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sbittrichsbittrich
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wip (TODO chemcomp parsing)
1 parent c290ea9 commit 993665a

30 files changed

Lines changed: 135 additions & 1091 deletions

‎biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java‎

Lines changed: 0 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -23,10 +23,6 @@
2323
import org.biojava.nbio.structure.Chain;
2424
import org.biojava.nbio.structure.Group;
2525
import org.biojava.nbio.structure.Structure;
26-
import org.biojava.nbio.structure.chem.AllChemCompProvider;
27-
import org.biojava.nbio.structure.chem.ChemCompGroupFactory;
28-
import org.biojava.nbio.structure.chem.ChemCompProvider;
29-
import org.biojava.nbio.structure.chem.DownloadChemCompProvider;
3026
import org.biojava.nbio.structure.io.FileParsingParameters;
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import org.biojava.nbio.structure.io.PDBFileReader;
3228

‎biojava-structure/src/main/java/demo/DemoMMCIFReader.java‎

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Original file line numberDiff line numberDiff line change
@@ -26,6 +26,7 @@
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2727
import org.biojava.nbio.structure.*;
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import org.biojava.nbio.structure.align.util.AtomCache;
29+
import org.biojava.nbio.structure.io.CifFileReader;
2930
import org.biojava.nbio.structure.io.StructureProvider;
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3132
import java.util.List;
@@ -79,7 +80,7 @@ public void loadSimple(){
7980
public void loadFromDirectAccess(){
8081
String pdbId = "1A4W";
8182

82-
StructureProvider pdbreader = new MMCIFFileReader();
83+
StructureProvider pdbreader = new CifFileReader();
8384

8485
try {
8586
Structure s = pdbreader.getStructureById(pdbId);

‎biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java‎

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Original file line numberDiff line numberDiff line change
@@ -32,6 +32,7 @@
3232
import java.util.NavigableMap;
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import java.util.TreeMap;
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35+
import org.biojava.nbio.structure.chem.ChemComp;
3536
import org.biojava.nbio.structure.chem.PolymerType;
3637
import org.biojava.nbio.structure.chem.ResidueType;
3738
import org.slf4j.Logger;

‎biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@
2424
package org.biojava.nbio.structure;
2525

2626

27-
import org.biojava.nbio.structure.chem.ChemCompGroupFactory;
27+
import org.biojava.nbio.structure.chem.ChemComp;
2828
import org.biojava.nbio.structure.chem.PolymerType;
2929
import org.biojava.nbio.structure.io.FileConvert;
3030
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;

‎biojava-structure/src/main/java/org/biojava/nbio/structure/DatabasePDBRevRecord.java‎

Lines changed: 0 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2,9 +2,6 @@
22

33
import org.biojava.nbio.structure.io.cif.CifBean;
44

5-
import java.util.ArrayList;
6-
import java.util.List;
7-
85
public class DatabasePDBRevRecord implements CifBean<org.rcsb.cif.schema.mm.DatabasePDBRevRecord> {
96
private static final long serialVersionUID = 1L;
107
private String revNum;

‎biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java‎

Lines changed: 3 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -23,11 +23,10 @@
2323
*/
2424
package org.biojava.nbio.structure;
2525

26-
import org.biojava.nbio.structure.chem.ChemCompGroupFactory;
26+
import org.biojava.nbio.structure.chem.ChemComp;
2727
import org.biojava.nbio.structure.chem.PolymerType;
2828
import org.biojava.nbio.structure.chem.ResidueType;
2929
import org.biojava.nbio.structure.io.GroupToSDF;
30-
import org.rcsb.cif.schema.mm.ChemComp;
3130
import org.slf4j.Logger;
3231
import org.slf4j.LoggerFactory;
3332

@@ -336,7 +335,7 @@ public boolean isAminoAcid() {
336335
return getType().equals(GroupType.AMINOACID);
337336

338337

339-
ResidueType rt = ResidueType.getResidueTypeFromString(cc.getType().get(0));
338+
ResidueType rt = ResidueType.getResidueTypeFromString(cc.getType());
340339

341340
if (ResidueType.nonPolymer.equals(rt))
342341
return false;
@@ -355,7 +354,7 @@ public boolean isNucleotide() {
355354
if ( cc == null)
356355
return getType().equals(GroupType.NUCLEOTIDE);
357356

358-
ResidueType rt = ResidueType.getResidueTypeFromString(cc.getType().get(0));
357+
ResidueType rt = ResidueType.getResidueTypeFromString(cc.getType());
359358

360359
if (ResidueType.nonPolymer.equals(rt))
361360
return false;

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1545,9 +1545,9 @@ public static double[][] updateMatrixWithSequenceConservation(double[][] max, At
15451545
Atom a2 = ca2[j];
15461546

15471547
AminoAcidCompound ac1 =
1548-
set.getCompoundForString(a1.getGroup().getChemComp().getOne_letter_code());
1548+
set.getCompoundForString(a1.getGroup().getChemComp().getOneLetterCode());
15491549
AminoAcidCompound ac2 =
1550-
set.getCompoundForString(a2.getGroup().getChemComp().getOne_letter_code());
1550+
set.getCompoundForString(a2.getGroup().getChemComp().getOneLetterCode());
15511551

15521552

15531553
if ( ac1 == null || ac2 == null)

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1442,7 +1442,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str
14421442
for ( int i =0 ; i < strBuf1.length; i++){
14431443
if ( strBuf1[i] == null)
14441444
break;
1445-
System.out.print(strBuf1[i].getGroup().getChemComp().getOne_letter_code());
1445+
System.out.print(strBuf1[i].getGroup().getChemComp().getOneLetterCode());
14461446
}
14471447
System.out.println();
14481448

@@ -1551,9 +1551,9 @@ public static double[][] updateMatrixWithSequenceConservation(double[][] max, At
15511551
Atom a2 = ca2[j];
15521552

15531553
AminoAcidCompound ac1 =
1554-
set.getCompoundForString(a1.getGroup().getChemComp().getOne_letter_code());
1554+
set.getCompoundForString(a1.getGroup().getChemComp().getOneLetterCode());
15551555
AminoAcidCompound ac2 =
1556-
set.getCompoundForString(a2.getGroup().getChemComp().getOne_letter_code());
1556+
set.getCompoundForString(a2.getGroup().getChemComp().getOneLetterCode());
15571557

15581558

15591559
if ( ac1 == null || ac2 == null)

‎biojava-structure/src/main/java/org/biojava/nbio/structure/chem/AllChemCompProvider.java‎

Lines changed: 0 additions & 185 deletions
This file was deleted.

‎biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ChemComp.java‎

Lines changed: 18 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -49,26 +49,24 @@ public class ChemComp implements CifBean<org.rcsb.cif.schema.mm.ChemComp>, Compa
4949

5050
@Override
5151
public String toString(){
52-
StringBuffer buf = new StringBuffer("ChemComp ");
53-
buf.append(id)
54-
.append(" ")
55-
.append(oneLetterCode)
56-
.append(" ")
57-
.append(threeLetterCode)
58-
.append(" poly:")
59-
.append(getPolymerType())
60-
.append(" resi:")
61-
.append(getResidueType())
62-
.append(isStandard() ? " standard" : " modified")
63-
.append(" ")
64-
.append(name)
65-
.append(" ")
66-
.append(pdbxType)
67-
.append(" ")
68-
.append(formula)
69-
.append(" parent:")
70-
.append(monNstdParentCompId);
71-
return buf.toString();
52+
return "ChemComp " + id +
53+
" " +
54+
oneLetterCode +
55+
" " +
56+
threeLetterCode +
57+
" poly:" +
58+
getPolymerType() +
59+
" resi:" +
60+
getResidueType() +
61+
(isStandard() ? " standard" : " modified") +
62+
" " +
63+
name +
64+
" " +
65+
pdbxType +
66+
" " +
67+
formula +
68+
" parent:" +
69+
monNstdParentCompId;
7270
}
7371

7472
public boolean hasParent(){

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