Package org.jmol.adapter.readers.quantum
Class NBOParser
java.lang.Object
org.jmol.adapter.readers.quantum.NBOParser
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionboolean
connectNBO
(int modelIndex, String type) getAllStructures
(String output, Lst<Object> list) get thegetStructureMap
(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 structureint
getStructures
(String data, String nrtType, Lst<Object> list) Reads the $NRTSTR $NRTSTRA, $NRTSTRB, and $CHOOSE blocks.static void
getStructures46
(String[] tokens, String type, Lst<Object> structures, int nAtoms) Use the .46 file NBO alpha/beta labels to identify bonds, lone pairs, and lone valences.boolean
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Constructor Details
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NBOParser
public NBOParser()
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Method Details
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set
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getAllStructures
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getStructures46
public static void getStructures46(String[] tokens, String type, 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
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getStructures
Reads the $NRTSTR $NRTSTRA, $NRTSTRB, and $CHOOSE blocks. Creates a Lst of Hashtables- Parameters:
data
- NBO output block not including $ENDnrtType
- "CHOOSE", "NRTSTRA", "NRTSTRB"list
- to fill- Returns:
- number of structures found or -1 for an error
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isOpenShell
public boolean isOpenShell() -
getStructureMap
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 filetype
- topoa, topob, nrtstra, nrtstrb, alpha, beta -- last two are from CHOOSEindex
- 0-based index for this type- Returns:
- Hashtable or null
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connectNBO
- Parameters:
modelIndex
-type
- one of alpha|beta|choosea|chooseb|nrtstr_n|nrtstra_n|topo_n|topoa_n| topob_n- Returns:
- true if successful
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getNBOAtomLabel
get the- Parameters:
a
-- Returns:
- label including (lp), (lv), and (if not open-spin) formal charge
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