Open babel

AN INTRODUCTION

1. 0pen Babel Submitted to Mr.Inam ul haq Submitted by M Atif Raza (3024) University of Education,Okara campus 1

2. C ontents Introduction Features Funtions Finger Printing University of Education,Okara campus 2

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 . University of Education,Okara campus 3

4. Features chemical expert system interconversion of many chemical file formats substructure search (based on SMARTS ) fingerprint calculation wrappers for Python , Perl , Java , Ruby , University of Education,Okara campus 4

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 : University of Education,Okara campus 5 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. University of Education,Okara campus 6 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 University of Education,Okara campus 7

8. Summary It is very useful software for Chemical Formats It is also useful in Cheminformatics It is applicable in Finger Printing Calculations University of Education,Okara campus 8

9. Conclusion It is a unique Software which is used to convert Chemical Formats accurately. University of Education,Okara campus 9

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 University of Education,Okara campus 10