Installing Cinfony on Windows¶

Cinfony contains the following modules (dependencies listed in parentheses):

pybel - Open Babel wrapper (Python or Java+Jython or IronPython)
cdk - CDK wrapper (Java and Python+JPype or Jython)
rdk - RDKit wrapper (Python)
opsin - OPSIN wrapper (Java and Python+JPype or Jython)
indy - Indigo wrapper (Python or Java+Jython or IronPython)
jchem - JChem wrapper (Java and Python+JPype or Jython)
webel - Uses web services

Installing dependencies¶

You should install the dependencies first. Depending on what wrappers you wish to use, you should install (32-bit versions of) some or all of the following: Python 2.7.x, Java 1.7 (“JRE 7”), Jython 2.5, IronPython 2.7. If you are installing Jython, you should install Java first.

Installing 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 1.2, and unzip it, for example, as C:\cinfony. This includes the following libraries so you don’t need to download them separately:
- JPype 0.5.4.2 - connects CPython to a JVM
- NumPy 1.6.2 - fast linear algebra for Python
- Pycairo 1.4.12 - Python interface to Cairo (drawing library)
- Python Imaging Library 1.1.7 - Image manipulation in Python
If interested in using Open Babel, download OpenBabel 2.3.2 and run the installer. Also download and run the installer for the Python 2.7 bindings.
If interested in using the Chemistry Development Kit, download CDK 1.4.15 and place in C:\cinfony\Java
If interested in using the RDKit, download RDKit 2012.09 (Greg Landrum) and unzip into C:\cinfony\RDKit
- If unzipped correctly, there should be a file C:\cinfony\RDKit\README
If interested in using OPSIN, download OPSIN 1.3 and place in C:\cinfony\Java
If interested in using Indigo, go to the Indigo 1.1 download page and...
- ...for CPython, follow the link for Windows builds: Python API to download a zip file. Unzip this and copy all of the contents into C:\cinfony\Python.
- ...for Jython, follow the link for Windows builds: Java API to download a zip file. Unzip this and place the four jar files within into C:\cinfony\Java.
- ...for IronPython, follow the link for Windows builds: .NET API to download a zip file. Unzip this and copy the three DLLs within into C:\cinfony\DLL.
If interested in using JChem, obtain a license from ChemAxon and then download and install JChem 5.11.
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 System Settings, 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 2.7 prompt type:
from cinfony import obabel, rdk, cdk, indy, jchem, opsin, webel
or at the Jython 2.5 prompt type:
from cinfony import obabel, cdk, indy, opsin, webel
or at the IronPython 2.7 prompt type:
from cinfony import obabel, indy, jchem, webel

C:\Documents and Settings\Noel> python
Python 2.7.1 (r271:86832, Nov 27 2010, 18:30:46) [MSC v.1500 32 bit (Intel)] on
win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from cinfony import obabel, rdk, cdk, indy, opsin, webel
>>> mol = obabel.readstring("smi", "CC=O")
>>> mol.draw()
>>> print rdk.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
>> print webel.Molecule(mol).write("names")
['acetaldehyde', 'ethanal', '75-07-0', 'NCI-C56326', 'PS2030_SUPELCO', 'NSC7594'
, 'NCGC00091753-01', 'Octowy aldehyd', 'METALDEHYDE',
...
'acetaldehydes', 'W200360_ALDRICH', 'C00084', 'ACETALD', 'ACETYL GROUP']
>>> (CTRL+Z, Enter)

C:\Documents and Settings\Noel> jython
*sys-package-mgr*: processing new jar, 'C:\cinfony\CDK\cdk-1.2.8.jar'
Jython 2.5.0 on java1.5.0_15
Type "copyright", "credits" or "license" for more information.
>>> from cinfony import obabel, cdk, indy, opsin, webel
>>> mol = cdk.readstring("smi", "CC=O")
>>> print obabel.Molecule(mol).molwt
44.05256
>>> (CTRL+Z, Enter)

Using Cinfony from IDLE¶

If you want to run Cinfony scripts from within IDLE, find the file idle.bat (on my computer this is in C:\Python27\Lib\idlelib\idle.bat) and make a copy called cinfony_idle.bat. Edit this file in Notepad and add the following just before the start idle.pyw line:

call cinfony.bat

Make a shortcut to cinfony_idle.bat on your desktop and use this to start IDLE. You can also drag-and-drop Python scripts onto this shortcut.