using alias for reactivity in cmd

Hi,

I could not figure out how could i use the alias defined in the mol.smarts file and use them by command line to run reactor. I tried using ..r: and writing the alias eg:.

react -r "Y:\RxnName.rxn" ..r:'alkene' -f sdf -t reaction -o "Y:\Product.sdf"        or

react -r "Y:\RxnName.rxn" ..r:reactant(1),"ether" && reactant(2),"aldehyde" -f sdf -t reaction -o "Y:\Product.sdf"   

or ratom(1) 'alias'. Please detail, how is it done.

the match function is mentioned in the help but using them in between like below gives error.

react -r "Y:\RxnName.rxn" ..r:match(reactant(1), (alkene) -f sdf -t reaction -o "Y:\Product.sdf"   

Also, how more than one alias for one Reactant is represented,  Is it by putting them w/in the {}. 

Thanks in advance.

Hi,

You are mixing "reaction file", and "reaction string" in reaction definition. Please see the documentation for more.

Zsolt

Thanks Zsolt.

react -i rxnID -c config.xml -r rxn1.rxn react.sd -o prod.smi

command works fine and it gives product but ignoring config file, removing the config file also i can get product as long as .rxn file is there.

1/ If i want to define my rxn with rules in the config file w/o including .rxn file, that willnot work, is it correct? or can i do that?

2/If i give rxnID in config file keeping the .rxn file in the same directory, shouldnot that work too.

3/I am wondering wny my config file is not read even though its presence or absence is not giving any errors. There might be minute mistakes which i am not aware of. Please guide me. Thanks a bunch.

PS.If you need to see config file please let me know i could send you by email.

From JChem version 3.2 (released on October 17, 2006) configuration XML files are no longer supported by Reactor (see JChem changes). We removed the description of the configuration XML file syntax from the documentation years ago.

Reactions for Reactor can be defined as reaction file, or reaction string. If the reaction is given in RDF or MRV file, then it
is also possible to set the reaction rules, the reactant standardization, and some additional properties
in RDF/MRV tags. The most convenient way to set the reaction rules in reaction files is using the reaction editor inside the  Reactor (GUI) application. It contains a reaction rule editor, which supports code competion and syntax highlighting.

I hope this helps.

Zsolt

Thanks a bunch for the clarification but how it is done in evaluator? Does evaluator still has a config file? I was looking to run the reactor in command line. If there is any local way to do this besides using the Reactor GUI? 

bhhataba wrote:

Does evaluator still has a config file?

Yes, it has. Details are described here: https://www.chemaxon.com/marvin/help/chemicalterms/Evaluator.html#config

bhhataba wrote:

I was looking to run the reactor in command line. If there is any local way to do this besides using the Reactor GUI?

You can use Reactor in command line with the reaction created in Reactor GUI. For example create a reaction named reaction.mrv using the reaction editor (in Reaction GUI), save it, and then use it from command line:

react -r reaction.mrv reactants1.sdf reactants2.sdf

It's just much easier to create a reaction with the reaction editor, then to do it manually.

I hope this helps.

Zsolt