Rosetta Core  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::chemical::sdf::MolFileIOMolecule Class Reference

#include <MolFileIOData.hh>

Public Member Functions

 MolFileIOMolecule ()
 
virtual ~MolFileIOMolecule ()
 
std::string name () const
 
void name (std::string name)
 
MolFileIOAtomOP atom_index (AtomIndex index)
 Retrieve a modifiable atom by index. More...
 
void add_atom (MolFileIOAtomOP atom)
 Add an atom (takes possession of object) More...
 
void add_bond (MolFileIOBondOP bond)
 Add a bond (takes possession of object) More...
 
void add_str_str_data (std::string const &key, std::string const &value)
 
StrStrMap const & get_str_str_data () const
 
void normalize ()
 Generate data for potentially missing fields. More...
 
ResidueTypeOP convert_to_ResidueType (chemical::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types)
 Make a ResidueType from this object rsd_type_set is used for context - the residue is not actually added to the set. More...
 

Private Member Functions

void set_from_extra_data (ResidueType &restype, std::map< mioAD, core::chemical::VD > &restype_from_mio)
 From the str/str data in MolFile, additional information Specifically, it's the overall atom and bond information. More...
 
bool index_valid (AtomIndex index, ResidueType const &restype, std::map< mioAD, core::chemical::VD > &restype_from_mio)
 

Private Attributes

std::string name_
 
MolFileIOGraph molgraph_
 
std::map< AtomIndex, mioADindex_atom_map_
 
StrStrMap molecule_string_data_
 

Constructor & Destructor Documentation

core::chemical::sdf::MolFileIOMolecule::MolFileIOMolecule ( )
core::chemical::sdf::MolFileIOMolecule::~MolFileIOMolecule ( )
virtual

Member Function Documentation

void core::chemical::sdf::MolFileIOMolecule::add_atom ( MolFileIOAtomOP  atom)

Add an atom (takes possession of object)

References index_atom_map_, and molgraph_.

Referenced by core::chemical::sdf::CtabV2000Parser::parse(), and core::chemical::sdf::CtabV3000Parser::parse().

void core::chemical::sdf::MolFileIOMolecule::add_bond ( MolFileIOBondOP  bond)

Add a bond (takes possession of object)

References index_atom_map_, and molgraph_.

Referenced by core::chemical::sdf::CtabV2000Parser::parse(), and core::chemical::sdf::CtabV3000Parser::parse().

void core::chemical::sdf::MolFileIOMolecule::add_str_str_data ( std::string const &  key,
std::string const &  value 
)
MolFileIOAtomOP core::chemical::sdf::MolFileIOMolecule::atom_index ( AtomIndex  index)

Retrieve a modifiable atom by index.

References core::chemical::sdf::has(), index_atom_map_, and molgraph_.

Referenced by core::chemical::sdf::CtabV2000Parser::parse_property_line().

ResidueTypeOP core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType ( chemical::AtomTypeSetCAP  atom_types,
chemical::ElementSetCAP  elements,
chemical::MMAtomTypeSetCAP  mm_atom_types 
)
StrStrMap const& core::chemical::sdf::MolFileIOMolecule::get_str_str_data ( ) const
inline

References molecule_string_data_.

bool core::chemical::sdf::MolFileIOMolecule::index_valid ( AtomIndex  index,
ResidueType const &  restype,
std::map< mioAD, core::chemical::VD > &  restype_from_mio 
)
private
std::string core::chemical::sdf::MolFileIOMolecule::name ( ) const
inline

References name_.

Referenced by set_from_extra_data().

void core::chemical::sdf::MolFileIOMolecule::name ( std::string  name)
inline

References name(), and name_.

Referenced by name().

void core::chemical::sdf::MolFileIOMolecule::normalize ( )

Generate data for potentially missing fields.

Referenced by convert_to_ResidueType().

void core::chemical::sdf::MolFileIOMolecule::set_from_extra_data ( ResidueType restype,
std::map< mioAD, core::chemical::VD > &  restype_from_mio 
)
private

Member Data Documentation

std::map< AtomIndex, mioAD > core::chemical::sdf::MolFileIOMolecule::index_atom_map_
private
StrStrMap core::chemical::sdf::MolFileIOMolecule::molecule_string_data_
private
MolFileIOGraph core::chemical::sdf::MolFileIOMolecule::molgraph_
private
std::string core::chemical::sdf::MolFileIOMolecule::name_
private

Referenced by convert_to_ResidueType(), and name().


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