I want to make a plot with Matplotlib in Python and therefore read some data from a PDB-file (protein data bank). I want to extract every column from the file and store these columns in separate vectors. The PDB-file consists of columns with both text and floats. I'm very new to Matplotlib and I have tried several methods suggested to extract these columns, but nothing seem to work. What would be the best way to extract these columns? I'm going to load a lot of data in a later stage, so it's good if the method isn't too inefficient.
The PDB-files looks something like this:
ATOM 1 CA MET A 1 38.012 8.932 -1.253
ATOM 2 CA GLU A 2 39.809 5.652 -1.702
ATOM 3 CA ALA A 3 43.007 5.013 0.368
ATOM 4 CA ALA A 4 41.646 7.577 2.820
ATOM 5 CA HIS A 5 42.611 4.898 5.481
ATOM 6 CA SER A 6 46.191 5.923 5.090
ATOM 7 CA LYS A 7 45.664 9.815 5.134
ATOM 8 CA SER A 8 45.898 12.022 8.181
ATOM 9 CA THR A 9 42.528 13.075 9.570
ATOM 10 CA GLU A 10 43.330 16.633 8.378
ATOM 11 CA GLU A 11 44.171 15.729 4.757
ATOM 12 CA CYS A 12 40.589 14.150 4.745
ATOM 13 CA LEU A 13 38.984 17.314 6.105
ATOM 14 CA ALA A 14 40.633 19.053 3.220
ATOM 15 CA TYR A 15 39.740 16.682 0.505
ATOM 16 CA PHE A 16 36.138 17.421 1.566
ATOM 17 CA GLY A 17 36.536 20.854 2.826
ATOM 18 CA VAL A 18 34.184 20.012 5.553
ATOM 19 CA SER A 19 34.483 20.966 9.177
Going off of @Kyle_S-C's recommendation, here's a way to do it using Biopython.
First read your file into a Biopython Structure object:
import Bio.PDB
path = '/path/to/PDB/file' # your file path here
p = Bio.PDB.PDBParser()
structure = p.get_structure('myStructureName', path)
Then, for example, you can get a list of just the Atom ids like this:
ids = [a.get_id() for a in structure.get_atoms()]
See the Biopython Structural Bioinformatics FAQ for more, including the following methods for accessing the PDB columns for an Atom:
How do I extract information from an Atom object?
Using the following methods:
# a.get_name() # atom name (spaces stripped, e.g. 'CA') # a.get_id() # id (equals atom name) # a.get_coord() # atomic coordinates # a.get_vector() # atomic coordinates as Vector object # a.get_bfactor() # isotropic B factor # a.get_occupancy() # occupancy # a.get_altloc() # alternative location specifier # a.get_sigatm() # std. dev. of atomic parameters # a.get_siguij() # std. dev. of anisotropic B factor # a.get_anisou() # anisotropic B factor # a.get_fullname() # atom name (with spaces, e.g. '.CA.')