Bindings for core::chemical::sdf namespace

Classes
		builtins.object BondData CtabParserBase CtabV2000Parser CtabV3000Parser MolFileIOAtom MolFileIOBond MolFileIOMolecule MolFileIOReader MolWriter SDFParser   class BondData(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.chemical.sdf.BondData, other : rosetta.core.chemical.sdf.BondData) -> bool __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.chemical.sdf.BondData, index1 : int, index2 : int, type : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: bondType lower upper   class CtabParserBase(builtins.object)       Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.chemical.sdf.CtabParserBase,  : rosetta.core.chemical.sdf.CtabParserBase) -> rosetta.core.chemical.sdf.CtabParserBase   class CtabV2000Parser(CtabParserBase)       Method resolution order: CtabV2000Parser CtabParserBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.chemical.sdf.CtabV2000Parser,  : rosetta.core.chemical.sdf.CtabV2000Parser) -> rosetta.core.chemical.sdf.CtabV2000Parser   class CtabV3000Parser(CtabParserBase)       Method resolution order: CtabV3000Parser CtabParserBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.chemical.sdf.CtabV3000Parser,  : rosetta.core.chemical.sdf.CtabV3000Parser) -> rosetta.core.chemical.sdf.CtabV3000Parser   class MolFileIOAtom(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.chemical.sdf.MolFileIOAtom) -> NoneType   2. __init__(self : rosetta.core.chemical.sdf.MolFileIOAtom,  : rosetta.core.chemical.sdf.MolFileIOAtom) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.chemical.sdf.MolFileIOAtom,  : rosetta.core.chemical.sdf.MolFileIOAtom) -> rosetta.core.chemical.sdf.MolFileIOAtom element(...) from builtins.PyCapsule element(*args, **kwargs) Overloaded function.   1. element(rosetta.core.chemical.sdf.MolFileIOAtom) -> str   2. element(self : rosetta.core.chemical.sdf.MolFileIOAtom, element : str) -> NoneType formal_charge(...) from builtins.PyCapsule formal_charge(*args, **kwargs) Overloaded function.   1. formal_charge(rosetta.core.chemical.sdf.MolFileIOAtom) -> int   2. formal_charge(self : rosetta.core.chemical.sdf.MolFileIOAtom, formal_charge : int) -> NoneType index(...) from builtins.PyCapsule index(*args, **kwargs) Overloaded function.   1. index(rosetta.core.chemical.sdf.MolFileIOAtom) -> int   2. index(self : rosetta.core.chemical.sdf.MolFileIOAtom, index : int) -> NoneType name(...) from builtins.PyCapsule name(*args, **kwargs) Overloaded function.   1. name(rosetta.core.chemical.sdf.MolFileIOAtom) -> str   2. name(self : rosetta.core.chemical.sdf.MolFileIOAtom, name : str) -> NoneType partial_charge(...) from builtins.PyCapsule partial_charge(*args, **kwargs) Overloaded function.   1. partial_charge(rosetta.core.chemical.sdf.MolFileIOAtom) -> float   2. partial_charge(self : rosetta.core.chemical.sdf.MolFileIOAtom, partial_charge : float) -> NoneType position(...) from builtins.PyCapsule position(*args, **kwargs) Overloaded function.   1. position(rosetta.core.chemical.sdf.MolFileIOAtom) -> rosetta.numeric.xyzVector_double_t   2. position(self : rosetta.core.chemical.sdf.MolFileIOAtom, position : rosetta.numeric.xyzVector_double_t) -> NoneType   class MolFileIOBond(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.chemical.sdf.MolFileIOBond) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.chemical.sdf.MolFileIOBond,  : rosetta.core.chemical.sdf.MolFileIOBond) -> rosetta.core.chemical.sdf.MolFileIOBond atom1(...) from builtins.PyCapsule atom1(*args, **kwargs) Overloaded function.   1. atom1(rosetta.core.chemical.sdf.MolFileIOBond) -> int   2. atom1(self : rosetta.core.chemical.sdf.MolFileIOBond, atom1 : int) -> NoneType atom2(...) from builtins.PyCapsule atom2(*args, **kwargs) Overloaded function.   1. atom2(rosetta.core.chemical.sdf.MolFileIOBond) -> int   2. atom2(self : rosetta.core.chemical.sdf.MolFileIOBond, atom2 : int) -> NoneType index(...) from builtins.PyCapsule index(*args, **kwargs) Overloaded function.   1. index(rosetta.core.chemical.sdf.MolFileIOBond) -> int   2. index(self : rosetta.core.chemical.sdf.MolFileIOBond, index : int) -> NoneType sdf_type(...) from builtins.PyCapsule sdf_type(*args, **kwargs) Overloaded function.   1. sdf_type(rosetta.core.chemical.sdf.MolFileIOBond) -> int   2. sdf_type(self : rosetta.core.chemical.sdf.MolFileIOBond, sdf_type : int) -> NoneType   class MolFileIOMolecule(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.chemical.sdf.MolFileIOMolecule) -> NoneType   2. __init__(self : rosetta.core.chemical.sdf.MolFileIOMolecule,  : rosetta.core.chemical.sdf.MolFileIOMolecule) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_atom(...) from builtins.PyCapsule add_atom(self : rosetta.core.chemical.sdf.MolFileIOMolecule, atom : rosetta.core.chemical.sdf.MolFileIOAtom) -> NoneType   Add an atom (takes possession of object) add_bond(...) from builtins.PyCapsule add_bond(self : rosetta.core.chemical.sdf.MolFileIOMolecule, bond : rosetta.core.chemical.sdf.MolFileIOBond) -> NoneType   Add a bond (takes possession of object) add_str_str_data(...) from builtins.PyCapsule add_str_str_data(self : rosetta.core.chemical.sdf.MolFileIOMolecule, key : str, value : str) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.chemical.sdf.MolFileIOMolecule,  : rosetta.core.chemical.sdf.MolFileIOMolecule) -> rosetta.core.chemical.sdf.MolFileIOMolecule atom_index(...) from builtins.PyCapsule atom_index(self : rosetta.core.chemical.sdf.MolFileIOMolecule, index : int) -> rosetta.core.chemical.sdf.MolFileIOAtom   Retrieve a modifiable atom by index convert_to_ResidueType(...) from builtins.PyCapsule convert_to_ResidueType(*args, **kwargs) Overloaded function.   1. convert_to_ResidueType(self : rosetta.core.chemical.sdf.MolFileIOMolecule, atom_types : rosetta.core.chemical.AtomTypeSet, elements : rosetta.core.chemical.ElementSet, mm_atom_types : rosetta.core.chemical.MMAtomTypeSet) -> rosetta.core.chemical.ResidueType   Make a ResidueType from this object      Not const as it calls normalize() to fix up missing data first.   2. convert_to_ResidueType(self : rosetta.core.chemical.sdf.MolFileIOMolecule, index_name_map : rosetta.std.map_unsigned_long_std_string, atom_types : rosetta.core.chemical.AtomTypeSet, elements : rosetta.core.chemical.ElementSet, mm_atom_types : rosetta.core.chemical.MMAtomTypeSet) -> rosetta.core.chemical.ResidueType   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. get_str_str_data(...) from builtins.PyCapsule get_str_str_data(rosetta.core.chemical.sdf.MolFileIOMolecule) -> rosetta.std.map_std_string_std_string name(...) from builtins.PyCapsule name(*args, **kwargs) Overloaded function.   1. name(rosetta.core.chemical.sdf.MolFileIOMolecule) -> str   2. name(self : rosetta.core.chemical.sdf.MolFileIOMolecule, name : str) -> NoneType normalize(...) from builtins.PyCapsule normalize(rosetta.core.chemical.sdf.MolFileIOMolecule) -> NoneType   Generate data for potentially missing fields.   class MolFileIOReader(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.chemical.sdf.MolFileIOReader) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.chemical.sdf.MolFileIOReader,  : rosetta.core.chemical.sdf.MolFileIOReader) -> rosetta.core.chemical.sdf.MolFileIOReader   class MolWriter(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.chemical.sdf.MolWriter) -> NoneType   2. __init__(self : rosetta.core.chemical.sdf.MolWriter, ctab_mode : str) -> NoneType   3. __init__(self : rosetta.core.chemical.sdf.MolWriter,  : rosetta.core.chemical.sdf.MolWriter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. output_residue(...) from builtins.PyCapsule output_residue(*args, **kwargs) Overloaded function.   1. output_residue(self : rosetta.core.chemical.sdf.MolWriter, file_name : str, residue : core::conformation::Residue) -> NoneType   2. output_residue(self : rosetta.core.chemical.sdf.MolWriter, file_name : str, residue_type : rosetta.core.chemical.ResidueType) -> NoneType   3. output_residue(self : rosetta.core.chemical.sdf.MolWriter, file_name : str, residue : core::conformation::Residue) -> NoneType   4. output_residue(self : rosetta.core.chemical.sdf.MolWriter, file_name : str, residue_type : rosetta.core.chemical.ResidueType) -> NoneType set_job_data(...) from builtins.PyCapsule set_job_data(self : rosetta.core.chemical.sdf.MolWriter, job_data : rosetta.std.map_std_string_std_string) -> NoneType   class SDFParser(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.chemical.sdf.SDFParser) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.chemical.sdf.SDFParser,  : rosetta.core.chemical.sdf.SDFParser) -> rosetta.core.chemical.sdf.SDFParser

Functions
		parse_atom_type_data(...) method of builtins.PyCapsule instance parse_atom_type_data(raw_data : str) -> rosetta.std.map_unsigned_long_std_string