core::chemical::sdf::V2Parser Class Reference

#include <v2_parser.hh>

Public Member Functions
	V2Parser (utility::vector1< std::string > const &connection_table_lines, core::chemical::ResidueTypeOP molecule_container, MolData const &mol_data)
virtual void	ParseTable ()
Public Member Functions inherited from core::chemical::sdf::CtabBase
	CtabBase (utility::vector1< std::string > const &connection_table_lines, core::chemical::ResidueTypeOP molecule_container, MolData const &mol_data)
virtual	~CtabBase ()
core::chemical::ResidueTypeOP	GetResidueType ()
core::Size	connection_table_length () const
std::string	connection_table_line (core::Size const line_number) const
void	add_index_name_pair (core::Size const index, std::string const atomname)
std::string	atom_name_from_index (core::Size const index) const
bool	check_for_aromatic (core::Size lower, core::Size upper)
void	set_atom_type (core::Size const atomno, std::string const atomname)
void	fix_atom_types ()

Private Member Functions
virtual void	ParseAtom (std::string const atom_line, core::Size const atom_number)
virtual void	ParseBond (std::string const bond_line)

Constructor & Destructor Documentation

core::chemical::sdf::V2Parser::V2Parser	(	utility::vector1< std::string > const &	connection_table_lines,
		core::chemical::ResidueTypeOP	molecule_container,
		MolData const &	mol_data
	)

Member Function Documentation

void core::chemical::sdf::V2Parser::ParseAtom ( std::string const  atom_line, core::Size const  atom_number  )

privatevirtual

Implements core::chemical::sdf::CtabBase.

References core::chemical::sdf::CtabBase::add_index_name_pair(), utility::add_spaces_left_align(), core::chemical::sdf::DEFAULT_MM_ATOM_TYPE_, core::chemical::sdf::element_to_default_type, core::chemical::sdf::elementToType::get(), core::chemical::sdf::CtabBase::GetResidueType(), and residue.

Referenced by ParseTable().

void core::chemical::sdf::V2Parser::ParseBond ( std::string const  bond_line )

privatevirtual

Implements core::chemical::sdf::CtabBase.

References core::chemical::AromaticBond, core::chemical::sdf::CtabBase::atom_name_from_index(), core::chemical::sdf::CtabBase::check_for_aromatic(), core::chemical::sdf::CtabBase::GetResidueType(), and residue.

Referenced by ParseTable().

void core::chemical::sdf::V2Parser::ParseTable ( )

virtual

Implements core::chemical::sdf::CtabBase.

References core::chemical::sdf::CtabBase::connection_table_length(), core::chemical::sdf::CtabBase::connection_table_line(), core::chemical::sdf::CtabBase::fix_atom_types(), ParseAtom(), and ParseBond().

Referenced by core::chemical::sdf::MolFileParser::parse_mol_file().

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

• symlinks/rosetta/src/core/chemical/sdf/v2_parser.hh
• symlinks/rosetta/src/core/chemical/sdf/v2_parser.cc