Protein Data Bank in Europe (PDBe; http://pdbe.org) mmCif/CIF/STAR parser and API
used to work with STAR, CIF, and mmCIF formatted files. The package contains modules for accessing mmCIF data in different ways depending on the type of task required.
Typical usage often looks like this:
from mmCif import *
from mmcifIO import mmcifIO##Reading from a file
cfr = mmcifIO.CifFileReader(input='dictionary')
cif_file = cfr.read(os.path.join(<your_path>, "usage-example.cif"), output='cif_file')
print "CifFile:", cif_file##Writing to a file
# create a file writer
cff = mmcifIO.CifFileWriter(os.path.join(<your_path>, "cif_output_test.cif"))
# write the file
cff.write(cif_file)##Using a CifFile object
Using the CifFile object to access, edit and update mmCIF data.
The following examples use a CifFile object with roughly the following structure.
Data are manipulated using the accessors and mutators provided:
NB: See the Test suite in mmCif.test for more examples
print "DataBlock ids:", cif_file.getDataBlockIds() #List all datablock ids
print "DataBlock objects:", cif_file.getDataBlocks() #List all datablock objects
data_block_1 = cif_file.getDataBlock("TEST_CIF") #Get a specific datablock
data_block_1 = cif_file.getDataBlocks()[0] #Get the first datablock
data_block_2 = cif_file.setDataBlock("BLOCK_2") # Create another empty datablock
data_block_3 = cif_file.setDataBlock("BLOCK_3") # Create another empty datablock
cif_file.removeChild(data_block_2) # Remove datablock (Method 1 - given object)
cif_file.removeChild("BLOCK_3") # Remove datablock (Method 2 - given ID)
print "RECYCLED DATABLOCKS:", cif_file.recycleBin # Removed objects are stored in a recycle binNB: Category and SaveFrame are handled in the same manner
data_block_1 = cif_file.getDataBlock("TEST_CIF") #Get a specific datablock
data_block_4 = cif_file.setDataBlock("BLOCK_4") # Create another empty datablock
data_block_5 = cif_file.setDataBlock("BLOCK_5") # Create another empty datablock
data_block_5.getId() # Get the datablock ID
data_block_5.updateId("BLOCK_5.1") # Change the datablock ID
print "Category ids:", data_block_1.getCategoryIds() #List all category ids
print "Category objects:", data_block_1.getCategories() #List all category objects
category_1 = data_block_1.getCategory("_test_keyword") #Get a specific category
category_2 = data_block_4.setCategory("CATEGORY_2") #Create an empty category
category_3 = data_block_4.setCategory("CATEGORY_3") #Create an empty category
data_block_4.removeChild(category_2) # Remove category (Method 1 - given object)
data_block_4.removeChild("CATEGORY_3") # Remove category (Method 2 - given ID)
data_block_5.remove() # Remove datablock from CifFile
print "RECYCLED CATEGORIES:", data_block_4.recycleBin # Removed objects are stored in a recycle bin category_1 = data_block_1.getCategory("_test_keyword") #Get a specific category
category_4 = data_block_4.setCategory("CATEGORY_4") # Create another empty category
category_5 = data_block_4.setCategory("CATEGORY_5") # Create another empty category
print "Item names:", category_1.getItemNames() #List all item names
print "Item objects:", category_1.getItems() #List all item objects
item_1 = category_1.getItem("field_1") #Get a specific item
item_2 = category_4.setItem("ITEM_2") #Create an empty item
item_3 = category_4.setItem("ITEM_3") #Create an empty item
category_4.removeChild(item_2) # Remove item (Method 1 - given object)
category_4.removeChild("ITEM_3") # Remove item (Method 2 - given ID)
category_5.remove() # Remove category from DataBlock
print "RECYCLED ITEMS:", category_4.recycleBin # Removed objects end up in the recycle bin item_1 = category_1.getItem("field_1") #Get a specific item
item_4 = category_4.setItem("ITEM_4") # Create another empty item
item_5 = category_4.setItem("ITEM_5") # Create another empty item
print "Value (raw):", item_1.getRawValue() #Get raw item value (Method 1 - using accessor)
print "Value (raw):", item_1.value #Get raw item value (Method 2 - using attribute)
print "Value (formated):", item_1.getFormattedValue() #Get the formated value (for file export)
item_4.setValue("VALUE_2") #Set the item value
item_5.setValue([9, 8, 7, 6, 5]) #Set the item value
item_5.remove() # Remove item from Category
print "RECYCLED ITEMS:", category_4.recycleBin # Removed objects end up in the recycle binFor every object the setXXXX() method always returns the this you are
trying to set. If no object is present it creates a new one and returns it.
setXXXX() can therefor be used as both accessor and mutator
cif_file.setDataBlock("BLOCK_6").setCategory("CATEGORY_6").setItem("ITEM_6").setValue("VALUE_6")