diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 008719d187af5161095fd75effb6d3ce5aedf825..5e5f4742a61cdf5830891233b3e067bcc9efc8d4 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -540,49 +540,73 @@ class LigandScorer:
min_mat1 = mat1.min()
return assignments
- def _assign_ligands_rmsd(self):
- """Assign (map) ligands between model and target
+ @staticmethod
+ def _reverse_lddt(lddt):
+ """Reverse lDDT means turning it from a number between 0 and 1 to a
+ number between infinity and 0 (0 being better).
+
+ In practice, this is 1/lDDT. If lDDT is 0, the result is infinity.
"""
- # Transform lddt_pli to be on the scale of RMSD
with warnings.catch_warnings(): # RuntimeWarning: divide by zero
warnings.simplefilter("ignore")
- mat2 = np.float64(1) / self.lddt_pli_matrix
+ return np.float64(1) / lddt
+
+ def _assign_ligands_rmsd(self):
+ """Assign (map) ligands between model and target.
- assignments = self._find_ligand_assignment(self.rmsd_matrix, mat2)
- self._rmsd = {}
- self._rmsd_assignment = {}
- self._rmsd_details = {}
+ Sets self._rmsd, self._rmsd_assignment and self._rmsd_details.
+ """
+ mat2 = self._reverse_lddt(self.lddt_pli_matrix)
+
+ mat_tuple = self._assign_matrices(self.rmsd_matrix,
+ mat2,
+ self._rmsd_full_matrix,
+ "rmsd")
+ self._rmsd = mat_tuple[0]
+ self._rmsd_assignment = mat_tuple[1]
+ self._rmsd_details = mat_tuple[2]
+
+ def _assign_matrices(self, mat1, mat2, data, main_key):
+ """
+ :param mat1: the main ligand assignment criteria (RMSD or lDDT-PLI)
+ :param mat2: the secondary ligand assignment criteria (lDDT-PLI or RMSD)
+ :param data: the data (either self._rmsd_full_matrix or self._lddt_pli_matrix
+ :return: a tuple with 3 dictionaries of matrices containing the main
+ data, assignement, and details, respectively.
+ """
+ assignments = self._find_ligand_assignment(mat1, mat2)
+ out_main = {}
+ out_assignment = {}
+ out_details = {}
for assignment in assignments:
trg_idx, mdl_idx = assignment
- mdl_lig_qname = self.model_ligands[mdl_idx].qualified_name
- self._rmsd[mdl_lig_qname] = self._rmsd_full_matrix[
- trg_idx, mdl_idx]["rmsd"]
- self._rmsd_assignment[mdl_lig_qname] = self._rmsd_full_matrix[
+ mdl_lig = self.model_ligands[mdl_idx]
+ mdl_cname = mdl_lig.chain.name
+ mdl_restuple = (mdl_lig.number.num, mdl_lig.number.ins_code)
+ if mdl_cname not in out_main:
+ out_main[mdl_cname] = {}
+ out_assignment[mdl_cname] = {}
+ out_details[mdl_cname] = {}
+ out_main[mdl_cname][mdl_restuple] = data[
+ trg_idx, mdl_idx][main_key]
+ out_assignment[mdl_cname][mdl_restuple] = data[
trg_idx, mdl_idx]["target_ligand"].qualified_name
- self._rmsd_details[mdl_lig_qname] = self._rmsd_full_matrix[
+ out_details[mdl_cname][mdl_restuple] = data[
trg_idx, mdl_idx]
+ return out_main, out_assignment, out_details
def _assign_ligands_lddt_pli(self):
""" Assign ligands based on lDDT-PLI.
"""
- # Transform lddt_pli to be on the scale of RMSD
- with warnings.catch_warnings(): # RuntimeWarning: divide by zero
- warnings.simplefilter("ignore")
- mat1 = np.float64(1) / self.lddt_pli_matrix
-
- assignments = self._find_ligand_assignment(mat1, self.rmsd_matrix)
- self._lddt_pli = {}
- self._lddt_pli_assignment = {}
- self._lddt_pli_details = {}
- for assignment in assignments:
- trg_idx, mdl_idx = assignment
- mdl_lig_qname = self.model_ligands[mdl_idx].qualified_name
- self._lddt_pli[mdl_lig_qname] = self._lddt_pli_full_matrix[
- trg_idx, mdl_idx]["lddt_pli"]
- self._lddt_pli_assignment[mdl_lig_qname] = self._lddt_pli_full_matrix[
- trg_idx, mdl_idx]["target_ligand"].qualified_name
- self._lddt_pli_details[mdl_lig_qname] = self._lddt_pli_full_matrix[
- trg_idx, mdl_idx]
+ mat1 = self._reverse_lddt(self.lddt_pli_matrix)
+
+ mat_tuple = self._assign_matrices(mat1,
+ self.rmsd_matrix,
+ self._lddt_pli_full_matrix,
+ "lddt_pli")
+ self._lddt_pli = mat_tuple[0]
+ self._lddt_pli_assignment = mat_tuple[1]
+ self._lddt_pli_details = mat_tuple[2]
@property
def rmsd_matrix(self):
diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py
index 4bff9e812cbbf3d3c191aa335923446ea1db4395..0116a948dbe26cc061351bb0901cd8d0db92e11a 100644
--- a/modules/mol/alg/tests/test_ligand_scoring.py
+++ b/modules/mol/alg/tests/test_ligand_scoring.py
@@ -24,6 +24,11 @@ class TestLigandScoring(unittest.TestCase):
mdl, mdl_seqres = io.LoadMMCIF(os.path.join('testfiles', "P84080_model_02.cif.gz"), seqres=True)
sc = LigandScorer(mdl, trg, None, None)
+ # import ipdb; ipdb.set_trace()
+ # import ost.mol.alg.scoring
+ # scr = ost.mol.alg.scoring.Scorer(sc.model, sc.target)
+ # scr.lddt
+ # scr.local_lddt
assert len(sc.target_ligands) == 7
assert len(sc.model_ligands) == 1
@@ -284,7 +289,7 @@ class TestLigandScoring(unittest.TestCase):
trg_4c0a, _ = io.LoadMMCIF(os.path.join('testfiles', "4c0a.cif.gz"), seqres=True)
sc = LigandScorer(trg, trg_4c0a, None, None, check_resnames=False)
- expected_keys = {"J.G3D1", "F.G3D1"}
+ expected_keys = {"J", "F"}
self.assertFalse(expected_keys.symmetric_difference(sc.rmsd.keys()))
self.assertFalse(expected_keys.symmetric_difference(sc.rmsd_assignment.keys()))
self.assertFalse(expected_keys.symmetric_difference(sc.rmsd_details.keys()))
@@ -293,42 +298,44 @@ class TestLigandScoring(unittest.TestCase):
self.assertFalse(expected_keys.symmetric_difference(sc.lddt_pli_details.keys()))
# rmsd
- self.assertAlmostEqual(sc.rmsd["J.G3D1"], 3.8498, 3)
- self.assertAlmostEqual(sc.rmsd["F.G3D1"], 57.6295, 3)
+ self.assertAlmostEqual(sc.rmsd["J"][(1, "\x00")], 3.8498, 3)
+ self.assertAlmostEqual(sc.rmsd["F"][(1, "\x00")], 57.6295, 3)
# rmsd_assignment
- self.assertEqual(sc.rmsd_assignment, {'J.G3D1': 'L.G3D1', 'F.G3D1': 'I.G3D1'})
+ self.assertEqual(sc.rmsd_assignment, {'J': {(1, "\x00"): 'L.G3D1'},
+ 'F': {(1, "\x00"): 'I.G3D1'}})
# rmsd_details
- self.assertEqual(sc.rmsd_details["J.G3D1"]["chain_mapping"], {'A': 'B', 'H': 'C'})
- self.assertEqual(sc.rmsd_details["J.G3D1"]["bs_num_res"], 16)
- self.assertEqual(sc.rmsd_details["J.G3D1"]["bs_num_overlap_res"], 16)
- self.assertEqual(sc.rmsd_details["J.G3D1"]["target_ligand"].qualified_name, 'L.G3D1')
- self.assertEqual(sc.rmsd_details["J.G3D1"]["model_ligand"].qualified_name, 'J.G3D1')
- self.assertEqual(sc.rmsd_details["F.G3D1"]["chain_mapping"], {'F': 'B', 'C': 'C'})
- self.assertEqual(sc.rmsd_details["F.G3D1"]["bs_num_res"], 15)
- self.assertEqual(sc.rmsd_details["F.G3D1"]["bs_num_overlap_res"], 15)
- self.assertEqual(sc.rmsd_details["F.G3D1"]["target_ligand"].qualified_name, 'I.G3D1')
- self.assertEqual(sc.rmsd_details["F.G3D1"]["model_ligand"].qualified_name, 'F.G3D1')
+ self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["chain_mapping"], {'A': 'B', 'H': 'C'})
+ self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["bs_num_res"], 16)
+ self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["bs_num_overlap_res"], 16)
+ self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["target_ligand"].qualified_name, 'L.G3D1')
+ self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["model_ligand"].qualified_name, 'J.G3D1')
+ self.assertEqual(sc.rmsd_details["F"][(1, "\x00")]["chain_mapping"], {'F': 'B', 'C': 'C'})
+ self.assertEqual(sc.rmsd_details["F"][(1, "\x00")]["bs_num_res"], 15)
+ self.assertEqual(sc.rmsd_details["F"][(1, "\x00")]["bs_num_overlap_res"], 15)
+ self.assertEqual(sc.rmsd_details["F"][(1, "\x00")]["target_ligand"].qualified_name, 'I.G3D1')
+ self.assertEqual(sc.rmsd_details["F"][(1, "\x00")]["model_ligand"].qualified_name, 'F.G3D1')
# lddt_pli
- self.assertAlmostEqual(sc.lddt_pli["J.G3D1"], 0.91194, 5)
- self.assertAlmostEqual(sc.lddt_pli["F.G3D1"], 0.0014598, 6)
+ self.assertAlmostEqual(sc.lddt_pli["J"][(1, "\x00")], 0.91194, 5)
+ self.assertAlmostEqual(sc.lddt_pli["F"][(1, "\x00")], 0.0014598, 6)
# lddt_pli_assignment
- self.assertEqual(sc.lddt_pli_assignment, {'J.G3D1': 'I.G3D1', 'F.G3D1': 'J.G3D1'})
+ self.assertEqual(sc.lddt_pli_assignment, {'J': {(1, "\x00"): 'I.G3D1'},
+ 'F': {(1, "\x00"): 'J.G3D1'}})
# lddt_pli_details
- self.assertAlmostEqual(sc.lddt_pli_details["J.G3D1"]["rmsd"], 4.1008, 4)
- self.assertEqual(sc.lddt_pli_details["J.G3D1"]["lddt_pli_n_contacts"], 5224)
- self.assertEqual(sc.lddt_pli_details["J.G3D1"]["chain_mapping"], {'F': 'B', 'C': 'C'})
- self.assertEqual(sc.lddt_pli_details["J.G3D1"]["bs_num_res"], 15)
- self.assertEqual(sc.lddt_pli_details["J.G3D1"]["bs_num_overlap_res"], 15)
- self.assertEqual(sc.lddt_pli_details["J.G3D1"]["target_ligand"].qualified_name, 'I.G3D1')
- self.assertEqual(sc.lddt_pli_details["J.G3D1"]["model_ligand"].qualified_name, 'J.G3D1')
- self.assertAlmostEqual(sc.lddt_pli_details["F.G3D1"]["rmsd"], 57.7868, 4)
- self.assertEqual(sc.lddt_pli_details["F.G3D1"]["lddt_pli_n_contacts"], 5480)
- self.assertEqual(sc.lddt_pli_details["F.G3D1"]["chain_mapping"], {'E': 'B', 'D': 'C'})
- self.assertEqual(sc.lddt_pli_details["F.G3D1"]["bs_num_res"], 16)
- self.assertEqual(sc.lddt_pli_details["F.G3D1"]["bs_num_overlap_res"], 16)
- self.assertEqual(sc.lddt_pli_details["F.G3D1"]["target_ligand"].qualified_name, 'J.G3D1')
- self.assertEqual(sc.lddt_pli_details["F.G3D1"]["model_ligand"].qualified_name, 'F.G3D1')
+ self.assertAlmostEqual(sc.lddt_pli_details["J"][(1, "\x00")]["rmsd"], 4.1008, 4)
+ self.assertEqual(sc.lddt_pli_details["J"][(1, "\x00")]["lddt_pli_n_contacts"], 5224)
+ self.assertEqual(sc.lddt_pli_details["J"][(1, "\x00")]["chain_mapping"], {'F': 'B', 'C': 'C'})
+ self.assertEqual(sc.lddt_pli_details["J"][(1, "\x00")]["bs_num_res"], 15)
+ self.assertEqual(sc.lddt_pli_details["J"][(1, "\x00")]["bs_num_overlap_res"], 15)
+ self.assertEqual(sc.lddt_pli_details["J"][(1, "\x00")]["target_ligand"].qualified_name, 'I.G3D1')
+ self.assertEqual(sc.lddt_pli_details["J"][(1, "\x00")]["model_ligand"].qualified_name, 'J.G3D1')
+ self.assertAlmostEqual(sc.lddt_pli_details["F"][(1, "\x00")]["rmsd"], 57.7868, 4)
+ self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["lddt_pli_n_contacts"], 5480)
+ self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["chain_mapping"], {'E': 'B', 'D': 'C'})
+ self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["bs_num_res"], 16)
+ self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["bs_num_overlap_res"], 16)
+ self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["target_ligand"].qualified_name, 'J.G3D1')
+ self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["model_ligand"].qualified_name, 'F.G3D1')
if __name__ == "__main__":