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Remove old mmCIF parsing and refactor chemcomp handling #912

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Merged
josemduarte merged 27 commits into from
Feb 26, 2021
Merged

Remove old mmCIF parsing and refactor chemcomp handling #912

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e3bad37
detach mmcif.model.DatabasePdbrevRecord
sbittrich Nov 18, 2020
c290ea9
wip (most of structure parsing done)
sbittrich Jan 13, 2021
993665a
wip (TODO chemcomp parsing)
sbittrich Jan 14, 2021
1b164a9
compiling
sbittrich Jan 20, 2021
b992e74
metal parsing
sbittrich Jan 25, 2021
61bd8e8
new filetype param
sbittrich Jan 25, 2021
e7f563d
fix bcif download
sbittrich Jan 25, 2021
0c00cac
fix chemcomp type
sbittrich Jan 25, 2021
16792bd
Merge remote-tracking branch 'upstream/master' into bcif-integration
sbittrich Jan 26, 2021
85b6c6b
chem comp parsing errors & missing crystal translation
sbittrich Jan 26, 2021
e9c59f6
fix entity parsing
sbittrich Jan 26, 2021
28815db
handle missing rfree/rwork
sbittrich Jan 26, 2021
f36f82c
SCOP hack to force loading of MMTF
sbittrich Jan 26, 2021
63d2ee7
bcif/models URL is a constant
sbittrich Jan 26, 2021
2d4cc74
StructureInterface#toMMCIF
sbittrich Jan 26, 2021
b7a40c5
TODO TestHardBioUnits
sbittrich Jan 27, 2021
2f91dbf
those aren't the FloatColumns you're looking for
sbittrich Jan 27, 2021
9f42c9c
trigger build
sbittrich Jan 27, 2021
454830a
docs
sbittrich Jan 27, 2021
4f44fce
Group.java from upstream
sbittrich Feb 1, 2021
53982b0
update CHANGELOG.md
sbittrich Feb 2, 2021
19766ca
update AtomCacheTest
sbittrich Feb 3, 2021
58efc46
Merge remote-tracking branch 'upstream/master' into bcif-integration
sbittrich Feb 4, 2021
e94f047
increase QCP precision threshold (try to fix #914)
sbittrich Feb 10, 2021
83cf763
Revert "increase QCP precision threshold (try to fix #914)"
sbittrich Feb 12, 2021
54f4c2b
dedicated test for SuperPositionQCP issues (#914)
sbittrich Feb 24, 2021
288b18c
switch from QCP to SVD
sbittrich Feb 24, 2021
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10 changes: 10 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -15,6 +15,16 @@ BioJava 6.0.0 (future release)
* Support for automatically fetching dssp files from RCSB (`org.biojava.nbio.structure.secstruc.DSSPParser.fetch()`)
* `org.biojava.nbio.structure.PDBStatus`: simplified `Status` enum to 3 states, with OBSOLETE now called REMOVED
* `org.biojava.nbio.structure.PDBStatus`: removed `getReplacement` and `getReplaces`
* Removed `org.biojava.nbio.structure.io.mmcif` package
* Removed functionality to write isolated CIF headers from `FileConvert`

### Breaking API changes
* Extracted `StructureIO.StructureFiletype` enum to `org.biojava.nbio.structure.io.StructureFiletype` (supports `PDB`, `MMTF`, `CIF`, and `BCIF`)
* `org.biojava.nbio.structure.align.util.AtomCache`: removed `setUseMmCif`, `setUseMmtf`, `isUseMmCif`, and `isUseMmtf` - replaced by `setFiletype` and `getFiletype` that controls parsed content via the `StructureFiletype`
* `org.biojava.nbio.structure.io.MMCIFFileReader` is now effectively `org.biojava.nbio.structure.io.CifFileReader`
* Moved `org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord` to `org.biojava.nbio.structure.DatabasePDBRevRecord.java`
* Moved all chem-comp model classes from `org.biojava.nbio.structure.io.mmcif.chem` to `org.biojava.nbio.structure.chem`
* Moved all chem-comp parsing classes from `org.biojava.nbio.structure.io.mmcif.chem` to `org.biojava.nbio.structure.io.cif`

BioJava 5.4.0
=============
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295 changes: 0 additions & 295 deletions biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/MMcifTest.java
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This file was deleted.

11 changes: 6 additions & 5 deletions ...ava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java
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Expand Up @@ -24,11 +24,12 @@

import org.biojava.nbio.structure.*;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.chem.ChemCompGroupFactory;
import org.biojava.nbio.structure.chem.ChemCompProvider;
import org.biojava.nbio.structure.chem.DownloadChemCompProvider;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.io.PDBFileParser;
import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
import org.biojava.nbio.structure.io.mmcif.ChemCompProvider;
import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
import org.biojava.nbio.structure.io.StructureFiletype;
import org.junit.Before;
import org.junit.Test;

Expand Down Expand Up @@ -186,12 +187,12 @@ public void testCAmmCIF() throws StructureException {

//mmCIF files left justify their atom names (eg "CA "), so can have different behavior
AtomCache pdbCache = new AtomCache();
pdbCache.setUseMmCif(false);
pdbCache.setFiletype(StructureFiletype.PDB);
FileParsingParameters params = new FileParsingParameters();
pdbCache.setFileParsingParams(params);

AtomCache mmcifCache = new AtomCache();
mmcifCache.setUseMmCif(true);
mmcifCache.setFiletype(StructureFiletype.CIF);
FileParsingParameters params2 = new FileParsingParameters();
mmcifCache.setFileParsingParams(params2);

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17 changes: 5 additions & 12 deletions biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1a4w.java
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Expand Up @@ -26,14 +26,13 @@

import org.biojava.nbio.structure.*;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.CifFileReader;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.io.PDBFileParser;
import org.biojava.nbio.structure.io.mmcif.MMcifParser;
import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.rcsb.cif.model.CifFile;

import java.io.IOException;
import java.io.InputStream;
Expand Down Expand Up @@ -87,17 +86,11 @@ public void test1a4wPDBFile() throws IOException
InputStream inStream = this.getClass().getResourceAsStream("/1a4w.cif");
Assert.assertNotNull(inStream);

MMcifParser pdbpars = new SimpleMMcifParser();
SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
FileParsingParameters params = new FileParsingParameters();
params.setAlignSeqRes(true);
consumer.setFileParsingParameters(params);
pdbpars.addMMcifConsumer(consumer);

pdbpars.parse(inStream) ;
structure2 = consumer.getStructure();


CifFileReader reader = new CifFileReader();
reader.setFileParsingParameters(params);
structure2 = reader.getStructure(inStream);

Assert.assertNotNull(structure2);

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3 changes: 2 additions & 1 deletion biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1o2f.java
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Expand Up @@ -22,6 +22,7 @@

import org.biojava.nbio.structure.Chain;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.io.StructureFiletype;
import org.biojava.nbio.structure.StructureIO;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
Expand All @@ -38,7 +39,7 @@ public class Test1o2f {
@Before
public void setUp() throws Exception {
AtomCache cache = new AtomCache();
cache.setUseMmCif(true);
cache.setFiletype(StructureFiletype.CIF);
cache.setFetchBehavior(FetchBehavior.FETCH_FILES);
StructureIO.setAtomCache(cache);
String pdbId = "1O2F";
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