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smilesbasedsimilaritykernels's Introduction

SMILESbasedSimilarityKernels

Source code containing different SMILES similarity functions written in Java, Eclipse.

Folders

"data" folder contains the chemical data that is used.

  • e: contains unique smiles created from mol files of enzyme data set

  • gpcr: contains unique smiles created from mol files of enzyme data set

  • ic: contains unique smiles created from mol files of enzyme data set

  • nr: contains unique smiles created from mol files of enzyme data set

  • sim_matrix: contains similarity matrices created by SMILES based algorithms.

"source code" folder contains java source code.

How to Run the Jar File

First, please place "data" folder under the same directory with SMILESSim.jar. Then, you can run the code below in the command line to see the results for the four data sets of Yamanishi et al. (enzyme, gpcr, nuclear receptors, ion channels),

java -jar SMILESSimv2.jar

If you want to calculate similarity of your own SMILES set, then you have to put SMILES files (.smi) under your folder. Then you can run the code below in the command line. This command computes similarity for 13 different similarity functions.

java -jar SMILESSimv2.jar [yourfoldername]

You can also choose to run only a function of your choice.

java -jar SMILESSimv2.jar [yourfoldername] [functionname]

To see the available functions:

java -jar SMILESSimv2.jar

How to Run the Source Code

You can open the project in Eclipse or NetBeans to run.

Input

You need to put data folder under source code/SMILESKernels folder for program the read data.

You can place your own folder (newFolder), containing SMILES files (.smi) under data folder with name newFolder.

Then you need to manually add the folder to SMILESKernels.java in the following line,

String[] dataset = {"e", "gpcr", "nr", "ic", "newFolder"};

or

String[] dataset = {"newFolder"};

Output

The program will produce text files containing a similarity matrix of the given inputs under the "simmatrix" folder for each function.

Citation to this work:

Öztürk, Hakime, Elif Ozkirimli, and Arzucan Özgür. "A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction." BMC bioinformatics 17.1 (2016): 128.

smilesbasedsimilaritykernels's People

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smilesbasedsimilaritykernels's Issues

Can't run on own folder

Hi :)

thanks for this piece of software! I'm having trouble running it (might be related to #1 ). I'm also running on OsX but I'm using my own SMILES.

I run: java -jar tools/SMILESSim.jar ../data/smiles and get:

---------edit------------------
---------../data/smiles------------------
0
1
2
3
... [cropping content for readability]...
1410
1411
Exception in thread "main" java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.io.FileNotFoundException: ./simmatrix/edit_../data/smiles_simmat_dc.txt (No such file or directory)
	at java.io.FileOutputStream.open0(Native Method)
	at java.io.FileOutputStream.open(FileOutputStream.java:270)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:101)
	at java.io.FileWriter.<init>(FileWriter.java:63)
	at smileskernels.SMILESKernels.writeSimMatrix(SMILESKernels.java:206)
	at smileskernels.SMILESKernels.main(SMILESKernels.java:171)
	... 5 more
  1. This is very strange, because my data folder and my tools folder lie in the same directory (thus the .. is somehow incorrect, but it's the only way to make it work).
    An ls of where I'm running the thing:
ls
PROCEDERE.md			libs				simmatrix			train.ipynb
SMILES_for_similarity.ipynb	models				src
create_features.ipynb		predict.ipynb			tests
data				process_data.ipynb		tools

  1. I believe it fails when trying to create the summary files, e.g.: the line ./simmatrix/edit_../data/smiles_simmat_dc.tx.

  2. If I copy the smiles folder over to my my tools dir and run everything from there, aka: java -jar SMILESSim.jar smiles or java -jar SMILESSim.jar smiles\ or java -jar SMILESSim.jar ./smiles or java -jar SMILESSim.jar ./smiles/ or java -jar SMILESSim.jar ../smiles or java -jar SMILESSim.jar ../smiles/ I always get:

---------edit------------------
---------[./|../|]smiles[/|]------------------
Exception in thread "main" java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.NullPointerException
	at ioops.readSMILES.readSMILESfromFolder(readSMILES.java:24)
	at smileskernels.SMILESKernels.main(SMILESKernels.java:74)
	... 5 more

Would greatly appreciate your help :)

eidt: notice how it created the folder simmatrix in my root. That wasn't there before running the command, but the content of the folder is empty :)

Can't run example code

Hi, we've cloned the repo on two separate machines and get the same error when trying to run the example code.

$ ls
README.md     SMILESSim.jar data          source code

$ dirtree
   |-data
   |---e
   |---gpcr
   |---ic
   |---nr
   |---sim_matrix

$ java -jar SMILESSim.jar
---------edit------------------
---------e------------------
Exception in thread "main" java.lang.NullPointerException
    at ioops.readSMILES.readSMILESfromFolder(readSMILES.java:24)
    at smileskernels.SMILESKernels.main(SMILESKernels.java:72)

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