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sbittrichsbittrich
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rewire ciftools-java
1 parent c5f42b6 commit faae1a1

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Lines changed: 134 additions & 130 deletions

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumer.java‎

Lines changed: 47 additions & 47 deletions
Original file line numberDiff line numberDiff line change
@@ -1,50 +1,50 @@
11
package org.biojava.nbio.structure.io.cif;
22

3-
import org.rcsb.cif.model.generated.AtomSite;
4-
import org.rcsb.cif.model.generated.AtomSites;
5-
import org.rcsb.cif.model.generated.AuditAuthor;
6-
import org.rcsb.cif.model.generated.Cell;
7-
import org.rcsb.cif.model.generated.ChemComp;
8-
import org.rcsb.cif.model.generated.ChemCompBond;
9-
import org.rcsb.cif.model.generated.DatabasePDBRemark;
10-
import org.rcsb.cif.model.generated.DatabasePDBRev;
11-
import org.rcsb.cif.model.generated.DatabasePDBRevRecord;
12-
import org.rcsb.cif.model.generated.Entity;
13-
import org.rcsb.cif.model.generated.EntityPoly;
14-
import org.rcsb.cif.model.generated.EntityPolySeq;
15-
import org.rcsb.cif.model.generated.EntitySrcGen;
16-
import org.rcsb.cif.model.generated.EntitySrcNat;
17-
import org.rcsb.cif.model.generated.Exptl;
18-
import org.rcsb.cif.model.generated.PdbxAuditRevisionHistory;
19-
import org.rcsb.cif.model.generated.PdbxChemCompIdentifier;
20-
import org.rcsb.cif.model.generated.PdbxDatabaseStatus;
21-
import org.rcsb.cif.model.generated.PdbxEntityDescriptor;
22-
import org.rcsb.cif.model.generated.PdbxEntitySrcSyn;
23-
import org.rcsb.cif.model.generated.PdbxMolecule;
24-
import org.rcsb.cif.model.generated.PdbxMoleculeFeatures;
25-
import org.rcsb.cif.model.generated.PdbxNonpolyScheme;
26-
import org.rcsb.cif.model.generated.PdbxReferenceEntityLink;
27-
import org.rcsb.cif.model.generated.PdbxReferenceEntityList;
28-
import org.rcsb.cif.model.generated.PdbxReferenceEntityPolyLink;
29-
import org.rcsb.cif.model.generated.PdbxStructAssembly;
30-
import org.rcsb.cif.model.generated.PdbxStructAssemblyGen;
31-
import org.rcsb.cif.model.generated.PdbxStructModResidue;
32-
import org.rcsb.cif.model.generated.PdbxStructOperList;
33-
import org.rcsb.cif.model.generated.Refine;
34-
import org.rcsb.cif.model.generated.Struct;
35-
import org.rcsb.cif.model.generated.StructAsym;
36-
import org.rcsb.cif.model.generated.StructConf;
37-
import org.rcsb.cif.model.generated.StructConn;
38-
import org.rcsb.cif.model.generated.StructConnType;
39-
import org.rcsb.cif.model.generated.StructKeywords;
40-
import org.rcsb.cif.model.generated.StructNcsOper;
41-
import org.rcsb.cif.model.generated.StructRef;
42-
import org.rcsb.cif.model.generated.StructRefSeq;
43-
import org.rcsb.cif.model.generated.StructRefSeqDif;
44-
import org.rcsb.cif.model.generated.StructSheetRange;
45-
import org.rcsb.cif.model.generated.StructSite;
46-
import org.rcsb.cif.model.generated.StructSiteGen;
47-
import org.rcsb.cif.model.generated.Symmetry;
3+
import org.rcsb.cif.schema.mm.AtomSite;
4+
import org.rcsb.cif.schema.mm.AtomSites;
5+
import org.rcsb.cif.schema.mm.AuditAuthor;
6+
import org.rcsb.cif.schema.mm.Cell;
7+
import org.rcsb.cif.schema.mm.ChemComp;
8+
import org.rcsb.cif.schema.mm.ChemCompBond;
9+
import org.rcsb.cif.schema.mm.DatabasePDBRemark;
10+
import org.rcsb.cif.schema.mm.DatabasePDBRev;
11+
import org.rcsb.cif.schema.mm.DatabasePDBRevRecord;
12+
import org.rcsb.cif.schema.mm.Entity;
13+
import org.rcsb.cif.schema.mm.EntityPoly;
14+
import org.rcsb.cif.schema.mm.EntityPolySeq;
15+
import org.rcsb.cif.schema.mm.EntitySrcGen;
16+
import org.rcsb.cif.schema.mm.EntitySrcNat;
17+
import org.rcsb.cif.schema.mm.Exptl;
18+
import org.rcsb.cif.schema.mm.PdbxAuditRevisionHistory;
19+
import org.rcsb.cif.schema.mm.PdbxChemCompIdentifier;
20+
import org.rcsb.cif.schema.mm.PdbxDatabaseStatus;
21+
import org.rcsb.cif.schema.mm.PdbxEntityBranchDescriptor;
22+
import org.rcsb.cif.schema.mm.PdbxEntitySrcSyn;
23+
import org.rcsb.cif.schema.mm.PdbxMolecule;
24+
import org.rcsb.cif.schema.mm.PdbxMoleculeFeatures;
25+
import org.rcsb.cif.schema.mm.PdbxNonpolyScheme;
26+
import org.rcsb.cif.schema.mm.PdbxReferenceEntityLink;
27+
import org.rcsb.cif.schema.mm.PdbxReferenceEntityList;
28+
import org.rcsb.cif.schema.mm.PdbxReferenceEntityPolyLink;
29+
import org.rcsb.cif.schema.mm.PdbxStructAssembly;
30+
import org.rcsb.cif.schema.mm.PdbxStructAssemblyGen;
31+
import org.rcsb.cif.schema.mm.PdbxStructModResidue;
32+
import org.rcsb.cif.schema.mm.PdbxStructOperList;
33+
import org.rcsb.cif.schema.mm.Refine;
34+
import org.rcsb.cif.schema.mm.Struct;
35+
import org.rcsb.cif.schema.mm.StructAsym;
36+
import org.rcsb.cif.schema.mm.StructConf;
37+
import org.rcsb.cif.schema.mm.StructConn;
38+
import org.rcsb.cif.schema.mm.StructConnType;
39+
import org.rcsb.cif.schema.mm.StructKeywords;
40+
import org.rcsb.cif.schema.mm.StructNcsOper;
41+
import org.rcsb.cif.schema.mm.StructRef;
42+
import org.rcsb.cif.schema.mm.StructRefSeq;
43+
import org.rcsb.cif.schema.mm.StructRefSeqDif;
44+
import org.rcsb.cif.schema.mm.StructSheetRange;
45+
import org.rcsb.cif.schema.mm.StructSite;
46+
import org.rcsb.cif.schema.mm.StructSiteGen;
47+
import org.rcsb.cif.schema.mm.Symmetry;
4848

4949
/**
5050
* Defines a rather generic interface which allows to populate some data structure with data parsed from a CIF file.
@@ -175,9 +175,9 @@ interface CifFileConsumer<S> {
175175

176176
/**
177177
* Consume a particular Cif category.
178-
* @param pdbxEntityDescriptor data
178+
* @param pdbxEntityBranchDescriptor data
179179
*/
180-
void consumePdbxEntityDescriptor(PdbxEntityDescriptor pdbxEntityDescriptor);
180+
void consumePdbxEntityBranchDescriptor(PdbxEntityBranchDescriptor pdbxEntityBranchDescriptor);
181181

182182
/**
183183
* Consume a particular Cif category.

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java‎

Lines changed: 46 additions & 46 deletions
Original file line numberDiff line numberDiff line change
@@ -40,51 +40,51 @@
4040
import org.rcsb.cif.model.FloatColumn;
4141
import org.rcsb.cif.model.IntColumn;
4242
import org.rcsb.cif.model.StrColumn;
43-
import org.rcsb.cif.model.generated.AtomSite;
44-
import org.rcsb.cif.model.generated.AtomSites;
45-
import org.rcsb.cif.model.generated.AuditAuthor;
46-
import org.rcsb.cif.model.generated.Cell;
47-
import org.rcsb.cif.model.generated.ChemComp;
48-
import org.rcsb.cif.model.generated.ChemCompBond;
49-
import org.rcsb.cif.model.generated.DatabasePDBRemark;
50-
import org.rcsb.cif.model.generated.DatabasePDBRev;
51-
import org.rcsb.cif.model.generated.DatabasePDBRevRecord;
52-
import org.rcsb.cif.model.generated.Entity;
53-
import org.rcsb.cif.model.generated.EntityPoly;
54-
import org.rcsb.cif.model.generated.EntityPolySeq;
55-
import org.rcsb.cif.model.generated.EntitySrcGen;
56-
import org.rcsb.cif.model.generated.EntitySrcNat;
57-
import org.rcsb.cif.model.generated.Exptl;
58-
import org.rcsb.cif.model.generated.PdbxAuditRevisionHistory;
59-
import org.rcsb.cif.model.generated.PdbxChemCompIdentifier;
60-
import org.rcsb.cif.model.generated.PdbxDatabaseStatus;
61-
import org.rcsb.cif.model.generated.PdbxEntityDescriptor;
62-
import org.rcsb.cif.model.generated.PdbxEntitySrcSyn;
63-
import org.rcsb.cif.model.generated.PdbxMolecule;
64-
import org.rcsb.cif.model.generated.PdbxMoleculeFeatures;
65-
import org.rcsb.cif.model.generated.PdbxNonpolyScheme;
66-
import org.rcsb.cif.model.generated.PdbxReferenceEntityLink;
67-
import org.rcsb.cif.model.generated.PdbxReferenceEntityList;
68-
import org.rcsb.cif.model.generated.PdbxReferenceEntityPolyLink;
69-
import org.rcsb.cif.model.generated.PdbxStructAssembly;
70-
import org.rcsb.cif.model.generated.PdbxStructAssemblyGen;
71-
import org.rcsb.cif.model.generated.PdbxStructModResidue;
72-
import org.rcsb.cif.model.generated.PdbxStructOperList;
73-
import org.rcsb.cif.model.generated.Refine;
74-
import org.rcsb.cif.model.generated.Struct;
75-
import org.rcsb.cif.model.generated.StructAsym;
76-
import org.rcsb.cif.model.generated.StructConf;
77-
import org.rcsb.cif.model.generated.StructConn;
78-
import org.rcsb.cif.model.generated.StructConnType;
79-
import org.rcsb.cif.model.generated.StructKeywords;
80-
import org.rcsb.cif.model.generated.StructNcsOper;
81-
import org.rcsb.cif.model.generated.StructRef;
82-
import org.rcsb.cif.model.generated.StructRefSeq;
83-
import org.rcsb.cif.model.generated.StructRefSeqDif;
84-
import org.rcsb.cif.model.generated.StructSheetRange;
85-
import org.rcsb.cif.model.generated.StructSite;
86-
import org.rcsb.cif.model.generated.StructSiteGen;
87-
import org.rcsb.cif.model.generated.Symmetry;
43+
import org.rcsb.cif.schema.mm.AtomSite;
44+
import org.rcsb.cif.schema.mm.AtomSites;
45+
import org.rcsb.cif.schema.mm.AuditAuthor;
46+
import org.rcsb.cif.schema.mm.Cell;
47+
import org.rcsb.cif.schema.mm.ChemComp;
48+
import org.rcsb.cif.schema.mm.ChemCompBond;
49+
import org.rcsb.cif.schema.mm.DatabasePDBRemark;
50+
import org.rcsb.cif.schema.mm.DatabasePDBRev;
51+
import org.rcsb.cif.schema.mm.DatabasePDBRevRecord;
52+
import org.rcsb.cif.schema.mm.Entity;
53+
import org.rcsb.cif.schema.mm.EntityPoly;
54+
import org.rcsb.cif.schema.mm.EntityPolySeq;
55+
import org.rcsb.cif.schema.mm.EntitySrcGen;
56+
import org.rcsb.cif.schema.mm.EntitySrcNat;
57+
import org.rcsb.cif.schema.mm.Exptl;
58+
import org.rcsb.cif.schema.mm.PdbxAuditRevisionHistory;
59+
import org.rcsb.cif.schema.mm.PdbxChemCompIdentifier;
60+
import org.rcsb.cif.schema.mm.PdbxDatabaseStatus;
61+
import org.rcsb.cif.schema.mm.PdbxEntityBranchDescriptor;
62+
import org.rcsb.cif.schema.mm.PdbxEntitySrcSyn;
63+
import org.rcsb.cif.schema.mm.PdbxMolecule;
64+
import org.rcsb.cif.schema.mm.PdbxMoleculeFeatures;
65+
import org.rcsb.cif.schema.mm.PdbxNonpolyScheme;
66+
import org.rcsb.cif.schema.mm.PdbxReferenceEntityLink;
67+
import org.rcsb.cif.schema.mm.PdbxReferenceEntityList;
68+
import org.rcsb.cif.schema.mm.PdbxReferenceEntityPolyLink;
69+
import org.rcsb.cif.schema.mm.PdbxStructAssembly;
70+
import org.rcsb.cif.schema.mm.PdbxStructAssemblyGen;
71+
import org.rcsb.cif.schema.mm.PdbxStructModResidue;
72+
import org.rcsb.cif.schema.mm.PdbxStructOperList;
73+
import org.rcsb.cif.schema.mm.Refine;
74+
import org.rcsb.cif.schema.mm.Struct;
75+
import org.rcsb.cif.schema.mm.StructAsym;
76+
import org.rcsb.cif.schema.mm.StructConf;
77+
import org.rcsb.cif.schema.mm.StructConn;
78+
import org.rcsb.cif.schema.mm.StructConnType;
79+
import org.rcsb.cif.schema.mm.StructKeywords;
80+
import org.rcsb.cif.schema.mm.StructNcsOper;
81+
import org.rcsb.cif.schema.mm.StructRef;
82+
import org.rcsb.cif.schema.mm.StructRefSeq;
83+
import org.rcsb.cif.schema.mm.StructRefSeqDif;
84+
import org.rcsb.cif.schema.mm.StructSheetRange;
85+
import org.rcsb.cif.schema.mm.StructSite;
86+
import org.rcsb.cif.schema.mm.StructSiteGen;
87+
import org.rcsb.cif.schema.mm.Symmetry;
8888
import org.slf4j.Logger;
8989
import org.slf4j.LoggerFactory;
9090

@@ -770,7 +770,7 @@ public void consumePdbxDatabaseStatus(PdbxDatabaseStatus pdbxDatabaseStatus) {
770770
}
771771

772772
@Override
773-
public void consumePdbxEntityDescriptor(PdbxEntityDescriptor pdbxEntityDescriptor) {
773+
public void consumePdbxEntityBranchDescriptor(PdbxEntityBranchDescriptor pdbxEntityBranchDescriptor) {
774774
// TODO not considered in ref
775775
}
776776

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConverter.java‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,9 @@
33
import org.biojava.nbio.structure.Structure;
44
import org.biojava.nbio.structure.io.FileParsingParameters;
55
import org.rcsb.cif.CifIO;
6-
import org.rcsb.cif.model.Block;
76
import org.rcsb.cif.model.CifFile;
7+
import org.rcsb.cif.schema.StandardSchemata;
8+
import org.rcsb.cif.schema.mm.MmCifBlock;
89

910
import java.io.IOException;
1011
import java.io.InputStream;
@@ -104,7 +105,7 @@ public static Structure fromCifFile(CifFile cifFile, FileParsingParameters param
104105
consumer.prepare();
105106

106107
// feed individual categories to consumer
107-
Block cifBlock = cifFile.getFirstBlock();
108+
MmCifBlock cifBlock = cifFile.as(StandardSchemata.MMCIF).getFirstBlock();
108109

109110
consumer.consumeAuditAuthor(cifBlock.getAuditAuthor());
110111
consumer.consumeAtomSite(cifBlock.getAtomSite());
@@ -125,7 +126,7 @@ public static Structure fromCifFile(CifFile cifFile, FileParsingParameters param
125126
consumer.consumePdbxAuditRevisionHistory(cifBlock.getPdbxAuditRevisionHistory());
126127
consumer.consumePdbxChemCompIdentifier(cifBlock.getPdbxChemCompIdentifier());
127128
consumer.consumePdbxDatabaseStatus(cifBlock.getPdbxDatabaseStatus());
128-
consumer.consumePdbxEntityDescriptor(cifBlock.getPdbxEntityDescriptor());
129+
consumer.consumePdbxEntityBranchDescriptor(cifBlock.getPdbxEntityBranchDescriptor());
129130
consumer.consumePdbxMolecule(cifBlock.getPdbxMolecule());
130131
consumer.consumePdbxMoleculeFeatures(cifBlock.getPdbxMoleculeFeatures());
131132
consumer.consumePdbxNonpolyScheme(cifBlock.getPdbxNonpolyScheme());

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImpl.java‎

Lines changed: 32 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -9,14 +9,16 @@
99
import org.biojava.nbio.structure.Structure;
1010
import org.biojava.nbio.structure.xtal.CrystalCell;
1111
import org.biojava.nbio.structure.xtal.SpaceGroup;
12+
import org.rcsb.cif.CifBuilder;
1213
import org.rcsb.cif.model.Category;
1314
import org.rcsb.cif.model.CifFile;
14-
import org.rcsb.cif.model.builder.BlockBuilder;
15-
import org.rcsb.cif.model.builder.CategoryBuilder;
16-
import org.rcsb.cif.model.builder.CifBuilder;
17-
import org.rcsb.cif.model.builder.FloatColumnBuilder;
18-
import org.rcsb.cif.model.builder.IntColumnBuilder;
19-
import org.rcsb.cif.model.builder.StrColumnBuilder;
15+
import org.rcsb.cif.model.FloatColumnBuilder;
16+
import org.rcsb.cif.model.IntColumnBuilder;
17+
import org.rcsb.cif.model.StrColumnBuilder;
18+
import org.rcsb.cif.schema.StandardSchemata;
19+
import org.rcsb.cif.schema.mm.MmCifBlockBuilder;
20+
import org.rcsb.cif.schema.mm.MmCifCategoryBuilder;
21+
import org.rcsb.cif.schema.mm.MmCifFileBuilder;
2022

2123
import java.util.ArrayList;
2224
import java.util.LinkedHashMap;
@@ -43,7 +45,7 @@ public CifFile get(Structure structure) {
4345
List<WrappedAtom> wrappedAtoms = collectWrappedAtoms(structure);
4446
Category atomSite = wrappedAtoms.stream().collect(toAtomSite());
4547

46-
BlockBuilder blockBuilder = new CifBuilder()
48+
MmCifBlockBuilder blockBuilder = CifBuilder.enterFile(StandardSchemata.MMCIF)
4749
.enterBlock(structure.getPDBCode());
4850

4951
if (atomSite.isDefined() && atomSite.getRowCount() > 0) {
@@ -187,30 +189,30 @@ int getAtomId() {
187189
}
188190

189191
static class AtomSiteCollector implements Consumer<WrappedAtom> {
190-
private final CategoryBuilder.AtomSiteBuilder atomSiteBuilder;
191-
private final StrColumnBuilder<CategoryBuilder.AtomSiteBuilder> groupPDB;
192-
private final IntColumnBuilder<CategoryBuilder.AtomSiteBuilder> id;
193-
private final StrColumnBuilder<CategoryBuilder.AtomSiteBuilder> typeSymbol;
194-
private final StrColumnBuilder<CategoryBuilder.AtomSiteBuilder> labelAtomId;
195-
private final StrColumnBuilder<CategoryBuilder.AtomSiteBuilder> labelAltId;
196-
private final StrColumnBuilder<CategoryBuilder.AtomSiteBuilder> labelCompId;
197-
private final StrColumnBuilder<CategoryBuilder.AtomSiteBuilder> labelAsymId;
198-
private final StrColumnBuilder<CategoryBuilder.AtomSiteBuilder> labelEntityId;
199-
private final IntColumnBuilder<CategoryBuilder.AtomSiteBuilder> labelSeqId;
200-
private final StrColumnBuilder<CategoryBuilder.AtomSiteBuilder> pdbxPDBInsCode;
201-
private final FloatColumnBuilder<CategoryBuilder.AtomSiteBuilder> cartnX;
202-
private final FloatColumnBuilder<CategoryBuilder.AtomSiteBuilder> cartnY;
203-
private final FloatColumnBuilder<CategoryBuilder.AtomSiteBuilder> cartnZ;
204-
private final FloatColumnBuilder<CategoryBuilder.AtomSiteBuilder> occupancy;
205-
private final FloatColumnBuilder<CategoryBuilder.AtomSiteBuilder> bIsoOrEquiv;
206-
private final IntColumnBuilder<CategoryBuilder.AtomSiteBuilder> authSeqId;
207-
private final StrColumnBuilder<CategoryBuilder.AtomSiteBuilder> authCompId;
208-
private final StrColumnBuilder<CategoryBuilder.AtomSiteBuilder> authAsymId;
209-
private final StrColumnBuilder<CategoryBuilder.AtomSiteBuilder> authAtomId;
210-
private final IntColumnBuilder<CategoryBuilder.AtomSiteBuilder> pdbxPDBModelNum;
192+
private final MmCifCategoryBuilder.AtomSiteBuilder atomSiteBuilder;
193+
private final StrColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> groupPDB;
194+
private final IntColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> id;
195+
private final StrColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> typeSymbol;
196+
private final StrColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> labelAtomId;
197+
private final StrColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> labelAltId;
198+
private final StrColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> labelCompId;
199+
private final StrColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> labelAsymId;
200+
private final StrColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> labelEntityId;
201+
private final IntColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> labelSeqId;
202+
private final StrColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> pdbxPDBInsCode;
203+
private final FloatColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> cartnX;
204+
private final FloatColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> cartnY;
205+
private final FloatColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> cartnZ;
206+
private final FloatColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> occupancy;
207+
private final FloatColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> bIsoOrEquiv;
208+
private final IntColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> authSeqId;
209+
private final StrColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> authCompId;
210+
private final StrColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> authAsymId;
211+
private final StrColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> authAtomId;
212+
private final IntColumnBuilder<MmCifCategoryBuilder.AtomSiteBuilder, MmCifBlockBuilder, MmCifFileBuilder> pdbxPDBModelNum;
211213

212214
AtomSiteCollector() {
213-
this.atomSiteBuilder = new CategoryBuilder.AtomSiteBuilder(null);
215+
this.atomSiteBuilder = new MmCifCategoryBuilder.AtomSiteBuilder(null);
214216
this.groupPDB = atomSiteBuilder.enterGroupPDB();
215217
this.id = atomSiteBuilder.enterId();
216218
this.typeSymbol = atomSiteBuilder.enterTypeSymbol();
@@ -286,7 +288,7 @@ public void accept(WrappedAtom wrappedAtom) {
286288
}
287289

288290
AtomSiteCollector combine(AtomSiteCollector other) {
289-
throw new UnsupportedOperationException("impl by calling addAll for all collection - not feeling like writing that code");
291+
throw new UnsupportedOperationException("impl by calling addAll for all collection");
290292
}
291293

292294
Category get() {

‎biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImplTest.java‎

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -9,9 +9,10 @@
99
import org.biojava.nbio.structure.io.PDBFileParser;
1010
import org.junit.Test;
1111
import org.rcsb.cif.CifIO;
12-
import org.rcsb.cif.model.CifFile;
13-
import org.rcsb.cif.model.Column;
12+
import org.rcsb.cif.model.IntColumn;
1413
import org.rcsb.cif.model.ValueKind;
14+
import org.rcsb.cif.schema.StandardSchemata;
15+
import org.rcsb.cif.schema.mm.MmCifFile;
1516

1617
import java.io.ByteArrayInputStream;
1718
import java.io.IOException;
@@ -210,8 +211,8 @@ public void specialCases() throws IOException {
210211
"7 1S32 . D . GB 30268542 MET 1 'INTIATING METHIONINE' ? ? 7\n"+
211212
"8 1S32 . H . GB 30268542 MET 1 'INTIATING METHIONINE' ? ? 8\n" +
212213
"#" ;
213-
CifFile cifFile = CifIO.readFromInputStream(new ByteArrayInputStream(mmcifStr.getBytes()));
214-
Column column = cifFile.getFirstBlock().getCategory("struct_ref_seq_dif").getColumn("seq_num");
214+
MmCifFile cifFile = CifIO.readFromInputStream(new ByteArrayInputStream(mmcifStr.getBytes())).as(StandardSchemata.MMCIF);
215+
IntColumn column = cifFile.getFirstBlock().getStructRefSeqDif().getSeqNum();
215216

216217
assertNotNull(column);
217218
assertTrue(column.isDefined());

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