Mychem 0.8.1: more than just a bug fix

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!

The version 0.7.0 of Mychem has been released

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

Mychem v0.6.0 is Released !

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

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)

New release of Mychem

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

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

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.

Mychem 0.2 is out !

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 mychem

The 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

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>

Chemical Structure 2.0 released !

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.