PDBeCIF
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
»
Index
Index
C
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D
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G
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I
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M
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P
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R
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S
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T
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U
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V
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W
C
Category (class in pdbecif.mmcif)
CifFile (class in pdbecif.mmcif)
CifFileReader (class in pdbecif.mmcif_io)
CifFileWriter (class in pdbecif.mmcif_io)
CIFWrapper (class in pdbecif.mmcif)
CIFWrapperTable (class in pdbecif.mmcif)
D
DataBlock (class in pdbecif.mmcif)
G
getCategories() (pdbecif.mmcif.DataBlock method)
(pdbecif.mmcif.SaveFrame method)
getCategoryIds() (pdbecif.mmcif.DataBlock method)
(pdbecif.mmcif.SaveFrame method)
getDataBlockIds() (pdbecif.mmcif.CifFile method)
getDataBlocks() (pdbecif.mmcif.CifFile method)
getFormattedValue() (pdbecif.mmcif.Item method)
getItemNames() (pdbecif.mmcif.Category method)
getItems() (pdbecif.mmcif.Category method)
getRawValue() (pdbecif.mmcif.Item method)
getSaveFrameIds() (pdbecif.mmcif.DataBlock method)
getSaveFrames() (pdbecif.mmcif.DataBlock method)
I
import_mmcif_data_map() (pdbecif.mmcif.CifFile method)
Item (class in pdbecif.mmcif)
M
MMCIF2Dict (class in pdbecif.mmcif_tools)
module
pdbecif.globalphasing
pdbecif.globalphasing.startools
pdbecif.mmcif
pdbecif.mmcif_io
pdbecif.mmcif_tools
pdbecif.utils
P
parse() (pdbecif.mmcif_tools.MMCIF2Dict method)
pdbecif.globalphasing
module
pdbecif.globalphasing.startools
module
pdbecif.mmcif
module
pdbecif.mmcif_io
module
pdbecif.mmcif_tools
module
pdbecif.utils
module
R
read() (pdbecif.mmcif_io.CifFileReader method)
remove() (pdbecif.mmcif.Category method)
(pdbecif.mmcif.DataBlock method)
(pdbecif.mmcif.Item method)
(pdbecif.mmcif.SaveFrame method)
removeChild() (pdbecif.mmcif.Category method)
(pdbecif.mmcif.CifFile method)
(pdbecif.mmcif.DataBlock method)
(pdbecif.mmcif.SaveFrame method)
reset() (pdbecif.mmcif.Item method)
S
SaveFrame (class in pdbecif.mmcif)
search() (pdbecif.mmcif.CIFWrapperTable method)
searchiter() (pdbecif.mmcif.CIFWrapperTable method)
start_matching() (pdbecif.globalphasing.startools.StarTokeniser method)
StarToken (class in pdbecif.globalphasing.startools)
StarTokeniser (class in pdbecif.globalphasing.startools)
T
type (pdbecif.globalphasing.startools.StarToken property)
type_string (pdbecif.globalphasing.startools.StarToken property)
U
unwrap() (pdbecif.mmcif.CIFWrapper method)
updateId() (pdbecif.mmcif.DataBlock method)
(pdbecif.mmcif.SaveFrame method)
V
value (pdbecif.globalphasing.startools.StarToken property)
W
write() (pdbecif.mmcif_io.CifFileWriter method)