Rosetta
|
Classes | |
class | EnumInfo |
Functions | |
def | read_lines_from_file (filename) |
def | separate_definitions_from_comments (lines_to_parse) |
def | write_lines_to_file_if_necessary (lines, filename) |
def | Doxygen_info (filename, brief, additional_note="") |
def | do_not_edit_warning (short_name, filename) |
def | generate_enum_header_file (enum_info, enum_defs, comments) |
def | generate_mappings_source_file (enum_info, enum_defs) |
def | generate_files (enum_info) |
Variables | |
list | HEADER |
list | AUTHOR_AND_NOTE |
list | NAMESPACE_OPENING |
list | NAMESPACE_CLOSING |
properties = EnumInfo('ResidueProperty') | |
short_name | |
short_name_plural | |
input_file | |
brief | |
variants = EnumInfo('VariantType') | |
def update_ResidueType_enum_files.do_not_edit_warning | ( | short_name, | |
filename | |||
) |
Return lines providing a 'do not edit' comment warning.
Referenced by generate_enum_header_file(), and generate_mappings_source_file().
def update_ResidueType_enum_files.Doxygen_info | ( | filename, | |
brief, | |||
additional_note = "" |
|||
) |
Return the lines of Doxygen info, given the filename and description.
Referenced by generate_enum_header_file(), and generate_mappings_source_file().
def update_ResidueType_enum_files.generate_enum_header_file | ( | enum_info, | |
enum_defs, | |||
comments | |||
) |
Write a header file from lists of enum definitions and their corresponding comments, if the data have changed. Return True if a new file has been written.
References do_not_edit_warning(), Doxygen_info(), protocols::sic_dock.range(), and write_lines_to_file_if_necessary().
Referenced by generate_files().
def update_ResidueType_enum_files.generate_files | ( | enum_info | ) |
def update_ResidueType_enum_files.generate_mappings_source_file | ( | enum_info, | |
enum_defs | |||
) |
Write the _mappings.cc file from a list of enum values, if the data have changed. Return True if a new file has been written.
References do_not_edit_warning(), Doxygen_info(), and write_lines_to_file_if_necessary().
Referenced by generate_files().
def update_ResidueType_enum_files.read_lines_from_file | ( | filename | ) |
Return each line of a file to a list.
References protocols::sparta.split().
Referenced by generate_files().
def update_ResidueType_enum_files.separate_definitions_from_comments | ( | lines_to_parse | ) |
Parse each line by searching for a # symbol and return two lists.
Referenced by generate_files().
def update_ResidueType_enum_files.write_lines_to_file_if_necessary | ( | lines, | |
filename | |||
) |
Compare the existing file with the proposed new file and only write the new file with different. Return True if a new file has been written.
Referenced by generate_enum_header_file(), and generate_mappings_source_file().
list update_ResidueType_enum_files.AUTHOR_AND_NOTE |
update_ResidueType_enum_files.brief |
list update_ResidueType_enum_files.HEADER |
update_ResidueType_enum_files.input_file |
Referenced by protocols::simple_moves::AddResidueCouplingConstraint.apply(), protocols::nmr::pcs::PCSEnergy.get_pcs_data_from_pose(), core::import_pose.get_pdb_and_cleanup(), core::import_pose.get_pdb_with_full_model_info(), protocols::nmr::pre::PREEnergy.get_pre_data_from_pose(), protocols::nmr::rdc::RDCEnergy.get_rdc_data_from_pose(), core::import_pose::libraries::BasePairStepLibrary.initialize_data(), protocols::frag_picker::scores::MakeJCoupling.make(), protocols::frag_picker::scores::MakePhiPsiRmsd.make(), protocols::frag_picker::scores::MakePhiPsiSquareWell.make(), core::scoring::epr_deer::DEERIO.parse_input(), core::import_pose.process_input_file(), protocols::noesy_assign::NoesyModule.read_input_files(), core::scoring::SS_Killhairpins_Info.setup_from_kill_hairpins_file(), core::scoring::SS_Killhairpins_Info.setup_from_psipred(), and core::scoring::SS_Killhairpins_Info.setup_killhairpins().
list update_ResidueType_enum_files.NAMESPACE_CLOSING |
list update_ResidueType_enum_files.NAMESPACE_OPENING |
update_ResidueType_enum_files.properties = EnumInfo('ResidueProperty') |
Referenced by core::pack::palette::PackerPalette.add_base_residue_types_by_properties(), core::conformation::parametric::ParametrizationCalculator.add_boolean_parameter(), core::conformation::parametric::ParametrizationCalculator.add_custom_parameter(), core::conformation::parametric::ParametrizationCalculator.add_parameter(), core::conformation::parametric::ParametrizationCalculator.add_real_parameter(), core::conformation::parametric::ParametrizationCalculator.add_realvector_parameter(), core::conformation::parametric::ParametrizationCalculator.add_size_parameter(), core::conformation::parametric::ParametrizationCalculator.add_sizevector_parameter(), core::chemical::Patch.adds_properties(), core::chemical::PatchCase.adds_properties_enums(), core::chemical::Patch.adds_properties_enums(), core::chemical.bond_order_to_property(), core::chemical::sdf::MolWriter.compose_rosetta_properties(), core::chemical::Patch.deletes_properties(), core::chemical::Patch.deletes_properties_enums(), core::pack::task::ResidueLevelTask_.disable_restypes_with_at_least_one_property(), core::chemical::AtomType.get_all_properties(), core::pack::palette::PackerPalette.get_base_names_by_properties(), protocols::abinitio::abscript::RigidChunkCM.initialize(), core::chemical::AtomProperties.operator==(), core::chemical::sdf::MolWriter.output_residue_impl(), core::select::residue_selector::ResiduePropertySelector.parse_my_tag(), core::io::pose_from_sfr::PoseFromSFRBuilder.pass_2_quick_and_dirty_resolve_residue_types(), core::chemical::carbohydrates::CarbohydrateInfo.read_and_set_properties(), core::chemical.residue_selector_single_from_line(), core::select::residue_selector::ResiduePropertySelector.ResiduePropertySelector(), core::pack::task::ResidueLevelTask_.restrict_to_restypes_with_all_properties(), core::pack::task::ResidueLevelTask_.restrict_to_restypes_with_at_least_one_property(), core::select::residue_selector::ResiduePropertySelector.set_properties(), core::chemical::ResidueTypeSelector.set_property(), core::chemical::AtomProperties.show(), core::chemical::ResidueProperties.show(), core::chemical::AtomTypeDatabaseIO.write_atom_type_properties_table(), and core::chemical.write_topology_file().
update_ResidueType_enum_files.short_name |
update_ResidueType_enum_files.short_name_plural |
update_ResidueType_enum_files.variants = EnumInfo('VariantType') |
Referenced by core::chemical::ResidueTypeSetCache.all_types_with_variants_aa_already_cached(), core::chemical::ResidueTypeSetCache.all_types_with_variants_residuetypecops_already_cached(), core::chemical::ResidueTypeSetCache.cache_all_types_with_variants_aa(), core::chemical::ResidueTypeSetCache.cache_all_types_with_variants_residuetypecops(), core::pack::palette::PackerPalette.decide_what_to_do_with_base_type(), core::pack::palette::PackerPalette.decide_what_to_do_with_existing_type(), core::chemical::Patch.deletes_variants(), core::chemical::PatchCase.deletes_variants_by_enum(), core::chemical::Patch.deletes_variants_by_enum(), core::chemical::ResidueTypeSet.get_all_types_with_variants_aa(), core::chemical::GlobalResidueTypeSet.get_all_types_with_variants_aa(), core::chemical::ResidueTypeSet.get_all_types_with_variants_by_basetype(), core::chemical::ResidueTypeSet.get_all_types_with_variants_name1(), core::chemical::ResidueTypeSet.get_all_types_with_variants_name3(), core::chemical::ResidueTypeSet.get_representative_type_aa(), core::chemical::ResidueTypeSet.get_representative_type_name1(), core::chemical::ResidueTypeSet.get_representative_type_name3(), core::conformation.get_residue_from_name1(), core::io::pose_from_sfr::PoseFromSFRBuilder.get_rsd_type(), core::pose.get_rsd_type_from_aa(), core::io::pose_from_sfr::PoseFromSFRBuilder.pass_2_quick_and_dirty_resolve_residue_types(), core::chemical::carbohydrates::CarbohydrateInfo.read_and_set_properties(), core::chemical::ResidueTypeSetCache.retrieve_all_types_with_variants_aa(), core::chemical::ResidueTypeSetCache.retrieve_all_types_with_variants_residuetypecops(), core::chemical::ResidueProperties.show(), core::pose::carbohydrates.tautomerize_anomer(), core::chemical::ResidueTypeFinder.variants(), core::pose::Pose.virtual_to_real(), and core::chemical.write_topology_file().