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jcf.standardize needs to be called repeatedly.
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Michael

Joined: 07 Jul 2011
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Link to postPosted: Mon Nov 12, 2012 9:44 pmPost subject: jcf.standardize needs to be called repeatedly. Reply with quote

Hi,

We are using jcf.standardize to standardize smiles.  I am finding that I need to call it twice times, using the output from one call as the input to the next call in order to make sure that the output smiles are in a standard state.

Our conversion options are:

 

sep=~ config:removeexplicitH..[NX3+:1](=[O:2])-[O-;X1:3]>>[N:1](=[O:2])=[O:3]..[SX4+:1](=[O:2])-[O-;X1:3]>>[S:1](=[O:2])=[O:3]..[CX1H0:1]=[NX2H0:2]>>[C-:1]#[N+:2]..[NX1H0:1]#[NX2H0:2]=[N:3]>>[N-:1]=[N+:2]=[N:3]..[P+:1][O-:2]>>[P:1]=[O:2]..[n:1]-[O-:2]>>[n:1]=[O:2]..tautomerize..aromatize~outFormat:smiles:u

 

The below examples have 4 smiles, the input is from a chemical vendor's catalog.

1). Input

2). Output from processing #1

3). Output from processing #2

4). Output from processing #3

In the below examples, you can see how standardizing the first output gives a different output.  


Could you please take a close look at our options, and see if this is a jc_convert issue or if we need to add more options to fix this behavior, or if we just need to run jc_convert multiple times for these cases.

 

 

---------------------

CCCCCCCCCOC(=O)C1=CC2=C(C=C1)N(CC)\C(=C\C=C\C1=[N+](CCCS([O-])(=O)=O)C3=C(C=CC(=C3)C(=O)OCCCCCCCCC)N1CC)N2CCCS([O-])(=O)=O

CCCCCCCCCOC(=O)c1ccc2N(CC)\C(=C\C=C\c3n(CC)c4ccc(cc4[n+]3CCCS([O-])(=O)=O)C(=O)OCCCCCCCCC)N(CCCS([O-])(=O)=O)c2c1

CCCCCCCCCOC(=O)c1ccc2N(CC)\C(=C/C=C/c3n(CC)c4ccc(cc4[n+]3CCCS([O-])(=O)=O)C(=O)OCCCCCCCCC)N(CCCS([O-])(=O)=O)c2c1

CCCCCCCCCOC(=O)c1ccc2N(CC)\C(=C/C=C/c3n(CC)c4ccc(cc4[n+]3CCCS([O-])(=O)=O)C(=O)OCCCCCCCCC)N(CCCS([O-])(=O)=O)c2c1

---------------------

---------------------

[I-].CCN1\C(S\C(=C\NC2=CC=CC=C2)C1=O)=C/C1=[N+](CC)C(=CS1)C1=CC=CC=C1

[I-].CCn1\c(=C\c2scc(-c3ccccc3)[n+]2CC)s\c(=C\Nc2ccccc2)c1=O

[I-].CCn1\c(=C\c2scc(-c3ccccc3)[n+]2CC)s\c(=C/Nc2ccccc2)c1=O

[I-].CCn1\c(=C\c2scc(-c3ccccc3)[n+]2CC)s\c(=C/Nc2ccccc2)c1=O

---------------------

---------------------

CN1C(=S)S\C(=C\C2=C(OCCSC3=CC=C(C)C=C3)C=CC=C2)C1=O

CN1C(=S)S\C(=C\c2ccccc2OCCSc2ccc(C)cc2)C1=O

CN1C(=S)S\C(=C/c2ccccc2OCCSc2ccc(C)cc2)C1=O

CN1C(=S)S\C(=C/c2ccccc2OCCSc2ccc(C)cc2)C1=O

---------------------

---------------------

CN1C(=S)S\C(=C\C2=C(OCCOC3=CC=CC(C)=C3)C=CC(Cl)=C2)C1=O

CN1C(=S)S\C(=C\c2cc(Cl)ccc2OCCOc2cccc(C)c2)C1=O

CN1C(=S)S\C(=C/c2cc(Cl)ccc2OCCOc2cccc(C)c2)C1=O

CN1C(=S)S\C(=C/c2cc(Cl)ccc2OCCOc2cccc(C)c2)C1=O

---------------------

---------------------

CCC1=CC(OCCOC2=C(\C=C3\SC(=S)N(C)C3=O)C=C(Br)C=C2)=CC(C)=C1

CCc1cc(C)cc(OCCOc2ccc(Br)cc2\C=C2\SC(=S)N(C)C2=O)c1

CCc1cc(C)cc(OCCOc2ccc(Br)cc2\C=C2/SC(=S)N(C)C2=O)c1

CCc1cc(C)cc(OCCOc2ccc(Br)cc2\C=C2/SC(=S)N(C)C2=O)c1

---------------------

---------------------

CCOC1=C(\C=C2\C(=O)NC(=S)N(C2=O)C2=CC=C(Cl)C=C2)C2=CC=CC=C2C=C1

CCOc1ccc2ccccc2c1\C=C1/C(=O)NC(=S)N(C1=O)c1ccc(Cl)cc1

CCOc1ccc2ccccc2c1\C=C1\C(=O)NC(=S)N(C1=O)c1ccc(Cl)cc1

CCOc1ccc2ccccc2c1\C=C1\C(=O)NC(=S)N(C1=O)c1ccc(Cl)cc1

---------------------

---------------------

[O-][N+](=O)C1=C(C=CC=C1)C1=CC=C(O1)\C=C1/C(=O)NC(=S)N(C1=O)C1=CC=CC(Br)=C1

Brc1cccc(c1)N1C(=S)NC(=O)\C(=C/c2ccc(o2)-c2ccccc2N(=O)=O)C1=O

Brc1cccc(c1)N1C(=S)NC(=O)C(=Cc2ccc(o2)-c2ccccc2N(=O)=O)C1=O

Brc1cccc(c1)N1C(=S)NC(=O)C(=Cc2ccc(o2)-c2ccccc2N(=O)=O)C1=O

---------------------

---------------------

[O-][N+](=O)C1=CC=C(O1)\C=C1\C(=O)NC(=O)N(C1=O)C1=CC=C(Cl)C=C1

Clc1ccc(cc1)N1C(=O)NC(=O)\C(=C\c2ccc(o2)N(=O)=O)C1=O

Clc1ccc(cc1)N1C(=O)NC(=O)C(=Cc2ccc(o2)N(=O)=O)C1=O

Clc1ccc(cc1)N1C(=O)NC(=O)C(=Cc2ccc(o2)N(=O)=O)C1=O

---------------------

---------------------

[O-][N+](=O)C1=CC=C(C=C1)C1=CC=C(O1)\C=C1\C(=O)NC(=S)N(C1=O)C1=CC=C(Br)C=C1

Brc1ccc(cc1)N1C(=S)NC(=O)\C(=C\c2ccc(o2)-c2ccc(cc2)N(=O)=O)C1=O

Brc1ccc(cc1)N1C(=S)NC(=O)C(=Cc2ccc(o2)-c2ccc(cc2)N(=O)=O)C1=O

Brc1ccc(cc1)N1C(=S)NC(=O)C(=Cc2ccc(o2)-c2ccc(cc2)N(=O)=O)C1=O

---------------------

---------------------

[O-][N+](=O)C1=CC=CC(=C1)C1=CC=C(O1)\C=C1\C(=O)NC(=S)N(C1=O)C1=CC=CC(Br)=C1

Brc1cccc(c1)N1C(=S)NC(=O)\C(=C\c2ccc(o2)-c2cccc(c2)N(=O)=O)C1=O

Brc1cccc(c1)N1C(=S)NC(=O)C(=Cc2ccc(o2)-c2cccc(c2)N(=O)=O)C1=O

Brc1cccc(c1)N1C(=S)NC(=O)C(=Cc2ccc(o2)-c2cccc(c2)N(=O)=O)C1=O

---------------------

---------------------

O=C1N(C2CCCC2)\C(S\C1=C\C1=CN(CC2=CC=CC=C2C#N)C2=C1C=CC=C2)=N/C1=CC=CC=C1

O=C1N(C2CCCC2)\C(S\C1=C\c1cn(Cc2ccccc2C#N)c2ccccc12)=N/c1ccccc1

O=C1N(C2CCCC2)\C(S\C1=C/c1cn(Cc2ccccc2C#N)c2ccccc12)=N/c1ccccc1

O=C1N(C2CCCC2)\C(S\C1=C\c1cn(Cc2ccccc2C#N)c2ccccc12)=N/c1ccccc1

---------------------

---------------------

CC1=C(\C=C2\S\C(=N\C3=CC=CC=C3)N(C3CCCC3)C2=O)C2=C(C=CC=C2)N1CC1=CC=CC=C1C#N

Cc1c(\C=C2/S\C(=N\c3ccccc3)N(C3CCCC3)C2=O)c2ccccc2n1Cc1ccccc1C#N

Cc1c(\C=C2\S\C(=N\c3ccccc3)N(C3CCCC3)C2=O)c2ccccc2n1Cc1ccccc1C#N

Cc1c(\C=C2/S\C(=N\c3ccccc3)N(C3CCCC3)C2=O)c2ccccc2n1Cc1ccccc1C#N

---------------------

---------------------

CCOC(=O)C1=C(C)N=C2S\C(=C/C3=CC(Cl)=C(OCC4=C5C=CC=CC5=CC=C4)C(OC)=C3)C(=O)N2C1C1=CC=CC=C1

CCOC(=O)C1=C(C)N=c2s\c(=C\c3cc(Cl)c(OCc4cccc5ccccc45)c(OC)c3)c(=O)n2C1c1ccccc1

CCOC(=O)C1=C(C)N=c2s\c(=C/c3cc(Cl)c(OCc4cccc5ccccc45)c(OC)c3)c(=O)n2C1c1ccccc1

CCOC(=O)C1=C(C)N=c2s\c(=C/c3cc(Cl)c(OCc4cccc5ccccc45)c(OC)c3)c(=O)n2C1c1ccccc1

---------------------

---------------------

CC1=C(C(N2C(=O)\C(SC2=N1)=C\C1=CN(CC2=C3C=CC=CC3=CC=C2)C2=C1C=CC=C2)C1=CC=CC=C1)C(=O)NC1=CC=CC=C1

CC1=C(C(c2ccccc2)n2c(=N1)s\c(=C/c1cn(Cc3cccc4ccccc34)c3ccccc13)c2=O)C(=O)Nc1ccccc1

CC1=C(C(c2ccccc2)n2c(=N1)s\c(=C\c1cn(Cc3cccc4ccccc34)c3ccccc13)c2=O)C(=O)Nc1ccccc1

CC1=C(C(c2ccccc2)n2c(=N1)s\c(=C/c1cn(Cc3cccc4ccccc34)c3ccccc13)c2=O)C(=O)Nc1ccccc1

---------------------



Last edited by Michael on Tue Nov 13, 2012 6:14 pm; edited 1 time in total
peter
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Link to postPosted: Tue Nov 13, 2012 12:56 amPost subject: Reply with quote

Hi,

We are using jc_convert to standardize smiles.

You meant jc_standardize, correct?

Peter

Michael

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Link to postPosted: Tue Nov 13, 2012 6:15 pmPost subject: Original post corrected. Reply with quote

pkovacs wrote:

Hi,

We are using jc_convert to standardize smiles.

You meant jc_standardize, correct?

Peter

YES! My Apologies.  I have corrected my post.

peter
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Link to postPosted: Wed Nov 14, 2012 9:52 amPost subject: Reply with quote

Thank you! We're looking into this.

Szilard
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Link to postPosted: Wed Nov 14, 2012 6:09 pmPost subject: Reply with quote

Mike,

We could reproduce the problem, the bug appeared in 5.11.2 (up to 5.11.1 it works fine).

It is realated to some core stereo handling methods, which are invoked at some point by the tautomerization task.

My colleagues will let you know soon when a fix is expected to be available.

Best regards,

Szilard

 

 

Zsolt
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Link to postPosted: Wed Nov 21, 2012 4:06 pmPost subject: Reply with quote

This bug will be fixed in JChem 5.12.

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