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Classes | Functions | Variables
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)

◆ 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:
1 = [
2  '/// @author Labonte <JWLabonte@jhu.edu>\n',
3  '/// @author Vikram K. Mulligan (vmullig@uw.edu) -- updated for multi-threading\n',
4  '/// @note DO NOT EDIT THIS FILE DIRECTLY! It is auto-generated.\n',
5  '/// If you wish to edit it, modify the update_ResidueType_enum_files.py '
6  'script.\n']

◆ brief

update_ResidueType_enum_files.brief

◆ HEADER

list update_ResidueType_enum_files.HEADER
Initial value:
1 = [
2  '// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;'
3  'rm-trailing-spaces:t -*-\n',
4  '// vi: set ts=2 noet:\n',
5  '//\n',
6  '// (c) Copyright Rosetta Commons Member Institutions.\n',
7  '// (c) This file is part of the Rosetta software suite and is made '
8  'available under license.\n',
9  '// (c) The Rosetta software is developed by the contributing members of '
10  'the Rosetta Commons.\n',
11  '// (c) For more information, see http://www.rosettacommons.org. Questions '
12  'about this can be\n',
13  '// (c) addressed to University of Washington UW CoMotion, email: '
14  'license@uw.edu.\n',
15  "\n"]

◆ input_file

update_ResidueType_enum_files.input_file

◆ NAMESPACE_CLOSING

list update_ResidueType_enum_files.NAMESPACE_CLOSING
Initial value:
1 = [
2  '} // namespace chemical\n',
3  '} // namespace core\n']

◆ NAMESPACE_OPENING

list update_ResidueType_enum_files.NAMESPACE_OPENING
Initial value:
1 = [
2  'namespace core {\n',
3  'namespace chemical {\n',
4  "\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

◆ 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().