Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Classes | Typedefs | Functions
core::chemical::sdf Namespace Reference

Classes

struct  BondData
 
class  CtabParserBase
 
class  CtabV2000Parser
 
class  CtabV3000Parser
 
class  MolFileIOAtom
 
class  MolFileIOBond
 
class  MolFileIOMolecule
 
class  MolFileIOReader
 
class  MolWriter
 
class  SDFParser
 

Typedefs

typedef
utility::pointer::shared_ptr
< MolFileIOAtom
MolFileIOAtomOP
 
typedef
utility::pointer::shared_ptr
< MolFileIOBond
MolFileIOBondOP
 
typedef
utility::pointer::shared_ptr
< MolFileIOMolecule
MolFileIOMoleculeOP
 
typedef
utility::pointer::shared_ptr
< const MolFileIOAtom
MolFileIOAtomCOP
 
typedef
utility::pointer::shared_ptr
< const MolFileIOBond
MolFileIOBondCOP
 
typedef
utility::pointer::shared_ptr
< const MolFileIOMolecule
MolFileIOMoleculeCOP
 
typedef
boost::undirected_graph
< MolFileIOAtomOP,
MolFileIOBondOP
MolFileIOGraph
 
typedef
MolFileIOGraph::vertex_descriptor 
mioAD
 
typedef
MolFileIOGraph::edge_descriptor 
mioBD
 
typedef core::Size AtomIndex
 
typedef core::Size BondIndex
 
typedef std::map< std::string,
std::string > 
StrStrMap
 

Functions

static basic::Tracer TR ("core.chemical.sdf.CtabV2000Parser")
 
static basic::Tracer TR ("core.chemical.sdf.CtabV3000Parser")
 
std::set< BondDataparse_bond_type_data (std::string raw_data)
 
std::map< core::Size, std::string > parse_atom_type_data (std::string raw_data)
 
static basic::Tracer tr ("core.chemical.sdf.mol_writer")
 
template<class Input_t >
void output_residue (std::string const &outfile, Input_t &residue)
 
template<class Input_t >
void output_residue (std::ostream &output_stream, Input_t &residue)
 
static basic::Tracer TR ("core.io.sdf.MolFileIOData")
 
void dump_graph (MolFileIOGraph const &graph)
 
bool has (MolFileIOGraph const &graph, mioAD vd)
 
bool has (MolFileIOGraph const &graph, mioBD ed)
 
static basic::Tracer TR ("core.io.sdf.MolFileIOReader")
 
MutableResidueTypeOP convert_to_ResidueType (utility::vector1< MolFileIOMoleculeOP > molfile_data, std::string atom_type_tag="fa_standard", std::string element_type_tag="default", std::string mm_atom_type_tag="fa_standard")
 Convert the vector of MolFileIOMolecules into a single residue type, using multiple entries as rotamers Can return a null pointer if there's something wrong with the underlying data. More...
 
MutableResidueTypeOP convert_to_ResidueType (utility::vector1< MolFileIOMoleculeOP > molfile_data, AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types)
 Convert the vector of MolFileIOMolecules into a single residue type, using multiple entries as rotamers Can return a null pointer if there's something wrong with the underlying data. More...
 
utility::vector1
< MutableResidueTypeOP
convert_to_ResidueTypes (utility::vector1< MolFileIOMoleculeOP > molfile_data, bool load_rotamers=true, std::string atom_type_tag="fa_standard", std::string element_type_tag="default", std::string mm_atom_type_tag="fa_standard")
 Convert the vector of MolFileIOMolecules into multiple residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers Will not return results for entries with bad Data. More...
 
utility::vector1
< MutableResidueTypeOP
convert_to_ResidueTypes (utility::vector1< MolFileIOMoleculeOP > molfile_data, bool load_rotamers, AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types)
 Convert the vector of MolFileIOMolecules into multiple residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers Will not return results for entries with bad Data. More...
 
utility::vector1
< MutableResidueTypeOP
convert_to_ResidueTypes (std::string const &filename, bool load_rotamers, std::string atom_type_tag, std::string elements_tag, std::string mm_atom_type_tag)
 Load a given file into one or more residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers. More...
 
utility::vector1
< MutableResidueTypeOP
convert_to_ResidueTypes (std::string const &filename, bool load_rotamers, AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types)
 Load a given file into one or more residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers. More...
 
static basic::Tracer TR ("core.chemical.sdf.SDFParser")
 

Typedef Documentation

typedef MolFileIOGraph::vertex_descriptor core::chemical::sdf::mioAD
typedef MolFileIOGraph::edge_descriptor core::chemical::sdf::mioBD
typedef utility::pointer::shared_ptr< const MolFileIOAtom > core::chemical::sdf::MolFileIOAtomCOP
typedef utility::pointer::shared_ptr< MolFileIOAtom > core::chemical::sdf::MolFileIOAtomOP
typedef utility::pointer::shared_ptr< const MolFileIOBond > core::chemical::sdf::MolFileIOBondCOP
typedef utility::pointer::shared_ptr< MolFileIOBond > core::chemical::sdf::MolFileIOBondOP
typedef utility::pointer::shared_ptr< const MolFileIOMolecule > core::chemical::sdf::MolFileIOMoleculeCOP
typedef utility::pointer::shared_ptr< MolFileIOMolecule > core::chemical::sdf::MolFileIOMoleculeOP
typedef std::map<std::string, std::string> core::chemical::sdf::StrStrMap

Function Documentation

MutableResidueTypeOP core::chemical::sdf::convert_to_ResidueType ( utility::vector1< MolFileIOMoleculeOP >  molfile_data,
std::string  atom_type_tag,
std::string  elements_tag,
std::string  mm_atom_type_tag 
)

Convert the vector of MolFileIOMolecules into a single residue type, using multiple entries as rotamers Can return a null pointer if there's something wrong with the underlying data.

Referenced by core::chemical::GlobalResidueTypeSet::attempt_readin(), and convert_to_ResidueTypes().

MutableResidueTypeOP core::chemical::sdf::convert_to_ResidueType ( utility::vector1< MolFileIOMoleculeOP >  molfile_data,
AtomTypeSetCOP  atom_types,
ElementSetCOP  element_type_set,
MMAtomTypeSetCOP  mm_atom_types 
)

Convert the vector of MolFileIOMolecules into a single residue type, using multiple entries as rotamers Can return a null pointer if there's something wrong with the underlying data.

References TR().

utility::vector1< MutableResidueTypeOP > core::chemical::sdf::convert_to_ResidueTypes ( utility::vector1< MolFileIOMoleculeOP >  molfile_data,
bool  load_rotamers,
std::string  atom_type_tag,
std::string  elements_tag,
std::string  mm_atom_type_tag 
)

Convert the vector of MolFileIOMolecules into multiple residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers Will not return results for entries with bad Data.

Referenced by convert_to_ResidueTypes(), and core::chemical::GlobalResidueTypeSet::extra_nonparam_restypes_from_commandline().

utility::vector1< MutableResidueTypeOP > core::chemical::sdf::convert_to_ResidueTypes ( utility::vector1< MolFileIOMoleculeOP >  molfile_data,
bool  load_rotamers,
AtomTypeSetCOP  atom_types,
ElementSetCOP  element_types,
MMAtomTypeSetCOP  mm_atom_types 
)

Convert the vector of MolFileIOMolecules into multiple residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers Will not return results for entries with bad Data.

References convert_to_ResidueType(), and TR().

utility::vector1< MutableResidueTypeOP > core::chemical::sdf::convert_to_ResidueTypes ( std::string const &  filename,
bool  load_rotamers,
std::string  atom_type_tag,
std::string  elements_tag,
std::string  mm_atom_type_tag 
)

Load a given file into one or more residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers.

References convert_to_ResidueTypes().

utility::vector1< MutableResidueTypeOP > core::chemical::sdf::convert_to_ResidueTypes ( std::string const &  filename,
bool  load_rotamers,
AtomTypeSetCOP  atom_types,
ElementSetCOP  element_types,
MMAtomTypeSetCOP  mm_atom_types 
)

Load a given file into one or more residue types If load_rotamers is false, each will be loaded as a single ResidueType Otherwise, entries with the same name will be loaded as rotamers.

References convert_to_ResidueTypes(), and core::chemical::sdf::MolFileIOReader::parse_file().

void core::chemical::sdf::dump_graph ( MolFileIOGraph const &  graph)

References has(), and TR().

bool core::chemical::sdf::has ( MolFileIOGraph const &  graph,
mioAD  vd 
)
inline
bool core::chemical::sdf::has ( MolFileIOGraph const &  graph,
mioBD  ed 
)
inline
template<class Input_t >
void core::chemical::sdf::output_residue ( std::string const &  outfile,
Input_t &  residue 
)
template<class Input_t >
void core::chemical::sdf::output_residue ( std::ostream &  output_stream,
Input_t &  residue 
)
std::map< core::Size, std::string > core::chemical::sdf::parse_atom_type_data ( std::string  raw_data)
std::set< BondData > core::chemical::sdf::parse_bond_type_data ( std::string  raw_data)
static basic::Tracer core::chemical::sdf::TR ( "core.chemical.sdf.CtabV2000Parser"  )
static
static basic::Tracer core::chemical::sdf::TR ( "core.chemical.sdf.CtabV3000Parser"  )
static
static basic::Tracer core::chemical::sdf::TR ( "core.io.sdf.MolFileIOReader"  )
static
static basic::Tracer core::chemical::sdf::TR ( "core.chemical.sdf.SDFParser"  )
static
static basic::Tracer core::chemical::sdf::tr ( "core.chemical.sdf.mol_writer"  )
static
static basic::Tracer core::chemical::sdf::TR ( "core.io.sdf.MolFileIOData"  )
static