core::chemical::sdf::MolFileIOMolecule Class Reference

#include <MolFileIOData.hh>

Inheritance diagram for core::chemical::sdf::MolFileIOMolecule:

Public Member Functions
	MolFileIOMolecule ()
	~MolFileIOMolecule () override
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...
MutableResidueTypeOP	convert_to_ResidueType (chemical::AtomTypeSetCOP atom_types, chemical::ElementSetCOP elements, chemical::MMAtomTypeSetCOP mm_atom_types)
	Make a ResidueType from this object. More...
MutableResidueTypeOP	convert_to_ResidueType (std::map< AtomIndex, std::string > &index_name_map, chemical::AtomTypeSetCOP atom_types, chemical::ElementSetCOP elements, chemical::MMAtomTypeSetCOP mm_atom_types)
	Make a ResidueType from this object Index_name_map will contain a mapping from this object's AtomIndexes to the atom names in the returned ResidueType. More...

Private Member Functions
void	set_from_extra_data (MutableResidueType &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, MutableResidueType const &restype, std::map< mioAD, core::chemical::VD > &restype_from_mio)
void	parse_multi (std::istream &estream, utility::vector1< std::string > &parsed, std::string label) const
	Parse a multiple value item, say for per-atom or per-bond data This assumes that the passed vector is pre-initialized to the appropriate size. Valid formats are a series of space-separated sequential items, or a space-separated set of items in the form of "(index,value)". Spaces are not valid in either entry. More...
void	create_dummy_atom (MutableResidueTypeOP restype, std::string atom_name, core::Vector const &xyz_offset, chemical::ElementSetCOP elements, chemical::MMAtomTypeSetCOP mm_atom_types)

Private Attributes
std::string	name_
MolFileIOGraph	molgraph_
std::map< AtomIndex, mioAD >	index_atom_map_
StrStrMap	molecule_string_data_

Constructor & Destructor Documentation

core::chemical::sdf::MolFileIOMolecule::MolFileIOMolecule

(

)

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

overridedefault

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
	)

References molecule_string_data_.

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

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().

MutableResidueTypeOP core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType ( chemical::AtomTypeSetCOP  atom_types, chemical::ElementSetCOP  elements, chemical::MMAtomTypeSetCOP  mm_atom_types  )

inline

Make a ResidueType from this object.

Not const as it calls normalize() to fix up missing data first.

MutableResidueTypeOP core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType	(	std::map< AtomIndex, std::string > &	index_name_map,
		chemical::AtomTypeSetCOP	atom_types,
		chemical::ElementSetCOP	elements,
		chemical::MMAtomTypeSetCOP	mm_atom_types
	)

Make a ResidueType from this object Index_name_map will contain a mapping from this object's AtomIndexes to the atom names in the returned ResidueType.

Not const as it calls normalize() to fix up missing data first.

References create_dummy_atom(), core::chemical::sdf::MolFileIOAtom::element(), core::chemical::Atom::element_type(), core::chemical::find_bonds_in_rings(), core::chemical::find_nbr_dist(), core::chemical::sdf::MolFileIOAtom::formal_charge(), core::chemical::element::H, core::chemical::sdf::has(), index_atom_map_, core::chemical::mainchain_path(), molgraph_, core::chemical::sdf::MolFileIOAtom::name(), name_, protocols::sic_dock::scores::nbr, normalize(), core::chemical::MutableResidueType::null_vertex, core::chemical::sdf::MolFileIOAtom::partial_charge(), core::chemical::sdf::MolFileIOAtom::position(), core::chemical::rename_atoms(), core::chemical::rosetta_recharge_fullatom(), core::chemical::rosetta_retype_fullatom(), core::chemical::element::S, core::chemical::sdf::MolFileIOBond::sdf_type(), set_from_extra_data(), and core::chemical::sdf::TR().

void core::chemical::sdf::MolFileIOMolecule::create_dummy_atom ( MutableResidueTypeOP  restype, std::string  atom_name, core::Vector const &  xyz_offset, chemical::ElementSetCOP  elements, chemical::MMAtomTypeSetCOP  mm_atom_types  )

private

References core::chemical::Atom::element_type(), and core::chemical::UnknownBond.

Referenced by convert_to_ResidueType().

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, MutableResidueType const &  restype, std::map< mioAD, core::chemical::VD > &  restype_from_mio  )

private

References core::chemical::MutableResidueType::has(), and index_atom_map_.

Referenced by set_from_extra_data().

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::parse_multi ( std::istream &  estream, utility::vector1< std::string > &  parsed, std::string  label  ) const

private

Parse a multiple value item, say for per-atom or per-bond data This assumes that the passed vector is pre-initialized to the appropriate size. Valid formats are a series of space-separated sequential items, or a space-separated set of items in the form of "(index,value)". Spaces are not valid in either entry.

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

Referenced by set_from_extra_data().

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

private

From the str/str data in MolFile, additional information Specifically, it's the overall atom and bond information.

References protocols::cluster::calibur::aa, core::chemical::ResidueTypeBase::aa(), core::chemical::ResidueTypeBase::add_property(), core::chemical::ResidueTypeBase::add_string_property(), core::chemical::ResidueTypeBase::atom_type_set(), core::chemical::AtomTypeSet::has_atom(), index_atom_map_, index_valid(), core::chemical::ResidueTypeBase::interchangeability_group(), molecule_string_data_, name(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), protocols::sic_dock::scores::nbr, core::chemical::MutableResidueType::nbr_atom(), core::chemical::MutableResidueType::nbr_radius(), parse_multi(), core::chemical::MutableResidueType::rename_atom(), core::chemical::MutableResidueType::set_atom_type(), and core::chemical::sdf::TR().

Referenced by convert_to_ResidueType().

Member Data Documentation

std::map< AtomIndex, mioAD > core::chemical::sdf::MolFileIOMolecule::index_atom_map_

private

Referenced by add_atom(), add_bond(), atom_index(), convert_to_ResidueType(), index_valid(), and set_from_extra_data().

StrStrMap core::chemical::sdf::MolFileIOMolecule::molecule_string_data_

private

Referenced by add_str_str_data(), get_str_str_data(), and set_from_extra_data().

MolFileIOGraph core::chemical::sdf::MolFileIOMolecule::molgraph_

private

Referenced by add_atom(), add_bond(), atom_index(), and convert_to_ResidueType().

std::string core::chemical::sdf::MolFileIOMolecule::name_

private

Referenced by convert_to_ResidueType(), and name().

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

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