Run workflow using API¶

In [1]:

from pathlib import Path

from rich import print as pprint

from pathlib import Path from rich import print as pprint

In [2]:

import logging

logging.basicConfig(level=logging.WARNING)
# Set to WARNING to see only warnings
# Set to INFO to see sparql queries
# Set to DEBUG to see raw results

import logging logging.basicConfig(level=logging.WARNING) # Set to WARNING to see only warnings # Set to INFO to see sparql queries # Set to DEBUG to see raw results

Setup session directory¶

In this directory files like PDB files are stored and a DuckDB database for meta data.

In [3]:

session_dir = Path("session1")
session_dir

session_dir = Path("session1") session_dir

Out[3]:

PosixPath('session1')

Search Uniprot for structures¶

In [4]:

from protein_detective.uniprot import Query
from protein_detective.workflow import search_structures_in_uniprot

from protein_detective.uniprot import Query from protein_detective.workflow import search_structures_in_uniprot

In [5]:

query = Query(
    taxon_id="9606",
    reviewed=True,
    subcellular_location_uniprot="nucleus",
    subcellular_location_go="GO:0005634",  # Cellular component - Nucleus
    molecular_function_go="GO:0003677",  # Molecular function - DNA binding
)

query = Query( taxon_id="9606", reviewed=True, subcellular_location_uniprot="nucleus", subcellular_location_go="GO:0005634", # Cellular component - Nucleus molecular_function_go="GO:0003677", # Molecular function - DNA binding )

In [6]:

nr_uniprot, nr_pdbe, nr_af = search_structures_in_uniprot(query, session_dir, limit=80)
nr_uniprot, nr_pdbe, nr_af

nr_uniprot, nr_pdbe, nr_af = search_structures_in_uniprot(query, session_dir, limit=80) nr_uniprot, nr_pdbe, nr_af

WARNING:protein_detective.uniprot:Search for uniprot accessions returned 80 results. There may be more results available, but they are not returned due to the limit of 80. Consider increasing the limit to get more results.

Out[6]:

(71, 14, 71)

Use database queries to see what was found.

Fetch structures from PDBe and Alphafold found in Uniprot¶

In [7]:

from protein_detective.workflow import retrieve_structures

from protein_detective.workflow import retrieve_structures

In [8]:

download_path, nr_pdbs, nr_alphafolds = retrieve_structures(session_dir)
download_path, nr_pdbs, nr_alphafolds

download_path, nr_pdbs, nr_alphafolds = retrieve_structures(session_dir) download_path, nr_pdbs, nr_alphafolds

Downloading PDBe mmCIF files: 100%|██████████| 14/14 [00:00<00:00, 14.65it/s]
Fetching Alphafold summaries: 100%|██████████| 71/71 [00:02<00:00, 30.69it/s]
Downloading AlphaFold files: 100%|██████████| 71/71 [00:00<00:00, 153.18it/s]

Out[8]:

(PosixPath('session1/downloads'), 14, 71)

Filter out AlphafoldDB structures with low confidence¶

And write PDB files without those low confidence residues to new directory.

In [9]:

from protein_detective.alphafold.density import DensityFilterQuery
from protein_detective.workflow import density_filter

from protein_detective.alphafold.density import DensityFilterQuery from protein_detective.workflow import density_filter

In [10]:

dquery = DensityFilterQuery(
    confidence=70.0,
    min_threshold=100,
    max_threshold=500,
)

dquery = DensityFilterQuery( confidence=70.0, min_threshold=100, max_threshold=500, )

In [11]:

result = density_filter(session_dir, dquery)
pprint(result)

result = density_filter(session_dir, dquery) pprint(result)

DensityFilterSessionResult(
    density_filtered_dir=PosixPath('session1/density_filtered'),
    nr_kept=32,
    nr_discarded=39
)

Prune PDBe files¶

Prune the PDB files to only keep the first chain of the found Uniprot entries and rename that chain to A.

In [12]:

from protein_detective.workflow import prune_pdbs

from protein_detective.workflow import prune_pdbs

In [13]:

(single_chain_dir, nr_passed) = prune_pdbs(session_dir)
(single_chain_dir, nr_passed)

(single_chain_dir, nr_passed) = prune_pdbs(session_dir) (single_chain_dir, nr_passed)

Saving single chain PDB files from PDBe: 100%|██████████| 14/14 [00:03<00:00,  3.95it/s]

Out[13]:

(PosixPath('session1/single_chain'), 14)

Powerfit¶

In [ ]:

from protein_detective.powerfit.options import PowerfitOptions
from protein_detective.powerfit.workflow import powerfit_commands

from protein_detective.powerfit.options import PowerfitOptions from protein_detective.powerfit.workflow import powerfit_commands

To run you must have cloned the https://github.com/haddocking/powerfit-tutorial repository in '../../powerfit-tutorial'.

In [15]:

options = PowerfitOptions(
    target=Path("../../powerfit-tutorial/ribosome-KsgA.map"),
    resolution=13,
    angle=20,
    laplace=True,
)

options = PowerfitOptions( target=Path("../../powerfit-tutorial/ribosome-KsgA.map"), resolution=13, angle=20, laplace=True, )

Run¶

Here we use printed commands to run powerfit, see powerfit.ipynb for running powerfits using the API.

In [16]:

commands, powerfit_run_id = powerfit_commands(session_dir, options)

commands, powerfit_run_id = powerfit_commands(session_dir, options)

In [17]:

powerfit_run_id

powerfit_run_id

Out[17]:

1

In [18]:

cwd = str(Path.cwd())
rel_commands = [c.replace(cwd, ".") for c in commands]
pprint(rel_commands)

cwd = str(Path.cwd()) rel_commands = [c.replace(cwd, ".") for c in commands] pprint(rel_commands)

[
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/single_chain/A8MT69_4dra_E2A.pdb --laplace 
--resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/A8MT69_4dra_E2A --delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/single_chain/A8MT69_4ne6_B2A.pdb --laplace 
--resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/A8MT69_4ne6_B2A --delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/single_chain/A8MT69_4ne3_B2A.pdb --laplace 
--resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/A8MT69_4ne3_B2A --delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/single_chain/A8MT69_7xhn_X2A.pdb --laplace 
--resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/A8MT69_7xhn_X2A --delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/single_chain/A8MT69_4drb_J2A.pdb --laplace 
--resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/A8MT69_4drb_J2A --delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/single_chain/A8MT69_7r5s_X2A.pdb --laplace 
--resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/A8MT69_7r5s_X2A --delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/single_chain/A8MT69_7xho_X2A.pdb --laplace 
--resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/A8MT69_7xho_X2A --delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/single_chain/A8MT69_4ne1_B2A.pdb --laplace 
--resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/A8MT69_4ne1_B2A --delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/single_chain/A8MT69_4ne5_B2A.pdb --laplace 
--resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/A8MT69_4ne5_B2A --delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/single_chain/A8MT69_7ywx_X2A.pdb --laplace 
--resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/A8MT69_7ywx_X2A --delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/single_chain/A8MT69_4ndy_B2A.pdb --laplace 
--resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/A8MT69_4ndy_B2A --delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/single_chain/A8MT69_4e44_B2A.pdb --laplace 
--resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/A8MT69_4e44_B2A --delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/single_chain/A8MT69_4e45_B2A.pdb --laplace 
--resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/A8MT69_4e45_B2A --delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/single_chain/A9YTQ3_5y7y_A2A.pdb --laplace 
--resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/A9YTQ3_5y7y_A2A --delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A0A087WUV0-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A0A087WUV0-F1-model_v4 
--delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A0A0U1RQI7-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A0A0U1RQI7-F1-model_v4 
--delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A0A1B0GTS1-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A0A1B0GTS1-F1-model_v4 
--delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A0A1B0GWH4-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A0A1B0GWH4-F1-model_v4 
--delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A0A1W2PPF3-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A0A1W2PPF3-F1-model_v4 
--delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A0A1W2PQL4-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A0A1W2PQL4-F1-model_v4 
--delimiter , --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A1YPR0-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A1YPR0-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A2RRD8-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A2RRD8-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A6NDX5-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A6NDX5-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A6NFD8-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A6NFD8-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A6NFI3-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A6NFI3-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A6NGD5-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A6NGD5-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A6NHJ4-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A6NHJ4-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A6NJL1-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A6NJL1-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A6NJT0-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A6NJT0-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A6NK53-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A6NK53-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A6NK75-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A6NK75-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A6NKF2-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A6NKF2-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A6NLW8-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A6NLW8-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A6NM28-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A6NM28-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A6NP11-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A6NP11-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A8K0S8-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A8K0S8-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A8K8V0-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A8K8V0-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A8MT65-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A8MT65-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A8MTY0-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A8MTY0-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A8MUV8-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A8MUV8-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A8MUZ8-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A8MUZ8-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A8MWA4-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A8MWA4-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-A9YTQ3-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-A9YTQ3-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-B2RPK0-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-B2RPK0-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-B4DU55-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-B4DU55-F1-model_v4 --delimiter
, --angle 20',
    'powerfit ./session1/powerfit/1/ribosome-KsgA.map 13 ./session1/density_filtered/AF-B4DX44-F1-model_v4.pdb 
--laplace --resampling-rate 2 --num 0 --nproc 1 --directory ./session1/powerfit/1/AF-B4DX44-F1-model_v4 --delimiter
, --angle 20'
]

These commands should be run on a cluster. Here we will just run a couple of them to show how it works.

In [19]:

!{rel_commands[6]}

!{rel_commands[6]}

Target file read from:                                                          
/home/stefanv/git/protein-detective/protein-detective/docs/session1/powerfit/1/r
ibosome-KsgA.map                                                                
Target resolution: 13.00                                                        
Initial shape of density: 128 128 128                                           
Shape after trimming: 60 73 67                                                  
Shape after extending: 60 75 70                                                 
Template file read from:                                                        
/home/stefanv/git/protein-detective/protein-detective/docs/session1/single_chain
/A8MT69_7xho_X2A.pdb                                                            
Reading in rotations.                                                           
Requested rotational sampling density: 20.00                                    
Real rotational sampling density: 20.83                                         
Requested number of processors: 1                                               
Starting search                                                                 
Processing rotations 100% ━━━━━━━━━━━╸ 647/648  [ 0:00:08 < 0:00:01 , 73 rot/s ]t/s ]
Time for search: 0m 10s                                                         
Analyzing results                                                               
Writing solutions to file.                                                      
Writing PDBs to file.                                                           
Total time: 0m 10s                                                              

In [20]:

!{rel_commands[0]}

!{rel_commands[0]}

Target file read from:                                                          
/home/stefanv/git/protein-detective/protein-detective/docs/session1/powerfit/1/r
ibosome-KsgA.map                                                                
Target resolution: 13.00                                                        
Initial shape of density: 128 128 128                                           
Shape after trimming: 60 73 67                                                  
Shape after extending: 60 75 70                                                 
Template file read from:                                                        
/home/stefanv/git/protein-detective/protein-detective/docs/session1/single_chain
/A8MT69_4dra_E2A.pdb                                                            
Reading in rotations.                                                           
Requested rotational sampling density: 20.00                                    
Real rotational sampling density: 20.83                                         
Requested number of processors: 1                                               
Starting search                                                                 
Processing rotations 100% ━━━━━━━━━━━╸ 647/648  [ 0:00:09 < 0:00:01 , 71 rot/s ]t/s ]
Time for search: 0m 9s                                                          
Analyzing results                                                               
Writing solutions to file.                                                      
Writing PDBs to file.                                                           
Total time: 0m 9s                                                               

In [21]:

!{rel_commands[-1]}

!{rel_commands[-1]}

Target file read from:                                                          
/home/stefanv/git/protein-detective/protein-detective/docs/session1/powerfit/1/r
ibosome-KsgA.map                                                                
Target resolution: 13.00                                                        
Initial shape of density: 128 128 128                                           
Shape after trimming: 60 73 67                                                  
Shape after extending: 60 75 70                                                 
Template file read from:                                                        
/home/stefanv/git/protein-detective/protein-detective/docs/session1/density_filt
ered/AF-B4DX44-F1-model_v4.pdb                                                  
Reading in rotations.                                                           
Requested rotational sampling density: 20.00                                    
Real rotational sampling density: 20.83                                         
Requested number of processors: 1                                               
Starting search                                                                 
Processing rotations 100% ━━━━━━━━━━━╸ 647/648  [ 0:00:09 < 0:00:01 , 69 rot/s ]t/s ]
Time for search: 0m 9s                                                          
Analyzing results                                                               
Writing solutions to file.                                                      
Writing PDBs to file.                                                           
Total time: 0m 10s                                                              

See powerfit.ipynb for running all powerfits using the API.

Report¶

Once all powerfit jobs are done the results can be parsed and reported.

In [ ]:

from protein_detective.powerfit.workflow import powerfit_report

from protein_detective.powerfit.workflow import powerfit_report

In [5]:

solutions = powerfit_report(session_dir)

solutions = powerfit_report(session_dir)

In [6]:

len(solutions)

len(solutions)

Out[6]:

62757

In [7]:

solutions

solutions

Out[7]:

	powerfit_run_id	structure	rank	cc	fishz	relz	translation	rotation	density_filter_id	af_id	pdb_id	pdb_file	uniprot_acc
0	1	A8MT69_4ne6_B2A	1	0.456	0.492	11.071	[227.18, 242.53, 211.83]	[0.0, -0.0, -1.0, 0.604, -0.797, 0.0, -0.797, ...	<NA>	None	4NE6	session1/single_chain/A8MT69_4ne6_B2A.pdb	A8MT69
1	1	A8MT69_4drb_J2A	1	0.444	0.477	10.588	[227.18, 242.53, 214.9]	[0.797, -0.604, 0.0, 0.604, 0.797, 0.0, 0.0, 0...	<NA>	None	4DRB	session1/single_chain/A8MT69_4drb_J2A.pdb	A8MT69
2	1	A8MT69_4dra_E2A	1	0.443	0.476	10.402	[214.9, 187.27, 214.9]	[1.0, -0.0, 0.0, 0.0, -0.0, 1.0, -0.0, -1.0, -...	<NA>	None	4DRA	session1/single_chain/A8MT69_4dra_E2A.pdb	A8MT69
3	1	A8MT69_4e44_B2A	1	0.440	0.472	10.099	[224.11, 236.39, 227.18]	[1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0]	<NA>	None	4E44	session1/single_chain/A8MT69_4e44_B2A.pdb	A8MT69
4	1	A8MT69_7xhn_X2A	1	0.439	0.471	10.136	[230.25, 242.53, 217.97]	[-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0]	<NA>	None	7XHN	session1/single_chain/A8MT69_7xhn_X2A.pdb	A8MT69
...	...	...	...	...	...	...	...	...	...	...	...	...	...
62752	1	AF-A8MTY0-F1-model_v4	1463	0.095	0.095	5.424	[168.85, 202.62, 236.39]	[0.0, 1.0, 0.0, 0.797, 0.0, -0.604, -0.604, 0....	1	A8MTY0	None	session1/density_filtered/AF-A8MTY0-F1-model_v...	A8MTY0
62753	1	AF-A8MTY0-F1-model_v4	1462	0.095	0.095	5.425	[122.8, 174.99, 147.36]	[0.797, 0.604, 0.0, 0.604, -0.797, 0.0, 0.0, 0...	1	A8MTY0	None	session1/density_filtered/AF-A8MTY0-F1-model_v...	A8MTY0
62754	1	AF-A8MTY0-F1-model_v4	1461	0.095	0.095	5.429	[150.43, 211.83, 104.38]	[0.548, 0.548, 0.632, 0.184, -0.816, 0.548, 0....	1	A8MTY0	None	session1/density_filtered/AF-A8MTY0-F1-model_v...	A8MTY0
62755	1	AF-A8MTY0-F1-model_v4	1460	0.095	0.096	5.437	[224.11, 282.44, 150.43]	[0.0, 0.797, 0.604, -1.0, 0.0, -0.0, 0.0, -0.6...	1	A8MTY0	None	session1/density_filtered/AF-A8MTY0-F1-model_v...	A8MTY0
62756	1	AF-A8MTY0-F1-model_v4	1459	0.095	0.096	5.445	[196.48, 196.48, 273.23]	[0.548, 0.548, 0.632, 0.184, -0.816, 0.548, 0....	1	A8MTY0	None	session1/density_filtered/AF-A8MTY0-F1-model_v...	A8MTY0

62757 rows × 13 columns

Fit model to solution¶

Rotate/translate the input model PDB files to the top 5 powerfit solutions.

In [ ]:

from protein_detective.powerfit.workflow import powerfit_fit_models

from protein_detective.powerfit.workflow import powerfit_fit_models

In [6]:

fitted = powerfit_fit_models(session_dir, top=5)
fitted

fitted = powerfit_fit_models(session_dir, top=5) fitted

Writing fitted model PDB files: 100%|██████████| 5/5 [00:00<00:00, 351.19it/s]

Out[6]:

	powerfit_run_id	structure	rank	fitted_model_file	unfitted_model_file
index
0	1	A8MT69_4ne6_B2A	1	session1/powerfit/1/A8MT69_4ne6_B2A/fit_1.pdb	session1/single_chain/A8MT69_4ne6_B2A.pdb
1	1	A8MT69_4drb_J2A	1	session1/powerfit/1/A8MT69_4drb_J2A/fit_1.pdb	session1/single_chain/A8MT69_4drb_J2A.pdb
2	1	A8MT69_4dra_E2A	1	session1/powerfit/1/A8MT69_4dra_E2A/fit_1.pdb	session1/single_chain/A8MT69_4dra_E2A.pdb
3	1	A8MT69_4e44_B2A	1	session1/powerfit/1/A8MT69_4e44_B2A/fit_1.pdb	session1/single_chain/A8MT69_4e44_B2A.pdb
4	1	A8MT69_7xhn_X2A	1	session1/powerfit/1/A8MT69_7xhn_X2A/fit_1.pdb	session1/single_chain/A8MT69_7xhn_X2A.pdb

In [ ]: