Examples with IChemModel org.openscience.cdk.interfaces.IChemModel used on opensource projects

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Example 26 with IChemModel

use of org.openscience.cdk.interfaces.IChemModel in project cdk by cdk.

the class Mol2ReaderTest method testBug1714794.

@Test
public void testBug1714794() throws Exception {
    String problematicMol2 = "@<TRIPOS>MOLECULE\n" + "mol_197219.smi\n" + " 129 135 0 0 0\n" + "SMALL\n" + "GASTEIGER\n" + "Energy = 0\n" + "\n" + "@<TRIPOS>ATOM\n" + "      1 N1          0.0000    0.0000    0.0000 N.am    1  <1>        -0.2782\n" + "      2 H1          0.0000    0.0000    0.0000 H       1  <1>         0.1552\n" + "      3 C1          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0886\n" + "      4 C2          0.0000    0.0000    0.0000 C.ar    1  <1>         0.1500\n" + "      5 C3          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0714\n" + "      6 C4          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0456\n" + "      7 C5          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0788\n" + "      8 C6          0.0000    0.0000    0.0000 C.ar    1  <1>         0.1435\n" + "      9 C7          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0342\n" + "     10 C8          0.0000    0.0000    0.0000 C.ar    1  <1>         0.1346\n" + "     11 O1          0.0000    0.0000    0.0000 O.3     1  <1>        -0.5057\n" + "     12 H2          0.0000    0.0000    0.0000 H       1  <1>         0.2922\n" + "     13 C9          0.0000    0.0000    0.0000 C.3     1  <1>        -0.0327\n" + "     14 H3          0.0000    0.0000    0.0000 H       1  <1>         0.0280\n" + "     15 H4          0.0000    0.0000    0.0000 H       1  <1>         0.0280\n" + "     16 H5          0.0000    0.0000    0.0000 H       1  <1>         0.0280\n" + "     17 O2          0.0000    0.0000    0.0000 O.3     1  <1>        -0.4436\n" + "     18 C10         0.0000    0.0000    0.0000 C.3     1  <1>         0.3143\n" + "     19 O3          0.0000    0.0000    0.0000 O.2     1  <1>        -0.4528\n" + "     20 C11         0.0000    0.0000    0.0000 C.2     1  <1>         0.0882\n" + "     21 H6          0.0000    0.0000    0.0000 H       1  <1>         0.1022\n" + "     22 C12         0.0000    0.0000    0.0000 C.2     1  <1>        -0.0208\n" + "     23 H7          0.0000    0.0000    0.0000 H       1  <1>         0.0628\n" + "     24 C13         0.0000    0.0000    0.0000 C.3     1  <1>         0.0854\n" + "     25 H8          0.0000    0.0000    0.0000 H       1  <1>         0.0645\n" + "     26 C14         0.0000    0.0000    0.0000 C.3     1  <1>         0.0236\n" + "     27 H9          0.0000    0.0000    0.0000 H       1  <1>         0.0362\n" + "     28 C15         0.0000    0.0000    0.0000 C.3     1  <1>         0.1131\n" + "     29 H10         0.0000    0.0000    0.0000 H       1  <1>         0.0741\n" + "     30 C16         0.0000    0.0000    0.0000 C.3     1  <1>         0.0200\n" + "     31 H11         0.0000    0.0000    0.0000 H       1  <1>         0.0359\n" + "     32 C17         0.0000    0.0000    0.0000 C.3     1  <1>         0.0661\n" + "     33 H12         0.0000    0.0000    0.0000 H       1  <1>         0.0600\n" + "     34 C18         0.0000    0.0000    0.0000 C.3     1  <1>         0.0091\n" + "     35 H13         0.0000    0.0000    0.0000 H       1  <1>         0.0348\n" + "     36 C19         0.0000    0.0000    0.0000 C.3     1  <1>         0.0661\n" + "     37 H14         0.0000    0.0000    0.0000 H       1  <1>         0.0602\n" + "     38 C20         0.0000    0.0000    0.0000 C.3     1  <1>         0.0009\n" + "     39 H15         0.0000    0.0000    0.0000 H       1  <1>         0.0365\n" + "     40 C21         0.0000    0.0000    0.0000 C.2     1  <1>        -0.0787\n" + "     41 H16         0.0000    0.0000    0.0000 H       1  <1>         0.0576\n" + "     42 C22         0.0000    0.0000    0.0000 C.2     1  <1>        -0.0649\n" + "     43 H17         0.0000    0.0000    0.0000 H       1  <1>         0.0615\n" + "     44 C23         0.0000    0.0000    0.0000 C.2     1  <1>        -0.0542\n" + "     45 H18         0.0000    0.0000    0.0000 H       1  <1>         0.0622\n" + "     46 C24         0.0000    0.0000    0.0000 C.2     1  <1>         0.0115\n" + "     47 C25         0.0000    0.0000    0.0000 C.2     1  <1>         0.2441\n" + "     48 O4          0.0000    0.0000    0.0000 O.2     1  <1>        -0.2702\n" + "     49 C26         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0348\n" + "     50 H19         0.0000    0.0000    0.0000 H       1  <1>         0.0279\n" + "     51 H20         0.0000    0.0000    0.0000 H       1  <1>         0.0279\n" + "     52 H21         0.0000    0.0000    0.0000 H       1  <1>         0.0279\n" + "     53 C27         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0566\n" + "     54 H22         0.0000    0.0000    0.0000 H       1  <1>         0.0236\n" + "     55 H23         0.0000    0.0000    0.0000 H       1  <1>         0.0236\n" + "     56 H24         0.0000    0.0000    0.0000 H       1  <1>         0.0236\n" + "     57 O5          0.0000    0.0000    0.0000 O.3     1  <1>        -0.3909\n" + "     58 H25         0.0000    0.0000    0.0000 H       1  <1>         0.2098\n" + "     59 C28         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0577\n" + "     60 H26         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n" + "     61 H27         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n" + "     62 H28         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n" + "     63 O6          0.0000    0.0000    0.0000 O.3     1  <1>        -0.3910\n" + "     64 H29         0.0000    0.0000    0.0000 H       1  <1>         0.2098\n" + "     65 C29         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0567\n" + "     66 H30         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n" + "     67 H31         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n" + "     68 H32         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n" + "     69 O7          0.0000    0.0000    0.0000 O.3     1  <1>        -0.4608\n" + "     70 C30         0.0000    0.0000    0.0000 C.2     1  <1>         0.3042\n" + "     71 O8          0.0000    0.0000    0.0000 O.2     1  <1>        -0.2512\n" + "     72 C31         0.0000    0.0000    0.0000 C.3     1  <1>         0.0332\n" + "     73 H33         0.0000    0.0000    0.0000 H       1  <1>         0.0342\n" + "     74 H34         0.0000    0.0000    0.0000 H       1  <1>         0.0342\n" + "     75 H35         0.0000    0.0000    0.0000 H       1  <1>         0.0342\n" + "     76 C32         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0564\n" + "     77 H36         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n" + "     78 H37         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n" + "     79 H38         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n" + "     80 O9          0.0000    0.0000    0.0000 O.3     1  <1>        -0.3753\n" + "     81 C33         0.0000    0.0000    0.0000 C.3     1  <1>         0.0372\n" + "     82 H39         0.0000    0.0000    0.0000 H       1  <1>         0.0524\n" + "     83 H40         0.0000    0.0000    0.0000 H       1  <1>         0.0524\n" + "     84 H41         0.0000    0.0000    0.0000 H       1  <1>         0.0524\n" + "     85 C34         0.0000    0.0000    0.0000 C.2     1  <1>         0.2505\n" + "     86 O10         0.0000    0.0000    0.0000 O.2     1  <1>        -0.2836\n" + "     87 C35         0.0000    0.0000    0.0000 C.3     1  <1>         0.0210\n" + "     88 H42         0.0000    0.0000    0.0000 H       1  <1>         0.0309\n" + "     89 H43         0.0000    0.0000    0.0000 H       1  <1>         0.0309\n" + "     90 H44         0.0000    0.0000    0.0000 H       1  <1>         0.0309\n" + "     91 C36         0.0000    0.0000    0.0000 C.ar    1  <1>         0.1361\n" + "     92 C37         0.0000    0.0000    0.0000 C.ar    1  <1>         0.0613\n" + "     93 C38         0.0000    0.0000    0.0000 C.2     1  <1>         0.0580\n" + "     94 H45         0.0000    0.0000    0.0000 H       1  <1>         0.0853\n" + "     95 N2          0.0000    0.0000    0.0000 N.2     1  <1>        -0.1915\n" + "     96 N3          0.0000    0.0000    0.0000 N.pl3   1  <1>        -0.2525\n" + "     97 C39         0.0000    0.0000    0.0000 C.3     1  <1>         0.0525\n" + "     98 C40         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0271\n" + "     99 H46         0.0000    0.0000    0.0000 H       1  <1>         0.0289\n" + "    100 H47         0.0000    0.0000    0.0000 H       1  <1>         0.0289\n" + "    101 C41         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0385\n" + "    102 H48         0.0000    0.0000    0.0000 H       1  <1>         0.0302\n" + "    103 C42         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0472\n" + "    104 H49         0.0000    0.0000    0.0000 H       1  <1>         0.0271\n" + "    105 H50         0.0000    0.0000    0.0000 H       1  <1>         0.0271\n" + "    106 C43         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0385\n" + "    107 H51         0.0000    0.0000    0.0000 H       1  <1>         0.0302\n" + "    108 C44         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0271\n" + "    109 H52         0.0000    0.0000    0.0000 H       1  <1>         0.0289\n" + "    110 H53         0.0000    0.0000    0.0000 H       1  <1>         0.0289\n" + "    111 C45         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0472\n" + "    112 H54         0.0000    0.0000    0.0000 H       1  <1>         0.0271\n" + "    113 H55         0.0000    0.0000    0.0000 H       1  <1>         0.0271\n" + "    114 C46         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0385\n" + "    115 H56         0.0000    0.0000    0.0000 H       1  <1>         0.0302\n" + "    116 C47         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0271\n" + "    117 H57         0.0000    0.0000    0.0000 H       1  <1>         0.0289\n" + "    118 H58         0.0000    0.0000    0.0000 H       1  <1>         0.0289\n" + "    119 C48         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0472\n" + "    120 H59         0.0000    0.0000    0.0000 H       1  <1>         0.0271\n" + "    121 H60         0.0000    0.0000    0.0000 H       1  <1>         0.0271\n" + "    122 C49         0.0000    0.0000    0.0000 C.3     1  <1>         0.0189\n" + "    123 H61         0.0000    0.0000    0.0000 H       1  <1>         0.0444\n" + "    124 H62         0.0000    0.0000    0.0000 H       1  <1>         0.0444\n" + "    125 H63         0.0000    0.0000    0.0000 H       1  <1>         0.0444\n" + "    126 O11         0.0000    0.0000    0.0000 O.3     1  <1>        -0.5054\n" + "    127 H64         0.0000    0.0000    0.0000 H       1  <1>         0.2922\n" + "    128 O12         0.0000    0.0000    0.0000 O.3     1  <1>        -0.5042\n" + "    129 H65         0.0000    0.0000    0.0000 H       1  <1>         0.2923\n" + "@<TRIPOS>BOND\n" + "     1     1     2    1\n" + "     2     1     3    1\n" + "     3     3     4   ar\n" + "     4     4     5   ar\n" + "     5     5     6   ar\n" + "     6     6     7   ar\n" + "     7     7     8   ar\n" + "     8     8     9   ar\n" + "     9     9    10   ar\n" + "    10     5    10   ar\n" + "    11    10    11    1\n" + "    12    11    12    1\n" + "    13     9    13    1\n" + "    14    13    14    1\n" + "    15    13    15    1\n" + "    16    13    16    1\n" + "    17     8    17    1\n" + "    18    17    18    1\n" + "    19    18    19    1\n" + "    20    19    20    1\n" + "    21    20    21    1\n" + "    22    20    22    2\n" + "    23    22    23    1\n" + "    24    22    24    1\n" + "    25    24    25    1\n" + "    26    24    26    1\n" + "    27    26    27    1\n" + "    28    26    28    1\n" + "    29    28    29    1\n" + "    30    28    30    1\n" + "    31    30    31    1\n" + "    32    30    32    1\n" + "    33    32    33    1\n" + "    34    32    34    1\n" + "    35    34    35    1\n" + "    36    34    36    1\n" + "    37    36    37    1\n" + "    38    36    38    1\n" + "    39    38    39    1\n" + "    40    38    40    1\n" + "    41    40    41    1\n" + "    42    40    42    2\n" + "    43    42    43    1\n" + "    44    42    44    1\n" + "    45    44    45    1\n" + "    46    44    46    2\n" + "    47    46    47    1\n" + "    48     1    47   am\n" + "    49    47    48    2\n" + "    50    46    49    1\n" + "    51    49    50    1\n" + "    52    49    51    1\n" + "    53    49    52    1\n" + "    54    38    53    1\n" + "    55    53    54    1\n" + "    56    53    55    1\n" + "    57    53    56    1\n" + "    58    36    57    1\n" + "    59    57    58    1\n" + "    60    34    59    1\n" + "    61    59    60    1\n" + "    62    59    61    1\n" + "    63    59    62    1\n" + "    64    32    63    1\n" + "    65    63    64    1\n" + "    66    30    65    1\n" + "    67    65    66    1\n" + "    68    65    67    1\n" + "    69    65    68    1\n" + "    70    28    69    1\n" + "    71    69    70    1\n" + "    72    70    71    2\n" + "    73    70    72    1\n" + "    74    72    73    1\n" + "    75    72    74    1\n" + "    76    72    75    1\n" + "    77    26    76    1\n" + "    78    76    77    1\n" + "    79    76    78    1\n" + "    80    76    79    1\n" + "    81    24    80    1\n" + "    82    80    81    1\n" + "    83    81    82    1\n" + "    84    81    83    1\n" + "    85    81    84    1\n" + "    86    18    85    1\n" + "    87     7    85    1\n" + "    88    85    86    2\n" + "    89    18    87    1\n" + "    90    87    88    1\n" + "    91    87    89    1\n" + "    92    87    90    1\n" + "    93     6    91   ar\n" + "    94    91    92   ar\n" + "    95     3    92   ar\n" + "    96    92    93    1\n" + "    97    93    94    1\n" + "    98    93    95    2\n" + "    99    95    96    1\n" + "   100    96    97    1\n" + "   101    97    98    1\n" + "   102    98    99    1\n" + "   103    98   100    1\n" + "   104    98   101    1\n" + "   105   101   102    1\n" + "   106   101   103    1\n" + "   107   103   104    1\n" + "   108   103   105    1\n" + "   109   103   106    1\n" + "   110   106   107    1\n" + "   111   106   108    1\n" + "   112   108   109    1\n" + "   113   108   110    1\n" + "   114    97   108    1\n" + "   115   106   111    1\n" + "   116   111   112    1\n" + "   117   111   113    1\n" + "   118   111   114    1\n" + "   119   114   115    1\n" + "   120   114   116    1\n" + "   121   116   117    1\n" + "   122   116   118    1\n" + "   123    97   116    1\n" + "   124   114   119    1\n" + "   125   119   120    1\n" + "   126   119   121    1\n" + "   127   101   119    1\n" + "   128    96   122    1\n" + "   129   122   123    1\n" + "   130   122   124    1\n" + "   131   122   125    1\n" + "   132    91   126    1\n" + "   133   126   127    1\n" + "   134     4   128    1\n" + "   135   128   129    1\n";
    Mol2Reader r = new Mol2Reader(new StringReader(problematicMol2));
    IChemModel model = r.read(SilentChemObjectBuilder.getInstance().newInstance(IChemModel.class));
    r.close();
    Assert.assertNotNull(model);
    List<IAtomContainer> containers = ChemModelManipulator.getAllAtomContainers(model);
    Assert.assertEquals(1, containers.size());
    IAtomContainer molecule = containers.get(0);
    Assert.assertNotNull(molecule);
    Assert.assertEquals(129, molecule.getAtomCount());
    Assert.assertEquals(135, molecule.getBondCount());
    for (IAtom atom : molecule.atoms()) {
        Assert.assertNotNull(atom.getAtomTypeName());
    }
}
Also used : IAtomContainer(org.openscience.cdk.interfaces.IAtomContainer) StringReader(java.io.StringReader) IChemModel(org.openscience.cdk.interfaces.IChemModel) IAtom(org.openscience.cdk.interfaces.IAtom) SimpleChemObjectReaderTest(org.openscience.cdk.test.io.SimpleChemObjectReaderTest) SlowTest(org.openscience.cdk.test.SlowTest) Test(org.junit.Test)

Example 27 with IChemModel

use of org.openscience.cdk.interfaces.IChemModel in project cdk by cdk.

the class PMPReaderTest method testTwoAceticAcid.

@Test
public void testTwoAceticAcid() throws Exception {
    String filename = "two_aceticacid.pmp";
    InputStream ins = this.getClass().getResourceAsStream(filename);
    PMPReader reader = new PMPReader(ins);
    ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
    reader.close();
    Assert.assertNotNull(chemFile);
    Assert.assertEquals(1, chemFile.getChemSequenceCount());
    IChemSequence seq = chemFile.getChemSequence(0);
    Assert.assertNotNull(seq);
    Assert.assertEquals(2, seq.getChemModelCount());
    IChemModel model = seq.getChemModel(0);
    Assert.assertNotNull(model);
    ICrystal crystal = model.getCrystal();
    Assert.assertNotNull(crystal);
    Assert.assertEquals(32, crystal.getAtomCount());
    Assert.assertEquals(28, crystal.getBondCount());
    model = seq.getChemModel(1);
    Assert.assertNotNull(model);
    crystal = model.getCrystal();
    Assert.assertNotNull(crystal);
    Assert.assertEquals(32, crystal.getAtomCount());
    Assert.assertEquals(28, crystal.getBondCount());
}
Also used : ICrystal(org.openscience.cdk.interfaces.ICrystal) ChemObject(org.openscience.cdk.ChemObject) InputStream(java.io.InputStream) ChemFile(org.openscience.cdk.ChemFile) IChemModel(org.openscience.cdk.interfaces.IChemModel) IChemSequence(org.openscience.cdk.interfaces.IChemSequence) SimpleChemObjectReaderTest(org.openscience.cdk.test.io.SimpleChemObjectReaderTest) Test(org.junit.Test)

Example 28 with IChemModel

use of org.openscience.cdk.interfaces.IChemModel in project cdk by cdk.

the class JumboTest method testCephNS.

/**
 * Special CML characteristics:
 * - use of cml: namespace
 * - X2D only
 */
@Test
public void testCephNS() throws Exception {
    String filename = "ceph-ns.xml";
    logger.info("Testing: " + filename);
    InputStream ins = this.getClass().getResourceAsStream(filename);
    CMLReader reader = new CMLReader(ins);
    IChemFile chemFile = reader.read(new org.openscience.cdk.ChemFile());
    reader.close();
    // test the resulting ChemFile content
    Assert.assertNotNull(chemFile);
    Assert.assertEquals(chemFile.getChemSequenceCount(), 1);
    IChemSequence seq = chemFile.getChemSequence(0);
    Assert.assertNotNull(seq);
    Assert.assertEquals(seq.getChemModelCount(), 1);
    IChemModel model = seq.getChemModel(0);
    Assert.assertNotNull(model);
    Assert.assertEquals(model.getMoleculeSet().getAtomContainerCount(), 1);
    // test the molecule
    IAtomContainer mol = model.getMoleculeSet().getAtomContainer(0);
    Assert.assertNotNull(mol);
    Assert.assertEquals(mol.getAtomCount(), 15);
    Assert.assertEquals(mol.getBondCount(), 16);
    Assert.assertFalse(GeometryUtil.has3DCoordinates(mol));
    Assert.assertTrue(GeometryUtil.has2DCoordinates(mol));
}
Also used : CMLReader(org.openscience.cdk.io.CMLReader) IAtomContainer(org.openscience.cdk.interfaces.IAtomContainer) InputStream(java.io.InputStream) IChemFile(org.openscience.cdk.interfaces.IChemFile) IChemModel(org.openscience.cdk.interfaces.IChemModel) IChemSequence(org.openscience.cdk.interfaces.IChemSequence) Test(org.junit.Test)

Example 29 with IChemModel

use of org.openscience.cdk.interfaces.IChemModel in project cdk by cdk.

the class JumboTest method testNucleustest.

/**
 * Special CML characteristics:
 * - <atomArray><stringArray builtin="atomId"/></atomArray>
 * - <bondArray><stringArray builtin="atomRef"/></atomArray>
 * - no coords
 */
@Test
public void testNucleustest() throws Exception {
    String filename = "nucleustest.xml";
    logger.info("Testing: " + filename);
    InputStream ins = this.getClass().getResourceAsStream(filename);
    CMLReader reader = new CMLReader(ins);
    IChemFile chemFile = reader.read(new org.openscience.cdk.ChemFile());
    reader.close();
    // test the resulting ChemFile content
    Assert.assertNotNull(chemFile);
    Assert.assertEquals(chemFile.getChemSequenceCount(), 1);
    IChemSequence seq = chemFile.getChemSequence(0);
    Assert.assertNotNull(seq);
    Assert.assertEquals(seq.getChemModelCount(), 1);
    IChemModel model = seq.getChemModel(0);
    Assert.assertNotNull(model);
    Assert.assertEquals(model.getMoleculeSet().getAtomContainerCount(), 1);
    // test the molecule
    IAtomContainer mol = model.getMoleculeSet().getAtomContainer(0);
    Assert.assertNotNull(mol);
    Assert.assertEquals("Incorrect number of atoms", 11, mol.getAtomCount());
    Assert.assertEquals("Incorrect number of bonds", 12, mol.getBondCount());
    Assert.assertFalse("File does not have 3D coordinates", GeometryUtil.has3DCoordinates(mol));
    Assert.assertFalse("File does not have 2D coordinates", GeometryUtil.has2DCoordinates(mol));
}
Also used : CMLReader(org.openscience.cdk.io.CMLReader) IAtomContainer(org.openscience.cdk.interfaces.IAtomContainer) InputStream(java.io.InputStream) IChemFile(org.openscience.cdk.interfaces.IChemFile) IChemModel(org.openscience.cdk.interfaces.IChemModel) IChemSequence(org.openscience.cdk.interfaces.IChemSequence) Test(org.junit.Test)

Example 30 with IChemModel

use of org.openscience.cdk.interfaces.IChemModel in project cdk by cdk.

the class CML25FragmentsTest method checkForXMoleculeFile.

private IAtomContainer checkForXMoleculeFile(IChemFile chemFile, int numberOfMolecules) {
    Assert.assertNotNull(chemFile);
    Assert.assertEquals(chemFile.getChemSequenceCount(), 1);
    IChemSequence seq = chemFile.getChemSequence(0);
    Assert.assertNotNull(seq);
    Assert.assertEquals(seq.getChemModelCount(), 1);
    IChemModel model = seq.getChemModel(0);
    Assert.assertNotNull(model);
    IAtomContainerSet moleculeSet = model.getMoleculeSet();
    Assert.assertNotNull(moleculeSet);
    Assert.assertEquals(moleculeSet.getAtomContainerCount(), numberOfMolecules);
    IAtomContainer mol = null;
    for (int i = 0; i < numberOfMolecules; i++) {
        mol = moleculeSet.getAtomContainer(i);
        Assert.assertNotNull(mol);
    }
    return mol;
}
Also used : IAtomContainer(org.openscience.cdk.interfaces.IAtomContainer) IAtomContainerSet(org.openscience.cdk.interfaces.IAtomContainerSet) IChemModel(org.openscience.cdk.interfaces.IChemModel) IChemSequence(org.openscience.cdk.interfaces.IChemSequence)

Aggregations

IChemModel (org.openscience.cdk.interfaces.IChemModel)138 Test (org.junit.Test)97 IAtomContainer (org.openscience.cdk.interfaces.IAtomContainer)85 IChemSequence (org.openscience.cdk.interfaces.IChemSequence)80 IAtomContainerSet (org.openscience.cdk.interfaces.IAtomContainerSet)53 IChemFile (org.openscience.cdk.interfaces.IChemFile)50 InputStream (java.io.InputStream)46 ChemFile (org.openscience.cdk.ChemFile)30 CMLReader (org.openscience.cdk.io.CMLReader)26 IAtom (org.openscience.cdk.interfaces.IAtom)24 ICrystal (org.openscience.cdk.interfaces.ICrystal)21 IOException (java.io.IOException)19 IRingSet (org.openscience.cdk.interfaces.IRingSet)18 CDKException (org.openscience.cdk.exception.CDKException)17 IReaction (org.openscience.cdk.interfaces.IReaction)17 IReactionSet (org.openscience.cdk.interfaces.IReactionSet)17 MDLV2000Reader (org.openscience.cdk.io.MDLV2000Reader)13 SimpleChemObjectReaderTest (org.openscience.cdk.test.io.SimpleChemObjectReaderTest)12 AbstractChemModelTest (org.openscience.cdk.test.interfaces.AbstractChemModelTest)11 ChemObject (org.openscience.cdk.ChemObject)10
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