Class TopoCifParser

    • 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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      • topol_link_node_label_2

        private static final byte topol_link_node_label_2
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      • topol_link_site_symmetry_symop_1

        private static final byte topol_link_site_symmetry_symop_1
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      • topol_link_site_symmetry_translation_1_x

        private static final byte topol_link_site_symmetry_translation_1_x
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      • topol_link_site_symmetry_translation_1_y

        private static final byte topol_link_site_symmetry_translation_1_y
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      • topol_link_site_symmetry_translation_1_z

        private static final byte topol_link_site_symmetry_translation_1_z
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      • topol_link_site_symmetry_symop_2

        private static final byte topol_link_site_symmetry_symop_2
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      • topol_link_site_symmetry_translation_2_x

        private static final byte topol_link_site_symmetry_translation_2_x
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      • topol_link_site_symmetry_translation_2_y

        private static final byte topol_link_site_symmetry_translation_2_y
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      • topol_link_site_symmetry_translation_2_z

        private static final byte topol_link_site_symmetry_translation_2_z
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      • topol_link_multiplicity

        private static final byte topol_link_multiplicity
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      • topol_link_voronoi_solidangle

        private static final byte topol_link_voronoi_solidangle
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      • topol_link_site_symmetry_translation_1

        private static final byte topol_link_site_symmetry_translation_1
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      • topol_link_site_symmetry_translation_2

        private static final byte topol_link_site_symmetry_translation_2
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      • cifParser

        javajs.api.GenericCifDataParser cifParser
    • Constructor Detail

      • TopoCifParser

        public TopoCifParser()
    • Method Detail

      • isEqualD

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