Feature Requests item #3173850, was opened at 2011-02-05 19:00
Message generated for change (Comment added) made by hansonr
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Category: None
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Simon Westrip (publcif)
Assigned to: Nobody/Anonymous (nobody)
Summary: SMILES for all connected moieties in model
Initial Comment:
I'm currently using e.g. var smiles={1.1}.find("SMILES") to obtain the smiles
for a model, but this returns smiles for the first connected moiety only.
So I then use the returned smiles to obtain an atom list using e.g. var
x={1.1}.find("SMARTS", smiles).
Then I 'remove' these atoms from the model using e.g. for (var
i=0;i<x.length;i++) assign atom @{x[i]} "X";
Then repeat the process until .find("SMILES") returns a single atom.
In most cases my script works fine, but there are a few 'gotchas' to overcome,
e.g. 'assign atom {} "X"', being part of the model kit, creates a 'logical'
atom in place of the last 'X' assignment so the model is altered and the next
.find("SMILES") call could return the added atom.
Is it possible for .find("SMILES") to return the smiles string for all distinct
molecules in the model? Or can anyone point me in the right direction with
regards to scripting a solution?
Cheers
Simon Westrip
PS I've been using the prerelease versions of 12.1.x, working with core CIFs.
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>Comment By: Bob Hanson (hansonr)
Date: 2011-02-05 20:05
Message:
Must be a better way than that. You can run through all the molecules
easily, selecting one at a time. This is not a place for answering usage
questions; please use the Jmol users list.
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