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

Lines changed: 98 additions & 33 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,27 @@
1+
/*
2+
* BioJava development code
3+
*
4+
* This code may be freely distributed and modified under the
5+
* terms of the GNU Lesser General Public Licence. This should
6+
* be distributed with the code. If you do not have a copy,
7+
* see:
8+
*
9+
* http://www.gnu.org/copyleft/lesser.html
10+
*
11+
* Copyright for this code is held jointly by the individual
12+
* authors. These should be listed in @author doc comments.
13+
*
14+
* For more information on the BioJava project and its aims,
15+
* or to join the biojava-l mailing list, visit the home page
16+
* at:
17+
*
18+
* http://www.biojava.org/
19+
*
20+
* Created on 07-20-2017
21+
*
22+
* @author Luke Czapla
23+
*
24+
*/
125
package org.biojava.nbio.structure.basepairs;
226

327
import org.biojava.nbio.structure.*;
@@ -11,12 +35,20 @@
1135
import java.io.ByteArrayInputStream;
1236
import java.io.IOException;
1337
import java.io.Serializable;
14-
import java.util.*;
38+
import java.util.List;
39+
import java.util.Arrays;
40+
import java.util.ArrayList;
41+
import java.util.Map;
42+
import java.util.HashMap;
1543

1644
import org.slf4j.Logger;
1745
import org.slf4j.LoggerFactory;
1846

19-
import static java.lang.Math.*;
47+
import static java.lang.Math.sin;
48+
import static java.lang.Math.cos;
49+
import static java.lang.Math.atan2;
50+
import static java.lang.Math.acos;
51+
import static java.lang.Math.PI;
2052

2153
/**
2254
* Contributed to BioJava under its LGPL
@@ -104,11 +136,7 @@ public class BasePairParameters implements Serializable {
104136
map.put("DG", 1); map.put("GUA", 1); map.put("G", 1);
105137
map.put("DT", 2); map.put("THY", 2); map.put("T", 2); map.put("U", 2); map.put("URA", 2);
106138
map.put("DC", 3); map.put("CYT", 3); map.put("C", 3);
107-
// chemically modified bases, leaving out to ignore (to treat as gaps) right now.
108-
//map.put("DZM", 0);
109-
//map.put("UCL", 2);
110-
//map.put("2DT", 2);
111-
//map.put("1CC", 3); map.put("5CM", 3);
139+
112140
ringMap = new HashMap<>();
113141
ringMap.put(0, Arrays.asList("C8", "C2", "N3", "C4", "C5", "C6", "N7", "N1", "N9"));
114142
ringMap.put(1, Arrays.asList("C8", "C2", "N3", "C4", "C5", "C6", "N7", "N1", "N9"));
@@ -191,7 +219,7 @@ public BasePairParameters analyze() {
191219
if (i != 0) {
192220
lastStep.invert();
193221
lastStep.mul(currentStep);
194-
double[] sparms = calculatetp(lastStep);
222+
double[] sparms = calculateTp(lastStep);
195223
for (int j = 0; j < 6; j++) stepParameters[i][j] = sparms[j];
196224
}
197225
}
@@ -205,7 +233,7 @@ public BasePairParameters analyze() {
205233
* @return An integer value, number of base pairs
206234
*/
207235
public int getLength() {
208-
if (structure == null || pairParameters == null) throw new IllegalArgumentException();
236+
if (structure == null || pairParameters == null) throw new IllegalArgumentException("Base pair number is out of range.");
209237
return pairingParameters.length;
210238
}
211239

@@ -261,7 +289,7 @@ public List<Matrix4d> getReferenceFrames() {
261289
* @return the value as a double (in degrees)
262290
*/
263291
public Double getBuckle(int bp) {
264-
if (bp < 0 || bp >= getPairingParameters().length) throw new IllegalArgumentException();
292+
if (bp < 0 || bp >= getPairingParameters().length) throw new IllegalArgumentException("Base pair number is out of range.");
265293
return pairingParameters[bp][0];
266294
}
267295

@@ -271,7 +299,7 @@ public Double getBuckle(int bp) {
271299
* @return the value as a double (in degrees)
272300
*/
273301
public Double getPropeller(int bp) {
274-
if (bp < 0 || bp >= getPairingParameters().length) throw new IllegalArgumentException();
302+
if (bp < 0 || bp >= getPairingParameters().length) throw new IllegalArgumentException("Base pair number is out of range.");
275303
return pairingParameters[bp][1];
276304
}
277305

@@ -281,7 +309,7 @@ public Double getPropeller(int bp) {
281309
* @return the value as a double (in degrees)
282310
*/
283311
public Double getOpening(int bp) {
284-
if (bp < 0 || bp >= getPairingParameters().length) throw new IllegalArgumentException();
312+
if (bp < 0 || bp >= getPairingParameters().length) throw new IllegalArgumentException("Base pair number is out of range.");
285313
return pairingParameters[bp][2];
286314
}
287315

@@ -291,7 +319,7 @@ public Double getOpening(int bp) {
291319
* @return the value as a double (in Å)
292320
*/
293321
public Double getShear(int bp) {
294-
if (bp < 0 || bp >= getPairingParameters().length) throw new IllegalArgumentException();
322+
if (bp < 0 || bp >= getPairingParameters().length) throw new IllegalArgumentException("Base pair number is out of range.");
295323
return pairingParameters[bp][3];
296324
}
297325

@@ -301,7 +329,7 @@ public Double getShear(int bp) {
301329
* @return the value as a double (in Å)
302330
*/
303331
public Double getStretch(int bp) {
304-
if (bp < 0 || bp >= getPairingParameters().length) throw new IllegalArgumentException();
332+
if (bp < 0 || bp >= getPairingParameters().length) throw new IllegalArgumentException("Base pair number is out of range.");
305333
return pairingParameters[bp][4];
306334
}
307335

@@ -311,7 +339,7 @@ public Double getStretch(int bp) {
311339
* @return the value as a double (in Å)
312340
*/
313341
public Double getStagger(int bp) {
314-
if (bp < 0 || bp >= getPairingParameters().length) throw new IllegalArgumentException();
342+
if (bp < 0 || bp >= getPairingParameters().length) throw new IllegalArgumentException("Base pair number is out of range.");
315343
return pairingParameters[bp][5];
316344
}
317345

@@ -321,7 +349,7 @@ public Double getStagger(int bp) {
321349
* @return the value as a double (in degrees)
322350
*/
323351
public Double getTilt(int bp) {
324-
if (bp < 0 || bp >= getStepParameters().length) throw new IllegalArgumentException();
352+
if (bp < 0 || bp >= getStepParameters().length) throw new IllegalArgumentException("Base pair number is out of range.");
325353
return stepParameters[bp][0];
326354
}
327355

@@ -331,7 +359,7 @@ public Double getTilt(int bp) {
331359
* @return the value as a double (in degrees)
332360
*/
333361
public Double getRoll(int bp) {
334-
if (bp < 0 || bp >= getStepParameters().length) throw new IllegalArgumentException();
362+
if (bp < 0 || bp >= getStepParameters().length) throw new IllegalArgumentException("Base pair number is out of range.");
335363
return stepParameters[bp][1];
336364
}
337365

@@ -341,7 +369,7 @@ public Double getRoll(int bp) {
341369
* @return the value as a double (in degrees)
342370
*/
343371
public Double getTwist(int bp) {
344-
if (bp < 0 || bp >= getStepParameters().length) throw new IllegalArgumentException();
372+
if (bp < 0 || bp >= getStepParameters().length) throw new IllegalArgumentException("Base pair number is out of range.");
345373
return stepParameters[bp][2];
346374
}
347375

@@ -351,7 +379,7 @@ public Double getTwist(int bp) {
351379
* @return the value as a double (in Å)
352380
*/
353381
public Double getShift(int bp) {
354-
if (bp < 0 || bp >= getStepParameters().length) throw new IllegalArgumentException();
382+
if (bp < 0 || bp >= getStepParameters().length) throw new IllegalArgumentException("Base pair number is out of range.");
355383
return stepParameters[bp][3];
356384
}
357385

@@ -361,7 +389,7 @@ public Double getShift(int bp) {
361389
* @return the value as a double (in Å)
362390
*/
363391
public Double getSlide(int bp) {
364-
if (bp < 0 || bp >= getStepParameters().length) throw new IllegalArgumentException();
392+
if (bp < 0 || bp >= getStepParameters().length) throw new IllegalArgumentException("Base pair number is out of range.");
365393
return stepParameters[bp][4];
366394
}
367395

@@ -371,7 +399,7 @@ public Double getSlide(int bp) {
371399
* @return the value as a double (in Å)
372400
*/
373401
public Double getRise(int bp) {
374-
if (bp < 0 || bp >= getStepParameters().length) throw new IllegalArgumentException();
402+
if (bp < 0 || bp >= getStepParameters().length) throw new IllegalArgumentException("Base pair number is out of range.");
375403
return stepParameters[bp][5];
376404
}
377405

@@ -416,7 +444,9 @@ public List<Pair<Group>> findPairs(List<Chain> chains) {
416444
for (int j = i+1; j < chains.size(); j++) {
417445
String complement = complement(chains.get(j).getAtomSequence(), useRNA);
418446
String match = longestCommonSubstring(c.getAtomSequence(), complement);
419-
//log.info(c.getAtomSequence() + " " + chains.get(j).getAtomSequence() + " " + match);
447+
if (log.isDebugEnabled()) {
448+
log.debug(c.getAtomSequence() + " " + chains.get(j).getAtomSequence() + " " + match);
449+
}
420450
int index1 = c.getAtomSequence().indexOf(match);
421451
int index2 = complement.length() - complement.indexOf(match) - 1;
422452
for (int k = 0; k < match.length(); k++) {
@@ -521,11 +551,10 @@ public Matrix4d basePairReferenceFrame(Pair<Group> pair) {
521551
}
522552
assert count == std2.getAtoms().size();
523553

524-
// log.info(ref1);
525554
Matrix4d temp = (Matrix4d)ref1.clone();
526555
Matrix4d temp2 = (Matrix4d)temp.clone();
527556
Matrix4d ref2 = sp.superposeAndTransform(pointact, pointref);
528-
// log.info(ref2);
557+
529558
double[][] v = new double[3][4];
530559
double[] y3 = new double[4];
531560
double[] z3 = new double[4];
@@ -568,7 +597,7 @@ public Matrix4d basePairReferenceFrame(Pair<Group> pair) {
568597
// calculate pairing parameters: buckle, propeller, opening, shear, stretch, stagger
569598
temp2.invert();
570599
temp2.mul(ref2);
571-
pairParameters = calculatetp(temp2);
600+
pairParameters = calculateTp(temp2);
572601
for (int i = 0; i < 6; i++) pairParameters[i] *= -1;
573602

574603
// return the central frame of the base pair
@@ -595,13 +624,14 @@ public String toString() {
595624
}
596625

597626

627+
// The following methods are just helper classes for the rapid analyze of base-pair geometry.
598628
/**
599-
* This method calculates pairing and step parameters from 4x4 transformation matrices
629+
* This method calculates pairing and step parameters from 4x4 transformation matrices (used internally)
600630
* that come out as Matrix4d;
601631
* @param input the 4x4 matrix representing the transformation from strand II -> strand I or pair i to pair i+1
602632
* @return Six parameters as double[6]
603633
*/
604-
public static double[] calculatetp(Matrix4d input) {
634+
public static double[] calculateTp(Matrix4d input) {
605635

606636
double[][] A = new double[4][4];
607637
for (int i = 0; i < 4; i++) for (int j = 0; j < 4; j++) {
@@ -646,8 +676,13 @@ public static double[] calculatetp(Matrix4d input) {
646676

647677
}
648678

649-
650-
public static char complementBase(char base, boolean RNA) {
679+
/**
680+
* Return the complement of a base (used internally)
681+
* @param base The letter of the base
682+
* @param RNA Whether it is RNA (if false, it is DNA)
683+
* @return The character representing the complement of the base
684+
*/
685+
protected static char complementBase(char base, boolean RNA) {
651686
if (base == 'A' && RNA) return 'U';
652687
if (base == 'A') return 'T';
653688
if (base == 'T' && !RNA) return 'A';
@@ -657,15 +692,26 @@ public static char complementBase(char base, boolean RNA) {
657692
return ' ';
658693
}
659694

660-
public static String complement(String sequence, boolean RNA) {
695+
/**
696+
* Simple helper method for quickly checking the complement of a sequence, see also DNASequence nad RNASequence classes
697+
* for more extensively useful functions not used in this narrow context of structural biology of base pairs. (Used internally)
698+
*/
699+
private static String complement(String sequence, boolean RNA) {
661700
String result = "";
662701
for (int i = sequence.length() - 1; i >= 0; i--) {
663702
result += complementBase(sequence.charAt(i), RNA);
664703
}
665704
return result;
666705
}
667706

668-
public static double[] cross(double[] a, double[] b) {
707+
/**
708+
* 3D Vector cross product of two vectors as double arrays (used internally)
709+
*
710+
* @param a An array of length 3 or 4 (4th component is ignored)
711+
* @param b An array of length 3 or 4 (4th component is ignored)
712+
* @return The cross product of the vectors (just the first three components
713+
*/
714+
private static double[] cross(double[] a, double[] b) {
669715
assert a.length >= 3 && b.length >= 3;
670716
double[] result = new double[4];
671717
result[0] = a[1]*b[2]-a[2]*b[1];
@@ -674,7 +720,13 @@ public static double[] cross(double[] a, double[] b) {
674720
return result;
675721
}
676722

677-
public static double[] removeComponent(double[] a, double[] b) {
723+
/**
724+
* Remove any component of vector a that is along vector b (used internally)
725+
* @param a The array (vector) to remove component from
726+
* @param b The component array (vector) to remove from the first
727+
* @return The original array a with any component along b removed from it.
728+
*/
729+
private static double[] removeComponent(double[] a, double[] b) {
678730
double dot = 0;
679731
double[] result = new double[4];
680732
for (int i = 0; i < 3; i++) {
@@ -687,7 +739,13 @@ public static double[] removeComponent(double[] a, double[] b) {
687739

688740
}
689741

690-
public static String longestCommonSubstring(String s1, String s2) {
742+
/**
743+
* Finds the longest common substring between two strings (used internally)
744+
* @param s1 The first string
745+
* @param s2 The second string
746+
* @return The substring itself
747+
*/
748+
private static String longestCommonSubstring(String s1, String s2) {
691749
int start = 0;
692750
int max = 0;
693751
for (int i = 0; i < s1.length(); i++) {
@@ -706,6 +764,13 @@ public static String longestCommonSubstring(String s1, String s2) {
706764
return s1.substring(start, (start + max));
707765
}
708766

767+
/**
768+
* Return true if a is the complement of b (used internally)
769+
* @param a First letter
770+
* @param b Potential matching letter
771+
* @param RNA Whether it is RNA (if false, DNA rules are used)
772+
* @return True if the bases are complementary.
773+
*/
709774
protected static boolean match(char a, char b, boolean RNA) {
710775
if (a == 'A' && b == 'T' && !RNA) return true;
711776
if (a == 'A' && b == 'U' && RNA) return true;

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

Lines changed: 22 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,24 @@
1+
/*
2+
* BioJava development code
3+
*
4+
* This code may be freely distributed and modified under the
5+
* terms of the GNU Lesser General Public Licence. This should
6+
* be distributed with the code. If you do not have a copy,
7+
* see:
8+
*
9+
* http://www.gnu.org/copyleft/lesser.html
10+
*
11+
* Copyright for this code is held jointly by the individual
12+
* authors. These should be listed in @author doc comments.
13+
*
14+
* For more information on the BioJava project and its aims,
15+
* or to join the biojava-l mailing list, visit the home page
16+
* at:
17+
*
18+
* http://www.biojava.org/
19+
*
20+
*
21+
*/
122
package org.biojava.nbio.structure.basepairs;
223

324
import org.biojava.nbio.structure.Atom;
@@ -12,7 +33,6 @@
1233
import java.util.List;
1334

1435
/**
15-
* Contributed to BioJava under its LGPL
1636
* This class allows for finding inter-strand base pairs that are not necessarily canonical Watson-Crick pairs.
1737
* The implementation of findPair is different than that of the base class.
1838
* @author Luke Czapla
@@ -66,6 +86,7 @@ public List<Pair<Group>> findPairs(List<Chain> chains) {
6686
Matrix4d data = basePairReferenceFrame(ga);
6787
// if the stagger is greater than 2 Å, it's not really paired.
6888
if (Math.abs(pairParameters[5]) > MaxStagger) continue;
89+
// similarly, extreme shear and stretch is not a good base pair
6990
if (Math.abs(pairParameters[3]) > MaxShear) continue;
7091
if (Math.abs(pairParameters[4]) > MaxStretch) continue;
7192

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