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Fixing issue with MTRIXn record parsing and adding test for it #845

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Merged
josemduarte merged 1 commit into from
Jul 26, 2019
Merged

Fixing issue with MTRIXn record parsing and adding test for it #845

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30 changes: 26 additions & 4 deletions biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/PDBFileParserTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,10 +24,6 @@
*/
package org.biojava.nbio.structure.test;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
Expand All @@ -49,6 +45,8 @@
import org.junit.Before;
import org.junit.Test;

import static org.junit.Assert.*;

/**
* Test the {@link PDBFileParser}.
*
Expand Down Expand Up @@ -654,4 +652,28 @@ public void testDates() throws IOException {
assertEquals(s.getPDBHeader().getRelDate().getYear() + 1900, 1992);

}

@Test
public void testMatrxn() throws IOException {
String pdb =
"MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1\n" +
"MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1\n" +
"MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1\n" +
"MTRIX1 2 0.302797 -0.436000 -0.847477 183.33000 \n" +
"MTRIX2 2 0.434555 0.854568 -0.284384 -74.97000 \n" +
"MTRIX3 2 0.848219 -0.282165 0.448227 -146.16000 \n" +
// no padding at end should also work
"MTRIX1 3 0.006722 0.856941 0.515371 176.52000\n" +
"MTRIX2 3 0.518827 0.437598 -0.734389 -69.86000\n" +
"MTRIX3 3 -0.854853 0.272325 -0.441662 242.75999\n";

BufferedReader br = new BufferedReader(new StringReader(pdb));
Structure s = parser.parsePDBFile(br);

assertNotNull(s.getCrystallographicInfo().getNcsOperators());
assertEquals(2, s.getCrystallographicInfo().getNcsOperators().length);

// making sure we read up to last character
assertEquals(242.75999, s.getCrystallographicInfo().getNcsOperators()[1].m23, 0.0000001);
}
}
6 changes: 3 additions & 3 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1553,8 +1553,8 @@ private void pdb_CRYST1_Handler(String line) {
private void pdb_MTRIXn_Handler(String line) {

// don't process incomplete records
if (line.length() < 60) {
logger.info("MTRIXn record has fewer than 60 columns: will ignore it");
if (line.length() < 55) {
logger.info("MTRIXn record has fewer than 55 columns: will ignore it");
return;
}

Expand All @@ -1567,7 +1567,7 @@ private void pdb_MTRIXn_Handler(String line) {
double col3Value = Double.parseDouble(line.substring(30,40));
double translValue = Double.parseDouble(line.substring(45,55));
int iGiven = 0;
if (!line.substring(59,60).trim().equals("")) {
if (line.length()>=60 && !line.substring(59,60).trim().isEmpty()) {
iGiven = Integer.parseInt(line.substring(59,60));
}

Expand Down