Calculate MolWeight and generate SMILES
/*
* Calculate Molweight and Smiles
*
*
* Usage:
* 1. Edit the name of the Structure field
* 2. Run button script
*
* For more details see:
* https://docs.chemaxon.com/display/jchembase/Utilities
*
* @author David Pech <[email protected]>
*/
import
com.im.df.api.*
import
com.im.df.api.support.SelectionDescription
import
com.im.ijc.core.api.util.IJCCoreUtils
import
chemaxon.struc.Molecule
import
chemaxon.util.MolHandler
init = { widget ->
}
destroy = { widget ->
}
evaluate = { widget ->
def
ety = dataTree.rootVertex.entity
// assumes you have reference to the data tree
def
molFld = ety.fields.items.
find
{ it.name ==
'Structure'
}
// find the structure field
def
rs = ety.schema.dataProvider.getDefaultResultSet(dataTree, false, DFEnvironmentRO.DEV_NULL)
// find the ResultSet
def
rootVS = rs.getVertexState(dataTree.rootVertex)
// obtain the VertexState
List ids = rootVS.getSelectedRowsIds()
// get the selected IDs
if
(ids.
size
==
1
) {
Map rows = rootVS.getData(ids, DFEnvironmentRO.DEV_NULL)
// get the data
Map row = rows[ids[
0
]]
// get the first and only row
MarvinStructure mol = row[molFld.id]
// Get the Structure. Its a com.im.df.api.chem.MarvinStructure instance
Molecule cxnMol = mol.getNative()
// obtain the chemaxon.struc.Molecule instance
// Convert molecule to SMILES
String molSmiles = cxnMol.toFormat(
"smiles"
)
// Canonical SMILES
// String molSmiles = cxnMol.toFormat("smiles:u")
println
molSmiles
// create a MolHandler instance
// set molecule from SMILES
// calculate molecular weight
MolHandler mh =
new
MolHandler();
mh.setMolecule(molSmiles);
println
mh.calcMolWeight()
}
else
{
println
"bad selection"
}
}
on_change = { widget, button ->
}