@@ -41,6 +41,7 @@ Richard L. Apodaca http://depth-first.com Duan Lian http://chemhack.com Fredrik Wallner http://www.wallner.nu/fredrik John Jaeger http://goeslightly.blogspot.com/ +Syed Asad Rahman http://www.ebi.ac.uk/~asad/Asad.html History: README @@ -23,7 +23,6 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ - package com.metamolecular.mx.test; import com.metamolecular.mx.io.Molecules; @@ -57,6 +56,13 @@ public class DefaultMapperTest extends TestCase private Molecule acetone; private Molecule propane; private Molecule cyclopropane; + private Molecule bigmol; + + public DefaultMapperTest() + { + // see: http://gist.github.com/144912 + bigmol = MoleculeKit.readMolfile("241\n -OEChem-07100913442D\n\n 67 72 0 0 1 0 999 V2000\n 5.3950 -3.1602 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0\n 4.9853 -3.8822 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0\n 5.4045 -4.6006 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0\n 6.2342 -4.5947 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0\n 6.6482 -3.8727 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0\n 6.2284 -3.1565 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 7.4799 -3.8687 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 4.9958 -5.3274 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 4.9776 -2.4425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 4.1536 -3.8873 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 6.6567 -5.3161 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 5.3878 -1.7207 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 4.1459 -2.4468 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 13.2577 -4.4546 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0\n 13.6743 -3.7340 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0\n 13.2533 -3.0100 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0\n 12.4237 -3.0128 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0\n 12.0114 -3.7375 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0\n 12.4243 -4.4553 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 11.1796 -3.7385 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 13.6691 -2.2889 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 13.6766 -5.1737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 14.5060 -3.7320 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 12.0081 -2.2941 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 13.2596 -5.8941 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.5084 -5.1726 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 12.8766 -8.3196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 13.5177 -8.8032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 13.1451 -7.5594 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 14.1838 -8.3419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 13.9476 -7.5771 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.8674 -8.3480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.2145 -8.8214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.6186 -7.5808 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 4.5139 -8.3857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.2048 -9.6520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 4.7732 -7.6213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 4.4315 -6.8694 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 10.1699 -8.3375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 10.4138 -7.5717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.3511 -8.7486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 10.8181 -8.8045 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 11.2181 -7.5717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 10.2013 -6.7887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.5504 -8.3375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 11.4662 -8.3375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 11.6152 -6.8705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 10.4104 -6.0055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.2980 -7.5787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 7.8973 -8.8158 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 12.1571 -8.7382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 10.1943 -5.2154 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 7.5009 -7.5787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.5043 -6.7992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 7.2456 -8.3375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.7266 -5.2224 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 7.0932 -6.8775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.2910 -6.0161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 6.5549 -8.7486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.4931 -5.2328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.0141 -5.2224 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 13.4995 -9.6348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 14.2100 -10.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.7211 -8.6383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.5455 -9.4504 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 14.9696 -8.6151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 14.4518 -6.9145 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 16 17 1 0 0 0 0\n 17 18 1 0 0 0 0\n 18 19 1 0 0 0 0\n 32 33 1 0 0 0 0\n 32 34 1 0 0 0 0\n 33 35 2 0 0 0 0\n 33 36 1 0 0 0 0\n 34 37 1 0 0 0 0\n 37 38 2 0 0 0 0\n 35 37 1 0 0 0 0\n 19 14 1 0 0 0 0\n 3 4 1 0 0 0 0\n 18 20 1 1 0 0 0\n 2 10 1 6 0 0 0\n 16 21 1 1 0 0 0\n 4 5 1 0 0 0 0\n 14 22 1 1 0 0 0\n 4 11 1 6 0 0 0\n 15 23 1 6 0 0 0\n 5 6 1 0 0 0 0\n 17 24 1 6 0 0 0\n 9 12 1 0 0 0 0\n 22 25 1 0 0 0 0\n 6 1 1 0 0 0 0\n 22 26 2 0 0 0 0\n 9 13 2 0 0 0 0\n 5 7 1 1 0 0 0\n 1 2 1 0 0 0 0\n 3 8 1 1 0 0 0\n 27 28 1 0 0 0 0\n 27 29 1 0 0 0 0\n 28 30 2 0 0 0 0\n 39 40 2 0 0 0 0\n 39 41 1 0 0 0 0\n 39 42 1 0 0 0 0\n 40 43 1 0 0 0 0\n 40 44 1 0 0 0 0\n 41 45 1 0 0 0 0\n 42 46 1 0 0 0 0\n 43 47 1 0 0 0 0\n 44 48 1 0 0 0 0\n 45 49 2 0 0 0 0\n 45 50 1 0 0 0 0\n 46 51 1 0 0 0 0\n 48 52 1 0 0 0 0\n 49 53 1 0 0 0 0\n 49 54 1 0 0 0 0\n 50 55 1 0 0 0 0\n 52 20 1 0 0 0 0\n 52 56 2 0 0 0 0\n 53 57 1 0 0 0 0\n 54 58 1 0 0 0 0\n 55 59 1 0 0 0 0\n 58 60 1 0 0 0 0\n 59 32 2 0 0 0 0\n 60 7 1 0 0 0 0\n 60 61 2 0 0 0 0\n 43 46 2 0 0 0 0\n 53 55 2 0 0 0 0\n 51 27 2 0 0 0 0\n 29 31 1 0 0 0 0\n 28 62 1 0 0 0 0\n 30 31 1 0 0 0 0\n 62 63 2 0 0 0 0\n 2 3 1 0 0 0 0\n 35 64 1 0 0 0 0\n 1 9 1 1 0 0 0\n 64 65 2 0 0 0 0\n 14 15 1 0 0 0 0\n 30 66 1 0 0 0 0\n 15 16 1 0 0 0 0\n 31 67 2 0 0 0 0\nM END"); + } @Override protected void setUp() throws Exception @@ -267,11 +273,10 @@ public class DefaultMapperTest extends TestCase // // assertTrue(mapper.hasMap(Molecules.createChargedDMSO())); // } - public void testItMapsPropaneToAcetone() { Mapper mapper = new DefaultMapper(Molecules.createPropane()); - + assertTrue(mapper.hasMap(Molecules.createAcetone())); } @@ -283,6 +288,20 @@ public class DefaultMapperTest extends TestCase assertEquals(0, map.size()); } + public void testItMapsBigmolToItself() + { + Mapper mapper = new DefaultMapper(bigmol); + + assertEquals(bigmol.countAtoms(), mapper.getFirstMap(bigmol).size()); + } + + public void testBigmolHasOneMap() + { + Mapper mapper = new DefaultMapper(bigmol); + + assertEquals(1, mapper.countMaps(bigmol)); + } + private Molecule createSimpleImine() { Molecule result = new DefaultMolecule(); src/com/metamolecular/mx/test/DefaultMapperTest.java 6c189d47537ebdbf1b2c55bd6ed5248dd1687e15 Rich Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/d2ab04b590f8167d57b253bdb7a60ad68220237b d2ab04b590f8167d57b253bdb7a60ad68220237b 2009-07-10T16:55:47-07:00 2009-07-10T16:55:47-07:00 added bigmol mapper tests a92e781a4c0c14aae1392f3748bf3b665a514d3b Rich Apodaca rapodaca@metamolecular.com