chemaxon.marvin.calculations
Class MolecularDynamicsPlugin

java.lang.Object
  chemaxon.marvin.plugin.CalculatorPlugin
      chemaxon.marvin.calculations.MolecularDynamicsPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

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);

    // read the input molecule
    MolImporter mi = new MolImporter("mol.sdf");
    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
    }
    
    mi.close();
 

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

Since:

Marvin 4.1, 05/11/2006

Version:

5.1.4, 11/07/2008

Author:

Imre Jakli, Zsolt Mohacsi

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

ATOM, BLUE, CALCRGB_OFF, COVALENT_HYDRATION_ERROR_REMARK, CRITICAL_ERROR_MSG, EPSILON, INCORRECT_AROMATIC_NITROGEN_REMARK, INSTABLE_TAUTOMERIC_FORM_REMARK, licenseEnvironment, MOLECULE, MOLECULES, NAN, PLUGIN_CLASS_KEY, PLUGIN_DIR, RED

Constructor Summary

MolecularDynamicsPlugin()
Creates a new instance of MolecularDynamicsPlugin

Method Summary

void	checkMolecule(Molecule mol) Checks the input molecule.
java.lang.String	getProductName() Returns the product identifier of the plugin as given by LicenseManager.
java.lang.Object	getResult(java.lang.Object type, int index) Returns the result item for the specified key and index.
java.lang.String	getResultAsString(java.lang.Object type, int index, java.lang.Object result) Returns the specified result in String format.
int	getResultCount(java.lang.Object type) Returns the number of result items for the given result key.
int	getResultDomain(java.lang.Object type) Returns the calculation domain.
chemaxon.marvin.plugin.PluginMDocSource	getResultSource() Returns the result as a document source object.
java.lang.Object[]	getResultTypes() Returns the result types.
Molecule	getStructure(int index) Returns a structure.
int	getStructureCount() Returns the number of different structures.
Molecule[]	getStructures() Returns all structures.
boolean	handlesMultiFragmentMolecules() Returns true if the plugin handles multifragment molecules, false otherwise.
boolean	run() Runs the tool.
void	setCenterMolecule(boolean centerMolecule) Center the molecule before MD calculation (It is not set by default.)
void	setForceField(java.lang.String forcefield) Sets the force field type.
void	setInitialTemperature(double temperature) Sets the initial temperature.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setIntegrator(java.lang.String integrator) Sets the integrator used for calculations.
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.
void	setProgressMonitor(chemaxon.common.util.MProgressMonitor pmon) Sets a progress observer to be used in run() to display progress status.
void	setSamplingInterval(double sampinterval) Number of trajectory frames to be stored from the sampling start time to the end of calculation.
void	setSamplingStart(double sampstart) Sets the beginning of trajectory sampling.
void	setStepNumber(int stepno) Sets the number of simulation steps.
void	setStepTime(double timestep) Sets the simulation timestep.
void	standardize(Molecule mol) Expands sgroups.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

canRepeat, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getInputMolDim, getMainMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecule, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getTypeString, getWarningMessage, isInputMoleculeAromatized, isLicensed, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, setDoublePrecision, setDoublePrecision, setDoublePrecision, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, standardizeIonicGroups, standardizeNeutralGroups

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MolecularDynamicsPlugin

public MolecularDynamicsPlugin()

Creates a new instance of MolecularDynamicsPlugin

Method Detail

setForceField

public void setForceField(java.lang.String forcefield)

Sets the force field type.

Parameters:

forcefield - force field type possible values: "dreiding", (default: "dreiding")

setIntegrator

public void setIntegrator(java.lang.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(chemaxon.common.util.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 java.lang.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(java.util.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:

CalculatorPlugin.getErrorMessage()

getResultSource

public chemaxon.marvin.plugin.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 java.lang.Object[] getResultTypes()

Returns the result types.

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain.

Overrides:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

the calculation domain

See Also:

getResultTypes()

getResultCount

public int getResultCount(java.lang.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:

getResultTypes()

getResult

public java.lang.Object getResult(java.lang.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:

CalculatorPlugin.getResultTypes()

getResultAsString

public java.lang.String getResultAsString(java.lang.Object type,
                                          int index,
                                          java.lang.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