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when generation of canonical SMILES fails, return generic SMILES #350

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Jul 10, 2024
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when generation of canonical SMILES fails, return generic SMILES #350

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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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Expand Up @@ -8,5 +8,13 @@

<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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Marvin 01132103242D

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13.0864 -3.4989 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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M END
217 changes: 217 additions & 0 deletions gsrs-module-substance-example/src/test/resources/molfiles/TG72BS085Y.mol
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Marvin 01132111442D

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M SCN 1 2 HT
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M SPA 2 1 45
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M SMT 2 3
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M SAL 3 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
M SAL 3 15 31 32 33 34 35 36 37 38 39 40 52 53 54 55 56
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M SAL 3 5 87 88 89 90 91
M SPA 3 15 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
M SPA 3 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
M SPA 3 10 31 32 33 34 35 36 37 38 39 40
M SDI 3 4 -5.1663 -7.3134 -5.1663 -2.6921
M SDI 3 4 5.4707 -2.6921 5.4707 -7.3134
M SMT 3 2
M END
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