diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 5a6d09b7fa3b7419ab2df9c97a1933d163a922fb..f2b9a58565f630d6a7757d4e4e0f7915aca723a5 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -17,7 +17,7 @@ Loads the structures and performs basic cleanup:
The cleaned structures are optionally dumped using -d/--dump-structures
Output is written in JSON format (default: out.json). In case of no additional
-options, this is a dictionary with 8 keys:
+options, this is a dictionary with 8 keys describing model/reference comparison:
* "reference_chains": Chain names of reference
* "model_chains": Chain names of model
@@ -36,7 +36,7 @@ options, this is a dictionary with 8 keys:
format.
* "inconsistent_residues": List of strings that represent name mismatches of
aligned residues in form
- <trg_cname>.<trg_rname><trg_rnum>-<mdl_cname>.<mdl_rname><mdl_rnum>.
+ <trg_cname>.<trg_rnum>.<trg_ins_code>-<mdl_cname>.<mdl_rnum>.<mdl_ins_code>.
Inconsistencies may lead to corrupt results but do not abort the program.
Program abortion in these cases can be enforced with
-ec/--enforce-consistency.
@@ -44,6 +44,20 @@ options, this is a dictionary with 8 keys:
content of the JSON output will be \"status\" set to FAILURE and an
additional key: "traceback".
+The following additional keys store relevant input parameters to reproduce
+results:
+
+ * "model"
+ * "reference"
+ * "fault_tolerant"
+ * "model_biounit"
+ * "reference_biounit"
+ * "residue_number_alignment"
+ * "enforce_consistency"
+ * "cad_exec"
+ * "usalign_exec"
+ * "lddt_no_stereochecks"
+
The pairwise sequence alignments are computed with Needleman-Wunsch using
BLOSUM62 (NUC44 for nucleotides). Many benchmarking scenarios preprocess the
structures to ensure matching residue numbers (CASP/CAMEO). In these cases,
@@ -216,13 +230,16 @@ def _ParseArgs():
default=False,
action="store_true",
help=("Compute per-residue lDDT scores with default parameterization "
- "and store as key \"local_lddt\". Score for model residue with "
- "number 42 in chain X can be extracted with: "
- "data[\"local_lddt\"][\"X\"][\"42\"]. If there is an insertion "
- "code, lets say A, the last key becomes \"42A\" Stereochemical "
- "irregularities affecting lDDT are reported as keys "
- "\"model_clashes\", \"model_bad_bonds\", \"model_bad_angles\" "
- "and the respective reference counterparts."))
+ "and store as key \"local_lddt\". Score for each residue is "
+ "accessible by key <chain_name>.<resnum>.<resnum_inscode>. "
+ "Residue with number 42 in chain X can be extracted with: "
+ "data[\"local_lddt\"][\"X.42.\"]. If there is an insertion "
+ "code, lets say A, the residue key becomes \"X.42.A\". "
+ "Stereochemical irregularities affecting lDDT are reported as "
+ "keys \"model_clashes\", \"model_bad_bonds\", "
+ "\"model_bad_angles\" and the respective reference "
+ "counterparts. Atoms specified in there follow the following "
+ "format: <chain_name>.<resnum>.<resnum_inscode>.<atom_name>"))
parser.add_argument(
"--bb-lddt",
@@ -241,10 +258,8 @@ def _ParseArgs():
help=("Compute per-residue lDDT scores with default parameterization "
"and store as key \"bb_local_lddt\". lDDT in this case is only "
"computed on backbone atoms: CA for peptides and C3' for "
- "nucleotides. Score for model residue with "
- "number 42 in chain X can be extracted with: "
- "data[\"local_lddt\"][\"X\"][\"42\"]. If there is an insertion "
- "code, lets say A, the last key becomes \"42A\""))
+ "nucleotides. Per-residue scores are accessible as described for "
+ "local_lddt."))
parser.add_argument(
"--cad-score",
@@ -262,12 +277,10 @@ def _ParseArgs():
default=False,
action="store_true",
help=("Compute local CAD's atom-atom (AA) scores and store as key "
- "\"local_cad_score\". Score for model residue with number 42 in "
- "chain X can be extracted with: "
- "data[\"local_cad_score\"][\"X\"][\"42\"]. "
- "--residue-number-alignments must be enabled to compute this "
- "score. Requires voronota_cadscore executable in PATH. "
- "Alternatively you can set cad-exec."))
+ "\"local_cad_score\". Per-residue scores are accessible as "
+ "described for local_lddt. --residue-number-alignments must be "
+ "enabled to compute this score. Requires voronota_cadscore "
+ "executable in PATH. Alternatively you can set cad-exec."))
parser.add_argument(
"--cad-exec",
@@ -350,8 +363,9 @@ def _ParseArgs():
"None. Model interface residues are available as key "
"\"model_interface_residues\", reference interface residues as "
"key \"reference_interface_residues\". Residues are represented "
- "as string in form <num><inscode>. The respective scores are "
- "available as keys \"patch_qs\" and \"patch_dockq\""))
+ "as string in form <chain_name>.<resnum>.<resnum_inscode>. "
+ "The respective scores are available as keys \"patch_qs\" and "
+ "\"patch_dockq\""))
parser.add_argument(
"--tm-score",
@@ -474,29 +488,47 @@ def _GetInconsistentResidues(alns):
r1 = col.GetResidue(0)
r2 = col.GetResidue(1)
if r1.IsValid() and r2.IsValid() and r1.GetName() != r2.GetName():
- lst.append((r1, r2))
- lst = [f"{x[0].GetQualifiedName()}-{x[1].GetQualifiedName()}" for x in lst]
+ ch_1 = r1.GetChain().name
+ num_1 = r1.number.num
+ ins_code_1 = r1.number.ins_code.strip("\u0000")
+ id_1 = f"{ch_1}.{num_1}.{ins_code_1}"
+ ch_2 = r2.GetChain().name
+ num_2 = r2.number.num
+ ins_code_2 = r2.number.ins_code.strip("\u0000")
+ id_2 = f"{ch_2}.{num_2}.{ins_code_2}"
+ lst.append(f"{id_1}-{id_2}")
return lst
def _LocalScoresToJSONDict(score_dict):
- """ Score for model residue with number rnum in chain X can be extracted
- with: data["local_cad_score"]["X"][rnum]. Convert ResNum object to str for
- JSON serialization
+ """ Convert ResNums to str for JSON serialization
"""
json_dict = dict()
for ch, ch_scores in score_dict.items():
- json_dict[ch] = {str(rnum): s for rnum, s in ch_scores.items()}
+ for num, s in ch_scores.items():
+ ins_code = num.ins_code.strip("\u0000")
+ json_dict[f"{ch}.{num.num}.{ins_code}"] = s
return json_dict
-def _InterfaceResiduesToJSONDict(interface_dict):
- """ Interface residues are stored as
- data["model_interface_residues"]["A"][rnum1, rnum2,...]. Convert ResNum
- object to str for JSON serialization.
+def _InterfaceResiduesToJSONList(interface_dict):
+ """ Convert ResNums to str for JSON serialization.
+
+ Changes in this function will affect _PatchScoresToJSONList
"""
- json_dict = dict()
+ json_list = list()
for ch, ch_nums in interface_dict.items():
- json_dict[ch] = [str(rnum) for rnum in ch_nums]
- return json_dict
+ for num in ch_nums:
+ ins_code = num.ins_code.strip("\u0000")
+ json_list.append(f"{ch}.{num.num}.{ins_code}")
+ return json_list
+
+def _PatchScoresToJSONList(interface_dict, score_dict):
+ """ Creates List of patch scores that are consistent with interface residue
+ lists
+ """
+ json_list = list()
+ for ch, ch_nums in interface_dict.items():
+ json_list += score_dict[ch]
+ return json_list
def _Process(model, reference, args):
@@ -579,11 +611,13 @@ def _Process(model, reference, args):
if args.patch_scores:
out["model_interface_residues"] = \
- _InterfaceResiduesToJSONDict(scorer.model_interface_residues)
+ _InterfaceResiduesToJSONList(scorer.model_interface_residues)
out["reference_interface_residues"] = \
- _InterfaceResiduesToJSONDict(scorer.target_interface_residues)
- out["patch_qs"] = scorer.patch_qs
- out["patch_dockq"] = scorer.patch_dockq
+ _InterfaceResiduesToJSONList(scorer.target_interface_residues)
+ out["patch_qs"] = _PatchScoresToJSONList(scorer.model_interface_residues,
+ scorer.patch_qs)
+ out["patch_dockq"] = _PatchScoresToJSONList(scorer.model_interface_residues,
+ scorer.patch_dockq)
if args.tm_score:
out["tm_score"] = scorer.tm_score
@@ -614,10 +648,6 @@ def _Process(model, reference, args):
"fails in this case.")
else:
raise
-
-
-
-
return out
def _Main():
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index 3178a2f5f4db18daf545281aaf3bcc1903f42ade..a71c8db2ec2cbc978da9de73001857e8718da23d 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -40,9 +40,11 @@ Details on the usage (output of ``ost compare-structures --help``):
[-c CHAIN_MAPPING [CHAIN_MAPPING ...]] [--lddt]
[--local-lddt] [--bb-lddt] [--bb-local-lddt]
[--cad-score] [--local-cad-score]
- [--cad-exec CAD_EXEC] [--qs-score]
+ [--cad-exec CAD_EXEC]
+ [--usalign-exec USALIGN_EXEC] [--qs-score]
[--rigid-scores] [--interface-scores]
- [--patch-scores]
+ [--patch-scores] [--tm-score]
+ [--lddt-no-stereochecks]
Evaluate model against reference
@@ -62,8 +64,8 @@ Details on the usage (output of ``ost compare-structures --help``):
The cleaned structures are optionally dumped using -d/--dump-structures
Output is written in JSON format (default: out.json). In case of no additional
- options, this is a dictionary with 8 keys:
-
+ options, this is a dictionary with 8 keys describing model/reference comparison:
+
* "reference_chains": Chain names of reference
* "model_chains": Chain names of model
* "chem_groups": Groups of polypeptides/polynucleotides from reference that
@@ -81,29 +83,43 @@ Details on the usage (output of ``ost compare-structures --help``):
format.
* "inconsistent_residues": List of strings that represent name mismatches of
aligned residues in form
- <trg_cname>.<trg_rname><trg_rnum>-<mdl_cname>.<mdl_rname><mdl_rnum>.
+ <trg_cname>.<trg_rnum>.<trg_ins_code>-<mdl_cname>.<mdl_rnum>.<mdl_ins_code>.
Inconsistencies may lead to corrupt results but do not abort the program.
Program abortion in these cases can be enforced with
-ec/--enforce-consistency.
* "status": SUCCESS if everything ran through. In case of failure, the only
content of the JSON output will be "status" set to FAILURE and an
additional key: "traceback".
-
+
+ The following additional keys store relevant input parameters to reproduce
+ results:
+
+ * "model"
+ * "reference"
+ * "fault_tolerant"
+ * "model_biounit"
+ * "reference_biounit"
+ * "residue_number_alignment"
+ * "enforce_consistency"
+ * "cad_exec"
+ * "usalign_exec"
+ * "lddt_no_stereochecks"
+
The pairwise sequence alignments are computed with Needleman-Wunsch using
BLOSUM62 (NUC44 for nucleotides). Many benchmarking scenarios preprocess the
structures to ensure matching residue numbers (CASP/CAMEO). In these cases,
enabling -rna/--residue-number-alignment is recommended.
-
+
Each score is opt-in and can be enabled with optional arguments.
-
+
Example to compute global and per-residue lDDT values as well as QS-score:
-
+
ost compare-structures -m model.pdb -r reference.cif --lddt --local-lddt --qs-score
-
+
Example to inject custom chain mapping
-
+
ost compare-structures -m model.pdb -r reference.cif -c A:B B:A
-
+
optional arguments:
-h, --help show this help message and exit
-m MODEL, --model MODEL
@@ -164,13 +180,17 @@ Details on the usage (output of ``ost compare-structures --help``):
counterparts.
--local-lddt Compute per-residue lDDT scores with default
parameterization and store as key "local_lddt". Score
- for model residue with number 42 in chain X can be
- extracted with: data["local_lddt"]["X"]["42"]. If
- there is an insertion code, lets say A, the last key
- becomes "42A" Stereochemical irregularities affecting
- lDDT are reported as keys "model_clashes",
- "model_bad_bonds", "model_bad_angles" and the
- respective reference counterparts.
+ for each residue is accessible by key
+ <chain_name>.<resnum>.<resnum_inscode>. Residue with
+ number 42 in chain X can be extracted with:
+ data["local_lddt"]["X.42."]. If there is an insertion
+ code, lets say A, the residue key becomes "X.42.A".
+ Stereochemical irregularities affecting lDDT are
+ reported as keys "model_clashes", "model_bad_bonds",
+ "model_bad_angles" and the respective reference
+ counterparts. Atoms specified in there follow the
+ following format:
+ <chain_name>.<resnum>.<resnum_inscode>.<atom_name>
--bb-lddt Compute global lDDT score with default
parameterization and store as key "bb_lddt". lDDT in
this case is only computed on backbone atoms: CA for
@@ -178,26 +198,26 @@ Details on the usage (output of ``ost compare-structures --help``):
--bb-local-lddt Compute per-residue lDDT scores with default
parameterization and store as key "bb_local_lddt".
lDDT in this case is only computed on backbone atoms:
- CA for peptides and C3' for nucleotides. Score for
- model residue with number 42 in chain X can be
- extracted with: data["local_lddt"]["X"]["42"]. If
- there is an insertion code, lets say A, the last key
- becomes "42A"
+ CA for peptides and C3' for nucleotides. Per-residue
+ scores are accessible as described for local_lddt.
--cad-score Compute global CAD's atom-atom (AA) score and store as
key "cad_score". --residue-number-alignment must be
enabled to compute this score. Requires
voronota_cadscore executable in PATH. Alternatively
you can set cad-exec.
--local-cad-score Compute local CAD's atom-atom (AA) scores and store as
- key "local_cad_score". Score for model residue with
- number 42 in chain X can be extracted with:
- data["local_cad_score"]["X"]["42"]. --residue-number-
- alignments must be enabled to compute this score.
- Requires voronota_cadscore executable in PATH.
+ key "local_cad_score". Per-residue scores are
+ accessible as described for local_lddt. --residue-
+ number-alignments must be enabled to compute this
+ score. Requires voronota_cadscore executable in PATH.
Alternatively you can set cad-exec.
--cad-exec CAD_EXEC Path to voronota-cadscore executable (installed from
https://github.com/kliment-olechnovic/voronota).
Searches PATH if not set.
+ --usalign-exec USALIGN_EXEC
+ Path to USalign executable to compute TM-score. If not
+ given, an OpenStructure internal copy of USalign code
+ is used.
--qs-score Compute QS-score, stored as key "qs_global", and the
QS-best variant, stored as key "qs_best".
--rigid-scores Computes rigid superposition based scores. They're
@@ -248,12 +268,13 @@ Details on the usage (output of ``ost compare-structures --help``):
"model_interface_residues", reference interface
residues as key "reference_interface_residues".
Residues are represented as string in form
- <num><inscode>. The respective scores are available as
- keys "patch_qs" and "patch_dockq"
+ <chain_name>.<resnum>.<resnum_inscode>. The respective
+ scores are available as keys "patch_qs" and
+ "patch_dockq"
--tm-score Computes TM-score with the USalign tool. Also computes
- a chain mapping in case of complexes that is stored
- in the same format as the default mapping. TM-score
- and the mapping are available as keys "tm_score" and
+ a chain mapping in case of complexes that is stored in
+ the same format as the default mapping. TM-score and
+ the mapping are available as keys "tm_score" and
"usalign_mapping"
--lddt-no-stereochecks
Disable stereochecks for lDDT computation
diff --git a/modules/mol/alg/pymod/stereochemistry.py b/modules/mol/alg/pymod/stereochemistry.py
index 625ee4ea15be6e0654a1048efb42d0b64cf86726..b3708648bf26a4e331f683e9fe7309196450f72c 100644
--- a/modules/mol/alg/pymod/stereochemistry.py
+++ b/modules/mol/alg/pymod/stereochemistry.py
@@ -9,6 +9,18 @@ from ost import geom
from ost import mol
+def _AtomToQualifiedName(a):
+ """ Returns string to uniquely identify atom
+
+ format: <chain_name>.<resnum>.<resnum_inscode>.<atom_name>
+ """
+ r = a.GetResidue()
+ ch = r.GetChain()
+ num = r.number.num
+ ins_code = r.number.ins_code.strip("\u0000")
+ return f"{ch.name}.{r.number.num}.{ins_code}.{a.name}"
+
+
def _PotentialDisulfid(a_one, a_two):
""" Returns whether two atoms can potentially build a disulfid bond
@@ -355,9 +367,12 @@ class ClashInfo:
def ToJSON(self):
""" Return JSON serializable dict
+
+ Atoms are represented by a string in format:
+ <chain_name>.<resnum>.<resnum_inscode>.<atom_name>
"""
- return {"a1": self.a1.GetQualifiedName(),
- "a2": self.a2.GetQualifiedName(),
+ return {"a1": _AtomToQualifiedName(self.a1),
+ "a2": _AtomToQualifiedName(self.a2),
"dist": self.dist,
"tolerated_dist": self.tolerated_dist}
@@ -382,9 +397,12 @@ class BondViolationInfo:
def ToJSON(self):
""" Return JSON serializable dict
+
+ Atoms are represented by a string in format:
+ <chain_name>.<resnum>.<resnum_inscode>.<atom_name>
"""
- return {"a1": self.a1.GetQualifiedName(),
- "a2": self.a2.GetQualifiedName(),
+ return {"a1": _AtomToQualifiedName(self.a1),
+ "a2": _AtomToQualifiedName(self.a2),
"length": self.length,
"exp_length": self.exp_length,
"std": self.std}
@@ -412,10 +430,13 @@ class AngleViolationInfo:
def ToJSON(self):
""" Return JSON serializable dict
+
+ Atoms are represented by a string in format:
+ <chain_name>.<resnum>.<resnum_inscode>.<atom_name>
"""
- return {"a1": self.a1.GetQualifiedName(),
- "a2": self.a2.GetQualifiedName(),
- "a3": self.a3.GetQualifiedName(),
+ return {"a1": _AtomToQualifiedName(self.a1),
+ "a2": _AtomToQualifiedName(self.a2),
+ "a3": _AtomToQualifiedName(self.a3),
"angle": self.angle,
"exp_angle": self.exp_angle,
"std": self.std}