sdf

Bindings for core::chemical::sdf namespace

class pyrosetta.rosetta.core.chemical.sdf.BondData

Bases: pybind11_builtins.pybind11_object

property bondType
property lower
property upper
class pyrosetta.rosetta.core.chemical.sdf.CtabParserBase

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.sdf.CtabParserBase, : pyrosetta.rosetta.core.chemical.sdf.CtabParserBase) pyrosetta.rosetta.core.chemical.sdf.CtabParserBase

C++: core::chemical::sdf::CtabParserBase::operator=(const class core::chemical::sdf::CtabParserBase &) –> class core::chemical::sdf::CtabParserBase &

parse(self: pyrosetta.rosetta.core.chemical.sdf.CtabParserBase, tablein: pyrosetta.rosetta.std.istream, headerline: str, molecule: core::chemical::sdf::MolFileIOMolecule) bool

C++: core::chemical::sdf::CtabParserBase::parse(std::istream &, const std::string &, class core::chemical::sdf::MolFileIOMolecule &) –> bool

class pyrosetta.rosetta.core.chemical.sdf.CtabV2000Parser

Bases: pyrosetta.rosetta.core.chemical.sdf.CtabParserBase

assign(self: pyrosetta.rosetta.core.chemical.sdf.CtabV2000Parser, : pyrosetta.rosetta.core.chemical.sdf.CtabV2000Parser) pyrosetta.rosetta.core.chemical.sdf.CtabV2000Parser

C++: core::chemical::sdf::CtabV2000Parser::operator=(const class core::chemical::sdf::CtabV2000Parser &) –> class core::chemical::sdf::CtabV2000Parser &

parse(self: pyrosetta.rosetta.core.chemical.sdf.CtabV2000Parser, tablein: pyrosetta.rosetta.std.istream, headerline: str, molecule: core::chemical::sdf::MolFileIOMolecule) bool

C++: core::chemical::sdf::CtabV2000Parser::parse(std::istream &, const std::string &, class core::chemical::sdf::MolFileIOMolecule &) –> bool

class pyrosetta.rosetta.core.chemical.sdf.CtabV3000Parser

Bases: pyrosetta.rosetta.core.chemical.sdf.CtabParserBase

assign(self: pyrosetta.rosetta.core.chemical.sdf.CtabV3000Parser, : pyrosetta.rosetta.core.chemical.sdf.CtabV3000Parser) pyrosetta.rosetta.core.chemical.sdf.CtabV3000Parser

C++: core::chemical::sdf::CtabV3000Parser::operator=(const class core::chemical::sdf::CtabV3000Parser &) –> class core::chemical::sdf::CtabV3000Parser &

parse(self: pyrosetta.rosetta.core.chemical.sdf.CtabV3000Parser, tablein: pyrosetta.rosetta.std.istream, headerline: str, molecule: core::chemical::sdf::MolFileIOMolecule) bool

C++: core::chemical::sdf::CtabV3000Parser::parse(std::istream &, const std::string &, class core::chemical::sdf::MolFileIOMolecule &) –> bool

class pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom, : pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom) pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom

C++: core::chemical::sdf::MolFileIOAtom::operator=(const class core::chemical::sdf::MolFileIOAtom &) –> class core::chemical::sdf::MolFileIOAtom &

element(*args, **kwargs)

Overloaded function.

  1. element(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom) -> str

C++: core::chemical::sdf::MolFileIOAtom::element() const –> const std::string &

  1. element(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom, element: str) -> None

C++: core::chemical::sdf::MolFileIOAtom::element(const std::string &) –> void

formal_charge(*args, **kwargs)

Overloaded function.

  1. formal_charge(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom) -> int

C++: core::chemical::sdf::MolFileIOAtom::formal_charge() const –> int

  1. formal_charge(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom, formal_charge: int) -> None

C++: core::chemical::sdf::MolFileIOAtom::formal_charge(int) –> void

index(*args, **kwargs)

Overloaded function.

  1. index(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom) -> int

C++: core::chemical::sdf::MolFileIOAtom::index() const –> unsigned long

  1. index(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom, index: int) -> None

C++: core::chemical::sdf::MolFileIOAtom::index(unsigned long) –> void

name(*args, **kwargs)

Overloaded function.

  1. name(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom) -> str

C++: core::chemical::sdf::MolFileIOAtom::name() const –> const std::string &

  1. name(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom, name: str) -> None

C++: core::chemical::sdf::MolFileIOAtom::name(const std::string &) –> void

partial_charge(*args, **kwargs)

Overloaded function.

  1. partial_charge(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom) -> float

C++: core::chemical::sdf::MolFileIOAtom::partial_charge() const –> double

  1. partial_charge(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom, partial_charge: float) -> None

C++: core::chemical::sdf::MolFileIOAtom::partial_charge(double) –> void

position(*args, **kwargs)

Overloaded function.

  1. position(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::chemical::sdf::MolFileIOAtom::position() const –> const class numeric::xyzVector<double> &

  1. position(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom, position: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::chemical::sdf::MolFileIOAtom::position(const class numeric::xyzVector<double> &) –> void

class pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond, : pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond) pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond

C++: core::chemical::sdf::MolFileIOBond::operator=(const class core::chemical::sdf::MolFileIOBond &) –> class core::chemical::sdf::MolFileIOBond &

atom1(*args, **kwargs)

Overloaded function.

  1. atom1(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond) -> int

C++: core::chemical::sdf::MolFileIOBond::atom1() const –> unsigned long

  1. atom1(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond, atom1: int) -> None

C++: core::chemical::sdf::MolFileIOBond::atom1(unsigned long) –> void

atom2(*args, **kwargs)

Overloaded function.

  1. atom2(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond) -> int

C++: core::chemical::sdf::MolFileIOBond::atom2() const –> unsigned long

  1. atom2(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond, atom2: int) -> None

C++: core::chemical::sdf::MolFileIOBond::atom2(unsigned long) –> void

index(*args, **kwargs)

Overloaded function.

  1. index(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond) -> int

C++: core::chemical::sdf::MolFileIOBond::index() const –> unsigned long

  1. index(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond, index: int) -> None

C++: core::chemical::sdf::MolFileIOBond::index(unsigned long) –> void

sdf_type(*args, **kwargs)

Overloaded function.

  1. sdf_type(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond) -> int

C++: core::chemical::sdf::MolFileIOBond::sdf_type() const –> unsigned long

  1. sdf_type(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond, sdf_type: int) -> None

C++: core::chemical::sdf::MolFileIOBond::sdf_type(unsigned long) –> void

class pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule

Bases: pybind11_builtins.pybind11_object

add_atom(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule, atom: pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom) None

Add an atom (takes possession of object)

C++: core::chemical::sdf::MolFileIOMolecule::add_atom(class std::shared_ptr<class core::chemical::sdf::MolFileIOAtom>) –> void

add_bond(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule, bond: pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond) None

Add a bond (takes possession of object)

C++: core::chemical::sdf::MolFileIOMolecule::add_bond(class std::shared_ptr<class core::chemical::sdf::MolFileIOBond>) –> void

add_str_str_data(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule, key: str, value: str) None

C++: core::chemical::sdf::MolFileIOMolecule::add_str_str_data(const std::string &, const std::string &) –> void

assign(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule, : pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule) pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule

C++: core::chemical::sdf::MolFileIOMolecule::operator=(const class core::chemical::sdf::MolFileIOMolecule &) –> class core::chemical::sdf::MolFileIOMolecule &

atom_index(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule, index: int) pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom

Retrieve a modifiable atom by index

C++: core::chemical::sdf::MolFileIOMolecule::atom_index(unsigned long) –> class std::shared_ptr<class core::chemical::sdf::MolFileIOAtom>

convert_to_ResidueType(*args, **kwargs)

Overloaded function.

  1. convert_to_ResidueType(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule, atom_types: pyrosetta.rosetta.core.chemical.AtomTypeSet, elements: pyrosetta.rosetta.core.chemical.ElementSet, mm_atom_types: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) -> pyrosetta.rosetta.core.chemical.MutableResidueType

Make a ResidueType from this object

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

C++: core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType(class std::shared_ptr<const class core::chemical::AtomTypeSet>, class std::shared_ptr<const class core::chemical::ElementSet>, class std::shared_ptr<const class core::chemical::MMAtomTypeSet>) –> class std::shared_ptr<class core::chemical::MutableResidueType>

  1. convert_to_ResidueType(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule, index_name_map: pyrosetta.rosetta.std.map_unsigned_long_std_string, atom_types: pyrosetta.rosetta.core.chemical.AtomTypeSet, elements: pyrosetta.rosetta.core.chemical.ElementSet, mm_atom_types: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) -> pyrosetta.rosetta.core.chemical.MutableResidueType

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.

C++: core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType(class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &, class std::shared_ptr<const class core::chemical::AtomTypeSet>, class std::shared_ptr<const class core::chemical::ElementSet>, class std::shared_ptr<const class core::chemical::MMAtomTypeSet>) –> class std::shared_ptr<class core::chemical::MutableResidueType>

get_str_str_data(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule) pyrosetta.rosetta.std.map_std_string_std_string

C++: core::chemical::sdf::MolFileIOMolecule::get_str_str_data() const –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

name(*args, **kwargs)

Overloaded function.

  1. name(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule) -> str

C++: core::chemical::sdf::MolFileIOMolecule::name() const –> std::string

  1. name(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule, name: str) -> None

C++: core::chemical::sdf::MolFileIOMolecule::name(std::string) –> void

normalize(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule) None

Generate data for potentially missing fields.

C++: core::chemical::sdf::MolFileIOMolecule::normalize() –> void

class pyrosetta.rosetta.core.chemical.sdf.MolFileIOReader

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOReader, : pyrosetta.rosetta.core.chemical.sdf.MolFileIOReader) pyrosetta.rosetta.core.chemical.sdf.MolFileIOReader

C++: core::chemical::sdf::MolFileIOReader::operator=(const class core::chemical::sdf::MolFileIOReader &) –> class core::chemical::sdf::MolFileIOReader &

parse_file(*args, **kwargs)

Overloaded function.

  1. parse_file(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOReader, filename: str) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t

  2. parse_file(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOReader, filename: str, type: str) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t

  3. parse_file(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOReader, filename: str, type: str, n_entries: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t

parse file, with the possibility of type autodetection.

C++: core::chemical::sdf::MolFileIOReader::parse_file(const std::string &, std::string, unsigned long) –> class utility::vector1<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule>, class std::allocator<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule> > >

  1. parse_file(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOReader, file: pyrosetta.rosetta.std.istream, type: str) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t

  2. parse_file(self: pyrosetta.rosetta.core.chemical.sdf.MolFileIOReader, file: pyrosetta.rosetta.std.istream, type: str, n_entries: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t

parse file from stream, type must be specified.

C++: core::chemical::sdf::MolFileIOReader::parse_file(std::istream &, std::string, unsigned long) –> class utility::vector1<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule>, class std::allocator<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule> > >

class pyrosetta.rosetta.core.chemical.sdf.MolWriter

Bases: pybind11_builtins.pybind11_object

output_residue(*args, **kwargs)

Overloaded function.

  1. output_residue(self: pyrosetta.rosetta.core.chemical.sdf.MolWriter, output_stream: pyrosetta.rosetta.std.ostream, residue: core::conformation::Residue) -> None

C++: core::chemical::sdf::MolWriter::output_residue(std::ostream &, class std::shared_ptr<const class core::conformation::Residue>) –> void

  1. output_residue(self: pyrosetta.rosetta.core.chemical.sdf.MolWriter, output_stream: pyrosetta.rosetta.std.ostream, residue_type: pyrosetta.rosetta.core.chemical.ResidueType) -> None

C++: core::chemical::sdf::MolWriter::output_residue(std::ostream &, class std::shared_ptr<const class core::chemical::ResidueType>) –> void

  1. output_residue(self: pyrosetta.rosetta.core.chemical.sdf.MolWriter, output_stream: pyrosetta.rosetta.std.ostream, residue_type: pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

C++: core::chemical::sdf::MolWriter::output_residue(std::ostream &, class std::shared_ptr<const class core::chemical::MutableResidueType>) –> void

  1. output_residue(self: pyrosetta.rosetta.core.chemical.sdf.MolWriter, output_stream: pyrosetta.rosetta.std.ostream, residue: core::conformation::Residue) -> None

C++: core::chemical::sdf::MolWriter::output_residue(std::ostream &, const class core::conformation::Residue &) –> void

  1. output_residue(self: pyrosetta.rosetta.core.chemical.sdf.MolWriter, output_stream: pyrosetta.rosetta.std.ostream, residue_type: pyrosetta.rosetta.core.chemical.ResidueType) -> None

C++: core::chemical::sdf::MolWriter::output_residue(std::ostream &, const class core::chemical::ResidueType &) –> void

  1. output_residue(self: pyrosetta.rosetta.core.chemical.sdf.MolWriter, output_stream: pyrosetta.rosetta.std.ostream, residue_type: pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

C++: core::chemical::sdf::MolWriter::output_residue(std::ostream &, const class core::chemical::MutableResidueType &) –> void

set_job_data(self: pyrosetta.rosetta.core.chemical.sdf.MolWriter, job_data: pyrosetta.rosetta.std.map_std_string_std_string) None

C++: core::chemical::sdf::MolWriter::set_job_data(const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &) –> void

class pyrosetta.rosetta.core.chemical.sdf.SDFParser

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.sdf.SDFParser, : pyrosetta.rosetta.core.chemical.sdf.SDFParser) pyrosetta.rosetta.core.chemical.sdf.SDFParser

C++: core::chemical::sdf::SDFParser::operator=(const class core::chemical::sdf::SDFParser &) –> class core::chemical::sdf::SDFParser &

parse(*args, **kwargs)

Overloaded function.

  1. parse(self: pyrosetta.rosetta.core.chemical.sdf.SDFParser, filein: pyrosetta.rosetta.std.istream) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t

  2. parse(self: pyrosetta.rosetta.core.chemical.sdf.SDFParser, filein: pyrosetta.rosetta.std.istream, n_entries: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t

parse the given input stream.

n_entries are the maximum number of entries to parse - of zero parse all the remaining ones.

C++: core::chemical::sdf::SDFParser::parse(std::istream &, unsigned long) –> class utility::vector1<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule>, class std::allocator<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule> > >

pyrosetta.rosetta.core.chemical.sdf.__PyRosetta_instantiate_vector1_MutableResidueType_and_MolFileIOMolecule_types(: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_MutableResidueType_t, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t) None

C++: core::chemical::sdf::__PyRosetta_instantiate_vector1_MutableResidueType_and_MolFileIOMolecule_types(class utility::vector1<class std::shared_ptr<class core::chemical::MutableResidueType>, class std::allocator<class std::shared_ptr<class core::chemical::MutableResidueType> > >, class utility::vector1<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule>, class std::allocator<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule> > >) –> void

pyrosetta.rosetta.core.chemical.sdf.convert_to_ResidueType(*args, **kwargs)

Overloaded function.

  1. convert_to_ResidueType(molfile_data: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t) -> pyrosetta.rosetta.core.chemical.MutableResidueType

  2. convert_to_ResidueType(molfile_data: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t, atom_type_tag: str) -> pyrosetta.rosetta.core.chemical.MutableResidueType

  3. convert_to_ResidueType(molfile_data: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t, atom_type_tag: str, element_type_tag: str) -> pyrosetta.rosetta.core.chemical.MutableResidueType

  4. convert_to_ResidueType(molfile_data: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t, atom_type_tag: str, element_type_tag: str, mm_atom_type_tag: str) -> pyrosetta.rosetta.core.chemical.MutableResidueType

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

C++: core::chemical::sdf::convert_to_ResidueType(class utility::vector1<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule>, class std::allocator<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule> > >, std::string, std::string, std::string) –> class std::shared_ptr<class core::chemical::MutableResidueType>

  1. convert_to_ResidueType(molfile_data: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t, atom_types: pyrosetta.rosetta.core.chemical.AtomTypeSet, element_types: pyrosetta.rosetta.core.chemical.ElementSet, mm_atom_types: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) -> pyrosetta.rosetta.core.chemical.MutableResidueType

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

C++: core::chemical::sdf::convert_to_ResidueType(class utility::vector1<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule>, class std::allocator<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule> > >, class std::shared_ptr<const class core::chemical::AtomTypeSet>, class std::shared_ptr<const class core::chemical::ElementSet>, class std::shared_ptr<const class core::chemical::MMAtomTypeSet>) –> class std::shared_ptr<class core::chemical::MutableResidueType>

pyrosetta.rosetta.core.chemical.sdf.convert_to_ResidueTypes(*args, **kwargs)

Overloaded function.

  1. convert_to_ResidueTypes(molfile_data: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_MutableResidueType_t

  2. convert_to_ResidueTypes(molfile_data: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t, load_rotamers: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_MutableResidueType_t

  3. convert_to_ResidueTypes(molfile_data: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t, load_rotamers: bool, atom_type_tag: str) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_MutableResidueType_t

  4. convert_to_ResidueTypes(molfile_data: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t, load_rotamers: bool, atom_type_tag: str, element_type_tag: str) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_MutableResidueType_t

  5. convert_to_ResidueTypes(molfile_data: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t, load_rotamers: bool, atom_type_tag: str, element_type_tag: str, mm_atom_type_tag: str) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_MutableResidueType_t

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

C++: core::chemical::sdf::convert_to_ResidueTypes(class utility::vector1<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule>, class std::allocator<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule> > >, bool, std::string, std::string, std::string) –> class utility::vector1<class std::shared_ptr<class core::chemical::MutableResidueType>, class std::allocator<class std::shared_ptr<class core::chemical::MutableResidueType> > >

  1. convert_to_ResidueTypes(molfile_data: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_sdf_MolFileIOMolecule_t, load_rotamers: bool, atom_types: pyrosetta.rosetta.core.chemical.AtomTypeSet, element_types: pyrosetta.rosetta.core.chemical.ElementSet, mm_atom_types: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_MutableResidueType_t

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

C++: core::chemical::sdf::convert_to_ResidueTypes(class utility::vector1<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule>, class std::allocator<class std::shared_ptr<class core::chemical::sdf::MolFileIOMolecule> > >, bool, class std::shared_ptr<const class core::chemical::AtomTypeSet>, class std::shared_ptr<const class core::chemical::ElementSet>, class std::shared_ptr<const class core::chemical::MMAtomTypeSet>) –> class utility::vector1<class std::shared_ptr<class core::chemical::MutableResidueType>, class std::allocator<class std::shared_ptr<class core::chemical::MutableResidueType> > >

  1. convert_to_ResidueTypes(filename: str) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_MutableResidueType_t

  2. convert_to_ResidueTypes(filename: str, load_rotamers: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_MutableResidueType_t

  3. convert_to_ResidueTypes(filename: str, load_rotamers: bool, atom_type_tag: str) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_MutableResidueType_t

  4. convert_to_ResidueTypes(filename: str, load_rotamers: bool, atom_type_tag: str, element_type_tag: str) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_MutableResidueType_t

  5. convert_to_ResidueTypes(filename: str, load_rotamers: bool, atom_type_tag: str, element_type_tag: str, mm_atom_type_tag: str) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_MutableResidueType_t

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

C++: core::chemical::sdf::convert_to_ResidueTypes(const std::string &, bool, std::string, std::string, std::string) –> class utility::vector1<class std::shared_ptr<class core::chemical::MutableResidueType>, class std::allocator<class std::shared_ptr<class core::chemical::MutableResidueType> > >

  1. convert_to_ResidueTypes(filename: str, load_rotamers: bool, atom_types: pyrosetta.rosetta.core.chemical.AtomTypeSet, element_types: pyrosetta.rosetta.core.chemical.ElementSet, mm_atom_types: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_chemical_MutableResidueType_t

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

C++: core::chemical::sdf::convert_to_ResidueTypes(const std::string &, bool, class std::shared_ptr<const class core::chemical::AtomTypeSet>, class std::shared_ptr<const class core::chemical::ElementSet>, class std::shared_ptr<const class core::chemical::MMAtomTypeSet>) –> class utility::vector1<class std::shared_ptr<class core::chemical::MutableResidueType>, class std::allocator<class std::shared_ptr<class core::chemical::MutableResidueType> > >

pyrosetta.rosetta.core.chemical.sdf.parse_atom_type_data(raw_data: str) pyrosetta.rosetta.std.map_unsigned_long_std_string

C++: core::chemical::sdf::parse_atom_type_data(std::string) –> class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > >