Package com.actelion.research.chem.io

Class Mol2FileParser

java.lang.Object

com.actelion.research.chem.io.AbstractParser

com.actelion.research.chem.io.Mol2FileParser

public class Mol2FileParser
extends AbstractParser

Author:

freyssj

Field Summary

Fields

Modifier and Type	Field	Description
static int	iAMPAC_CHARGES
static int	iDEL_RE
static int	iDICT_CHARGES
static int	iGAST_HUCK
static int	iGASTEIGER
static int	iGAUSS80_CHARGES
static int	iHUCKEL
static int	iMMFF94_CHARGES
static int	iMULLIKEN_CHARGES
static int	iNO_CHARGES
static int	iPULLMAN
static int	iUSER_CHARGES

Fields inherited from class com.actelion.research.chem.io.AbstractParser

errors, NEWLINE, optimize3D

Constructor Summary

Constructors

Constructor	Description
Mol2FileParser()

Method Summary

Modifier and Type	Method	Description
static java.lang.String	getChargeType(int type)
java.util.List<Molecule3D>	loadGroup(java.lang.String fileName, java.io.Reader in, int from, int to)
static void	main(java.lang.String[] args)
void	save(Molecule3D mol, java.io.Writer writer)
void	save(java.util.List<Molecule3D> mols, int chargeType, java.io.Writer writer)	Writes also the partial charges
void	save(java.util.List<Molecule3D> mols, java.io.Writer writer)	If not subclassed, save the files separately

Methods inherited from class com.actelion.research.chem.io.AbstractParser

convertDataToPrimitiveTypes, getErrors, is3D, isOptimize3D, load, load, load, loadGroup, loadGroup, save, save, setOptimize3D, writeL, writeR

Methods inherited from class java.lang.Object

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

Field Detail

iNO_CHARGES

public static final int iNO_CHARGES

See Also:

Constant Field Values

iDEL_RE

public static final int iDEL_RE

See Also:

Constant Field Values

iGASTEIGER

public static final int iGASTEIGER

See Also:

Constant Field Values

iGAST_HUCK

public static final int iGAST_HUCK

See Also:

Constant Field Values

iHUCKEL

public static final int iHUCKEL

See Also:

Constant Field Values

iPULLMAN

public static final int iPULLMAN

See Also:

Constant Field Values

iGAUSS80_CHARGES

public static final int iGAUSS80_CHARGES

See Also:

Constant Field Values

iAMPAC_CHARGES

public static final int iAMPAC_CHARGES

See Also:

Constant Field Values

iMULLIKEN_CHARGES

public static final int iMULLIKEN_CHARGES

See Also:

Constant Field Values

iDICT_CHARGES

public static final int iDICT_CHARGES

See Also:

Constant Field Values

iMMFF94_CHARGES

public static final int iMMFF94_CHARGES

See Also:

Constant Field Values

iUSER_CHARGES

public static final int iUSER_CHARGES

See Also:

Constant Field Values

Constructor Detail

Mol2FileParser

public Mol2FileParser()

Method Detail

getChargeType

public static java.lang.String getChargeType(int type)

loadGroup

public java.util.List<Molecule3D> loadGroup(java.lang.String fileName,
                                            java.io.Reader in,
                                            int from,
                                            int to)
                                     throws java.lang.Exception

Specified by:

loadGroup in class AbstractParser

Throws:

java.lang.Exception

See Also:

com.actelion.research.chem.parsers.AbstractParser#parse(java.io.Reader, com.actelion.research.chem.Molecule3D)

save

public void save(Molecule3D mol,
                 java.io.Writer writer)
          throws java.lang.Exception

Overrides:

save in class AbstractParser

Throws:

java.lang.Exception

save

public void save(java.util.List<Molecule3D> mols,
                 java.io.Writer writer)
          throws java.lang.Exception

Description copied from class: AbstractParser

If not subclassed, save the files separately

Overrides:

save in class AbstractParser

Throws:

java.lang.Exception

save

public void save(java.util.List<Molecule3D> mols,
                 int chargeType,
                 java.io.Writer writer)
          throws java.lang.Exception

Writes also the partial charges

Parameters:

mols -

chargeType -

writer -

Throws:

java.lang.Exception

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Throws:

java.lang.Exception