Rosetta 3.5: core::chemical::sdf::ctabV3000Parser Class Reference

#include <ctab_parser.hh>

Collaboration diagram for core::chemical::sdf::ctabV3000Parser:

Collaboration graph

Public Member Functions
	ctabV3000Parser (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)

void	ParseBond (const std::string bond_line)

core::Real	FindExtraParameter (std::vector< std::string > extra_parameters, const std::string query)

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 83 of file ctab_parser.hh.

Constructor & Destructor Documentation

core::chemical::sdf::ctabV3000Parser::ctabV3000Parser	(	const utility::vector1< std::string >	connection_table_lines,
		core::chemical::ResidueTypeOP	molecule_container,
		MolData	mol_data
	)

Definition at line 263 of file ctab_parser.cc.

Member Function Documentation

core::Real core::chemical::sdf::ctabV3000Parser::FindExtraParameter	(	std::vector< std::string >	extra_parameters,
		const std::string	query
	)

private

Definition at line 309 of file ctab_parser.cc.

Referenced by ParseAtom().

core::chemical::ResidueTypeOP core::chemical::sdf::ctabV3000Parser::GetResidueType ( )

Definition at line 267 of file ctab_parser.cc.

References molecule_container_.

void core::chemical::sdf::ctabV3000Parser::ParseAtom ( const std::string atom_line)

private

Definition at line 404 of file ctab_parser.cc.

References core::chemical::sdf::element_to_default_type, FindExtraParameter(), core::chemical::sdf::elementToType::get(), index_to_names_map_, molecule_container_, and core::io::pdb::split().

Referenced by ParseTable().

std::map< core::Size, std::string > core::chemical::sdf::ctabV3000Parser::ParseAtomTypeData ( )

private

Definition at line 451 of file ctab_parser.cc.

References core::chemical::sdf::MolData::get_mol_data_string_vector(), and mol_data_.

Referenced by ParseTable().

void core::chemical::sdf::ctabV3000Parser::ParseBond ( const std::string bond_line)

private

Definition at line 432 of file ctab_parser.cc.

References index_to_names_map_, molecule_container_, and core::io::pdb::split().

Referenced by ParseTable().

void core::chemical::sdf::ctabV3000Parser::ParseTable ( )

Definition at line 328 of file ctab_parser.cc.

References added_H_, core::chemical::sdf::addedH::atom_number, index_to_names_map_, molecule_container_, ParseAtom(), ParseAtomTypeData(), ParseBond(), set_atom_type(), and core::io::pdb::split().

void core::chemical::sdf::ctabV3000Parser::set_atom_type	(	core::Size	atomno,
		std::string	atomname
	)

private

Definition at line 273 of file ctab_parser.cc.

References added_H_, core::chemical::sdf::addedH::atom_number, core::chemical::sdf::addedH::atom_type, core::chemical::sdf::addedH::bonded_atom_name, current_atom_, core::chemical::sdf::DEFAULT_MM_ATOM_TYPE_, core::chemical::sdf::atomTyper::get_element(), 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::ctabV3000Parser::added_H_

private

Definition at line 105 of file ctab_parser.hh.

Referenced by ParseTable(), and set_atom_type().

utility::vector1<std::string> core::chemical::sdf::ctabV3000Parser::connection_table_lines_

private

Definition at line 101 of file ctab_parser.hh.

core::Size core::chemical::sdf::ctabV3000Parser::current_atom_

private

Definition at line 106 of file ctab_parser.hh.

Referenced by set_atom_type().

std::map<core::Size, std::string> core::chemical::sdf::ctabV3000Parser::index_to_names_map_

private

Definition at line 103 of file ctab_parser.hh.

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

MolData core::chemical::sdf::ctabV3000Parser::mol_data_

private

Definition at line 102 of file ctab_parser.hh.

Referenced by ParseAtomTypeData().

core::chemical::ResidueTypeOP core::chemical::sdf::ctabV3000Parser::molecule_container_

private

Definition at line 104 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