Package org.jmol.adapter.readers.cif


package org.jmol.adapter.readers.cif
  • Class
    Description
    Fully implemented 2016.12.1 see http://journals.iucr.org/j/issues/2016/01/00/aj5269/index.html Will deliver JSON versions of the data while file reading and Java List/Map structures when called by x = getProperty("cifInfo", filename) Validated using the test-data suite by John Bollinger (John.Bollinger@stjude.org) found at https://github.com/COMCIFS/cif_api
    Preliminary Cif2 reader.
    A true line-free CIF file reader for CIF files.
    Allows checking specific blocks e.g.
    mmCIF files are recognized prior to class creation.
     
    JmolData RCSB MMTF (macromolecular transmission format) file reader see https://github.com/rcsb/mmtf/blob/master/spec.md full specification Version: v0.2+dev (as of 2016.08.08) is implemented,including: reading atoms, bonds, and DSSP 1.0 secondary structure load =1f88.mmtf filter "DSSP1" [Note that the filter "DSSP1" is required, since mmtf included DSSP 1.0 calculations, while the standard for Jmol itself is DSSP 2.0.
     
    generalized modulated structure reader class for CIF and Jana -- includes Fourier, Crenel, Sawtooth; displacement, occupancy, and Uij -- handles up to 6 modulation wave vectors -- commensurate and incommensurate, including composites -- not handling _cell_commen_t_section_1
     
    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.