openchemlib-extended

openchemlib-extended

Openchemlib extended

DB

RXN

Create an instance of the RXN object based on a text file in RXN format. This will also calculate for each reagent and product:

• SMILES
• Molecular formula
• Molecular weight
• idCode

var rxn = new RXN(rxnFile)

methods on rxn:

• addReagent(molfile)
• addProduct(molfile)
• toRXN() : create a new RXN file

Molecule extension

getGroupedDiastereotopicAtomIDs(options)

Returns an array containing all the different diastereotopic atoms in the molecule with the occurence of each of them. It may be useful to first create the implicit hydrogens before using the method ``Molecule.addImplicitHydrogens()```.

options:

• atomLabel: filter to show only a specific atom (default: '')

getAtomsInfo(options)

Returns an array containing many informations about the atoms. It may be useful to first create the implicit hydrogens before using the method ``Molecule.addImplicitHydrogens()```.

toDiastereotopicSVG(options)

Return a SVG containing a circle at the level of each atom having a data-atomid a diastereoisotopic unique identifier.

options:

• height (default: 300)
• width (default: 200)
• prefix : prefix for the id of each SVG element (default: ocl)

getDiastereotopicHoseCodes(options)

Returns an array containing diastereotopic hoses codes

options:

• maxSphereSize: maxSphere for hose code calculation

getGroupedHOSECodes(options)

Returns an extended groupedDiastereotopicID with hoses

options:

• atomLabel: filter to show only a specific atom (default: '')
• maxSphereSize: maxSphere for hose code calculation

toVisualizerMolfile()

getNumberOfAtoms()

getExtendedDiastereotopicAtomIDs()

Return an array of explicit hydrogens added molecule of diastereotopicAtomIDs. Extra information like the diastereotopicIDs of the molecule are added

getConnectivityMatrix()

Returns an array of array (matrix) containing a '1' for all the connected atoms. An atom is considered connected to itself (dialog is equal to 1)

License

BSD-3-Clause