Extracting 3D coordinates from PDB files with Groovy CDK
BioStar featured a question today about how to extract 3D coordinates from PDB files . Now, a simple script may actually do, and BioJava was mentioned too . Of course, it can also be done with the CDK . For example using this Groovy code:
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.io.*;
import org.openscience.cdk.tools.manipulator.*;
import org.openscience.cdk.io.IChemObjectReader.Mode;
import org.openscience.cdk.*;
import java.io.File;
import java.util.zip.GZIPInputStream;
reader = new PDBReader(
new GZIPInputStream(
new URL(
"http://www.pdb.org/pdb/files/1CRN.pdb.gz"
).openStream()
)
);
crambin = reader.read(new ChemFile());
for (container in
ChemFileManipulator.getAllAtomContainers(
crambin
)) {
for (atom in container.atoms()) {
println atom.point3d;
}
}
Wondering what the Bioclipse Scripting Language version would look like… and, it can likely be done with Jmol script too.