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V0.21 Refactor and add ligand and target neighbor data. Keep all nea…
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…rest residue level interacitons.
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@jdwestbrook
jdwestbrook committed Feb 24, 2021
1 parent 61512f2 commit cc96d22
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Showing 9 changed files with 344 additions and 163 deletions.
3 changes: 2 additions & 1 deletion HISTORY.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -9,4 +9,5 @@
21-Feb-2021 - V0.17 Separate the computation and presentation of validation scores and target interactions
22-Feb-2021 - V0.18 Tweak sorting of unique target interactions and interaction and score attributes
23-Feb-2021 - V0.19 Change the default serialization and provide and format conversion method.
24-Feb-2021 - V0.20 Avoid reload with target updates when updateOnly=True
24-Feb-2021 - V0.20 Avoid reload with target updates when updateOnly=True
24-Feb-2021 - V0.21 Refactor and add ligand and target neighbor data. Keep all nearest residue level interacitons.
166 changes: 146 additions & 20 deletions rcsb/utils/dictionary/DictMethodCommonUtils.py
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178 changes: 111 additions & 67 deletions rcsb/utils/dictionary/DictMethodEntityInstanceHelper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1693,7 +1693,7 @@ def buildInstanceValidationScores(self, dataContainer, catName, **kwargs):
#
instanceModelValidationD = self.__commonU.getInstanceNonpolymerValidationInfo(dataContainer)
#
# NonpolymerValidationFields = ("rsr", "rscc", "mogul_bonds_rmsz", "mogul_angles_rmsz", "missing_heavy_atom_count")
# NonpolymerValidationFields = ("rsr", "rscc", "mogul_bonds_rmsz", "mogul_angles_rmsz")
#
logger.debug("Length instanceModelValidationD %d", len(instanceModelValidationD))
#
Expand All @@ -1704,23 +1704,15 @@ def buildInstanceValidationScores(self, dataContainer, catName, **kwargs):
rankD = {}
scoreD = {}
# -- Get existing interactions or calculate on the fly
if self.__tiP.hasEntry(entryId):
intD = self.__tiP.getInteractions(entryId)
ligandAtomCountD = self.__tiP.getAtomCounts(entryId)
if False and self.__tiP.hasEntry(entryId):
pass
# intD = self.__tiP.getInteractions(entryId)
# ligandAtomCountD = self.__tiP.getAtomCounts(entryId)
else:
intD, ligandAtomCountD = self.__commonU.getNonpolymerInstanceNeighbors(dataContainer)

intTargetD = {}
intNeighborD = {}
intIsBoundD = {}
for asymId, neighborL in intD.items():
isBound = False
for neighbor in neighborL:
intTargetD.setdefault(asymId, set()).add((neighbor.partnerEntityId, neighbor.partnerAsymId, neighbor.connectType))
intNeighborD.setdefault((neighbor.partnerEntityId, neighbor.partnerAsymId, neighbor.connectType), []).append(neighbor)
if neighbor.connectType != "non-bonded":
isBound = True
intIsBoundD[asymId] = isBound
# intD, ligandAtomCountD = self.__commonU.getNonpolymerInstanceNeighbors(dataContainer)
ligandAtomCountD = self.__commonU.getLigandAtomCountD(dataContainer)
intIsBoundD = self.__commonU.getLigandNeighborBoundState(dataContainer)

# --
# calculate scores and ranks and find best ranking
for (modelId, asymId, altId, compId), vTup in instanceModelValidationD.items():
Expand Down Expand Up @@ -1859,41 +1851,16 @@ def __calculateGeometryScore(self, bondsRmsZ, anglesRmsZ, meanD, stdD, loadingD)

return geoScore, geoRanking

def buildInstanceTargetInteractions(self, dataContainer, catName, **kwargs):
"""Build category rcsb_nonpolymer_instance_target_interactions ...
def buildInstanceTargetNeighbors(self, dataContainer, catName, **kwargs):
"""Build category rcsb_target_neighbors ...
Example:
loop_
_rcsb_nonpolymer_instance_target_interactions.ordinal
_rcsb_nonpolymer_instance_target_interactions.entry_id
_rcsb_nonpolymer_instance_target_interactions.model_id
_rcsb_nonpolymer_instance_target_interactions.entity_id
_rcsb_nonpolymer_instance_target_interactions.asym_id
_rcsb_nonpolymer_instance_target_interactions.auth_asym_id
_rcsb_nonpolymer_instance_target_interactions.comp_id
_rcsb_nonpolymer_instance_target_interactions.atom_id
_rcsb_nonpolymer_instance_target_interactions.alt_id
_rcsb_nonpolymer_instance_target_interactions.target_model_id
_rcsb_nonpolymer_instance_target_interactions.target_entity_id
_rcsb_nonpolymer_instance_target_interactions.target_asym_id
_rcsb_nonpolymer_instance_target_interactions.target_seq_id
_rcsb_nonpolymer_instance_target_interactions.target_comp_id
_rcsb_nonpolymer_instance_target_interactions.target_atom_id
_rcsb_nonpolymer_instance_target_interactions.target_is_bound
1 6TTM 1 2 B A PEG O4 A 1 1 A 270 GLU O N
2 6TTM 1 3 C A HYO N04 . 1 1 A 119 GLU OE2 N
3 6TTM 1 4 D A NI NI . 1 1 A 277 HIS NE2 Y
4 6TTM 1 6 F A EDO O1 . 1 1 A 232 ASP OD2 N
5 6TTM 1 6 G A EDO C1 . 1 1 A 102 GLU OE2 N
6 6TTM 1 7 H A SR SR . 1 1 A 101 GLY O Y
7 6TTM 1 8 I A UNX UNK . 1 1 A 148 ASN O N
8 6TTM 1 8 J A UNX UNK . 1 1 A 344 LYS NZ N
#
"""
logger.debug("Starting with %s %r %r", dataContainer.getName(), catName, kwargs)
startTime = time.time()
try:
if catName != "rcsb_nonpolymer_instance_target_interactions":
if catName != "rcsb_target_neighbors":
return False
if not dataContainer.exists("entry"):
return False
Expand All @@ -1910,27 +1877,22 @@ def buildInstanceTargetInteractions(self, dataContainer, catName, **kwargs):
asymIdD = self.__commonU.getInstanceEntityMap(dataContainer)
asymAuthIdD = self.__commonU.getAsymAuthIdMap(dataContainer)
# -- Get existing interactions or calculate on the fly
if self.__tiP.hasEntry(entryId):
intD = self.__tiP.getInteractions(entryId)
# TODO
if False and self.__tiP.hasEntry(entryId):
# intD = self.__tiP.getInteractions(entryId)
pass
else:
intD, _ = self.__commonU.getNonpolymerInstanceNeighborInfo(dataContainer)

# intD[asymId for each ligand] -> [LigandTargetInstance(),]
intTargetD = {}
intNeighborD = {}
intIsBoundD = {}
for asymId, neighborL in intD.items():
isBound = False
for neighbor in neighborL:
intTargetD.setdefault(asymId, set()).add((neighbor.partnerEntityId, neighbor.partnerAsymId, neighbor.connectType))
intNeighborD.setdefault(asymId, {}).setdefault((neighbor.partnerEntityId, neighbor.partnerAsymId, neighbor.connectType), []).append(neighbor)
if neighbor.connectType != "non-bonded":
isBound = True
intIsBoundD[asymId] = isBound
#
for asymId, nS in intTargetD.items():
for (partnerEntityId, partnerAsymId, pConnectType) in nS:
neighbor = intNeighborD[asymId][(partnerEntityId, partnerAsymId, pConnectType)][0]
ligandIndexD = self.__commonU.getLigandNeighborIndex(dataContainer)
nearestNeighborL = self.__commonU.getNearestNeighborList(dataContainer)
#
logger.debug("%s (%d) ligandIndexD %r", entryId, len(nearestNeighborL), ligandIndexD)
#
for asymId, nD in ligandIndexD.items():
for (partnerAsymId, partnerAuthSeqId), nIndex in nD.items():
logger.debug("%s pAsym %r pAuthSeqId %r nIndex %d", entryId, partnerAsymId, partnerAuthSeqId, nIndex)
#
neighbor = nearestNeighborL[nIndex]
# neighbor = intNeighborD[asymId][(partnerEntityId, partnerAsymId, pConnectType)][0]
#
entityId = asymIdD[asymId]
authAsymId = asymAuthIdD[asymId]
Expand All @@ -1946,11 +1908,12 @@ def buildInstanceTargetInteractions(self, dataContainer, catName, **kwargs):
cObj.setValue(neighbor.ligandAltId if neighbor.ligandAltId and neighbor.ligandAltId not in ["?"] else ".", "alt_id", ii)
cObj.setValue(neighbor.ligandCompId, "comp_id", ii)
#
cObj.setValue(neighbor.partnerEntityId, "target_model_id", ii)
cObj.setValue(neighbor.partnerModelId, "target_model_id", ii)
cObj.setValue(neighbor.partnerEntityId, "target_entity_id", ii)
cObj.setValue(neighbor.partnerAsymId, "target_asym_id", ii)
cObj.setValue(neighbor.partnerCompId, "target_comp_id", ii)
cObj.setValue(neighbor.partnerSeqId, "target_seq_id", ii)
cObj.setValue(neighbor.partnerAuthSeqId, "target_auth_seq_id", ii)
cObj.setValue(neighbor.partnerAtomId, "target_atom_id", ii)
cObj.setValue("N" if neighbor.connectType == "non-bonded" else "Y", "target_is_bound", ii)
cObj.setValue("%.3f" % neighbor.distance, "distance", ii)
Expand All @@ -1964,3 +1927,84 @@ def buildInstanceTargetInteractions(self, dataContainer, catName, **kwargs):
except Exception as e:
logger.exception("For %s %r failing with %s", dataContainer.getName(), catName, str(e))
return False

def buildInstanceLigandNeighbors(self, dataContainer, catName, **kwargs):
"""Build category rcsb_target_neighbors ...
Example:
"""
logger.debug("Starting with %s %r %r", dataContainer.getName(), catName, kwargs)
startTime = time.time()
try:
if catName != "rcsb_ligand_neighbors":
return False
if not dataContainer.exists("entry"):
return False
#
eObj = dataContainer.getObj("entry")
entryId = eObj.getValue("id", 0)
#
# Create the new target category
if not dataContainer.exists(catName):
dataContainer.append(DataCategory(catName, attributeNameList=self.__dApi.getAttributeNameList(catName)))
cObj = dataContainer.getObj(catName)
ii = cObj.getRowCount()
#
asymIdD = self.__commonU.getInstanceEntityMap(dataContainer)
asymAuthIdD = self.__commonU.getAsymAuthIdMap(dataContainer)
# -- Get existing interactions or calculate on the fly
# TODO
if False and self.__tiP.hasEntry(entryId):
# intD = self.__tiP.getInteractions(entryId)
pass
else:
targetIndexD = self.__commonU.getTargetNeighborIndex(dataContainer)
nearestNeighborL = self.__commonU.getNearestNeighborList(dataContainer)
#
logger.debug("%s (%d) targetIndexD %r", entryId, len(nearestNeighborL), targetIndexD)
#
for (asymId, authSeqId), nD in targetIndexD.items():
for ligandAsymId, nIndex in nD.items():
logger.debug("%s asymId %s authSeqId %s ligandAsym %rnIndex %d", entryId, asymId, authSeqId, ligandAsymId, nIndex)
#
neighbor = nearestNeighborL[nIndex]
#
entityId = asymIdD[asymId]
authAsymId = asymAuthIdD[asymId]
#
cObj.setValue(ii + 1, "ordinal", ii)
cObj.setValue(neighbor.ligandModelId, "model_id", ii)
cObj.setValue(entryId, "entry_id", ii)
cObj.setValue(entityId, "entity_id", ii)
cObj.setValue(asymId, "asym_id", ii)
cObj.setValue(authAsymId, "auth_asym_id", ii)
cObj.setValue(neighbor.partnerCompId, "comp_id", ii)
#
cObj.setValue(neighbor.partnerSeqId, "seq_id", ii)
cObj.setValue(neighbor.partnerAuthSeqId, "auth_seq_id", ii)

cObj.setValue(neighbor.partnerAtomId, "atom_id", ii)
cObj.setValue(neighbor.partnerAltId if neighbor.partnerAltId and neighbor.partnerAltId not in ["?"] else ".", "alt_id", ii)
#
cObj.setValue(neighbor.ligandModelId, "ligand_model_id", ii)
cObj.setValue(asymIdD[neighbor.ligandAsymId], "ligand_entity_id", ii)
cObj.setValue(neighbor.ligandAsymId, "ligand_asym_id", ii)
cObj.setValue(neighbor.ligandCompId, "ligand_comp_id", ii)
cObj.setValue(neighbor.ligandAtomId, "ligand_atom_id", ii)
cObj.setValue(neighbor.ligandAltId, "ligand_alt_id", ii)
cObj.setValue(neighbor.ligandAltId if neighbor.ligandAltId and neighbor.ligandAltId not in ["?"] else ".", "ligand_alt_id", ii)
cObj.setValue("N" if neighbor.connectType == "non-bonded" else "Y", "ligand_is_bound", ii)
cObj.setValue("%.3f" % neighbor.distance, "distance", ii)
# ----
ii += 1
#
##

#
endTime = time.time()
logger.debug("Completed at %s (%.4f seconds)", time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - startTime)
return True
except Exception as e:
logger.exception("For %s %r failing with %s", dataContainer.getName(), catName, str(e))
return False
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