file_basename(), utility::file::file_exists(), file_exists(), and pair.

Referenced by main().

main()

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

References argv, calc_outputCoordCsts(), basic::options::OptionKeys::chemical::chemical, minimalCstHomology::coordCstFiles, test.T009_Exceptions::e, in::file::fasta(), utility::file_basename(), basic::init(), input_alignments(), input_alignmentsMapped(), input_coordCstsMapped(), minimalCstHomology::only_res_out, option, poses_from_cmd_line(), basic::options::OptionKeys::in::file::silent, and in::file::template_pdb().

output_alignments()

void output_alignments	(	vector1< SequenceAlignment >	alns,
		std::ostream &	out
	)

References create_a3b_hbs::ii.

Referenced by calc_outputCoordCsts().

poses_from_cmd_line()

std::map< std::string, core::pose::Pose > poses_from_cmd_line

(

utility::vector1< std::string > const &

fn_list

)

References basic::options::OptionKeys::chemical::chemical, end, utility::file_basename(), utility::file::file_exists(), file_exists(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::mp::assembly::poses.

Referenced by main().

removeConstraintsNearGap()

std::set< Size > removeConstraintsNearGap	(	std::set< Size >	caAtomsToConstrainAll,
		SequenceAlignment	aln,
		Size	gapSize
	)

References aln, get_terminal_aln_res(), create_a3b_hbs::ii, enumerate_junctions::int, subloop_histogram::iterator, create_a3b_hbs::nres, pna::resi, and basic::options::OptionKeys::relax::sequence.

Referenced by calc_outputCoordCsts().

Variable Documentation

tr

basic::Tracer tr("minimalCstHomology") ( "minimalCstHomology"  )

static