# $Id$ # # Copyright (C) 2016 Novartis Institute of BioMedical Research # All Rights Reserved # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are # met: # # * Redistributions of source code must retain the above copyright # notice, this list of conditions and the following disclaimer. # * Redistributions in binary form must reproduce the above # copyright notice, this list of conditions and the following # disclaimer in the documentation and/or other materials provided # with the distribution. # * Neither the name of Novartis Institutes for BioMedical Research Inc. # nor the names of its contributors may be used to endorse or promote # products derived from this software without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT # OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT # LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY # THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. # from __future__ import print_function from rdkit import Chem from rdkit.Chem import rdStructChecker import unittest data = """310929550 -OEChem-07211613022D 55 60 0 0 0 0 0 0 0999 V2000 -3.6737 1.4194 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8298 2.0868 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7144 1.2798 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5968 2.8875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8579 0.8673 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4302 1.2798 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0013 -1.1952 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.5736 0.8673 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.7170 1.2798 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.8605 0.8673 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0093 2.1731 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 -3.5724 -0.3702 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.1434 -0.3702 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.1434 1.2798 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.5724 1.2798 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.8579 0.0423 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.2868 0.8673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0013 1.2798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2868 0.0423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7158 0.0423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7158 0.8673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0013 -0.3702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4302 -0.3702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7144 -0.3702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4290 0.0423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.8673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8579 0.0423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4290 0.8673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7144 1.2798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7144 -1.1952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7144 -0.3702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4290 0.8673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4302 -1.1952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1447 -0.7827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1447 0.0423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.6077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7144 -1.1952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8579 0.8673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4290 0.0423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2868 0.8673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1434 -0.3702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0013 1.2798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7158 0.8673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2868 0.0423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0013 -0.3702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7158 0.0423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1447 0.8673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2868 -1.6077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8592 1.2798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.2881 1.2798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0026 0.8673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.4316 0.8673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1460 1.2798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.5750 1.2798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 11 1 0 0 0 0 1 17 1 0 0 0 0 2 11 1 0 0 0 0 2 18 1 0 0 0 0 3 27 1 0 0 0 0 3 33 1 0 0 0 0 4 11 2 0 0 0 0 5 28 2 0 0 0 0 6 44 1 0 0 0 0 6 48 1 0 0 0 0 7 46 1 0 0 0 0 7 49 1 0 0 0 0 8 50 1 0 0 0 0 8 51 1 0 0 0 0 9 52 1 0 0 0 0 9 53 1 0 0 0 0 10 54 1 0 0 0 0 10 55 1 0 0 0 0 12 19 1 0 0 0 0 12 28 1 0 0 0 0 13 26 1 0 0 0 0 13 28 1 0 0 0 0 14 33 2 0 0 0 0 14 39 1 0 0 0 0 15 39 1 0 0 0 0 15 41 1 0 0 0 0 16 39 2 0 0 0 0 16 42 1 0 0 0 0 17 18 1 0 0 0 0 17 19 2 0 0 0 0 18 21 2 0 0 0 0 19 22 1 0 0 0 0 20 21 1 0 0 0 0 20 22 2 0 0 0 0 20 23 1 0 0 0 0 23 34 1 0 0 0 0 23 35 1 0 0 0 0 23 36 1 0 0 0 0 24 25 1 0 0 0 0 24 26 2 0 0 0 0 24 31 1 0 0 0 0 25 27 2 0 0 0 0 25 32 1 0 0 0 0 26 29 1 0 0 0 0 27 30 1 0 0 0 0 29 30 2 0 0 0 0 31 37 2 0 0 0 0 32 38 2 0 0 0 0 33 40 1 0 0 0 0 37 38 1 0 0 0 0 40 42 2 0 0 0 0 41 43 2 0 0 0 0 41 45 1 0 0 0 0 43 44 1 0 0 0 0 44 47 2 0 0 0 0 45 46 2 0 0 0 0 46 47 1 0 0 0 0 48 50 1 0 0 0 0 51 52 1 0 0 0 0 53 54 1 0 0 0 0 M CHG 1 11 1 M END """ class TestCase(unittest.TestCase): def testStructOptions(self): rdStructChecker.StructCheckerOptions() def testStructChecker(self): checker = rdStructChecker.StructChecker() m = Chem.MolFromMolBlock(data) self.assertTrue(m) res = checker.CheckMolStructure(m) self.assertEquals(res, rdStructChecker.StructureFlags.ATOM_CHECK_FAILED) if __name__ == '__main__': unittest.main()