Package com.actelion.research.chem
Class MolfileParser
- java.lang.Object
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- com.actelion.research.chem.MolfileParser
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public class MolfileParser extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static boolean
debug
static int
MODE_KEEP_HYDROGEN_MAP
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Constructor Summary
Constructors Constructor Description MolfileParser()
Constructor of a MolFileParser, which will mirror Y,Z coordinatesMolfileParser(int mode)
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Method Summary
All Methods Instance Methods Concrete Methods 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_MAPboolean
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.
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Field Detail
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MODE_KEEP_HYDROGEN_MAP
public static final int MODE_KEEP_HYDROGEN_MAP
- See Also:
- Constant Field Values
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debug
public static boolean debug
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Method Detail
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getHandleHydrogenMap
public int[] getHandleHydrogenMap()
If this MoflileParser was instantiated with MODE_KEEP_HYDROGEN_MAP- Returns:
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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
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isChiralFlagSet
public boolean isChiralFlagSet()
- Returns:
- whether the previous molfile's chiral flag was set
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isV3000
public boolean isV3000()
- Returns:
- whether the previous molfile was a V3000
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parse
public boolean parse(StereoMolecule mol, java.io.File file)
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parse
public boolean parse(StereoMolecule mol, java.lang.String molFile)
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parse
public boolean parse(StereoMolecule mol, java.lang.StringBuffer molFile)
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parse
public boolean parse(StereoMolecule m, java.io.BufferedReader rd)
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getCompactMolecule
public StereoMolecule getCompactMolecule(java.lang.String molFile)
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getCompactMolecule
public StereoMolecule getCompactMolecule(java.io.BufferedReader reader)
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getCompactMolecule
public StereoMolecule getCompactMolecule(java.io.File file)
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