Reactiion file format

User e213d45538

29-06-2011 05:20:10

 


Dear All,


I am newbie to reactor for combinatorial library enumeration and facing a strange problem which should not occur.  I
have downloaded reaction file from chemaxon site in available mrv
format. But reactor does not support mrv file as reaction file. Then I
converted this mrv file to rdf file using molconvert, even then results
are not coming out. I have taken acid halide nucleophile acylation.
When I run reactor by using converted rdf file it is not giving result
but when I took supplied example nucleophile acylation rdf file with
Jchem it gave me correct and perfect result. Then I compared both rdf
file ie converted from mrv and example rdf I can see there is some difference, the diff file is attached please see


My question are


1. Is this is due to incorrect rdf file format.


2. Where can I get correct rdf files for all reaction.


Best regards


 


Prashant

ChemAxon d76e6e95eb

29-06-2011 07:34:35

Interesting issue. Reactor does support the mrv format for reactions, our entire reaction library is in mrv format. I tried the reaction you mentioned and did not experience any issues. Which reactor version are you using? Do you use the Reactor wizard or the command line application?

ChemAxon e08c317633

29-06-2011 09:40:14

Hi Prashant,


Could you attach the mrv file which didn't work?


Zsolt

User e213d45538

30-06-2011 05:35:47










Zsolt wrote:

Hi Prashant,


Could you attach the mrv file which didn't work?


Zsolt



Dear Zsolt,


I am using reactor 5.5 command line version. Please find my input file and reaction mrv file in attachment. I have also attached an rdf file which is supplied by Jchem. The reaction goes well with rdf but not with mrv. Please see and let me know where I am doing mistake. I also would like ask you that is there is some other flag rather tha -r for give reaction mrv file.


 


Best regards

User e213d45538

30-06-2011 05:37:50










Gyuri wrote:

Interesting issue. Reactor does support the mrv format for reactions, our entire reaction library is in mrv format. I tried the reaction you mentioned and did not experience any issues. Which reactor version are you using? Do you use the Reactor wizard or the command line application?



Dear Gyuri,


I am using reactor 5.5 command line version. Please find my input
file and reaction mrv file in attachment. I have also attached an rdf
file which is supplied by Jchem. The reaction goes well with rdf but
not with mrv. Please see and let me know where I am doing mistake. I
also would like ask you that is there is some other flag rather tha -r
for give reaction mrv file.



Best regards

ChemAxon d76e6e95eb

30-06-2011 08:21:16

Both reactions work (please see below), but there is one trick with your reactions.You need to feed the input compounds exactly in the order as they appear in the reaction scheme. However, the reactants in your two reactions are swapped (and the products too)! So you have to swap the input files as well to get the products.


How did you convert the mrv to rdf? I tried it with molconvert, but it keeps the original order of the reaction components.


$ react -r nucleophile_acylation_with_acid_halide.mrv nucleophiles_614-download
8519.smiles rosiglitazone_scaffold_732-download8518.smiles -m comb -x 1
CCCCNC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CCN(CC)CCNCCNC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CCN(CC)CCN(CCN)C(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CC1CC1COC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CC(CS)OC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
Cc1ccc(NNC(=O)c2cc(N)cc(CC3SC(=O)NC3=O)c2)cc1C
Nc1cc(CC2SC(=O)NC2=O)cc(c1)C(=O)NOC1CCCCO1
CC(=O)Nc1ccc(Cl)c(NC(=O)c2cc(N)cc(CC3SC(=O)NC3=O)c2)c1
CC(C)(S)C(NC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1)C(O)=O
Nc1cc(CC2SC(=O)NC2=O)cc(c1)C(=O)O[C@@H]1CNC(=O)C1
CC(=O)N1C[C@@H](C[C@H]1C(O)=O)OC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1

$ react -r acid-halide+nucleophile.rdf rosiglitazone_scaffold_732-download8518.
smiles nucleophiles_614-download8519.smiles -m comb -x 2
CCCCNC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CCN(CC)CCN(CCN)C(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CCN(CC)CCNCCNC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CC1CC1COC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CC(CS)OC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CC(O)CSC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
Cc1ccc(NNC(=O)c2cc(N)cc(CC3SC(=O)NC3=O)c2)cc1C
Nc1cc(CC2SC(=O)NC2=O)cc(c1)C(=O)NOC1CCCCO1
CC(=O)Nc1ccc(Cl)c(NC(=O)c2cc(N)cc(CC3SC(=O)NC3=O)c2)c1
CC(C)(SC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1)C(N)C(O)=O
CC(C)(S)C(NC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1)C(O)=O
Nc1cc(CC2SC(=O)NC2=O)cc(c1)C(=O)O[C@@H]1CNC(=O)C1
CC(=O)N1C[C@@H](C[C@H]1C(O)=O)OC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1

User e213d45538

30-06-2011 09:00:52










Gyuri wrote:

Both reactions work (please see below), but there is one trick with your reactions.You need the feed the input cmpounds in the order as they appear in the reaction scheme. However, the order of reactants and products in your reactions is swapped! So you have to swap the order of the input files as well to get the products.


How did you convert the mrv to rdf? I tried it with molconvert, but it keeps the original order of the reaction components.


$ react -r nucleophile_acylation_with_acid_halide.mrv nucleophiles_614-download
8519.smiles rosiglitazone_scaffold_732-download8518.smiles -m comb -x 1
CCCCNC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CCN(CC)CCNCCNC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CCN(CC)CCN(CCN)C(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CC1CC1COC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CC(CS)OC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
Cc1ccc(NNC(=O)c2cc(N)cc(CC3SC(=O)NC3=O)c2)cc1C
Nc1cc(CC2SC(=O)NC2=O)cc(c1)C(=O)NOC1CCCCO1
CC(=O)Nc1ccc(Cl)c(NC(=O)c2cc(N)cc(CC3SC(=O)NC3=O)c2)c1
CC(C)(S)C(NC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1)C(O)=O
Nc1cc(CC2SC(=O)NC2=O)cc(c1)C(=O)O[C@@H]1CNC(=O)C1
CC(=O)N1C[C@@H](C[C@H]1C(O)=O)OC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1

$ react -r acid-halide+nucleophile.rdf rosiglitazone_scaffold_732-download8518.
smiles nucleophiles_614-download8519.smiles -m comb -x 2
CCCCNC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CCN(CC)CCN(CCN)C(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CCN(CC)CCNCCNC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CC1CC1COC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CC(CS)OC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
CC(O)CSC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1
Cc1ccc(NNC(=O)c2cc(N)cc(CC3SC(=O)NC3=O)c2)cc1C
Nc1cc(CC2SC(=O)NC2=O)cc(c1)C(=O)NOC1CCCCO1
CC(=O)Nc1ccc(Cl)c(NC(=O)c2cc(N)cc(CC3SC(=O)NC3=O)c2)c1
CC(C)(SC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1)C(N)C(O)=O
CC(C)(S)C(NC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1)C(O)=O
Nc1cc(CC2SC(=O)NC2=O)cc(c1)C(=O)O[C@@H]1CNC(=O)C1
CC(=O)N1C[C@@H](C[C@H]1C(O)=O)OC(=O)c1cc(N)cc(CC2SC(=O)NC2=O)c1



Dear Gyuri,


 


Thanks for your reply.  I got you point and hope this will fine. Well I have converted mrv to rdf using molconvert using  "molconvert rdf nucleophile_acylation_with_acid_halide.mrv | less" . But while converting it also append mrv file.


 


Best regards


 


Prashant