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3f7caf0147
* Extend RDKit::MolStandardize with a validation and standardization Pipeline * suggested changes * apply clang-format * apply yapf * MolStandardize::FeaturesValidation optionally disallow dative bonds * add allowDativeBondType to MolStandardize::PipelineOptions * apply clang-format * make the API of other validation classes more consistent with MolStandardize::FeaturesValidation * apply clang-format * PipelineStage to enum class remove virtual functions from Pipeline class be explicit about enums * light refactoring to avoid what I think is an unnecessary call to `parse` * a bit of modernization * make the pipeline configurable * make parse and serialize configurable too * switch to storing pipeline stages using uints * add a simple test for providing a pipeline * update pointer alignment for clang-format * test modifying the parser and serializer * update swig requirement * changes in response to review * changes in response to review * rename PipelineResult's *MolBlock members to *MolData * upgrade swig to 4.2 in the CI environments * add a few missing export directives --------- Co-authored-by: greg landrum <greg.landrum@gmail.com>
68 lines
2.0 KiB
Java
68 lines
2.0 KiB
Java
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.*;
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/**
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* JUnit tests for MolStandardize wrappers.
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*/
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public class MolStandardizeTest extends GraphMolTest {
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@Test
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public void testStandardize1() {
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assertEquals("fail", RDKFuncs.standardizeSmiles("[Na]OC(=O)c1ccccc1"),"O=C([O-])c1ccccc1.[Na+]");
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}
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@Test
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public void testPipelineBadInput() {
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Pipeline pipeline = new Pipeline();
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PipelineResult result = pipeline.run(
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"\n" +
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" sldfj;ldskfj sldkjfsd;lkf\n" +
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"M V30 BEGIN CTAB"
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);
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assertEquals(result.getStage(), PipelineStage.PARSING_INPUT);
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assertFalse(result.getStatus() == PipelineStatus.NO_EVENT);
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assertTrue((result.getStatus() & PipelineStatus.INPUT_ERROR) != PipelineStatus.NO_EVENT);
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result.delete();
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pipeline.delete();
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}
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@Test
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public void testPipelineUnsupportedFeatures() {
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Pipeline pipeline = new Pipeline();
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PipelineResult result = pipeline.run(
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"\n" +
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" Mrv2311 01162413552D \n" +
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"\n" +
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" 0 0 0 0 0 999 V3000\n" +
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"M V30 BEGIN CTAB\n" +
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"M V30 COUNTS 2 1 0 0 0\n" +
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"M V30 BEGIN ATOM\n" +
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"M V30 1 R# -17.3747 6.9367 0 0 RGROUPS=(1 0)\n" +
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"M V30 2 C -18.7083 6.1667 0 0\n" +
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"M V30 END ATOM\n" +
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"M V30 BEGIN BOND\n" +
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"M V30 1 1 2 1\n" +
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"M V30 END BOND\n" +
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"M V30 END CTAB\n" +
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"M END"
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);
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assertEquals(result.getStage(), PipelineStage.COMPLETED);
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assertFalse(result.getStatus() == PipelineStatus.NO_EVENT);
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assertTrue((result.getStatus() & PipelineStatus.VALIDATION_ERROR) != PipelineStatus.NO_EVENT);
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assertTrue((result.getStatus() & PipelineStatus.FEATURES_VALIDATION_ERROR) != PipelineStatus.NO_EVENT);
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result.delete();
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pipeline.delete();
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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.MolStandardizeTest");
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}
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}
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