Refactoring of code to remove it from main and more #539

Job	Run time
Run pipeline with test data (24.04.2 \| docker \| test)	5m 26s
Run pipeline with test data (24.04.2 \| docker \| test_alphafold2_split)	4m 1s
Run pipeline with test data (24.04.2 \| docker \| test_alphafold2_download)	4m 58s
Run pipeline with test data (24.04.2 \| docker \| test_colabfold_local)	5m 41s
Run pipeline with test data (24.04.2 \| docker \| test_colabfold_webserver)	6m 30s
Run pipeline with test data (24.04.2 \| docker \| test_colabfold_download)	4m 9s
Run pipeline with test data (24.04.2 \| docker \| test_esmfold)	3m 53s
Run pipeline with test data (latest-everything \| docker \| test)	3m 56s
Run pipeline with test data (latest-everything \| docker \| test_alphafold2_split)	3m 57s
Run pipeline with test data (latest-everything \| docker \| test_alphafold2_download)	4m 10s
Run pipeline with test data (latest-everything \| docker \| test_colabfold_local)	3m 48s
Run pipeline with test data (latest-everything \| docker \| test_colabfold_webserver)	5m 6s
Run pipeline with test data (latest-everything \| docker \| test_colabfold_download)	4m 49s
Run pipeline with test data (latest-everything \| docker \| test_esmfold)	3m 50s
	1h 4m 14s

Provide feedback