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kohchuanhockkohchuanhock
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Removed line 460-462 of PeptidePropertiesImpl.java which caused getNetCharge of Innovagen to return 0.0 if the net charge excluding the n-terminal and c-terminal are 0.0 regardless of the charge of n-terminal and c-terminal
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@9637 7c6358e6-4a41-0410-a743-a5b2a554c398
1 parent 5817d83 commit 5f57b39

2 files changed

Lines changed: 73 additions & 62 deletions

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‎biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/PeptidePropertiesImpl.java‎

Lines changed: 6 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -260,7 +260,7 @@ private double getIsoelectricPointInnovagen(ProteinSequence sequence){
260260
final double difference = 0.0001;
261261

262262
while(true){
263-
margin = this.getNetCharge(chargedAA2Count, currentPH, nTerminalChar, cTerminalChar);
263+
margin = this.getNetChargeInnovagen(chargedAA2Count, currentPH, nTerminalChar, cTerminalChar);
264264
//Within allowed difference
265265
if(margin <= difference && margin >= -difference) break;
266266
changeSize /= 2.0;
@@ -402,16 +402,7 @@ private double getNetChargeExpasy(String sequence, double pHPoint){
402402
// Look up N-terminal and C-terminal residue.
403403
//
404404
int nTermResidue = sequence.charAt(0) - 'A';
405-
// int index = 0;
406-
// while((nTermResidue < 0 || nTermResidue >= 26) && index < 25){
407-
// nTermResidue
408-
// }
409-
410405
int cTermResidue = sequence.charAt(sequence.length() - 1) - 'A';
411-
// index = 1;
412-
// while((cTermResidue < 0 || cTermResidue >= 26) && index < 25){
413-
// cTermResidue = sequence.charAt(sequence.length() - index++) - 'A';
414-
// }
415406
return getNetChargeExpasy(comp, nTermResidue, cTermResidue, pHPoint);
416407
}
417408

@@ -437,10 +428,10 @@ private double getNetChargeExpasy(int comp[], int nTermResidue, int cTermResidue
437428
private double getNetChargeInnovagen(ProteinSequence sequence, double pHPoint) {
438429
Map<AminoAcidCompound, Integer> chargedAA2Count = this.getChargedAACount(sequence);
439430
String sequenceString = sequence.getSequenceAsString();
440-
return getNetCharge(chargedAA2Count, pHPoint, sequenceString.charAt(0), sequenceString.charAt(sequenceString.length() - 1));
431+
return getNetChargeInnovagen(chargedAA2Count, pHPoint, sequenceString.charAt(0), sequenceString.charAt(sequenceString.length() - 1));
441432
}
442433

443-
private double getNetCharge(Map<AminoAcidCompound, Integer> chargedAA2Count, double ph, char nTerminalChar, char cTerminalChar){
434+
private double getNetChargeInnovagen(Map<AminoAcidCompound, Integer> chargedAA2Count, double ph, char nTerminalChar, char cTerminalChar){
444435
//Constraints.aa2PKa is aleady reinitialized in getChargedAACount hence no need to do it again
445436

446437
//Lys => K, Arg => R, His => H
@@ -466,9 +457,9 @@ private double getNetCharge(Map<AminoAcidCompound, Integer> chargedAA2Count, dou
466457
double eCharge = chargedAA2Count.get(aaSet.getCompoundForString("E")) * this.getNegCharge(Constraints.aa2PKa.get(aaSet.getCompoundForString("E")), ph);
467458
double cCharge = chargedAA2Count.get(aaSet.getCompoundForString("C")) * this.getNegCharge(Constraints.aa2PKa.get(aaSet.getCompoundForString("C")), ph);
468459
double yCharge = chargedAA2Count.get(aaSet.getCompoundForString("Y")) * this.getNegCharge(Constraints.aa2PKa.get(aaSet.getCompoundForString("Y")), ph);
469-
if((kCharge + rCharge + hCharge) == 0.0 && (dCharge + eCharge + cCharge + yCharge) == 0.0){
470-
return 0.0;
471-
}
460+
// if((nTerminalCharge + kCharge + rCharge + hCharge) == 0.0 && (cTerminalCharge + dCharge + eCharge + cCharge + yCharge) == 0.0){
461+
// return 0.0;
462+
// }
472463
return (nTerminalCharge + kCharge + rCharge + hCharge) - (dCharge + eCharge + cCharge + yCharge + cTerminalCharge);
473464
}
474465

‎biojava3-aa-prop/src/test/java/org/biojava3/aaproperties/PeptidePropertiesImplTester.java‎

Lines changed: 67 additions & 47 deletions
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ public class PeptidePropertiesImplTester {
1717
*/
1818
private final String sequence = "MTADGPCRELLCQLRAAVRHRWWC1";
1919
private final String fullInvalidSequence = "3176412372301230183--2310";
20-
20+
2121
@Test
2222
public void testAAComposition() {
2323
//'W', 'C', 'M', 'H', 'Y', 'F', 'Q', 'N', 'I', 'R', 'D', 'P', 'T', 'K', 'E', 'V', 'S', 'G', 'A', 'L'
@@ -43,7 +43,7 @@ public void testAAComposition() {
4343
assertEquals(1.0/sequenceLength, composition.get("G"));
4444
assertEquals(3.0/sequenceLength, composition.get("A"));
4545
assertEquals(3.0/sequenceLength, composition.get("L"));
46-
46+
4747
Map<String, Double> iComposition = PeptideProperties.getAACompositionString(fullInvalidSequence);
4848
assertEquals(0.0, iComposition.get("W"));
4949
assertEquals(0.0, iComposition.get("C"));
@@ -72,7 +72,7 @@ public void testAAComposition() {
7272
assertNull(composition.get(""));
7373
assertNull(composition.get("1"));
7474
}
75-
75+
7676
@Test()
7777
public void testEnrichment() {
7878
//'W', 'C', 'M', 'H', 'Y', 'F', 'Q', 'N', 'I', 'R', 'D', 'P', 'T', 'K', 'E', 'V', 'S', 'G', 'A', 'L'
@@ -97,7 +97,7 @@ public void testEnrichment() {
9797
assertEquals(1.0/sequenceLength, PeptideProperties.getEnrichment(sequence, "G"));
9898
assertEquals(3.0/sequenceLength, PeptideProperties.getEnrichment(sequence, "A"));
9999
assertEquals(3.0/sequenceLength, PeptideProperties.getEnrichment(sequence, "L"));
100-
100+
101101
assertEquals(0.0, PeptideProperties.getEnrichment(fullInvalidSequence, "W"));
102102
assertEquals(0.0, PeptideProperties.getEnrichment(fullInvalidSequence, "C"));
103103
assertEquals(0.0, PeptideProperties.getEnrichment(fullInvalidSequence, "M"));
@@ -120,13 +120,13 @@ public void testEnrichment() {
120120
assertEquals(0.0, PeptideProperties.getEnrichment(fullInvalidSequence, "L"));
121121
assertEquals(0.0, PeptideProperties.getEnrichment(sequence, "X"));
122122
}
123-
123+
124124
@Test (expected = NullPointerException.class)
125125
public void testEnrichmentNull(){
126126
assertNull(PeptideProperties.getEnrichment(sequence, "1"));
127127
assertEquals(0.0, PeptideProperties.getEnrichment(sequence, ""));
128128
}
129-
129+
130130
@Test
131131
public void testMolecularWeight(){
132132
//http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator.asp
@@ -135,113 +135,113 @@ public void testMolecularWeight(){
135135
assertEquals(2872.4, Utils.roundToDecimals(PeptideProperties.getMolecularWeight(sequence), 1));
136136
assertEquals(0.0, PeptideProperties.getMolecularWeight("Z"));
137137
assertEquals(0.0, PeptideProperties.getMolecularWeight("1"));
138-
138+
139139
assertEquals(0.0, PeptideProperties.getMolecularWeight(fullInvalidSequence));
140140
}
141-
141+
142142
@Test
143143
public void testMolecularWeightXML() throws FileNotFoundException, JAXBException{
144144
File elementMassFile = new File("./src/main/resources/ElementMass.xml");
145145
File aminoAcidCompositionFile = new File("./src/main/resources/AminoAcidComposition.xml");
146-
146+
147147
assertEquals(
148-
Utils.roundToDecimals(PeptideProperties.getMolecularWeight("A", elementMassFile, aminoAcidCompositionFile)
149-
* 5.0 - 4 * (17.0073 + 1.0079), 5),
150-
Utils.roundToDecimals(PeptideProperties.getMolecularWeight("AAAAA", elementMassFile, aminoAcidCompositionFile), 5));
148+
Utils.roundToDecimals(PeptideProperties.getMolecularWeight("A", elementMassFile, aminoAcidCompositionFile)
149+
* 5.0 - 4 * (17.0073 + 1.0079), 5),
150+
Utils.roundToDecimals(PeptideProperties.getMolecularWeight("AAAAA", elementMassFile, aminoAcidCompositionFile), 5));
151151
}
152-
152+
153153
@Test
154154
public void testMolecularWeightXMLSingleFile() throws FileNotFoundException, JAXBException{
155155
File aminoAcidCompositionFile = new File("./src/main/resources/AminoAcidComposition.xml");
156-
156+
157157
assertEquals(
158-
Utils.roundToDecimals(PeptideProperties.getMolecularWeight("A", aminoAcidCompositionFile) * 5.0 - 4 * (17.0073 + 1.0079), 5),
159-
Utils.roundToDecimals(PeptideProperties.getMolecularWeight("AAAAA", aminoAcidCompositionFile), 5));
158+
Utils.roundToDecimals(PeptideProperties.getMolecularWeight("A", aminoAcidCompositionFile) * 5.0 - 4 * (17.0073 + 1.0079), 5),
159+
Utils.roundToDecimals(PeptideProperties.getMolecularWeight("AAAAA", aminoAcidCompositionFile), 5));
160160
}
161-
161+
162162
@Test
163163
public void testMolecularWeightBasedOnAminoAcidCompositionTable() throws Exception{
164164
File elementMassFile = new File("./src/main/resources/ElementMass.xml");
165165
File aminoAcidCompositionFile = new File("./src/main/resources/AminoAcidComposition.xml");
166166
AminoAcidCompositionTable table = PeptideProperties.obtainAminoAcidCompositionTable(elementMassFile, aminoAcidCompositionFile);
167-
167+
168168
assertEquals(
169-
Utils.roundToDecimals(PeptideProperties.getMolecularWeightBasedOnXML("A", table) * 5.0 - 4 * (17.0073 + 1.0079), 5),
170-
Utils.roundToDecimals(PeptideProperties.getMolecularWeightBasedOnXML("AAAAA", table), 5));
169+
Utils.roundToDecimals(PeptideProperties.getMolecularWeightBasedOnXML("A", table) * 5.0 - 4 * (17.0073 + 1.0079), 5),
170+
Utils.roundToDecimals(PeptideProperties.getMolecularWeightBasedOnXML("AAAAA", table), 5));
171171
}
172-
172+
173173
@Test (expected = NullPointerException.class)
174174
public void testMolecularWeightXMLNull() throws FileNotFoundException, JAXBException{
175175
PeptideProperties.getMolecularWeight(sequence, null, null);
176176
}
177-
177+
178178
@Test
179179
public void testExtinctionCoefficient(){
180180
//http://au.expasy.org/cgi-bin/protparam
181181
assertEquals(11125.0, PeptideProperties.getExtinctionCoefficient(sequence, false));
182182
assertEquals(11000.0, PeptideProperties.getExtinctionCoefficient(sequence, true));
183-
183+
184184
assertEquals(0.0, PeptideProperties.getExtinctionCoefficient(fullInvalidSequence, true));
185185
assertEquals(0.0, PeptideProperties.getExtinctionCoefficient(fullInvalidSequence, false));
186186
}
187-
187+
188188
@Test (expected = NullPointerException.class)
189189
public void testExtinctionCoefficientNull(){
190190
assertEquals(11000.0, PeptideProperties.getExtinctionCoefficient(null, true));
191191
}
192-
192+
193193
@Test
194194
public void testAbsorbance(){
195195
//http://au.expasy.org/cgi-bin/protparam
196196
assertEquals(3.830, Utils.roundToDecimals(PeptideProperties.getAbsorbance(sequence, true), 3));
197197
assertEquals(3.873, Utils.roundToDecimals(PeptideProperties.getAbsorbance(sequence, false), 3));
198-
198+
199199
assertEquals(0.0, Utils.roundToDecimals(PeptideProperties.getAbsorbance(fullInvalidSequence, true), 3));
200200
assertEquals(0.0, Utils.roundToDecimals(PeptideProperties.getAbsorbance(fullInvalidSequence, false), 3));
201201
}
202-
202+
203203
@Test (expected = NullPointerException.class)
204204
public void testAbsorbanceNull(){
205205
assertEquals(3.830, PeptideProperties.getAbsorbance(null, false));
206206
}
207-
208-
207+
208+
209209
@Test
210210
public void testInstabilityIndex(){
211211
//http://au.expasy.org/cgi-bin/protparam
212212
assertEquals(38.48, Utils.roundToDecimals(PeptideProperties.getInstabilityIndex(sequence), 2));
213213
assertEquals(0.0, Utils.roundToDecimals(PeptideProperties.getInstabilityIndex(fullInvalidSequence), 2));
214214
}
215-
215+
216216
@Test (expected = NullPointerException.class)
217217
public void testInstabilityIndexNull(){
218218
assertEquals(38.48, PeptideProperties.getInstabilityIndex(null));
219219
}
220-
220+
221221
@Test
222222
public void testApliphaticIndex(){
223223
//http://au.expasy.org/cgi-bin/protparam
224224
assertEquals(73.33, Utils.roundToDecimals(PeptideProperties.getApliphaticIndex(sequence), 2));
225225
assertEquals(0.0, Utils.roundToDecimals(PeptideProperties.getApliphaticIndex(fullInvalidSequence), 2));
226226
}
227-
227+
228228
@Test (expected = NullPointerException.class)
229229
public void testApliphaticIndexNull(){
230230
assertEquals(73.33, Utils.roundToDecimals(PeptideProperties.getApliphaticIndex(null), 2));
231231
}
232-
232+
233233
@Test
234234
public void testAverageHydropathy(){
235235
//http://au.expasy.org/cgi-bin/protparam
236236
assertEquals(-0.242, Utils.roundToDecimals(PeptideProperties.getAvgHydropathy(sequence), 3));
237237
assertEquals(0.0, Utils.roundToDecimals(PeptideProperties.getAvgHydropathy(fullInvalidSequence), 3));
238238
}
239-
239+
240240
@Test (expected = NullPointerException.class)
241241
public void testAverageHydropathyNull(){
242242
assertEquals(-0.242, Utils.roundToDecimals(PeptideProperties.getAvgHydropathy(null), 3));
243243
}
244-
244+
245245
@Test
246246
public void testIsoelectricPointInnovagen(){
247247
/*
@@ -250,41 +250,41 @@ public void testIsoelectricPointInnovagen(){
250250
//http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator.asp
251251
assertEquals(9.01, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint(sequence, false), 2));
252252
assertEquals(7.00, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint(fullInvalidSequence, false), 2));
253-
253+
254254
assertEquals(2.70, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint("ACCACAAADADADACA", false), 2));
255255
}
256-
256+
257257
@Test
258258
public void testIsoelectricPointExpasy(){
259259
/*
260260
* Test for Expasy
261261
*/
262262
assertEquals(3.42, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint("ACCACAAADADADACA"), 2));
263263
assertEquals(3.42, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint("ACCACAAADADADACM"), 2));
264-
//
264+
//
265265
assertEquals(3.37, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint("ECCACAAADADADACS", true), 2));
266-
267-
266+
267+
268268
assertEquals(3.24, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint("ADCCACAAADADADACDAAAAAAAAAAAA", true), 2));
269-
269+
270270
//3.32 at Expasy
271271
assertEquals(3.32, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint("DCCACAAADADADACS", true), 2));
272-
272+
273273
assertEquals(3.17, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint("DCCACAAADADADACDAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAD", true), 2));
274274
assertEquals(3.37, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint("ACCACAAADADADACE", true), 2));
275275
assertEquals(3.32, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint("ACCACAAADADADACAAAAAAAAAAAAAAD", true), 2));
276276
assertEquals(3.28, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint("DCCACAAADADADACE", true), 2));
277-
277+
278278
assertEquals(8.71, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint("MTADGPCRELLCQLRAAVRHRWWC", true), 2));
279279
assertEquals(8.71, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint(sequence, true), 2));
280280
assertEquals(0.0, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint(fullInvalidSequence, true), 1));
281281
}
282-
282+
283283
@Test (expected = NullPointerException.class)
284284
public void testIsoelectricPointNull(){
285285
assertEquals(8.6, Utils.roundToDecimals(PeptideProperties.getIsoelectricPoint(null), 1));
286286
}
287-
287+
288288
@Test
289289
public void testNetCharge(){
290290
/*
@@ -293,15 +293,35 @@ public void testNetCharge(){
293293
//http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator.asp
294294
assertEquals(2.9, Utils.roundToDecimals(PeptideProperties.getNetCharge(sequence, false), 1));
295295
assertEquals(0.0, Utils.roundToDecimals(PeptideProperties.getNetCharge(fullInvalidSequence, false), 1));
296-
296+
297297
assertEquals(-3.2, Utils.roundToDecimals(PeptideProperties.getNetCharge("ACCACAAADADADACA", false), 1));
298298
/*
299299
* Did not test for Expasy because in their website, net charge is not given.
300300
* However, since Isoelectric point is given which rely on getNetCharge values therefore,
301301
* we infer that if getIsoelectricPoint is correct, getNetCharge would be correct for Expasy.
302302
*/
303+
304+
305+
/*
306+
* Provided by Steve Darnell to compare the difference between Innovagen and Expasy
307+
*/
308+
String[] alpha = {"A",/*"B",*/"C","D","E","F","G","H","I",/*"J",*/
309+
"K","L","M","N",/*"O",*/"P","Q","R","S","T",
310+
/*"U",*/"V","W",/*"X",*/"Y"/*,"Z"*/};
311+
for (String aa : alpha) {
312+
String p = String.format("AA%sAA", aa);
313+
System.out.println(p);
314+
System.out.println("pH\tInnovagen\tExpasy\tdiff");
315+
for ( int i = 1; i < 15; i++) {
316+
double phPoint = (new Double(i)).doubleValue();
317+
double chrgInnovagen = PeptideProperties.getNetCharge(p,false,phPoint);
318+
double chrgExpasy = PeptideProperties.getNetCharge(p,true,phPoint);
319+
System.out.println(String.format("%2.1f\t%2.2f\t%2.2f\t%2.2f", phPoint, chrgInnovagen,
320+
chrgExpasy, chrgInnovagen - chrgExpasy));
321+
}
322+
}
303323
}
304-
324+
305325
@Test (expected = NullPointerException.class)
306326
public void testNetChargeNull(){
307327
assertEquals(8.6, PeptideProperties.getNetCharge(null));

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