https://github.com/a-r-j/cpdb
Cython implementation of PDB -> DataFrame parsing
https://github.com/a-r-j/cpdb
bioinformatics deep-learning machine-learning pdb pdb-files pdb-parser protein protein-structure structural-biology
Last synced: 6 months ago
JSON representation
Cython implementation of PDB -> DataFrame parsing
- Host: GitHub
- URL: https://github.com/a-r-j/cpdb
- Owner: a-r-j
- License: mit
- Created: 2023-04-03T20:22:20.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2023-06-26T16:54:59.000Z (over 2 years ago)
- Last Synced: 2025-03-16T03:05:00.662Z (7 months ago)
- Topics: bioinformatics, deep-learning, machine-learning, pdb, pdb-files, pdb-parser, protein, protein-structure, structural-biology
- Language: Cython
- Homepage:
- Size: 18.7 MB
- Stars: 23
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://badge.fury.io/py/cpdb-protein)
[](https://opensource.org/licenses/MIT)
# CPDB
Cython implementation of PDB -> DataFrame parsing
## Installation
```bash
pip install cpdb-protein
```
## Usage
### To Dictionary
```python
# 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
```python
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
```