core::chemical::sdf Namespace Reference

Classes
struct	addedH
class	elementToType
class	CtabBase
class	ctabV2000Parser
class	ctabV3000Parser
class	atomTyper
class	MolFileParser
struct	BondData
class	MolWriter
class	MolData
class	SDFParser
class	V2Parser
class	V3Parser

Enumerations
enum	typerBond {   Csingle =0, Cdouble =1, Ctriple =2, Caro =3,   Nsingle =4, Ndouble =5, Ntriple =6, Naro =7,   Osingle =8, Odouble =9, Oaro =11, Hsingle =12,   AroBonds =13 }

Functions
static basic::Tracer	ctabParserTracer ("core.io.sdf.ctab_parser")
static basic::Tracer	ctabParserTracer ("core.io.sdf.ctab_parser")
static basic::Tracer	MolParserTracer ("core.chemical.sdf.mol_parser")
std::set< BondData >	parse_bond_type_data (std::string raw_data)
std::map< core::Size, std::string >	parse_atom_type_data (std::string raw_data)
static basic::Tracer	MolDataTracer ("core.io.sdf.MolData")
static basic::Tracer	SDFParserTracer ("core.io.sdf.sdf_parser")

Variables
static std::string const	DEFAULT_ATOM_TYPE_ ="CH3"
static std::string const	DEFAULT_MM_ATOM_TYPE_ ="X"
static elementToType	element_to_default_type
static std::string const	DEFAULT_ATOM_TYPE_ ="CH3"
static std::string const	DEFAULT_MM_ATOM_TYPE_ ="X"
static elementToType	element_to_default_type

Enumeration Type Documentation

enum core::chemical::sdf::typerBond

Enumerator
Csingle
Cdouble
Ctriple
Caro
Nsingle
Ndouble
Ntriple
Naro
Osingle
Odouble
Oaro
Hsingle
AroBonds

Definition at line 33 of file ctab_typer.hh.

Function Documentation

static basic::Tracer core::chemical::sdf::ctabParserTracer ( "core.io.sdf.ctab_parser"  )

static

static basic::Tracer core::chemical::sdf::ctabParserTracer ( "core.io.sdf.ctab_parser"  )

static

static basic::Tracer core::chemical::sdf::MolDataTracer ( "core.io.sdf.MolData"  )

static

static basic::Tracer core::chemical::sdf::MolParserTracer ( "core.chemical.sdf.mol_parser"  )

static

Referenced by core::chemical::sdf::MolFileParser::GetResidueTypeOP(), core::chemical::sdf::MolFileParser::MolFileParser(), and core::chemical::sdf::MolFileParser::parse_mol_file().

std::map< core::Size, std::string > core::chemical::sdf::parse_atom_type_data

(

std::string

raw_data)

Definition at line 78 of file mol_util.cc.

Referenced by core::chemical::sdf::CtabBase::CtabBase().

std::set< BondData > core::chemical::sdf::parse_bond_type_data

(

std::string

raw_data)

Definition at line 49 of file mol_util.cc.

References core::io::pdb::split().

Referenced by core::chemical::sdf::CtabBase::CtabBase().

static basic::Tracer core::chemical::sdf::SDFParserTracer ( "core.io.sdf.sdf_parser"  )

static

Variable Documentation

std::string const core::chemical::sdf::DEFAULT_ATOM_TYPE_ ="CH3"

static

Definition at line 33 of file ctab_base.hh.

std::string const core::chemical::sdf::DEFAULT_ATOM_TYPE_ ="CH3"

static

Definition at line 35 of file ctab_parser.hh.

std::string const core::chemical::sdf::DEFAULT_MM_ATOM_TYPE_ ="X"

static

Definition at line 34 of file ctab_base.hh.

Referenced by core::chemical::sdf::V2Parser::ParseAtom(), core::chemical::sdf::V3Parser::ParseAtom(), core::chemical::sdf::ctabV2000Parser::ParseAtom(), core::chemical::sdf::ctabV2000Parser::set_atom_type(), and core::chemical::sdf::ctabV3000Parser::set_atom_type().

std::string const core::chemical::sdf::DEFAULT_MM_ATOM_TYPE_ ="X"

static

Definition at line 36 of file ctab_parser.hh.

elementToType core::chemical::sdf::element_to_default_type

static

Definition at line 52 of file ctab_base.hh.

Referenced by core::chemical::sdf::V2Parser::ParseAtom(), core::chemical::sdf::V3Parser::ParseAtom(), core::chemical::sdf::ctabV2000Parser::ParseAtom(), and core::chemical::sdf::ctabV3000Parser::ParseAtom().

elementToType core::chemical::sdf::element_to_default_type

static

Definition at line 55 of file ctab_parser.hh.