Set PDB predicted scores x 100

README.md

@@ -159,36 +159,36 @@ The CSV output files contains per-residue outputs, with the following column hea
 - PDB ID and chain name
 - Relative residue index (re-numbered from 1)
 - Amino-acid residue, 1-letter
-- DiscoTope-3.0 score
+- DiscoTope-3.0 score (theoretical range 0.00 - 1.00)
 - Relative surface accessibility (Shrake-Rupley, normalized using Sander scale)
-- AlphaFold pLDDT score (set to 100 for non-AlphaFold structures)
+- AlphaFold pLDDT score (0-100, set to 100 for non-AlphaFold structures)
 - Chain length
 - A binary feature set to 1 for AlphaFold structures.
 
 Example input:
 ```bash
 python src/predict_webserver.py \
---pdb_or_zip_file data/example_pdbs_solved/7lkh.pdb \
+--pdb_or_zip_file data/example_pdbs_solved/7c4s.pdb \
 --struc_type solved \
---out_dir output/7lkh
+--out_dir output/7c4s
 ```
 
-Example output CSV (see [output/7lkh/7lkh_A_discotope3.csv](./output/7lkh/7lkh_A_discotope3.csv)):
+Example output CSV (see [output/7c4s/7c4s_A_discotope3.csv](./output/7c4s/7c4s_A_discotope3.csv)):
 ```text
 pdb,res_id,residue,DiscoTope-3.0_score,rsa,pLDDTs,length,alphafold_struc_flag
-7lkh_A,53,G,0.04597,1.30833,100,286,0
-7lkh_A,54,P,0.05957,0.26530,100,286,0
-7lkh_A,55,V,0.05202,0.43499,100,286,0
+7c4s_A,14,G,0.15186,0.80634,100,282,0
+7c4s_A,15,Q,0.13953,0.45077,100,282,0
+7c4s_A,16,E,0.23955,0.72919,100,282,0
 ```
 
-The PDB output files contain individual single chains with the B-factor column replaced with per-residue DiscoTope-3.0 scores (2nd right-most column).
+The PDB output files contain individual single chains with the B-factor column replaced with per-residue DiscoTope-3.0 scores (2nd right-most column). Note that the scores are multiplied by 100 as PDB files only allow 2 decimals of precision.
 
-Example output PDB (see [output/7lkh/7lkh_A_discotope3.pdb](./output/7lkh/7lkh_A_discotope3.pdb)):
+Example output PDB (see [output/7c4s/7c4s_A_discotope3.pdb](./output/7c4s/7c4s_A_discotope3.pdb)):
 ```text
-ATOM 1 N GLY A  1  143.756 170.612 143.660 1.00  4.60 N 
-ATOM 2 CA GLY A  1  142.861 169.851 142.747 1.00  4.60 C 
-ATOM 3 C GLY A  1  143.525 169.536 141.422 1.00  4.60 C 
-ATOM 4 O GLY A  1  144.482 170.199 141.027 1.00  4.60 O 
+ATOM 1 N GLY A 14  -16.773 -32.069 23.105 1.00 15.19 N 
+ATOM 2 CA GLY A 14  -15.595 -32.029 23.955 1.00 15.19 C 
+ATOM 3 C GLY A 14  -14.287 -31.844 23.204 1.00 15.19 C 
+ATOM 4 O GLY A 14  -13.284 -32.465 23.555 1.00 15.19 O 
 ```
 
 # Common issues

output/7c4s/output/7c4s_A_discotope3.csv

@@ -154,7 +154,7 @@ pdb,res_id,residue,DiscoTope-3.0_score,rsa,pLDDTs,length,alphafold_struc_flag
 7c4s_A,172,P,0.05415,0.01292,100,282,0
 7c4s_A,173,I,0.31203,0.36754,100,282,0
 7c4s_A,174,L,0.24067,0.89415,100,282,0
-7c4s_A,175,G,0.21472,0.58958,100,282,0
+7c4s_A,175,G,0.21481,0.58958,100,282,0
 7c4s_A,176,W,0.19280,0.40581,100,282,0
 7c4s_A,177,N,0.18728,0.17860,100,282,0
 7c4s_A,178,C,0.00766,0.00000,100,282,0
@@ -180,7 +180,7 @@ pdb,res_id,residue,DiscoTope-3.0_score,rsa,pLDDTs,length,alphafold_struc_flag
 7c4s_A,198,A,0.10805,0.38232,100,282,0
 7c4s_A,199,F,0.12337,0.45795,100,282,0
 7c4s_A,200,C,0.03853,0.03893,100,282,0
-7c4s_A,201,I,0.14309,0.10800,100,282,0
+7c4s_A,201,I,0.14298,0.10800,100,282,0
 7c4s_A,202,S,0.04062,0.49121,100,282,0
 7c4s_A,203,I,0.06358,0.31119,100,282,0
 7c4s_A,204,F,0.05302,0.08356,100,282,0