OEMonomerData

Attention

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

class OEMonomerData

Stores the basic definition required for a monomer (OEMonomer) to be used as a building block for representing biological macromolecules.

**Example of monomer definition of L-Alanine**
Property	Value	Required/Optional/Generated
Smiles	`[H:1]N[C@@H](C)C(=O)[OH:2]`	required
Canonical Smiles	`C[C@@H](C(=O)O)N`	generated
Name	`L-Alanine` (optional)	optional
Polymer type	`OEPolymerType::Peptide`	required
Monomer type	`OEMonomerType::Backbone`	required
Monomer code-set/code pair	`A` in code-set `Standard`	required for at least one code-set

OEMonomerData monomerData("[H:1]N[C@@H](C)C(=O)[OH:2]");
monomerData.SetName("L-Alanine");
monomerData.AddCode("Standard", "A");
OEMonomerValidationResult result;
if (!OEIsValidMonomerData(monomerData, result))
{
  OEThrow.Error("Invalid monomer definition for '%s' [warning=%s]", monomerData.GetName().c_str(),
                result.GetWarning().c_str());
}

See also

OEIsValidMonomerData function
OEMonomerValidationResult class

Constructors

OEMonomerData()

Default constructor that creates an OEMonomerData object.

OEMonomerData(const std::string& smiles,
              unsigned polymerType = OEPolymerType::Peptide,
              unsigned monomerType = OEMonomerType::Backbone)

Constructor that initializes an OEMonomerData object.

See also

OEPolymerType namespace
OEMonomerType namespace

OEMonomerData(const OEMonomerData &)

Copy constructor.

operator=

OEMonomerData &operator=(const OEMonomerData &)

Assignment operator.

AddCode

void AddCode(const std::string& codeSet, const std::string& code)

Adds a code to a monomer for a given code-set.

GetCode

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

Returns the code of the monomer for the given code-set. Returns an empty string if there is no code defined for the code-set.

GetCodes

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

Returns the map that contains all the code-set and code pairs defined for the monomer.

GetMonomerType

unsigned int GetMonomerType() const

Returns the monomer type of the monomer.

See also

OEMonomerType namespace

GetName

std::string GetName() const

Returns the full name of the monomer. It is optional to define and only used to reference name.

GetPolymerType

unsigned int GetPolymerType() const

Returns the polymer type of the monomer.

See also

OEPolymerType namespace

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.

GetCanonicalSmiles

std::string GetCanonicalSmiles() const

Returns the canonical smiles representation of the monomer (without atom mapping) Such as C[C@@H](C(=O)O)N] for alanine.

HasCode

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

Returns whether the monomer has a code defined for the given code set.

IsValid

bool IsValid() const

Returns whether the OEMonomerData object is fully defined and correct.

See also

OEIsValidMonomerData function

NumCodes

unsigned int NumCodes() const

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

SetCodes

void SetCodes(const std::map<std::string, std::string>& codes)

Sets a code of the monomer for a specific code-set.

SetMonomerType

void SetMonomerType(unsigned int)

Sets the monomer type of the monomer.

See also

OEMonomerType namespace

SetName

void SetName(const std::string &)

Sets the name of the monomer. The name can be arbitrary, but it is recommended use the IUPAC name or any other name that well the monomer. For example, the name of the C[C@@H](C(=O)O)N] monomer of can be Alanine , L-alanine or L-alpha-Alanine or (2S)-2-aminopropanoic acid. Setting the name is optional.

SetPolymerType

void SetPolymerType(unsigned int)

Sets the polymer type of the monomer.

See also

OEPolymerType namespace

SetSmiles

void SetSmiles(const std::string &)

Sets the smiles of the monomer. The given smiles has to define possible attachment points of the monomer using map indices. For example, [H:1]N[C@@H](C)C(=O)[OH:2] defining alanine with two connection points to from a peptide bonds with adjacent amino acid monomers.

See also

OEPerceivePeptideMonomerConnections function

Validate

bool Validate() const

Calls the OEIsValidMonomerData function to validate the monomer data object.