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58c21baeba
* ChemDraw Document and read/write support for the RDKit * Add missing test file * Rev chemdraw version * Rev chemdraw version * Rev chemdraw version for g++11 * Update CMakeLists.txt Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Build chemdraw from an external CMake file * Remove unused platform bigendian check * Revert changes to constants, remove unused ones * Keep the original constant names * Remove __main__ section * Use as much of the ChemDraw CMakeList as possible * Skip installing expat * Rev chemdraw version to fix windows issue * Don't install expat, set the appropriate CHEMDRAW_BUILD definition * resolve windows builds * Fix minimal lib builds * Move ChemDraw document to private header * Move utility functions to ChemDraw namespace * Move ChemDraw to v2 unique ptr api namespace * Make class enum * Switch to camelCase * Response to review * Move ChemDrawToDocument to ChemDraw namespace * Update External/ChemDraw/Wrap/rdChemDraw.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Fix typo * Update External/ChemDraw/Wrap/rdChemDraw.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Add better documentation * Rev chemdraw version --------- Co-authored-by: Brian Kelley <bkelley@glysade.com> Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
278 lines
6.7 KiB
Python
278 lines
6.7 KiB
Python
# Copyright (c) 2025 Glysade Inc
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# All rights reserved.
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#
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# This file is part of the RDKit.
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# The contents are covered by the terms of the BSD license
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# which is included in the file license.txt, found at the root
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# of the RDKit source tree.
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import copy
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import os
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import sys
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import unittest
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from rdkit import Chem
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from rdkit.Chem import rdChemDraw, rdChemDrawReaction
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class TestChemDraw(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 = rdChemDraw.MolsFromChemDraw(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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