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Hashing of pseudo atoms changed, see 214361c
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@johnmay
johnmay committed Apr 25, 2017
1 parent 8749924 commit b7135e5
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Showing 2 changed files with 38 additions and 11 deletions.
46 changes: 36 additions & 10 deletions ...builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/TemplateHandler3DTest.java
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Expand Up @@ -64,16 +64,16 @@ private static BitSet parseBitSet(String str) throws Exception {
@Test
public void testFingerprints() throws Exception {
BitSet[] expected = new BitSet[]{
parseBitSet("{1, 4, 10, 14, 24, 28, 37, 40, 41, 44, 50, 53, 54, 59, 61, 65, 67, 73, 74, 77, 86, 94, 103, 104, 112, 117, 119, 120, 125, 127, 131, 134, 154, 155, 160, 162, 166, 182, 186, 187, 189, 196, 198, 205, 221, 222, 223, 224, 228, 232, 234, 248, 249, 253, 255, 262, 286, 287, 293, 296, 299, 300, 303, 305, 308, 309, 317, 320, 325, 331, 335, 337, 339, 342, 344, 354, 357, 371, 374, 376, 385, 386, 388, 395, 398, 408, 424, 429, 432, 438, 443, 447, 454, 463, 464, 473, 482, 489, 490, 492, 506, 510, 511, 515, 522, 523, 533, 534, 544, 548, 555, 557, 561, 562, 568, 571, 573, 576, 588, 590, 602, 606, 608, 612, 628, 652, 665, 670, 671, 672, 678, 680, 681, 709, 711, 714, 729, 730, 741, 742, 747, 752, 753, 760, 766, 769, 770, 773, 794, 798, 800, 808, 816, 832, 833, 834, 839, 841, 843, 847, 850, 859, 868, 873, 876, 879, 881, 882, 884, 887, 905, 911, 921, 922, 924, 925, 930, 936, 939, 944, 946, 949, 952, 953, 954, 955, 960, 963, 986, 987, 995, 998, 1003, 1006, 1009, 1010, 1017, 1020}"),
parseBitSet("{1, 4, 10, 14, 24, 28, 44, 50, 54, 59, 61, 65, 67, 73, 77, 79, 86, 94, 103, 104, 112, 119, 120, 134, 153, 154, 155, 160, 162, 166, 182, 186, 187, 189, 196, 222, 223, 224, 228, 234, 236, 239, 242, 253, 262, 264, 287, 291, 293, 296, 300, 303, 305, 308, 309, 317, 320, 323, 325, 335, 337, 339, 354, 356, 357, 371, 376, 381, 383, 385, 386, 395, 398, 422, 424, 432, 443, 464, 473, 482, 489, 490, 492, 506, 510, 515, 522, 523, 533, 544, 548, 561, 562, 573, 578, 588, 597, 602, 609, 645, 652, 653, 665, 671, 672, 678, 709, 711, 714, 726, 730, 740, 741, 742, 747, 752, 760, 766, 769, 770, 773, 781, 792, 793, 798, 801, 808, 816, 825, 832, 833, 834, 841, 843, 850, 851, 856, 876, 884, 885, 888, 914, 921, 922, 924, 925, 933, 936, 944, 949, 952, 955, 963, 977, 980, 981, 986, 987, 993, 995, 998, 1001, 1003, 1010, 1020}"),
parseBitSet("{4, 17, 51, 52, 58, 110, 114, 162, 177, 182, 208, 224, 230, 231, 242, 259, 262, 266, 270, 277, 289, 307, 309, 325, 335, 339, 349, 351, 354, 363, 371, 376, 387, 406, 433, 437, 489, 491, 500, 504, 513, 522, 533, 539, 545, 561, 573, 588, 601, 603, 611, 614, 618, 665, 686, 735, 746, 747, 752, 755, 764, 776, 777, 784, 795, 798, 801, 808, 822, 823, 851, 876, 882, 886, 944, 969, 987}"),
parseBitSet("{4, 10, 77, 162, 522, 714, 747, 752, 816}"),
parseBitSet("{4, 14, 16, 17, 18, 27, 30, 37, 40, 44, 50, 51, 52, 54, 55, 58, 61, 65, 67, 73, 75, 78, 79, 86, 103, 104, 106, 110, 112, 114, 120, 125, 127, 141, 142, 144, 151, 153, 154, 158, 162, 177, 178, 182, 189, 196, 199, 204, 205, 208, 210, 215, 216, 220, 222, 224, 228, 230, 231, 236, 239, 245, 253, 255, 259, 262, 264, 266, 280, 286, 287, 289, 291, 296, 297, 300, 303, 305, 308, 309, 311, 317, 320, 321, 322, 323, 325, 329, 334, 335, 337, 339, 342, 344, 347, 349, 351, 354, 356, 359, 363, 370, 371, 376, 377, 378, 381, 382, 383, 385, 386, 387, 395, 398, 400, 406, 412, 415, 425, 432, 433, 437, 439, 467, 473, 475, 485, 489, 490, 491, 492, 495, 500, 502, 504, 506, 510, 512, 515, 522, 523, 526, 531, 534, 536, 539, 544, 545, 548, 550, 555, 557, 561, 562, 566, 568, 572, 573, 575, 578, 588, 592, 597, 601, 602, 603, 609, 611, 614, 615, 616, 618, 624, 626, 638, 644, 645, 646, 651, 653, 654, 655, 658, 665, 666, 671, 674, 680, 686, 691, 700, 733, 735, 740, 742, 745, 746, 747, 752, 755, 764, 766, 768, 770, 773, 777, 781, 792, 793, 795, 798, 800, 801, 822, 825, 830, 832, 834, 843, 845, 851, 856, 857, 874, 876, 882, 884, 885, 886, 888, 896, 905, 910, 912, 914, 921, 922, 924, 925, 930, 931, 933, 939, 944, 946, 952, 955, 957, 961, 963, 977, 978, 979, 980, 987, 998, 999, 1001, 1003, 1008, 1010, 1017, 1020}"),
parseBitSet("{4, 10, 14, 16, 24, 28, 40, 50, 61, 65, 67, 77, 86, 92, 103, 104, 108, 117, 120, 132, 136, 154, 155, 158, 160, 162, 182, 185, 189, 196, 198, 222, 223, 228, 231, 255, 275, 280, 287, 295, 299, 300, 303, 308, 317, 320, 328, 339, 352, 357, 369, 385, 386, 395, 398, 401, 424, 429, 432, 443, 449, 464, 473, 481, 488, 490, 505, 506, 507, 510, 513, 515, 522, 527, 533, 544, 546, 548, 561, 562, 566, 596, 598, 599, 613, 628, 645, 652, 671, 672, 678, 680, 683, 686, 696, 709, 714, 729, 730, 736, 747, 752, 760, 770, 773, 777, 779, 794, 797, 808, 816, 829, 834, 843, 868, 886, 889, 910, 911, 921, 922, 923, 925, 936, 944, 946, 952, 955, 958, 963, 971, 988, 995, 998, 1003, 1010, 1020, 1022}"),
parseBitSet("{4, 10, 77, 162, 522, 714, 747, 752, 816}"),
parseBitSet("{4, 10, 162, 522, 714, 747, 752, 816}"),
parseBitSet("{4, 17, 51, 52, 58, 110, 114, 162, 177, 182, 208, 224, 230, 231, 242, 259, 262, 266, 270, 277, 289, 307, 309, 325, 335, 339, 349, 351, 354, 363, 371, 376, 387, 406, 433, 437, 489, 491, 500, 504, 513, 522, 533, 539, 545, 561, 573, 588, 601, 603, 611, 614, 618, 665, 686, 735, 746, 747, 752, 755, 764, 776, 777, 784, 795, 798, 801, 808, 822, 823, 851, 876, 882, 886, 944, 969, 987}"),
parseBitSet("{4, 14, 50, 61, 65, 67, 83, 86, 91, 103, 104, 120, 133, 154, 162, 166, 188, 192, 222, 300, 308, 317, 320, 398, 426, 429, 432, 465, 468, 473, 475, 490, 505, 506, 510, 515, 522, 671, 682, 689, 704, 739, 747, 770, 782, 834, 921, 922, 925, 944, 952, 953, 960, 963, 998, 1020}")};
parseBitSet("{3, 5, 8, 18, 29, 33, 39, 65, 71, 90, 105, 125, 140, 170, 182, 192, 199, 203, 209, 213, 226, 271, 272, 287, 301, 304, 319, 368, 386, 423, 433, 540, 590, 605, 618, 620, 629, 641, 649, 672, 681, 690, 694, 696, 697, 716, 726, 745, 748, 751, 760, 765, 775, 777, 780, 792, 799, 805, 810, 825, 829, 836, 844, 850, 876, 880, 882, 888, 899, 914, 924, 929, 932, 935, 967, 971, 1004, 1013, 1015, 1023}"),
parseBitSet("{3, 8, 18, 29, 33, 65, 90, 101, 109, 117, 125, 127, 140, 170, 190, 192, 209, 213, 218, 226, 271, 272, 286, 287, 301, 304, 319, 386, 423, 433, 566, 590, 605, 618, 629, 641, 646, 649, 672, 690, 694, 696, 716, 726, 745, 748, 765, 775, 777, 780, 783, 792, 805, 810, 825, 829, 836, 844, 850, 876, 882, 899, 914, 924, 932, 934, 956, 967, 971, 994, 1004, 1013, 1015, 1023}"),
parseBitSet("{3, 18, 26, 32, 33, 43, 140, 155, 188, 189, 226, 238, 262, 267, 287, 315, 319, 326, 375, 450, 577, 629, 644, 690, 719, 732, 745, 746, 751, 775, 847, 850, 881, 959, 971, 995, 1015, 1019}"),
parseBitSet("{3, 18, 33, 192, 319, 745, 780, 882}"),
parseBitSet("{3, 13, 18, 22, 26, 29, 33, 43, 71, 85, 90, 101, 103, 109, 117, 118, 125, 127, 140, 145, 153, 155, 182, 188, 189, 190, 199, 218, 225, 226, 238, 269, 272, 286, 287, 301, 304, 315, 319, 326, 370, 375, 386, 408, 423, 433, 450, 493, 502, 556, 566, 577, 590, 598, 605, 617, 618, 629, 644, 649, 672, 679, 690, 691, 694, 696, 716, 719, 727, 732, 745, 748, 751, 760, 762, 765, 775, 777, 783, 805, 806, 810, 821, 829, 844, 847, 850, 876, 888, 899, 914, 923, 924, 926, 927, 929, 934, 956, 959, 966, 971, 990, 995, 1006, 1013, 1015, 1019}"),
parseBitSet("{3, 18, 29, 33, 53, 65, 90, 105, 125, 192, 203, 269, 271, 272, 293, 301, 319, 345, 364, 376, 386, 433, 540, 569, 590, 605, 618, 641, 649, 672, 675, 681, 696, 745, 748, 765, 780, 790, 798, 799, 801, 805, 825, 829, 836, 837, 844, 853, 876, 882, 891, 899, 914, 924, 932, 967, 996, 1004, 1013}"),
parseBitSet("{3, 18, 33, 192, 319, 745, 780, 882}"),
parseBitSet("{3, 18, 33, 192, 319, 745, 780, 882}"),
parseBitSet("{3, 18, 26, 32, 33, 43, 140, 155, 188, 189, 226, 238, 262, 267, 287, 315, 319, 326, 375, 450, 577, 629, 644, 690, 719, 732, 745, 746, 751, 775, 847, 850, 881, 959, 971, 995, 1015, 1019}"),
parseBitSet("{3, 18, 29, 33, 90, 105, 125, 272, 280, 301, 433, 521, 590, 618, 651, 672, 696, 698, 745, 760, 829, 844, 876, 890, 899, 924, 1013}")};

String filename = "data/mdl/fingerprints_from_modelbuilder3d.sdf";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
Expand All @@ -87,6 +87,32 @@ public void testFingerprints() throws Exception {
}
}

@Test
public void testAnonFingerprints() throws Exception {
BitSet[] expected = new BitSet[]{
parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}")};

String filename = "data/mdl/fingerprints_from_modelbuilder3d.sdf";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
List<IBitFingerprint> data = new TemplateExtractor().makeFingerprintsFromSdf(true, true,
new HashMap<String, Integer>(), new BufferedReader(new InputStreamReader(ins)), 10);
QueryChemObject obj = new QueryChemObject(DefaultChemObjectBuilder.getInstance());
obj.getBuilder();
for (int i = 0; i < data.size(); i++) {
IBitFingerprint bs = data.get(i);
Assert.assertEquals(expected[i], bs.asBitSet());
}
}

@Test
public void testMapTemplates_IAtomContainer_double() throws Exception {
IAtomContainer ac = TestMoleculeFactory.makeBicycloRings();
Expand Down
3 changes: 2 additions & 1 deletion ...uilder3dtools/src/main/java/org/openscience/cdk/modeling/builder3d/TemplateExtractor.java
View file
Expand Up @@ -365,8 +365,9 @@ public void makeCanonicalSmileFromRingSystems(String dataFileIn, String dataFile
public List<IBitFingerprint> makeFingerprintsFromSdf(boolean anyAtom, boolean anyAtomAnyBond,
Map<String, Integer> timings, BufferedReader fin, int limit) throws Exception {

IFingerprinter fingerPrinter = new HybridizationFingerprinter(HybridizationFingerprinter.DEFAULT_SIZE,
HybridizationFingerprinter fingerPrinter = new HybridizationFingerprinter(HybridizationFingerprinter.DEFAULT_SIZE,
HybridizationFingerprinter.DEFAULT_SEARCH_DEPTH);
fingerPrinter.setHashPseudoAtoms(true);
IAtomContainer m = null;
IteratingSDFReader imdl = null;
//QueryAtomContainer query=null;
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