AN INTRODUCTION

1. 0pen Babel
Submitted to Mr.Inam ul haq
Submitted by M Atif Raza(3024)
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2. Contents
• Introduction
• Features
• Funtions
• Finger Printing
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3. Introduction
• Open Babel is free software, a chemical expert system mainly used
for converting chemical file formats.[1] Due to the strong relationship
to informatics this program belongs more to the category
cheminformatics than to molecular modelling. It is available for
Windows, Unix, and Mac OS. It is distributed under the GNU GPL.
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4. Features
• chemical expert system
• interconversion of many chemical file formats
• substructure search (based on SMARTS)
• fingerprint calculation
• wrappers for Python, Perl, Java, Ruby,
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5. Function
• For relatively small datasets (<10,000’s) it is possible to do similarity
searches without the need to build a similarity index, however larger
datasets (up to a few million) can be searched rapidly once a
fastsearch index has been built.
• On small datasets these fingerprints can be used in a variety of ways.
The following command gives you the Tanimoto coefficient between a
SMILES string in mysmiles.smi and all the molecules in mymols.sdf:
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Small Datasets

6. Function
• On larger datasets it is necessary to first build a fastsearch index. This
is an new file that stores a database of fingerprints for the files
indexed. You will still need to keep both the new .fs fastsearch index
and the original files. However, the new index will allow significantly
faster searching and similarity comparisons.
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Large Datasets

7. Moleculer Fingerprinting
• Molecular fingerprints encode molecular structure in a series of binary
digits (bits) that represent the presence or absence of particular
substructures in the molecule. Comparing fingerprints will allow you to
determine the similarity between two molecules, search databases, etc.,
but does not include full structural data (such as coordinates).
• The Open Babel fingerprints can be accessed through the following Utility
file formats:
• Fingerprint format (fpt): the path-based fingerprint FP2; substructure
based fingerprints FP2, FP3 and MACCS; user-defined substructures
• Multilevel Neighborhoods of Atoms (MNA) (mna): a circular fingerprint
• MolPrint2D format (mpd): a circular fingerprint
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8. Summary
• It is very useful software for Chemical Formats
• It is also useful in Cheminformatics
• It is applicable in Finger Printing Calculations
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9. Conclusion
• It is a unique Software which is used to convert Chemical Formats
accurately.
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10. References
• Jump up ^ O'Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.;
Vandermeersch, T.; Hutchison, G. R. (2011). "Open Babel: An open chemical
toolbox". Journal of Cheminformatics 3: 33. doi:10.1186/1758-2946-3-33.
PMC 3198950. PMID 21982300. edit
• Jump up ^ http://openbabel.org/
• Jump up ^ Guha, R.; Howard, M. T.; Hutchison, G. R.; Murray-Rust, P.; Rzepa,
H.; Steinbeck, C.; Wegner, J.; Willighagen, E. L. (2006). "The Blue Obelisk -
Interoperability in Chemical Informatics". Journal of Chemical Information and
Modeling 46 (3): 991–998. doi:10.1021/ci050400b. PMID 16711717. edit
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