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Commit 0647fa56 authored by Rafal Gumienny's avatar Rafal Gumienny
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feat: SCHWED-3120 Map back to mmCIF chain names

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actions/ost-compare-structures
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......@@ -371,6 +371,39 @@ def _ParseArgs():
return opts
def _RevertChainNames(ent):
"""Revert chain names to original names."""
editor = ent.EditXCS()
suffix = "_tmp" # just a suffix for temporary chain name
used_names = dict()
reverted_chains = dict()
for chain in ent.chains:
try:
original_name = chain.GetStringProp("original_name")
except Exception as ex:
ost.LogError("Cannot revert chain %s back to original: %s" % (
chain.name,
str(ex)))
reverted_chains[chain.name] = chain.name
editor.RenameChain(chain, chain.name + suffix)
continue
new_name = original_name
if new_name not in used_names:
used_names[original_name] = 1
reverted_chains[chain.name] = new_name
editor.RenameChain(chain, chain.name + suffix)
else:
new_name = "%s_%i" % (original_name, # dot causes selection error
used_names[original_name])
reverted_chains[chain.name] = new_name
editor.RenameChain(chain, chain.name + suffix)
used_names[original_name] += 1
for chain in ent.chains:
editor.RenameChain(chain, reverted_chains[chain.name[:-len(suffix)]])
rev_out = ["%s -> %s" % (on, nn) for on, nn in reverted_chains.iteritems()]
ost.LogInfo("Reverted chains: %s" % ", ".join(rev_out))
def _ReadStructureFile(path):
"""Safely read structure file into OST entity.
......@@ -389,9 +422,7 @@ def _ReadStructureFile(path):
if not entity.IsValid():
raise IOError("Provided file does not contain valid entity.")
entity.SetName(os.path.basename(path))
chain_mapping = {c.name: c.name for c in entity.chains}
entities.append({"entity": entity,
"chain_mapping": chain_mapping})
entities.append(entity)
except Exception:
try:
tmp_entity, cif_info = LoadMMCIF(path, info=True)
......@@ -407,11 +438,8 @@ def _ReadStructureFile(path):
tbu.AddOperations(tinfo.GetOperations())
entity = tbu.PDBize(tmp_entity, min_polymer_size=0)
entity.SetName(os.path.basename(path) + ".au")
chain_mapping = {c.name: c.GetStringProp("original_name")
for c in entity.chains}
entities.append({
"entity": entity,
"chain_mapping": chain_mapping})
_RevertChainNames(entity)
entities.append(entity)
elif len(cif_info.biounits) > 1:
for i, biounit in enumerate(cif_info.biounits):
entity = biounit.PDBize(tmp_entity, min_polymer_size=0)
......@@ -419,11 +447,8 @@ def _ReadStructureFile(path):
raise IOError(
"Provided file does not contain valid entity.")
entity.SetName(os.path.basename(path) + "." + str(i))
chain_mapping = {c.name: c.GetStringProp("original_name")
for c in entity.chains}
entities.append({
"entity": entity,
"chain_mapping": chain_mapping})
_RevertChainNames(entity)
entities.append(entity)
else:
biounit = cif_info.biounits[0]
entity = biounit.PDBize(tmp_entity, min_polymer_size=0)
......@@ -431,11 +456,8 @@ def _ReadStructureFile(path):
raise IOError(
"Provided file does not contain valid entity.")
entity.SetName(os.path.basename(path))
chain_mapping = {c.name: c.GetStringProp("original_name")
for c in entity.chains}
entities.append({
"entity": entity,
"chain_mapping": chain_mapping})
_RevertChainNames(entity)
entities.append(entity)
except Exception as exc:
raise exc
......@@ -471,22 +493,22 @@ def _Main():
references = _ReadStructureFile(opts.reference)
if opts.molck:
for i in range(len(references)):
_MolckEntity(references[i]["entity"], opts)
references[i]["entity"] = references[i]["entity"].CreateFullView()
_MolckEntity(references[i], opts)
references[i] = references[i].CreateFullView()
for i in range(len(models)):
_MolckEntity(models[i]["entity"], opts)
models[i]["entity"] = models[i]["entity"].CreateFullView()
_MolckEntity(models[i], opts)
models[i] = models[i].CreateFullView()
else:
for i in range(len(references)):
references[i]["entity"] = references[i]["entity"].CreateFullView()
references[i] = references[i].CreateFullView()
for i in range(len(models)):
models[i]["entity"] = models[i]["entity"].CreateFullView()
models[i] = models[i].CreateFullView()
if opts.structural_checks:
stereochemical_parameters = ReadStereoChemicalPropsFile(
opts.parameter_file)
ost.LogInfo("Performing structural checks for reference(s)")
for reference in references:
CheckStructure(reference["entity"],
CheckStructure(reference,
stereochemical_parameters.bond_table,
stereochemical_parameters.angle_table,
stereochemical_parameters.nonbonded_table,
......@@ -494,7 +516,7 @@ def _Main():
opts.angle_tolerance)
ost.LogInfo("Performing structural checks for model(s)")
for model in models:
CheckStructure(model["entity"],
CheckStructure(model,
stereochemical_parameters.bond_table,
stereochemical_parameters.angle_table,
stereochemical_parameters.nonbonded_table,
......@@ -511,12 +533,10 @@ def _Main():
result["options"]["cwd"] = os.path.abspath(os.getcwd())
#
# Perform scoring
for model_data in models:
model = model_data["entity"]
for model in models:
model_name = model.GetName()
model_results = dict()
for reference_data in references:
reference = reference_data["entity"]
for reference in references:
reference_name = reference.GetName()
reference_results = dict()
ost.LogInfo("#\nComparing %s to %s" % (
......@@ -530,11 +550,6 @@ def _Main():
"Using custom chain mapping: %s" % str(
opts.chain_mapping))
qs_scorer.chain_mapping = opts.chain_mapping
original_chain_mapping = dict()
for mdl_cname, ref_cname in qs_scorer.chain_mapping.iteritems():
orig_mdl_cname = model_data["chain_mapping"][mdl_cname]
orig_ref_cname = reference_data["chain_mapping"][ref_cname]
original_chain_mapping[orig_mdl_cname] = orig_ref_cname
if opts.qs_score:
ost.LogInfo("Computing QS-score")
try:
......@@ -545,8 +560,7 @@ def _Main():
"reference_name": reference_name,
"global_score": qs_scorer.global_score,
"best_score": qs_scorer.best_score,
"chain_mapping": qs_scorer.chain_mapping,
"original_chain_mapping": original_chain_mapping
"chain_mapping": qs_scorer.chain_mapping
}
except qsscoring.QSscoreError as ex:
# default handling: report failure and set score to 0
......@@ -558,8 +572,7 @@ def _Main():
"reference_name": reference.GetName(),
"global_score": 0.0,
"best_score": 0.0,
"chain_mapping": qs_scorer.chain_mapping,
"original_chain_mapping": original_chain_mapping
"chain_mapping": qs_scorer.chain_mapping
}
# Calculate lDDT
if opts.lddt:
......@@ -594,8 +607,6 @@ def _Main():
lddt_results["single_chain_lddt"].append({
"status": "SUCCESS",
"error": "",
"original_model_chain": model_data["chain_mapping"][model_chain],
"original_reference_chain": reference_data["chain_mapping"][reference_chain],
"model_chain": model_chain,
"reference_chain": reference_chain,
"global_score": lddt_scorer.global_score,
......@@ -606,8 +617,6 @@ def _Main():
lddt_results["single_chain_lddt"].append({
"status": "FAILURE",
"error": str(ex),
"original_model_chain": model_data["chain_mapping"][model_chain],
"original_reference_chain": reference_data["chain_mapping"][reference_chain],
"model_chain": model_chain,
"reference_chain": reference_chain,
"global_score": 0.0,
......
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