Package chemaxon.marvin.calculations

Class MolecularDynamicsPlugin

java.lang.Object
chemaxon.marvin.plugin.CalculatorPlugin
chemaxon.marvin.calculations.MolecularDynamicsPlugin
All Implemented Interfaces:
TaggedCalculator, chemaxon.license.Licensable
@PublicApi public class MolecularDynamicsPlugin extends CalculatorPlugin
Molecular Dynamics plugin.

API usage example: 


 // create plugin
 MolecularDynamicsPlugin plugin = new MolecularDynamicsPlugin();

 // set parameters
 plugin.setStepNumber(10000);
 plugin.setStepTime(1);
 plugin.setSamplingInterval(10);

 try (MolImporter mi = new MolImporter("mol.sdf")) {
    // read the input molecule
    Molecule mol = mi.read();

    // set the input molecule
    plugin.setMolecule(mol);

    // run the calculation
    plugin.run();

    // get the results
    int structureCount = plugin.getStructureCount();
    for (int i = 0; i < structureCount; i++) {
        Molecule mdMol = plugin.getStructure(i);
        // do something with results
    }
 }

For concurrent plugin example applications using ChemAxon's concurrent framework, refer to the Concurrent plugin examples.

Since:
Marvin 4.1, 05/11/2006

  • Constructor Details

    • MolecularDynamicsPlugin

      public MolecularDynamicsPlugin()
      Creates a new instance of MolecularDynamicsPlugin

  • Method Details

    • setForceField

      public void setForceField(String forcefield)
      Sets the force field type.
      Parameters:
      forcefield - force field type possible values: "dreiding", (default: "dreiding")

    • setIntegrator

      public void setIntegrator(String integrator)
      Sets the integrator used for calculations.
      Parameters:
      integrator - integrator type possible values: "positionverlet","velocityverlet","leapfrog","projectedvelocityverlet" (default: "velocityverlet")

    • setStepNumber

      public void setStepNumber(int stepno)
      Sets the number of simulation steps.
      Parameters:
      stepno - number of simulation steps (default: 1000)

    • setStepTime

      public void setStepTime(double timestep)
      Sets the simulation timestep.
      Parameters:
      timestep - duration of one simulation step in femtoseconds (default: 0.1fs)

    • setInitialTemperature

      public void setInitialTemperature(double temperature)
      Sets the initial temperature. (default: 300K)
      Parameters:
      temperature - temperature in Kelvins

    • setSamplingStart

      public void setSamplingStart(double sampstart)
      Sets the beginning of trajectory sampling. (default: 0)
      Parameters:
      sampstart - number of first trajectory frame to be saved

    • setSamplingInterval

      public void setSamplingInterval(double sampinterval)
      Number of trajectory frames to be stored from the sampling start time to the end of calculation. (default: 10)
      Parameters:
      sampinterval - trajectory sampling interval in femtoseconds

    • setCenterMolecule

      public void setCenterMolecule(boolean centerMolecule)
      Center the molecule before MD calculation (It is not set by default.)
      Parameters:
      centerMolecule - is the molecule will be centered

    • setProgressMonitor

      public void setProgressMonitor(MProgressMonitor pmon)
      Sets a progress observer to be used in run() to display progress status. Short calculations may ignore the observer object. The default implementation does nothing.
      Overrides:
      setProgressMonitor in class CalculatorPlugin
      Parameters:
      pmon - is the progress monitor, may be null

    • getProductName

      public String getProductName()
      Returns the product identifier of the plugin as given by LicenseManager.
      Specified by:
      getProductName in class CalculatorPlugin
      Returns:
      The identifier LicenseManager.CONFORMATION_PLUGIN_GROUP

    • setParameters

      public void setParameters(Properties params) throws PluginException
      Sets the input parameters for the plugin. Parameters:
      • forcefield: forcefield used for calculation (default: "Dreiding")
        • "dreiding"
        • "newdreiding"
      • integrator: integrator type, possible values:
        • "positionverlet"
        • "velocityverlet"
        • "leapfrog"
        • "projectedvelocityverlet"
        (default: velocityverlet)
      • stepno: step number to be calculated (default: 1000)
      • steptime: step time in femtoseconds (default: 0.1fs)
      • temperature: initial temperature of the system in Kelvin(default: 300K)
      • trajectorytype: type of trajectory output
        • mol - multiple "mol" frames
        • xtc - Gromacs XTC compressed frames
      • trajectoryfile: file, where trajectory is stored (default:-)
      • xtcprecision: number of decimal digits (default:4)
      • debuglevel: (default: 0)
      • debugfile: (default: stderr)
      Overrides:
      setParameters in class CalculatorPlugin
      Parameters:
      params - is the parameter table
      Throws:
      PluginException - on error

    • handlesMultiFragmentMolecules

      public boolean handlesMultiFragmentMolecules()
      Returns true if the plugin handles multifragment molecules, false otherwise. In the latter case the plugin takes the fragment with more atoms if a multifragment molecule is given as input. Returns true if parameter "single" is set to "false", false otherwise (default: false).
      Overrides:
      handlesMultiFragmentMolecules in class CalculatorPlugin
      Returns:
      true if the plugin handles multifragment molecules, false otherwise

    • checkMolecule

      public void checkMolecule(Molecule mol) throws PluginException
      Checks the input molecule. Throws exception if the molecule is RxnMolecule or if the molecule contains R-groups.
      Overrides:
      checkMolecule in class CalculatorPlugin
      Parameters:
      mol - is the input molecule
      Throws:
      PluginException - with error message for the user if the molecule is refused

    • setInputMolecule

      protected void setInputMolecule(Molecule mol) throws PluginException
      Sets the input molecule.
      Specified by:
      setInputMolecule in class CalculatorPlugin
      Parameters:
      mol - is the input molecule
      Throws:
      PluginException - on error

    • run

      public boolean run() throws PluginException
      Runs the tool.
      Specified by:
      run in class CalculatorPlugin
      Returns:
      true if the calculation was successful, false on calculation problems
      Throws:
      PluginException - on error
      See Also:

    • getResultSource

      public PluginMDocSource getResultSource() throws PluginException
      Returns the result as a document source object. This is useful for displaying the molecules in a viewer dynamically as they become available instead of collecting all results before display.
      Overrides:
      getResultSource in class CalculatorPlugin
      Returns:
      the document source interface
      Throws:
      PluginException - on error
      Since:
      Marvin 5.0

    • getStructureCount

      public int getStructureCount()
      Returns the number of different structures.
      Returns:
      the number of different structures

    • getStructure

      public Molecule getStructure(int index) throws PluginException
      Returns a structure.
      Parameters:
      index - is the structure index
      Returns:
      the structure
      Throws:
      PluginException

    • getStructures

      public Molecule[] getStructures() throws PluginException
      Returns all structures.
      Returns:
      all structures
      Throws:
      PluginException

    • getResultTypes

      public Object[] getResultTypes()
      Returns the result types.
      Overrides:
      getResultTypes in class CalculatorPlugin
      Returns:
      the result types

    • getResultDomain

      public int getResultDomain(Object type)
      Returns the calculation domain.
      Overrides:
      getResultDomain in class CalculatorPlugin
      Parameters:
      type - is the result type
      Returns:
      the calculation domain
      See Also:

    • getResultCount

      public int getResultCount(Object type)
      Returns the number of result items for the given result key.
      Overrides:
      getResultCount in class CalculatorPlugin
      Parameters:
      type - is the result type
      Returns:
      the number of result items
      See Also:

    • getResult

      public Object getResult(Object type, int index) throws PluginException
      Returns the result item for the specified key and index.
      Overrides:
      getResult in class CalculatorPlugin
      Parameters:
      type - is the result type
      index - is the result index
      Returns:
      the result item for the specified key and index
      Throws:
      PluginException - if the result cannot be returned
      See Also:

    • getResultAsString

      public String getResultAsString(Object type, int index, Object result) throws PluginException
      Returns the specified result in String format.
      Overrides:
      getResultAsString in class CalculatorPlugin
      Parameters:
      type - is the result type
      index - is the result index
      result - is the result item
      Returns:
      the specified result in String format
      Throws:
      PluginException - if an invalid result item is given

    • standardize

      public void standardize(Molecule mol)
      Expands sgroups.
      Overrides:
      standardize in class CalculatorPlugin
      Parameters:
      mol - is the molecule to be standardized