Objects description¶

CifFileReader¶

There are two types of behaviour that can be configured when instantiating the CifFileReader. You can specify the file type as either ‘data’ (default) or ‘dictionary’.

If ‘dictionary’ is specified the reader will always return a CifFile object regardless of the ‘output’ flag in the read() method.
If ‘data’ is specified (this is the default behaviour), the ‘output’ flag in the read method.

import pdbecif.mmcif_io as mmcif
cfr = mmcif.CifFileReader(input='dictionary')

By changing the ‘output’ parameter, users can customize the way in which mmCIF is returned. output takes one of three values i.e.:

‘cif_dictionary’ returns a tuple of datablock_id and mmCIF data

(cif_id, cif_dictionary) = cfr.read("../../resources/dodgy.cif", output='cif_dictionary')

‘cif_wrapper’ returns a CIFWrapper object that encapsulates mmCIF-like dictionaries for python ‘dot’ notation data access
```
cif_wrapper = cfr.read("../../resources/dodgy.cif", output='cif_wrapper')
```
‘cif_file’ returns a CifFile object that fully encapsulates all components of mmCIF files
```
 cif_file = cfr.read("../../resources/dodgy.cif", output='cif_file')
```

NB: if ‘input’ is set as ‘dictionary’ when instantiating CifFileReader, ‘output’ will have no effect

CifFileWriter¶

CifFileWriter accepts mmCIF-like dictionaries, CIFWrapper objects, and CifFile objects to write. Files can be compressed while writing using the compress=True flag.

Examples continued from above:

cfd = mmcif.CifFileWriter("../../resources/cif_dictionary_test.cif")
cfd.write(cif_dictionary)
cfw = mmcif.CifFileWriter("../../resources/cif_wrapper_test.cif")
cfw.write(cif_wrapper)
cff = mmcif.CifFileWriter("../../resources/cif_file_test.cif")
cff.write(cif_file)

MMCIF2Dict¶

A very low level access to mmCIF data files. MMCIF2Dict has one method parse() that returns (datablock_id, mmCIF_data) tuples as (str, dict)

MMCIF2Dict is very fast at reading mmCIF data.

from pdbecif.mmcif_tools import MMCIF2Dict

>>> obj = MMCIF2Dict().parse('1tqn_updated.cif')
>>> print(obj)

Resulting structure is a plain python dictionary with mmCIF category names organized as keys. Value to that key is another python dictionary with mmCIF fields being keys and value is either a string (provided there is just a single value) or an array if _loop element was present and there are multiple values to a given field.

Category examples¶

Category with a single value per field¶

{
    "1TQN": {
        "_entry": {
            "id": "1TQN"
        },
        "_symmetry": {
            "entry_id": "1TQN",
            "space_group_name_H-M": "I 2 2 2",
            "pdbx_full_space_group_name_H-M": "?",
            "cell_setting": "?",
            "Int_Tables_number": "23",
            "space_group_name_Hall": "?"
        }
}

Multivalue category per field¶

{
        "_entity": {
            "id": ["1", "2", "3"],
            "type": ["polymer", "non-polymer", "water"],
            "src_method": ["man", "syn", "nat"],
            "pdbx_description": ["cytochrome P450 3A4", "PROTOPORPHYRIN IX CONTAINING FE", "water"],
            "formula_weight": ["55594.637", "616.487", "18.015"],
            "pdbx_number_of_molecules": ["1", "1", "190"],
            "pdbx_ec": ["1.14.14.1", "?", "?"],
            "pdbx_mutation": ["?", "?", "?"],
            "pdbx_fragment": ["?", "?", "?"],
            "details": ["?", "?", "?"]
        }
}