ideaconsult/apps-ambit

Applications using AMBIT and examples how to call AMBIT modules

apps-ambit's Issues

cdk version for this example

Which cdk version was this? I was unable to run the example using cdk 1.5.13

please add what people should type on the command line

please add what people should type on the command line to convert a SD file into a webpage with the "molbrowser"

project not buliding - compliation errors

the project has compilation errors

[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] ..../appdomain-example/src/main/java/net/idea/example/ambit/appdomain/AppDomainModel.java:[18,31] error: package org.apache.commons.lang3 does not exist

and after adding common-lang3 to the pom.xml

[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] .../appdomain-example/src/main/java/net/idea/example/ambit/appdomain/AppDomainModel.java:[271,87] error: cannot find symbol

feature request: command line option to provide the input molecule via stream instead of file

Java API usage

Can you point to an example of using the Java API for generating tautomers.
For instance, if I have CDK IAtomContainer how can I generate tautomers for that molecule, along with this associated information such as the energy score.

feature request: consistent rank-formatting in .sdf by Ambit‐Tautomer

I'm starting to use ambit-tautomer (ambit-tautomers-2.0.0-SNAPSHOT.jar, downloaded today). With O=C(c1c2cccc1)N([C@H](CCC(N1)=O)C1=O)C2=O provided in a .smi file, I run

java -jar ambit-tautomers-2.0.0-SNAPSHOT.jar -f thalomid.smi -o thalo.sdf

and read the results in DataWarrior. While browsing across the table, I noticed an inconsitent formatting of the rank order:

and

While I'm surprised about the occurence of negative rank orders, my first intent is to suggest a consistent formatting of this type of result; if it is a floating number, perhaps consistently to five decimals and -- so necessary -- with the addition of padding zeroes.

To ease replication of the observation, I add both start and resulting file; both padded by .txt to pass GitHub's settings.
thalomid.smi.txt
thalo.sdf.txt

feature request: command line option to suppress output of the input molecule