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Rosetta
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Program which scans for backbone positions in a list of scaffolds with low rmsd to specific positions in a reference structure by building inverse rotamers. More...
#include <basic/options/util.hh>#include <basic/Tracer.hh>#include <ObjexxFCL/format.hh>#include <utility/file/file_sys_util.hh>#include <utility/file/FileName.hh>#include <utility/vector1.hh>#include <core/conformation/Residue.fwd.hh>#include <utility/graph/Graph.hh>#include <core/id/AtomID.hh>#include <core/id/AtomID_Map.hh>#include <core/io/pdb/pdb_writer.hh>#include <core/import_pose/import_pose.hh>#include <core/pack/packer_neighbors.hh>#include <core/pack/task/TaskFactory.hh>#include <core/pack/rotamer_set/RotamerSet.hh>#include <core/pack/rotamer_set/RotamerSetFactory.hh>#include <core/pose/Pose.hh>#include <core/pose/PDBInfo.hh>#include <core/pose/init_id_map.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/rms_util.hh>#include <devel/init.hh>#include <iostream>#include <cstdio>Namespaces | |
| find_position_matches_using_inverse_rotamers | |
Functions | |
| void | init_usage_prompt (std::string exe) |
| the usage prompt that gets printed when the user doesn't enter all the required command line arguments More... | |
| void | build_bb_independent_rotamers (core::chemical::ResidueTypeCOP target_res_restype, utility::vector1< core::conformation::ResidueOP > &rotamers) |
| function which returns a set of backbone-independent rotamers for the given ResidueType. basically a copy of the function in core::pack::rotamer_set::bb_independent_rotamers.hh, but it samples more chi angles thereby building more rotamers. More... | |
| void | tokenize_string (const std::string &str, utility::vector1< std::string > &tokens, const std::string &delimiters=" ") |
| void | parse_position (std::string position, char &chain, core::Size &pdb_resnum, char &icode) |
| void | dump_rotamerset_pdb (utility::vector1< core::conformation::ResidueCOP > const &rotamers, std::string const &filename) |
| function which writes out a PDB file of the rotamers in the passed in vector this should really be a function of the RotamerSet class, but it's not. there is a similar function in the class RotamerSets, but I don't want the multiple MODELS in there. only using this function to check that the inverse rotamers are aligned properly to the reference residue(s). More... | |
| int | main (int argc, char *argv[]) |
Program which scans for backbone positions in a list of scaffolds with low rmsd to specific positions in a reference structure by building inverse rotamers.
| void build_bb_independent_rotamers | ( | core::chemical::ResidueTypeCOP | target_res_restype, |
| utility::vector1< core::conformation::ResidueOP > & | rotamers | ||
| ) |
function which returns a set of backbone-independent rotamers for the given ResidueType. basically a copy of the function in core::pack::rotamer_set::bb_independent_rotamers.hh, but it samples more chi angles thereby building more rotamers.
References utility::options::IntegerOptionKey::clone(), create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, rot, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::hotspot::target_res, and vancomycin::task.
Referenced by main().
| void dump_rotamerset_pdb | ( | utility::vector1< core::conformation::ResidueCOP > const & | rotamers, |
| std::string const & | filename | ||
| ) |
function which writes out a PDB file of the rotamers in the passed in vector this should really be a function of the RotamerSet class, but it's not. there is a similar function in the class RotamerSets, but I don't want the multiple MODELS in there. only using this function to check that the inverse rotamers are aligned properly to the reference residue(s).
References lactamize::filename, create_a3b_hbs::ii, and erraser_single_res_analysis::out.
Referenced by main().
| void init_usage_prompt | ( | std::string | exe | ) |
the usage prompt that gets printed when the user doesn't enter all the required command line arguments
References usage_string.
Referenced by main().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References argv, find_position_matches_using_inverse_rotamers::assume_command_line_has_pose_numbering, utility::file::FileName::base(), build_bb_independent_rotamers(), utility::io::oc::cerr, predPRE::chain, find_position_matches_using_inverse_rotamers::check_for_valid_chi3_chi4_dihedrals, utility::io::oc::cout, dump_rotamerset_pdb(), test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, ObjexxFCL::format::F(), fclose(), PREcst::FILE, utility::file::file_exists(), val2thr::fout, fprintf(), create_a3b_hbs::ii, basic::init(), init_usage_prompt(), find_position_matches_using_inverse_rotamers::ir_rmsd, test.T008_Serialization::iss, natoms(), find_position_matches_using_inverse_rotamers::number_glycan_clashes_allowed, option, erraser_single_res_analysis::out, find_position_matches_using_inverse_rotamers::output_aligned_scaffold, find_position_matches_using_inverse_rotamers::output_inverse_rotamers, parse_position(), utility::file::FileName::path(), pyrosetta.distributed.io::pose_from_file, find_position_matches_using_inverse_rotamers::reference_structure, find_position_matches_using_inverse_rotamers::reference_structure_epitope_residue_range, find_position_matches_using_inverse_rotamers::reference_structure_glycan_residues, find_position_matches_using_inverse_rotamers::reference_structure_positions_to_match, average_rmsds::rmsd, runtime_assert, find_position_matches_using_inverse_rotamers::scaffold_epitope_residue_range, subloop_histogram::size, challenge::ss, basic::options::start_files(), sum(), superimpose_pose(), TR, usage_string, basic::options::OptionKeys::inout::dbms::user, utility_exit, and basic::Tracer::Warning.
| void parse_position | ( | std::string | position, |
| char & | chain, | ||
| core::Size & | pdb_resnum, | ||
| char & | icode | ||
| ) |
References predPRE::chain, test.T008_Serialization::iss, subloop_histogram::iterator, challenge::ss, and tokenize_string().
Referenced by main().
| void tokenize_string | ( | const std::string & | str, |
| utility::vector1< std::string > & | tokens, | ||
| const std::string & | delimiters = " " |
||
| ) |
References make_symmdef_file_denovo::pos, and str().
Referenced by parse_position().
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static |
Core headers.
Referenced by main().
| std::string usage_string |
Referenced by init_usage_prompt(), and main().
1.9.1