Reading files
*************

There are two types of files we typically work with, models and maps.  TEMPy loads these files using parsing functions.

Reading models
--------------
To read a PDB file, use the PDBParser.

.. doctest::
   :options: -ELLIPSIS, +NORMALIZE_WHITESPACE

   >>> from TEMPy.protein.structure_parser import PDBParser
   >>> model = PDBParser.read_PDB_file("", "../tests/test_data/1CS4.pdb")
   >>> model
   Gemmi_Structure: 1CS4 
   , Filename: ../tests/test_data/1CS4.pdb
   No Of Atoms: 5647
   First Atom: (MET 377 A: 28.568, -27.770, 32.255)
   Last Atom: (LEU 388 C: 16.116, -21.409, 27.123)

To read a mmCIF file, use the mmCIFParser.

.. doctest::
   :options: -ELLIPSIS, +NORMALIZE_WHITESPACE

   >>> from TEMPy.protein.structure_parser import mmCIFParser
   >>> model = mmCIFParser.read_mmCIF_file("../tests/test_data/1CS4.cif")
   >>> model
   Gemmi_Structure: 1CS4 
   , Filename: ../tests/test_data/1CS4.cif
   No Of Atoms: 5647
   First Atom: (MET 377 A: 28.568, -27.770, 32.255)
   Last Atom: (LEU 388 C: 16.116, -21.409, 27.123)

Operations on models
--------------------

To get a list of chains:

.. doctest::

   >>> from TEMPy.protein.structure_parser import mmCIFParser
   >>> model = mmCIFParser.read_mmCIF_file("../tests/test_data/1CS4.cif")
   >>> model.get_chain_list()
   ['A', 'B', 'C']


To get a particular chain, use the `get_chain` method. This will return
a new structure.

.. doctest::
   :options: -ELLIPSIS, +NORMALIZE_WHITESPACE

   >>> from TEMPy.protein.structure_parser import mmCIFParser
   >>> model = mmCIFParser.read_mmCIF_file("../tests/test_data/1CS4.cif")
   >>> model.get_chain('A')
   Gemmi_Structure: 1CS4chainA 
   No Of Atoms: 1476
   First Atom: (MET 377 A: 28.568, -27.770, 32.255)
   Last Atom: (LEU 565 A: 45.328, -2.249, 79.025)


Often, we only want to work with backbone atoms. This can be a useful for example
at low resolutions.

.. doctest::
   :options: -ELLIPSIS, +NORMALIZE_WHITESPACE

   >>> from TEMPy.protein.structure_parser import mmCIFParser
   >>> model = mmCIFParser.read_mmCIF_file("../tests/test_data/1CS4.cif")
   >>> model.get_backbone()
   No Of Atoms: 2124
   First Atom: (MET 377 A: 28.568, -27.770, 32.255)
   Last Atom: (LEU 388 C: 13.015, -22.394, 30.319)
   <BLANKLINE>

For more information about the methods available, consult the API reference: Link

Reading maps
------------

.. doctest::

   >>> from TEMPy.maps.map_parser import MapParser
   >>> map = MapParser.readMRC("../tests/test_data/1CS4.mrc")
   >>> map
   Obtained from ../tests/test_data/1CS4.mrc
   Origin: [-18.572 -51.218 -21.575]
   Box size (x,y,z): [32, 31, 35]
   Grid spacing: [3.500 3.500 3.500]
   Min, max, mean, std: 0.000, 0.630, 0.026, 0.087
   <BLANKLINE>
   

You can get information about the dimensions of the box in voxels:

.. doctest::

   >>> from TEMPy.maps.map_parser import MapParser
   >>> map = MapParser.readMRC("../tests/test_data/1CS4.mrc")
   >>> map.box_size()
   (35, 31, 32)


Or the size of each voxel in units of Angstroms:

.. doctest::

   >>> from TEMPy.maps.map_parser import MapParser
   >>> map = MapParser.readMRC("../tests/test_data/1CS4.mrc")
   >>> map.apix
   array([3.5, 3.5, 3.5], dtype=float32)

For more information about the methods available, consult the API reference: Link