extended smarts - bond types - ChemAxon Forum Archive

User d2950aa5e4

09-03-2006 17:56:56

I wonder if there is a way how to define in ChemAxon Extended Smarts bond type "aromatic" equal to bond type "4" used in (extended) molfiles.

ChemAxon a3d59b832c

10-03-2006 21:28:31

Dear Jiri,

As far as I know, the smarts aromatic bond type (':') does correspond to mol bond type 4. For example:

Code:

$ molconvert mol -s '[#6]:[#6]{cxsmarts}'

Marvin 03100622222D

2 1 0 0 0 0 999 V2000

0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

0.8250 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

1 2 4 0 0 0 0

M END

Could you explain the problem in more detail?

Best regards,

Szabolcs

User d2950aa5e4

20-03-2006 16:29:18

I would like to use extended smarts for construction of systems with

R-groups with the aim to convert them later into extended molfiles.

As a simple example let's consider bicycle that in extended molfile looks

like the following:

Code:

Marvin 03200617072D

0 0 0 0 0 999 V3000

M V30 BEGIN CTAB

M V30 COUNTS 8 9 0 0 0

M V30 BEGIN ATOM

M V30 1 C -0 0.77 0 0

M V30 2 R# -1.4646 1.2459 0 0 RGROUPS=(1 1)

M V30 3 C -2.3698 -0 0 0

M V30 4 C -1.4646 -1.2459 0 0

M V30 5 C 0 -0.77 0 0

M V30 6 R# 1.4646 -1.2459 0 0 RGROUPS=(1 2)

M V30 7 C 2.3698 0 0 0

M V30 8 C 1.4646 1.2459 0 0

M V30 END ATOM

M V30 BEGIN BOND

M V30 1 4 1 2

M V30 2 4 2 3

M V30 3 4 3 4

M V30 4 4 4 5

M V30 5 4 1 5

M V30 6 4 5 6

M V30 7 4 6 7

M V30 8 4 7 8

M V30 9 4 1 8

M V30 END BOND

M V30 END CTAB

M END

When I try to write the structure in extended smarts:

C12:[$([#1,*])]:C:C:C:1:[$([#1,*])]:C:C:2 |$;_R1;;;;_R2;;;$|

and convert it into extended molfile, I receive the following:

Code:

Marvin 03200617082D

0 0 0 0 0 999 V3000

M V30 BEGIN CTAB

M V30 COUNTS 8 9 0 0 0

M V30 BEGIN ATOM

M V30 1 C -0 0.77 0 0

M V30 2 R# -1.4646 1.2459 0 0 RGROUPS=(1 1)

M V30 3 C -2.3698 -0 0 0

M V30 4 C -1.4646 -1.2459 0 0

M V30 5 C 0 -0.77 0 0

M V30 6 R# 1.4646 -1.2459 0 0 RGROUPS=(1 2)

M V30 7 C 2.3698 0 0 0

M V30 8 C 1.4646 1.2459 0 0

M V30 END ATOM

M V30 BEGIN BOND

M V30 1 4 1 2

M V30 2 4 2 3

M V30 3 4 3 4

M V30 4 4 4 5

M V30 5 6 1 5

M V30 6 4 5 6

M V30 7 4 6 7

M V30 8 4 7 8

M V30 9 4 1 8

M V30 END BOND

M V30 END CTAB

M END

where the 1-5 bond is of type "6", single or aromatic, but I would like to have it of type "4" aromatic, as the other ones.

ChemAxon 25dcd765a3

21-03-2006 19:58:33

Hi!

It was a bug in the import. I fixed it right now.

Thank you for the report.

Andras

User d2950aa5e4

21-03-2006 20:12:39

Thanks for explanation. Will the fixed version be available soon ?

User d2950aa5e4

21-03-2006 20:37:16

Further to my previous question I should better specify that I currently work with version 4.1.0alpha4.

User d2950aa5e4

24-03-2006 10:29:04

Seems I found another shape of the problem. Now trying to write down bicyclic structure consisting from saturated and aromatic ring:

Code:

[C,N]12[$([*])][$([*])][$([*])][C,N]:1:[$([*])]:[$([*])]:[$([*])]:C:2[$([*])] |$;_R1;_R2;_R2;;_R3;_R3;_R3;;_R4;$|

Converted to extended molfiles I get the following:

Code:

Marvin 03240611222D

0 0 0 0 0 999 V3000

M V30 BEGIN CTAB

M V30 COUNTS 10 11 0 0 0

M V30 BEGIN ATOM

M V30 1 [C,N] -0.4037 0.462 0 0

M V30 2 R# -1.8683 0.9379 0 0 RGROUPS=(1 1)

M V30 3 R# -2.7735 -0.308 0 0 RGROUPS=(1 2)

M V30 4 R# -1.8683 -1.5539 0 0 RGROUPS=(1 2)

M V30 5 [C,N] -0.4037 -1.078 0 0

M V30 6 R# 0.93 -1.848 0 0 RGROUPS=(1 3)

M V30 7 R# 2.2637 -1.078 0 0 RGROUPS=(1 3)

M V30 8 R# 2.2637 0.462 0 0 RGROUPS=(1 3)

M V30 9 C 0.93 1.232 0 0

M V30 10 R# 0.93 2.772 0 0 RGROUPS=(1 4)

M V30 END ATOM

M V30 BEGIN BOND

M V30 1 1 1 2

M V30 2 6 2 3

M V30 3 6 3 4

M V30 4 1 4 5

M V30 5 4 1 5

M V30 6 4 5 6

M V30 7 4 6 7

M V30 8 4 7 8

M V30 9 4 8 9

M V30 10 4 1 9

M V30 11 1 9 10

M V30 END BOND

M V30 END CTAB

M END

but I need the bonds 2-3 and 3-4, respectively, to be single and not "6".

Currently working with 4.1.0alpha13. Thanks for a hint.

ChemAxon a3d59b832c

25-03-2006 14:42:35

Dear Jiri,

If you would like to get single bonds there, then I think the input cxsmarts is wrong in your case. This input works correctly:

Code:

[C,N]12[$([*])]-[$([*])]-[$([*])][C,N]:1:[$([*])]:[$([*])]:[$([*])]:C:2[$([*])] |$;_R1;_R2;_R2;;_R3;_R3;_R3;;_R4;$|

Best regards,

Szabolcs

User d2950aa5e4

25-03-2006 16:44:34

Thanks, it explains a lot, I did not know it, expecting that no sign between centers implicitly means single bond. Is there any document detailed enough that covers such features ? I would be also indebted for an answer to my previous question regarding availability of the bug-free marvin version (cf. my post Tue Mar 21). Currently working with the 4.1.0alpha13.

ChemAxon a3d59b832c

25-03-2006 17:26:08

Dear Jiri,

Alpha13 is the latest alpha release, hopefully we will be able to issue a new alpha release next week.

Implicit bond type in SMARTS is generally "single or aromatic", but it can be guessed more specific in some specific cases. Below is the corresponding section of our SMARTS documentation.

http://www.chemaxon.com/marvin/doc/user/smiles-doc.html#SMARTS

"Implicit bond types: The default bond types for import and export strongly depend on the atoms connected by the bond.

Aromatic bonds are not written explicitly if neither atoms are aliphatic and they are in a ring.

Eg: c1ccccc1 But: c:c, c:[c;a], [#6]:c
Single bonds are not written explicitly if at least one atom is not aromatic.

Eg: CC, C[c;a], Cc, C[C;A], [#6]C But: [#6]-[c;a], c1ccc(cc1)-c2ccccc2
Single_or_aromatic bonds are not written explicitly if both atoms of the bond are aromatic and any of them is not in the same ring.

Eg: [#6]cc, [#6][c;a], [#6][#6]"

Best regards,

Szabolcs

User d2950aa5e4

25-03-2006 17:40:31

Thanks, I see that for my purposes it is more didactic to write explicit bond types to avoid mistakes. Your next release of alpha version will cover the aromatic bond input bug discussed earlier this week (to wait for it or make the changes in few dozens thus generated extended molfiles manually) ? And the last question, is cxsmarts capable to somehow depict link nodes (I guess it is not since I did not find a hint in documentation you kindly pointed to but I do better ask).

ChemAxon a3d59b832c

25-03-2006 20:44:25

jirikrechl wrote:

Your next release of alpha version will cover the aromatic bond input bug discussed earlier this week (to wait for it or make the changes in few dozens thus generated extended molfiles manually) ?

I have to check that with Volfi, but I guess so.

jirikrechl wrote:

And the last question, is cxsmarts capable to somehow depict link nodes (I guess it is not since I did not find a hint in documentation you kindly pointed to but I do better ask).

You are right, link nodes cannot be represented by cxsmiles, only in mol and mrv formats.

Szabolcs

ChemAxon 25dcd765a3

26-03-2006 14:21:21

Quote:

Your next release of alpha version will cover the aromatic bond input bug discussed earlier this week

Yes. I have fixed it. The next release will contain the fix.

User d2950aa5e4

10-04-2006 09:43:54

volfi wrote:

Quote:

Your next release of alpha version will cover the aromatic bond input bug discussed earlier this week

Yes. I have fixed it. The next release will contain the fix.

Could you please give a rought estimate when the next release with the bug fix will be made public ? THX

ChemAxon 7c2d26e5cf

11-04-2006 13:20:14

I can not tell you an exact date for new major Marvin release. I hope we can release it soon. This week we will build a pre-release where the required bugfix will be already available.

ChemAxon a3d59b832c

21-04-2006 07:29:45

Dear Jiri,

The new alpha (Marvin 4.1.0alpha14) is now available:

http://www.chemaxon.com/shared/alpha/

Best regards,

Szabolcs