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Cannot find output #15

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marcabrus opened this issue May 10, 2018 · 3 comments
Open

Cannot find output #15

marcabrus opened this issue May 10, 2018 · 3 comments

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@marcabrus
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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
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caodac commented May 10, 2018

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
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marcabrus commented May 11, 2018

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
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caodac commented May 11, 2018

Will do, thanks for the suggestion!

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