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org.openscience.compchem
Class ChemFileUtils  

java.lang.Object
  org.openscience.compchem.ChemFileUtils

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public class ChemFileUtils

extends java.lang.Object

A collection of static methods to return an array of Nodes from various commonly used file formats, so far only MDL Mol files and SMILES strings

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Constructor Summary

ChemFileUtils()

 

Method Summary
private static java.lang.String	formatMDLFloat(float fl)
private static java.lang.String	formatMDLInt(int i, int l)
private static java.lang.String	formatMDLString(java.lang.String s, int le)
private static java.lang.String	getElementSymbol(java.lang.String s, int pos)
private static java.lang.String	getRingNumber(java.lang.String s, int pos)
static Node[]	parseSmiles(java.lang.String args)           Parses a SMILES string and returns an array of nodes.
static Node[]	readLUCYStructure(java.lang.String args)
static Node[]	readMDLMolFile(java.io.File args)
static Node[]	readMDLMolFile(java.lang.String args)           This needs to be fixed according to JICS (1992) 32/3, 244-255 I have written this by trial and error.
static void	writeMDLMolFile(java.io.File file, java.lang.String name, Node[] setOfNodes)
static void	writeMDLMolFile(java.lang.String fQFilename, java.lang.String name, Node[] setOfNodes)

 

Methods inherited from class java.lang.Object

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

 

Constructor Detail

ChemFileUtils

public ChemFileUtils()

Method Detail

readMDLMolFile

public static Node[] readMDLMolFile(java.lang.String args)

This needs to be fixed according to JICS (1992) 32/3, 244-255 I have written this by trial and error. Parses an MDL Mol file and returns an array of nodes. So far, the coordinates are ignored because I only use the method to extract the connectivity info from the file, but the code to read the coordinates into the x and y coordinates of the Node class is easily added

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readMDLMolFile

public static Node[] readMDLMolFile(java.io.File args)

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writeMDLMolFile

public static void writeMDLMolFile(java.lang.String fQFilename,
                                   java.lang.String name,
                                   Node[] setOfNodes)

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writeMDLMolFile

public static void writeMDLMolFile(java.io.File file,
                                   java.lang.String name,
                                   Node[] setOfNodes)

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parseSmiles

public static Node[] parseSmiles(java.lang.String args)

Parses a SMILES string and returns an array of nodes. So far only the SSMILES subset and the '%' tag for more than 10 rings at a time are supported, but this should be sufficient for most organic molecules.

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getElementSymbol

private static java.lang.String getElementSymbol(java.lang.String s,
                                                 int pos)

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getRingNumber

private static java.lang.String getRingNumber(java.lang.String s,
                                              int pos)

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formatMDLInt

private static java.lang.String formatMDLInt(int i,
                                             int l)

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formatMDLFloat

private static java.lang.String formatMDLFloat(float fl)

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formatMDLString

private static java.lang.String formatMDLString(java.lang.String s,
                                                int le)

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readLUCYStructure

public static Node[] readLUCYStructure(java.lang.String args)

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> openscience >> [ compchem overview ]	PREV CLASS  NEXT CLASS
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