CPDB
Cython implementation of PDB -> DataFrame parsing
Installation
pip install cpdb-proteinUsage
To Dictionary
# To dictionary
from cpdb import parse
# From Disk
data = parse("path_to_pdb.pdb", df=False)
data = parse("path_to_pdb.pdb.gz", df=False)
# From str
with open("tests/test_data/1htq.pdb") as f:
pdb_file = f.readlines()
data = parse(pdb_str=pdb_file, df=False)
# From PDB
data = parse(pdb_code="3eiy", df=False)
# From AF2
data = parse(uniprot_id="Q8W3K0", df=False){'record_name': array(['ATOM', 'ATOM', 'ATOM', ..., 'HETATM', 'HETATM', 'HETATM'],
dtype=object), 'atom_number': array([ 1, 2, 3, ..., 1773, 1774, 1775], dtype=int32), 'atom_name': array(['N', 'CA', 'C', ..., 'O', 'O', 'O'], dtype=object), 'alt_loc': array(['', '', '', ..., '', '', ''], dtype=object), 'residue_name': array(['GLY', 'GLY', 'GLY', ..., 'HOH', 'HOH', 'HOH'], dtype=object), 'chain_id': array(['A', 'A', 'A', ..., 'A', 'A', 'A'], dtype=object), 'residue_number': array([ 30, 30, 30, ..., 2276, 2277, 2278], dtype=int32), 'insertion': array(['', '', '', ..., '', '', ''], dtype=object), 'x_coord': array([31.203, 32.02 , 33.358, ..., 44.665, 41.786, 38.498], dtype=float32), 'y_coord': array([26.31 , 27.046, 26.387, ..., 13.172, 10.059, 12.491], dtype=float32), 'z_coord': array([ 6.06 , 5.069, 4.79 , ..., 18.445, 22.316, 15.004], dtype=float32), 'occupancy': array([0.5, 0.5, 0.5, ..., 1. , 1. , 1. ], dtype=float32), 'b_factor': array([26.27, 29.29, 30.21, ..., 24.67, 34.64, 41.14], dtype=float32), 'element_symbol': array(['N', 'C', 'C', ..., 'O', 'O', 'O'], dtype=object), 'charge': array(['', '', '', ..., '', '', ''], dtype=object), 'model_idx': array([1, 1, 1, ..., 1, 1, 1], dtype=int32)}
To Pandas DataFrame
from cpdb import parse
# From Disk
data = parse("path_to_pdb.pdb", df=True)
data = parse("path_to_pdb.pdb.gz", df=True)
# From str
with open("tests/test_data/1htq.pdb") as f:
pdb_file = f.readlines()
data = parse(pdb_str=pdb_file, df=True)
# From PDB
data = parse(pdb_code="3eiy", df=True)
# From AF2
data = parse(uniprot_id="Q8W3K0", df=True) record_name atom_number atom_name alt_loc residue_name chain_id residue_number insertion x_coord y_coord z_coord occupancy b_factor element_symbol charge model_idx
0 ATOM 1 N GLY A 30 31.202999 26.309999 6.060000 0.50 26.270000 N 1
1 ATOM 2 CA GLY A 30 32.020000 27.046000 5.069000 0.50 29.290001 C 1
2 ATOM 3 C GLY A 30 33.358002 26.386999 4.790000 0.50 30.209999 C 1
3 ATOM 4 O GLY A 30 33.810001 25.535999 5.552000 0.50 29.299999 O 1
4 ATOM 5 N GLY A 31 33.987000 26.789000 3.684000 0.50 31.889999 N 1
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
1769 HETATM 1771 O HOH A 2274 42.688999 61.925999 29.589001 1.00 39.950001 O 1
1770 HETATM 1772 O HOH A 2275 32.055000 62.648998 30.961000 0.66 15.680000 O 1
1771 HETATM 1773 O HOH A 2276 44.665001 13.172000 18.445000 1.00 24.670000 O 1
1772 HETATM 1774 O HOH A 2277 41.785999 10.059000 22.316000 1.00 34.639999 O 1
1773 HETATM 1775 O HOH A 2278 38.498001 12.491000 15.004000 1.00 41.139999 O 1
