convert smile format molecules into individual .pdb files

Hi

I have an excel sheet with 1st column containing the name of the molecule and 2nd column containing the structures of each respective molecule in smile format .

May i request for some help with converting each molecule into individual pdb file in a batch mode.

Will greatly appreciate your help.

Best

Rinku

 

Hi,

First of all export you excel sheet to text file such a way that the first column contains the SMILES and the second column is the molecule name (I guess you would like to keep the molecule name also) separated by space character.

Eg. pdbexcel.smi:

CCCC name
CCC name2

After you have this file (pdbexcel.smi), give it as a parameter to the attached java program (to run this program you need the chemaxon library: eg files in MarvinBeans/lib ). The code will export each line of the smi file into separate pdb file with the filename containing the line number in the smi followed by the .pdb extension.

As you read the molecule from smiles I have included a 3D cleaning for the molecule (I guess you don't want pdb file with every atom sitting at the origin). This 3D cleaning may be slow.

You can compile and run it from the MarvinBeans directory:

javac -cp ".:./lib/MarvinBeans-beans.jar" ConvertToPdb.java


java -cp ".:./lib/MarvinBeans-beans.jar" ConvertToPdb pdbexcel.smi

I hope this helps.

I am looking for such java programs converting smiles to pdb file. Where can I get the ConvertToPDB.java file?

 

Thanks.

After I reloaded the web page, I found the file. Please ignore my post. Thanks.

Hello

 

I have tried this as it is exactly what I need, but it doesn't work. I follow the steps and it says:

$ javac -cp "MarvinBeans-beans.jar" ConvertToPdb.java


Note: ConvertToPdb.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.

When I try to run the next line it says:

$ java -cp "MarvinBeans-beans.jar" ConvertToPdb test.smi 


Exception in thread "main" java.lang.NoClassDefFoundError: ConvertToPdb


Caused by: java.lang.ClassNotFoundException: ConvertToPdb


	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)


	at java.security.AccessController.doPrivileged(Native Method)


	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)


	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)


	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)


	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)

I have no idea what to do! Can someone help please? Thank you in advance.

Hi you should add the current directory to the classpath as well:

java -cp ".:MarvinBeans-beans.jar" ConvertToPdb test.smi

 

Best Regards,

Peter

Thanks! Are the conversions accurate?

You can find information about PDB export on this page:

http://www.chemaxon.com/marvin/help/formats/pdb-doc.html

Hi, I was excited to find this script... it is exactly what I need! However I cannot get it to compile... it seems I am missing some dependencies? the main error seems to read chemaxon.formats does not exist.  I have MarvinBeans and JChem installed, machnine is 32 bit Linux.  The classpath and path set as follows:

#.jars go below

export CLASSPATH=$/home/aiden/ChemAxon/MarvinBeans/lib/*:

 

#executables go below

export PATH=${PATH}:/home/aiden/ChemAxon/MarvinBeans/bin/*:/home/aiden/Desktop/openMAXWELL/FDA/*:.

 

and here is the full output of the error

 

aiden@aiden-ThinkPad-T400:~/Desktop/openMAXWELL/FDA$ javac -cp ".:./lib/MarvinBeans-beans.jar" ConvertToPdb.java

ConvertToPdb.java:4: error: package chemaxon.formats does not exist

import chemaxon.formats.MolExporter;

                       ^

ConvertToPdb.java:5: error: package chemaxon.formats does not exist

import chemaxon.formats.MolFormatException;

                       ^

ConvertToPdb.java:6: error: package chemaxon.formats does not exist

import chemaxon.formats.MolImporter;

                       ^

ConvertToPdb.java:7: error: package chemaxon.struc does not exist

import chemaxon.struc.Molecule;

                     ^

ConvertToPdb.java:32: error: cannot find symbol

    public static void main(String[] args) throws MolFormatException, IOException {

                                                  ^

  symbol:   class MolFormatException

  location: class ConvertToPdb

ConvertToPdb.java:40: error: cannot find symbol

        MolImporter mi = new MolImporter(new FileInputStream(args[0]), "smiles");

        ^

  symbol:   class MolImporter

  location: class ConvertToPdb

ConvertToPdb.java:40: error: cannot find symbol

        MolImporter mi = new MolImporter(new FileInputStream(args[0]), "smiles");

                             ^

  symbol:   class MolImporter

  location: class ConvertToPdb

ConvertToPdb.java:41: error: cannot find symbol

        Molecule m = null;

        ^

  symbol:   class Molecule

  location: class ConvertToPdb

ConvertToPdb.java:45: error: cannot find symbol

            MolExporter exporter = new MolExporter(filename, "pdb");

            ^

  symbol:   class MolExporter

  location: class ConvertToPdb

ConvertToPdb.java:45: error: cannot find symbol

            MolExporter exporter = new MolExporter(filename, "pdb");

                                       ^

  symbol:   class MolExporter

  location: class ConvertToPdb

10 errors

Hi Aiden,

You should use the MarvinBeans.jar instead of MarvinBeans-beans.jar:

~/Desktop/openMAXWELL/FDA$ javac -cp ".:./lib/MarvinBeans.jar" ConvertToPdb.java

BRs,

Peter

Hi Peter, 

Thank you for your quick reply. I tried executing the modified command you gave me,  but still no luck. The exact same error message prints. Upon searching my system for the packages listed in the error message, nothing is found except html pages describing the packages. Should these be jars in the lib file? (ie MolFormatException)? I have both JChem and MarvinBeans installed so i am baffled these packages are still missing. Best regards, 

Aiden

Hi Aiden,

I've downoladed the MarvinBeans-6.2.1.sh from our website and run it.

It created a ChemAxon folder in my home. In the folder ~/ChemAxon/MarvinBeans/lib there should be several jars with names like com.chemaxon-* and MarvinBeans*. You should include the MarvinBeans.jar from there.

The command should be something like:

~/Desktop/openMAXWELL/FDA$ javac -cp ".:/home/aiden/ChemAxon/MarvinBeans/lib/MarvinBeans.jar" ConvertToPdb.java

I've just tried it and it worked for me. I think something may be missing from the classpath.

BR, 

Peter

it was indeed a classpath error. I was using the wildcard incorrectly. Thanks for your time!

 

javac -cp ".:/lib/MarvinBeans-beans.jar" ConvertToPdb.java

javac: file not found: ConvertToPdb.java

Usage: javac <options> <source files>

 

javac -cp ".:/lib/MarvinBeans-beans.jar" ConvertToPdb test.smi

error: Class names, 'ConvertToPdb,test.smi', are only accepted if annotation processing is explicitly requested

 

1 error

the above error persists for me.... could anyone help me to sort it out 

Hi,

Did you try to use the MarvinBeans.jar instead of MarvinBeans-beans.jar and the full path of ConvertToPdb.java?

thanks for your reply,

but even after trying with full path it didn't work for me 

javac -cp ".:/Applications/ChemAxon/MarvinBeans/lib/MarvinBeans-beans.jar"  ConvertToPdb.java

javac: file not found: ConvertToPdb.java

 

Try this in the folder containing the ConvertToPdb file:

javac -cp ".:/Applications/ChemAxon/MarvinBeans/lib/MarvinBeans.jar"  ConvertToPdb.java

DearJkendi,

I tried as you suggested but .still the error persists ..

javac -cp ".:./Applications/ChemAxon/MarvinBeans/lib/MarvinBeans.jar"  ConvertToPdb.java

javac: file not found: ConvertToPdb.java

Usage: javac <options> <source files>

It seems, this is a javac usage problem, not a problem with our API. I don't have any idea, try to get some personal help from somebody who is familiar with javac.

 

You can also try molconvert:

https://docs.chemaxon.com/display/docs151214/Molecule+File+Conversion+with+MolConverter

hi,

I got one new error 

javac -cp ".:./MarvinBeans.jar" ConvertToPdb c.smi 

error: Class names, 'ConvertToPdb,c.smi', are only accepted if annotation processing is explicitly requested

 

1 error

could you help with it ....

javac -cp ".:./MarvinBeans.jar" ConvertToPdb.java


java -cp ".:./MarvinBeans.jar" ConvertToPdb c.smi

 

First, you have to compile the source with javac and then using the java (not javac) to run the program.

This may help: 

http://www.codejava.net/java-core/tools/using-javac-command

http://stackoverflow.com/questions/11965818/how-to-run-java-program-in-command-prompt