Finding doublets & finding salts

Probably straightforward, but right now I can't see the forest from all the trees.

How do I find doublets/multiplets in IJchem ? And will that include (different) salt forms of same neutral compound?

Also, how can one find a salt (with a simple extra calculation column)? E.g. in a text file I would probably search the smiles for "." (dot).

Hi,

to address your last issue, you could add a smiles column as a Chemical Term, and then query on this for the dot.

Good luck,

Evert

Hello,

all the possible options for search are described here in the documentation. Plus I am forwarding the issue to JChem team.

Best 

David

Hi Alexander,

 

There are a few possibilities to do so.

One is to strip the salts with standardizer

https://docs.chemaxon.com/display/standardizer/Strip+Salts

https://www.chemaxon.com/jchem/doc/dev/java/api/chemaxon/standardizer/advancedactions/StripSaltsAction.html 

and compare the stripped molecules.

 

The other way is to search with the ionic molecule (no counterion added) against salts with the following options:

t:ff

stereoSearchType:e

charge:e

isotope:e

radical:e

exactQueryAtomMatching:y

exactBondMatching:y

transformMonomer:n

 

I hope it helps,

Norbert

Thanks for the replies.

It helps and it doesn't help. For example searching for salt is for me faster to export to excel or knime and search for the dot in the string, flag and re-import. I guess I need more time to get into the details, but when learning multiple software suites at once... might be just an excuse of course. Sorry for blabbering.

For finding of duplicates by any field (i.e. for Smiles, if you need find same structures) you can use the script:

import java.awt.Dimension

import java.awt.BorderLayout

import javax.swing.*

import javax.swing.border.*

import org.openide.*

import com.im.ijc.core.api.lists.TemporaryListsAndQueries

import com.im.df.util.ui.DFObjectListCellRenderer



def ety = dataTree.rootVertex.entity

def edp = ety.schema.dataProvider.getEntityDataProvider(ety)

def field = selectFromList(ety.fields.items)

if (field == null) {

    return

}



sort = SortDirective.create(field, true)

ids = edp.queryForIds(DFTermExpression.ALL_DATA, sort, env)



List duplicates = []

List buffer = []

lastValue = null

ids.each { rowId ->

   value = edp.getData([ rowId ], env).get(rowId).get(field.id)

   if (lastValue != value) {

       if (buffer.size() > 1) {

           duplicates.addAll(buffer)

       }

       buffer.clear()

       lastValue = value

   }

   buffer.add(rowId)

}

println "Found " + duplicates.size() + " duplicates"

if (!duplicates.empty) {

    TemporaryListsAndQueries.getListsFor(ety).addList(duplicates, "Duplicates in " + field.name + " field")

}



Object selectFromList(List values) {

    JList list = new JList(values.toArray())

    list.cellRenderer = new DFObjectListCellRenderer()

    list.selectionModel.selectionMode = ListSelectionModel.SINGLE_SELECTION

    list.visibleRowCount = 15

    panel = new JPanel()

    panel.layout = new BorderLayout()

    panel.add(new JScrollPane(list), BorderLayout.CENTER)

    panel.border = new EmptyBorder(5,5,5,5)

    panel.preferredSize = new Dimension(250, 300)

    DialogDescriptor dd = new DialogDescriptor(panel, "Select field")

    if (DialogDisplayer.getDefault().notify(dd) != DialogDescriptor.OK_OPTION) {

        println "  Cancel pressed => exit"

        return null

    }

    selected = list.selectedValue

    println "  Selected field: $selected"

    if (selected == null) {

        println "  No field selected => exit"

        return null

    }

    return selected

}

all duplicates will be recorded in a temporary list.

Thanks!

Though... how do I use a java script within IJChem...

Thanks to Igorlab for this nice script. It is a Groovy Script that uses Instant JChem's API. We support possibility to script your own functionality and tricks into IJC that you can run on Schema level, Data Tree level, View level and even custom buttons. 

How to use Groovy in Instant JChem is described in the documentation.

 

I hope this helps

David

Actually, I have found this script in some topic, but I'm not author of this script :)

Awesome! Thanks a million!