
####################################################################

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_ligand1/1a30_target.cif" \
  -m ./input/protein_ligand1/*.cif \
  --scoring-levels atom residue \
  --scoring-types contacts sites \
  --subselect-contacts "[-a1 [-chain A,B] -a2 [-chain X]]" \
  --subselect-atoms "[-chain A,B]" \
| column -t
target           model            t_id  m_id  residue_residue_cadscore  atom_atom_cadscore  residue_sites_cadscore  atom_sites_cadscore
1a30_target.cif  1a30_model4.cif  4     3     0.809186                  0.220007            0.809186                0.772563
1a30_target.cif  1a30_model2.cif  4     1     0.795893                  0.413699            0.795893                0.774953
1a30_target.cif  1a30_model3.cif  4     2     0.692567                  0.290539            0.692567                0.675844
1a30_target.cif  1a30_model1.cif  4     0     0.493151                  0.038371            0.493151                0.436639

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_ligand1/1a30_target.cif" \
  -m ./input/protein_ligand1/*.cif \
  --scoring-levels atom residue \
  --scoring-types contacts sites \
  --subselect-contacts "[-a1 [-protein] -a2! [-protein]]" \
  --subselect-atoms "[-protein]" \
| column -t
target           model            t_id  m_id  residue_residue_cadscore  atom_atom_cadscore  residue_sites_cadscore  atom_sites_cadscore
1a30_target.cif  1a30_model4.cif  4     3     0.809186                  0.220007            0.809186                0.772563
1a30_target.cif  1a30_model2.cif  4     1     0.795893                  0.413699            0.795893                0.774953
1a30_target.cif  1a30_model3.cif  4     2     0.692567                  0.290539            0.692567                0.675844
1a30_target.cif  1a30_model1.cif  4     0     0.493151                  0.038371            0.493151                0.436639

####################################################################

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_ligand1/1a30_target.cif" \
  -m ./input/protein_ligand1/*.cif \
  --scoring-levels atom residue \
  --scoring-types contacts sites \
  --subselect-contacts "[-a1 [-chain A,B] -a2 [-chain X]]" \
  --subselect-atoms "[-chain A,B]" \
  --conflate-atom-types \
  --conflation-config-file "./input/protein_ligand1/1a30_target_groups_of_equivalent_atoms.tsv" \
| column -t
target           model            t_id  m_id  residue_residue_cadscore  atom_atom_cadscore  residue_sites_cadscore  atom_sites_cadscore
1a30_target.cif  1a30_model4.cif  4     3     0.809186                  0.230513            0.809186                0.78498
1a30_target.cif  1a30_model2.cif  4     1     0.795893                  0.468029            0.795893                0.793089
1a30_target.cif  1a30_model3.cif  4     2     0.692567                  0.35366             0.692567                0.692399
1a30_target.cif  1a30_model1.cif  4     0     0.493151                  0.058834            0.493151                0.444203

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_ligand1/1a30_target.cif" \
  -m ./input/protein_ligand1/*.cif \
  --scoring-levels atom residue \
  --scoring-types contacts sites \
  --subselect-contacts "[-a1 [-protein] -a2! [-protein]]" \
  --subselect-atoms "[-protein]" \
  --conflate-atom-types \
  --conflation-config-file "./input/protein_ligand1/1a30_target_groups_of_equivalent_atoms.tsv" \
| column -t
target           model            t_id  m_id  residue_residue_cadscore  atom_atom_cadscore  residue_sites_cadscore  atom_sites_cadscore
1a30_target.cif  1a30_model4.cif  4     3     0.809186                  0.230513            0.809186                0.78498
1a30_target.cif  1a30_model2.cif  4     1     0.795893                  0.468029            0.795893                0.793089
1a30_target.cif  1a30_model3.cif  4     2     0.692567                  0.35366             0.692567                0.692399
1a30_target.cif  1a30_model1.cif  4     0     0.493151                  0.058834            0.493151                0.444203

####################################################################

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_ligand1/1a30_target.cif" \
  -m ./input/protein_ligand1/*.cif \
  --scoring-levels atom \
  --scoring-types contacts \
  --subselect-contacts "[-a1 [-chain A,B] -a2 [-chain X]]" \
  --subselect-atoms "[-chain A,B]" \
  --conflate-atom-types \
  --conflation-config-file "./input/protein_ligand1/1a30_target_groups_of_equivalent_atoms.tsv" \
  --output-with-f1 \
  --output-with-identities \
| column -t
target           model            t_id  m_id  atom_atom_cadscore  atom_atom_F1_of_areas  identity_of_residues  identity_of_atoms  identity_of_chains
1a30_target.cif  1a30_model2.cif  4     1     0.468029            0.61711                100                   100                100
1a30_target.cif  1a30_model3.cif  4     2     0.35366             0.476373               100                   100                100
1a30_target.cif  1a30_model4.cif  4     3     0.230513            0.304661               100                   100                100
1a30_target.cif  1a30_model1.cif  4     0     0.058834            0.074674               100                   100                100

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_ligand1/1a30_target.cif" \
  -m ./input/protein_ligand1/*.cif \
  --scoring-levels atom \
  --scoring-types contacts \
  --subselect-contacts "[-a1 [-protein] -a2! [-protein]]" \
  --subselect-atoms "[-protein]" \
  --conflate-atom-types \
  --conflation-config-file "./input/protein_ligand1/1a30_target_groups_of_equivalent_atoms.tsv" \
  --output-with-f1 \
  --output-with-identities \
| column -t
target           model            t_id  m_id  atom_atom_cadscore  atom_atom_F1_of_areas  identity_of_residues  identity_of_atoms  identity_of_chains
1a30_target.cif  1a30_model2.cif  4     1     0.468029            0.61711                100                   100                100
1a30_target.cif  1a30_model3.cif  4     2     0.35366             0.476373               100                   100                100
1a30_target.cif  1a30_model4.cif  4     3     0.230513            0.304661               100                   100                100
1a30_target.cif  1a30_model1.cif  4     0     0.058834            0.074674               100                   100                100

####################################################################

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_ligand1/1a30_target.cif" \
  -m ./input/protein_ligand1/*.cif \
  --scoring-levels atom \
  --scoring-types contacts \
  --subselect-contacts "[-a1 [-chain A,B] -a2 [-chain X]]" \
  --subselect-atoms "[-chain A,B]" \
  --conflate-atom-types \
  --conflation-config-file "./input/protein_ligand1/1a30_target_groups_of_equivalent_atoms.tsv" \
  --output-with-areas \
| column -t
target           model            t_id  m_id  atom_atom_cadscore  atom_atom_target_area  atom_atom_model_area  atom_atom_TP_area  atom_atom_FP_area  atom_atom_FN_area
1a30_target.cif  1a30_model2.cif  4     1     0.468029            377.407683             310.204839            234.191802         147.396062         143.215881
1a30_target.cif  1a30_model3.cif  4     2     0.35366             377.407683             254.791682            178.512831         193.546205         198.894852
1a30_target.cif  1a30_model4.cif  4     3     0.230513            377.407683             184.052817            117.927722         278.822145         259.479961
1a30_target.cif  1a30_model1.cif  4     0     0.058834            377.407683             49.54308              29.486256          382.833971         347.921427

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_ligand1/1a30_target.cif" \
  -m ./input/protein_ligand1/*.cif \
  --scoring-levels atom \
  --scoring-types contacts \
  --subselect-contacts "[-a1 [-protein] -a2! [-protein]]" \
  --subselect-atoms "[-protein]" \
  --conflate-atom-types \
  --conflation-config-file "./input/protein_ligand1/1a30_target_groups_of_equivalent_atoms.tsv" \
  --output-with-areas \
| column -t
target           model            t_id  m_id  atom_atom_cadscore  atom_atom_target_area  atom_atom_model_area  atom_atom_TP_area  atom_atom_FP_area  atom_atom_FN_area
1a30_target.cif  1a30_model2.cif  4     1     0.468029            377.407683             310.204839            234.191802         147.396062         143.215881
1a30_target.cif  1a30_model3.cif  4     2     0.35366             377.407683             254.791682            178.512831         193.546205         198.894852
1a30_target.cif  1a30_model4.cif  4     3     0.230513            377.407683             184.052817            117.927722         278.822145         259.479961
1a30_target.cif  1a30_model1.cif  4     0     0.058834            377.407683             49.54308              29.486256          382.833971         347.921427

####################################################################

cadscore-lt \
  --include-heteroatoms \
  -t "./input/protein_ligand1/1a30_target.cif" \
  -m ./input/protein_ligand1/*.cif \
  --scoring-levels atom \
  --subselect-contacts "[-a1 [-chain A,B] -a2 [-chain X]]" \
  --subselect-atoms "[-chain A,B]" \
  --conflate-atom-types \
  --conflation-config-file "./input/protein_ligand1/1a30_target_groups_of_equivalent_atoms.tsv" \
  --output-with-f1 \
  --output-with-areas \
  --output-with-identities \
  --local-output-formats pdb contactmap graphics-pymol \
  --local-output-levels atom \
  --output-dir ./output/protein_ligand1/output_dit_01 \
| column -t
target           model            t_id  m_id  atom_atom_cadscore  atom_atom_F1_of_areas  atom_atom_target_area  atom_atom_model_area  atom_atom_TP_area  atom_atom_FP_area  atom_atom_FN_area  identity_of_residues  identity_of_atoms  identity_of_chains
1a30_target.cif  1a30_model2.cif  4     1     0.468029            0.61711                377.407683             310.204839            234.191802         147.396062         143.215881         100                   100                100
1a30_target.cif  1a30_model3.cif  4     2     0.35366             0.476373               377.407683             254.791682            178.512831         193.546205         198.894852         100                   100                100
1a30_target.cif  1a30_model4.cif  4     3     0.230513            0.304661               377.407683             184.052817            117.927722         278.822145         259.479961         100                   100                100
1a30_target.cif  1a30_model1.cif  4     0     0.058834            0.074674               377.407683             49.54308              29.486256          382.833971         347.921427         100                   100                100

####################################################################


