Regarding synthesizer....

I have two doubt regarding the synthesizer program


(1)I have successfully run the program in memory and file mode with the


examples provided. I need to give my own input. Is this program support only


amine, carboxylic acid and alkynes? Can I give my own SETId other than


amine, carboxylic acid and alkyne(program is showing error) ? In synthesizer


xml file do I need to make changes to give user defined input?


(2)To open synthesis browser connection to database is required. From where


will get the user name and password.Is there any example database provided


with package.

1) It is a general tool, so you can configure it for your own reactions and sets. The examples are provided as illustrations.





2) Synthesis browser can be used when you generated your library to a jchem database. It does not support files, and we are currently reengineering our approach to synthesis databases. We will add Reactor's functionality to Instant JChem soon, which will provide an easy to access interface for reaction processing in databases. Please sign up for our newsletter to be informed as soon as this integration process has been finished.

hi,


i am tryin the synthesizer program..


now i am trying to add more input molecules(as example xml and file have only three (alkyne, amines and carboxylic acid)). also i am trying to upload your reaction library in rdf format(instead of three). also i edited the xml file according to that. but its still showing some error, so do i need to make any other change??/\


how can i do this with my own input molecules??/


see the attached files...(reaction library in rdf format and edited XML file)


please see and tell me any other change needed?? or what will i do in set id in this case?/?

jijibio wrote:

hi, i am tryin the synthesizer program.. now i am trying to add more input molecules(as example xml and file have only three (alkyne, amines and carboxylic acid)). also i am trying to upload your reaction library in rdf format(instead of three). also i edited the xml file according to that. but its still showing some error, so do i need to make any other change??/\ how can i do this with my own input molecules??/ see the attached files...(reaction library in rdf format and edited XML file) please see and tell me any other change needed?? or what will i do in set id in this case?/?

The problem is that "reactions.rdf" file contains more than one reaction (contains the whole library).

Code:

<Reaction ID="r1" Structure="reactions.rdf"/>

After the "Structure=" tag you can only specify a reaction SMARTS, or a reaction file containing one reaction.





Regards,


Zsolt

Hi,





my doubt is that the output of the synthesiser conains the input molecules also (scaffold, groups).


But i need only the output molecules for further procees, so can u help me..


please see the attached file.


The first four molecules and 5,6,7 molecules are also the same input molecules...


help me to solve this..





Jiji

In exhaustive algorithm working examples provided in help, some reactions (e.g 2-oxopent-4-enoic_acid_hydrolase.mrv, 4-hydroxy-2-oxovalerate_aldolase.mrv etc) are used. so is this reactions are also there in your reaction library(contains 72 reactions type)??





if i want to do synthsise with my own inputs, how can i refer the reaction type?








Jiji

jijibio wrote:

Hi, my doubt is that the output of the synthesiser conains the input molecules also (scaffold, groups). But i need only the output molecules for further procees, so can u help me.. please see the attached file. The first four molecules and 5,6,7 molecules are also the same input molecules... help me to solve this.. Jiji

Hi,





Please specify the exact command line call you have used, and attach the input files.





Thanks,


Zsolt

jijibio wrote:

if i want to do synthsise with my own inputs, how can i refer the reaction type?

As follows:

Code:

<Reaction ID="r1" Structure="[H:2][c:1]1ccccc1>>[Cl:3][c:1]1ccccc1" Type="string"> ... </Reaction> <Reaction ID="r2" Structure="reactions/reaction.mrv" Type="path"> ... </Reaction>

If the Type attribute is omitted then the structure type is automatically decided based on its format which gives the correct result in most cases.





See: http://www.chemaxon.com/jchem/doc/user/Synthesizer.html#reactions





Best regards,


Zsolt

Hi ,


Thanks for your response..


Its really helpful for me..





now, my doubt is about the 'Graph' part of the synthsizer.xml file.


QUESTION :1





<Graph>


<Sets Result="RESULT"/>


<Rule>


<![CDATA[


Ncount(product(0)) + Ocount(product(0)) + Scount(product(0)) <= 10


&& mass(product(0)) <= 700


]]>


</Rule>


<Edge From="alkyne,scaffold" To="product1" RID="r1"/>


<Edge From="product1,amine" To="product2" RID="r2"/>


<Edge From="carboxylic-acid,product2" To="RESULT" RID="r3"/>


</Graph>








can you explain that part as above example, like how it works?





QUESTION :2





If i have a scaffold, and i need to generate a combinatorial library. For that i know that i need to select the recation type and, R-gropus(Here like alkyne, amines etc).


So DO I NEED TO SPECIFY THAT GROUPS IN SEPARATE FILE as amines.smiles, alkynes.smiles here) or in one file?





then according to thos my own reaction how can i edit the EDGE part of the xml.???





help me to solve this problem...

Please try using Reactor. It has graphical user interface that helps you in reaction design (including specifying reaction rules and reaction library management), and provides an easy to use interface for selecting the input and the output files.





Best regards,


Zsolt

Hi,


in synthesizer.xml, i have edited the edge tag and tried the following commands separately with the same inputs.





eg. first one is <Edge From="scaffolds,halo" To="RESULT" RID="r1"/>





second one is <Edge From="halo, scaffolds" To="RESULT" RID="r1"/>





i am attaching the input files, reaction type and both result.can you tell how i got this result??


RESULT1.smiles, is the result of first tag and RESULT2.smiles is the result of secong tag.


can you explain how can i edit this <edge> tag appropriately to get all the possible molecule set?





regards,


jiji