diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index 07a687467f4aaf74b17f298db09bbd3476fe8cd6..12b3d7bfc27f4f9dd2af49c1f30507a29206b989 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -320,8 +320,6 @@ def _LoadStructure(structure_path, sformat, fault_tolerant, bu_id):
The returned structure has structure_path attached as structure name
"""
- # increase loglevel, as we would pollute the info log with weird stuff
- ost.PushVerbosityLevel(ost.LogLevel.Error)
# Load the structure
if sformat == "mmcif":
if bu_id is not None:
@@ -346,7 +344,6 @@ def _LoadStructure(structure_path, sformat, fault_tolerant, bu_id):
raise Exception(f"No residues found in file: {structure_path}")
# restore old loglevel and return
- ost.PopVerbosityLevel()
entity.SetName(structure_path)
return entity
@@ -528,6 +525,7 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
##################
if args.lddt_pli:
+ LogScript("Computing lDDT-PLI scores")
out["lddt_pli"] = dict()
out["lddt_pli"]["assigned_scores"] = list()
for lig_pair in lddtpli_scorer.assignment:
@@ -590,6 +588,7 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
if args.rmsd:
+ LogScript("Computing BiSyRMSD scores")
out["rmsd"] = dict()
out["rmsd"]["assigned_scores"] = list()
for lig_pair in scrmsd_scorer.assignment:
@@ -680,12 +679,15 @@ def _Main():
_CheckCompoundLib()
try:
# Load structures
+ LogScript("Loading data")
+ LogInfo("Loading reference structure")
reference_format = _GetStructureFormat(args.reference,
sformat=args.reference_format)
reference = _LoadStructure(args.reference,
sformat=reference_format,
bu_id=args.reference_biounit,
fault_tolerant = args.fault_tolerant)
+ LogInfo("Loading model structure")
model_format = _GetStructureFormat(args.model,
sformat=args.model_format)
model = _LoadStructure(args.model,
@@ -694,13 +696,19 @@ def _Main():
fault_tolerant = args.fault_tolerant)
# Load ligands
- model_ligands = _LoadLigands(args.model_ligands)
+ LogInfo("Loading reference ligands")
reference_ligands = _LoadLigands(args.reference_ligands)
+ LogInfo("Loading model ligands")
+ model_ligands = _LoadLigands(args.model_ligands)
# Cleanup
+ LogVerbose("Cleaning up reference structure")
cleaned_reference = _CleanupStructure(reference)
+ LogVerbose("Cleaning up model structure")
cleaned_model = _CleanupStructure(model)
+ LogVerbose("Cleaning up reference ligands")
cleaned_reference_ligands = _CleanupLigands(reference_ligands)
+ LogVerbose("Cleaning up model ligands")
cleaned_model_ligands = _CleanupLigands(model_ligands)
# Validate
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index b19107ba5fc0640ed6a068a27517b0acd257a0aa..9d025f3161fa5b1f1fa586935eb6cfde1f6286fe 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -1438,6 +1438,10 @@ class ChainMapper:
substructure_chem_mapping,
self.n_max_naive))
+ # This step can be slow so give some hints in logs
+ msg = "Computing initial ranking of %d chain mappings" % len(mappings)
+ (ost.LogWarning if len(mappings) > 10000 else ost.LogInfo)(msg)
+
for mapping in mappings:
# chain_mapping and alns as input for lDDT computation
lddt_chain_mapping = dict()
diff --git a/modules/mol/alg/pymod/ligand_scoring_base.py b/modules/mol/alg/pymod/ligand_scoring_base.py
index 3be4a958e5a08fe217d3e8846c053cfdcf2b4feb..19e8d617cbd7414ed3b944dee05d11a489848b63 100644
--- a/modules/mol/alg/pymod/ligand_scoring_base.py
+++ b/modules/mol/alg/pymod/ligand_scoring_base.py
@@ -1,10 +1,30 @@
+from contextlib import contextmanager
import numpy as np
import networkx
from ost import mol
-from ost import LogWarning, LogScript, LogVerbose, LogDebug
+from ost import LogWarning, LogScript, LogInfo, LogVerbose, LogDebug, GetVerbosityLevel, PushVerbosityLevel, PopVerbosityLevel
from ost.mol.alg import chain_mapping
+
+@contextmanager
+def _SinkVerbosityLevel(n=1):
+ """ Context manager to temporarily reduce the verbosity level by n.
+
+ Example usage:
+ with _SinkVerbosityLevel(2):
+ LogVerbose("Test")
+ Will only write "Test" in script level (2 above)
+ """
+ PushVerbosityLevel(GetVerbosityLevel() - n)
+ try:
+ yield
+ except:
+ raise
+ finally:
+ PopVerbosityLevel()
+
+
class LigandScorer:
""" Scorer to compute various small molecule ligand (non polymer) scores.
@@ -426,6 +446,7 @@ class LigandScorer:
raise RuntimeError("LigandScorer._score_dir must return one in "
"['+', '-']")
+ LogScript("Computing ligand assignment")
while len(tmp) > 0:
# select high coverage ligand pairs in working array
coverage_thresh = max([x[1] for x in tmp]) - self.coverage_delta
@@ -712,10 +733,11 @@ class LigandScorer:
:type: :class:`ost.mol.alg.chain_mapping.ChainMapper`
"""
if self.__chain_mapper is None:
- self.__chain_mapper = \
- chain_mapping.ChainMapper(self.target,
- n_max_naive=1e9,
- resnum_alignments=self.resnum_alignments)
+ with _SinkVerbosityLevel():
+ self.__chain_mapper = \
+ chain_mapping.ChainMapper(self.target,
+ n_max_naive=1e9,
+ resnum_alignments=self.resnum_alignments)
return self.__chain_mapper
@staticmethod
@@ -887,7 +909,7 @@ class LigandScorer:
self._state_matrix[g_idx,:] = 6
msg = "Disconnected graph observed for target ligand "
msg += str(self.target_ligands[g_idx])
- LogVerbose(msg)
+ LogWarning(msg)
for g_idx, g in enumerate(model_graphs):
if not networkx.is_connected(g):
@@ -895,11 +917,11 @@ class LigandScorer:
self._state_matrix[:,g_idx] = 6
msg = "Disconnected graph observed for model ligand "
msg += str(self.model_ligands[g_idx])
- LogVerbose(msg)
+ LogWarning(msg)
for target_id, target_ligand in enumerate(self.target_ligands):
- LogVerbose("Analyzing target ligand %s" % target_ligand)
+ LogInfo("Analyzing target ligand %s" % target_ligand)
if self._target_ligand_states[target_id] == 4:
# Disconnected graph - already updated states and reported
@@ -907,7 +929,7 @@ class LigandScorer:
continue
for model_id, model_ligand in enumerate(self.model_ligands):
- LogVerbose("Compare to model ligand %s" % model_ligand)
+ LogInfo("Comparing to model ligand %s" % model_ligand)
#########################################################
# Compute symmetries for given target/model ligand pair #
@@ -926,30 +948,30 @@ class LigandScorer:
max_symmetries=self.max_symmetries,
model_graph = model_graphs[model_id],
target_graph = target_graphs[target_id])
- LogVerbose("Ligands %s and %s symmetry match" % (
+ LogInfo("Ligands %s and %s symmetry match" % (
str(model_ligand), str(target_ligand)))
except NoSymmetryError:
# Ligands are different - skip
- LogVerbose("No symmetry between %s and %s" % (
+ LogInfo("No symmetry between %s and %s" % (
str(model_ligand), str(target_ligand)))
self._state_matrix[target_id, model_id] = 1
continue
except TooManySymmetriesError:
# Ligands are too symmetrical - skip
- LogVerbose("Too many symmetries between %s and %s" % (
+ LogWarning("Too many symmetries between %s and %s" % (
str(model_ligand), str(target_ligand)))
self._state_matrix[target_id, model_id] = 2
continue
except NoIsomorphicSymmetryError:
# Ligands are different - skip
- LogVerbose("No isomorphic symmetry between %s and %s" % (
+ LogInfo("No isomorphic symmetry between %s and %s" % (
str(model_ligand), str(target_ligand)))
self._state_matrix[target_id, model_id] = 3
continue
except DisconnectedGraphError:
# this should never happen as we guard against
# DisconnectedGraphError when precomputing the graph
- LogVerbose("Disconnected graph observed for %s and %s" % (
+ LogError("Disconnected graph observed for %s and %s" % (
str(model_ligand), str(target_ligand)))
# just set both ligand states to 4
self._model_ligand_states[model_id] = 4
diff --git a/modules/mol/alg/pymod/ligand_scoring_lddtpli.py b/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
index 5710e3efd07d91da727424a59f050e4f39c18ba9..5ba88920d39b424b6f328fa0b2b9b3d26d6bb575 100644
--- a/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
+++ b/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
@@ -935,10 +935,11 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
@property
def _chain_mapping_mdl(self):
- if self.__chain_mapping_mdl is None:
- self.__chem_mapping, self.__chem_group_alns, \
- self.__chain_mapping_mdl = \
- self._chain_mapper.GetChemMapping(self.model)
+ if self.__chain_mapping_mdl is None:
+ with ligand_scoring_base._SinkVerbosityLevel():
+ self.__chem_mapping, self.__chem_group_alns, \
+ self.__chain_mapping_mdl = \
+ self._chain_mapper.GetChemMapping(self.model)
return self.__chain_mapping_mdl
# specify public interface
diff --git a/modules/mol/alg/pymod/ligand_scoring_scrmsd.py b/modules/mol/alg/pymod/ligand_scoring_scrmsd.py
index 56ef24a9e9cccf354e2b286aac1794ae40526ae2..5dc6e61e815c494b70641211e6bb603ed9770e17 100644
--- a/modules/mol/alg/pymod/ligand_scoring_scrmsd.py
+++ b/modules/mol/alg/pymod/ligand_scoring_scrmsd.py
@@ -1,11 +1,12 @@
import numpy as np
-from ost import LogWarning
+from ost import LogWarning, LogScript, LogInfo, LogVerbose
from ost import geom
from ost import mol
from ost.mol.alg import ligand_scoring_base
+
class SCRMSDScorer(ligand_scoring_base.LigandScorer):
""" :class:`LigandScorer` implementing symmetry corrected RMSD.
@@ -174,6 +175,9 @@ class SCRMSDScorer(ligand_scoring_base.LigandScorer):
"inconsistent_residues": list()}
representations = self._get_repr(target_ligand, model_ligand)
+ # This step can be slow so give some hints in logs
+ msg = "Computing BiSyRMSD with %d chain mappings" % len(representations)
+ (LogWarning if len(representations) > 10000 else LogInfo)(msg)
for r in representations:
rmsd = _SCRMSD_symmetries(symmetries, model_ligand,
@@ -231,6 +235,8 @@ class SCRMSDScorer(ligand_scoring_base.LigandScorer):
if key not in self._repr:
ref_bs = self._get_target_binding_site(target_ligand)
+ LogVerbose("%d chains are in proximity of the target ligand: %s" % (
+ ref_bs.chain_count, ", ".join([c.name for c in ref_bs.chains])))
if self.full_bs_search:
reprs = self._chain_mapper.GetRepr(
ref_bs, self.model, inclusion_radius=self.lddt_lp_radius,
@@ -262,7 +268,8 @@ class SCRMSDScorer(ligand_scoring_base.LigandScorer):
h = ref_res.handle.GetHashCode()
if h not in ref_residues_hashes and \
h not in ignored_residue_hashes:
- view = self._chain_mapper.target.ViewForHandle(ref_res)
+ with ligand_scoring_base._SinkVerbosityLevel(1):
+ view = self._chain_mapper.target.ViewForHandle(ref_res)
if view.IsValid():
h = ref_res.handle.GetHashCode()
ref_residues_hashes.add(h)
@@ -341,12 +348,15 @@ class SCRMSDScorer(ligand_scoring_base.LigandScorer):
radius = self.model_bs_radius
chains = set()
for at in mdl_ligand.atoms:
- close_atoms = self._chain_mapping_mdl.FindWithin(at.GetPos(),
- radius)
+ with ligand_scoring_base._SinkVerbosityLevel(1):
+ close_atoms = self._chain_mapping_mdl.FindWithin(at.GetPos(),
+ radius)
for close_at in close_atoms:
chains.add(close_at.GetChain().GetName())
if len(chains) > 0:
+ LogVerbose("%d chains are in proximity of the model ligand: %s" % (
+ len(chains), ", ".join(chains)))
# the chain mapping model which only contains close chains
query = "cname="