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CDK-R / cdkr

Integrating R and the CDK
https://cdk-r.github.io/cdkr/
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Include hydrogens in plots #9

Closed trljcl closed 7 years ago

trljcl commented 11 years ago

Hydrogens are not included in plots (using view.image.2d or view.molecule.2d) functions. This is confusing when plotting structures containing, for example, hydroxyl groups. I suspect this is caused by the following default assigment in these functions of:

molecule = AtomContainerManipulator.removeHydrogens(molecule)

This assignment should be updated to include the following options:

1) No hydrogens (default; current behaviour) 2) All atoms (i.e. including all hydrogens; less useful but probably easy to implement) 3) All hydrogens not attached to a carbon (most useful option)

rajarshi commented 7 years ago

Should be fixed in current version