core::chemical::sdf::MolFileParser Class Reference

#include <mol_parser.hh>

Collaboration diagram for core::chemical::sdf::MolFileParser:

Public Member Functions
	MolFileParser (const utility::vector1< std::string > mol_file_lines)
	MolFileParser (const std::string file_name)
void	parse_mol_file (core::chemical::AtomTypeSetCAP atom_types, ElementSetCAP elements, core::chemical::MMAtomTypeSetCAP mm_atom_types, core::chemical::orbitals::OrbitalTypeSetCAP orbital_type_set)
core::chemical::ResidueTypeOP	GetResidueTypeOP ()
core::chemical::ResidueType	GetResidueType ()
std::string	GetMoleculeName ()
std::string	GetMoleculeInfo ()
std::string	GetMoleculeComments ()

Private Member Functions
std::string	FindNbrAtom ()

Private Attributes
utility::vector1< std::string >	mol_file_lines_
core::chemical::ResidueTypeOP	molecule_container_
MolData	mol_data_
std::string	molecule_name_
std::string	molecule_info_
std::string	molecule_comments_

Detailed Description

Definition at line 41 of file mol_parser.hh.

Constructor & Destructor Documentation

core::chemical::sdf::MolFileParser::MolFileParser

(

const utility::vector1< std::string >

mol_file_lines)

Definition at line 36 of file mol_parser.cc.

References core::chemical::sdf::MolParserTracer().

core::chemical::sdf::MolFileParser::MolFileParser

(

const std::string

file_name)

Definition at line 41 of file mol_parser.cc.

References mol_file_lines_.

Member Function Documentation

std::string core::chemical::sdf::MolFileParser::FindNbrAtom ( )

private

Definition at line 177 of file mol_parser.cc.

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

Referenced by parse_mol_file().

std::string core::chemical::sdf::MolFileParser::GetMoleculeComments

(

)

Definition at line 162 of file mol_parser.cc.

References molecule_comments_.

std::string core::chemical::sdf::MolFileParser::GetMoleculeInfo

(

)

Definition at line 172 of file mol_parser.cc.

References molecule_info_.

std::string core::chemical::sdf::MolFileParser::GetMoleculeName

(

)

Definition at line 167 of file mol_parser.cc.

References molecule_name_.

core::chemical::ResidueType core::chemical::sdf::MolFileParser::GetResidueType

(

)

Definition at line 56 of file mol_parser.cc.

References molecule_container_.

core::chemical::ResidueTypeOP core::chemical::sdf::MolFileParser::GetResidueTypeOP

(

)

Definition at line 61 of file mol_parser.cc.

References molecule_container_, and core::chemical::sdf::MolParserTracer().

Referenced by core::chemical::sdf::SDFParser::GenerateResidues().

void core::chemical::sdf::MolFileParser::parse_mol_file	(	core::chemical::AtomTypeSetCAP	atom_types,
		ElementSetCAP	elements,
		core::chemical::MMAtomTypeSetCAP	mm_atom_types,
		core::chemical::orbitals::OrbitalTypeSetCAP	orbital_type_set
	)

Definition at line 67 of file mol_parser.cc.

References FindNbrAtom(), core::chemical::sdf::CtabBase::GetResidueType(), mol_data_, mol_file_lines_, molecule_comments_, molecule_container_, molecule_info_, molecule_name_, core::chemical::sdf::MolParserTracer(), core::chemical::sdf::MolData::parse_mol_data(), and core::chemical::sdf::V2Parser::ParseTable().

Referenced by core::chemical::sdf::SDFParser::GenerateResidues(), and core::chemical::ChemicalManager::residue_type_set().

Member Data Documentation

MolData core::chemical::sdf::MolFileParser::mol_data_

private

Definition at line 61 of file mol_parser.hh.

Referenced by FindNbrAtom(), and parse_mol_file().

utility::vector1<std::string> core::chemical::sdf::MolFileParser::mol_file_lines_

private

Definition at line 59 of file mol_parser.hh.

Referenced by MolFileParser(), and parse_mol_file().

std::string core::chemical::sdf::MolFileParser::molecule_comments_

private

Definition at line 65 of file mol_parser.hh.

Referenced by GetMoleculeComments(), and parse_mol_file().

core::chemical::ResidueTypeOP core::chemical::sdf::MolFileParser::molecule_container_

private

Definition at line 60 of file mol_parser.hh.

Referenced by FindNbrAtom(), GetResidueType(), GetResidueTypeOP(), and parse_mol_file().

std::string core::chemical::sdf::MolFileParser::molecule_info_

private

Definition at line 64 of file mol_parser.hh.

Referenced by GetMoleculeInfo(), and parse_mol_file().

std::string core::chemical::sdf::MolFileParser::molecule_name_

private

Definition at line 63 of file mol_parser.hh.

Referenced by GetMoleculeName(), and parse_mol_file().

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

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