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:

operator=

GetData

IsDataType

operator+=

GetDataIter

SetBaseData

AddBaseData

GetDataType

SetBoolData

AddData

GetDoubleData

SetData

Clear

GetFloatData

SetDoubleData

CreateCopy

GetIntData

SetFloatData

DeleteData

GetStringData

SetIntData

GetBoolData

HasData

SetStringData

Constructors

OEMonomer(const OEMonomerData &)

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(const OEMonomer &)

Copy constructor.

operator=

OEMonomer &operator=(const OEMonomer &)

Assignment operator.

GetAminoAcidType

unsigned GetAminoAcidType() const

Returns the amino acid of the monomer.

See also

GetCanonicalSmiles

std::string GetCanonicalSmiles() const

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

GetCode

std::string GetCode(const std::string& codeSet) const

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

GetCodes

const std::map<std::string, std::string>& GetCodes() const

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

GetMonomerType

unsigned GetMonomerType() const

Returns the monomer type of the monomer.

See also

GetName

std::string GetName() const

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

GetPolymerType

unsigned GetPolymerType() const

Returns the polymer type of the monomer.

See also

GetSmiles

std::string GetSmiles() const

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

HasCode

bool HasCode(const std::string& codeSet) const

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

HasRGroup

bool HasRGroup(unsigned idx) const

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

IsCTerminal

bool IsCTerminal() const

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

IsNTerminal

bool IsNTerminal() const

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

IsValid

bool IsValid() const

Returns whether the monomer was initialized successfully.

NumCodes

unsigned NumCodes() const

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

NumRGroups

unsigned NumRGroups() const

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