Package com.actelion.research.chem

Class MolfileParser

java.lang.Object

com.actelion.research.chem.MolfileParser

public class MolfileParser
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	debug
static int	MODE_KEEP_HYDROGEN_MAP

Constructor Summary

Constructors

Constructor	Description
MolfileParser()	Constructor of a MolFileParser, which will mirror Y,Z coordinates
MolfileParser(int mode)

Method Summary

Modifier and Type	Method	Description
StereoMolecule	getCompactMolecule(java.io.BufferedReader reader)
StereoMolecule	getCompactMolecule(java.io.File file)
StereoMolecule	getCompactMolecule(java.lang.String molFile)
int[]	getHandleHydrogenMap()	If this MoflileParser was instantiated with MODE_KEEP_HYDROGEN_MAP
boolean	isChiralFlagSet()
boolean	isV3000()
boolean	parse(StereoMolecule m, java.io.BufferedReader rd)
boolean	parse(StereoMolecule mol, java.io.File file)
boolean	parse(StereoMolecule mol, java.lang.String molFile)
boolean	parse(StereoMolecule mol, java.lang.StringBuffer molFile)
void	setAssumeChiralTrue(boolean b)	Some software exports mol/sd-files with an unset chiral flag despite the original molecule is a pure enantiomer.

Methods inherited from class java.lang.Object

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

Field Detail

MODE_KEEP_HYDROGEN_MAP

public static final int MODE_KEEP_HYDROGEN_MAP

See Also:

Constant Field Values

debug

public static boolean debug

Constructor Detail

MolfileParser

public MolfileParser()

Constructor of a MolFileParser, which will mirror Y,Z coordinates

MolfileParser

public MolfileParser(int mode)

Method Detail

getHandleHydrogenMap

public int[] getHandleHydrogenMap()

If this MoflileParser was instantiated with MODE_KEEP_HYDROGEN_MAP

Returns:

setAssumeChiralTrue

public void setAssumeChiralTrue(boolean b)

Some software exports mol/sd-files with an unset chiral flag despite the original molecule is a pure enantiomer. This method allows the MolfileParser to override the molfile's chiral flag for such cases.

Parameters:

b -

isChiralFlagSet

public boolean isChiralFlagSet()

Returns:

whether the previous molfile's chiral flag was set

isV3000

public boolean isV3000()

Returns:

whether the previous molfile was a V3000

parse

public boolean parse(StereoMolecule mol,
                     java.io.File file)

parse

public boolean parse(StereoMolecule mol,
                     java.lang.String molFile)

parse

public boolean parse(StereoMolecule mol,
                     java.lang.StringBuffer molFile)

parse

public boolean parse(StereoMolecule m,
                     java.io.BufferedReader rd)

getCompactMolecule

public StereoMolecule getCompactMolecule(java.lang.String molFile)

getCompactMolecule

public StereoMolecule getCompactMolecule(java.io.BufferedReader reader)

getCompactMolecule

public StereoMolecule getCompactMolecule(java.io.File file)