JavaGenes, NASA Ames. Written largely by Al Globus

gov.nasa.javaGenes.chemistry
Class xyzFormat

java.lang.Object
  extended bygov.nasa.javaGenes.chemistry.xyzFormat

public class xyzFormat
extends java.lang.Object

read and write mol files representing molecules


Constructor Summary
xyzFormat()
           
 
Method Summary
static void appendToFile(Molecule molecule, java.lang.String filename)
           
static Molecule read(java.io.BufferedReader input)
          read an xyz file
static Molecule read(java.lang.String filename)
          read an xyz file
protected static java.lang.String readLine(java.io.BufferedReader input)
           
static Molecules readMolecules(java.lang.String filename)
          read many molecules from a xyz file
static void write(Molecule molecule, java.io.PrintWriter out)
          write the file to PrintWriter out
static void writeMolecules(ExtendedVector molecules, java.lang.String filename)
           
static void writeToFile(Molecule molecule, java.lang.String filename)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

xyzFormat

public xyzFormat()
Method Detail

appendToFile

public static void appendToFile(Molecule molecule,
                                java.lang.String filename)

writeToFile

public static void writeToFile(Molecule molecule,
                               java.lang.String filename)

writeMolecules

public static void writeMolecules(ExtendedVector molecules,
                                  java.lang.String filename)

write

public static void write(Molecule molecule,
                         java.io.PrintWriter out)
write the file to PrintWriter out


read

public static Molecule read(java.lang.String filename)
read an xyz file

Parameters:
filename - the file to read
Returns:
the molecule

readMolecules

public static Molecules readMolecules(java.lang.String filename)
read many molecules from a xyz file


read

public static Molecule read(java.io.BufferedReader input)
                     throws java.io.IOException,
                            java.io.EOFException
read an xyz file

Returns:
the molecule
Throws:
java.io.IOException
java.io.EOFException

readLine

protected static java.lang.String readLine(java.io.BufferedReader input)
                                    throws java.io.IOException,
                                           java.io.EOFException
Throws:
java.io.IOException
java.io.EOFException

JavaGenes, NASA Ames. Written largely by Al Globus