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CONECT/LINK line-length bug fix for the PDB Parser (already in BioJava Master branch). #707

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Merged
josemduarte merged 2 commits into from
Oct 19, 2017
Merged

CONECT/LINK line-length bug fix for the PDB Parser (already in BioJava Master branch). #707

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50c34d3
Added exception handler for out-of-bounds errors when parsing lines, …
Nov 30, 2016
e88637c
Changes for CONECT/LINK
larsonmattr Oct 18, 2017
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115 changes: 64 additions & 51 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 @@ -2017,6 +2017,8 @@ private void switchCAOnly(){

/** safes repeating a few lines ... */
private Integer conect_helper (String line,int start,int end) {
if (line.length() < end) return null;

String sbond = line.substring(start,end).trim();
int bond = -1 ;
Integer b = null ;
Expand Down Expand Up @@ -2343,7 +2345,15 @@ private void pdb_SSBOND_Handler(String line){
private void pdb_LINK_Handler(String line) {

if (params.isHeaderOnly()) return;

// Check for the minimal set of fields.
if (line.length()<56) {
logger.info("LINK line has length under 56. Ignoring it.");
return;
}

int len = line.length();

String name1 = line.substring(12, 16).trim();
String altLoc1 = line.substring(16, 17).trim();
String resName1 = line.substring(17, 20).trim();
Expand All @@ -2356,10 +2366,13 @@ private void pdb_LINK_Handler(String line) {
String resName2 = line.substring(47, 50).trim();
String chainID2 = line.substring(51, 52).trim();
String resSeq2 = line.substring(52, 56).trim();
String iCode2 = line.substring(56, 57).trim();
String iCode2 = null; // Might get trimmed if blank.
if (len > 56) iCode2 = line.substring(56, 57).trim();

String sym1 = line.substring(59, 65).trim();
String sym2 = line.substring(66, 72).trim();
String sym1 = null;
if (len > 64) sym1 = line.substring(59, 65).trim();
String sym2 = null;
if (len > 71) sym2 = line.substring(66, 72).trim();

// System.err.println("LINK");
// System.err.println("\tName: " + name1);
Expand Down Expand Up @@ -2690,54 +2703,54 @@ public Structure parsePDBFile(BufferedReader buf)

String recordName = line.substring (0, 6).trim ();

if (recordName.equals("ATOM"))
pdb_ATOM_Handler(line);
else if (recordName.equals("SEQRES"))
pdb_SEQRES_Handler(line);
else if (recordName.equals("HETATM"))
pdb_ATOM_Handler(line);
else if (recordName.equals("MODEL"))
pdb_MODEL_Handler(line);
else if (recordName.equals("HEADER"))
pdb_HEADER_Handler(line);
else if (recordName.equals("AUTHOR"))
pdb_AUTHOR_Handler(line);
else if (recordName.equals("TITLE"))
pdb_TITLE_Handler(line);
else if (recordName.equals("SOURCE"))
sourceLines.add(line); //pdb_SOURCE_Handler
else if (recordName.equals("COMPND"))
compndLines.add(line); //pdb_COMPND_Handler
else if (recordName.equals("JRNL"))
pdb_JRNL_Handler(line);
else if (recordName.equals("EXPDTA"))
pdb_EXPDTA_Handler(line);
else if (recordName.equals("CRYST1"))
pdb_CRYST1_Handler(line);
else if (recordName.startsWith("MTRIX"))
pdb_MTRIXn_Handler(line);
else if (recordName.equals("REMARK"))
pdb_REMARK_Handler(line);
else if (recordName.equals("CONECT"))
pdb_CONECT_Handler(line);
else if (recordName.equals("REVDAT"))
pdb_REVDAT_Handler(line);
else if (recordName.equals("DBREF"))
pdb_DBREF_Handler(line);
else if (recordName.equals("SITE"))
pdb_SITE_Handler(line);
else if (recordName.equals("SSBOND"))
pdb_SSBOND_Handler(line);
else if (recordName.equals("LINK"))
pdb_LINK_Handler(line);
else if ( params.isParseSecStruc()) {
if ( recordName.equals("HELIX") ) pdb_HELIX_Handler ( line ) ;
else if (recordName.equals("SHEET")) pdb_SHEET_Handler(line ) ;
else if (recordName.equals("TURN")) pdb_TURN_Handler( line ) ;
}
else {
// this line type is not supported, yet.
// we ignore it
try {
if (recordName.equals("ATOM"))
pdb_ATOM_Handler(line);
else if (recordName.equals("SEQRES"))
pdb_SEQRES_Handler(line);
else if (recordName.equals("HETATM"))
pdb_ATOM_Handler(line);
else if (recordName.equals("MODEL"))
pdb_MODEL_Handler(line);
else if (recordName.equals("HEADER"))
pdb_HEADER_Handler(line);
else if (recordName.equals("AUTHOR"))
pdb_AUTHOR_Handler(line);
else if (recordName.equals("TITLE"))
pdb_TITLE_Handler(line);
else if (recordName.equals("SOURCE"))
sourceLines.add(line); //pdb_SOURCE_Handler
else if (recordName.equals("COMPND"))
compndLines.add(line); //pdb_COMPND_Handler
else if (recordName.equals("JRNL"))
pdb_JRNL_Handler(line);
else if (recordName.equals("EXPDTA"))
pdb_EXPDTA_Handler(line);
else if (recordName.equals("CRYST1"))
pdb_CRYST1_Handler(line);
else if (recordName.startsWith("MTRIX"))
pdb_MTRIXn_Handler(line);
else if (recordName.equals("REMARK"))
pdb_REMARK_Handler(line);
else if (recordName.equals("CONECT"))
pdb_CONECT_Handler(line);
else if (recordName.equals("REVDAT"))
pdb_REVDAT_Handler(line);
else if (recordName.equals("DBREF"))
pdb_DBREF_Handler(line);
else if (recordName.equals("SITE"))
pdb_SITE_Handler(line);
else if (recordName.equals("SSBOND"))
pdb_SSBOND_Handler(line);
else if (recordName.equals("LINK"))
pdb_LINK_Handler(line);
else if ( params.isParseSecStruc()) {
if ( recordName.equals("HELIX") ) pdb_HELIX_Handler ( line ) ;
else if (recordName.equals("SHEET")) pdb_SHEET_Handler(line ) ;
else if (recordName.equals("TURN")) pdb_TURN_Handler( line ) ;
}
} catch (StringIndexOutOfBoundsException ex) {
logger.warn("Unable to parse [" + line + "]");
}


Expand Down
71 changes: 71 additions & 0 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestShortLines.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,71 @@
package org.biojava.nbio.structure.io;

import static org.junit.Assert.assertEquals;

import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;

import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Chain;
import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.Structure;
import org.junit.Test;

/**
* This class will test parsing short CONECT lines.
*/
public class TestShortLines {

@Test
public void testConect() throws IOException {
PDBFileParser pdbPars = new PDBFileParser();
FileParsingParameters params = pdbPars.getFileParsingParameters();
params.setCreateAtomBonds(true);

// CONECTS will be deprecated, but will we create bonds?
// Like the LINK records, should BioJava create BondImpl when params.setCreateAtomBonds(true)?

StringBuilder sb = new StringBuilder();
sb.append("HETATM 2398 P FAD A 500 8.398 46.448 73.490 1.00 13.51 P \n");
sb.append("HETATM 2399 PA FAD A 500 6.089 45.580 75.235 1.00 15.88 P \n");
sb.append("HETATM 2400 O1P FAD A 500 7.908 47.684 72.869 1.00 4.19 O \n");
sb.append("CONECT 2400 2398\n");
String shortLine = sb.toString();
Structure s;
// Parse short
try(InputStream is = new ByteArrayInputStream(shortLine.getBytes())) {
s = pdbPars.parsePDBFile(is);
}

// After 4.2, CONECTS are deprecated, but there is not yet an implementation
// describing how CONECTS will be replaced - will Bonds be created?
assertEquals(1, s.getConnections().size());
}

@Test
public void testLINK() throws IOException {
Structure s;
PDBFileParser pdbPars = new PDBFileParser();
FileParsingParameters params = pdbPars.getFileParsingParameters();
params.setCreateAtomBonds(true);

StringBuilder sb = new StringBuilder();
sb.append("ATOM 2412 C21 2EG A 7 0.888 44.973 72.238 1.00 29.17 C \n");
sb.append("ATOM 2413 C22 2EG B 19 0.888 44.973 72.238 1.00 29.17 C \n");
//sb.append("LINK C21 2EG A 7 C22 2EG B 19 1555 1555 1.56 ");
sb.append("LINK C21 2EG A 7 C22 2EG B 19\n");
String shortLine = sb.toString();

// Parse short
try(InputStream is = new ByteArrayInputStream(shortLine.getBytes())) {
s = pdbPars.parsePDBFile(is);
}

// Should be a bond present in the Atoms.
Chain c = s.getChain(0, 0);
Group g = c.getAtomGroups().get(0);
Atom a = g.getAtom(0);
assertEquals(1, a.getBonds().size());
}
}