core::chemical::sdf::CtabBase Class Reference

#include <ctab_base.hh>

Inheritance diagram for core::chemical::sdf::CtabBase:

Collaboration diagram for core::chemical::sdf::CtabBase:

Public Member Functions
	CtabBase (utility::vector1< std::string > const &connection_table_lines, core::chemical::ResidueTypeOP molecule_container, MolData const &mol_data)
virtual	~CtabBase ()
virtual void	ParseTable ()=0
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)=0
virtual void	ParseBond (std::string const bond_line)=0

Private Attributes
utility::vector1< std::string >	connection_table_lines_
core::chemical::ResidueTypeOP	molecule_container_
MolData	mol_data_
std::map< core::Size, std::string >	index_to_names_map_
std::map< core::Size, std::string >	atom_type_data_map_
std::set< BondData >	bond_type_data_set_

Detailed Description

Definition at line 54 of file ctab_base.hh.

Constructor & Destructor Documentation

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

Definition at line 64 of file ctab_base.cc.

References atom_type_data_map_, bond_type_data_set_, core::chemical::sdf::MolData::get_mol_data(), mol_data_, core::chemical::sdf::parse_atom_type_data(), and core::chemical::sdf::parse_bond_type_data().

core::chemical::sdf::CtabBase::~CtabBase ( )

virtual

Definition at line 74 of file ctab_base.cc.

Member Function Documentation

void core::chemical::sdf::CtabBase::add_index_name_pair	(	core::Size const	index,
		std::string const	atomname
	)

Definition at line 94 of file ctab_base.cc.

References index_to_names_map_.

Referenced by core::chemical::sdf::V2Parser::ParseAtom(), and core::chemical::sdf::V3Parser::ParseAtom().

std::string core::chemical::sdf::CtabBase::atom_name_from_index

(

core::Size const

index)

const

Definition at line 99 of file ctab_base.cc.

References index_to_names_map_.

Referenced by core::chemical::sdf::V2Parser::ParseBond(), and core::chemical::sdf::V3Parser::ParseBond().

bool core::chemical::sdf::CtabBase::check_for_aromatic	(	core::Size	lower,
		core::Size	upper
	)

Definition at line 148 of file ctab_base.cc.

References bond_type_data_set_.

Referenced by core::chemical::sdf::V2Parser::ParseBond(), and core::chemical::sdf::V3Parser::ParseBond().

core::Size core::chemical::sdf::CtabBase::connection_table_length

(

)

const

Definition at line 84 of file ctab_base.cc.

References connection_table_lines_.

Referenced by core::chemical::sdf::V2Parser::ParseTable(), and core::chemical::sdf::V3Parser::ParseTable().

std::string core::chemical::sdf::CtabBase::connection_table_line

(

core::Size const

line_number)

const

Definition at line 89 of file ctab_base.cc.

References connection_table_lines_.

Referenced by core::chemical::sdf::V2Parser::ParseTable(), and core::chemical::sdf::V3Parser::ParseTable().

void core::chemical::sdf::CtabBase::fix_atom_types

(

)

Definition at line 206 of file ctab_base.cc.

References atom_type_data_map_, index_to_names_map_, molecule_container_, and set_atom_type().

Referenced by core::chemical::sdf::V2Parser::ParseTable(), and core::chemical::sdf::V3Parser::ParseTable().

core::chemical::ResidueTypeOP core::chemical::sdf::CtabBase::GetResidueType

(

)

Definition at line 79 of file ctab_base.cc.

References molecule_container_.

Referenced by core::chemical::sdf::MolFileParser::parse_mol_file(), core::chemical::sdf::V2Parser::ParseAtom(), core::chemical::sdf::V3Parser::ParseAtom(), core::chemical::sdf::V2Parser::ParseBond(), and core::chemical::sdf::V3Parser::ParseBond().

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

privatepure virtual

Implemented in core::chemical::sdf::V3Parser, and core::chemical::sdf::V2Parser.

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

privatepure virtual

Implemented in core::chemical::sdf::V3Parser, and core::chemical::sdf::V2Parser.

virtual void core::chemical::sdf::CtabBase::ParseTable ( )

pure virtual

Implemented in core::chemical::sdf::V2Parser, and core::chemical::sdf::V3Parser.

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

Definition at line 159 of file ctab_base.cc.

References core::chemical::ChemicalManager::atom_type_set(), core::chemical::ChemicalManager::get_instance(), core::chemical::sdf::atomTyper::getType(), and molecule_container_.

Referenced by fix_atom_types().

Member Data Documentation

std::map<core::Size,std::string> core::chemical::sdf::CtabBase::atom_type_data_map_

private

Definition at line 87 of file ctab_base.hh.

Referenced by CtabBase(), and fix_atom_types().

std::set<BondData> core::chemical::sdf::CtabBase::bond_type_data_set_

private

Definition at line 88 of file ctab_base.hh.

Referenced by check_for_aromatic(), and CtabBase().

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

private

Definition at line 82 of file ctab_base.hh.

Referenced by connection_table_length(), and connection_table_line().

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

private

Definition at line 85 of file ctab_base.hh.

Referenced by add_index_name_pair(), atom_name_from_index(), and fix_atom_types().

MolData core::chemical::sdf::CtabBase::mol_data_

private

Definition at line 84 of file ctab_base.hh.

Referenced by CtabBase().

core::chemical::ResidueTypeOP core::chemical::sdf::CtabBase::molecule_container_

private

Definition at line 83 of file ctab_base.hh.

Referenced by fix_atom_types(), GetResidueType(), and set_atom_type().

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

• src/core/chemical/sdf/ctab_base.hh
• src/core/chemical/sdf/ctab_base.cc