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sblivenjosemduarte
sbliven
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josemduarte
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Fix #480. Correct spelling of _symmetry.space_group_name_H-M in CIF output
CIF categories are represented as a simple bean, typically extending AbstractBean. By default, all fields from the bean are taken as the CIF labels. Fields may be omitted by annotating them as @IgnoreField. The CIF label for a field may be changed by defining a function, `static Map<String,String> getCIFLabelMap();`, mapping from the field's name to the correct label. This commit also changes the MMCIFFileTools.toMMCIF method to be generic, so that we enforce at compile time that all loop rows must be of the same type.
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6 files changed

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java‎

Lines changed: 17 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -20,25 +20,33 @@
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*/
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package org.biojava.nbio.structure.contact;
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23-
import org.biojava.nbio.structure.*;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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import java.util.TreeMap;
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29+
import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.Chain;
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import org.biojava.nbio.structure.Element;
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import org.biojava.nbio.structure.Compound;
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import org.biojava.nbio.structure.Group;
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import org.biojava.nbio.structure.GroupType;
35+
import org.biojava.nbio.structure.ResidueNumber;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.asa.AsaCalculator;
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import org.biojava.nbio.structure.asa.GroupAsa;
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import org.biojava.nbio.structure.io.FileConvert;
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import org.biojava.nbio.structure.io.FileParsingParameters;
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import org.biojava.nbio.structure.io.mmcif.MMCIFFileTools;
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import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
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import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
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import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
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import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
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import org.biojava.nbio.structure.xtal.CrystalTransform;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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36-
import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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import java.util.TreeMap;
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/**
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* An interface between 2 molecules (2 sets of atoms).
@@ -753,7 +761,7 @@ public String toMMCIF() {
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// we reassign atom ids if sym related (otherwise atom ids would be duplicated and some molecular viewers can't cope with that)
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int atomId = 1;
756-
List<Object> atomSites = new ArrayList<Object>();
764+
List<AtomSite> atomSites = new ArrayList<>();
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for (Atom atom:this.molecules.getFirst()) {
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if (isSymRelated()) {
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atomSites.add(MMCIFFileTools.convertAtomToAtomSite(atom, 1, molecId1, molecId1, atomId));
@@ -771,7 +779,7 @@ public String toMMCIF() {
771779
atomId++;
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}
773781

774-
sb.append(MMCIFFileTools.toMMCIF(atomSites));
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sb.append(MMCIFFileTools.toMMCIF(atomSites,AtomSite.class));
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return sb.toString();
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}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java‎

Lines changed: 4 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -680,12 +680,10 @@ public String toMMCIF() {
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str.append(getAtomSiteHeader());
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@SuppressWarnings("unchecked")
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List<Object> list =
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(List<Object>) (List<?>) MMCIFFileTools.convertStructureToAtomSites(structure);
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List<AtomSite> list = MMCIFFileTools.convertStructureToAtomSites(structure);
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687685

688-
str.append(MMCIFFileTools.toMMCIF(list));
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str.append(MMCIFFileTools.toMMCIF(list,AtomSite.class));
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return str.toString();
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}
@@ -697,11 +695,9 @@ public static String toMMCIF(Chain chain, String chainId, String internalChainId
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str.append(getAtomSiteHeader());
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@SuppressWarnings("unchecked")
701-
List<Object> list =
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(List<Object>) (List<?>) MMCIFFileTools.convertChainToAtomSites(chain, 1, chainId, internalChainId);
698+
List<AtomSite> list = MMCIFFileTools.convertChainToAtomSites(chain, 1, chainId, internalChainId);
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704-
str.append(MMCIFFileTools.toMMCIF(list));
700+
str.append(MMCIFFileTools.toMMCIF(list,AtomSite.class));
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return str.toString();
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}
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