[URGENT] Handling explicit H atoms in Superstructure search

Hello everyone,

I have another question regarding the superstructure search while considering explicit H atoms.

the mini_smarts_base.sdf is a file containing the following pattern P1='[H]C([H])(OC=O)C([H])(OC=O)C([H])([H])OC1OC(C)C(O)C(O)C1O', with explicit atoms. It also contains structural paterns that do not contain expliciti H atoms.

If I am looking for substructures (in mini_smarts_base) for 2 query compounds:

q1='[H]C([H])(OC1OC(C)C(O)C(O)C1O)C([H])(OC=O)C([H])([H])OC(=O)CCCC' and,

q2='[H]C([H])(OC1OC(C)C(O)C(O)C1O)C([H])(OC(=O)CCC)C(C)(CCC)OC(=O)CCCC'

How do I set the search options so that Jcsearch, while browsing the table (mini_smarts_base), so that the explicit H atoms are considered. This means,  the superstructure search of  q1 BUT NOT q2 should return P1.

Adding  the option  --implicitHMatching:n does not improve/change the results.

Attached is the mini_base that I imported in a table of type  "Query Structures"

Thank you.

Mr Yan

  Hello Mr Yan,

Before we can respond your post, please fill in the Company field in your Profile

and use an institutional mail address. These data will not be displayed at the forum.

Thank you,
Krisztina

Thanks Krisztina,

My profile has been updated. How to change my e-mail address? I addeda second address, but how to I make that one the primary address?

Hoepfully, I can get answers to my previous questions.

Thank you,

Mr Yan

Hello Mr Yan,

Thank you for flling out the Profile sheet.

We suppose your question relates to the environment described in the other topic:

https://www.chemaxon.com/forum/ftopic10079.html

that is JChem 5.11.x, Query table with default standardization.

We found that if only molecule P1 is imported in a Query-type table having default standardization, then the superstrcuture search gives the expected results (q1 results HIT, q2 results NO HIT) without using any special search option.

We used the latest version of JChem:  5.11.5.

jcsearch -q '[H]C([H])(OC1OC(C)C(O)C(O)C1O)C([H])(OC=O)C([H])([H])OC(=O)CCCC' DB:P1querytable -t:u
[H]C([H])(OC=O)C([H])(OC=O)C([H])([H])OC1OC(C)C(O)C(O)C1O

jcsearch -q '[H]C([H])(OC1OC(C)C(O)C(O)C1O)C([H])(OC(=O)CCC)C(C)(CCC)OC(=O)CCCC' DB:P1querytable -t:u

Unfortunately if the whole mini_smarts_base.sdf was imported in the table, then the superstructure search with jcsearch resulted the same errors as you described in the other topic. We start to investigate, find, and correct the cause of this erroneous behavior.

Best reagrds,

Krisztina

Helllo Mr Yan,

Investigating the moleucles in the attached mini_smarts_base.sdf we found that the 9th compound causes the error messages, especially the chn property of the bonds.

We suggest the following workaround until the bugfix will be done.

Remove chn property from the bonds and add R0 property to the atoms concerned. (R0 means: the atom is not part of any ring.)

You can find documentation about query atom properties here:

https://www.chemaxon.com/jchem/doc/user/query_features.html#atprop

https://www.chemaxon.com/marvin/help/sketch/sketch-chem.html#atom-props

See attached the modified 9th molecule.

Best regards,

Krisztina

This is going to be a big problem,

 

because I have many more structures with those topological features in my whole database (mini_smarts was just a tiny subset.)

Please let me know when you manage to fix the problem,

Thank you.

MrYan

Hi MrYan,

Sorry, but we couldn't reproduce the problems you found. We experienced that superstructure search works as expected in case of targets with and without explicit H atoms in Query tables created with JChem 5.11.5 and default standardization.

Default standardization means only aromatization in case of Query tables, but in case of other table types the removal of explicit hydrogens (conversion of explicit hydrogens to implicit hydrogens) is part of default standardization too. Are you sure you are using Query tables?

Because of the problem with handling of bond query features, I suggest to test superstructure search in tables without structures with bond query features.

See this examples again:

jcman c q_p1_only --t:query  //create table

jcman a q_p1_only p1.mrv   //import

jcsearch -q "[H]C([H])(OC1OC(C)C(O)C(O)C1O)C([H])(OC=O)C([H])([H])OC(=O)CCCC" DB:q_p1_only -t:u
[H]C([H])(OC1OC(C)C(O)C(O)C1O)C([H])(OC=O)C([H])([H])OC(=O)CCCC

jcsearch -q " [H]C([H])(OC1OC(C)C(O)C(O)C1O)C([H])(OC(=O)CCC)C(C)(CCC)OC(=O)CCCC " DB:q_p1_only -t:u

Best regards,

Krisztina