Metadata-Version: 1.1
Name: NAMS
Version: 0.9.1
Summary: NAMS is a module to calculate similarity between molecules based on the structural/topological relationships of each atom towards all the others within a molecule.
Home-page: http://nams.lasige.di.fc.ul.pt/
Author: Andre O Falcao and Ana L. Teixeira
Author-email: afalcao@di.fc.ul.pt; ateixeira@lasige.di.fc.ul.pt
License: The NAMS python package calculates the similarity between molecules based on the 
structural/topological relationships of each atom towards all the others 
within a molecule.

This program is free software: you can redistribute it and/or modify
it under the terms of the MIT License as published on the official site of Open Source Initiative
and attached below.

-------------------------------------------------------------------------------------------------
Copyright (C) 2013, Andre Falcao and Ana Teixeira, University of Lisbon - LaSIGE

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and 
associated documentation files (the "Software"), to deal in the Software without restriction, including 
without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 
copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the 
 following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial 
portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT 
LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, 
WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE 
OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Please cite the authors in any work or product based on this material: 
AL Teixeira, AO Falcao. 2013. A non-contiguous atom matching structural similarity function. J. Chem. Inf. Model. 
DOI: 10.1021/ci400324u.
Description: NAMS: Non-contiguous Atom Matching Structural Similarity
        =========================================================
        
        NAMS is a similarity method based on atom alignment for the analysis of structural similarity between molecules. This method is based on the comparison 
        of the bonding profiles of atoms on comparable molecules, including features that are seldom found in other structural or graph matching approaches like 
        chirality or double bond stereoisomerism. The similarity measure is then defined on the annotated molecular graph, based on an iterative directed graph 
        similarity procedure and  optimal atom alignment between atoms using a pairwise matching algorithm. With the proposed approach the similarities detected 
        are more intuitively understood because similar atoms in the molecules are explicitly shown. This module implements NAMS and also supports the classification 
        of the type of isomerism present in a given atom or bond of a molecule. 
        
        For background and cite the authors in any work or product based on this material:
        
        - Ana L. Teixeira and Andre O. Falcao 2013: A non-contiguous atom matching structural similarity function. Journal of Chemical Information and Modeling(DOI: 10.1021/ci400324u)
        
        - Ana L. Teixeira, Joao P. Leal and Andre O. Falcao, Automated Identification and Classification of Stereochemistry: Chirality and Double Bond Stereoisomerism. Technical Report . LaSIGE, Department of Informatics, Faculty of Sciences, University of Lisbon, February 2013. (DOI: arXiv:1303.1724)	
        
        Visit our webtool at http://nams.lasige.di.fc.ul.pt/
        
        
        Disclaimer
        ==========
        
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS 
        IN THE SOFTWARE.
        
        
        
        Typical usage
        =============
        Usage examples::
        
            from nams import nams
            from nams import chirality
            from nams import doubleb_e_z
            
            ms=nams.Nams()
            
            #Define 2 molecules: (molecular_representation_type, molecular_representation) 
            mol_t1 = ("smi", "CCC(=O)C(c1ccccc1)c2ccccc2")
            mol_t2= ("smi", "O=C(CC)N(c1ccncc1)c3ccccc3")
            
            #Extract the set of characteristics of the atoms/bonds 
            mol1, mol_info1 = ms.get_mol_info(mol_t1[0],mol_t1[1])
            mol2, mol_info2 = ms.get_mol_info(mol_t2[0],mol_t2[1])
            
            #Calculate the similarity between the pair of molecules
            sim11, d_atoms = ms.get_similarity(mol_info1, mol_info1) 
            sim22, d_atoms = ms.get_similarity(mol_info2, mol_info2)
            sim12, d_atoms = ms.get_similarity(mol_info1, mol_info2)
            
            #Chirality detection and classification classification
            chir=chirality.Chirality("C([C@@H](C(=O)O)N)S", "smi")
            chir.get_chirality(atom_id)
            
            #Double bond stereoisomerism detection and classification
            stereo=doubleb_e_z.Stereodoubleb("I/C=C/Cl", "smi")
            stereo.get_e_z_at(at1, at2)
        
        More examples: http://nams.lasige.di.fc.ul.pt/downloads.php
        
        Dependencies and Requirements
        =============================
        Python
        ------
        Python 2.7
        
        Modules
        -------
        * openbabel, a chemical toolbox designed to handle chemical data <http://openbabel.org/>. 
        
        * pybel, which provides convenience functions and classes that make it simpler to use the Open Babel libraries from Python, especially for file input/output and for accessing the attributes of atoms and molecules. <http://openbabel.org/docs/current/UseTheLibrary/PythonInstall.html>. 
        
        * munkres, which provides an implementation of the Munkres algorithm (also called the Hungarian algorithm or the Kuhn-Munkres algorithm), useful for solving the Assignment Problem. <https://pypi.python.org/pypi/munkres/>. 
        
        
        License
        ===========
        
        The NAMS python package calculates the similarity between molecules based on the 
        structural/topological relationships of each atom towards all the others 
        within a molecule.
        
        This program is free software: you can redistribute it and/or modify
        it under the terms of the MIT License as published on the official site of Open Source Initiative
        and attached below.
        
        Copyright (C) 2013, Andre Falcao and Ana Teixeira, University of Lisbon - LaSIGE
        
        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files 
        (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, 
        publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, 
        subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
        
        Please cite the authors in any work or product based on this material:
        
        AL Teixeira, AO Falcao. 2013. A non-contiguous atom matching structural similarity function. J. Chem. Inf. Model. DOI: 10.1021/ci400324u.
        
        
Keywords: molecular similarity,chemoinformatics,atom matching,structural similarity
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
