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| MutableResidueTypeOP | core::chemical::read_topology_file (std::string const &filename, chemical::ResidueTypeSetCOP rsd_type_set) |
| | function to convert params files into ResidueType objects (repackages string filename into istream, gets needed subsidiary type sets from rsd_type_set More...
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| MutableResidueTypeOP | core::chemical::read_topology_file (utility::io::izstream &istream, chemical::ResidueTypeSetCOP rsd_type_set) |
| | function to convert params files into ResidueType objects, gets needed subsidiary type sets from rsd_type_set More...
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| MutableResidueTypeOP | core::chemical::read_topology_file (std::istream &istream, std::string const &filename, chemical::ResidueTypeSetCOP rsd_type_set) |
| | function to convert params files into ResidueType objects, gets needed subsidiary type sets from rsd_type_set More...
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| MutableResidueTypeOP | core::chemical::read_topology_file (std::string const &filename, chemical::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types, chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types) |
| | function to convert params files into ResidueType objects (repackages string filename into istream) More...
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| MutableResidueTypeOP | core::chemical::read_topology_file (std::istream &data, std::string const &filename, chemical::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types, chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types) |
| | main function to convert params files into ResidueType objects More...
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| void | core::chemical::write_topology_file (ResidueType const &rsd, std::string filename="") |
| | writes a .params file from a given ResidueType object More...
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| void | core::chemical::write_graphviz (ResidueType const &rsd, std::ostream &out, bool header) |
| | Produces a graphviz dot representation of the ResidueType to the given output stream If header is true (the default) a line with an explanitory message will be printed first. More...
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| void | core::chemical::write_graphviz (MutableResidueType const &rsd, std::ostream &out, bool header) |
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| void | core::chemical::set_up_mapfile_reassignments_from_commandline (ResidueTypeBaseOP rsd) |
| | Certain commandline flags override the default RamaPrePro maps used by the 20 canonical amino acids. This function applies those overrides. More...
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| void | core::chemical::setup_atom_type_reassignments_from_commandline (std::string const &rsd_type_name, TypeSetMode rsd_type_set_mode, std::map< std::string, std::string > &atom_type_reassignments) |
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| void | core::chemical::setup_atomic_charge_reassignments_from_commandline (std::string const &rsd_type_name, TypeSetMode rsd_type_set_mode, std::map< std::string, Real > &atomic_charge_reassignments) |
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| void | core::chemical::setup_icoor_reassignments_from_commandline (std::string const &rsd_type_name, TypeSetMode rsd_type_set_mode, std::map< std::string, utility::vector1< std::string > > &icoor_reassignments) |
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| void | core::chemical::apply_symm_gly_corrections (std::string const &child_atom, core::Real &phi, core::Real &, core::Real &d, std::string &, std::string &, std::string &torsion_atom) |
| | Symmetrize the glycine params file (if the user has used the -symmetric_gly_tables option). More...
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| void | core::chemical::apply_symm_b3g_corrections (std::string const &child_atom, core::Real &phi, core::Real &theta, core::Real &d, std::string &, std::string &, std::string &torsion_atom) |
| | Symmetrize the glycine params file (if the user has used the -symmetric_gly_tables option). More...
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