core::chemical::sdf::ctabV3000Parser Class Reference

#include <ctab_parser.hh>

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_

Constructor & Destructor Documentation

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

Member Function Documentation

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

private

Referenced by ParseAtom().

core::chemical::ResidueTypeOP core::chemical::sdf::ctabV3000Parser::GetResidueType

(

)

References molecule_container_.

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

private

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

Referenced by ParseTable().

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

private

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

Referenced by ParseTable().

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

private

References index_to_names_map_, molecule_container_, utility::split(), and type.

Referenced by ParseTable().

void core::chemical::sdf::ctabV3000Parser::ParseTable

(

)

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

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

private

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

Referenced by ParseTable(), and set_atom_type().

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

private

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

private

Referenced by set_atom_type().

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

private

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

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

private

Referenced by ParseAtomTypeData().

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

private

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

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

• symlinks/rosetta/src/core/chemical/sdf/ctab_parser.hh
• symlinks/rosetta/src/core/chemical/sdf/ctab_parser.cc