Reproduce colabfold paper results

[Luke-ebbis]

I think it has to do with the grouped command. This may be needed as I cannot assemble the ungrouped example data too

[Luke-ebbis]

• implement this with a switch directive using data from a config file.

[Luke-ebbis]

Correct colabfold output for test data

$pixi run python3 scripts/run_on_pdbs.py  example/subunits.json example/pdbs/ test_example
--- Searching for subunits in supplied PDB files
found full A0 in AFM_A0_G0_unrelaxed_rank_1_model_2.pdb chain B
found full G0 in AFM_A0_G0_unrelaxed_rank_1_model_2.pdb chain C
found full A0 in AFM_A0_G0_unrelaxed_rank_2_model_3.pdb chain B
found full G0 in AFM_A0_G0_unrelaxed_rank_2_model_3.pdb chain C
found full A0 in AFM_A0_A0_A0_unrelaxed_rank_1_model_3.pdb chain B
found full A0 in AFM_A0_A0_A0_unrelaxed_rank_1_model_3.pdb chain C
found full A0 in AFM_A0_A0_A0_unrelaxed_rank_1_model_3.pdb chain D
found full A0 in AFM_A0_A0_unrelaxed_rank_1_model_1.pdb chain B
found full A0 in AFM_A0_A0_unrelaxed_rank_1_model_1.pdb chain C
found full A0 in AFM_A0_A0_G0_unrelaxed_rank_1_model_1.pdb chain B
found full A0 in AFM_A0_A0_G0_unrelaxed_rank_1_model_1.pdb chain C
found full G0 in AFM_A0_A0_G0_unrelaxed_rank_1_model_1.pdb chain D
found full A0 in AFM_A0_A0_unrelaxed_rank_2_model_4.pdb chain B
found full A0 in AFM_A0_A0_unrelaxed_rank_2_model_4.pdb chain C
found full G0 in AFM_G0_G0_unrelaxed_rank_2_model_5.pdb chain B
found full G0 in AFM_G0_G0_unrelaxed_rank_2_model_5.pdb chain C
found full G0 in AFM_G0_G0_unrelaxed_rank_1_model_4.pdb chain B
found full G0 in AFM_G0_G0_unrelaxed_rank_1_model_4.pdb chain C
found full A0 in AFM_A0_A0_A0_unrelaxed_rank_2_model_1.pdb chain B
found full A0 in AFM_A0_A0_A0_unrelaxed_rank_2_model_1.pdb chain C
found full A0 in AFM_A0_A0_A0_unrelaxed_rank_2_model_1.pdb chain D
found full A0 in AFM_A0_A0_G0_unrelaxed_rank_2_model_3.pdb chain B
found full A0 in AFM_A0_A0_G0_unrelaxed_rank_2_model_3.pdb chain C
found full G0 in AFM_A0_A0_G0_unrelaxed_rank_2_model_3.pdb chain D
--- Extracting representative subunits (for each subunit, its best scored model in the PDBs folder)
rep A0 has plddt score 96.00915686274507
rep G0 has plddt score 89.0577211394304
--- Extracting pairwise transformations between subunits (from each PDB file with 2 or more subunits)
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_G0_unrelaxed_rank_1_model_2.pdb
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_G0_unrelaxed_rank_2_model_3.pdb
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_A0_A0_unrelaxed_rank_1_model_3.pdb
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
Skipping transformation, missing interface between A0 A0
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_A0_unrelaxed_rank_1_model_1.pdb
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_A0_G0_unrelaxed_rank_1_model_1.pdb
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_A0_unrelaxed_rank_2_model_4.pdb
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_G0_G0_unrelaxed_rank_2_model_5.pdb
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_G0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_G0_G0_unrelaxed_rank_1_model_4.pdb
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_G0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_A0_A0_unrelaxed_rank_2_model_1.pdb
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
Skipping transformation, missing interface between A0 A0
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_A0_G0_unrelaxed_rank_2_model_3.pdb
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
/home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
found 6 transformations between A0 and G0
found 8 transformations between A0 and A0
found 2 transformations between G0 and G0
--- Finished building unified representation
--- Running combinatorial assembly algorithm, may take a while
--- Finished combinatorial assembly, writing output models
--- Assembled 3 complexes, confidence: 88.9885-88.9885

incorrect output

--- Searching for subunits in supplied PDB files
found full A0 in A0_A0_unrelaxed_rank_003_alphafold2_multimer_v3_model_1_seed_000.pdb chain A
found full A0 in A0_A0_unrelaxed_rank_003_alphafold2_multimer_v3_model_1_seed_000.pdb chain B
found full A0 in A0_A0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb chain A
found full A0 in A0_A0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb chain B
found full G0 in A0_A0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb chain C
found full A0 in A0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb chain A
found full G0 in A0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb chain B
found full G0 in G0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb chain A
found full G0 in G0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb chain B
found full G0 in G0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb chain A
found full G0 in G0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb chain B
found full A0 in A0_A0_unrelaxed_rank_005_alphafold2_multimer_v3_model_4_seed_000.pdb chain A
found full A0 in A0_A0_unrelaxed_rank_005_alphafold2_multimer_v3_model_4_seed_000.pdb chain B
found full A0 in A0_A0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb chain A
found full A0 in A0_A0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb chain B
found full G0 in A0_A0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb chain C
found full A0 in A0_A0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb chain A
found full A0 in A0_A0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb chain B
found full A0 in A0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb chain A
found full G0 in A0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb chain B
found full A0 in A0_A0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb chain A
found full A0 in A0_A0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb chain B
found full G0 in A0_A0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb chain C
found full A0 in A0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb chain A
found full G0 in A0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb chain B
found full A0 in A0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb chain A
found full G0 in A0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb chain B
found full A0 in A0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb chain A
found full G0 in A0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb chain B
found full A0 in A0_A0_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb chain A
found full A0 in A0_A0_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb chain B
found full G0 in G0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_000.pdb chain A
found full G0 in G0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_000.pdb chain B
found full G0 in G0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_5_seed_000.pdb chain A
found full G0 in G0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_5_seed_000.pdb chain B
found full A0 in A0_A0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb chain A
found full A0 in A0_A0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb chain B
found full G0 in A0_A0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb chain C
found full A0 in A0_A0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb chain A
found full A0 in A0_A0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb chain B
found full G0 in A0_A0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb chain C
found full A0 in A0_A0_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb chain A
found full A0 in A0_A0_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb chain B
found full G0 in G0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb chain A
found full G0 in G0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb chain B
--- Extracting representative subunits (for each subunit, its best scored model in the PDBs folder)
rep A0 has plddt score 95.11188235294117
rep G0 has plddt score 92.22199400299847
--- Extracting pairwise transformations between subunits (from each PDB file with 2 or more subunits)
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_unrelaxed_rank_003_alphafold2_multimer_v3_model_1_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
Skipping transformation, missing interface between A0 G0
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/G0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_G0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/G0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_G0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_unrelaxed_rank_005_alphafold2_multimer_v3_model_4_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
Skipping transformation, missing interface between A0 G0
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
Skipping transformation, missing interface between A0 G0
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/G0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_G0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/G0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_5_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_G0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
Skipping transformation, missing interface between A0 G0
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb 
- Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/G0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb
/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_G0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb 
found 10 transformations between A0 and A0
found 11 transformations between A0 and G0
found 5 transformations between G0 and G0
--- Finished building unified representation
--- Running combinatorial assembly algorithm, may take a while
--- Finished combinatorial assembly, writing output models
Could not assemble, exiting
made the following files in output