[Cdk-devel] [ cdk-Patches-3568970 ] single/double bond order and better atom types

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Patches item #3568970, was opened at 2012-09-18 07:57
Message generated for change (Comment added) made by jwmay
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Category: None
Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: John May (jwmay)
Assigned to: Rajarshi Guha (rajarshi)
Summary: single/double bond order and better atom types

Initial Comment:
Hi,

I've been working with the satChecker some part of this week. And
today I think I got i working, at least all the molecules that I have
tested work (including the horribly one that I think Cristopher
mailed, i.e the one that has the SMILES:
c1ccc(C[C@@H](C(N[C@H](Cc2c3ccccc3[nH]c2)C(N[C@@H](CCCN)C(N[C@@H](Cc2ccc(cc2)O)C(N[C@H](C(N[C@@H]
). =)

What i does is this:
First it see if it can find a solution where all atoms are saturated,
if not it settles with the solution with most saturated atoms. If so
it makes an notice in the log (as a warning).

I don't know if you want to look at the code, but I attach the files
so you can if you want to.

/Klas


Egon has reviewed Klas' patch and add new explicit atom types to owl. I have checked these changes and signed off as well as add some additional unit tests for the BondManipulator.

(me) Signed off Egon's commits: https://github.com/johnmay/cdk/tree/421-14x-betterAtomTypes


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Comment By: John May (jwmay)
Date: 2012-09-23 10:15

Message:
Just adding incase it gets missed but someone from Bioclipse pointed out
the cdk.module was wrong.
Looks like it should be valencycheck not valency (unless the module making
handles this).

J

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Comment By: Egon Willighagen (egonw)
Date: 2012-09-23 08:40

Message:
Rajarshi, your independent, second review please.

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