Molfile compression using molCompress()

Using the MdlCompressor class in Java

The chemaxon.formats.MdlCompressor can compress or decompress MDL Molfiles, SDfiles, RGfiles and Rxnfiles in two ways:

In one step: if the input file contents are in a byte array or in a String.
MdlCompressor has two static methods that convert in one step:
```
public static byte[] convert(byte[] mol, int flags) throws IOException;
public static String convert(String mol, int flags) throws IOException;
```
The following flags can be specified:
- COMPRESS for compression
- DECOMPRESS for decompression

Molecule by molecule: using an InputStream and an OutputStream.

import java.io.*;
import chemaxon.formats.*;
 
public class Example {
    public static void main(String args[]) {
        int n = 0;
        try {
            FileInputStream in = new FileInputStream("2000.sdf");
            MdlCompressor mc = new MdlCompressor(in, System.out,
						 MdlCompressor.COMPRESS);
            while(mc.convert())
                ++n;
        } catch(FileNotFoundException ex) {
            System.err.println("File not found");
        } catch(MolFormatException ex) {
            System.err.println("Bad file format");
        } catch(IOException ex) {
            System.err.println("Unexpected end of file");
        }
	System.out.println("Number of molecules: "+n);
    }
}

Note that there is a more general converter class in the Chemaxon class library (too general to be open source), chemaxon.formats.MolConverter, that is also a command line application (it has a main() method). In a Java program, it can be used similarly to MdlCompressor. Only the constructor differs:

            MolConverter mc = new MolConverter(in, System.out, "csmol");

Decompression:

            MolConverter mc = new MolConverter(in, System.out, "mol");

Using molCompress() in JavaScript

Note that the JavaScript version of molCompress can only compress simple Molfiles. SDfiles, RGfiles and Rxnfiles are not supported.

At first you should include the file molcompress.js in the HTML page, in the following way:


<script LANGUAGE="JavaScript1.1" SRC="molcompress.js"></script>

Because of the difference of operating systems in text file formats, you might need a function that converts a string to DOS/Windows format:


<script LANGUAGE="JavaScript1.1">
<!--
// molCompress() returns a string with \n newline characters.
// The <textarea> HTML element needs \r\n end-of-line characters
// in MS Windows, so we must fix the molCompress() output before
// setting the value of a <textarea>.
function eolfix(s) {
        if(navigator.userAgent.lastIndexOf("(Win") >= 0) {
                return s.split("\n").join("\r\n");
        } else {
                return s;
        }
}
//-->
</script>

In this example, an HTML textarea is used to display the input and output of the molfile compression or decompression.


<form onSubmit="return false;">
<textarea NAME="mol" ROWS=5 COLS=60>

  MSketch 11289810322D

  1  0  0  0  0  0  0  0  0  0999 V2000
   -2.5313    0.7188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
M  END
</textarea>

The second argument of molCompress() must be true for compression, false for decompession.


<input TYPE="BUTTON" VALUE="Compress"
	onClick="mol.value=eolfix(molCompress(mol.value, true))">
<input TYPE="BUTTON" VALUE="Inflate"
	onClick="mol.value=eolfix(molCompress(mol.value, false))">
</form>

You may want to try the compression demo and view its source.

Using molCompress() in C and C++

Note that the C version of molCompress can only compress simple Molfiles. SDfiles, RGfiles and Rxnfiles are not supported.

This C program converts an MDL Molfile into compressed mol format:


#include <stdio.h>

char* molCompress(const char* s, int compress);

int main(int argc, char* argv[])
{
    char* mol = "\n\
  MSketch 11289810322D\n\
\n\
  1  0  0  0  0  0  0  0  0  0999 V2000\n\
   -2.5313    0.7188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n\
M  END";
    char* csmol = molCompress(mol, 1);
    printf("%s", csmol);
    free(csmol);
    return 0;
}

When you run the program, the result should be



  MSketch 11289810322D

  1  0  0  0  0  0  0  0  0  0999 V2000
VqvVKm1W60
M  END

If you develop in C++ and compile molCompress() as a C++ function (usually by simply renaming the "c" extension of molcompress.c to C, cc, or cxx, etc.), then you should free the memory allocated for the compressed mol string by using the C++ delete operator instead of the C function free().


#include <iostream.h>

char* molCompress(const char* s, int compress);

int main(int argc, char* argv[])
{
    char* mol = "\n\
  MSketch 11289810322D\n\
\n\
  1  0  0  0  0  0  0  0  0  0999 V2000\n\
   -2.5313    0.7188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n\
M  END";
    char* csmol = molCompress(mol, 1);
    cout<<csmol;
    delete csmol;
    return 0;
}

For decompression, the second parameter of molCompress must be 0: char* mol = molCompress(csmol, 0);

Note that the second parameter only affects the return value, the first argument can be a compressed or decompressed mol regardless of the type of return. In other words, all of the following calls are valid:


char* csmol = molCompress(mol, 1);
char* csmol2 = molCompress(csmol, 1);
char* mol = molCompress(csmol, 0);
char* mol2 = molCompress(mol, 0);