Jerome's Blog Space

Mychem 0.8.1: more than just a bug fix

2010-09-17T00:12:00.000-07:00

Mychem 0.8.1 has been released on 2010-09-07.

This version fix an important bug. All functions using serialized obmol type were impacted. The problem has been resolved by using the solution published by the pgchem project.

Mychem is now fully usable with MySQL 5.0 and 5.1. It should also be working with MySQL 4.1, but it has not been tested.

The bug list is now empty. I'm waiting for new providers!

chem-bla-ics: Warren DeLano and the future of PyMOL

2010-05-04T03:50:00.000-07:00

chem-bla-ics: Warren DeLano and the future of PyMOL

The version 0.7.0 of Mychem has been released

2009-10-14T10:05:00.000-07:00

The version 0.7.0 of Mychem has been released on 2009-09-30.

This release represents a major bug-fix release and is a stable upgrade, strongly recommended for all users of Mychem.
While there may not be many new functions, several crashes and other bugs have been fixed since 0.6.0. The main changes are:

Added the mol2_to_molecule() function
Added the molecule_to_mol2() function
Added the inchi_version() function
Added the pdb_to_molecule() function
Added the molecule_to_serializedOBMol() function
Added the serialized OBMol type
The code has been entirely rewritten
The documentation has been updated
Several bug fixes and small feature improvements

The version 2.2.0 of Chemical Structures is released!

2009-07-10T05:06:00.000-07:00

The Chemical Structures Project
The Chemical Structures Project provides a set of molecular structures. Each structure is stored in a CML file, that contains the 3D coordinates and some properties of the chemical compound. The project provides also a HTML interface for accessing the data. Two types of archive are available to download:
- a source archive, that contains only CML files and tools for building the HTML files
- a binary archive, that contains the HTML files and the structure as CML and MOL files.

For a better overview, look at the online version!

The version 2.2.0 of Chemical Structure has been released on 2009-07-08. It is a stable upgrade and provides several enhancement. The main changes and fixes are:

Traditional Chinese translation added
New compound categories:
- Natural products
- Peptides
New structures added:
- 4-Aminobutanoic acid
- Tetrahydropyran
- Pyrrol-2-one
- 1,5-Dihydro-2H-pyrrol-2-one
- Norepinephrine
- Coelenterazine
- D-Luciferin.
- R-Adrenaline
- Aspartame
New version of Jmol included (v11.6.25)
The license and contributions notices have been added to the HTML pages
The build system has been updated. The out-of-source build is now supported.
Compounds and directories are now sorted by alphabetic order
Several bug fixes

As this project is Free Software, it can be freely downloaded from the SourceForge repository!

chem-bla-ics: Bioclipse-JChemPaint

2009-06-20T06:29:00.000-07:00

Les équipes de développement CDK à l'université d'Uppsala et à l'EBI ont travaillé intensivement à la ré-écriture de JChemPaint. La nouvelle version est maintenant stable et devrait être prochainement annoncée officiellement. Ci-dessous, le lien vers l'annonce sur le blog d'Egon Willighagen, l'un des fondateurs du projet CDK :
chem-bla-ics: Bioclipse-JChemPaint

Mychem v0.6.0 is Released !

2009-01-04T07:01:00.000-08:00

The version 0.6.0 of Mychem has been released on 2008-12-30. The main changes are:

New functions:
- bit_fp_or
- bit_fp_count
- bit_fp_and
- molecule_to_inchi
- inchi_to_molecule

Bug fixes

Updated documentation

Molecule type is now MDL Molfile

Works with Open Babel v2.1.1 and v2.2.0.

Two versions of Mychem are now available:

Mychem² - Designed for Open Babel v2.1.1.

Mychem³ - Designed for Open Babel v2.2.0.

Major fix in Mychem

2008-11-10T05:58:00.001-08:00

A major bug has been fixed into Mychem. Fredrik Wallner has posted the main patch.
In some case, the return value of Mychem functions was blank and no error were raised.
Fredrik Wallner has founded that setting a character at the end of the string to '\0' fixes this issue.

The old code:
const char *inputMol = args->args[0];

The new code:
char *inputMol = (char *) malloc(sizeof(char)*(args->lengths[0]+1));
strncpy(inputMol, args->args[0], args->lengths[0]);
inputMol[args->lengths[0]] = 0;

This indicates that the character string given by MySQL as parameter does not contains the '\0' character at the end.

Many thanks to Fredrik Wallner !

The road is now open to go to the next release (0.6.0)

Mychem works on Windows XP

2008-06-14T13:05:00.000-07:00

After some works on the source files and tuning Microsoft Visual Express C++, I'm proud to announce that Mychem is working on Microsoft Windows XP.

The Microsoft Windows version of Mychem will be released soon. The Mychem documentation will also contain a section about the compilation and the installation of Mychem on Windows XP.

New release of Mychem

2008-04-08T04:52:00.000-07:00

The version 0.5.5 of Mychem has been released on 2008-04-08. The main changes are:

New functions:
- strip_salts
- molecule_to_canonical_smiles
- is_2D
- is_3D
- is_chiral
- number_of_rings
- number_of_acceptors
- number_of_donors
- molpsa
- molmr
- mollogp

Bug fixes

Updated documentation

The Tanimoto function has been enhanced by two methods. The first was to store the
fingerprint as binary string. The second was to implement directly the tanimoto algorithm. Now, the Tanimoto coefficient computation of more than 70.000 entries takes less than 0.4 second on my laptop.

At least, a short article has been published about Pgchem and Mychem on Alchem.org.

Some news about Mychem

2008-02-22T15:03:00.000-08:00

Mychem is an Open Source package providing a set of chemical functions for MySQL. These functions are designed to permit you to handle chemical data within a MySQL database.

The last version is v0.4.5 and has been released on 2008-02-18.

There are three major updates in this version:

The build system has been modified (each module is in a directory)
Five function have been added to the property module
The documentation has now a troubleshooting appendix

The development of v0.5.0 has began on 2008-02-19. A new directory has been created for tests. The CTest tool, provided by CMake, is used to perform unit testing. The preliminary tests are working well.

Chemical Structures v2.1

2008-01-15T12:59:00.000-08:00

The Chemical Structures is a complete set of molecular structures. The last version (v2.1) contains over 550 structures of organic compounds and has been released on 2008-01-03. In addition to structural data, each file contains complementary informations, like molecular weight, boiling point, melting point or InChI code.

Each structure can be accessed through a web interface. Structure are displayed with the Jmol applet. These html pages contain also Microformat data (InChI and SMILES).

The project has been translated into 5 languages (english, dutch, french, german and spanish) and new languages can be easily added by editing a single file.

The project is actually used in german and french schools.

New European Initiatives about Open Access

2007-12-05T03:51:00.000-08:00

Open Access (OA) is a free and unrestricted online availability of scientific and scholarly materials (data, literature, ...). The Budapest Open Access Initiative in December 2001 published the first major international statement on OA in February 2002. Since then, OA has become a popular subject. For more details about Open Access, you can read the dedicated wikipedia page.

Recently, two documents have been published:

a document published by the Council of the European Union concerning access to scientific data (starting on page 37):
http://www.consilium.europa.eu/ueDocs/cms_Data/docs/pressData/en/intm/97225.pdf

a document published by the French National Research Agency (ANR) recommends to use the HAL service. The HAL service is one of the Open Archives Initiative projects in France:
http://www.agence-nationale-recherche.fr/actualite/13

Mychem 0.2 is out !

2007-08-17T07:25:00.000-07:00

Mychem is an extension for MySQL that provides chemical functions. It's based on Open Babel 2 and is distributed under GPL-v2 license. In the current Mychem version, the following functions are supported:
- conversion of chemical files (CML, InChI, SMILES, MDL Mol)
- calculation of some chemical properties (formula, molecular weight)

Other functions, like fingerprint generation or tanimoto calculation are available on the SVN trunk:
svn co https://mychem.svn.sourceforge.net/svnroot/mychem/trunk mychemThe package contains also:
- a short documentation (mychem.docbook)
- MychemAdmin, a graphical interface for creating MySQL chemical database (fig. 1)

Figure 1. MychemAdmin, a chemical database creator

CML file reloaded

2007-07-27T00:50:00.000-07:00

Here's an updated version of a valid CML file:


<?xml version="1.0"?>
<molecule xmlns="http://www.xml-cml.org/schema"
xmlns:cml="http://www.xml-cml.org/dict/cml"
xmlns:units="http://www.xml-cml.org/units/units"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns:iupac="http://www.iupac.org" id="CS_oxolane">
<formula concise=" C 4 H 8 O 1 "/>
<identifier convention="iupac:inchi" value="1/C4H8O/c1-2-4-5-3-1/h1-4H2"/>
<name convention="IUPAC">Oxolan</name>
<atomArray>
<atom id="a1" elementType="C" x3="-0.03" y3="1.09" z3="-0.03"/>
<atom id="a2" elementType="C" x3="-1.33" y3="0.28" z3="0.024"/>
<atom id="a3" elementType="O" x3="-1.01" y3="-1.10" z3="-0.13"/>
<atom id="a4" elementType="C" x3="0.39" y3="-1.30" z3="0.02"/>
<atom id="a5" elementType="C" x3="1.09" y3="0.06" z3="-0.04"/>
<atom id="a6" elementType="H" x3="0.04" y3="1.79" z3="0.82"/>
<atom id="a7" elementType="H" x3="-0.00" y3="1.73" z3="-0.94"/>
<atom id="a8" elementType="H" x3="-2.03" y3="0.51" z3="-0.79"/>
<atom id="a9" elementType="H" x3="-1.86" y3="0.39" z3="0.98"/>
<atom id="a10" elementType="H" x3="0.68" y3="-1.98" z3="-0.79"/>
<atom id="a11" elementType="H" x3="0.55" y3="-1.81" z3="0.98"/>
<atom id="a12" elementType="H" x3="1.72" y3="0.15" z3="-0.94"/>
<atom id="a13" elementType="H" x3="1.78" y3="0.20" z3="0.82"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a2 a3" order="1"/>
<bond atomRefs2="a3 a4" order="1"/>
<bond atomRefs2="a4 a5" order="1"/>
<bond atomRefs2="a5 a1" order="1"/>
<bond atomRefs2="a1 a6" order="1"/>
<bond atomRefs2="a1 a7" order="1"/>
<bond atomRefs2="a2 a8" order="1"/>
<bond atomRefs2="a2 a9" order="1"/>
<bond atomRefs2="a4 a10" order="1"/>
<bond atomRefs2="a4 a11" order="1"/>
<bond atomRefs2="a5 a12" order="1"/>
<bond atomRefs2="a5 a13" order="1"/>
</bondArray>
<propertyList>
<property dictRef="cml:molwt" title="Molecular weight">
 <scalar dataType="xsd:double" dictRef="cml:molwt" units="units:g">
 72.11
 </scalar>
</property>
<property dictRef="cml:isotopicwt" title="Monoisotopic mass">
 <scalar dataType="xsd:double" dictRef="cml:monoisotopicwt" units="units:g">
 72.06
 </scalar>
</property>
<property dictRef="cml:mp" title="Melting point">
 <scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:mp" units="units:celsius">
 -108
 </scalar>
</property>
<property dictRef="cml:bp" title="Boiling point">
 <scalar dataType="xsd:double" errorValue="1.0" dictRef="cml:bp" units="units:celsius">
 65
 </scalar>
</property>
</propertyList>
</molecule>

PyMOL 1.0 is released

2007-07-19T01:50:00.000-07:00

The version 1.0 of PyMOL has been released on 2007-06-21.

PyMOL 1.0 executables are available for download by current PyMOL Subscribers. The open-source code for 1.0 is freely available from the b10 branche of the subversion repository:

svn co https://pymol.svn.sourceforge.net/svnroot/pymol/branches/b10/pymol pymol-1.0

Read the entire news on the Alchem Website !

Chemical Structure 2.0 released !

2007-02-27T05:20:00.000-08:00

The news. The version 2.0 of Chemical Structures released today. This release has many new features and fixes:
- the project contains 524 structures
- the build system is based on CMake
- the user interface has been improved by using a new html design
- SMILES string is displayed on the molecule page
- Python scripts are used to generate html pages (instead of XSLT)
- name and formula indexes are available
- many bug fixes
- ...

Screenshot.

Chemical Structure Project. An online version is available on the following website:
http://chem-file.sourceforge.net/

Download. The last version can be downloaded on this page:
https://sourceforge.net/project/showfiles.php?group_id=169897

About Chemical Structures. The Chemical Structures project aims to provide a complete set of molecular structures. The version 2.0 contains over 500 structures of organic compounds. In addition to structural data, each file contains complementary informations, like molecular weight, boiling point, melting point or InChI code.
Chemical Structures is part of the Blue Obelisk Data Repository.

KOpenBabel: a new building block for a chemistry-aware desktop

2007-02-22T23:13:00.000-08:00

KOpenBabel is a graphical interface to Open Babel. It permits the conversion of chemical files (more than 70 file formats are supported).
KOpenBabel is divided in three parts:
- KOpenBabel3: a KDE3 interface
- KOpenBabel4: a KDE4 interface
- QOpenBabel: a Qt4 interface

KOpenBabel3 and QOpenBabel are the most advanced projects. Translastions are available in french and german. All basic features are working. Some works are needed on the translation of KOpenBabel4. Each packages are released under the GNU Public License.

QOpenBabel has been successfully compiled on Microsoft Windows XP.

A screenshot of KOpenBabel3

For furthers informations, visit the project website:
http://kopenbabel.sourceforge.net

A simple CML parser written in Python

2007-01-08T11:00:00.000-08:00

Python is a powerful programming language. It can be easily extended by importing modules.
Below is a simple module for parsing CML file. As you can see, it's really easy to add the support for another tags.


import xml.sax.handler

class CMLHandler(xml.sax.handler.ContentHandler):
  def __init__(self):
      self.id = ""
      self.formula = ""
      self.inIdentifier = False
      self.inchi = "InChI/1="
      self.inInChI = False
      self.inBasic = False
      self.name = ""
      self.inName = False
      self.weight = ""
      self.inWeight = False
      self.mpt = ""
      self.mptSet = False
      self.inMpt = False
      self.bpt = ""
      self.inBpt = False
      self.bptSet = False

  def startElement(self, name, attributes):
      if name == "molecule":
          self.id = attributes["id"]

      if name == "formula":
          self.formula = attributes["concise"]

      if name == "identifier":
          self.inIdentifier = True
          if attributes.has_key("version") and attributes["version"] == "InChI/1":
              self.inInChI = True

      if name == "basic":
          self.inBasic = True

      if name == "name":
          self.inName = True

      if name == "scalar":
          if attributes["dictRef"] == "cml:molwt":
              self.inWeight = True
          elif attributes["dictRef"] == "cml:mpt":
              self.inMpt = True
          elif attributes["dictRef"] == "cml:bpt":
              self.inBpt = True

  def characters(self, data):
      if self.inName:
          self.name += data

      if self.inWeight:
          self.weight += data

      if self.inMpt:
          self.mpt += data

      if self.inBpt:
          self.bpt += data

      if self.inBasic and self.inInChI:
          self.inchi += data

  def endElement(self,name):
      if name == "identifier":
          self.inIdenfitier = False

      if name == "basic":
          self.inBasic = False
          if self.inInChI:
            self.inInChI = False

      if name == "name":
          self.inName = False

      if name == "inchi":
          self.inInChI = False

      if name == "scalar":
          if self.inWeight:
              self.inWeight = False
          elif self.inMpt:
              self.inMpt = False
              self.mptSet = True
          elif self.inBpt:
              self.inBpt = False
              self.bptSet = True

CML, a powerful chemical file type

2006-06-15T06:45:00.000-07:00

CML (Chemical Markup Language) is a chemistry-oriented file format, based on a markup language. It's capable of holding many informations, like chemical structures, chemical properties or reactions.

By using the right style sheet, it's possible to transform or to render easily the information. For example, it's used in the chemical-structures project to generate html datasheet of each compound.

Some papers relevant to this topic have been published.

Here is an example of molecule (D-Alanine) in cml format:

<?xml version="1.0"?>
<molecule xmlns="http://www.xml-cml.org/schema/cml2/core"
   id="D-alanine">
<name convention="IUPAC">(2R)-2-Aminopropanoic acid</name>
<atomArray>
 <atom id="a1" elementType="H" x3="-3.496" y3="1.763" z3="-2.499"/>
 <atom id="a2" elementType="C" x3="-3.687" y3="0.754" z3="-2.120"/>
 <atom id="a3" elementType="N" x3="-2.411" y3="0.067" z3="-1.892"/>
 <atom id="a4" elementType="H" x3="-1.649" y3="0.745" z3="-1.865"/>
 <atom id="a5" elementType="H" x3="-2.208" y3="-0.558" z3="-2.672"/>
 <atom id="a6" elementType="C" x3="-4.450" y3="0.847" z3="-0.803"/>
 <atom id="a7" elementType="H" x3="-5.398" y3="1.380" z3="-0.932"/>
 <atom id="a8" elementType="H" x3="-3.872" y3="1.391" z3="-0.048"/>
 <atom id="a9" elementType="H" x3="-4.682" y3="-0.144" z3="-0.401"/>
 <atom id="a10" elementType="C" x3="-4.453" y3="-0.004" z3="-3.198"/>
 <atom id="a11" elementType="O" x3="-4.044" y3="-0.991" z3="-3.791"/>
 <atom id="a12" elementType="O" x3="-5.639" y3="0.577" z3="-3.501"/>
 <atom id="a13" elementType="H" x3="-6.093" y3="0.057" z3="-4.197"/>
</atomArray>
<bondArray>
 <bond atomRefs2="a1 a2" order="1"/>
 <bond atomRefs2="a2 a3" order="1"/>
 <bond atomRefs2="a2 a6" order="1"/>
 <bond atomRefs2="a2 a10" order="1"/>
 <bond atomRefs2="a3 a4" order="1"/>
 <bond atomRefs2="a3 a5" order="1"/>
 <bond atomRefs2="a6 a7" order="1"/>
 <bond atomRefs2="a6 a8" order="1"/>
 <bond atomRefs2="a6 a9" order="1"/>
 <bond atomRefs2="a10 a11" order="2"/>
 <bond atomRefs2="a10 a12" order="1"/>
 <bond atomRefs2="a12 a13" order="1"/>
</bondArray>
</molecule>