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Updated Aug 11, 2008 by baoilleach
NewInstallationInstructions  
This page describes how to install cinfony on Windows

Installing cinfony on Windows

Cinfony contains the following five wrappers (dependencies listed in parentheses):

  1. pybel - OpenBabel wrapper (Python)
  2. jybel - OpenBabel wrapper (Java, Jython)
  3. cdkjpype - CDK wrapper (Python, Java)
  4. cdkjython - CDK wrapper (Java, Jython)
  5. rdkit - RDKit wrapper (Python)

Installing dependencies

You should install the dependencies first. Depending on what wrappers you wish to use, you should install Python 2.5, Java 1.5 ("JRE 5.0") and/or Jython 2.2. If you are installing Jython, you should install Java first.

Installing cinfony

Here I describe how to download and install the main part of cinfony. I will assume that you want to install cinfony into the folder C:\cinfony. If you install it somewhere else, remember this when you are following the instructions.

  • Download cinfony 0.8, and unzip it, for example, as C:\cinfony. This includes the following libraries so you don't need to download them separately:
    • OpenBabel 2.2.0 - Many contributors including Geoff Hutchison, Tim Vandermeesch and Chris Morley
    • OASA 0.12.1 - Beda Kosata
    • JPype 0.5.3 (Steve Menard) - connects CPython to a JVM
    • Numeric 24.2 (many) - fast linear algebra for Python
    • Pycairo 1.4.12 - Python interface to Cairo (drawing library)
    • AggDraw 1.2a3 (Fredrik Lundh) - Python interface to Agg (drawing library)
    • Python Imaging Library 1.1.6 (Fredrik Lundh) - Image manipulation in Python
  • Download CDK 1.0.3 (many contributors) and place in C:\cinfony\Java
  • Download RDKit May2008 (Greg Landrum) and unzip into C:\cinfony\RDKit
    • If unzipped correctly, there should be a file C:\cinfony\RDKit\README
  • Open the file C:\cinfony\cinfony.bat with Notepad and follow the instructions therein to configure cinfony
  • Add the cinfony directory to the Windows PATH or just copy C:\cinfony\cinfony.bat to a folder that's already on the Windows PATH
    • To add a folder to the Windows PATH, you need to go to Control Panel, System, Advanced, Environment Variables
    • In the top panel (user variables) search for one called PATH
      • If it's there, click Edit and add ;C:\cinfony to the end
      • If it's not there, click New, and enter PATH for the name and C:\cinfony for the value
  • If you are using Jython, open the folder where you installed Jython, and edit the file named registry as follows:
    • Before the line # This is how Jim sets his path etc, add 
      • python.path=C:\\cinfony

Testing cinfony

Open a command prompt anywhere on your computer and type the following 

C:\Documents and Settings\Noel> cinfony
cinfony is configured for user! At the Python 2.5 prompt type:
   from cinfony import pybel, rdkit, cdk
or at the Jython 2.2 prompt type:
   from cinfony import jybel, cdk

C:\Documents and Settings\Noel> python

Python 2.5 (r25:51908, Sep 19 2006, 09:52:17) [MSC v.1310 32 bit (Intel)] on win
32
Type "help", "copyright", "credits" or "license" for more information.
>>> from cinfony import rdkit, cdk, pybel
>>> mol = pybel.readstring("smi", "CC=O")
>>> mol.draw()
>>> print rdkit.Molecule(mol).calcdesc()
{'BertzCT': 10.264662506490405, 'fr_C_O_noCOO': 1, 'Chi4v': 0.0, 'fr_Ar_COO': 0,
 'Chi4n': 0.0, 'SMR_VSA4': 0.0, 'fr_urea': 0, 'fr_para_hydroxylation': 0, 'fr_ba
...
one': 0, 'fr_nitro_arom_nonortho': 0, 'Chi0v': 1.9855985596534889, 'fr_ArN': 0,
'NumRotatableBonds': 0}
>>> cdkmol = cdk.Molecule(mol)
>>> cdkmol.addh()
>>> print cdkmol.molwt
44.0525588989
>>> (CTRL+Z, Enter)


C:\Documents and Settings\Noel> jython
*sys-package-mgr*: processing new jar, 'C:\cinfony\CDK\cdk-1.0.3.jar'
Jython 2.2.1 on java1.5.0_15
Type "copyright", "credits" or "license" for more information.
>>> from cinfony import cdk, jybel
>>> mol = cdk.readstring("smi", "CC=O")
>>> mol.draw()
>>> print jybel.Molecule(mol).molwt
44.05256
>>> (CTRL+Z, Enter)

Using cinfony from IDLE

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