Some CML Fun

These are some notes on some initial work to create a chemical properties pipeline. End result will be calculated properties in an RDF triple store that can be exported using ORE/Atom. If I don't write this stuff down, I'll forget it.

Step 0: get Jumbo CML converter tools from SourceForge. Peter Murray Rust was kind enough to write a little README, now in the SVN. I did an SVN checkout rather than download the tagged Jumbo versio 5.4 or 5.5.

svn co https://cml.svn.sourceforge.net/svnroot/cml/jumbo-converter/trunk jumbo-converter

Step 0.5: Compile as an executable jar. I used "mvn assembly:assembly". See http://www.springone2gx.com/blog/scott_leberknight/2008/06/creating_executable_jars_using_the_maven_assembly_plugin.html


Step 0.75: Run with sample data using the command (must set classpath):

java -jar target/jumbo-converters-jar-with-dependencies.jar -converter org.xmlcml.cml.converters.molecule.pubchem.PubchemXML2CMLConverter
-sd examples/input -odir ../output -is pubchem.xml -os pubchem.cml


Step 1: get XML descriptions of molecules from Pubchem. I'm not a chemist, so I did a structure similarity search on caffeine, applied the Rule of Five, and got 1298 matches. That's pretty good.


Step 2: Unfortunately the PubChem download gives everything in one big XML file, but Jumbo's converter expects each molecule to be in a separate file. I googled around and made a little Perl script to do this:

#!/usr/bin/perl

use File::Basename;

$file = @ARGV[0];

open(_FH, "< $file") or die "Unable to open file: $file\n";

$count=0;
$max_records=1;
$files_counter=0;

while(<_FH>)
{
if($count == 0)
{

my @suffix=qw(.pubchem.xml);
my ($basefilename, $path, $suffix)=fileparse($file,@suffix);
$filename=$basefilename . "_part_" . $files_counter . $suffix;
open(FH2, "> $filename") or die "Unable to open file: $filenam
e\n";
$count++;
print FH2 "\<\?xml version=\"1.0\"\?\>\n";
}

if (grep /<\/PC-Compound>/, $_ )
{
print FH2 $_;
$count++;
}
elsif (grep /<PC-Compound>/, $_ )
{
print FH2 "<PC-Compound xmlns=\"http://www.ncbi.nlm.nih.gov\"
xmlns:xs=\"http://www.w3.org/2001/XMLSchema-instance\" xs:schemaLocation=\"http:
//www.ncbi.nlm.nih.gov ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem
.xsd\">\n";

}
else {
print FH2 $_;
}

if ($count == $max_records + 1)
{
$count = 0;
$files_counter++;
close(FH2);
}
}

I stole a lot of this from http://www.mysysad.com/2008/01/parse-xml-records-with-perl-script.html


Step 2.5: Rerun the converter command on the new files. Jumbo was able to handle most but barfed on a few, so I'll have to follow up on this.

Step 3: Go to lunch. Next need PMR and Co. to decide on the best way to change the CML into Gaussian input files.

Step 4: Realize you downloaded a bunch of 2D structures, so repeat steps 0-3 with 3D structures.

Step 5: Make Gaussian input files from CML with

java -jar target/jumbo-converters-jar-with-dependencies.jar -converter org.xmlcml.cml.converters.compchem.gaussian.input.CML2GaussianInputConverter -sd examples/output -odir ../gaussian -is pubchem.cml -os pubchem.gauss

Current SVN of jumbo-converters won't compile without first checking out and compiling also cmlxom and jumbo5 from SVN (they are peers in the directory structure).

Step 6. Run Gaussian on TeraGrid machines. See http://communitygrids.blogspot.com/2009/07/running-gaussian-on-big-red.html. Welcome to 2009!

Step 7. Get the data back and convert the Gaussian standard output to CML. I used the command

java -jar target/jumbo-converters-jar-with-dependencies.jar -converter org.xmlcml.cml.converters.compchem.gaussian.log.GaussianLog2CMLConverter -sd examples/gaussOut -odir ../gaussOut -is out -os cml

I put the Gaussian output files in the examples/gaussOut directory.

Step 8. Convert the output CML to RDF:

java -jar target/jumbo-converters-jar-with-dependencies.jar -converter org.xmlcml.cml.converters.compchem.gaussian.GaussianCML2OWLRDFConverter -sd examples/gaussOut -odir ../gaussOut -is cml -os rdf