#1249 Overlapped atoms from branched compounds
I had a problem with the 2D depiction of a large set of molecules using LICCS which uses jchempaint v 3.2 as teh base depictor. i ahev since reproduced the same problem directly with jchempaint which indicates the problem is not with the use of jchempaint by LICCS but a base problem with jchempaint. To exemplify the problem, I found a couple publicly available compounds that are not behaving properly. Here is my original post to the LICCS support group which again highlights the exact problem I am finding.
The depictions coming up from my smiles strings seem to have a large amount of overlapping in the structure images. I searched online for some public examples that fail in a similar fashion and I found a few. Here are two.
Example 1: CC1(C)(CC(=O)C(C(=O)C1)C(c2ccc(o2)N+[O-])C=3C(=O)CC(C)(C)CC=3(O)) (BAS 03161502 from Asinex collection)
See this link for example of non-overlaped structure on pubchem. http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=3145896
Example 2: O=C2C1=CC=CC=C1C@H=C(O)\C(NC3=CC(C(C)=O)=CC=C3)=O)O2 (NSC 640982)
See this link for example of non-overlaped structure on pubchem. http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=369251&loc=ec_rcs
The attached file is a jpg with the two depictions from LICCS (using jchempaint 3.2: reproduced when using jchempaint standalone) in them (left is example 2, right is example 1).
Thanks ,
Dale
depictions
see also https://github.com/JChemPaint/jchempaint/issues/167
Hi Egan,
I installed the latest jchempaint jar (3.3-1210), desktop app, just now, and the two exemplified smiles still fail for me.
SMILES for BAS 03161502 from the Pubchem (CC1(CC(=O)C(C(=O)C1)C(C2=CC=C(O2)N+[O-])C3=C(CC(CC3=O)(C)C)O)C)overlaps the two carbonyl oxygens. See attached jpg from Jchempaint.
SMILES for NSC640982 from the Pubchen (CC(=O)C1=CC(=CC=C1)NC(=O)C(=O)C(C2C3=CC=CC=C3C(=O)O2)C(=O)C4=CC=CC=C4F) overlap the fluorine attached to the phenyl with the bicycle.
See the attached jpg files I generated just now showing what I am seeing.
Dale
From: Egon Willighagen [mailto:egonw@users.sf.net]
Sent: Thursday, August 11, 2016 3:34 AM
To: [cdk:bugs] 1249@bugs.cdk.p.re.sf.net
Subject: [cdk:bugs] #1249 Overlapped atoms from branched compounds
Dear Dale,
the SMILESes in the report don't work for me (not valid), but I looked them up from the PubChem records you linked to. Using the new code stack, they seem to work fine:
https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=CC(=O)C1=CC(=CC=C1)NC(=O)C(=O)C(C2C3=CC=CC=C3C(=O)O2)C(=O)C4=CC=CC=C4F&abbr=on&suppressh=true&showtitle=false&zoom=1.3&annotate=none
https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=CC1(CC(=O)C(C(=O)C1)C(C2=CC=C(O2)N%2Bhttps://sourceforge.net/../=O[O-])C3=C(CC(CC3=O)(C)C)O)C&abbr=on&suppressh=true&showtitle=false&zoom=1.3&annotate=none
[bugs:#1249]https://sourceforge.net/p/cdk/bugs/1249/ Overlapped atoms from branched compounds
Status: closed
Group: cdk-1.6.x
Labels: jchempaint
Created: Thu Aug 16, 2012 04:12 PM UTC by Dale Cameron
Last Updated: Fri Feb 06, 2015 01:48 AM UTC
Owner: nobody
I had a problem with the 2D depiction of a large set of molecules using LICCS which uses jchempaint v 3.2 as teh base depictor. i ahev since reproduced the same problem directly with jchempaint which indicates the problem is not with the use of jchempaint by LICCS but a base problem with jchempaint. To exemplify the problem, I found a couple publicly available compounds that are not behaving properly. Here is my original post to the LICCS support group which again highlights the exact problem I am finding.
The depictions coming up from my smiles strings seem to have a large amount of overlapping in the structure images. I searched online for some public examples that fail in a similar fashion and I found a few. Here are two.
Example 1: CC1(C)(CC(=O)C(C(=O)C1)C(c2ccc(o2)N+https://sourceforge.net/../=O[O-])C=3C(=O)CC(C)(C)CC=3(O)) (BAS 03161502 from Asinex collection)
See this link for example of non-overlaped structure on pubchem. http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=3145896
Example 2: O=C2C1=CC=CC=C1C@Hhttps://sourceforge.net/%5bC@%5d(C(C4=CC=CC=C4F)=O=C(O)\C(NC3=CC(C(C)=O)=CC=C3)=O)O2 (NSC 640982)
See this link for example of non-overlaped structure on pubchem. http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=369251&loc=ec_rcs
The attached file is a jpg with the two depictions from LICCS (using jchempaint 3.2: reproduced when using jchempaint standalone) in them (left is example 2, right is example 1).
Thanks ,
Dale
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#1249Hi Dale,
JChemPaint is no longer in active development, Egon was refering to the CDK code base, here's what they look like in CDK Depict.
Aah, I realize now that this was to cdk bugs.
I guess it's back in the cdk-Excel folks lap then since they still use jchempaint. Agree the base code seems to have fixed the problem with these two.
Thanks,
Dale
From: John May [mailto:jwmay@users.sf.net]
Sent: Monday, August 15, 2016 1:44 PM
To: [cdk:bugs] 1249@bugs.cdk.p.re.sf.net
Subject: [cdk:bugs] Re: #1249 Overlapped atoms from branched compounds
Hi Dale,
JChemPaint is no longer in active development, Egon was refering to the CDK code base, here's what they look like in CDK Depicthttps://cdkdepict-openchem.rhcloud.com/depict.html.
[bugs:#1249]https://sourceforge.net/p/cdk/bugs/1249/ Overlapped atoms from branched compounds
Status: closed
Group: cdk-1.6.x
Labels: jchempaint
Created: Thu Aug 16, 2012 04:12 PM UTC by Dale Cameron
Last Updated: Thu Aug 11, 2016 10:33 AM UTC
Owner: nobody
I had a problem with the 2D depiction of a large set of molecules using LICCS which uses jchempaint v 3.2 as teh base depictor. i ahev since reproduced the same problem directly with jchempaint which indicates the problem is not with the use of jchempaint by LICCS but a base problem with jchempaint. To exemplify the problem, I found a couple publicly available compounds that are not behaving properly. Here is my original post to the LICCS support group which again highlights the exact problem I am finding.
The depictions coming up from my smiles strings seem to have a large amount of overlapping in the structure images. I searched online for some public examples that fail in a similar fashion and I found a few. Here are two.
Example 1: CC1(C)(CC(=O)C(C(=O)C1)C(c2ccc(o2)N+https://sourceforge.net/../=O[O-])C=3C(=O)CC(C)(C)CC=3(O)) (BAS 03161502 from Asinex collection)
See this link for example of non-overlaped structure on pubchem. http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=3145896
Example 2: O=C2C1=CC=CC=C1C@Hhttps://sourceforge.net/%5bC@%5d(C(C4=CC=CC=C4F)=O=C(O)\C(NC3=CC(C(C)=O)=CC=C3)=O)O2 (NSC 640982)
See this link for example of non-overlaped structure on pubchem. http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=369251&loc=ec_rcs
The attached file is a jpg with the two depictions from LICCS (using jchempaint 3.2: reproduced when using jchempaint standalone) in them (left is example 2, right is example 1).
Thanks ,
Dale
Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/cdk/bugs/1249/
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Bugs:
#1249Dear Dale,
the SMILESes in the report don't work for me (not valid), but I looked them up from the PubChem records you linked to. Using the new code stack, they seem to work fine:
https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=CC(=O)C1=CC(=CC=C1)NC(=O)C(=O)C(C2C3=CC=CC=C3C(=O)O2)C(=O)C4=CC=CC=C4F&abbr=on&suppressh=true&showtitle=false&zoom=1.3&annotate=none
https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=CC1(CC(=O)C(C(=O)C1)C(C2=CC=C(O2)N%2B[O-])C3=C(CC(CC3=O)(C)C)O)C&abbr=on&suppressh=true&showtitle=false&zoom=1.3&annotate=none