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