Package etomica.parser

Class ParmedParser

java.lang.Object

etomica.parser.ParmedParser

public class ParmedParser
extends java.lang.Object

Class that generates ParmedStructure objects by invoking the ParmEd library and serializing its Structure object using JSON.

See Also:

ParmedStructure

Constructor Summary

Constructors

Constructor	Description
ParmedParser()

Method Summary

Modifier and Type	Method	Description
static ParmedStructure	parseGromacs(java.io.File topFile, java.io.File groFile)	Parses the given Gromacs .top and .gro files using the ParmEd python library.
static ParmedStructure	parseGromacsResourceFiles(java.lang.String topFileName, java.lang.String groFileName)	Convenience method to parse gromacs files located in the etomica-core/src/main/resources directory.

Methods inherited from class java.lang.Object

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

Constructor Detail

ParmedParser

public ParmedParser()

Method Detail

parseGromacs

public static ParmedStructure parseGromacs(java.io.File topFile,
                                           java.io.File groFile)
                                    throws java.io.IOException

Parses the given Gromacs .top and .gro files using the ParmEd python library.

Parameters:

topFile - File object containing the path to a Gromacs .top file

groFile - File object containing the path to a Gromacs .gro file

Returns:

a ParmedStructure for extracting Etomica simulation components from the ParmEd Structure object

Throws:

java.io.IOException

parseGromacsResourceFiles

public static ParmedStructure parseGromacsResourceFiles(java.lang.String topFileName,
                                                        java.lang.String groFileName)
                                                 throws java.io.IOException

Convenience method to parse gromacs files located in the etomica-core/src/main/resources directory.

Parameters:

topFileName - the plain name of the .top file, e.g. "test.top"

groFileName - the plain name of the .gro file, e.g. "test.gro"

Returns:

a ParmedStructure containing the parsed data.

Throws:

java.io.IOException - if the files do not exist.