Add some hybrid DCA-LLM commands to CLI scripts/"tests"

Author: niklases

scripts/CLI/run_cli_tests_linux.sh

@@ -307,6 +307,17 @@ echo
 $pypef hybrid extrapolation -i 37_ANEH_variants_dca_encoded.csv --conc
 echo
 
+# 0.4.0 features: hybrid DCA-LLM modeling
+$pypef hybrid --ts TS.fasl --params GREMLIN --llm esm
+echo
+$pypef hybrid --ts TS.fasl --params GREMLIN --llm prosst --wt P42212_F64L.fasta --pdb GFP_AEQVI.pdb
+echo
+$pypef hybrid --ls LS.fasl --ts TS.fasl --params GREMLIN --llm esm
+echo
+$pypef hybrid --ls LS.fasl --ts TS.fasl --params GREMLIN --llm prosst --wt P42212_F64L.fasta --pdb GFP_AEQVI.pdb
+echo
+
+
 rm 37_ANEH_variants_plmc_dca_encoded.csv
 echo
 rm 37_ANEH_variants_gremlin_dca_encoded.csv

scripts/CLI/run_cli_tests_win.ps1

@@ -432,6 +432,20 @@ pypef hybrid extrapolation -i 37_ANEH_variants_dca_encoded.csv --conc
 ExitOnExitCode
 Write-Host
 
+# 0.4.0 features: hybrid DCA-LLM modeling
+pypef hybrid --ts TS.fasl --params GREMLIN --llm esm
+ExitOnExitCode
+Write-Host
+pypef hybrid --ts TS.fasl --params GREMLIN --llm prosst --wt P42212_F64L.fasta --pdb GFP_AEQVI.pdb
+ExitOnExitCode
+Write-Host
+pypef hybrid --ls LS.fasl --ts TS.fasl --params GREMLIN --llm esm
+ExitOnExitCode
+Write-Host
+pypef hybrid --ls LS.fasl --ts TS.fasl --params GREMLIN --llm prosst --wt P42212_F64L.fasta --pdb GFP_AEQVI.pdb
+ExitOnExitCode
+Write-Host
+
 Remove-Item 37_ANEH_variants_plmc_dca_encoded.csv
 ExitOnExitCode
 Write-Host

scripts/ProteinGym_runs/run_performance_tests_proteingym_hybrid_dca_llm.py

@@ -569,7 +569,7 @@ def plot_csv_data(csv, plot_name):
 
     compute_performances(
         mut_data=combined_mut_data, 
-        start_i=start_i, 
+        start_i=0, 
         already_tested_is=already_tested_is
     )