%load_ext autoreload
%autoreload 2
import requests
import io
from pymolint import mol_int
# import numpy as np
# import sys
from pytexshade import ipyshade
# from seqplot.p9tools import
import MDAnalysis as mda
from seqplot.pdb_plot import plot_prof4pdb
The autoreload extension is already loaded. To reload it, use: %reload_ext autoreload
h=io.StringIO(requests.get('https://files.rcsb.org/download/1KX5.pdb').content.decode("utf-8") )
struct=mda.Universe(h,format='PDB')
/opt/miniconda3/envs/moldyn/lib/python3.7/site-packages/MDAnalysis/topology/guessers.py:80: UserWarning: Failed to guess the mass for the following atom types: MN warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
d=mol_int.struct2cont(struct,'segid B and protein','nucleic')
0it [00:00, ?it/s]
df=d.get_df()
df
A_atom_id | A_atom_name | A_resname | A_segid | A_resid | B_atom_id | B_atom_name | B_resname | B_segid | B_resid | dist | Time | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | 7365 | NH1 | ARG | B | 36 | 1223 | P | DA | I | -13 | 3.688779 | 0 |
1 | 7364 | CZ | ARG | B | 36 | 1224 | OP1 | DA | I | -13 | 3.517523 | 0 |
2 | 7365 | NH1 | ARG | B | 36 | 1224 | OP1 | DA | I | -13 | 3.285111 | 0 |
3 | 7366 | NH2 | ARG | B | 36 | 1224 | OP1 | DA | I | -13 | 2.872054 | 0 |
4 | 7329 | CB | PRO | B | 32 | 1225 | OP2 | DA | I | -13 | 3.450700 | 0 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
130 | 7706 | N | LYS | B | 79 | 5080 | OP2 | DC | J | 28 | 3.583109 | 0 |
131 | 7700 | CG | ARG | B | 78 | 5081 | O5' | DC | J | 28 | 3.665597 | 0 |
132 | 7701 | CD | ARG | B | 78 | 5081 | O5' | DC | J | 28 | 3.722939 | 0 |
133 | 7719 | CB | THR | B | 80 | 5082 | C5' | DC | J | 28 | 3.744557 | 0 |
134 | 7720 | OG1 | THR | B | 80 | 5082 | C5' | DC | J | 28 | 3.508114 | 0 |
135 rows × 12 columns
dp=d.get_num_int_profile()
dp
segid | resid | num_int | |
---|---|---|---|
0 | B | 5 | 7.0 |
1 | B | 6 | 2.0 |
2 | B | 8 | 4.0 |
3 | B | 9 | 3.0 |
4 | B | 10 | 1.0 |
5 | B | 14 | 1.0 |
6 | B | 15 | 1.0 |
7 | B | 16 | 9.0 |
8 | B | 17 | 17.0 |
9 | B | 18 | 3.0 |
10 | B | 19 | 17.0 |
11 | B | 30 | 3.0 |
12 | B | 32 | 5.0 |
13 | B | 35 | 1.0 |
14 | B | 36 | 5.0 |
15 | B | 45 | 14.0 |
16 | B | 46 | 8.0 |
17 | B | 47 | 3.0 |
18 | B | 48 | 4.0 |
19 | B | 78 | 6.0 |
20 | B | 79 | 13.0 |
21 | B | 80 | 8.0 |
%%time
import warnings
warnings.filterwarnings('ignore')
plot_prof4pdb(pdb_chain_id='1KX5_B',column='num_int',data=dp,ymin=0,feature_types=['SecStr'])
Starting resid 1 CPU times: user 8.93 s, sys: 101 ms, total: 9.03 s Wall time: 15.9 s
<ggplot: (8774699024227)>
%%time
import warnings
warnings.filterwarnings('ignore')
h=io.StringIO(requests.get('https://files.rcsb.org/download/1ZLA.pdb').content.decode("utf-8") )
dp=struct_int.struct2cont(h,'segid K and protein',format='pdb').get_num_int_profile()
plot_prof4pdb(pdb_chain_id='1ZLA_K',column='num_int',data=dp,ymin=0,feature_types=['SecStr'],aspect_ratio=0.3)
Exception ignored in: <function ReaderBase.__del__ at 0x7f29ee8661e0> Traceback (most recent call last): File "/opt/miniconda3/envs/moldyn/lib/python3.7/site-packages/MDAnalysis/coordinates/base.py", line 2106, in __del__ self.close() File "/opt/miniconda3/envs/moldyn/lib/python3.7/site-packages/MDAnalysis/coordinates/PDB.py", line 424, in close self._pdbfile.close() File "/opt/miniconda3/envs/moldyn/lib/python3.7/site-packages/MDAnalysis/lib/util.py", line 736, in close self.flush() File "/opt/miniconda3/envs/moldyn/lib/python3.7/site-packages/MDAnalysis/lib/util.py", line 842, in flush return self.stream.flush() ValueError: I/O operation on closed file.
CPU times: user 2.82 s, sys: 184 ms, total: 3 s Wall time: 8.16 s
<ggplot: (8738737358600)>