kaibioinfo/computefp

Contains the code for computing fingerprints for CSI:FingerID

computefp

Contains the code for computing fingerprints for CSI:FingerID

install

gradle installDist

usage

computefp/bin/computefp [INPUTFILES]

where INPUTFILES is a list of files containing SMILES. The files can either be text files with one SMILES per line, or TAB separated text files with SMILES as last column. The previous columns are then treated as metadata (e.g. Ids or names).

output

For each input file a new file with same path but different ending (.fp) is created. The file is TAB separated, with the first columns are the metadata (if given), first 14 characters of the InChI-Key, the 2D InChI, the SMILES, and the fingerprint.

The fingerprint is given as comma separated list of indizes. Note that the definition of fingerprints might change with

fingerprint definitions

To get a list of all indizes with their meaning, run

computefp/bin/computefp --info

computefp's Issues

Missing dependencies in the build-file

Hei,

unfortunately I receive the errors when using gradle distInstall. It seems that a couple of dependencies cannot be found, such as: jmzml (in version 1.7.11), cpdetector, ... I added them manually to the build.gradle file:

repositories {
    mavenLocal()
    mavenCentral()
    maven {//public libs only so anybody can build the frontend without login
        url "https://bio.informatik.uni-jena.de/repository/libs-oss"
    }
    maven {
        url "https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo"
    }
    maven {
        url "https://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/"
    }
    maven {
        url "https://mvnrepository.com/artifact/antlr/antlr"
    }
}

dependencies {
    compile group: 'uk.ac.ebi.jmzml', name: 'jmzml', version: '1.7.11'
    compile group: 'cpdetector', name: 'cpdetector', version: '1.0.7'
    compile "de.unijena.bioinf.ms:fingerprinter_oss:1.3.0-SNAPSHOT"
    compile "de.unijena.bioinf.ms:chemistry_base:4.3.0-SNAPSHOT"
}

However, still I receive "missing dependency" exceptions for other packages:

> Could not resolve all files for configuration ':compileClasspath'.
   > Could not find org.antlr:com.springsource.antlr:2.7.7.
     Searched in the following locations:
       - file:/home/bach/.m2/repository/org/antlr/com.springsource.antlr/2.7.7/com.springsource.antlr-2.7.7.pom
       - https://repo.maven.apache.org/maven2/org/antlr/com.springsource.antlr/2.7.7/com.springsource.antlr-2.7.7.pom
       - https://bio.informatik.uni-jena.de/repository/libs-oss/org/antlr/com.springsource.antlr/2.7.7/com.springsource.antlr-2.7.7.pom
       - https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/org/antlr/com.springsource.antlr/2.7.7/com.springsource.antlr-2.7.7.pom
       - https://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/org/antlr/com.springsource.antlr/2.7.7/com.springsource.antlr-2.7.7.pom
       - https://mvnrepository.com/artifact/antlr/antlr/org/antlr/com.springsource.antlr/2.7.7/com.springsource.antlr-2.7.7.pom
     Required by:
         project :
         project : > cpdetector:cpdetector:1.0.7
   > Could not find net.sourceforge.cpdetector:cpdetector:1.0.7.
     Searched in the following locations:
       - file:/home/bach/.m2/repository/net/sourceforge/cpdetector/cpdetector/1.0.7/cpdetector-1.0.7.pom
       - https://repo.maven.apache.org/maven2/net/sourceforge/cpdetector/cpdetector/1.0.7/cpdetector-1.0.7.pom
       - https://bio.informatik.uni-jena.de/repository/libs-oss/net/sourceforge/cpdetector/cpdetector/1.0.7/cpdetector-1.0.7.pom
       - https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/net/sourceforge/cpdetector/cpdetector/1.0.7/cpdetector-1.0.7.pom
       - https://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/net/sourceforge/cpdetector/cpdetector/1.0.7/cpdetector-1.0.7.pom
       - https://mvnrepository.com/artifact/antlr/antlr/net/sourceforge/cpdetector/cpdetector/1.0.7/cpdetector-1.0.7.pom
     Required by:
         project : > uk.ac.ebi.jmzml:jmzml:1.7.11 > uk.ac.ebi.pride.architectural:pride-xml-handling:1.0.3 > psidev.psi.tools:xxindex:0.23

Could you indicate how to set the dependencies properly?

Best regards,

Eric

Missing Gradle build file?

Hei,

could you add a 'build.gradle' file to the repository?

Best regards,
Eric