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Verified Commit 7f0022fa authored by Xavier Robin's avatar Xavier Robin
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refactor: drop check_resnames and set it to False

This is in order to be consistent with the behavior of the Scorer
parent 42fb612c
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...@@ -82,9 +82,6 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer): ...@@ -82,9 +82,6 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
:param max_symmetries: Passed to parent constructor - see :param max_symmetries: Passed to parent constructor - see
:class:`LigandScorer`. :class:`LigandScorer`.
:type max_symmetries: :class:`int` :type max_symmetries: :class:`int`
:param check_resnames: On by default. Enforces residue name matches
between mapped model and target residues.
:type check_resnames: :class:`bool`
:param lddt_pli_radius: lDDT inclusion radius for lDDT-PLI. :param lddt_pli_radius: lDDT inclusion radius for lDDT-PLI.
:type lddt_pli_radius: :class:`float` :type lddt_pli_radius: :class:`float`
:param add_mdl_contacts: Whether to add mdl contacts. :param add_mdl_contacts: Whether to add mdl contacts.
...@@ -105,7 +102,7 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer): ...@@ -105,7 +102,7 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
def __init__(self, model, target, model_ligands=None, target_ligands=None, def __init__(self, model, target, model_ligands=None, target_ligands=None,
resnum_alignments=False, rename_ligand_chain=False, resnum_alignments=False, rename_ligand_chain=False,
substructure_match=False, coverage_delta=0.2, substructure_match=False, coverage_delta=0.2,
max_symmetries=1e5, check_resnames=True, lddt_pli_radius=6.0, max_symmetries=1e5, lddt_pli_radius=6.0,
add_mdl_contacts=False, add_mdl_contacts=False,
lddt_pli_thresholds = [0.5, 1.0, 2.0, 4.0], lddt_pli_thresholds = [0.5, 1.0, 2.0, 4.0],
lddt_pli_binding_site_radius=None): lddt_pli_binding_site_radius=None):
...@@ -118,7 +115,6 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer): ...@@ -118,7 +115,6 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
coverage_delta = coverage_delta, coverage_delta = coverage_delta,
max_symmetries = max_symmetries) max_symmetries = max_symmetries)
self.check_resnames = check_resnames
self.lddt_pli_radius = lddt_pli_radius self.lddt_pli_radius = lddt_pli_radius
self.add_mdl_contacts = add_mdl_contacts self.add_mdl_contacts = add_mdl_contacts
self.lddt_pli_thresholds = lddt_pli_thresholds self.lddt_pli_thresholds = lddt_pli_thresholds
...@@ -427,7 +423,7 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer): ...@@ -427,7 +423,7 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
scorer._ProcessModel(mdl_bs, lddt_chain_mapping, scorer._ProcessModel(mdl_bs, lddt_chain_mapping,
residue_mapping = lddt_alns, residue_mapping = lddt_alns,
thresholds = self.lddt_pli_thresholds, thresholds = self.lddt_pli_thresholds,
check_resnames = self.check_resnames) check_resnames = False)
# estimate a penalty for unsatisfied model contacts from chains # estimate a penalty for unsatisfied model contacts from chains
# that are not in the local trg binding site, but can be mapped in # that are not in the local trg binding site, but can be mapped in
...@@ -650,7 +646,7 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer): ...@@ -650,7 +646,7 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
scorer._ProcessModel(mdl_bs, lddt_chain_mapping, scorer._ProcessModel(mdl_bs, lddt_chain_mapping,
residue_mapping = lddt_alns, residue_mapping = lddt_alns,
thresholds = self.lddt_pli_thresholds, thresholds = self.lddt_pli_thresholds,
check_resnames = self.check_resnames) check_resnames = False)
for (trg_sym, mdl_sym) in symmetries: for (trg_sym, mdl_sym) in symmetries:
for mdl_i, trg_i in zip(mdl_sym, trg_sym): for mdl_i, trg_i in zip(mdl_sym, trg_sym):
......
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