Package org.jmol.adapter.readers.quantum

Class NBOParser

java.lang.Object

org.jmol.adapter.readers.quantum.NBOParser

public class NBOParser
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
private boolean	haveBeta
private Viewer	vwr

Constructor Summary

Constructors

Constructor	Description
NBOParser()

Method Summary

Modifier and Type	Method	Description
boolean	connectNBO(int modelIndex, String type)
private static void	dumpMatrix(String nrtType, int index, int[][] matrix)
javajs.util.Lst<Object>	getAllStructures(String output, javajs.util.Lst<Object> list)
private static int	getAtomIndex(String xx99)
private String	getBlock(String output, String key)
private String	getData(String output, String start, String end, int n)
String	getNBOAtomLabel(Atom a)	get the
static Map<String,Object>	getStructureMap(javajs.util.Lst<Object> structureList, String type, int index)	Find the map for a specified structure, producing a structure that can be used to generate lone pairs and bonds for a Lewis structure
int	getStructures(String data, String nrtType, javajs.util.Lst<Object> list)	Reads the $NRTSTR $NRTSTRA, $NRTSTRB, and $CHOOSE blocks.
static void	getStructures46(String[] tokens, String type, javajs.util.Lst<Object> structures, int nAtoms)	Use the .46 file NBO alpha/beta labels to identify bonds, lone pairs, and lone valences.
private void	getStructuresTOPO(String data, String nrtType, javajs.util.Lst<Object> list)
boolean	isOpenShell()
NBOParser	set(Viewer vwr)
private boolean	setJmolLewisStructure(Map<String,Object> structureMap, int modelIndex, int resNo)	Starting with a structure map, do what needs to be done to change the current Jmol structure to that in terms of bonding and formal charge.

Methods inherited from class java.lang.Object

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

Field Detail

vwr

private Viewer vwr

haveBeta

private boolean haveBeta

Constructor Detail

NBOParser

public NBOParser()

Method Detail

set

public NBOParser set(Viewer vwr)

getAllStructures

public javajs.util.Lst<Object> getAllStructures(String output,
                                                javajs.util.Lst<Object> list)

getBlock

private String getBlock(String output,
                        String key)

getStructures46

public static void getStructures46(String[] tokens,
                                   String type,
                                   javajs.util.Lst<Object> structures,
                                   int nAtoms)

Use the .46 file NBO alpha/beta labels to identify bonds, lone pairs, and lone valences.

Parameters:

tokens -

type -

structures -

nAtoms -

getAtomIndex

private static int getAtomIndex(String xx99)

getStructuresTOPO

private void getStructuresTOPO(String data,
                               String nrtType,
                               javajs.util.Lst<Object> list)

dumpMatrix

private static void dumpMatrix(String nrtType,
                               int index,
                               int[][] matrix)

getData

private String getData(String output,
                       String start,
                       String end,
                       int n)

getStructures

public int getStructures(String data,
                         String nrtType,
                         javajs.util.Lst<Object> list)

Reads the $NRTSTR $NRTSTRA, $NRTSTRB, and $CHOOSE blocks. Creates a Lst of Hashtables

Parameters:

data - NBO output block not including $END

nrtType - "CHOOSE", "NRTSTRA", "NRTSTRB"

list - to fill

Returns:

number of structures found or -1 for an error

isOpenShell

public boolean isOpenShell()

getStructureMap

public static Map<String,Object> getStructureMap(javajs.util.Lst<Object> structureList,
                                                       String type,
                                                       int index)

Find the map for a specified structure, producing a structure that can be used to generate lone pairs and bonds for a Lewis structure

Parameters:

structureList - a list of structural information from this class created from an NBO file

type - topoa, topob, nrtstra, nrtstrb, alpha, beta -- last two are from CHOOSE

index - 0-based index for this type

Returns:

Hashtable or null

connectNBO

public boolean connectNBO(int modelIndex,
                          String type)

Parameters:

modelIndex -

type - one of alpha|beta|choosea|chooseb|nrtstr_n|nrtstra_n|topo_n|topoa_n| topob_n

Returns:

true if successful

setJmolLewisStructure

private boolean setJmolLewisStructure(Map<String,Object> structureMap,
                                      int modelIndex,
                                      int resNo)

Starting with a structure map, do what needs to be done to change the current Jmol structure to that in terms of bonding and formal charge. Three map configurations are supported: bond/lone/3c data from $CHOOSE or $NRTSTR, $NRTSTRA, or $NRTSTRB matrix from TOPO map of atom names from the .46 file NBO alpha/beta lists

Parameters:

structureMap -

modelIndex -

resNo -

Returns:

true if successful

getNBOAtomLabel

public String getNBOAtomLabel(Atom a)

get the

Parameters:

a -

Returns:

label including (lp), (lv), and (if not open-spin) formal charge