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Fix wrong description in README.md and a bug in the RMSD calc script. #14

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Fix wrong description in README.md and a bug in the RMSD calc script. #14

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5129b37
Fix README.md
eunos-1128 Jan 25, 2024
2f1f866
Fix a `NameError` bug
eunos-1128 Jan 25, 2024
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6 changes: 3 additions & 3 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# AF-Cluster

Code and data corresponding to Wayment-Steele*, Ojoawo*, ... Ovchinnikov, Colwell, Kern (2023) "Predicting multiple conformations via sequence clustering with AlphaFold2" *Nature*. [link](https://www.nature.com/articles/s41586-023-06832-9)
Code and data corresponding to Wayment-Steele*, Ojoawo*, ... Ovchinnikov, Colwell, Kern (2023) "Predicting multiple conformations via sequence clustering with AlphaFold2" *Nature*. [link](https://www.nature.com/articles/s41586-023-06832-9)

[original bioRxiv](https://www.biorxiv.org/content/10.1101/2022.10.17.512570v1)

Expand Down Expand Up @@ -50,7 +50,7 @@ To also perform PCA and/or tSNE embedding at the same time and save it in `EX_cl

`python scripts/ClusterMSA.py -i <my_alignment.a3m> -o <outdir> --run_PCA`

or
or

`python scripts/ClusterMSA.py -i <my_alignment.a3m> -o <outdir> --run_tSNE`

Expand Down Expand Up @@ -92,7 +92,7 @@ See https://github.com/jproney/AF2Rank for more information on compiling an Alph

### To calculate RMSD to provided reference structure(s):

`python scripts/CalculateModelFeatures.py path/to/pdbs/* -o <my_output_file>.json.zip --ref_struct REF_PDB_1.pdb REF_PDB_2.pdb`
`python scripts/CalculateModelFeatures.py path/to/pdbs/* -o <my_output_file>.json --ref_struct REF_PDB.pdb`

### To reproduce figures in preprint:

Expand Down
7 changes: 3 additions & 4 deletions scripts/CalculateModelFeatures.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ def calc_rmsd(decoy, ref_obj, debug=False):
string='name CA and ('+ ' or '.join("resid %d" % x for x in ref_atoms)+')'

if debug:

print(ref_seq)
print(decoy_seq)
if len(decoy.top.select(string)) != len(ref_obj.top.select(string)):
Expand Down Expand Up @@ -83,12 +83,12 @@ def calc_dssp(decoy):

if args.ref_struct is not None:
pdb_name = os.path.basename(args.ref_struct).replace('.pdb','')
ref_obj = md.load_pdb(args.ref_struct)
df['rmsd_ref'] = df.parallel_apply(lambda row: calc_rmsd(row['pdb'], ref_obj), axis=1)

ref_obj = md.load_pdb(args.ref_struct)
ref_dssp = calc_dssp(ref_obj)
df['dist_dssp'] = df.parallel_apply(lambda row: levenshtein(row['dssp_string'], ref_dssp), axis=1)

df.head()

if args.plot_results and args.ref_struct is not None:
Expand All @@ -115,4 +115,3 @@ def calc_dssp(decoy):

df.to_json(args.o)
print('Wrote to', args.o)