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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (1.8.0_222) on Fri Sep 06 15:20:46 PDT 2019 -->
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title>Deprecated List (biojava 5.3.0 API)</title>
<meta name="date" content="2019-09-06">
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<div class="header">
<h1 title="Deprecated API" class="title">Deprecated API</h1>
<h2 title="Contents">Contents</h2>
<ul>
<li><a href="#method">Deprecated Methods</a></li>
</ul>
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<table class="deprecatedSummary" border="0" cellpadding="3" cellspacing="0" summary="Deprecated Methods table, listing deprecated methods, and an explanation">
<caption><span>Deprecated Methods</span><span class="tabEnd"> </span></caption>
<tr>
<th class="colOne" scope="col">Method and Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#findChain-java.lang.String-">org.biojava.nbio.structure.Structure.findChain(String)</a></td>
</tr>
<tr class="rowColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#findChain-java.lang.String-int-">org.biojava.nbio.structure.Structure.findChain(String, int)</a></td>
</tr>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Chain.html#getAtomLigands--">org.biojava.nbio.structure.Chain.getAtomLigands()</a>
<div class="block"><span class="deprecationComment">since biojava 5.0 this does not apply anymore. Chains contain either
polymeric groups or non-polymeric groups</span></div>
</td>
</tr>
<tr class="rowColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#getChainByPDB-java.lang.String-">org.biojava.nbio.structure.Structure.getChainByPDB(String)</a>
<div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Structure.html#getPolyChainByPDB-java.lang.String-"><code>Structure.getPolyChainByPDB(String)</code></a> instead</span></div>
</td>
</tr>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#getChainByPDB-java.lang.String-int-">org.biojava.nbio.structure.Structure.getChainByPDB(String, int)</a>
<div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Structure.html#getPolyChainByPDB-java.lang.String-int-"><code>Structure.getPolyChainByPDB(String,int)</code></a> instead</span></div>
</td>
</tr>
<tr class="rowColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Chain.html#getChainID--">org.biojava.nbio.structure.Chain.getChainID()</a>
<div class="block"><span class="deprecationComment">use getId() instead</span></div>
</td>
</tr>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#getCompoundById-int-">org.biojava.nbio.structure.Structure.getCompoundById(int)</a>
<div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Structure.html#getEntityById-int-"><code>Structure.getEntityById(int)</code></a> instead</span></div>
</td>
</tr>
<tr class="rowColor">
<td class="colOne"><a href="org/biojava/nbio/structure/contact/Grid.html#getContacts--">org.biojava.nbio.structure.contact.Grid.getContacts()</a>
<div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/contact/Grid.html#getAtomContacts--"><code>Grid.getAtomContacts()</code></a> instead</span></div>
</td>
</tr>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Chain.html#getInternalChainID--">org.biojava.nbio.structure.Chain.getInternalChainID()</a>
<div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Chain.html#getId--"><code>Chain.getId()</code></a> instead</span></div>
</td>
</tr>
<tr class="rowColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Chain.html#getParent--">org.biojava.nbio.structure.Chain.getParent()</a>
<div class="block"><span class="deprecationComment">use getStructure(Structure) instead.</span></div>
</td>
</tr>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/ChainImpl.html#getParent--">org.biojava.nbio.structure.ChainImpl.getParent()</a>
<div class="block"><span class="deprecationComment">use getStructure instead.</span></div>
</td>
</tr>
<tr class="rowColor">
<td class="colOne"><a href="org/biojava/nbio/structure/StructureImpl.html#getPdbId--">org.biojava.nbio.structure.StructureImpl.getPdbId()</a></td>
</tr>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#getPdbId--">org.biojava.nbio.structure.Structure.getPdbId()</a>
<div class="block"><span class="deprecationComment">From BioJava 4.2, use <a href="org/biojava/nbio/structure/Structure.html#getPDBCode--"><code>Structure.getPDBCode()</code></a> or
<code>getStructureIdentifier().toCanonical().getPdbId()</code></span></div>
</td>
</tr>
<tr class="rowColor">
<td class="colOne"><a href="org/biojava/nbio/structure/StructureTools.html#getPredominantGroupType-org.biojava.nbio.structure.Chain-">org.biojava.nbio.structure.StructureTools.getPredominantGroupType(Chain)</a>
<div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Chain.html#getPredominantGroupType--"><code>Chain.getPredominantGroupType()</code></a> instead.</span></div>
</td>
</tr>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/StructureImpl.html#getRanges--">org.biojava.nbio.structure.StructureImpl.getRanges()</a></td>
</tr>
<tr class="rowColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#getRanges--">org.biojava.nbio.structure.Structure.getRanges()</a>
<div class="block"><span class="deprecationComment">From BioJava 4.2, use
<code>getStructureIdentifier().toCanonical().getRanges()</code></span></div>
</td>
</tr>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/StructureTools.html#getReducedStructure-org.biojava.nbio.structure.Structure-java.lang.String-">org.biojava.nbio.structure.StructureTools.getReducedStructure(Structure, String)</a>
<div class="block"><span class="deprecationComment">Use <a href="org/biojava/nbio/structure/StructureIdentifier.html#reduce-org.biojava.nbio.structure.Structure-"><code>StructureIdentifier.reduce(Structure)</code></a> instead (v. 4.2.0)</span></div>
</td>
</tr>
<tr class="rowColor">
<td class="colOne"><a href="org/biojava/nbio/structure/StructureImpl.html#getResidueRanges--">org.biojava.nbio.structure.StructureImpl.getResidueRanges()</a></td>
</tr>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#getResidueRanges--">org.biojava.nbio.structure.Structure.getResidueRanges()</a>
<div class="block"><span class="deprecationComment">From BioJava 4.2, use
<code>getStructureIdentifier().toCanonical().getResidueRanges()</code></span></div>
</td>
</tr>
<tr class="rowColor">
<td class="colOne"><a href="org/biojava/nbio/structure/StructureTools.html#isChainPureNonPolymer-org.biojava.nbio.structure.Chain-">org.biojava.nbio.structure.StructureTools.isChainPureNonPolymer(Chain)</a>
<div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Chain.html#isPureNonPolymer--"><code>Chain.isPureNonPolymer()</code></a> instead.</span></div>
</td>
</tr>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/StructureTools.html#isChainWaterOnly-org.biojava.nbio.structure.Chain-">org.biojava.nbio.structure.StructureTools.isChainWaterOnly(Chain)</a>
<div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Chain.html#isWaterOnly--"><code>Chain.isWaterOnly()</code></a> instead.</span></div>
</td>
</tr>
<tr class="rowColor">
<td class="colOne"><a href="org/biojava/nbio/structure/StructureTools.html#isNucleicAcid-org.biojava.nbio.structure.Chain-">org.biojava.nbio.structure.StructureTools.isNucleicAcid(Chain)</a>
<div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Chain.html#isNucleicAcid--"><code>Chain.isNucleicAcid()</code></a> instead.</span></div>
</td>
</tr>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/StructureTools.html#isProtein-org.biojava.nbio.structure.Chain-">org.biojava.nbio.structure.StructureTools.isProtein(Chain)</a>
<div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Chain.html#isProtein--"><code>Chain.isProtein()</code></a> instead.</span></div>
</td>
</tr>
<tr class="rowColor">
<td class="colOne"><a href="org/biojava/nbio/genome/parsers/gff/LocIterator.html#main-java.lang.String:A-">org.biojava.nbio.genome.parsers.gff.LocIterator.main(String[])</a> </td>
</tr>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Chain.html#setChainID-java.lang.String-">org.biojava.nbio.structure.Chain.setChainID(String)</a>
<div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Chain.html#setId-java.lang.String-"><code>Chain.setId(String asymId)</code></a> instead</span></div>
</td>
</tr>
<tr class="rowColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Chain.html#setInternalChainID-java.lang.String-">org.biojava.nbio.structure.Chain.setInternalChainID(String)</a>
<div class="block"><span class="deprecationComment">use <code>#setId()</code> instead</span></div>
</td>
</tr>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/Chain.html#setParent-org.biojava.nbio.structure.Structure-">org.biojava.nbio.structure.Chain.setParent(Structure)</a>
<div class="block"><span class="deprecationComment">use setStructure instead</span></div>
</td>
</tr>
<tr class="rowColor">
<td class="colOne"><a href="org/biojava/nbio/structure/ChainImpl.html#setParent-org.biojava.nbio.structure.Structure-">org.biojava.nbio.structure.ChainImpl.setParent(Structure)</a></td>
</tr>
<tr class="altColor">
<td class="colOne"><a href="org/biojava/nbio/structure/symmetry/internal/CESymmParameters.html#setRefineResult-boolean-">org.biojava.nbio.structure.symmetry.internal.CESymmParameters.setRefineResult(boolean)</a></td>
</tr>
</tbody>
</table>
</li>
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