Rosetta 3.5: core::chemical::sdf::ctabV2000Parser Class Reference

#include <ctab_parser.hh>

Collaboration diagram for core::chemical::sdf::ctabV2000Parser:

Collaboration graph

Public Member Functions
	ctabV2000Parser (const utility::vector1< std::string > connection_table_lines, core::chemical::ResidueTypeOP molecule_container, MolData mol_data)

void	ParseTable ()

core::chemical::ResidueTypeOP	GetResidueType ()

Private Member Functions
void	set_atom_type (core::Size atomno, std::string atomname)

void	ParseAtom (const std::string atom_line, core::Size atom_number)

void	ParseBond (const std::string bond_line)

std::map< core::Size, std::string >	ParseAtomTypeData ()

Private Attributes
utility::vector1< std::string >	connection_table_lines_

MolData	mol_data_

std::map< core::Size, std::string >	index_to_names_map_

core::chemical::ResidueTypeOP	molecule_container_

utility::vector1< addedH >	added_H_

core::Size	current_atom_

Detailed Description

Definition at line 57 of file ctab_parser.hh.

Constructor & Destructor Documentation

core::chemical::sdf::ctabV2000Parser::ctabV2000Parser	(	const utility::vector1< std::string >	connection_table_lines,
		core::chemical::ResidueTypeOP	molecule_container,
		MolData	mol_data
	)

Definition at line 74 of file ctab_parser.cc.

Member Function Documentation

core::chemical::ResidueTypeOP core::chemical::sdf::ctabV2000Parser::GetResidueType ( )

Definition at line 257 of file ctab_parser.cc.

References molecule_container_.

void core::chemical::sdf::ctabV2000Parser::ParseAtom	(	const std::string	atom_line,
		core::Size	atom_number
	)

private

Definition at line 173 of file ctab_parser.cc.

References current_atom_, core::chemical::sdf::DEFAULT_MM_ATOM_TYPE_, core::chemical::sdf::element_to_default_type, core::chemical::sdf::elementToType::get(), index_to_names_map_, and molecule_container_.

Referenced by ParseTable().

std::map< core::Size, std::string > core::chemical::sdf::ctabV2000Parser::ParseAtomTypeData ( )

private

Definition at line 220 of file ctab_parser.cc.

References connection_table_lines_, and core::io::pdb::split().

void core::chemical::sdf::ctabV2000Parser::ParseBond ( const std::string bond_line)

private

Definition at line 208 of file ctab_parser.cc.

References index_to_names_map_, and molecule_container_.

Referenced by ParseTable().

void core::chemical::sdf::ctabV2000Parser::ParseTable ( )

Definition at line 80 of file ctab_parser.cc.

References added_H_, core::chemical::sdf::addedH::atom_number, connection_table_lines_, index_to_names_map_, molecule_container_, ParseAtom(), ParseBond(), and set_atom_type().

void core::chemical::sdf::ctabV2000Parser::set_atom_type	(	core::Size	atomno,
		std::string	atomname
	)

private

Definition at line 129 of file ctab_parser.cc.

References added_H_, core::chemical::sdf::addedH::atom_number, core::chemical::sdf::addedH::atom_type, core::chemical::ChemicalManager::atom_type_set(), core::chemical::sdf::addedH::bonded_atom_name, current_atom_, core::chemical::sdf::DEFAULT_MM_ATOM_TYPE_, core::chemical::sdf::atomTyper::get_element(), core::chemical::ChemicalManager::get_instance(), core::chemical::sdf::atomTyper::getNumBonds(), core::chemical::sdf::atomTyper::getType(), molecule_container_, and core::chemical::SingleBond.

Referenced by ParseTable().

Member Data Documentation

utility::vector1<addedH> core::chemical::sdf::ctabV2000Parser::added_H_

private

Definition at line 78 of file ctab_parser.hh.

Referenced by ParseTable(), and set_atom_type().

utility::vector1<std::string> core::chemical::sdf::ctabV2000Parser::connection_table_lines_

private

Definition at line 74 of file ctab_parser.hh.

Referenced by ParseAtomTypeData(), and ParseTable().

core::Size core::chemical::sdf::ctabV2000Parser::current_atom_

private

Definition at line 79 of file ctab_parser.hh.

Referenced by ParseAtom(), and set_atom_type().

std::map<core::Size, std::string> core::chemical::sdf::ctabV2000Parser::index_to_names_map_

private

Definition at line 76 of file ctab_parser.hh.

Referenced by ParseAtom(), ParseBond(), and ParseTable().

MolData core::chemical::sdf::ctabV2000Parser::mol_data_

private

Definition at line 75 of file ctab_parser.hh.

core::chemical::ResidueTypeOP core::chemical::sdf::ctabV2000Parser::molecule_container_

private

Definition at line 77 of file ctab_parser.hh.

Referenced by GetResidueType(), ParseAtom(), ParseBond(), ParseTable(), and set_atom_type().

The documentation for this class was generated from the following files:

src/core/chemical/sdf/ctab_parser.hh
src/core/chemical/sdf/ctab_parser.cc