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luke czaplaluke czapla
luke czapla
authored and
luke czapla
committed
fixed nomenclature for constants
1 parent c9a1dd9 commit e99cad7

1 file changed

Lines changed: 39 additions & 27 deletions

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/basepairs/BasePairParameters.java‎

Lines changed: 39 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -72,7 +72,7 @@ public class BasePairParameters implements Serializable {
7272
// See URL http://ndbserver.rutgers.edu/ndbmodule/archives/reports/tsukuba/Table1.html
7373
// and the paper cited at the top of this class (also as Table 1).
7474
// These are hard-coded to avoid problems with resource paths.
75-
public static String[] standardBases = new String[] {
75+
public static final String[] STANDARD_BASES = new String[] {
7676
"SEQRES 1 A 1 A\n" +
7777
"ATOM 2 N9 A A 1 -1.291 4.498 0.000\n" +
7878
"ATOM 3 C8 A A 1 0.024 4.897 0.000\n" +
@@ -121,24 +121,24 @@ public class BasePairParameters implements Serializable {
121121
};
122122

123123
// this is also hard-coded data about standard WC base pairs for both DNA and RNA
124-
protected static String[] baseListDNA = {"A", "G", "T", "C"};
125-
protected static String[] baseListRNA = {"A", "G", "U", "C"};
126-
protected static Map<String, Integer> map;
124+
protected static final String[] BASE_LIST_DNA = {"A", "G", "T", "C"};
125+
protected static final String[] BASE_LIST_RNA = {"A", "G", "U", "C"};
126+
protected static final Map<String, Integer> BASE_MAP;
127127
// private static List<String> RNAspecific = Arrays.asList("U", "URA"),
128128
// DNAspecific = Arrays.asList("DC", "C", "CYT");
129-
protected static Map<Integer, List<String>> ringMap;
129+
protected static final Map<Integer, List<String>> RING_MAP;
130130
static {
131-
map = new HashMap<>();
132-
map.put("DA", 0); map.put("ADE", 0); map.put("A", 0);
133-
map.put("DG", 1); map.put("GUA", 1); map.put("G", 1);
134-
map.put("DT", 2); map.put("THY", 2); map.put("T", 2); map.put("U", 2); map.put("URA", 2);
135-
map.put("DC", 3); map.put("CYT", 3); map.put("C", 3);
136-
137-
ringMap = new HashMap<>();
138-
ringMap.put(0, Arrays.asList("C8", "C2", "N3", "C4", "C5", "C6", "N7", "N1", "N9"));
139-
ringMap.put(1, Arrays.asList("C8", "C2", "N3", "C4", "C5", "C6", "N7", "N1", "N9"));
140-
ringMap.put(2, Arrays.asList("C6", "C2", "N3", "C4", "C5", "N1"));
141-
ringMap.put(3, Arrays.asList("C6", "C2", "N3", "C4", "C5", "N1"));
131+
BASE_MAP = new HashMap<>();
132+
BASE_MAP.put("DA", 0); BASE_MAP.put("ADE", 0); BASE_MAP.put("A", 0);
133+
BASE_MAP.put("DG", 1); BASE_MAP.put("GUA", 1); BASE_MAP.put("G", 1);
134+
BASE_MAP.put("DT", 2); BASE_MAP.put("THY", 2); BASE_MAP.put("T", 2); BASE_MAP.put("U", 2); BASE_MAP.put("URA", 2);
135+
BASE_MAP.put("DC", 3); BASE_MAP.put("CYT", 3); BASE_MAP.put("C", 3);
136+
137+
RING_MAP = new HashMap<>();
138+
RING_MAP.put(0, Arrays.asList("C8", "C2", "N3", "C4", "C5", "C6", "N7", "N1", "N9"));
139+
RING_MAP.put(1, Arrays.asList("C8", "C2", "N3", "C4", "C5", "C6", "N7", "N1", "N9"));
140+
RING_MAP.put(2, Arrays.asList("C6", "C2", "N3", "C4", "C5", "N1"));
141+
RING_MAP.put(3, Arrays.asList("C6", "C2", "N3", "C4", "C5", "N1"));
142142
}
143143

144144
protected transient Structure structure;
@@ -172,10 +172,22 @@ public BasePairParameters(Structure structure, boolean useRNA, boolean removeDup
172172

173173
}
174174

175+
/**
176+
* Constructor takes a Structure object, whether to use RNA, and whether to remove duplicate sequences.
177+
* @param structure The already-loaded structure to analyze.
178+
* @param useRNA if true, the RNA standard bases will be used. Otherwise, if false, it will work on standard DNA bases.
179+
* @param removeDups if true, duplicate sequences will not be considered. This is for the analysis of X-ray structures from
180+
* RCSB, where there may be identical or similar units.
181+
*/
175182
public BasePairParameters(Structure structure, boolean useRNA, boolean removeDups) {
176183
this(structure, useRNA, removeDups, false);
177184
}
178185

186+
/**
187+
* Constructor takes a Structure object, and whether to use the RNA standard bases
188+
* @param structure The already-loaded structure to analyze.
189+
* @param useRNA if true, the RNA standard bases will be used. Otherwise, if false, it will work on standard DNA bases.
190+
*/
179191
public BasePairParameters(Structure structure, boolean useRNA) {
180192
this(structure, useRNA, false, false);
181193
}
@@ -449,14 +461,14 @@ public List<Pair<Group>> findPairs(List<Chain> chains) {
449461
for (int k = 0; k < match.length(); k++) {
450462
Group g1 = c.getAtomGroup(index1+k);
451463
Group g2 = chains.get(j).getAtomGroup(index2-k);
452-
Integer type1 = map.get(g1.getPDBName());
453-
Integer type2 = map.get(g2.getPDBName());
464+
Integer type1 = BASE_MAP.get(g1.getPDBName());
465+
Integer type2 = BASE_MAP.get(g2.getPDBName());
454466
if (type1 == null || type2 == null) {
455467
if (pairSequence.length() != 0 && pairSequence.charAt(pairSequence.length()-1) != ' ') pairSequence += ' ';
456468
continue;
457469
}
458-
Atom a1 = g1.getAtom(ringMap.get(type1).get(0));
459-
Atom a2 = g2.getAtom(ringMap.get(type2).get(0));
470+
Atom a1 = g1.getAtom(RING_MAP.get(type1).get(0));
471+
Atom a2 = g2.getAtom(RING_MAP.get(type2).get(0));
460472

461473
if (a1 == null) {
462474
log.info("Error processing " + g1.getPDBName());
@@ -477,17 +489,17 @@ public List<Pair<Group>> findPairs(List<Chain> chains) {
477489
// could be a base pair
478490
if (Math.abs(distance-10.0) < 4.0) {
479491
boolean valid = true;
480-
for (String atomname : ringMap.get(type1)) {
492+
for (String atomname : RING_MAP.get(type1)) {
481493
Atom a = g1.getAtom(atomname);
482494
if (a == null) valid = false;
483495
}
484-
if (valid) for (String atomname: ringMap.get(type2)) {
496+
if (valid) for (String atomname: RING_MAP.get(type2)) {
485497
Atom a = g2.getAtom(atomname);
486498
if (a == null) valid = false;
487499
}
488500
if (valid) {
489501
result.add(new Pair<Group>(g1, g2));
490-
pairingNames.add((useRNA ? baseListRNA[type1]+baseListRNA[type2] : baseListDNA[type1]+baseListDNA[type2]));
502+
pairingNames.add((useRNA ? BASE_LIST_RNA[type1]+ BASE_LIST_RNA[type2] : BASE_LIST_DNA[type1]+ BASE_LIST_DNA[type2]));
491503
pairSequence += c.getAtomSequence().charAt(index1 + k);
492504
} else if (pairSequence.length() != 0 && pairSequence.charAt(pairSequence.length()-1) != ' ') pairSequence += ' ';
493505
} else if (pairSequence.length() != 0 && pairSequence.charAt(pairSequence.length()-1) != ' ') pairSequence += ' ';
@@ -507,15 +519,15 @@ public List<Pair<Group>> findPairs(List<Chain> chains) {
507519
* @return The middle frame of the center of the base-pair formed
508520
*/
509521
public Matrix4d basePairReferenceFrame(Pair<Group> pair) {
510-
Integer type1 = map.get(pair.getFirst().getPDBName());
511-
Integer type2 = map.get(pair.getSecond().getPDBName());
522+
Integer type1 = BASE_MAP.get(pair.getFirst().getPDBName());
523+
Integer type2 = BASE_MAP.get(pair.getSecond().getPDBName());
512524
SuperPosition sp = new SuperPositionQCP(true);
513525
if (type1 == null || type2 == null) return null;
514526
PDBFileReader pdbFileReader = new PDBFileReader();
515527
Structure s1, s2;
516528
try {
517-
s1 = pdbFileReader.getStructure(new ByteArrayInputStream(standardBases[type1].getBytes()));
518-
s2 = pdbFileReader.getStructure(new ByteArrayInputStream(standardBases[type2].getBytes()));
529+
s1 = pdbFileReader.getStructure(new ByteArrayInputStream(STANDARD_BASES[type1].getBytes()));
530+
s2 = pdbFileReader.getStructure(new ByteArrayInputStream(STANDARD_BASES[type2].getBytes()));
519531
} catch (IOException e) {
520532
e.printStackTrace();
521533
return null;

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