Depth-First: Tag inchi

A Simple and Portable Ruby Interface to InChI - Part 2: Silencing Console Output

Rich Apodaca — Fri, 30 May 2008 10:04:00 -0400

The previous article in this series described a simple and portable method for interfacing Ruby to the cInChI-1 binary. One disadvantage was noisy console output. This article offers a minor modification to disable it.

The Code

module InChI
  def inchi_for molfile
    output = %x[echo "#{molfile}" | cInChI-1 -STDIO 2>/dev/null]

    output.eql?("") ? "" : output.split(/\n/)[1]
  end
end

Here, we're taking advantage of the ability to redirect certain output streams to /dev/null.

Testing the Code

Saving the above in a file called inchi.rb, we can test it from IRB. To make things interesting, let's pull a molfile from Chempedia:

$ irb
irb(main):001:0> require 'open-uri'
=> true
irb(main):002:0> require 'inchi'
=> true
irb(main):003:0> include InChI
=> Object
irb(main):004:0> open 'http://chempedia.com/compounds/83490.mol' do |f|
irb(main):005:1*   puts inchi_for(f.read)
irb(main):006:1> end
InChI=1/C15H15NO3S/c17-14(16-18)11-20(19)15(12-7-3-1-4-8-12)13-9-5-2-6-10-13/h1-10,15,18H,11H2,(H,16,17)
=> nil

We should be able to run this code unmodified on any UNIX-like system in which the cInChI-1 binary is on the path. And of course we could take this one step further by allowing command line options to be passed in as parameters to the inchi_for method.

Simplicity has its advantages.

A Simple and Portable Ruby Interface to InChI

Rich Apodaca — Thu, 29 May 2008 12:12:00 -0400

Although the InChI software itself is written in C, it can still be used via Ruby. Rino offers one implementation of a Ruby InChI interface that makes use of a C extension. This article describes a more concise and portable solution.

The Code

The following code will accept a String encoding a molfile and return either its InChI, or an empty String if no InChI could be found:

module InChI
  def inchi_for molfile
    output = %x[echo "#{molfile}" | cInChI-1 -STDIO]

    output.eql?("") ? "" : output.split(/\n/)[1]
  end
end

This code takes advantage of Ruby's built-in support for Command Expansion.

Testing the Code

The code below tests the library:

require 'inchi'
include InChI

molfile =
"http://chempedia.com/compounds/106.mol
  -OEChem-03010811072D

 12 12  0     0  0  0  0  0  0999 V2000
    2.8660    1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0000    0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7321    0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0000   -0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7321   -0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660   -1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660    1.6200    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4631    0.8100    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690    0.8100    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4631   -0.8100    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690   -0.8100    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660   -1.6200    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  7  1  0  0  0  0
  2  4  1  0  0  0  0
  2  8  1  0  0  0  0
  3  5  2  0  0  0  0
  3  9  1  0  0  0  0
  4  6  2  0  0  0  0
  4 10  1  0  0  0  0
  5  6  1  0  0  0  0
  5 11  1  0  0  0  0
  6 12  1  0  0  0  0
M  END"

puts "Found InChI: #{inchi_for(molfile)}"

We can run the test by saving it in a file called test.rb and executing it:

$ ruby test.rb
InChI version 1, Software version 1.02-beta August 2007
Log file not specified. Using standard error output.
Input file not specified. Using standard input.
Output file not specified. Using standard output.
Options: Mobile H Perception ON
Isotopic ON, Absolute Stereo ON
Omit undefined/unknown stereogenic centers and bonds
Full Aux. info
Input format: MOLfile
Output format: Plain text
Timeout per structure: 60.000 sec; Up to 1024 atoms per structure
End of file detected after structure #1.
Finished processing 1 structure: 0 errors, processing time 0:00:00.00
Found InChI: InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H

Prerequisites

The above approach only requires that it be run on a UNIX-like system, and that a copy of the InChI library be present on your path.

Advantages

The approach described here offers some important advantages over Rino:

It works without modification on both the Matz Ruby Interpreter (C-Ruby) and JRuby.
It neither creates nor uses files.

Disadvantages

This approach creates a lot of noisy log output to the console. There must be a way to suppress it, but so far I haven't found out how.

Conclusions

Using Ruby's support for Command Expansions has enabled the creation of a concise and portable Ruby interface to the InChI toolkit. Similar principles would apply to any Unix command-line binary, including for example, Open Babel.

From C Source Code to Platform-Independent Executable Jarfile: Using NestedVM to Build JInChI

Rich Apodaca — Mon, 03 Dec 2007 08:42:00 -0500

A recent series of articles discussed in some detail the process of compiling source code written in C and C++ to pure Java bytecode with NestedVM. But the full conversion process, starting with source and finishing with an executable jarfile, has to my knowledge never been documented. This article uses the InChI toolkit to illustrate the complete process for converting a real-world C source distribution into a platform-independent, executable jarfile that can be run with any modern Java Virtual Machine (JVM).

About InChI

The previous article in this series introduced JInChI, the first and only pure Java implementation of the IUPAC/NIST InChI toolkit. This toolkit is used to convert molecular connection tables encoded in MDL's SD File format into ASCII character strings called 'InChIs' that have a variety of applications in the field of cheminformatics. Although an excellent JNI-InChI interface is available, JNI won't be a viable option in every situation. Our pure Java implementation nicely complements the JNI-InChI library.

In this tutorial, we'll build version 1.0.2b of the InChI toolkit. This version, among other features, supports the generation of InChI Keys.

Prerequisites

This article assumes you've already installed NestedVM on your system. Building NestedVM required the installation of many dependencies and was a fairly lengthy, but straightforward, process on my Linux system.

Step 1: Prepare Your Environment

Before building anything, we'll need to set up our environment. NestedVM makes this simple:

$ cd /your/path/to/nestedvm/
$ source env.sh

Next, let's create a directory to hold the various components we'll need during the build process:

$ cd /your/projects/directory
$ mkdir jinchi
$ cd jinchi

Next, we'll download and unpack the InChI source distribution:

$ wget http://www.iupac.org/inchi/download/inchi102b.zip
$ unzip inchi102b.zip

Step 2: Cross-Compile InChI

We now have everything we need to begin cross-compiling. NestedVM uses a two-part process in which source code is first cross-compiled to a MIPS binary. That MIPS binary is then translated to Java bytecode. We start by invoking make with the appropriate cross-compiler flags (which I found by looking through the InChI Makefile):

$ make C_COMPILER=mips-unknown-elf-gcc LINKER=mips-unknown-elf-gcc

This creates a MIPS binary (cInChI-1). Unless you're running on a MIPS machine, this binary won't be executable.

$ ./cInChI-1
bash: ./cInChI-1: cannot execute binary file

We can now translate the MIPS binary into pure Java bytecode:

$ java org.ibex.nestedvm.Compiler -outfile JInChI.class JInChI cInChI-1

This produces a Java class file:

$ ll JInChI.class
-rw-r--r-- 1 rich rich 4372362 Nov 30 08:27 JInChI.class

We can verify that the classfile has been compiled correctly by running it:

$ java JInChI
InChI ver 1, Software version 1.02-beta August 2007.

Usage:
cInChI-1 inputFile [outputFile [logFile [problemFile]]] [-option[ -option...]]

Options:
  SNon        Exclude stereo (Default: Include Absolute stereo)
  SRel        Relative stereo

-- truncated --

We have now done something truly remarkable: we've taken a standard C source code distribution and converted it into an executable Java class file. It runs, but only because the NestedVM runtime is on our classpath (thanks to the source command we used at the beginning of the process).

What we really want is a self-contained, executable jarfile that can be run, unmodified, on any system with Java installed.

Step 3: Build the JInChI Jarfile

We begin by moving up the the root directory of our jinchi project, creating a new directory to hold our java-specific files (the JInChI.class file and the NestedVM runtime), and copying them into it:

$ cd ../../..
$ mkdir jinchi-1.0.2b.1
$ mv InChI-1-software-1-02-beta/cInChI/gcc_makefile/JInChI.class jinchi-1.0.2b.1/
$ cp -r /your/path/to/nestedvm/build/org/ jinchi-1.0.2b.1

An executable jarfile generally needs a manifest to point to the main execution class. One way to do that is to first create a manifest:

$ vi jinchi-1.0.2b.1/MANIFEST.MF

It's essential that this file end with a newline.

$ cat jinchi-1.0.2b.1/MANIFEST.MF
Main-Class: JInChI

With everything in place, we can create the jarfile:

$ cd jinchi-1.0.2b.1/
$ ls
JInChI.class  MANIFEST.MF  org/
$ jar -cfm jinchi-1.0.2b.1.jar MANIFEST.MF *
$ ls
jinchi-1.0.2b.1.jar  JInChI.class  MANIFEST.MF  org/

We've successfully converted standard C source code into a platform independent executable jarfile. But does it work?

Step 4: Test JInChI

We can confirm that the process has worked by running the jarfile (you should do this in a new shell session to verify that the jarfile is indeed independent of your NestedVM installation).

$ java -jar jinchi-1.0.2b.1.jar
InChI ver 1, Software version 1.02-beta August 2007.

Usage:
cInChI-1 inputFile [outputFile [logFile [problemFile]]] [-option[ -option...]]

Options:
  SNon        Exclude stereo (Default: Include Absolute stereo)
  SRel        Relative stereo

That's all there is to it! Your shiny new jarfile can be run on any system with a JVM installed. The one created here has been successfully tested on Mac OS X, Linux, and Windows.

If you'd prefer to download the JInChI jarfile, it can be obtained from SourceForge.

Conclusions

This article has illustrated in detail the process of converting a standard C source distribution into a platform-independent executable jarfile. Given the appropriate MIPS cross-compiler (many of which come with the NestedVM distribution), the same process can be repeated with code written in a variety of other languages.

You may be wondering what kind of performance hit you can expect with the approach outlined here. After all, we'd be comparing a native binary to something running on top of two abstraction layers: the NestedVM runtime and a JVM. It's not as bad as you might think, but that's a story for another time.

Image Credit: smithco

JInChI: Run InChI Anywhere Java Runs

Rich Apodaca — Wed, 31 Oct 2007 10:59:00 -0400

Regardless of your views on Java the Programming Language, Java the Platform has a lot going for it. The ability to run the same executable on any system with a Java Virtual Machine (JVM), without recompilation, is a significant advantage in today's heterogeneous computing environment. Combine that with Java the Platform's battle-tested security model, stability and performance, and you have some compelling reasons to actually prefer that code execute on a JVM rather than bare metal.

Cheminformatics has many useful libraries, legacy and otherwise, that don't yet run on a JVM. Many of these can trace their roots back to the 1960s and 1970s and FORTRAN; others were written in C or C++ more recently. What they all have in common is that they're compiled to native binaries rather than Java bytecode.

Wouldn't it be great if this software could be easily compiled to Java bytecode instead?

A recent Depth-First article described how the InChI toolkit, an open source C library distributed by IUPAC, was successfully compiled to a Java classfile with the remarkable NestedVM library. This article describes the creation and use of a new platform-independent jarfile that runs the InChI program.

The procedure was not difficult. The two files previously released ( JInChI.class and nestedvm.jar) were combined into a single executable jarfile with a Manifest pointing to the JInChI classfile as the Main class.

The full cInChI jarfile can be downloaded here.

The jinchi.jar file can be tested from the command line:

$ java -jar jinchi.jar
InChI ver 1, Software version 1.01 release 07/21/2006.

Usage:
cInChI-1 inputFile [outputFile [logFile [problemFile]]] [-option[ -option...]]

Options:
  SNon        Exclude stereo (Default: Include Absolute stereo)
  SRel        Relative stereo
  SRac        Racemic stereo

[truncated]

If we wanted to process a molfile representing toluene, we'd use something like the following:

$ java -jar jinchi.jar test/toluene.mol
InChI version 1, Software version 1.01 release 07/21/2006
Opened log file 'test/toluene.mol.log'
Opened input file 'test/toluene.mol'
Opened output file 'test/toluene.mol.txt'
Opened problem file 'test/toluene.mol.prb'
Options: Mobile H Perception ON
Isotopic ON, Absolute Stereo ON
Omit undefined/unknown stereogenic centers and bonds
Full Aux. info
Input format: MOLfile
Output format: Plain text
Timeout per structure: 60.000 sec; Up to 1024 atoms per structure
End of file detected after structure #1.
Finished processing 1 structure: 0 errors, processing time 0:00:00.00

This command would produce the following output file, just like the cInChI program:

$ cat test/toluene.mol.txt
* Input_File: "test/toluene.mol"
Structure: 1
InChI=1/C7H8/c1-7-5-3-2-4-6-7/h2-6H,1H3
AuxInfo=1/0/N:1,2,3,4,5,6,7/E:(3,4)(5,6)/rA:7nCCCCCCC/rB:;d2;s2;s3;d4;s1d5s6;/rC:3.6373,2.8,0;0,.7,0;0,2.1,0;1.2124,0,0;1.2124,2.8,0;2.4249,.7,0;2.4249,2.1,0;

We can also convert InChIs into molfiles (command line options work the same as in cInChI):

$ java -jar jinchi.jar test/toluene.mol.txt -OutputSDF
InChI version 1, Software version 1.01 release 07/21/2006
Opened log file 'test/toluene.mol.txt.log'
Opened input file 'test/toluene.mol.txt'
Opened output file 'test/toluene.mol.txt.txt'
Opened problem file 'test/toluene.mol.txt.prb'
Options: Output SDfile only
End of file detected after structure #1.
Finished processing 1 structure: 0 errors, processing time 0:00:00.00

In this case the output is:

$ cat test/toluene.mol.txt.txt
Structure #1
  InChI v1 SDfile Output

  7  7  0  0  0  0  0  0  0  0  1 V2000
    3.6373    2.8000    0.0000 C   0  0  0     0  0  0  0  0  0
    0.0000    0.7000    0.0000 C   0  0  0     0  0  0  0  0  0
    0.0000    2.1000    0.0000 C   0  0  0     0  0  0  0  0  0
    1.2124    0.0000    0.0000 C   0  0  0     0  0  0  0  0  0
    1.2124    2.8000    0.0000 C   0  0  0     0  0  0  0  0  0
    2.4249    0.7000    0.0000 C   0  0  0     0  0  0  0  0  0
    2.4249    2.1000    0.0000 C   0  0  0     0  0  0  0  0  0
  1  7  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  2  0  0  0  0
  5  7  2  0  0  0  0
  6  7  1  0  0  0  0
M  END
$$$$

Similar tests worked on both Linux and Windows using the same jarfile.

There are still some issues to be addressed with this approach. For example, various reports indicate that NestedVM code runs about four to ten times slower than native execution. Benchmarking may be useful at this point.

Another issue is how to go about making a Java InChI library with NestedVM. If you decompile the jinchi.jar file, you'll find that the JInChI.class file is a large and complex beast in which almost all methods are named as hex numbers. It may be possible to create a library by renaming certain methods and breaking the code into smaller classfiles, but the NestedVM documentation seems sparse on this subject.

Despite these difficulties, this article demonstrates the power of NestedVM and describes the first (and currently only) example of a 100% Java InChI implementation.

Image Credit: smithco

Compiling the InChI Toolkit to Pure Java Bytecode with NestedVM

Rich Apodaca — Mon, 29 Oct 2007 11:13:00 -0400

Some time ago, a Depth-First article discussed some methods for compiling C to Java bytecode. Many factors make this approach attractive compared to the JNI approach. Some of them include security, portability, and use within applets. Unfortunately, none of the approaches discussed in the earlier article seemed particularly general.

Many cheminformatics libraries are written in C and C++; being able to reliably and automatically port them to Java could potentially save a great deal of effort.

One of the more important cheminformatics C libraries written in recent years is the InChI toolkit. With no pure Java port of this library, JNI is the only way to use InChI with Java. In some situations, this approach is either overly complicated or simply unacceptable.

All of this leaves us with the question: how can the InChI toolkit be converted into a pure Java library without writing any new code?

A partial answer to this question came from Evan Jones, who suggested I look at NestedVM. From the website:

NestedVM provides binary translation for Java Bytecode. This is done by having GCC compile to a MIPS binary which is then translated to a Java class file. Hence any application written in C, C++, Fortran, or any other language supported by GCC can be run in 100% pure Java with no source changes.

And it worked!

NestedVM was successfully used compile the InChI-API distribution to a Java class file that executed on nothing more than a standard JVM -- and with no JNI code. The InChI classfile and nestedvm runtime jarfile can be downloaded from SourceForge. Future articles in this series will describe the compilation, installation, and use of NestedVM, as well as the Java class file that it produced.

Image Credit: pmorgan

Easily Convert IUPAC Nomenclature to SMILES, InChI, or Molfile with Rubidium

Rich Apodaca — Fri, 19 Oct 2007 10:05:00 -0400

A recent article introduced Rubidium, a cheminformatics toolkit written in Ruby. One of Ruby's strengths is the speed with which it enables disparate pieces of code to be glued together - even if they're written in different programming languages. In this article, we'll see how Rubidium can be extended to provide support for converting IUPAC nomenclature into SMILES, InChI, or Molfile formats.

About Rubidium

Rubidium is a cheminformatics toolkit written in Ruby. Rubidium is currently configured to run on JRuby, although future versions may also work with Matz' Ruby Implementation) (MRI) via Ruby Java Bridge.

Rubidium will eventually be packaged as a RubyGem and hosted on RubyForge. For now, the toolkit consists of a running library that will updated and documented on this blog.

The Library

The library extends the CDK module presented in the previous article in this series. The main change is the addition of an IUPACReader class, based on Peter Corbett's excellent OPSIN library:

class IUPACReader
  import 'java.io.StringReader'
  import 'uk.ac.cam.ch.wwmm.opsin.NameToStructure'
  import 'org.openscience.cdk.io.CMLReader'
  import 'org.openscience.cdk.ChemFile'

  def initialize
    @iupac_reader = NameToStructure.new
    @cml_reader = CMLReader.new
  end

  def read name
    cml = @iupac_reader.parse_to_cml(name)

    raise "Could not parse '#{name}'." unless cml

    @cml_reader.set_reader StringReader.new(cml.to_xml)

    chem_file = @cml_reader.read ChemFile.new

    chem_file.chem_sequence(0).chem_model(0).molecule_set.molecule(0)
  end
end

Using this additional functionality requires nothing more than copying the OPSIN jarfile into the lib directory of your JRuby installation. You'll also need to place the CDK jarfile in this directory if you haven't done so already.

The complete Rubidium library can be downloaded here.

A Test

We can test Rubidium's IUPAC nomenclature parsing abilities with jirb. For example, to convert from name to SMILES:

$ jirb
irb(main):001:0> require 'cdk'
=> true
irb(main):002:0> c=CDK::Conversion.new
=> #<CDK::Conversion:0x46ca65 ... >
irb(main):003:0> c.set_formats 'iupac', 'smi'
=> "smi"
irb(main):004:0> c.convert '1,4-dichlorobenzene'
=> "C=1C=C(C=CC=1Cl)Cl"

To convert from name to InChI (in the same jirb session):

irb(main):005:0> c.set_out_format 'inchi'
=> "inchi"
irb(main):006:0> c.convert '1,4-dichlorobenzene'
=> "InChI=1/C6H4Cl2/c7-5-1-2-6(8)4-3-5/h1-4H"

And to convert from name to Molfile (also in the same jirb session):

irb(main):007:0> c.set_out_format 'mol'
=> "mol"
irb(main):008:0> c.convert '1,4-dichlorobenzene'
=> "\n  CDK    10/19/07,7:59\n\n  8  8  0  0  0  0  0  0  0  0999 V2000\n    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000    0.0000    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000    0.0000    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  2  0  0  0  0 \n  2  3  1  0  0  0  0 \n  3  4  2  0  0  0  0 \n  4  5  1  0  0  0  0 \n  5  6  2  0  0  0  0 \n  6  1  1  0  0  0  0 \n  7  1  1  0  0  0  0 \n  8  4  1  0  0  0  0 \nM  END\n"

Conclusions

By re-using a simple conversion API together with another Java library, we've given Rubidium the ability to translate IUPAC nomenclature into other molecular languages. The additional code was both easy to write and easy to test. Future articles will discuss the packaging, distribution, and further elaboration of Rubidium.

JRuby for Cheminformatics: Reading and Writing InChIs Via the Java Native Interface

Rich Apodaca — Wed, 10 Oct 2007 08:21:00 -0400

The increased use of the InChI identifier is making the reading and writing of InChIs a standard cheminformatics capability. Recent articles have discussed the advantages of JRuby for cheminformatics. One disadvantage of JRuby is that code written in C can't be directly used. The presents a potential problem for libraries, such as the InChI toolkit, that are written in C. Fortunately, the solution is simple. Today's tutorial will demonstrate how InChIs can be both read and written using the C-InChI toolkit via JRuby and the excellent JNI-InChI library.

About JNI-InChI

The JNI-InChI library, written by Jim Downing and Sam Adams, wraps the C InChI toolkit in a Java Native Interface. This low-level toolkit is suitable for building more complex software, but lacks many features present in the C InChI toolkit. For example, JNI-InChI doesn't directly interconvert SMILES or molfile with InChI. For that you'd need to build a support library. If you're building a toolkit from scratch, this lightweight approach can be a significant advantage.

The JNI-InChI binary distribution jarfile includes the compiled native InChI library. In this sense it's virtually indistinguishable from any other Java library. This simplified packaging makes it exceptionally easy to use JNI-InChI from JRuby, as we'll see below.

Installation

JRuby can be installed as described previously. To install the JNI-InChI library for JRuby, simply copy the current release jarfile into the lib directory of your JRuby installation. That's all there is to it.

A Simple Library

We can now write a simple library to read InChIs via JRuby:

require 'java'

include_class 'net.sf.jniinchi.JniInchiInput'
include_class 'net.sf.jniinchi.JniInchiInputInchi'
include_class 'net.sf.jniinchi.JniInchiWrapper'

module IUPAC
  def read_inchi inchi
    input = JniInchiInputInchi.new inchi

    JniInchiWrapper.getStructureFromInchi input
  end
end

Testing the Library

By saving the above library to a file called iupac.rb, we can parse InChIs via JRuby:

$ jirb
irb(main):001:0> require 'iupac'
=> true
irb(main):002:0> include IUPAC
=> Object
irb(main):003:0> output = read_inchi 'InChI=1/C14H10/c1-3-7-13-11(5-1)9-10-12-6-2-4-8-14(12)13/h1-10H'
=> #
irb(main):004:0> output.num_atoms
=> 14
irb(main):005:0> output.num_bonds
=> 16

Writing InChIs

Because JNI-InChI is a low-level toolkit, writing InChIs is feasible, but not trivial. We must first construct a representation, and then get the InChI for it. For example, we could get the InChI for methane as follows:

$ jirb
irb(main):001:0> require 'java'
=> true
irb(main):002:0> include_class 'net.sf.jniinchi.JniInchiInput'
=> ["net.sf.jniinchi.JniInchiInput"]
irb(main):003:0> include_class 'net.sf.jniinchi.JniInchiAtom'
=> ["net.sf.jniinchi.JniInchiAtom"]
irb(main):004:0> include_class 'net.sf.jniinchi.JniInchiWrapper'
=> ["net.sf.jniinchi.JniInchiWrapper"]
irb(main):005:0> input = JniInchiInput.new
=> #
irb(main):006:0> a1 = input.add_atom JniInchiAtom.new(0,0,0, "C")
=> #
irb(main):007:0> a1.set_implicit_h(4)
=> nil
irb(main):008:0> output = JniInchiWrapper.get_inchi input
=> #
irb(main):009:0> output.get_inchi
=> "InChI=1/CH4/h1H4"

Fortunately, we don't have to work that hard. The Chemistry Development Kit, through JNI-InChI, supports reading and writing of InChIs via a variety of molecular languages, including SMILES and molfile. More on that later, though.

Conclusions

Provided that a Java Native Interface exists for a C library, it can be used from JRuby. Future articles will discuss the use of other cheminformatics libraries written in either C or C++ from JRuby, and their integration with pure Java and Ruby libraries.

Streamlining Cheminformatics on the Web: Let InChI Do the Heavy Lifting and Get Some REST

Rich Apodaca — Mon, 01 Oct 2007 10:53:00 -0400

A recent Depth-First article discussed the advantages of minimal Web APIs in Cheminformatics. Recently, Antony Williams unveiled some simplified ChemSpider URL schemes, mainly from the perspective of enabling Google indexing. However, it's possible to take this scheme much, much further. Here I present a proposal for radically simplifying (and unifying) the development of cheminformatics Web APIs and the software that interacts with them.

The New ChemSpider URLs

ChemSpider now has several new kinds of URLs. For the purposes of this article, the most interesting of these are of the format:

These URLs may seem unremarkable, but there's much more than meets the eye. They let anonymous developers query ChemSpider about specific substances - without needing to know much at all about how ChemSpider itself works. Goodbye API. Goodbye API support. Goodbye API documentation. Goodbye angle brackets. Hello to getting stuff done. It's all very RESTful. Well, at least it could be that way with some minor modification.

Some Recommendations

ChemSpider hasn't quite reached that place where the API just disappears. The problem is that the ChemSpider URLs listed above point to query results pages, not compound summary pages. Were these URLs to redirect to a summary page, we could construct the following URLs to extract ChemSpider resources (I've replaced the '=' sign with a '/' for simplicity):

.../InChIKey/DEIYFTQMQPDXOT-RERXVCSDCZ Get all resources for the molecule identified by the given InChIKey - i.e., "Compound summary page"
.../InChIKey/DEIYFTQMQPDXOT-RERXVCSDCZ/molfile.mol Get the molfile for the molecule identified by the given InChIKey
.../InChIKey/DEIYFTQMQPDXOT-RERXVCSDCZ/small_image.png Get the small image for the molecule indentified by the given InChIKey.
.../InChIKey/DEIYFTQMQPDXOT-RERXVCSDCZ/large_image.png Get the large image for the molecule identified by the given InChIKey.
.../InChIKey/DEIYFTQMQPDXOT-RERXVCSDCZ/citations.xml Get the list of citations for the molecule identified by the given InchIKey, in XML format.

Jane, a developer building Web applications on top of this new ChemSpider API, would immediately notice that things just work. Let's say her online database stores IC₅₀s at the dopamine D₂ receptor. On the summary page for each molecule, she wants to link out to the ChemSpider compound summary page, if available. She would simply construct the InChIKey on her server, build the needed ChemSpider URL and GET it. An HTTP 404 would indicate no molecule with that Key exists on ChemSpider and so no link would be shown. An HTTP 200 would indicate ChemSpider has the molecule, and so the link would appear.

Conclusions

It would be interesting enough if ChemSpider adopted a system like that described here. But the real power of this approach would emerge if multiple Web services were to adopt it. By following a simple set of conventions, these services would enable third party developers to elegantly mashup all manner of cheminformatics resources into applications unimaginable today.

Technically, there's nothing that prevents this system from being implemented on every free chemistry database in existence today. However, doing so would transfer a significant degree of control from service operators to third-party developers. Not all providers will be comfortable with that idea.

Cheminformatics Web service providers need to carefully consider whether they're trying to develop a platform or an integrated service. As history has shown, the strategies, and upside potential, for each approach can differ dramatically.

InChI for Newbies

Rich Apodaca — Thu, 27 Sep 2007 08:39:00 -0400

The IUPAC International Chemical Indentifier (InChI) provides an open system for converting molecular representations into strings of text. Because text processing is one of the things computers do very well, InChI serves as an important link between chemistry and computer science.

Unfortunately, the InChI documentation is rather scattered. To help remedy this problem, I have selected some links to Depth-First articles discussing InChI. These articles span a wide range of perspectives. They have been divided into categories for easier navigation, although many contain information that any user of InChI could find useful.

InChI in Context

Interconvert Almost Any SMILES and InChI with Ruby Open Babel The risk-free way to test InChI.
Eleven Qualities of the Perfect Line Notation for the Web Whatever limitations it may have, designing InChI was no easy task.
How to Find Chemical Information on the Internet: Why Open Source, Open Access and Open Data Matter InChI is also part of the process.
Thirty-Two Free Chemistry Databases Many of them use InChI already.
The Automatic Encoding of Chemical Structures Why InChI needs to be heard but not seen.
Debabelization Why InChI probably isn't the last line notation you'll ever need.
107 Years of Line Formula Notations 1861-1968 InChI is the latest in a long ...ummm... line of indexing systems.
Everything Old is New Again: Wiswesser Line Notation (WLN) The early roots of InChI.

Hacking InChI

Hacking ChemSpider: Query by SMILES and InChI with Ruby The easy way to mash-up ChemSpider.
Decoding InChIs: An Introduction to Ninja Putting InChI together again.
From InChI to Image with Ruby Open Babel and Ruby CDK Inscrutable InChIs got you down? Visualize them in color!
Decoding InChIs with Rino Instructive, but no longer recommended.
Taking a SWIG of InChI It may leave a doozy of a hangover, but it'll cure what ails ya.
InChI Canonization Algorithm More detail than you probably wanted to know.

InChI and the Web

My InChI Runneth Over Why InChI makes grown Web designers cry.
Hashing InChIs One-way ticket to Web harmony.
Why the Web Isn't Ready for Chemistry Still!?
InChI Spam Remember when Spam was funny?
The Chemically-Aware Web: Are We There Yet? Google and InChI don't always mix.

InChIMatic

Google for Molecules with InChIMatic Title says it all.
Building the Chemically-Aware Web: TotallySynthetic and InChIMatic Hey, this thing is useful for something!
Googling for Molecules with InChIMatic and Firefly A comfortable editor for structure searching the Web.
Open Notebook Science Using InChIMatic One way to use InChI in Open Science
Anatomy of a Cheminformatics Web Application: InChIMatic It's never been so easy to build software for chemists.

Please feel free to link to your favorite InChI resource in the comments section.

Image Generator Credit: txt2pic.com

Building the Chemically-Aware Web: TotallySynthetic and InChIMatic

Rich Apodaca — Mon, 24 Sep 2007 10:54:00 -0400

Recent D-F articles have discussed InChIMatic, a Web application that lets you search the Web for chemical structures by simply drawing them. InChIMatic takes advantage of InChI, a system for representing molecular structures as a strings of text, and Google, which indexes these text strings. In this article, I'll show InChIMatic in action as it quickly finds a molecule discussed in a review of Overman's Sarain A synthesis appearing in Paul Docherty's TotallySynthetic blog.

You Can Skip this Step

The TotallySynthetic review lists three InChIs at the bottom, but which structures, out of the many discussed, do these represent? We need to know so that we can enter these structures into InChIMatic. This is, of course a step only needed because we're testing the system, not because we're using the system the way it was designed to be used.

A recent D-F article discussed a method for converting InChIs into 2D structures using Ruby. It has the advantage of being easily adaptable to building chemically-aware Web spiders. And it's 100% Open Source.

Running this library over TotallySynthetic's InChIs yields the three images above. Notice, we have some problems. The first and third images lack stereochemistry. The second has a trans- double bond instead of the cis- stereochemistry encoded by the InChI. There are good reasons for each of these problems, which I hope to address in later articles. For now, it's sufficient that we can clearly make the connection between the TotallySynthetic InChIs and structures in the Sarain A review.

Run the Search

We can test this system by pointing our browser to inchimatic.com. Entering one of the structures and clicking "Search" takes us directly to a link for the TotallySynthetic site, courtesy of Google. Unfortunately, the link doesn't currently point to the article itself. This issue may resolve itself as the Googlebot continues to index the TotallySynthetic site.

A Technical Note

If you spend any time working with InChIs, you'll notice that they're very long. So long, in fact, that they break many Web page layouts. There have been many attempts to fix the long-InChI problem, but Paul may have found the answer by trying the simplest thing that could possibly work.

If you inspect the HTML source for the TotallySynthetic article, you'll find that Paul has inserted hard returns (br elements) to manually break his InChIs, including ~~the one we just located with InChIMatic (first in the list)~~ the first and last structures above, both of which can be found with InChIMatic:

<p><small>InChI=1/C29H33NO4Si/c1-5-32-28(31)26-25(34-27(30-26)22-15-9-6-10-16-22)21-33-35(29(2,3)4,23-17-11-7-12-18-23)24-19-13-8-14-20-24<br />
/h6-20,25-26H,5,21H2,1-4H3/t25-,26-/m0/s1 InChI=1/C18H25NO6S/c1-14-9-11-15(12-10-14)26(22,23)19(17(21)25-18(2,3)4)13-7-6-8-16(20)24-5/h6,8-12H,7,13H2,1-5H3/b8-6- InChI=1/C47H58N2O10SSi/c1-10-56-43(51)47(36(32-41(50)55-9)30-31-49(44(52)59-45(3,4)5)60(53,54)37-28-26-34(2)27-29-37)40<br />

(58-42(48-47)35-20-14-11-15-21-35)33-57-61(46(6,7)8,38-22-16-12-17-23-38)39-24-18-13-19-25-39/h11-29,36,40H,10,30-33H2,1-9H3<br />
/t36-,40-,47-/m0/s1</small>
</p>

In other words, fixing the long InChI/Google indexing problem may be as simple as just inserting br elements when needed. More on this later, though.

Conclusions

This article has shown a working demonstration that uses free tools to build self-organizing, highly distributed, searchable chemical databases. Although the system is far from perfect, it does provide a glimpse at what can be done right now with relatively little effort. Starting with this basic idea, we can begin to think about a variety of fast, free, user-friendly services that make finding molecules on the Web, and publishing their wherabouts, as easy as using Google and WordPress. But that's a story for another time.