OEMonomer

Attention

This is a preliminary API and may be improved based on user feedback. It is currently available in C++ and Python.

class OEMonomer : public OESystem::OEBase

Stores validated and pre-computed information for a monomer to be used as a building block for representing biological macromolecules.

The following methods are publicly inherited from OEBase:

Constructors

OEMonomer(arg2: OEMonomerData) -> OEMonomer
OEMonomer(arg2: OEMonomerImpl) -> OEMonomer

Initializes a monomer from OEMonomerData object. If the OEMonomerData is not valid an error will be thrown and the the generated OEMonomer object will be invalid too.

OEMonomer(arg2: OEMonomerImpl) -> OEMonomer
OEMonomer(arg2: OEMonomer) -> OEMonomer

Copy constructor.

GetAminoAcidType

GetAminoAcidType() -> int

Returns the amino acid of the monomer.

See also

OEAminoAcidType namespace

GetCanonicalSmiles

GetCanonicalSmiles() -> str

Returns the canonical smiles of the monomer without the R-group definitions. In case of alanine, that is defined with [H:1]N[C@@H](C)C(=O)[OH:2], its canonical smiles will be C[C@@H](C(=O)O)N.

See also

OEMonomer.GetSmiles method

GetCode

GetCode(codeSet: str) -> str

Returns the code of the monomer in the given code set. Empty string is returned if the monomer has no code specified.

GetCodes

GetCodes() -> OEStringStringMap

Returns all the code/code-set pairs defined for the monomer.

GetMonomerType

GetMonomerType() -> int

Returns the monomer type of the monomer.

See also

OEMonomerType namespace

GetName

GetName() -> str

Returns the full name of the monomer, or an empty string if the name was not specified at initialization.

GetPolymerType

GetPolymerType() -> int

Returns the polymer type of the monomer.

See also

OEPolymerType namespace

GetSmiles

GetSmiles() -> str

Returns the smiles representation of the monomer that contains the atom map indices representing connection points. Such as [H:1]N[C@@H](C)C(=O)[OH:2] defining alanine.

See also

OEMonomer.GetCanonicalSmiles method

HasCode

HasCode(codeSet: str) -> bool

Return whether the monomer has a code defined in the given code-set.

HasRGroup

HasRGroup(idx: int) -> bool

Returns whether the monomer has a specific (R-groups) connections.

IsCTerminal

IsCTerminal() -> bool

Returns whether a monomer can be used at the C-terminal of a peptide chain.

IsNTerminal

IsNTerminal() -> bool

Returns whether a monomer can be used at the N-terminal of a peptide chain.

IsValid

IsValid() -> bool

Returns whether the monomer was initialized successfully.

NumCodes

NumCodes() -> int

Returns the number of codes the monomer is defined in various code-sets.

NumRGroups

NumRGroups() -> int

Returns the number of connections (R-groups) of the monomer.

`operator=`	`GetData`	`IsDataType`
`operator+=`	`GetDataIter`	`SetBaseData`
`AddBaseData`	`GetDataType`	`SetBoolData`
`AddData`	`GetDoubleData`	`SetData`
`Clear`	`GetFloatData`	`SetDoubleData`
`CreateCopy`	`GetIntData`	`SetFloatData`
`DeleteData`	`GetStringData`	`SetIntData`
`GetBoolData`	`HasData`	`SetStringData`