Extracting CML from a Chem4Word authored document (C#)

January 21, 2010

My previous post was the first in a series demonstrating how CML embedded in DOCX files could be extracted (in that case using Java). For completeness I thought I ought to post some code to accomplish the same thing in C#. This should also allow people to get used to the packaging tools before we build up functionality in later posts.

If you would like a file containing CML to test this out with, one is available here.

Now for the code:


using System.Collections.Generic;
using System.IO;
using System.IO.Packaging;
using System.Linq;
using System.Xml.Linq;
using System.Xml.XPath;

namespace Chem4Word.Tools 
{
  public class OOXMLTools 
  {
    public ICollection GetCML(string path) 
    {
      ICollection list = new List();
      using (Package package = Package.Open(path, FileMode.Open)) 
      {
        foreach (PackagePart packagePart in package.GetParts()) 
        {
          if (packagePart.ContentType == "application/xml") 
          {
            using (StreamReader streamReader = 
               new StreamReader(packagePart.GetStream())) 
            {
              try 
              {
                XDocument xDocument = 
                  XDocument.Parse(streamReader.ReadToEnd());
                if (xDocument.XPathSelectElements(
              "//*[local-name()='cml' and namespace-uri()=
              'http://www.xml-cml.org/schema']").Count() > 0) 
                {
                  list.Add(xDocument);
                }
              }
              catch 
              {
                  // not valid XML so therefore can't be CML
              }
            }
          }
        }
      }
      return list;
    }
  }
}

So there we go. Pretty similar to the Java version really. Just in case you were wondering, I know I haven’t done a load of exception checking.

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Extracting CML from a Chem4Word authored document (Java)

January 20, 2010

I have been meaning to write this post for ages and thanks to a recent tweet from Egon I’ve finally got round to it. Basically what I am going to do over a series of posts is explain how CML can be extracted from a DOCX (OOXML) file authored using Chem4Word. I’ll post methods in both Java and C# but I am starting off in Java.

A very quick into to DOCX and OOXML

There are plenty of blogs, papers, videos and the like out there which explain OOXML in various levels of detail. I don’t want to replicate that here but I think it will be useful to have a quick overview for reference. Microsoft developed the Open Packaging Convention (OPC) specification as a successor to its binary Microsoft Office file formats. The file-extension DOCX indicates an OPC document which should be edited using Microsoft Office Word 2007 (as opposed to the XSLX file extension for example which are OPC documents editable using Excel). A DOCX document is effectively a zip-file (the package) which contains the original text as a marked-up XML component (document.xml), with images and other embedded objects stored as separate files.

the simplified structure of an OPC document

The package-part word\document.xml contains the main text and body of the document. Chem4Word stores CML files in the customXml folder within the package. This directory contains pairs of files with names item[\d].xml and itemProps[\d].xml – itemProps[n] contains a list of all the namespaces and schemas used in item[n].

Getting the CML out – the brute force extraction method

The first method of extracting the CML files is the simplest. This method does not allow us to know anything more about the data other than it has been included somewhere in the document by the user. For example, we don’t know where and how it is being used in the document (or how many times). So, for the algorithm: iterate through all those files where the CML may be found, attempt to build each file as a XOM document, if it builds then search within it for a cml element from the cml namespace (see code below).

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.zip.ZipEntry;
import java.util.zip.ZipException;
import java.util.zip.ZipFile;

import nu.xom.Builder;
import nu.xom.Document;

public class OOXMLTools {

  public static List<Document> GetCML(File file)
    throws ZipException, IOException  {

    ZipFile zipFile = new ZipFile(file);
    List<Document> list = new ArrayList<Document>();
    Builder builder = new Builder();
    Matcher m =
      Pattern.compile("customXml/item([1-9][0-9]*)\\.xml")
        .matcher("");

    for (Enumeration <? extends ZipEntry>
      entries = zipFile.entries(); entries.hasMoreElements();) {

      ZipEntry entry = entries.nextElement();
      if (m.reset(entry.getName()).matches()) {
        try {
          Document doc =
            builder.build(zipFile.getInputStream(entry));

          if (doc.query("//*[local-name()='cml' and
            namespace-uri()='http://www.xml-cml.org/schema']")
              .size() > 0) {

            list.add(doc);
          }

        } catch (Exception e) {
          // not an XML file so can't be CML
        }
      }
    }
    return list;
  }
}

If you would like to try it out here is a DOCX file with some chemistry in it. There are three chemistry zones in the document (containing testosterone [item1] and acetic acid [item3]) but only two CML files in the customXml directory because both testosterone instances point to the same backing CML file.

In following posts I will go further into how you can discover which representation is being used in the document, how many times a particular CML file is referenced and how the data is converted into the on screen representation.


A challenge for Chemists and OOXML

July 27, 2008

Not all that long ago there were a series of competitions (of the new BBC version in that you could win kudos and little else) on various blogs (PMR, chemspiderman) to identify the number of chemicals in a paragraph of text. These focused largely on the difficultly of deciding what is and what is not a chemical – and consequently there was not necessarily a right answer.

Now I would like to propose a new challenge… and there is a right answer this time. I have randomly selected a preparation from an organic chemistry article a version of which is shown below. There is also a DOCX version available for download, which is fully and correctly formatted – to get the right answer I strongly suggest that you use the DOCX (although the latest version of Microsoft Office Word is not required).

So now for the challenge: how many chemicals do I think there are in the preparation – and for a further bonus point, which chemical did I get wrong?

((4S,5S)-5-Ethynyl-2,2-dimethyl-1,3-dioxolan-4-yl)methanol (14)

To a stirring mixture of 13 (10.0 g, 62.5 mmol) and anhydrous K2CO3 (11.37 g, 81.25 mmol) in dry MeOH (240 mL) at 65 °C was added a solution of Bestmann–Ohira reagent (15.6 g, 81.25 mmol) in dry MeOH (80 mL) dropwise over a period of 6 h under an argon atmosphere. After neutralization with acetic acid, the solvent was removed in vacuo, water was added and the mixture extracted with ethyl acetate (2 × 100 mL). The combined organic extracts were dried over anhydrous Na2SO4, concentrated under reduced pressure and purified by column chromatography (pet. ether–ethyl acetate, 4 : 1) to obtain 14 (6.82 g, 70%) as a colorless liquid. [α]27D -8.6 (c 1.0, MeOH); anal. calcd for C8H12O3: C, 61.52; H, 7.74; found: C, 61.79; H, 7.84; IR (neat) ν max/cm-1, 3452, 3284, 2121, 848, 665; 1H NMR (200 MHz, CDCl3, D2O exchange), δ 1.42 (s, 3H), 1.48 (s, 3H), 2.53 (d, 1H, J = 2.15 Hz), 3.64 (dd, 1H, J = 12.25, 3.67 Hz), 3.87 (dd, 1H, J = 12.25, 3.03 Hz), 4.16 (ddd, 1H, J = 7.58, 3.67, 3.03 Hz), 4.56 (dd, 1H, J = 7.57, 2.15 Hz).