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util.hh File Reference

Utilities for modifying and utilizing Residues and other core::chemical classes. More...

#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/AtomTypeSet.fwd.hh>
#include <core/chemical/MMAtomTypeSet.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/chemical/MutableResidueType.fwd.hh>
#include <core/chemical/ResidueTypeBase.fwd.hh>
#include <core/chemical/VariantType.hh>
#include <utility/vector1.hh>
#include <string>
#include <map>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::chemical
 

Functions

core::chemical::ResidueTypeSetCAP core::chemical::rsd_set_from_cmd_line ()
 Return a constant access pointer to the ResidueTypeSet specified by the command-line options. More...
 
void core::chemical::add_atom_type_set_parameters_from_command_line (std::string const &atom_type_set_tag, AtomTypeSet &atom_type_set)
 Add additional parameter files not present in <atom-set-name>/extras.txt. More...
 
void core::chemical::add_atom_types_from_command_line (std::string const &atom_type_set_tag, AtomTypeSet &atom_type_set)
 Add additional atomy types not present in <atom-set-name>/atom_properties.txt. More...
 
void core::chemical::add_mm_atom_type_set_parameters_from_command_line (std::string const &mm_atom_type_set_tag, MMAtomTypeSet &atom_type_set)
 Add additional mm atom parameters not present in <mm-atom-type-set-name>/mm_atom_properties.txt. More...
 
void core::chemical::modify_atom_properties_from_command_line (std::string const &atom_type_set_tag, AtomTypeSet &atom_type_set)
 Modify atom_type properties from the command line. More...
 
std::string core::chemical::formatted_icoord_tree (core::chemical::ResidueType const &restype)
 Return a string representing the internal coordinates tree of this ResidueType. More...
 
std::string core::chemical::formatted_icoord_tree (core::chemical::MutableResidueType const &restype)
 Return a string representing the internal coordinates tree of this MutableResidueType (if any) More...
 
void core::chemical::print_chis (std::ostream &out, ResidueType const &res)
 Utility to examine chi output. More...
 
void core::chemical::print_chis (std::ostream &out, MutableResidueType const &res)
 Utility to examine chi output. More...
 
std::string core::chemical::fixup_patches (std::string const &string_in)
 Replaces the deprecated "_p:" linker connecting ResidueType base names with their patch names with ":". More...
 
bool core::chemical::variants_match_with_exceptions (ResidueTypeBase const &res1, ResidueTypeBase const &res2, utility::vector1< VariantType > list_of_variants_to_ignore)
 Are these two residues patched in exactly the same way, ignoring any VariantTypes in the list of exceptions? More...
 
utility::vector1< VariantTypecore::chemical::pH_mode_exceptions ()
 check if user has set -pH_mode. More...
 
bool core::chemical::variants_match (ResidueTypeBase const &res1, ResidueTypeBase const &res2)
 Are these two residues patched in exactly the same way? More...
 
bool core::chemical::nonadduct_variants_match (ResidueTypeBase const &res1, ResidueTypeBase const &res2)
 Similar to variants_match(), but allows different adduct-modified states. More...
 
utility::vector1< VariantTypecore::chemical::get_terminal_varianttypes ()
 Get a list of those VariantTypes that affect termini. More...
 
ResidueTypeCOP core::chemical::find_best_match (ResidueTypeCOPs const &rsd_type_list, utility::vector1< std::string > const &atom_names, bool const ignore_atom_named_H)
 look for best match to atom_names More...
 
void core::chemical::enlarge_h_lj_wdepth (utility::vector1< Real > &lj_wdepth, AtomTypeSet const &atom_type_set)
 Fang-Chieh Chou 8/10/2012. Use larger LJ_WDEPTH for protons to avoid clashes in RNA. More...
 
void core::chemical::enlarge_h_lj_wdepth (AtomTypeSet &atom_type_set)
 Fang-Chieh Chou 8/10/2012. Use larger LJ_WDEPTH for protons to avoid clashes in RNA. More...
 
void core::chemical::unset_acceptor_ether_oxygens (AtomTypeSet &atom_type_set)
 Rhiju. O3', O4', O5' in nucleic acids are ethers – turn them off as acceptors for H-bonds. More...
 
void core::chemical::detect_ld_chirality_from_polymer_residue (core::chemical::MutableResidueType const &restype, bool &is_d_aa, bool &is_l_aa)
 
void core::chemical::detect_ld_chirality_from_polymer_residue (std::map< std::string, Vector > const &xyz, std::string const &name3, bool &is_d_aa, bool &is_l_aa)
 
bool core::chemical::heavy_atom_names_match (ResidueType const &first, ResidueType const &second)
 Return true if the two residues have the same number and name of heavy atoms. More...
 
bool core::chemical::is_mainchain_torsion_also_ring_torsion (ResidueType const &res_type, uint torsion_index)
 Are these main-chain torsions also ring torsions? More...
 

Detailed Description

Utilities for modifying and utilizing Residues and other core::chemical classes.