mol2readertest.java

化学图形处理软件

            + "     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 = (IChemModel)r.read(
        	NoNotificationChemObjectBuilder.getInstance().newChemModel()
        );
        assertNotNull(model);
        List containers = ChemModelManipulator.getAllAtomContainers(model);
        assertEquals(1, containers.size());
        IAtomContainer molecule = (IAtomContainer)containers.get(0);
        assertNotNull(molecule);
        assertEquals(129, molecule.getAtomCount());
        assertEquals(135, molecule.getBondCount());
        Iterator atoms = molecule.atoms();
        while (atoms.hasNext()) {
        	IAtom atom = (IAtom)atoms.next();
        	assertNotNull(atom.getAtomTypeName());
        }
    }
    
    
    private void checkMol(StringBuilder buf) throws CDKException {
        StringReader sr = new StringReader(buf.toString());
        Mol2Reader reader = new Mol2Reader(sr);
        IChemFile mol = (IChemFile)reader.read(NoNotificationChemObjectBuilder.getInstance().newChemFile());
        assertTrue(mol.getChemSequenceCount() > 0);
        assertTrue(mol.getChemSequence(0).getChemModelCount() > 0);
        assertTrue(mol.getChemSequence(0).getChemModel(0).getMoleculeSet().getAtomContainerCount() > 0);
        assertTrue(mol.getChemSequence(0).getChemModel(0).getMoleculeSet().getAtomContainer(0).getAtomCount() > 0);        
    }
}