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Commit da46b61e authored by Rafal Gumienny's avatar Rafal Gumienny
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feat: Save chain mappings

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actions/ost-compare-structures
+ 56
− 31
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......@@ -15,7 +15,7 @@ from ost.io import (LoadPDB, LoadMMCIF, MMCifInfoBioUnit, MMCifInfo,
MMCifInfoTransOp, ReadStereoChemicalPropsFile)
from ost import PushVerbosityLevel
from ost.mol.alg import (qsscoring, Molck, MolckSettings, lDDTSettings,
lDDTScorer, CheckStructure)
CheckStructure)
from ost.conop import CompoundLib
......@@ -150,7 +150,8 @@ def _ParseArgs():
dest="residue_number_alignment",
default=False,
action="store_true",
help=("Make alignment based on residue number instead using Clustal."))
help=("Make alignment based on residue number instead of using "
"Clustal."))
#
# lDDT options
#
......@@ -331,7 +332,9 @@ def _ReadStructureFile(path):
if not entity.IsValid():
raise IOError("Provided file does not contain valid entity.")
entity.SetName(os.path.basename(path))
entities.append(entity)
chain_mapping = {c.name: c.name for c in entity.chains}
entities.append({"entity": entity,
"chain_mapping": chain_mapping})
except Exception:
try:
tmp_entity, cif_info = LoadMMCIF(path, info=True)
......@@ -347,7 +350,11 @@ def _ReadStructureFile(path):
tbu.AddOperations(tinfo.GetOperations())
entity = tbu.PDBize(tmp_entity, min_polymer_size=0)
entity.SetName(os.path.basename(path) + ".au")
entities.append(entity)
chain_mapping = {c.name: c.GetStringProp("original_name")
for c in entity.chains}
entities.append({
"entity": entity,
"chain_mapping": chain_mapping})
elif len(cif_info.biounits) > 1:
for i, biounit in enumerate(cif_info.biounits):
entity = biounit.PDBize(tmp_entity, min_polymer_size=0)
......@@ -355,7 +362,11 @@ def _ReadStructureFile(path):
raise IOError(
"Provided file does not contain valid entity.")
entity.SetName(os.path.basename(path) + "." + str(i))
entities.append(entity)
chain_mapping = {c.name: c.GetStringProp("original_name")
for c in entity.chains}
entities.append({
"entity": entity,
"chain_mapping": chain_mapping})
else:
biounit = cif_info.biounits[0]
entity = biounit.PDBize(tmp_entity, min_polymer_size=0)
......@@ -363,7 +374,11 @@ def _ReadStructureFile(path):
raise IOError(
"Provided file does not contain valid entity.")
entity.SetName(os.path.basename(path))
entities.append(entity)
chain_mapping = {c.name: c.GetStringProp("original_name")
for c in entity.chains}
entities.append({
"entity": entity,
"chain_mapping": chain_mapping})
except Exception as exc:
raise exc
......@@ -386,17 +401,6 @@ def _MolckEntity(entity, options):
Molck(entity, lib, ms)
def _AveragelDDT(scorers):
scores = [s.global_score for s in scorers]
weights = [s.total_contacts for s in scorers]
nominator = sum([s * w for s, w in zip(scores, weights)])
denominator = sum(weights)
if denominator > 0:
return nominator / float(denominator)
else:
return 0.0
def _Main():
"""Do the magic."""
......@@ -410,17 +414,22 @@ def _Main():
references = _ReadStructureFile(opts.reference)
if opts.molck:
for i in range(len(references)):
_MolckEntity(references[i], opts)
references[i] = references[i].CreateFullView()
_MolckEntity(references[i]["entity"], opts)
references[i]["entity"] = references[i]["entity"].CreateFullView()
for i in range(len(models)):
_MolckEntity(models[i], opts)
models[i] = models[i].CreateFullView()
_MolckEntity(models[i]["entity"], opts)
models[i]["entity"] = models[i]["entity"].CreateFullView()
else:
for i in range(len(references)):
references[i]["entity"] = references[i]["entity"].CreateFullView()
for i in range(len(models)):
models[i]["entity"] = models[i]["entity"].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,
CheckStructure(reference["entity"],
stereochemical_parameters.bond_table,
stereochemical_parameters.angle_table,
stereochemical_parameters.nonbonded_table,
......@@ -428,7 +437,7 @@ def _Main():
opts.angle_tolerance)
ost.LogInfo("Performing structural checks for model(s)")
for model in models:
CheckStructure(model,
CheckStructure(model["entity"],
stereochemical_parameters.bond_table,
stereochemical_parameters.angle_table,
stereochemical_parameters.nonbonded_table,
......@@ -445,10 +454,12 @@ def _Main():
result["options"]["cwd"] = os.path.abspath(os.getcwd())
#
# Perform scoring
for model in models:
for model_data in models:
model = model_data["entity"]
model_name = model.GetName()
model_results = dict()
for reference in references:
for reference_data in references:
reference = reference_data["entity"]
reference_name = reference.GetName()
reference_results = dict()
ost.LogInfo("#\nComparing %s to %s" % (
......@@ -462,6 +473,11 @@ 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:
......@@ -472,7 +488,8 @@ def _Main():
"reference_name": reference_name,
"global_score": qs_scorer.global_score,
"best_score": qs_scorer.best_score,
"chain_mapping": qs_scorer.chain_mapping
"chain_mapping": qs_scorer.chain_mapping,
"original_chain_mapping": original_chain_mapping
}
except qsscoring.QSscoreError as ex:
# default handling: report failure and set score to 0
......@@ -484,7 +501,8 @@ def _Main():
"reference_name": reference.GetName(),
"global_score": 0.0,
"best_score": 0.0,
"chain_mapping": None
"chain_mapping": qs_scorer.chain_mapping,
"original_chain_mapping": original_chain_mapping
}
# Calculate lDDT
if opts.lddt:
......@@ -513,11 +531,16 @@ def _Main():
for lddt_scorer in oligo_lddt_scorer.sc_lddt_scorers:
# Get chains and renumber according to alignment (for lDDT)
try:
model_chain = lddt_scorer.model.chains[0].GetName()
reference_chain = \
lddt_scorer.references[0].chains[0].GetName()
lddt_results["single_chain_lddt"].append({
"status": "SUCCESS",
"error": "",
"model_chain": lddt_scorer.model.chains[0].GetName(),
"reference_chain": lddt_scorer.references[0].chains[0].GetName(),
"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,
"conserved_contacts": lddt_scorer.conserved_contacts,
"total_contacts": lddt_scorer.total_contacts})
......@@ -526,8 +549,10 @@ def _Main():
lddt_results["single_chain_lddt"].append({
"status": "FAILURE",
"error": str(ex),
"model_chain": lddt_scorer.model.chains[0].GetName(),
"reference_chain": lddt_scorer.references[0].chains[0].GetName(),
"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,
"conserved_contacts": 0.0,
"total_contacts": 0.0})
......
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