[Open Babel] new tools: obfit & obrotate

[Fabien F. <ffo...@im...>]

Dear all,


I have commited two new utilities in the 'tools' directory of the 
openbabel module.

The new tools have a usage very similar to obgrep, i.e. they all require 
a SMART pattern and at least one input files, they guess the input file 
format from the filename extention, and they print the results to the 
standard output.

The first one is obfit, It uses the qtrfit function of the library to 
superimpose two molecules. Its most interesting feature is that the 
atoms to fit are defined by the SMART pattern given by the user. I found 
it pretty useful to align congeneric series of molecules on a common 
structural scaffold for 3D-QSAR studies. Probably, It can be useful for 
the overlay of outputs of conformational sampling.
here is an example:
obfit "N1(C)CCCCC1" fixed.sdf moving.sdf

align all the molecules of 'moving.sdf' on a single molecule of 
'fixed.sdf' by superimposing them on its N-methylpiperidyl moiety.
If a molecule in 'moving.sdf' doesn't have the N-methylpiperidyl 
substructure, it is printed without any transformation.


The second tool is called obrotate. It rotates the tortional angle of a 
molecules so that its angle value is equal to the one defined by the 
user. In other words, it does the same as what would do a user setting 
an angle in a mollecular modelling package, but much faster and in batch 
mode.
Imagine you want to define the conformation of a lot of molecules with a 
pyridyl scaffold and substituted with an aliphatic chain at 3-position, 
for example for docking or 3D-QSAR puposes.
To set the value of the first tortional to 90 degrees, the command line 
would be:
obrotate "c1ccncc1CCC" pyridines.sdf 5 6 7 8 90

6 and 7 define the bond to rotate in the SMART pattern, i.e. c1C bond, 5 
and 8 are the atoms of the SMART pattern used to set the angle value. 
The two atoms used to set the angle value do not have to be connected to 
the atoms of the bond to rotate, for example, the following line:
obrotate "c1ccncc1CCC" pyridines.sdf 4 6 7 8 90

produces the same output, but uses the nitrogen atom as a reference for 
the angle value instead of the aromatic carbon. The order of the atom's 
definition matters, so the program knows which part of the molecule is 
moving and which part is kept fixed, i.e.:
obrotate "c1ccncc1CCC" pyridines.sdf 5 6 7 8 90

keeps the pyridyl ring fixed and moves the aliphatic chain while
obrotate "c1ccncc1CCC" pyridines.sdf 8 7 6 5 90

keeps the aliphatic chain fixed and moves the pyridyl ring


That's all,
Hope these utilities will be useful for people work

Fabien


-- 
Fabien Fontaine
Engineer in Biotechnology
Computer-Assisted Drug Design Laboratory
Research Group on Biomedical Informatics (GRIB) - IMIM/UPF

Passeig Maritim de la Barceloneta, 37-49	Tel: +34 93 224 08 94
E-08003 Barcelona (Spain)		       	Fax: +34 93 224 08 75
e-mail: ffo...@im...			http://www.imim.es/grib