mmcif: mmCIF input/output

mmcif: mmCIF format support

Read mmCIF files.

class MMCIFTable(table_name, tags=None, data=None)

Bases: object

Present a table interface for a mmCIF category

Tags should be in the mixed case version given in the associated dictionary

extend(table)

Experimental API . Extend mmCIF table

Parameters:
table : MMCIFTable to add on to current table
If a column with a given tag exists, then that column is extended.
Otherwise, a new column is added to the table.
field_has(field_name, value)

Experimental API . Return if given field has the given value

fields(field_names, *, allow_missing_fields=False, missing_value='')

Experimental API . Return subset of rows of the table for the given fields

Parameters:
field_names : a sequence of the field names
allow_missing_fields : optional boolean (default False)
missing_value : optional missing_value object (default ‘’)
A list of tuples is return where each tuple’s items are the values
corresponding to the given field names in the given order. If
missing fields are allowed, then the corresponding items are the
missing_value object.
has_field(field_name)

Experimental API . Return if given field name is in the table

mapping(key_names, value_names, foreach_names=None)

Experimental API . Return a dictionary for subset of the table

Parameters:
key_names : a field name or list of field names
value_names : a field name or list of field names
foreach_names : optional field name or list of field names
If foreach_names is not given, then the resulting dictionary is whose
keys are the values of the key field(s) and the values are the values
of the value field(s). If foreach_names is given, then the result is
a dicttionary of dictionaries, with the nested dictionaries as above,
and the outer dictionary’s keys are the values of the foreach fields.
num_rows()

Experimental API . Return number of rows in table

print(file=None, *, fixed_width=False)

Experimental API . Print contents of table to given file

citations(model, only=None)

Experimental API . Return APA-style HTML citations for model

Parameters:
model : instance of a AtomicStructure

The model.

get_mmcif_tables(filename, table_names)

Experimental API . Extract mmCIF tables from a file

Parameters:
filename : str

The name of the file.

table_names : list of str

A list of mmCIF category names.

get_mmcif_tables_from_metadata(model, table_names)

Experimental API . Extract mmCIF tables from previously read metadata

Parameters:
model : instance of a AtomicStructure

The model.

table_names : list of str

A list of mmCIF category names.

quote(s)

Experimental API . Return CIF 1.1 data value version of string