Package org.jmol.adapter.readers.cif

Class TopoCifParser

java.lang.Object

org.jmol.adapter.readers.cif.TopoCifParser

All Implemented Interfaces:

CifReader.Parser

public class TopoCifParser
extends Object
implements CifReader.Parser

See https://www.iucr.org/resources/cif/dictionaries/cif_topology

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private class	TopoCifParser.TopoLink	A class to hold the _topol block information and transform it as needed.
private class	TopoCifParser.TopoPrimitive	A class to hold the result of a "primitive" operation on a given link with a given operator.

Field Summary

Fields

Modifier and Type	Field	Description
(package private) String	bondlist
(package private) javajs.api.GenericCifDataParser	cifParser
private javajs.util.Lst<TopoCifParser.TopoLink>	links
(package private) CifReader	reader
private static byte	topol_link_distance
private static byte	topol_link_multiplicity
private static byte	topol_link_node_label_1
private static byte	topol_link_node_label_2
private static byte	topol_link_site_symmetry_symop_1
private static byte	topol_link_site_symmetry_symop_2
private static byte	topol_link_site_symmetry_translation_1
private static byte	topol_link_site_symmetry_translation_1_x
private static byte	topol_link_site_symmetry_translation_1_y
private static byte	topol_link_site_symmetry_translation_1_z
private static byte	topol_link_site_symmetry_translation_2
private static byte	topol_link_site_symmetry_translation_2_x
private static byte	topol_link_site_symmetry_translation_2_y
private static byte	topol_link_site_symmetry_translation_2_z
private static byte	topol_link_type
private static byte	topol_link_voronoi_solidangle
private static String[]	topolFields
private String	types

Constructor Summary

Constructors

Constructor	Description
TopoCifParser()

Method Summary

Modifier and Type	Method	Description
boolean	finalizeReader()
void	finalizeSymmetry(boolean haveSymmetry)	Create a list of cartesians and then set the bonds.
(package private) static boolean	isEqualD(javajs.util.T3 p1, javajs.util.T3 p2, double d, double err)
void	processBlock(String key)
private int	setBonds(int index, Atom[] atoms, javajs.util.P3[] carts, TopoCifParser.TopoLink link, SymmetryInterface sym, int nOps, javajs.util.BS bsConnected)	Find all bonds associated with this link by matching unitized atom positions to unitized "primitive" operations on the link.
TopoCifParser	setReader(CifReader reader)	filter "TOPOS_TYPES=hb" will only load hydrogen bonds; options include v, vw, and hb

Methods inherited from class java.lang.Object

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

Field Detail

topolFields

private static final String[] topolFields

topol_link_node_label_1

private static final byte topol_link_node_label_1

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Constant Field Values

topol_link_node_label_2

private static final byte topol_link_node_label_2

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Constant Field Values

topol_link_distance

private static final byte topol_link_distance

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Constant Field Values

topol_link_site_symmetry_symop_1

private static final byte topol_link_site_symmetry_symop_1

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Constant Field Values

topol_link_site_symmetry_translation_1_x

private static final byte topol_link_site_symmetry_translation_1_x

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Constant Field Values

topol_link_site_symmetry_translation_1_y

private static final byte topol_link_site_symmetry_translation_1_y

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Constant Field Values

topol_link_site_symmetry_translation_1_z

private static final byte topol_link_site_symmetry_translation_1_z

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Constant Field Values

topol_link_site_symmetry_symop_2

private static final byte topol_link_site_symmetry_symop_2

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Constant Field Values

topol_link_site_symmetry_translation_2_x

private static final byte topol_link_site_symmetry_translation_2_x

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Constant Field Values

topol_link_site_symmetry_translation_2_y

private static final byte topol_link_site_symmetry_translation_2_y

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Constant Field Values

topol_link_site_symmetry_translation_2_z

private static final byte topol_link_site_symmetry_translation_2_z

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Constant Field Values

topol_link_type

private static final byte topol_link_type

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Constant Field Values

topol_link_multiplicity

private static final byte topol_link_multiplicity

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Constant Field Values

topol_link_voronoi_solidangle

private static final byte topol_link_voronoi_solidangle

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Constant Field Values

topol_link_site_symmetry_translation_1

private static final byte topol_link_site_symmetry_translation_1

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Constant Field Values

topol_link_site_symmetry_translation_2

private static final byte topol_link_site_symmetry_translation_2

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Constant Field Values

reader

CifReader reader

cifParser

javajs.api.GenericCifDataParser cifParser

types

private String types

links

private javajs.util.Lst<TopoCifParser.TopoLink> links

bondlist

String bondlist

Constructor Detail

TopoCifParser

public TopoCifParser()

Method Detail

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

finalizeReader

public boolean finalizeReader()
                       throws Exception

Specified by:

finalizeReader in interface CifReader.Parser

Throws:

Exception

isEqualD

static boolean isEqualD(javajs.util.T3 p1,
                        javajs.util.T3 p2,
                        double d,
                        double err)

finalizeSymmetry

public void finalizeSymmetry(boolean haveSymmetry)
                      throws Exception

Create a list of cartesians and then set the bonds.

Specified by:

finalizeSymmetry in interface CifReader.Parser

Throws:

Exception

setBonds

private int setBonds(int index,
                     Atom[] atoms,
                     javajs.util.P3[] carts,
                     TopoCifParser.TopoLink link,
                     SymmetryInterface sym,
                     int nOps,
                     javajs.util.BS bsConnected)

Find all bonds associated with this link by matching unitized atom positions to unitized "primitive" operations on the link. The basic idea: 1. We comparing all atom positions from site 1 with all atom positions from site 2. 2.

Parameters:

index -

atoms -

carts -

link -

sym -

nOps -

bsConnected -

processBlock

public void processBlock(String key)
                  throws Exception

Specified by:

processBlock in interface CifReader.Parser

Throws:

Exception