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ncats / lychi

Layered Chemical Identifier
Apache License 2.0
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Cannot find output #15

Open marcabrus opened 6 years ago

marcabrus commented 6 years ago

when i run the test java -jar dist/lychi-all-v0.1.jar tests/standardizer_case1.smi i'm not able to find output, it only print results on command line

caodac commented 6 years ago

You can use the -Doutput={name} option to write the output to a file {name}, e.g.,

java -Doutput=test.smi -jar dist/lychi-all-v0.1.jar tests/standardizer_case1.smi
marcabrus commented 6 years ago

thanks a lot so if I checked correctly the options I can insert for now are: -Doutput-format={smi,smiles,sdf} default= smi -Dkeep-salt={true|false} default = true -Dlychi-keto-enol={true|false} - default=false Is it possible to add these options in readme? N.B. reading the comments the option to keto-enol tautomerism activation is -Dketo-enol=true, but as I desumed from the code the correct one is -Dlychi-keto-enol=true

caodac commented 6 years ago

Will do, thanks for the suggestion!