cct.adf
Class ADF

java.lang.Object
  extended by cct.adf.ADF

public class ADF
extends java.lang.Object


Field Summary
(package private)  float angleUnits
           
(package private)  java.util.ArrayList<ADFAtom> Atoms
           
(package private)  java.util.ArrayList<int[]> connectionTable
           
(package private)  boolean defaultChargeUsed
           
(package private) static float DEGREES_TO_RADIANS
           
(package private)  float distanceUnits
           
(package private) static java.lang.String FF_LABEL_PROP
           
(package private)  java.util.HashSet<java.lang.String> frozenParameters
           
(package private)  boolean includesFrozenAtoms
           
(package private)  boolean internalCoordinates
           
(package private) static java.util.HashMap<java.lang.String,KEY_WORDS> keyWords
           
(package private)  MathExpressionParser mathExpressionParser
           
(package private) static java.lang.String MM_TYPE_PROP
           
(package private) static double ONE_BOHR
           
(package private)  boolean symbolicParamResolved
           
(package private)  java.util.HashMap<java.lang.String,java.lang.Float> symbolicStrings
           
(package private)  int totalCharge
           
 
Constructor Summary
ADF()
           
 
Method Summary
static void fromZMatrixToCartesians(java.util.ArrayList<ADFAtom> atoms)
           
 void getMolecularInterface(MoleculeInterface molec)
           
(package private)  boolean isNumber(java.lang.String token)
           
static void main(java.lang.String[] args)
           
static int parseAtomLabel(java.lang.String label)
          Returns element number (0 for dummy atom)
 void parseATOMS(java.lang.String keyword, java.io.BufferedReader in)
          ATOMS {Cartesian / Zmatrix / MOPAC / Internal / ZCart} {N} Atom Coords {F=Fragment} ...
 void parseCartesianCoordinates(java.io.BufferedReader in)
           
 void parseCHARGE(java.lang.String charge)
           
 void parseDEFINE(java.io.BufferedReader in)
           
 void parseGEOVAR(java.io.BufferedReader in)
          GEOVAR Name Data ...
 void parseInput(java.lang.String file_name, int fileType)
           
 void parseQMMM(java.io.BufferedReader in)
           
 void parseUNITS(java.io.BufferedReader in)
          Geometric lengths and angles are in units defined by: UNITS length Angstrom / Bohr angle Degree / Radian end
 void parseZmatrix(java.io.BufferedReader in)
           
 void resolveSymbolicParamaters()
           
(package private)  void skipSection(java.io.BufferedReader in)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

ONE_BOHR

static final double ONE_BOHR
See Also:
Constant Field Values

DEGREES_TO_RADIANS

static final float DEGREES_TO_RADIANS
See Also:
Constant Field Values

FF_LABEL_PROP

static final java.lang.String FF_LABEL_PROP
See Also:
Constant Field Values

MM_TYPE_PROP

static final java.lang.String MM_TYPE_PROP
See Also:
Constant Field Values

keyWords

static java.util.HashMap<java.lang.String,KEY_WORDS> keyWords

distanceUnits

float distanceUnits

angleUnits

float angleUnits

symbolicParamResolved

boolean symbolicParamResolved

includesFrozenAtoms

boolean includesFrozenAtoms

defaultChargeUsed

boolean defaultChargeUsed

internalCoordinates

boolean internalCoordinates

totalCharge

int totalCharge

Atoms

java.util.ArrayList<ADFAtom> Atoms

connectionTable

java.util.ArrayList<int[]> connectionTable

symbolicStrings

java.util.HashMap<java.lang.String,java.lang.Float> symbolicStrings

frozenParameters

java.util.HashSet<java.lang.String> frozenParameters

mathExpressionParser

MathExpressionParser mathExpressionParser
Constructor Detail

ADF

public ADF()
Method Detail

main

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

getMolecularInterface

public void getMolecularInterface(MoleculeInterface molec)
                           throws java.lang.Exception
Throws:
java.lang.Exception

parseInput

public void parseInput(java.lang.String file_name,
                       int fileType)
                throws java.lang.Exception
Throws:
java.lang.Exception

resolveSymbolicParamaters

public void resolveSymbolicParamaters()
                               throws java.lang.Exception
Throws:
java.lang.Exception

parseCHARGE

public void parseCHARGE(java.lang.String charge)
                 throws java.lang.Exception
Throws:
java.lang.Exception

parseQMMM

public void parseQMMM(java.io.BufferedReader in)
               throws java.lang.Exception
Throws:
java.lang.Exception

skipSection

void skipSection(java.io.BufferedReader in)
           throws java.lang.Exception
Throws:
java.lang.Exception

parseUNITS

public void parseUNITS(java.io.BufferedReader in)
                throws java.lang.Exception
Geometric lengths and angles are in units defined by: UNITS length Angstrom / Bohr angle Degree / Radian end

Parameters:
in - BufferedReader
Throws:
java.lang.Exception

parseATOMS

public void parseATOMS(java.lang.String keyword,
                       java.io.BufferedReader in)
                throws java.lang.Exception
ATOMS {Cartesian / Zmatrix / MOPAC / Internal / ZCart} {N} Atom Coords {F=Fragment} ... End

Parameters:
keyword - String
in - BufferedReader
Throws:
java.lang.Exception

parseZmatrix

public void parseZmatrix(java.io.BufferedReader in)
                  throws java.lang.Exception
Throws:
java.lang.Exception

isNumber

boolean isNumber(java.lang.String token)

parseCartesianCoordinates

public void parseCartesianCoordinates(java.io.BufferedReader in)
                               throws java.lang.Exception
Throws:
java.lang.Exception

parseAtomLabel

public static int parseAtomLabel(java.lang.String label)
                          throws java.lang.Exception
Returns element number (0 for dummy atom)

Parameters:
label - String
Returns:
int
Throws:
java.lang.Exception

parseGEOVAR

public void parseGEOVAR(java.io.BufferedReader in)
                 throws java.lang.Exception
GEOVAR Name Data ... end

Parameters:
in - BufferedReader
Throws:
java.lang.Exception

parseDEFINE

public void parseDEFINE(java.io.BufferedReader in)
                 throws java.lang.Exception
Throws:
java.lang.Exception

fromZMatrixToCartesians

public static void fromZMatrixToCartesians(java.util.ArrayList<ADFAtom> atoms)
                                    throws java.lang.Exception
Throws:
java.lang.Exception