update_ResidueType_enum_files Namespace Reference

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')

Function Documentation

do_not_edit_warning()

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().

Doxygen_info()

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().

generate_enum_header_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().

generate_files()

def update_ResidueType_enum_files.generate_files

(

enum_info

)

References generate_enum_header_file(), generate_mappings_source_file(), read_lines_from_file(), and separate_definitions_from_comments().

generate_mappings_source_file()

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().

read_lines_from_file()

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().

separate_definitions_from_comments()

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().

write_lines_to_file_if_necessary()

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().

Variable Documentation

AUTHOR_AND_NOTE

list update_ResidueType_enum_files.AUTHOR_AND_NOTE

Initial value:

=  [
    '/// @author  Labonte <JWLabonte@jhu.edu>\n',
    '/// @author  Vikram K. Mulligan (vmullig@uw.edu) -- updated for multi-threading\n',
    '/// @note    DO NOT EDIT THIS FILE DIRECTLY!  It is auto-generated.\n',
    '/// If you wish to edit it, modify the update_ResidueType_enum_files.py '
                                                                    'script.\n']

brief

update_ResidueType_enum_files.brief

HEADER

list update_ResidueType_enum_files.HEADER

Initial value:

=  [
    '// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;'
                                                   'rm-trailing-spaces:t -*-\n',
    '// vi: set ts=2 noet:\n',
    '//\n',
    '// (c) Copyright Rosetta Commons Member Institutions.\n',
    '// (c) This file is part of the Rosetta software suite and is made '
                                                   'available under license.\n',
    '// (c) The Rosetta software is developed by the contributing members of '
                                                       'the Rosetta Commons.\n',
    '// (c) For more information, see http://www.rosettacommons.org. Questions '
                                                          'about this can be\n',
    '// (c) addressed to University of Washington UW CoMotion, email: '
                                                  'license@uw.edu.\n',
    "\n"]

input_file

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().

NAMESPACE_CLOSING

list update_ResidueType_enum_files.NAMESPACE_CLOSING

Initial value:

=  [
    '}  // namespace chemical\n',
    '}  // namespace core\n']

NAMESPACE_OPENING

list update_ResidueType_enum_files.NAMESPACE_OPENING

Initial value:

=  [
    'namespace core {\n',
    'namespace chemical {\n',
    "\n"]

properties

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().

short_name

update_ResidueType_enum_files.short_name

Referenced by core::chemical::GlobalResidueTypeSet.lazy_load_base_type_already_write_locked(), and core::chemical::carbohydrates.read_short_names_to_iupac_format_string().

short_name_plural

update_ResidueType_enum_files.short_name_plural

variants

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().