Package org.jmol.adapter.readers.cif
Class TopoCifParser
- java.lang.Object
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- org.jmol.adapter.readers.cif.TopoCifParser
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- All Implemented Interfaces:
CifReader.Parser
public class TopoCifParser extends Object implements CifReader.Parser
See https://www.iucr.org/resources/cif/dictionaries/cif_topology
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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.
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Field Summary
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Constructor Summary
Constructors Constructor Description TopoCifParser()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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
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Field Detail
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topolFields
private static final String[] topolFields
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topol_link_node_label_1
private static final byte topol_link_node_label_1
- See Also:
- Constant Field Values
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topol_link_node_label_2
private static final byte topol_link_node_label_2
- See Also:
- Constant Field Values
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topol_link_distance
private static final byte topol_link_distance
- See Also:
- Constant Field Values
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topol_link_site_symmetry_symop_1
private static final byte topol_link_site_symmetry_symop_1
- See Also:
- Constant Field Values
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topol_link_site_symmetry_translation_1_x
private static final byte topol_link_site_symmetry_translation_1_x
- See Also:
- Constant Field Values
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topol_link_site_symmetry_translation_1_y
private static final byte topol_link_site_symmetry_translation_1_y
- See Also:
- Constant Field Values
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topol_link_site_symmetry_translation_1_z
private static final byte topol_link_site_symmetry_translation_1_z
- See Also:
- Constant Field Values
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topol_link_site_symmetry_symop_2
private static final byte topol_link_site_symmetry_symop_2
- See Also:
- Constant Field Values
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topol_link_site_symmetry_translation_2_x
private static final byte topol_link_site_symmetry_translation_2_x
- See Also:
- Constant Field Values
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topol_link_site_symmetry_translation_2_y
private static final byte topol_link_site_symmetry_translation_2_y
- See Also:
- Constant Field Values
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topol_link_site_symmetry_translation_2_z
private static final byte topol_link_site_symmetry_translation_2_z
- See Also:
- Constant Field Values
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topol_link_type
private static final byte topol_link_type
- See Also:
- Constant Field Values
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topol_link_multiplicity
private static final byte topol_link_multiplicity
- See Also:
- Constant Field Values
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topol_link_voronoi_solidangle
private static final byte topol_link_voronoi_solidangle
- See Also:
- Constant Field Values
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topol_link_site_symmetry_translation_1
private static final byte topol_link_site_symmetry_translation_1
- See Also:
- Constant Field Values
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topol_link_site_symmetry_translation_2
private static final byte topol_link_site_symmetry_translation_2
- See Also:
- Constant Field Values
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reader
CifReader reader
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cifParser
javajs.api.GenericCifDataParser cifParser
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types
private String types
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links
private javajs.util.Lst<TopoCifParser.TopoLink> links
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bondlist
String bondlist
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Method Detail
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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 interfaceCifReader.Parser
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finalizeReader
public boolean finalizeReader() throws Exception
- Specified by:
finalizeReader
in interfaceCifReader.Parser
- Throws:
Exception
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isEqualD
static boolean isEqualD(javajs.util.T3 p1, javajs.util.T3 p2, double d, double err)
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finalizeSymmetry
public void finalizeSymmetry(boolean haveSymmetry) throws Exception
Create a list of cartesians and then set the bonds.- Specified by:
finalizeSymmetry
in interfaceCifReader.Parser
- Throws:
Exception
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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
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processBlock
public void processBlock(String key) throws Exception
- Specified by:
processBlock
in interfaceCifReader.Parser
- Throws:
Exception
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