Package name.mjw.jamber.IO.AMBER

Examples of name.mjw.jamber.IO.AMBER.ParameterStore

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
  }

  private static ParameterStore openAndReadGaffFile(String gaffFileName) {

    InputStream inputStream = null;
    ParameterStore gaffParameterStore = null;

    try {
      inputStream = new FileInputStream(gaffFileName);
    } catch (FileNotFoundException e) {
      System.out.println("Cannot open file" + gaffFileName);
      e.printStackTrace();
    }

    try {
      gaffParameterStore = new ParameterStore();
      gaffParameterStore.readParm(inputStream);
    } catch (IOException e) {
      System.out.println("Cannot parse ParameterStore file"
          + gaffFileName);
      e.printStackTrace();
    }

    LOG.debug(gaffParameterStore.getTitle());
    return gaffParameterStore;

  }
View Full Code Here
36
37
38
39
40
41
42
43
44
45
46
    InputStream frcmodIs = OpenMMXMLWithMol2RitonavirTest.class.getClass()
        .getResourceAsStream(
            "/name/mjw/jamber/IO/OpenMM/ritonavir/ritonavir.frcmod");

    try {
      parameterStore = new ParameterStore();
      parameterStore.readParm(gaffIs);
      parameterStore.readFrcmod(frcmodIs);

    } catch (Exception e) {
View Full Code Here
25
26
27
28
29
30
31
32
33
34
35
    InputStream parmIs = OpenMMXMLWithLibTest.class
        .getClass()
        .getResourceAsStream("/name/mjw/jamber/IO/AMBER/lib/parm99.dat");

    try {
      parameterStore = new ParameterStore();
      parameterStore.readParm(parmIs);

    } catch (IOException e) {

      e.printStackTrace();
View Full Code Here
40
41
42
43
44
45
46
47
48
49
50
        .getClass()
        .getResourceAsStream(
            "/name/mjw/jamber/IO/OpenMM/bromoergocryptine/bromoergocryptine.frcmod");

    try {
      parameterStore = new ParameterStore();
      parameterStore.readParm(gaffIs);
      parameterStore.readFrcmod(frcmodIs);

    } catch (Exception e) {
View Full Code Here
45
46
47
48
49
50
51
52
53
54
55
    InputStream parmLiteFrcmod = OpenMMXMLWithMol2CYPCPDITest.class
        .getClass().getResourceAsStream(
            "/name/mjw/jamber/IO/AMBER/CPDI/parm99_lite.dat");

    try {
      parameterStore = new ParameterStore();

      parameterStore.readParm(gaffIs);

      // TODO make consistent with other methods
      try {
View Full Code Here
38
39
40
41
42
43
44
45
46
47
48
        .getClass()
        .getResourceAsStream(
            "/name/mjw/jamber/IO/OpenMM/erythromycin/erythromycin.frcmod");

    try {
      parameterStore = new ParameterStore();
      parameterStore.readParm(gaffIs);
      parameterStore.readFrcmod(frcmodIs);

    } catch (Exception e) {
View Full Code Here
33
34
35
36
37
38
39
40
41
42
43
    InputStream gaffIs = OpenMMXMLWithMol2KetoconazoleTest.class.getClass()
        .getResourceAsStream("/name/mjw/jamber/IO/AMBER/lib/gaff.dat");

    try {
      parameterStore = new ParameterStore();
      parameterStore.readParm(gaffIs);

    } catch (IOException e) {

      e.printStackTrace();
View Full Code Here
34
35
36
37
38
39
40
41
42
43
44
        .getResourceAsStream("/name/mjw/jamber/IO/AMBER/lib/gaff.dat");



    try {
      parameterStore = new ParameterStore();
      parameterStore.readParm(gaffIs);

    } catch (Exception e) {

      e.printStackTrace();
View Full Code Here
34
35
36
37
38
39
40
41
42
43
44
        .getResourceAsStream("/name/mjw/jamber/IO/AMBER/lib/gaff.dat");



    try {
      parameterStore = new ParameterStore();
      parameterStore.readParm(gaffIs);

    } catch (Exception e) {

      e.printStackTrace();
View Full Code Here
TOP

Related Classes of name.mjw.jamber.IO.AMBER.ParameterStore

  • name.mjw.jamber.IO.FortranFormat
  • name.mjw.jamber.IO.OpenMM.AmberToOpenMM
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithLibTest
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2AceticAcidTest
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2BenzeneTest
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2BromoergocryptineTest
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2CYPCPDITest
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2ErythromycinTest
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2KetoconazoleTest
  • name.mjw.jamber.IO.OpenMM.OpenMMXMLWithMol2RitonavirTest
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.