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1.6
  • Quick start
    • Reading using CifFileReader
    • Reading using MMCIF2Dict
    • Writing data
  • Biological use cases
    • Reading PDB macromolecular files in the mmCIF format
      • Speed optimization for large entires
    • Reading wwPDB Biologically Interesting molecule Reference Dictionary
  • Objects description
    • CifFileReader
    • CifFileWriter
    • MMCIF2Dict
      • Category examples
      • Category with a single value per field
      • Multivalue category per field
  • Use cases
    • Creating objects
      • Example 1 - Creating an mmCIF like dictionary by hand (manually)
      • Example 2 - Creating a CifWrapper object from mmCif-like dictionaries
      • Example 3 - Creating an mmCif-like dictionary from a CifWrapper object
      • Example 4 - Creating a CifFile object from an mmCif-like dictionary
        • Method 1: (instantiation)
        • Method 2: (dictionary import)
    • Reading from files
      • Example 5 - INPUT: mmCif data files, OUTPUT: mmCif-like dictionary
      • Example 6 - INPUT: mmCif data files, OUTPUT: CIFWrapper object
      • Example 7 - INPUT: mmCif data files, OUTPUT: CifFile object
    • Writing to files
      • Example 8 - INPUT: mmCif-like dictionary
        • Method 1
        • Method 2: DataBlocks defined in mmCIF-like dictionary
      • Example 9 - INPUT: CIFWrapper object
      • Example 10 - INPUT: CifFile object
    • Using an mmCIF-like python dictionary
      • Example 11 - Accessing the value of an item
      • Example 12 - Accessing all items of a category
    • Using a CIFWrapper object
    • Using a CifFile object
      • Example 18 - Working with CifFile
      • Example 19 - Working with DataBlock
      • Example 20 - Working with Category
      • Example 21 - Working with Item
      • Example 22 - Method chaining
  • API documentation
    • Startools toolkit
      • pdbecif.globalphasing.startools
    • pdbecif
      • pdbecif.mmcif
        • mmCIF data files
        • mmCIF dictionaries
      • pdbecif.mmcif_io
      • pdbecif.mmcif_tools
      • pdbecif.ordereddict
      • pdbecif.utils
    • Objects description
      • CifFileReader
      • CifFileWriter
      • MMCIF2Dict
        • Category examples
        • Category with a single value per field
        • Multivalue category per field
PDBeCIF
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  • API documentation
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API documentationΒΆ

This part of the documentation is automatically generated from the PDBeCif source code and comments.

The pdbecif package is made up of the following modules:

  • Startools toolkit
    • pdbecif.globalphasing.startools
  • pdbecif
    • pdbecif.mmcif
      • mmCIF data files
      • mmCIF dictionaries
    • pdbecif.mmcif_io
    • pdbecif.mmcif_tools
    • pdbecif.ordereddict
    • pdbecif.utils
  • Objects description
    • CifFileReader
    • CifFileWriter
    • MMCIF2Dict
      • Category examples
      • Category with a single value per field
      • Multivalue category per field
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© Copyright 2020, Glen van Ginkel (Protein Data Bank in Europe; https://pdbe.org).

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