SMILES parsing doesn't set atom types

CDK-R / cdkr

Integrating R and the CDK

https://cdk-r.github.io/cdkr/

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SMILES parsing doesn't set atom types #109

Open rajarshi opened 4 years ago

rajarshi commented 4 years ago

Atom types can be perceived using the following code

acm <- J("org.openscience.cdk.tools.manipulator.AtomContainerManipulator")
acm$percieveAtomTypesAndConfigureAtoms(mol)

This does not happen by default when parsing a SMILES or reading an SDF. Either provide this as a function (e..g, set.atom.types) or else include in the molecule parsing/loading function as a optional parameter.

In both cases, should support the possibility of different atom typing schemes

rajarshi commented 4 years ago

There was a function, do.typing that implemented this. Renamed to set.atom.types and updated the code to use J notation. Currently only supports CDK atom types