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Rosetta
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Utilities for modifying and utilizing ResidueTypes and other core::chemical classes. More...
#include <core/chemical/util.hh>#include <core/chemical/ChemicalManager.hh>#include <core/chemical/AtomTypeSet.hh>#include <core/chemical/AtomType.hh>#include <core/chemical/MMAtomTypeSet.hh>#include <core/chemical/ResidueType.hh>#include <core/chemical/MutableResidueType.hh>#include <core/chemical/ResidueProperties.hh>#include <core/chemical/Patch.hh>#include <core/types.hh>#include <basic/options/option.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/chemical.OptionKeys.gen.hh>#include <basic/options/keys/pH.OptionKeys.gen.hh>#include <basic/Tracer.hh>#include <utility/vector1.hh>#include <utility/tools/make_vector1.hh>#include <utility/file/file_sys_util.hh>#include <utility/string_util.hh>#include <numeric/xyz.functions.hh>#include <ObjexxFCL/string.functions.hh>#include <core/chemical/MutableICoorRecord.hh>Namespaces | |
| core | |
| A class for reading in the atom type properties. | |
| core::chemical | |
Functions | |
| static basic::Tracer | core::chemical::TR ("core.chemical.util") |
| 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_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::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::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< VariantType > | core::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< VariantType > | core::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... | |
Utilities for modifying and utilizing ResidueTypes and other core::chemical classes.
1.9.1