Repository navigation
Expand file tree
/
Copy pathCalc.java
More file actions
1350 lines (1164 loc) · 33.1 KB
/
Copy pathCalc.java
File metadata and controls
1350 lines (1164 loc) · 33.1 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on 08.05.2004
*
*/
package org.biojava.nbio.structure;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import javax.vecmath.Matrix3d;
import javax.vecmath.Matrix4d;
import javax.vecmath.Point3d;
import javax.vecmath.Vector3d;
import org.biojava.nbio.structure.geometry.CalcPoint;
import org.biojava.nbio.structure.geometry.Matrices;
import org.biojava.nbio.structure.geometry.SuperPositionSVD;
import org.biojava.nbio.structure.jama.Matrix;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Utility operations on Atoms, AminoAcids, Matrices, Point3d, etc.
* <p>
* Currently the coordinates of an Atom are stored as an array of size 3
* (double[3]). It would be more powerful to use Point3d from javax.vecmath.
* Overloaded methods for Point3d operations exist in the {@link CalcPoint}
* Class.
*
* @author Andreas Prlic
* @author Aleix Lafita
* @since 1.4
* @version %I% %G%
*/
public class Calc {
private final static Logger logger = LoggerFactory.getLogger(Calc.class);
/**
* calculate distance between two atoms.
*
* @param a
* an Atom object
* @param b
* an Atom object
* @return a double
*/
public static final double getDistance(Atom a, Atom b) {
double x = a.getX() - b.getX();
double y = a.getY() - b.getY();
double z = a.getZ() - b.getZ();
double s = x * x + y * y + z * z;
return Math.sqrt(s);
}
/**
* Will calculate the square of distances between two atoms. This will be
* faster as it will not perform the final square root to get the actual
* distance. Use this if doing large numbers of distance comparisons - it is
* marginally faster than getDistance().
*
* @param a
* an Atom object
* @param b
* an Atom object
* @return a double
*/
public static double getDistanceFast(Atom a, Atom b) {
double x = a.getX() - b.getX();
double y = a.getY() - b.getY();
double z = a.getZ() - b.getZ();
return x * x + y * y + z * z;
}
public static final Atom invert(Atom a) {
double[] coords = new double[] { 0.0, 0.0, 0.0 };
Atom zero = new AtomImpl();
zero.setCoords(coords);
return subtract(zero, a);
}
/**
* add two atoms ( a + b).
*
* @param a
* an Atom object
* @param b
* an Atom object
* @return an Atom object
*/
public static final Atom add(Atom a, Atom b) {
Atom c = new AtomImpl();
c.setX(a.getX() + b.getX());
c.setY(a.getY() + b.getY());
c.setZ(a.getZ() + b.getZ());
return c;
}
/**
* subtract two atoms ( a - b).
*
* @param a
* an Atom object
* @param b
* an Atom object
* @return n new Atom object representing the difference
*/
public static final Atom subtract(Atom a, Atom b) {
Atom c = new AtomImpl();
c.setX(a.getX() - b.getX());
c.setY(a.getY() - b.getY());
c.setZ(a.getZ() - b.getZ());
return c;
}
/**
* Vector product (cross product).
*
* @param a
* an Atom object
* @param b
* an Atom object
* @return an Atom object
*/
public static final Atom vectorProduct(Atom a, Atom b) {
Atom c = new AtomImpl();
c.setX(a.getY() * b.getZ() - a.getZ() * b.getY());
c.setY(a.getZ() * b.getX() - a.getX() * b.getZ());
c.setZ(a.getX() * b.getY() - a.getY() * b.getX());
return c;
}
/**
* Scalar product (dot product).
*
* @param a
* an Atom object
* @param b
* an Atom object
* @return a double
*/
public static final double scalarProduct(Atom a, Atom b) {
return a.getX() * b.getX() + a.getY() * b.getY() + a.getZ() * b.getZ();
}
/**
* Gets the length of the vector (2-norm)
*
* @param a
* an Atom object
* @return Square root of the sum of the squared elements
*/
public static final double amount(Atom a) {
return Math.sqrt(scalarProduct(a, a));
}
/**
* Gets the angle between two vectors
*
* @param a
* an Atom object
* @param b
* an Atom object
* @return Angle between a and b in degrees, in range [0,180]. If either
* vector has length 0 then angle is not defined and NaN is returned
*/
public static final double angle(Atom a, Atom b) {
Vector3d va = new Vector3d(a.getCoordsAsPoint3d());
Vector3d vb = new Vector3d(b.getCoordsAsPoint3d());
return Math.toDegrees(va.angle(vb));
}
/**
* Returns the unit vector of vector a .
*
* @param a
* an Atom object
* @return an Atom object
*/
public static final Atom unitVector(Atom a) {
double amount = amount(a);
double[] coords = new double[3];
coords[0] = a.getX() / amount;
coords[1] = a.getY() / amount;
coords[2] = a.getZ() / amount;
a.setCoords(coords);
return a;
}
/**
* Calculate the torsion angle, i.e. the angle between the normal vectors of
* the two plains a-b-c and b-c-d. See
* http://en.wikipedia.org/wiki/Dihedral_angle
*
* @param a
* an Atom object
* @param b
* an Atom object
* @param c
* an Atom object
* @param d
* an Atom object
* @return the torsion angle in degrees, in range +-[0,180]. If either first
* 3 or last 3 atoms are colinear then torsion angle is not defined
* and NaN is returned
*/
public static final double torsionAngle(Atom a, Atom b, Atom c, Atom d) {
Atom ab = subtract(a, b);
Atom cb = subtract(c, b);
Atom bc = subtract(b, c);
Atom dc = subtract(d, c);
Atom abc = vectorProduct(ab, cb);
Atom bcd = vectorProduct(bc, dc);
double angl = angle(abc, bcd);
/* calc the sign: */
Atom vecprod = vectorProduct(abc, bcd);
double val = scalarProduct(cb, vecprod);
if (val < 0.0)
angl = -angl;
return angl;
}
/**
* Calculate the phi angle.
*
* @param a
* an AminoAcid object
* @param b
* an AminoAcid object
* @return a double
* @throws StructureException
* if aminoacids not connected or if any of the 4 needed atoms
* missing
*/
public static final double getPhi(AminoAcid a, AminoAcid b)
throws StructureException {
if (!isConnected(a, b)) {
throw new StructureException(
"can not calc Phi - AminoAcids are not connected!");
}
Atom a_C = a.getC();
Atom b_N = b.getN();
Atom b_CA = b.getCA();
Atom b_C = b.getC();
// C and N were checked in isConnected already
if (b_CA == null)
throw new StructureException(
"Can not calculate Phi, CA atom is missing");
return torsionAngle(a_C, b_N, b_CA, b_C);
}
/**
* Calculate the psi angle.
*
* @param a
* an AminoAcid object
* @param b
* an AminoAcid object
* @return a double
* @throws StructureException
* if aminoacids not connected or if any of the 4 needed atoms
* missing
*/
public static final double getPsi(AminoAcid a, AminoAcid b)
throws StructureException {
if (!isConnected(a, b)) {
throw new StructureException(
"can not calc Psi - AminoAcids are not connected!");
}
Atom a_N = a.getN();
Atom a_CA = a.getCA();
Atom a_C = a.getC();
Atom b_N = b.getN();
// C and N were checked in isConnected already
if (a_CA == null)
throw new StructureException(
"Can not calculate Psi, CA atom is missing");
return torsionAngle(a_N, a_CA, a_C, b_N);
}
/**
* Test if two amino acids are connected, i.e. if the distance from C to N <
* 2.5 Angstrom.
*
* If one of the AminoAcids has an atom missing, returns false.
*
* @param a
* an AminoAcid object
* @param b
* an AminoAcid object
* @return true if ...
*/
public static final boolean isConnected(AminoAcid a, AminoAcid b) {
Atom C = null;
Atom N = null;
C = a.getC();
N = b.getN();
if (C == null || N == null)
return false;
// one could also check if the CA atoms are < 4 A...
double distance = getDistance(C, N);
return distance < 2.5;
}
/**
* Rotate a single Atom aroud a rotation matrix. The rotation Matrix must be
* a pre-multiplication 3x3 Matrix.
*
* If the matrix is indexed m[row][col], then the matrix will be
* pre-multiplied (y=atom*M)
*
* @param atom
* atom to be rotated
* @param m
* a rotation matrix represented as a double[3][3] array
*/
public static final void rotate(Atom atom, double[][] m) {
double x = atom.getX();
double y = atom.getY();
double z = atom.getZ();
double nx = m[0][0] * x + m[0][1] * y + m[0][2] * z;
double ny = m[1][0] * x + m[1][1] * y + m[1][2] * z;
double nz = m[2][0] * x + m[2][1] * y + m[2][2] * z;
atom.setX(nx);
atom.setY(ny);
atom.setZ(nz);
}
/**
* Rotate a structure. The rotation Matrix must be a pre-multiplication
* Matrix.
*
* @param structure
* a Structure object
* @param rotationmatrix
* an array (3x3) of double representing the rotation matrix.
* @throws StructureException
* ...
*/
public static final void rotate(Structure structure,
double[][] rotationmatrix) throws StructureException {
if (rotationmatrix.length != 3) {
throw new StructureException("matrix does not have size 3x3 !");
}
AtomIterator iter = new AtomIterator(structure);
while (iter.hasNext()) {
Atom atom = iter.next();
Calc.rotate(atom, rotationmatrix);
}
}
/**
* Rotate a Group. The rotation Matrix must be a pre-multiplication Matrix.
*
* @param group
* a group object
* @param rotationmatrix
* an array (3x3) of double representing the rotation matrix.
* @throws StructureException
* ...
*/
public static final void rotate(Group group, double[][] rotationmatrix)
throws StructureException {
if (rotationmatrix.length != 3) {
throw new StructureException("matrix does not have size 3x3 !");
}
AtomIterator iter = new AtomIterator(group);
while (iter.hasNext()) {
Atom atom = null;
atom = iter.next();
rotate(atom, rotationmatrix);
}
}
/**
* Rotate an Atom around a Matrix object. The rotation Matrix must be a
* pre-multiplication Matrix.
*
* @param atom
* atom to be rotated
* @param m
* rotation matrix to be applied to the atom
*/
public static final void rotate(Atom atom, Matrix m) {
double x = atom.getX();
double y = atom.getY();
double z = atom.getZ();
double[][] ad = new double[][] { { x, y, z } };
Matrix am = new Matrix(ad);
Matrix na = am.times(m);
atom.setX(na.get(0, 0));
atom.setY(na.get(0, 1));
atom.setZ(na.get(0, 2));
}
/**
* Rotate a group object. The rotation Matrix must be a pre-multiplication
* Matrix.
*
* @param group
* a group to be rotated
* @param m
* a Matrix object representing the rotation matrix
*/
public static final void rotate(Group group, Matrix m) {
AtomIterator iter = new AtomIterator(group);
while (iter.hasNext()) {
Atom atom = iter.next();
rotate(atom, m);
}
}
/**
* Rotate a structure object. The rotation Matrix must be a
* pre-multiplication Matrix.
*
* @param structure
* the structure to be rotated
* @param m
* rotation matrix to be applied
*/
public static final void rotate(Structure structure, Matrix m) {
AtomIterator iter = new AtomIterator(structure);
while (iter.hasNext()) {
Atom atom = iter.next();
rotate(atom, m);
}
}
/**
* Transform an array of atoms at once. The transformation Matrix must be a
* post-multiplication Matrix.
*
* @param ca
* array of Atoms to shift
* @param t
* transformation Matrix4d
*/
public static void transform(Atom[] ca, Matrix4d t) {
for (Atom atom : ca)
Calc.transform(atom, t);
}
/**
* Transforms an atom object, given a Matrix4d (i.e. the vecmath library
* double-precision 4x4 rotation+translation matrix). The transformation
* Matrix must be a post-multiplication Matrix.
*
* @param atom
* @param m
*/
public static final void transform(Atom atom, Matrix4d m) {
Point3d p = new Point3d(atom.getX(), atom.getY(), atom.getZ());
m.transform(p);
atom.setX(p.x);
atom.setY(p.y);
atom.setZ(p.z);
}
/**
* Transforms a group object, given a Matrix4d (i.e. the vecmath library
* double-precision 4x4 rotation+translation matrix). The transformation
* Matrix must be a post-multiplication Matrix.
*
* @param group
* @param m
*/
public static final void transform(Group group, Matrix4d m) {
for (Atom atom : group.getAtoms()) {
transform(atom, m);
}
for (Group altG : group.getAltLocs()) {
transform(altG, m);
}
}
/**
* Transforms a structure object, given a Matrix4d (i.e. the vecmath library
* double-precision 4x4 rotation+translation matrix). The transformation
* Matrix must be a post-multiplication Matrix.
*
* @param structure
* @param m
*/
public static final void transform(Structure structure, Matrix4d m) {
for (int n=0; n<structure.nrModels();n++) {
for (Chain c : structure.getChains(n)) {
transform(c, m);
}
}
}
/**
* Transforms a chain object, given a Matrix4d (i.e. the vecmath library
* double-precision 4x4 rotation+translation matrix). The transformation
* Matrix must be a post-multiplication Matrix.
*
* @param chain
* @param m
*/
public static final void transform(Chain chain, Matrix4d m) {
for (Group g : chain.getAtomGroups()) {
transform(g, m);
}
}
/**
* Translates an atom object, given a Vector3d (i.e. the vecmath library
* double-precision 3-d vector)
*
* @param atom
* @param v
*/
public static final void translate(Atom atom, Vector3d v) {
atom.setX(atom.getX() + v.x);
atom.setY(atom.getY() + v.y);
atom.setZ(atom.getZ() + v.z);
}
/**
* Translates a group object, given a Vector3d (i.e. the vecmath library
* double-precision 3-d vector)
*
* @param group
* @param v
*/
public static final void translate(Group group, Vector3d v) {
for (Atom atom : group.getAtoms()) {
translate(atom, v);
}
for (Group altG : group.getAltLocs()) {
translate(altG, v);
}
}
/**
* Translates a chain object, given a Vector3d (i.e. the vecmath library
* double-precision 3-d vector)
*
* @param chain
* @param v
*/
public static final void translate(Chain chain, Vector3d v) {
for (Group g : chain.getAtomGroups()) {
translate(g, v);
}
}
/**
* Translates a Structure object, given a Vector3d (i.e. the vecmath library
* double-precision 3-d vector)
*
* @param structure
* @param v
*/
public static final void translate(Structure structure, Vector3d v) {
for (int n=0; n<structure.nrModels();n++) {
for (Chain c : structure.getChains(n)) {
translate(c, v);
}
}
}
/**
* calculate structure + Matrix coodinates ...
*
* @param s
* the structure to operate on
* @param matrix
* a Matrix object
*/
public static final void plus(Structure s, Matrix matrix) {
AtomIterator iter = new AtomIterator(s);
Atom oldAtom = null;
Atom rotOldAtom = null;
while (iter.hasNext()) {
Atom atom = null;
atom = iter.next();
try {
if (oldAtom != null) {
logger.debug("before {}", getDistance(oldAtom, atom));
}
} catch (Exception e) {
logger.error("Exception: ", e);
}
oldAtom = (Atom) atom.clone();
double x = atom.getX();
double y = atom.getY();
double z = atom.getZ();
double[][] ad = new double[][] { { x, y, z } };
Matrix am = new Matrix(ad);
Matrix na = am.plus(matrix);
double[] coords = new double[3];
coords[0] = na.get(0, 0);
coords[1] = na.get(0, 1);
coords[2] = na.get(0, 2);
atom.setCoords(coords);
try {
if (rotOldAtom != null) {
logger.debug("after {}", getDistance(rotOldAtom, atom));
}
} catch (Exception e) {
logger.error("Exception: ", e);
}
rotOldAtom = (Atom) atom.clone();
}
}
/**
* shift a structure with a vector.
*
* @param structure
* a Structure object
* @param a
* an Atom object representing a shift vector
*/
public static final void shift(Structure structure, Atom a) {
AtomIterator iter = new AtomIterator(structure);
while (iter.hasNext()) {
Atom atom = null;
atom = iter.next();
Atom natom = add(atom, a);
double x = natom.getX();
double y = natom.getY();
double z = natom.getZ();
atom.setX(x);
atom.setY(y);
atom.setZ(z);
}
}
/**
* Shift a vector.
*
* @param a
* vector a
* @param b
* vector b
*/
public static final void shift(Atom a, Atom b) {
Atom natom = add(a, b);
double x = natom.getX();
double y = natom.getY();
double z = natom.getZ();
a.setX(x);
a.setY(y);
a.setZ(z);
}
/**
* Shift a Group with a vector.
*
* @param group
* a group object
* @param a
* an Atom object representing a shift vector
*/
public static final void shift(Group group, Atom a) {
AtomIterator iter = new AtomIterator(group);
while (iter.hasNext()) {
Atom atom = null;
atom = iter.next();
Atom natom = add(atom, a);
double x = natom.getX();
double y = natom.getY();
double z = natom.getZ();
atom.setX(x);
atom.setY(y);
atom.setZ(z);
}
}
/**
* Returns the centroid of the set of atoms.
*
* @param atomSet
* a set of Atoms
* @return an Atom representing the Centroid of the set of atoms
*/
public static final Atom getCentroid(Atom[] atomSet) {
// if we don't catch this case, the centroid returned is (NaN,NaN,NaN), which can cause lots of problems down the line
if (atomSet.length==0)
throw new IllegalArgumentException("Atom array has length 0, can't calculate centroid!");
double[] coords = new double[3];
coords[0] = 0;
coords[1] = 0;
coords[2] = 0;
for (Atom a : atomSet) {
coords[0] += a.getX();
coords[1] += a.getY();
coords[2] += a.getZ();
}
int n = atomSet.length;
coords[0] = coords[0] / n;
coords[1] = coords[1] / n;
coords[2] = coords[2] / n;
Atom vec = new AtomImpl();
vec.setCoords(coords);
return vec;
}
/**
* Returns the center of mass of the set of atoms. Atomic masses of the
* Atoms are used.
*
* @param points
* a set of Atoms
* @return an Atom representing the center of mass
*/
public static Atom centerOfMass(Atom[] points) {
Atom center = new AtomImpl();
float totalMass = 0.0f;
for (Atom a : points) {
float mass = a.getElement().getAtomicMass();
totalMass += mass;
center = scaleAdd(mass, a, center);
}
center = scaleEquals(center, 1.0f / totalMass);
return center;
}
/**
* Multiply elements of a by s (in place)
*
* @param a
* @param s
* @return the modified a
*/
public static Atom scaleEquals(Atom a, double s) {
double x = a.getX();
double y = a.getY();
double z = a.getZ();
x *= s;
y *= s;
z *= s;
// Atom b = new AtomImpl();
a.setX(x);
a.setY(y);
a.setZ(z);
return a;
}
/**
* Multiply elements of a by s
*
* @param a
* @param s
* @return A new Atom with s*a
*/
public static Atom scale(Atom a, double s) {
double x = a.getX();
double y = a.getY();
double z = a.getZ();
Atom b = new AtomImpl();
b.setX(x * s);
b.setY(y * s);
b.setZ(z * s);
return b;
}
/**
* Perform linear transformation s*X+B, and store the result in b
*
* @param s
* Amount to scale x
* @param x
* Input coordinate
* @param b
* Vector to translate (will be modified)
* @return b, after modification
*/
public static Atom scaleAdd(double s, Atom x, Atom b) {
double xc = s * x.getX() + b.getX();
double yc = s * x.getY() + b.getY();
double zc = s * x.getZ() + b.getZ();
// Atom a = new AtomImpl();
b.setX(xc);
b.setY(yc);
b.setZ(zc);
return b;
}
/**
* Returns the Vector that needs to be applied to shift a set of atoms to
* the Centroid.
*
* @param atomSet
* array of Atoms
* @return the vector needed to shift the set of atoms to its geometric
* center
*/
public static final Atom getCenterVector(Atom[] atomSet) {
Atom centroid = getCentroid(atomSet);
return getCenterVector(atomSet, centroid);
}
/**
* Returns the Vector that needs to be applied to shift a set of atoms to
* the Centroid, if the centroid is already known
*
* @param atomSet
* array of Atoms
* @return the vector needed to shift the set of atoms to its geometric
* center
*/
public static final Atom getCenterVector(Atom[] atomSet, Atom centroid) {
double[] coords = new double[3];
coords[0] = 0 - centroid.getX();
coords[1] = 0 - centroid.getY();
coords[2] = 0 - centroid.getZ();
Atom shiftVec = new AtomImpl();
shiftVec.setCoords(coords);
return shiftVec;
}
/**
* Center the atoms at the Centroid.
*
* @param atomSet
* a set of Atoms
* @return an Atom representing the Centroid of the set of atoms
* @throws StructureException
* */
public static final Atom[] centerAtoms(Atom[] atomSet)
throws StructureException {
Atom centroid = getCentroid(atomSet);
return centerAtoms(atomSet, centroid);
}
/**
* Center the atoms at the Centroid, if the centroid is already know.
*
* @param atomSet
* a set of Atoms
* @return an Atom representing the Centroid of the set of atoms
* @throws StructureException
* */
public static final Atom[] centerAtoms(Atom[] atomSet, Atom centroid)
throws StructureException {
Atom shiftVector = getCenterVector(atomSet, centroid);
Atom[] newAtoms = new AtomImpl[atomSet.length];
for (int i = 0; i < atomSet.length; i++) {
Atom a = atomSet[i];
Atom n = add(a, shiftVector);
newAtoms[i] = n;
}
return newAtoms;
}
/**
* creates a virtual C-beta atom. this might be needed when working with GLY
*
* thanks to Peter Lackner for a python template of this method.
*
* @param amino
* the amino acid for which a "virtual" CB atom should be
* calculated
* @return a "virtual" CB atom
* @throws StructureException
*/
public static final Atom createVirtualCBAtom(AminoAcid amino)
throws StructureException {
AminoAcid ala = StandardAminoAcid.getAminoAcid("ALA");
Atom aN = ala.getN();
Atom aCA = ala.getCA();
Atom aC = ala.getC();
Atom aCB = ala.getCB();
Atom[] arr1 = new Atom[3];
arr1[0] = aN;
arr1[1] = aCA;
arr1[2] = aC;
Atom[] arr2 = new Atom[3];
arr2[0] = amino.getN();
arr2[1] = amino.getCA();
arr2[2] = amino.getC();
// ok now we got the two arrays, do a Superposition:
SuperPositionSVD svd = new SuperPositionSVD(false);