public class NBOParser
extends java.lang.Object
| Modifier and Type | Field and Description |
|---|---|
private boolean |
haveBeta |
private Viewer |
vwr |
| Constructor and Description |
|---|
NBOParser() |
| Modifier and Type | Method and Description |
|---|---|
boolean |
connectNBO(int modelIndex,
java.lang.String type) |
private static void |
dumpMatrix(java.lang.String nrtType,
int index,
int[][] matrix) |
javajs.util.Lst<java.lang.Object> |
getAllStructures(java.lang.String output,
javajs.util.Lst<java.lang.Object> list) |
private static int |
getAtomIndex(java.lang.String xx99) |
private java.lang.String |
getBlock(java.lang.String output,
java.lang.String key) |
private java.lang.String |
getData(java.lang.String output,
java.lang.String start,
java.lang.String end,
int n) |
java.lang.String |
getNBOAtomLabel(Atom a)
get the
|
static java.util.Map<java.lang.String,java.lang.Object> |
getStructureMap(javajs.util.Lst<java.lang.Object> structureList,
java.lang.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(java.lang.String data,
java.lang.String nrtType,
javajs.util.Lst<java.lang.Object> list)
Reads the $NRTSTR $NRTSTRA, $NRTSTRB, and $CHOOSE blocks.
|
static void |
getStructures46(java.lang.String[] tokens,
java.lang.String type,
javajs.util.Lst<java.lang.Object> structures,
int nAtoms)
Use the .46 file NBO alpha/beta labels to identify bonds, lone pairs, and lone valences.
|
private void |
getStructuresTOPO(java.lang.String data,
java.lang.String nrtType,
javajs.util.Lst<java.lang.Object> list) |
boolean |
isOpenShell() |
NBOParser |
set(Viewer vwr) |
private boolean |
setJmolLewisStructure(java.util.Map<java.lang.String,java.lang.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.
|
private Viewer vwr
private boolean haveBeta
public javajs.util.Lst<java.lang.Object> getAllStructures(java.lang.String output,
javajs.util.Lst<java.lang.Object> list)
private java.lang.String getBlock(java.lang.String output,
java.lang.String key)
public static void getStructures46(java.lang.String[] tokens,
java.lang.String type,
javajs.util.Lst<java.lang.Object> structures,
int nAtoms)
tokens - type - structures - nAtoms - private static int getAtomIndex(java.lang.String xx99)
private void getStructuresTOPO(java.lang.String data,
java.lang.String nrtType,
javajs.util.Lst<java.lang.Object> list)
private static void dumpMatrix(java.lang.String nrtType,
int index,
int[][] matrix)
private java.lang.String getData(java.lang.String output,
java.lang.String start,
java.lang.String end,
int n)
public int getStructures(java.lang.String data,
java.lang.String nrtType,
javajs.util.Lst<java.lang.Object> list)
data - NBO output block not including $ENDnrtType - "CHOOSE", "NRTSTRA", "NRTSTRB"list - to fillpublic boolean isOpenShell()
public static java.util.Map<java.lang.String,java.lang.Object> getStructureMap(javajs.util.Lst<java.lang.Object> structureList,
java.lang.String type,
int index)
structureList - a list of structural information from this class created from an NBO filetype - topoa, topob, nrtstra, nrtstrb, alpha, beta -- last two are from CHOOSEindex - 0-based index for this typepublic boolean connectNBO(int modelIndex,
java.lang.String type)
modelIndex - type - one of alpha|beta|choosea|chooseb|nrtstr_n|nrtstra_n|topo_n|topoa_n|
topob_nprivate boolean setJmolLewisStructure(java.util.Map<java.lang.String,java.lang.Object> structureMap,
int modelIndex,
int resNo)
structureMap - modelIndex - resNo - public java.lang.String getNBOAtomLabel(Atom a)
a -