Merge pull request #63 from haddocking/spelling

Improve spelling

Author: sverhoeven

benchmark/README.md

@@ -10,7 +10,7 @@ to execute a protein-detective pipeline.
 
 * The remote.sh script does search+retrieve as it talks to remote servers and is better to run sequentially.
 * The filter.sh script can run in parallel on CPU.
-* The powerfit.sh script can be run in seqeuntially on GPU. Each script uses all GPUs available.
+* The powerfit.sh script can be run sequentially on GPU. Each script uses all GPUs available.
 
 The "Benchmarklist.csv" file is not included in the repository, but you can create your own
 by looking in print-commands.py for the expected columns.

benchmark/print-commands.py

@@ -3,7 +3,7 @@
 from pdconfig import Dataset, benchmark_dir, datasets, map_root
 
 
-def soft_residue_range(number_of_residues_modelled: str | int | float) -> tuple[int, int, int, int]:
+def residue_ranges(number_of_residues_modelled: str | int | float) -> tuple[int, int, int, int]:
     """Calculate soft/hard minimum and maximum residues based on modelled residues count.
 
     Uses a range fraction of 0.1 (+- 10%) around the modelled residues.
@@ -15,10 +15,10 @@ def soft_residue_range(number_of_residues_modelled: str | int | float) -> tuple[
         Tuple of (soft_min_res, soft_max_res, hard_min_res, hard_max_res)
     """
     # TODO use better logic to determine min/max residues based on the volume of the unknown density
-    sorf_res_range_fraction = 0.1  # +- 10%
+    soft_res_range_fraction = 0.1  # +- 10%
     base_count = float(number_of_residues_modelled)
-    soft_min_res = int(base_count * (1 - sorf_res_range_fraction))
-    soft_max_res = int(base_count * (1 + sorf_res_range_fraction))
+    soft_min_res = int(base_count * (1 - soft_res_range_fraction))
+    soft_max_res = int(base_count * (1 + soft_res_range_fraction))
     hard_min_res = int(base_count * (0.8))  # at least 80%
     hard_max_res = int(base_count * (1.5))  # at most 150%
     return soft_min_res, soft_max_res, hard_min_res, hard_max_res
@@ -35,7 +35,7 @@ def create_remote_script_content(row: Dataset, interaction_partner_seeds: set[st
     chain = row.Chain
     # Use a range around the modelled residues for filtering
     # TODO use better logic to determine min/max residues based on the volume of the unknown density
-    soft_min_res, _, hard_min_res, hard_max_res = soft_residue_range(row.Number_of_residues_modelled)
+    soft_min_res, _, hard_min_res, hard_max_res = residue_ranges(row.Number_of_residues_modelled)
 
     interaction_partner_exclude = uniprot
     interaction_partner_seed = " \\\n".join(f'--interaction-partner-seed "{s}"' for s in interaction_partner_seeds)
@@ -87,7 +87,7 @@ def create_filter_script_content(row: Dataset) -> str:
     pdb_id = row.PDB_id
     chain = row.Chain
     # Use a range around the modelled residues for filtering
-    soft_min_res, soft_max_res, _, _ = soft_residue_range(row.Number_of_residues_modelled)
+    soft_min_res, soft_max_res, _, _ = residue_ranges(row.Number_of_residues_modelled)
 
     return dedent(f"""\
         #!/bin/bash