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Merge pull request #350 from ncats/smiles_force
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when generation of canonical SMILES fails, return generic SMILES
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@blueSwordfish
blueSwordfish authored Jul 10, 2024
2 parents b1a472d + d436d41 commit 098666f
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61 changes: 61 additions & 0 deletions gsrs-module-substance-example/src/test/java/example/chem/SmilesGenerationTest.java
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package example.chem;

import ix.core.chem.InchiStandardizer;
import ix.ginas.models.v1.GinasChemicalStructure;
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Test;

import java.io.IOException;

import static org.junit.jupiter.api.Assertions.assertNotNull;

@Slf4j
public class SmilesGenerationTest {

@Test
void generateSmiles1() throws IOException {
String molfileText = IOUtils.toString(
this.getClass().getResourceAsStream("/molfiles/TG72BS085Y.mol"),
"UTF-8"
);
GinasChemicalStructure structure = new GinasChemicalStructure();
structure.molfile = molfileText;
InchiStandardizer standardizer = new InchiStandardizer();
String smiles = standardizer.canonicalSmiles(structure, molfileText);
log.warn("canonical SMILES within first test: {}", smiles);
assertNotNull(smiles);
}

@Test
void generateSmiles2() throws IOException {
String molfileText = IOUtils.toString(
this.getClass().getResourceAsStream("/molfiles/TG72BS085Y_cleaned2.mol"),
"UTF-8"
);
GinasChemicalStructure structure = new GinasChemicalStructure();
structure.molfile = molfileText;
InchiStandardizer standardizer = new InchiStandardizer();
String smiles = standardizer.canonicalSmiles(structure, molfileText);
log.warn("canonical SMILES: {}", smiles);
assertNotNull(smiles);
}

/*
No Sgroups
*/
@Test
void generateSmiles3() throws IOException {
String molfileText = IOUtils.toString(
this.getClass().getResourceAsStream("/molfiles/6L522LAQ9U.mol"),
"UTF-8"
);
GinasChemicalStructure structure = new GinasChemicalStructure();
structure.molfile = molfileText;
InchiStandardizer standardizer = new InchiStandardizer();
String smiles = standardizer.canonicalSmiles(structure, molfileText);
log.warn("canonical SMILES: {}", smiles);
assertNotNull(smiles);
}

}
10 changes: 9 additions & 1 deletion gsrs-module-substance-example/src/test/resources/logback.xml
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<root level="ERROR">
<appender-ref ref="STDOUT" />
</root>
</root>

<logger name="example.chem" level="TRACE">
<appender-ref ref="STDOUT" />
</logger>

<logger name="ix.core.chem" level="TRACE">
<appender-ref ref="STDOUT" />
</logger>
</configuration>
58 changes: 58 additions & 0 deletions gsrs-module-substance-example/src/test/resources/molfiles/6L522LAQ9U.mol
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217 changes: 217 additions & 0 deletions gsrs-module-substance-example/src/test/resources/molfiles/TG72BS085Y.mol
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M END
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