mirror of
https://github.com/rdkit/rdkit.git
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cf269aa813
* Fist pass at CDX support * Enable CDX support for reading (also) in the CDXMLParser API * Add cdxml test files * Update swig wrappers for CDXMLFormat and Parameters * Add constructor to ChemDrawParserParams * Add Java SWIG support for ChemDraw * Add chemdraw define to rdconfig * Add missing chemdraw deps * Remove direct expat link * Fix Java linkages for ChemDraw * Remove bad merge code * Remove bad merge code * Fix csharp builds * Add sniffer for the ChemDraw DataStream * Include filesystem * Fix test on windows * Add more CDX tests * Ensure streams are open in binary mode to support CDX on windows * Fix text to show that a Block is the text input, not a file * Fix CSharp test * Disable CDX tests when not building chemdraw * Turn back on chemdraw * Response to review * Turn off chemdraw support for the limited external test --------- Co-authored-by: Brian Kelley <bkelley@glysade.com>
92 lines
3.7 KiB
Java
92 lines
3.7 KiB
Java
/*
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* Copyright (c) 2025, Glysade Inc
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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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package org.RDKit;
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import static org.junit.Assert.*;
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import java.io.File;
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import org.junit.Test;
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public class ChemDrawTest extends GraphMolTest {
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@Test public void testChemDrawReader() {
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String rdpath = System.getenv("RDBASE");
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if (rdpath == null)
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org.junit.Assert.fail("No definition for RDBASE");
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File base = new File(rdpath);
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File testFile = new File(base, "Code" + File.separator + "GraphMol"
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+ File.separator + "test_data" + File.separator +
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"CDXML" + File.separator + "beta-cypermethrin.cdxml");
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String fn = testFile.getAbsolutePath();
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RWMol_Vect prods = RDKFuncs.MolsFromChemDrawFile(fn);
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assertEquals(prods.size(), 1);
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for(int idx = 0; idx < prods.size(); idx++) {
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if(idx == 0) {
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System.out.print(prods.get(idx).MolToSmiles(true));
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System.out.print("\n");
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assertEquals(prods.get(idx).MolToSmiles(true), "CC1(C)[C@H](C=C(Cl)Cl)[C@H]1C(=O)O[C@@H](C#N)c1cccc(Oc2ccccc2)c1");
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}
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}
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ChemDrawParserParams params = new ChemDrawParserParams();
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prods = RDKFuncs.MolsFromChemDrawFile(fn, params);
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assertEquals(prods.size(), 1);
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for(int idx = 0; idx < prods.size(); idx++) {
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if(idx == 0) {
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System.out.print(prods.get(idx).MolToSmiles(true));
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System.out.print("\n");
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assertEquals(prods.get(idx).MolToSmiles(true), "CC1(C)[C@H](C=C(Cl)Cl)[C@H]1C(=O)O[C@@H](C#N)c1cccc(Oc2ccccc2)c1");
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}
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}
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testFile = new File(base, "Code" + File.separator + "GraphMol"
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+ File.separator + "test_data" + File.separator +
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"CDXML" + File.separator + "ring-stereo1.cdx");
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fn = testFile.getAbsolutePath();
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params = new ChemDrawParserParams(true, true, CDXFormat.CDX);
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prods = RDKFuncs.MolsFromChemDrawFile(fn, params);
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assertEquals(prods.size(), 1);
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params = new ChemDrawParserParams(true, true, CDXFormat.CDXML);
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boolean e = false;
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try {
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prods = RDKFuncs.MolsFromChemDrawFile(fn, params);
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} catch(GenericRDKitException ex) {
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e = true;
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}
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assertEquals(true, e);
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}
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public static void main(String args[]) {
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org.junit.runner.JUnitCore.main("org.RDKit.ChemDrawTest");
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}
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}
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