java.lang.Object
- org.jmol.adapter.readers.cif.TopoCifParser

All Implemented Interfaces:

CifReader.Parser
```
public class TopoCifParser
extends java.lang.Object
implements CifReader.Parser
```
see https://github.com/COMCIFS/TopoCif Basic idea: We have TLinks, TNodes, and TAtoms TLinks each have two TNodes and may also be associated with bridging TAtom sets. TNode extends TAtom and may also maintain a list of TAtoms. TAtoms extend Atom and may have symmetry aspects.

Author:

Bob Hanson hansonr@stolaf.edu 2020.11.17 2021.05.07

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`private class`	`TopoCifParser.TAtom`
`private class`	`TopoCifParser.TLink`	A class to hold the TOPOL_LINK data item information and transform it as needed.
`private class`	`TopoCifParser.TNet`
`private class`	`TopoCifParser.TNode`
`private static interface`	`TopoCifParser.TPoint`

Field Summary

Fields
Modifier and Type	Field	Description
`private int`	`ac0`
`private java.lang.String`	`allowedTypes`
`(package private) int`	`atomCount`
`(package private) javajs.util.Lst<TopoCifParser.TAtom>`	`atoms`	list of TOPOL_ATOM loop data
`(package private) int`	`b0`	base bond index to be added to any bond bitsets
`private int`	`bc0`
`private javajs.api.GenericCifDataParser`	`cifParser`
`(package private) static double`	`ERROR_TOLERANCE`
`(package private) java.lang.String`	`failed`	and indictor that we should abort, and why
`(package private) int`	`i0`	base atom index to be added to any atom bitsets
`static int`	`LINK_TYPE_AROM`
`static int`	`LINK_TYPE_BITS`
`static int`	`LINK_TYPE_DELO`
`static int`	`LINK_TYPE_DOUBLE`
`static int`	`LINK_TYPE_GENERIC_LINK`	types set by filter TOPOSE_TYPES in the format of one or more of {v, vw, hb} separated by "+"; default is v+hb
`static int`	`LINK_TYPE_HBOND`
`static int`	`LINK_TYPE_OCTUPLE`
`static int`	`LINK_TYPE_OTHER`
`static int`	`LINK_TYPE_PI`
`static int`	`LINK_TYPE_POLY`
`static int`	`LINK_TYPE_QUADRUPLE`
`static int`	`LINK_TYPE_QUINTUPLE`
`static int`	`LINK_TYPE_SEPTUPLE`
`static int`	`LINK_TYPE_SEXTUPLE`
`static int`	`LINK_TYPE_SINGLE`
`static int`	`LINK_TYPE_TRIPLE`
`static int`	`LINK_TYPE_VDW`
`(package private) int`	`linkCount`
`(package private) javajs.util.Lst<TopoCifParser.TLink>`	`links`	list of TOPOL_LINK loop data
`static java.lang.String`	`linkTypes`
`(package private) int`	`netCount`
`(package private) java.lang.String`	`netNotes`
`(package private) javajs.util.Lst<TopoCifParser.TNet>`	`nets`	list of TOPOL_NET loop or single data item data
`(package private) javajs.util.Lst<TopoCifParser.TNode>`	`nodes`	list of TOPOL_NODE loop data
`(package private) javajs.util.M4[]`	`ops`	symmetry operations for this space group
`(package private) CifReader`	`reader`	reader will be null if filter includes TOPOS_IGNORE
`(package private) java.lang.String`	`selectedNet`
`(package private) TopoCifParser.TNet`	`singleNet`	storage for a single net from a non-looped data item
`private SymmetryInterface`	`sym`
`(package private) javajs.util.T3`	`temp1`
`(package private) javajs.util.T3`	`temp2`
`private static byte`	`topol_atom_atom_label`
`private static byte`	`topol_atom_element_symbol`
`private static byte`	`topol_atom_fract_x`
`private static byte`	`topol_atom_fract_y`
`private static byte`	`topol_atom_fract_z`
`private static byte`	`topol_atom_id`
`private static byte`	`topol_atom_link_id`
`private static byte`	`topol_atom_node_id`
`private static byte`	`topol_atom_symop_id`
`private static byte`	`topol_atom_translation`
`private static byte`	`topol_atom_translation_x`
`private static byte`	`topol_atom_translation_y`
`private static byte`	`topol_atom_translation_z`
`(package private) static int`	`TOPOL_GROUP`
`(package private) static int`	`TOPOL_LINK`
`private static byte`	`topol_link_distance`
`private static byte`	`topol_link_id`
`private static byte`	`topol_link_multiplicity`
`private static byte`	`topol_link_net_id`
`private static byte`	`topol_link_node_id_1`
`private static byte`	`topol_link_node_id_2`
`private static byte`	`topol_link_node_label_1_DEPRECATED`
`private static byte`	`topol_link_node_label_2_DEPRECATED`
`private static byte`	`topol_link_order`
`private static byte`	`topol_link_site_symmetry_symop_1_DEPRECATED`
`private static byte`	`topol_link_site_symmetry_symop_2_DEPRECATED`
`private static byte`	`topol_link_site_symmetry_translation_1_DEPRECATED`
`private static byte`	`topol_link_site_symmetry_translation_1_x_DEPRECATED`
`private static byte`	`topol_link_site_symmetry_translation_1_y_DEPRECATED`
`private static byte`	`topol_link_site_symmetry_translation_1_z_DEPRECATED`
`private static byte`	`topol_link_site_symmetry_translation_2_DEPRECATED`
`private static byte`	`topol_link_site_symmetry_translation_2_x_DEPRECATED`
`private static byte`	`topol_link_site_symmetry_translation_2_y_DEPRECATED`
`private static byte`	`topol_link_site_symmetry_translation_2_z_DEPRECATED`
`private static byte`	`topol_link_symop_id_1`
`private static byte`	`topol_link_symop_id_2`
`private static byte`	`topol_link_translation_1`
`private static byte`	`topol_link_translation_1_x`
`private static byte`	`topol_link_translation_1_y`
`private static byte`	`topol_link_translation_1_z`
`private static byte`	`topol_link_translation_2`
`private static byte`	`topol_link_translation_2_x`
`private static byte`	`topol_link_translation_2_y`
`private static byte`	`topol_link_translation_2_z`
`private static byte`	`topol_link_type`
`private static byte`	`topol_link_voronoi_solidangle`
`private static byte`	`topol_net_id`
`private static byte`	`topol_net_label`
`private static byte`	`topol_net_special_details`
`(package private) static int`	`TOPOL_NODE`
`private static byte`	`topol_node_fract_x`
`private static byte`	`topol_node_fract_y`
`private static byte`	`topol_node_fract_z`
`private static byte`	`topol_node_id`
`private static byte`	`topol_node_label`
`private static byte`	`topol_node_net_id`
`private static byte`	`topol_node_symop_id`
`private static byte`	`topol_node_translation`
`private static byte`	`topol_node_translation_x`
`private static byte`	`topol_node_translation_y`
`private static byte`	`topol_node_translation_z`
`private static java.lang.String[]`	`topolFields`
`private static javajs.util.P3`	`ZERO`

Constructor Summary

Constructors
Constructor Description

TopoCifParser()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`(package private) static void`	`applySymmetry(Atom a, javajs.util.M4[] ops, int op, javajs.util.T3 t)`	Apply the symmetry and translation
`(package private) float`	`calculateDistance(javajs.util.P3 p1, javajs.util.P3 p2)`
`boolean`	`finalizeReader()`	PRIOR to symmetry application, process all internal symop/translation aspects.
`void`	`finalizeSymmetry(boolean haveSymmetry)`	Symmetry has been applied.
`TopoCifParser.TNode`	`findNode(java.lang.String nodeID, int op, javajs.util.P3 trans)`	Called from TLink and TAtom to find a node with the given symmetry.
`(package private) TopoCifParser.TNode`	`getAssociatedNodeByIdx(int idx)`	Find the node for this TAtom.
`(package private) TopoCifParser.TLink`	`getAssoiatedLinkByIdx(int idx)`	Find the link for this TAtom.
`Atom`	`getAtomFromName(java.lang.String atomLabel)`
`(package private) static int`	`getBondType(java.lang.String type, int order)`
`private java.lang.String`	`getDataValue(byte key)`	Read the data value.
`private float`	`getFloat(java.lang.String f)`
`private int`	`getInt(java.lang.String f)`
`(package private) static java.lang.String`	`getMF(javajs.util.Lst<TopoCifParser.TAtom> tatoms)`
`TopoCifParser.TNet`	`getNetByID(java.lang.String id)`	Find or create a net with this netID, giving it a default name "Net"+id
`TopoCifParser.TNet`	`getNetFor(java.lang.String id, java.lang.String label, boolean forceNew)`	Find or create a TNet for this id and label.
`(package private) static boolean`	`isEqualD(javajs.util.T3 p1, javajs.util.T3 p2, double d)`
`private int`	`processAssociations(javajs.util.BS bsConnected, javajs.util.BS bsAtoms)`	Find and process all "bonds" associated with all links and nodes.
`private void`	`processAtoms()`
`boolean`	`processBlock(java.lang.String key)`
`private void`	`processLinks()`
`private void`	`processNets()`	Process all nets.
`private void`	`processNodes()`
`void`	`ProcessRecord(java.lang.String key, java.lang.String data)`	process _topol_node.id 1
`private int[]`	`processTranslation(int p, int[] t, java.lang.String field)`
`private void`	`selectNet()`
`(package private) static void`	`setElementSymbol(Atom a, java.lang.String sym)`
`TopoCifParser`	`setReader(CifReader reader)`	filter "TOPOS_TYPES=hb" will only load hydrogen bonds; options include v, vw, and hb
`(package private) static void`	`setTAtom(Atom a, Atom b)`
`(package private) static javajs.util.BS`	`shiftBits(javajs.util.BS bsAtoms, javajs.util.BS bs)`	Shift bits to the left to account for missing atoms in the final atom list.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - TOPOL_LINK
```
static final int TOPOL_LINK
```
    See Also:
    
    Constant Field Values
  - TOPOL_GROUP
```
static final int TOPOL_GROUP
```
    See Also:
    
    Constant Field Values
  - TOPOL_NODE
```
static final int TOPOL_NODE
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_GENERIC_LINK
```
public static final int LINK_TYPE_GENERIC_LINK
```
    types set by filter TOPOSE_TYPES in the format of one or more of {v, vw, hb} separated by "+"; default is v+hb
    
    See Also:
    
    Constant Field Values
  - LINK_TYPE_SINGLE
```
public static final int LINK_TYPE_SINGLE
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_DOUBLE
```
public static final int LINK_TYPE_DOUBLE
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_TRIPLE
```
public static final int LINK_TYPE_TRIPLE
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_QUADRUPLE
```
public static final int LINK_TYPE_QUADRUPLE
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_QUINTUPLE
```
public static final int LINK_TYPE_QUINTUPLE
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_SEXTUPLE
```
public static final int LINK_TYPE_SEXTUPLE
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_SEPTUPLE
```
public static final int LINK_TYPE_SEPTUPLE
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_OCTUPLE
```
public static final int LINK_TYPE_OCTUPLE
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_AROM
```
public static final int LINK_TYPE_AROM
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_POLY
```
public static final int LINK_TYPE_POLY
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_DELO
```
public static final int LINK_TYPE_DELO
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_PI
```
public static final int LINK_TYPE_PI
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_HBOND
```
public static final int LINK_TYPE_HBOND
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_VDW
```
public static final int LINK_TYPE_VDW
```
    See Also:
    
    Constant Field Values
  - LINK_TYPE_OTHER
```
public static final int LINK_TYPE_OTHER
```
    See Also:
    
    Constant Field Values
  - linkTypes
```
public static java.lang.String linkTypes
```
  - LINK_TYPE_BITS
```
public static final int LINK_TYPE_BITS
```
    See Also:
    
    Constant Field Values
  - ERROR_TOLERANCE
```
static double ERROR_TOLERANCE
```
  - reader
```
CifReader reader
```
    reader will be null if filter includes TOPOS_IGNORE
  - atoms
```
javajs.util.Lst<TopoCifParser.TAtom> atoms
```
    list of TOPOL_ATOM loop data
  - nodes
```
javajs.util.Lst<TopoCifParser.TNode> nodes
```
    list of TOPOL_NODE loop data
  - links
```
javajs.util.Lst<TopoCifParser.TLink> links
```
    list of TOPOL_LINK loop data
  - nets
```
javajs.util.Lst<TopoCifParser.TNet> nets
```
    list of TOPOL_NET loop or single data item data
  - singleNet
```
TopoCifParser.TNet singleNet
```
    storage for a single net from a non-looped data item
  - netCount
```
int netCount
```
  - linkCount
```
int linkCount
```
  - atomCount
```
int atomCount
```
  - temp1
```
javajs.util.T3 temp1
```
  - temp2
```
javajs.util.T3 temp2
```
  - ac0
```
private int ac0
```
  - bc0
```
private int bc0
```
  - cifParser
```
private javajs.api.GenericCifDataParser cifParser
```
  - failed
```
java.lang.String failed
```
    and indictor that we should abort, and why
  - ops
```
javajs.util.M4[] ops
```
    symmetry operations for this space group
  - i0
```
int i0
```
    base atom index to be added to any atom bitsets
  - b0
```
int b0
```
    base bond index to be added to any bond bitsets
  - allowedTypes
```
private java.lang.String allowedTypes
```
  - netNotes
```
java.lang.String netNotes
```
  - sym
```
private SymmetryInterface sym
```
  - selectedNet
```
java.lang.String selectedNet
```
  - topolFields
```
private static final java.lang.String[] topolFields
```
  - topol_net_id
```
private static final byte topol_net_id
```
    See Also:
    
    Constant Field Values
  - topol_net_label
```
private static final byte topol_net_label
```
    See Also:
    
    Constant Field Values
  - topol_net_special_details
```
private static final byte topol_net_special_details
```
    See Also:
    
    Constant Field Values
  - topol_link_id
```
private static final byte topol_link_id
```
    See Also:
    
    Constant Field Values
  - topol_link_net_id
```
private static final byte topol_link_net_id
```
    See Also:
    
    Constant Field Values
  - topol_link_node_id_1
```
private static final byte topol_link_node_id_1
```
    See Also:
    
    Constant Field Values
  - topol_link_node_id_2
```
private static final byte topol_link_node_id_2
```
    See Also:
    
    Constant Field Values
  - topol_link_symop_id_1
```
private static final byte topol_link_symop_id_1
```
    See Also:
    
    Constant Field Values
  - topol_link_translation_1
```
private static final byte topol_link_translation_1
```
    See Also:
    
    Constant Field Values
  - topol_link_translation_1_x
```
private static final byte topol_link_translation_1_x
```
    See Also:
    
    Constant Field Values
  - topol_link_translation_1_y
```
private static final byte topol_link_translation_1_y
```
    See Also:
    
    Constant Field Values
  - topol_link_translation_1_z
```
private static final byte topol_link_translation_1_z
```
    See Also:
    
    Constant Field Values
  - topol_link_symop_id_2
```
private static final byte topol_link_symop_id_2
```
    See Also:
    
    Constant Field Values
  - topol_link_translation_2
```
private static final byte topol_link_translation_2
```
    See Also:
    
    Constant Field Values
  - topol_link_translation_2_x
```
private static final byte topol_link_translation_2_x
```
    See Also:
    
    Constant Field Values
  - topol_link_translation_2_y
```
private static final byte topol_link_translation_2_y
```
    See Also:
    
    Constant Field Values
  - topol_link_translation_2_z
```
private static final byte topol_link_translation_2_z
```
    See Also:
    
    Constant Field Values
  - topol_link_distance
```
private static final byte topol_link_distance
```
    See Also:
    
    Constant Field Values
  - topol_link_type
```
private static final byte topol_link_type
```
    See Also:
    
    Constant Field Values
  - topol_link_multiplicity
```
private static final byte topol_link_multiplicity
```
    See Also:
    
    Constant Field Values
  - topol_link_voronoi_solidangle
```
private static final byte topol_link_voronoi_solidangle
```
    See Also:
    
    Constant Field Values
  - topol_link_order
```
private static final byte topol_link_order
```
    See Also:
    
    Constant Field Values
  - topol_node_id
```
private static final byte topol_node_id
```
    See Also:
    
    Constant Field Values
  - topol_node_net_id
```
private static final byte topol_node_net_id
```
    See Also:
    
    Constant Field Values
  - topol_node_label
```
private static final byte topol_node_label
```
    See Also:
    
    Constant Field Values
  - topol_node_symop_id
```
private static final byte topol_node_symop_id
```
    See Also:
    
    Constant Field Values
  - topol_node_translation
```
private static final byte topol_node_translation
```
    See Also:
    
    Constant Field Values
  - topol_node_translation_x
```
private static final byte topol_node_translation_x
```
    See Also:
    
    Constant Field Values
  - topol_node_translation_y
```
private static final byte topol_node_translation_y
```
    See Also:
    
    Constant Field Values
  - topol_node_translation_z
```
private static final byte topol_node_translation_z
```
    See Also:
    
    Constant Field Values
  - topol_node_fract_x
```
private static final byte topol_node_fract_x
```
    See Also:
    
    Constant Field Values
  - topol_node_fract_y
```
private static final byte topol_node_fract_y
```
    See Also:
    
    Constant Field Values
  - topol_node_fract_z
```
private static final byte topol_node_fract_z
```
    See Also:
    
    Constant Field Values
  - topol_atom_id
```
private static final byte topol_atom_id
```
    See Also:
    
    Constant Field Values
  - topol_atom_atom_label
```
private static final byte topol_atom_atom_label
```
    See Also:
    
    Constant Field Values
  - topol_atom_node_id
```
private static final byte topol_atom_node_id
```
    See Also:
    
    Constant Field Values
  - topol_atom_link_id
```
private static final byte topol_atom_link_id
```
    See Also:
    
    Constant Field Values
  - topol_atom_symop_id
```
private static final byte topol_atom_symop_id
```
    See Also:
    
    Constant Field Values
  - topol_atom_translation
```
private static final byte topol_atom_translation
```
    See Also:
    
    Constant Field Values
  - topol_atom_translation_x
```
private static final byte topol_atom_translation_x
```
    See Also:
    
    Constant Field Values
  - topol_atom_translation_y
```
private static final byte topol_atom_translation_y
```
    See Also:
    
    Constant Field Values
  - topol_atom_translation_z
```
private static final byte topol_atom_translation_z
```
    See Also:
    
    Constant Field Values
  - topol_atom_fract_x
```
private static final byte topol_atom_fract_x
```
    See Also:
    
    Constant Field Values
  - topol_atom_fract_y
```
private static final byte topol_atom_fract_y
```
    See Also:
    
    Constant Field Values
  - topol_atom_fract_z
```
private static final byte topol_atom_fract_z
```
    See Also:
    
    Constant Field Values
  - topol_atom_element_symbol
```
private static final byte topol_atom_element_symbol
```
    See Also:
    
    Constant Field Values
  - topol_link_site_symmetry_symop_1_DEPRECATED
```
private static final byte topol_link_site_symmetry_symop_1_DEPRECATED
```
    See Also:
    
    Constant Field Values
  - topol_link_site_symmetry_translation_1_x_DEPRECATED
```
private static final byte topol_link_site_symmetry_translation_1_x_DEPRECATED
```
    See Also:
    
    Constant Field Values
  - topol_link_site_symmetry_translation_1_y_DEPRECATED
```
private static final byte topol_link_site_symmetry_translation_1_y_DEPRECATED
```
    See Also:
    
    Constant Field Values
  - topol_link_site_symmetry_translation_1_z_DEPRECATED
```
private static final byte topol_link_site_symmetry_translation_1_z_DEPRECATED
```
    See Also:
    
    Constant Field Values
  - topol_link_site_symmetry_symop_2_DEPRECATED
```
private static final byte topol_link_site_symmetry_symop_2_DEPRECATED
```
    See Also:
    
    Constant Field Values
  - topol_link_site_symmetry_translation_2_x_DEPRECATED
```
private static final byte topol_link_site_symmetry_translation_2_x_DEPRECATED
```
    See Also:
    
    Constant Field Values
  - topol_link_site_symmetry_translation_2_y_DEPRECATED
```
private static final byte topol_link_site_symmetry_translation_2_y_DEPRECATED
```
    See Also:
    
    Constant Field Values
  - topol_link_site_symmetry_translation_2_z_DEPRECATED
```
private static final byte topol_link_site_symmetry_translation_2_z_DEPRECATED
```
    See Also:
    
    Constant Field Values
  - topol_link_site_symmetry_translation_1_DEPRECATED
```
private static final byte topol_link_site_symmetry_translation_1_DEPRECATED
```
    See Also:
    
    Constant Field Values
  - topol_link_site_symmetry_translation_2_DEPRECATED
```
private static final byte topol_link_site_symmetry_translation_2_DEPRECATED
```
    See Also:
    
    Constant Field Values
  - topol_link_node_label_1_DEPRECATED
```
private static final byte topol_link_node_label_1_DEPRECATED
```
    See Also:
    
    Constant Field Values
  - topol_link_node_label_2_DEPRECATED
```
private static final byte topol_link_node_label_2_DEPRECATED
```
    See Also:
    
    Constant Field Values
  - ZERO
```
private static final javajs.util.P3 ZERO
```
- Constructor Detail
  - TopoCifParser
```
public TopoCifParser()
```
- Method Detail
  - getBondType
```
static int getBondType(java.lang.String type,
                       int order)
```
  - setReader
```
public TopoCifParser setReader(CifReader reader)
```
    filter "TOPOS_TYPES=hb" will only load hydrogen bonds; options include v, vw, and hb
    
    Specified by:
    
    setReader in interface CifReader.Parser
  - ProcessRecord
```
public void ProcessRecord(java.lang.String key,
                          java.lang.String data)
                   throws java.lang.Exception
```
    process _topol_node.id 1
    
    Specified by:
    
    ProcessRecord in interface CifReader.Parser
    
    Throws:
    
    java.lang.Exception
  - processBlock
```
public boolean processBlock(java.lang.String key)
                     throws java.lang.Exception
```
    Specified by:
    
    processBlock in interface CifReader.Parser
    
    Throws:
    
    java.lang.Exception
  - processNets
```
private void processNets()
                  throws java.lang.Exception
```
    Process all nets. Note that the nets list is self-populating with a "Net1" value if there is no TOPOL_NET section.
    
    Throws:
    
    java.lang.Exception
  - processLinks
```
private void processLinks()
                   throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - processNodes
```
private void processNodes()
                   throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - processAtoms
```
private void processAtoms()
                   throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - processTranslation
```
private int[] processTranslation(int p,
                                 int[] t,
                                 java.lang.String field)
```
  - finalizeReader
```
public boolean finalizeReader()
                       throws java.lang.Exception
```
    PRIOR to symmetry application, process all internal symop/translation aspects.
    
    Specified by:
    
    finalizeReader in interface CifReader.Parser
    
    Throws:
    
    java.lang.Exception
  - selectNet
```
private void selectNet()
```
  - finalizeSymmetry
```
public void finalizeSymmetry(boolean haveSymmetry)
                      throws java.lang.Exception
```
    Symmetry has been applied. Identify all of the connected atoms and process the group associations
    
    Specified by:
    
    finalizeSymmetry in interface CifReader.Parser
    
    Throws:
    
    java.lang.Exception
  - shiftBits
```
static javajs.util.BS shiftBits(javajs.util.BS bsAtoms,
                                javajs.util.BS bs)
```
    Shift bits to the left to account for missing atoms in the final atom list.
    
    Parameters:
    
    bsAtoms -
    
    bs -
    
    Returns:
    
    shifted bitset
  - processAssociations
```
private int processAssociations(javajs.util.BS bsConnected,
                                javajs.util.BS bsAtoms)
```
    Find and process all "bonds" associated with all links and nodes. This method runs AFTER generation of all the symmetry-related atoms. BOND_LINK + index indicates linked nodes BOND_GROUP + index indicates associated nodes
    
    Parameters:
    
    bsConnected - prevent Jmol from adding bonds to this atom
    
    bsAtoms - allow Jmol to add bonds to these atoms, inclusively
    
    Returns:
    
    number of bonds created
  - isEqualD
```
static boolean isEqualD(javajs.util.T3 p1,
                        javajs.util.T3 p2,
                        double d)
```
  - getDataValue
```
private java.lang.String getDataValue(byte key)
```
    Read the data value.
    
    Parameters:
    
    key -
    
    Returns:
    
    the value or null if does not exist or is '.' or '?'
  - getInt
```
private int getInt(java.lang.String f)
```
  - getFloat
```
private float getFloat(java.lang.String f)
```
  - getMF
```
static java.lang.String getMF(javajs.util.Lst<TopoCifParser.TAtom> tatoms)
```
  - setTAtom
```
static void setTAtom(Atom a,
                     Atom b)
```
  - setElementSymbol
```
static void setElementSymbol(Atom a,
                             java.lang.String sym)
```
    Parameters:
    
    a - TNode or TAtom
    
    sym -
  - applySymmetry
```
static void applySymmetry(Atom a,
                          javajs.util.M4[] ops,
                          int op,
                          javajs.util.T3 t)
```
    Apply the symmetry and translation
    
    Parameters:
    
    a - TNode or TAtom
    
    ops -
    
    op -
    
    t -
  - getNetByID
```
public TopoCifParser.TNet getNetByID(java.lang.String id)
```
    Find or create a net with this netID, giving it a default name "Net"+id
    
    Parameters:
    
    id -
    
    Returns:
    
    net, never null
  - getAtomFromName
```
public Atom getAtomFromName(java.lang.String atomLabel)
```
  - calculateDistance
```
float calculateDistance(javajs.util.P3 p1,
                        javajs.util.P3 p2)
```
  - getNetFor
```
public TopoCifParser.TNet getNetFor(java.lang.String id,
                                    java.lang.String label,
                                    boolean forceNew)
```
    Find or create a TNet for this id and label.
    
    Parameters:
    
    id - or null
    
    label - or null
    
    forceNew - true to create a new net
    
    Returns:
    
    a net, or null if not forceNew and not found
  - getAssociatedNodeByIdx
```
TopoCifParser.TNode getAssociatedNodeByIdx(int idx)
```
    Find the node for this TAtom.
    
    Parameters:
    
    idx -
    
    Returns:
    
    the node or null
  - getAssoiatedLinkByIdx
```
TopoCifParser.TLink getAssoiatedLinkByIdx(int idx)
```
    Find the link for this TAtom.
    
    Parameters:
    
    idx -
    
    Returns:
    
    the link or null
  - findNode
```
public TopoCifParser.TNode findNode(java.lang.String nodeID,
                                    int op,
                                    javajs.util.P3 trans)
```
    Called from TLink and TAtom to find a node with the given symmetry.
    
    Parameters:
    
    nodeID -
    
    op - match for linkSymop
    
    trans - match for linkTrans
    
    Returns:
    
    the node, or null if no such node was found

Class TopoCifParser

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

TOPOL_LINK

TOPOL_GROUP

TOPOL_NODE

LINK_TYPE_GENERIC_LINK

LINK_TYPE_SINGLE

LINK_TYPE_DOUBLE

LINK_TYPE_TRIPLE

LINK_TYPE_QUADRUPLE

LINK_TYPE_QUINTUPLE

LINK_TYPE_SEXTUPLE

LINK_TYPE_SEPTUPLE

LINK_TYPE_OCTUPLE

LINK_TYPE_AROM

LINK_TYPE_POLY

LINK_TYPE_DELO

LINK_TYPE_PI

LINK_TYPE_HBOND

LINK_TYPE_VDW

LINK_TYPE_OTHER

linkTypes

LINK_TYPE_BITS

ERROR_TOLERANCE

reader

atoms

nodes

links

nets

singleNet

netCount

linkCount

atomCount

temp1

temp2

ac0

bc0

cifParser

failed

ops

i0

b0

allowedTypes

netNotes

sym

selectedNet

topolFields

topol_net_id

topol_net_label

topol_net_special_details

topol_link_id

topol_link_net_id

topol_link_node_id_1

topol_link_node_id_2

topol_link_symop_id_1

topol_link_translation_1

topol_link_translation_1_x

topol_link_translation_1_y

topol_link_translation_1_z

topol_link_symop_id_2

topol_link_translation_2

topol_link_translation_2_x

topol_link_translation_2_y

topol_link_translation_2_z

topol_link_distance

topol_link_type

topol_link_multiplicity

topol_link_voronoi_solidangle

topol_link_order

topol_node_id

topol_node_net_id

topol_node_label

topol_node_symop_id

topol_node_translation

topol_node_translation_x