mirror of
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b417465e93
* Adds MolToCDXMLBlock to FileParsers * Simplified code, removed warning * Fix C# wrapper for MolToCDX * Add C# test, fix cscode in swig * Fix typo in tests * Set default format to CDXML for MolToCDXML Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Add CDXML writer smoke tests --------- Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
406 lines
11 KiB
Python
406 lines
11 KiB
Python
#
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# Copyright (C) 2003-2021 Greg Landrum and other RDKit contributors
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# All Rights Reserved
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#
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""" This is a rough coverage test of the python wrapper
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it's intended to be shallow, but broad
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"""
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import doctest
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import gc
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import gzip
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import logging
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import os
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import sys
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import tempfile
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import unittest
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from io import StringIO
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from rdkit import Chem
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class TestCase(unittest.TestCase):
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def test_cdxml(self):
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cdxml = """<?xml version="1.0" encoding="UTF-8" ?>
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<!DOCTYPE CDXML SYSTEM "http://www.cambridgesoft.com/xml/cdxml.dtd" >
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<CDXML
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CreationProgram="ChemDraw JS 2.0.0.9"
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Name="ACS Document 1996"
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BoundingBox="94.75 178.16 154.89 211.17"
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WindowPosition="0 0"
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WindowSize="0 0"
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FractionalWidths="yes"
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InterpretChemically="yes"
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ShowAtomQuery="yes"
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ShowAtomStereo="no"
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ShowAtomEnhancedStereo="yes"
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ShowAtomNumber="no"
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ShowResidueID="no"
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ShowBondQuery="yes"
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ShowBondRxn="yes"
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ShowBondStereo="no"
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ShowTerminalCarbonLabels="no"
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ShowNonTerminalCarbonLabels="no"
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HideImplicitHydrogens="no"
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Magnification="666"
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LabelFont="24"
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LabelSize="10"
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LabelFace="96"
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CaptionFont="24"
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CaptionSize="10"
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HashSpacing="2.50"
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MarginWidth="1.60"
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LineWidth="0.60"
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BoldWidth="2"
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BondLength="14.40"
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BondSpacing="18"
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ChainAngle="120"
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LabelJustification="Auto"
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CaptionJustification="Left"
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AminoAcidTermini="HOH"
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ShowSequenceTermini="yes"
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ShowSequenceBonds="yes"
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ShowSequenceUnlinkedBranches="no"
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ResidueWrapCount="40"
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ResidueBlockCount="10"
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ResidueZigZag="yes"
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NumberResidueBlocks="no"
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PrintMargins="36 36 36 36"
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MacPrintInfo="0003000001200120000000000B6608A0FF84FF880BE309180367052703FC0002000001200120000000000B6608A0000100000064000000010001010100000001270F000100010000000000000000000000000002001901900000000000400000000000000000000100000000000000000000000000000000"
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ChemPropName=""
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ChemPropFormula="Chemical Formula: "
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ChemPropExactMass="Exact Mass: "
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ChemPropMolWt="Molecular Weight: "
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ChemPropMOverZ="m/z: "
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ChemPropAnalysis="Elemental Analysis: "
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ChemPropBoilingPt="Boiling Point: "
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ChemPropMeltingPt="Melting Point: "
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ChemPropCritTemp="Critical Temp: "
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ChemPropCritPres="Critical Pres: "
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ChemPropCritVol="Critical Vol: "
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ChemPropGibbs="Gibbs Energy: "
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ChemPropLogP="Log P: "
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ChemPropMR="MR: "
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ChemPropHenry="Henry's Law: "
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ChemPropEForm="Heat of Form: "
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ChemProptPSA="tPSA: "
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ChemPropID=""
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ChemPropFragmentLabel=""
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color="0"
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bgcolor="1"
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RxnAutonumberStart="1"
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RxnAutonumberConditions="no"
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RxnAutonumberStyle="Roman"
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><colortable>
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<color r="1" g="1" b="1"/>
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<color r="0" g="0" b="0"/>
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<color r="1" g="0" b="0"/>
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<color r="1" g="1" b="0"/>
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<color r="0" g="1" b="0"/>
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<color r="0" g="1" b="1"/>
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<color r="0" g="0" b="1"/>
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<color r="1" g="0" b="1"/>
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</colortable><fonttable>
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<font id="24" charset="utf-8" name="Arial"/>
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</fonttable><page
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id="32"
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BoundingBox="0 0 542 354"
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Width="542"
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Height="354"
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HeaderPosition="36"
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FooterPosition="36"
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PageOverlap="0"
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PrintTrimMarks="yes"
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HeightPages="1"
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WidthPages="1"
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DrawingSpace="poster"
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><fragment
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id="10"
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BoundingBox="94.75 178.16 154.89 211.17"
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Z="4"
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><n
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id="7"
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p="95.05 187.47"
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Z="1"
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AS="N"
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/><n
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id="9"
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p="95.05 201.87"
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Z="3"
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AS="N"
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/><n
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id="11"
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p="106.31 210.84"
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Z="5"
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AS="N"
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/><n
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id="13"
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p="120.35 207.64"
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Z="7"
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AS="N"
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/><n
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id="15"
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p="126.59 194.67"
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Z="9"
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AS="N"
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/><n
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id="17"
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p="120.35 181.69"
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Z="11"
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AS="N"
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/><n
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id="19"
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p="106.31 178.49"
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Z="13"
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AS="N"
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/><n
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id="28"
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p="140.99 194.67"
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Z="22"
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NodeType="Nickname"
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NeedsClean="yes"
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AS="N"
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><fragment
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id="33"
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><n
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id="34"
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p="148.17 207.09"
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Element="8"
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NumHydrogens="0"
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/><n
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id="35"
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p="162.52 207.09"
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/><n
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id="36"
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p="176.87 207.09"
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/><n
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id="37"
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p="169.69 194.67"
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/><n
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id="38"
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p="169.69 219.52"
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/><n
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id="39"
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p="140.99 194.67"
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/><n
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id="40"
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p="148.17 182.24"
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Element="8"
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NumHydrogens="0"
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/><n
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id="41"
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p="126.64 194.67"
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NodeType="ExternalConnectionPoint"
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/><b
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id="42"
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B="39"
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E="40"
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Order="2"
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/><b
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id="43"
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B="35"
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E="38"
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/><b
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id="44"
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B="35"
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E="36"
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/><b
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id="45"
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B="35"
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E="37"
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/><b
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id="46"
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B="34"
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E="35"
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/><b
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id="47"
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B="34"
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E="39"
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/><b
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id="48"
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B="41"
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E="39"
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/></fragment><t
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p="137.66 198.28"
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BoundingBox="137.66 189.64 154.89 198.28"
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LabelJustification="Left"
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LabelAlignment="Left"
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><s font="24" size="9.95" color="0" face="96">Boc</s></t></n><b
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id="21"
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Z="15"
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B="7"
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E="9"
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BS="N"
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/><b
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id="22"
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Z="16"
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B="9"
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E="11"
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BS="N"
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/><b
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id="23"
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Z="17"
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B="11"
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E="13"
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BS="N"
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/><b
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id="24"
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Z="18"
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B="13"
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E="15"
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BS="N"
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/><b
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id="25"
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Z="19"
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B="15"
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E="17"
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BS="N"
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/><b
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id="26"
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Z="20"
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B="17"
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E="19"
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BS="N"
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/><b
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id="27"
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Z="21"
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B="19"
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E="7"
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BS="N"
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/><b
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id="29"
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Z="23"
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B="15"
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E="28"
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BS="N"
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/></fragment></page></CDXML>"""
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mols = Chem.MolsFromCDXML(cdxml)
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self.assertEqual(len(mols), 1)
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self.assertEqual(Chem.MolToSmiles(mols[0]), "CC(C)(C)OC(=O)C1CCCCCC1")
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mols = Chem.MolsFromCDXML(cdxml, True, False)
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self.assertEqual(len(mols), 1)
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self.assertEqual(Chem.MolToSmiles(mols[0]), "CC(C)(C)OC(=O)C1CCCCCC1")
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mols = Chem.MolsFromCDXML(cdxml, False, False)
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self.assertEqual(len(mols), 1)
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self.assertEqual(Chem.MolToSmiles(mols[0]), "CC(C)(C)OC(=O)C1CCCCCC1")
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params = Chem.CDXMLParserParams()
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mols = Chem.MolsFromCDXML(cdxml, params)
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self.assertEqual(len(mols), 1)
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self.assertEqual(Chem.MolToSmiles(mols[0]), "CC(C)(C)OC(=O)C1CCCCCC1")
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params.sanitize = True
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params.removeHs = False
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mols = Chem.MolsFromCDXML(cdxml, params)
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self.assertEqual(len(mols), 1)
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self.assertEqual(Chem.MolToSmiles(mols[0]), "CC(C)(C)OC(=O)C1CCCCCC1")
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params.sanitize = False
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params.removeHs = False
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mols = Chem.MolsFromCDXML(cdxml, params)
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self.assertEqual(len(mols), 1)
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self.assertEqual(Chem.MolToSmiles(mols[0]), "CC(C)(C)OC(=O)C1CCCCCC1")
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def test_cdxml(self):
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try: from rdkit.Chem import rdChemDraw
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except:
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return
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rdbase = os.environ['RDBASE']
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cdxfilename = os.path.join(rdbase,
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'Code/GraphMol/test_data/CDXML/ring-stereo1.cdx')
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mols = Chem.MolsFromCDXMLFile(cdxfilename)
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filename = os.path.join(rdbase,
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'Code/GraphMol/test_data/CDXML/ring-stereo1.cdxml')
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mols2 = Chem.MolsFromCDXMLFile(filename)
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smi1 = [Chem.MolToSmiles(m) for m in mols]
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smi2 = [Chem.MolToSmiles(m) for m in mols2]
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self.assertEqual(smi1, smi2)
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self.assertEqual(smi1, ['C1CC[C@H]2CCCC[C@H]2C1'])
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with open(cdxfilename, 'rb') as f:
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data = f.read()
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params = Chem.CDXMLParserParams(True, True, Chem.CDXMLFormat.CDX)
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mols3 = Chem.MolsFromCDXML(data, params)
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smi3 = [Chem.MolToSmiles(m) for m in mols3]
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self.assertEqual(smi1, smi3)
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if Chem.HasChemDrawCDXSupport():
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# ensure we can round trip through CDXML, CDX
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for smi, mol in zip(smi3, mols3):
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cdxml = Chem.MolToCDXMLBlock(mol)
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cdxml2 = Chem.MolToCDXMLBlock(mol, Chem.CDXMLFormat.CDXML)
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# check default is cdxml
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self.assertEqual(cdxml, cdxml2)
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cdx = Chem.MolToCDXMLBlock(mol, Chem.CDXMLFormat.CDX)
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self.assertEqual(type(cdx), bytes)
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self.assertEqual(Chem.MolToSmiles(Chem.MolsFromCDXML(cdxml)[0]),
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smi)
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self.assertEqual(Chem.MolToSmiles(Chem.MolsFromCDXML(cdx, params)[0]),
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smi)
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def test_formats(self):
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try:
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from rdkit.Chem import rdChemDraw
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self.assertEqual(Chem.HasChemDrawCDXSupport(),True)
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except:
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self.assertEqual(Chem.HasChemDrawCDXSupport(),False)
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return
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rdbase = os.environ['RDBASE']
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cdxfilename = os.path.join(rdbase,
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'Code/GraphMol/test_data/CDXML/ring-stereo1.cdx')
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mols = Chem.MolsFromCDXMLFile(cdxfilename)
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cdxmlfilename = os.path.join(rdbase,
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'Code/GraphMol/test_data/CDXML/ring-stereo1.cdxml')
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tests = [
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# we can deduce extensions from filenames, but not from streams (yet!)
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# filename, Stream, IsCDX, CDX res, CDXML res, Auto Res
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(cdxfilename, True, True, True, False, False),
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(cdxfilename, False, True, True, False, True),
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(cdxmlfilename, True, False, False, True, True),
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(cdxmlfilename, False, False, False, True, True),
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]
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for filename, stream, iscdx, cdxres, cdxmlres, autores in tests:
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for format, res in zip([Chem.CDXMLFormat.CDX, Chem.CDXMLFormat.CDXML, Chem.CDXMLFormat.Auto],
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[cdxres, cdxmlres, autores]):
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if stream:
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with open(filename, 'rb') as f:
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data = f.read()
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try:
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mols = Chem.MolsFromCDXML(data, Chem.CDXMLParserParams(True, True, format))
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if res: assert mols
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except RuntimeError:
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assert res == False
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else:
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mols = Chem.MolsFromCDXMLFile(filename, Chem.CDXMLParserParams(True, True, format))
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if res: assert mols
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if __name__ == '__main__':
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if "RDTESTCASE" in os.environ:
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suite = unittest.TestSuite()
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testcases = os.environ["RDTESTCASE"]
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for name in testcases.split(':'):
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suite.addTest(TestCase(name))
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runner = unittest.TextTestRunner()
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runner.run(suite)
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else:
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unittest.main()
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