diff --git a/actions/CMakeLists.txt b/actions/CMakeLists.txt
index 8597f5aecd26ea1c0d09bd966d529620ec2833cc..ce6e23204e1a1b3b08332c428e78d29384c48808 100644
--- a/actions/CMakeLists.txt
+++ b/actions/CMakeLists.txt
@@ -1,5 +1,4 @@
add_custom_target(actions ALL)
ost_action_init()
-ost_action(ost-qs-score actions)
ost_action(ost-compare-structures actions)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 554c24a8b3cc0d057c7adbac2029c13851a949a1..a16c76f06ce60137bff4fc2f9ac9de443e672585 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -718,8 +718,6 @@ def _Main():
reference_results["qs_score"] = {
"status": "SUCCESS",
"error": "",
- "model_name": model_name,
- "reference_name": reference_name,
"global_score": qs_scorer.global_score,
"best_score": qs_scorer.best_score}
except qsscoring.QSscoreError as ex:
@@ -728,8 +726,6 @@ def _Main():
reference_results["qs_score"] = {
"status": "FAILURE",
"error": str(ex),
- "model_name": model_name,
- "reference_name": reference_name,
"global_score": 0.0,
"best_score": 0.0}
# Calculate lDDT
diff --git a/actions/ost-qs-score b/actions/ost-qs-score
deleted file mode 100644
index 0a92262a70688ba535ee902a6599a14ff0f10c29..0000000000000000000000000000000000000000
--- a/actions/ost-qs-score
+++ /dev/null
@@ -1,188 +0,0 @@
-"""Calculate Quaternary Structure score (QS-score) between two complexes."""
-
-import os
-import sys
-import json
-import argparse
-
-import ost
-from ost.io import (LoadPDB, LoadMMCIF, MMCifInfoBioUnit, MMCifInfo,
- MMCifInfoTransOp)
-from ost import PushVerbosityLevel
-from ost.mol.alg import qsscoring
-
-
-def _ParseArgs():
- """Parse command-line arguments."""
- parser = argparse.ArgumentParser(
- formatter_class=argparse.ArgumentDefaultsHelpFormatter,
- description=__doc__,
- prog="ost qs-score")
-
- parser.add_argument(
- '-v',
- '--verbosity',
- type=int,
- default=3,
- help="Set verbosity level.")
- parser.add_argument(
- "-m",
- "--model",
- dest="model",
- required=True,
- help=("Path to the model file."))
- parser.add_argument(
- "-r",
- "--reference",
- dest="reference",
- required=True,
- help=("Path to the reference file."))
- parser.add_argument(
- "-c",
- "--chain-mapping",
- nargs="+",
- type=lambda x: x.split(":"),
- dest="chain_mapping",
- help=("Mapping of chains between the model and the reference. "
- "Each separate mapping consist of key:value pairs where key "
- "is the chain name in model and value is the chain name in "
- "reference."))
- parser.add_argument(
- "-o",
- "--output",
- dest="output",
- help=("Output file name. The output will be saved as a JSON file."))
-
- opts = parser.parse_args()
- if opts.chain_mapping is not None:
- try:
- opts.chain_mapping = dict(opts.chain_mapping)
- except ValueError:
- raise ValueError("Cannot parse chain mapping into dictionary. The "
- "correct format is: key:value.")
-
- return opts
-
-
-def _ReadStructureFile(path):
- """Safely read structure file into OST entity.
-
- The functin can read both PDB and mmCIF files.
-
- :param path: Path to the file.
- :type path: :class:`str`
- :returns: Entity
- :rtype: :class:`~ost.mol.EntityHandle`
- """
- entities = list()
- if not os.path.isfile(path):
- raise IOError("%s is not a file" % path)
- try:
- entity = LoadPDB(path)
- if not entity.IsValid():
- raise IOError("Provided file does not contain valid entity.")
- entity.SetName(os.path.basename(path))
- entities.append(entity)
- except Exception:
- try:
- tmp_entity, cif_info = LoadMMCIF(path, info=True)
- if len(cif_info.biounits) == 0:
- tbu = MMCifInfoBioUnit()
- tbu.id = 'ASU of ' + entity.pdb_id
- tbu.details = 'asymmetric unit'
- for chain in tmp_entity.chains:
- tbu.AddChain(str(chain))
- tinfo = MMCifInfo()
- tops = MMCifInfoTransOp()
- tinfo.AddOperation(tops)
- tbu.AddOperations(tinfo.GetOperations())
- entity = tbu.PDBize(tmp_entity, min_polymer_size=0)
- entity.SetName(os.path.basename(path) + ".au")
- 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)
- if not entity.IsValid():
- raise IOError(
- "Provided file does not contain valid entity.")
- entity.SetName(os.path.basename(path) + "." + str(i))
- entities.append(entity)
- else:
- biounit = cif_info.biounits[0]
- entity = biounit.PDBize(tmp_entity, min_polymer_size=0)
- if not entity.IsValid():
- raise IOError(
- "Provided file does not contain valid entity.")
- entity.SetName(os.path.basename(path))
- entities.append(entity)
-
- except Exception as exc:
- raise exc
- return entities
-
-
-def _Main():
- """Do the magic."""
-
- opts = _ParseArgs()
- PushVerbosityLevel(opts.verbosity)
- #
- # Read the input files
- ost.LogInfo("Reading model from %s" % opts.model)
- models = _ReadStructureFile(opts.model)
- ost.LogInfo("Reading reference from %s" % opts.reference)
- references = _ReadStructureFile(opts.reference)
-
- if len(models) > 1 or len(references) > 1:
- ost.LogInfo(
- "Multiple complexes detected. All combinations will be tried.")
-
- result = {"result": []}
- #
- # Perform scoring
- for model in models:
- for reference in references:
- ost.LogInfo("#\nComparing %s to %s" % (
- model.GetName(),
- reference.GetName()))
- try:
- qs_scorer = qsscoring.QSscorer(reference,
- model)
- if opts.chain_mapping is not None:
- ost.LogInfo(
- "Using custom chain mapping: %s" % str(
- opts.chain_mapping))
- qs_scorer.chain_mapping = opts.chain_mapping
- result["result"].append({
- "status": "SUCCESS",
- "error": "",
- "model_name": model.GetName(),
- "reference_name": reference.GetName(),
- "global_score": qs_scorer.global_score,
- "oligo_lddt_score": qs_scorer.lddt_score,
- "best_score": qs_scorer.best_score,
- "chain_mapping": qs_scorer.chain_mapping
- })
- except qsscoring.QSscoreError as ex:
- # default handling: report failure and set score to 0
- ost.LogError('QSscore failed:', str(ex))
- result["result"].append({
- "status": "FAILURE",
- "error": str(ex),
- "model_name": model.GetName(),
- "reference_name": reference.GetName(),
- "global_score": 0.0,
- "oligo_lddt_score": 0.0,
- "best_score": 0.0,
- "chain_mapping": None
- })
- if opts.output is not None:
- with open(opts.output, "w") as outfile:
- outfile.write(json.dumps(result, indent=4))
-
-
-if __name__ == '__main__':
- # make script 'hot'
- unbuffered = os.fdopen(sys.stdout.fileno(), 'w', 0)
- sys.stdout = unbuffered
- _Main()
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index ed8bf52c558e94c0e00914ac34129204ec41eb42..0ef131cf61d3aca7469c06ab7d5bf670f1c14bde 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -9,43 +9,97 @@ you can type ``ost <ACTION> -h`` to get a description on its usage.
Here we list the most prominent actions with simple examples.
-.. ost-qs-score:
+.. ost-compare-structures:
-Calculating QS-Score
+Comparing two structures
--------------------------------------------------------------------------------
-You can calculate quaternary structure score between two complexes
-from the command line with
+You can compare two structures in terms of quaternary structure score and
+lDDT scores between two complexes from the command line with:
.. code-block:: console
- $ ost qs-score [-h] [-v VERBOSITY] -m MODEL -r REFERENCE
- [-c CHAIN_MAPPING [CHAIN_MAPPING ...]] [-o OUTPUT]
+ $ ost compare-structures [-h] [-v VERBOSITY] -m MODEL -r REFERENCE
+ [-o OUTPUT] [-d] [-ds DUMP_SUFFIX]
+ [-rs REFERENCE_SELECTION] [-ms MODEL_SELECTION]
+ [-ca] [-ft] [-qs]
+ [-c CHAIN_MAPPING [CHAIN_MAPPING ...]] [-rna]
+ [-l] [-sc] [-p PARAMETER_FILE]
+ [-bt BOND_TOLERANCE] [-at ANGLE_TOLERANCE]
+ [-ir INCLUSION_RADIUS] [-ss SEQUENCE_SEPARATION]
+ [-cc] [-spr] [-ml] [-cl COMPOUND_LIBRARY]
+ [-rm REMOVE [REMOVE ...]] [-ce] [-mn]
By default the verbosity is set to 3 which will result in the informations
being shown in the console. The result can be (optionally) saved as JSON file
which is the preferred way of parsing it as the log output might change in the
-future. The output file has following format:
+future. Optionally, the local scores for lDDT can also be dumped to the output
+file. Additionally, cleaned up structures can be saved to the disk.
+The output file has following format:
.. code-block:: python
{
- "result": [
- {
- "status": <SUCCESS or FAILURE>,
- "reference_name": <Reference name extracted from the file name>,
- "model_name": <Model name extracted from the file name>,
- "error": <ERROR message if any>,
- "best_score": <Best QS-score>,
- "lddt_score": <lDDT score>
- "global_score": <Global QS-score>,
- "chain_mapping": <Mapping of chains eg. {"A": "B", "B": "A"}>,
+ "result": {
+ "<MODEL NAME>": { # Model name extracted from the file name
+ "<REFERENCE NAME>": { # Reference name extracted from the file name
+ "info": {
+ "residue_names_consistent": <Are the residue numbers consistent? true or false>,
+ "mapping": <Mapping of chains eg. {"A": "B", "B": "A"}>,
+ "alignments": <list of chain-chain alignments in FASTA format>
+ }
+ },
+ "lddt": { # calculated when --lddt (-l) option is selected
+ "oligo_lddt": {
+ "status": <SUCCESS or FAILURE>,
+ "error": <ERROR message if any>,
+ "global_score": <calculated oligomeric lddt score>,
+ },
+ "weighted_lddt": {
+ "status": <SUCCESS or FAILURE>,
+ "error": <ERROR message if any>,
+ "global_score": <calculated weighted lddt score>,
+ },
+ "single_chain_lddt": [ # a list of chain-chain lDDts
+ {
+ "status": <SUCCESS or FAILURE>,
+ "error": <ERROR message if any>,
+ "reference_chain": <name of the chain in reference>,
+ "model_chain": <name of the chain in model>
+ "global_score": <calculated single-chain lddt score>,
+ "conserved_contacts": <number of conserved contacts between model and reference>,
+ "total_contacts": <total number of contacts between model and reference>,
+ "per_residue_scores": [ # per-residue lDDT scores - calculated when --save-per-residue-scores (-spr) option is selected
+ {
+ "total_contacts": <total number of contacts between model and reference>,
+ "residue_name": <three letter code of the residue>,
+ "lddt": <residue lDDT score>,
+ "conserved_contacts": <number of conserved contacts between model and reference for given residue>,
+ "residue_number": <total number of contacts between model and reference for given residue>
+ },
+ .
+ .
+ .
+ ]
+ }
+ ]
+ },
+ "qs_score": { # calculated when --qs-score (-q) option is selected
+ "status": <SUCCESS or FAILURE>,
+ "error": <ERROR message if any>,
+ "global_score": <Global QS-score>,
+ "best_score": <Best QS-score>,
+ }
+
+ }
}
- ]
+ },
+ "options": {} # Options used to run the script
}
-The "result" filed is a list as eg. in mmCIF file there can be many entities and
-the script will compare all combinations.
+The "result" filed is a dictionary mapping from model to reference as eg. in
+mmCIF file there can be many entities and the script will compare all
+combinations.
Example usage:
@@ -53,13 +107,247 @@ Example usage:
$ curl https://www.cameo3d.org/static/data/modeling/2018.03.03/5X7J_B/bu_target_01.pdb > reference.pdb
$ curl https://www.cameo3d.org/static/data/modeling/2018.03.03/5X7J_B/servers/server11/oligo_model-1/superposed_oligo_model-1.pdb > model.pdb
- $ ost qs-score -r reference.pdb -m model.pdb -o qs.json
+ $ $OST_ROOT/bin/ost compare-structures --model model.pdb --reference reference.pdb --output output.json --qs-score --residue-number-alignment --lddt --structural-checks --consistency-checks --inclusion-radius 15.0 --bond-tolerance 15.0 --angle-tolerance 15.0 --molck --remove oxt hyd unk --clean-element-column --map-nonstandard-residues
+
+ ################################################################################
+ Reading input files (fault_tolerant=False)
+ --> reading model from model.pdb
+ imported 2 chains, 396 residues, 3106 atoms; with 0 helices and 0 strands
+ --> reading reference from reference.pdb
+ imported 3 chains, 408 residues, 3011 atoms; with 0 helices and 0 strands
+ ################################################################################
+ Cleaning up input with Molck
+ removing hydrogen atoms
+ --> removed 0 hydrogen atoms
+ removing OXT atoms
+ --> removed 0 OXT atoms
+ residue A.GLN54 is missing 4 atoms: 'CG', 'CD', 'OE1', 'NE2'
+ residue A.GLU55 is missing 4 atoms: 'CG', 'CD', 'OE1', 'OE2'
+ residue A.ARG139 is missing 6 atoms: 'CG', 'CD', 'NE', 'CZ', 'NH1', 'NH2'
+ residue B.THR53 is missing 1 atom: 'CG2'
+ residue B.GLN54 is missing 4 atoms: 'CG', 'CD', 'OE1', 'NE2'
+ residue B.GLU55 is missing 4 atoms: 'CG', 'CD', 'OE1', 'OE2'
+ residue B.GLU61 is missing 1 atom: 'OE2'
+ residue B.GLU117 is missing 1 atom: 'O'
+ residue B.ARG120 is missing 2 atoms: 'NH1', 'NH2'
+ residue B.ARG142 is missing 2 atoms: 'NH1', 'NH2'
+ residue B.GLU148 is missing 4 atoms: 'CG', 'CD', 'OE1', 'OE2'
+ residue B.PRO198 is missing 1 atom: 'O'
+ _.CL1 is not a standard amino acid
+ _.CL2 is not a standard amino acid
+ _.CL3 is not a standard amino acid
+ _.CL4 is not a standard amino acid
+ _.CA5 is not a standard amino acid
+ _.CA6 is not a standard amino acid
+ _.CA7 is not a standard amino acid
+ _.CA8 is not a standard amino acid
+ _.CA9 is not a standard amino acid
+ _.CL10 is not a standard amino acid
+ _.CL11 is not a standard amino acid
+ _.CL12 is not a standard amino acid
+ _.CL13 is not a standard amino acid
+ _.CL14 is not a standard amino acid
+ _.CL15 is not a standard amino acid
+ _.CA16 is not a standard amino acid
+ _.CA17 is not a standard amino acid
+ _.CA18 is not a standard amino acid
+ _.CA19 is not a standard amino acid
+ _.CA20 is not a standard amino acid
+ _.EDO21 is not a standard amino acid
+ _.EDO22 is not a standard amino acid
+ _.EDO23 is not a standard amino acid
+ _.EDO24 is not a standard amino acid
+ removing hydrogen atoms
+ --> removed 0 hydrogen atoms
+ removing OXT atoms
+ --> removed 0 OXT atoms
+ ################################################################################
+ Performing structural checks
+ --> for reference(s)
+ Checking
+ Checking stereo-chemistry
+ Average Z-Score for bond lengths: -nan
+ Bonds outside of tolerance range: 0 out of 0
+ Bond Avg Length Avg zscore Num Bonds
+ Average Z-Score angle widths: 0.00000
+ Angles outside of tolerance range: 0 out of 1
+ Filtering non-bonded clashes
+ 0 non-bonded short-range distances shorter than tolerance distance
+ Distances shorter than tolerance are on average shorter by: 0.00000
+ --> for model(s)
+ Checking
+ Checking stereo-chemistry
+ Average Z-Score for bond lengths: -nan
+ Bonds outside of tolerance range: 0 out of 0
+ Bond Avg Length Avg zscore Num Bonds
+ Average Z-Score angle widths: 0.00000
+ Angles outside of tolerance range: 0 out of 1
+ Filtering non-bonded clashes
+ 0 non-bonded short-range distances shorter than tolerance distance
+ Distances shorter than tolerance are on average shorter by: 0.00000
+ ################################################################################
+ Comparing to
+ Chains removed from : _
+ Chains in : AB
+ Chains in : AB
+ Chemically equivalent chain-groups in pdb_1: [['B', 'A']]
+ Chemically equivalent chain-groups in pdb_2: [['A', 'B']]
+ Chemical chain-groups mapping: {('B', 'A'): ('A', 'B')}
+ Identifying Symmetry Groups...
+ Symmetry threshold 0.1 used for angles of pdb_1
+ Symmetry threshold 0.1 used for axis of pdb_1
+ Symmetry threshold 0.1 used for angles of pdb_2
+ Symmetry threshold 0.1 used for axis of pdb_2
+ Selecting Symmetry Groups...
+ Symmetry-groups used in pdb_1: [('B',), ('A',)]
+ Symmetry-groups used in pdb_2: [('A',), ('B',)]
+ Closed Symmetry with strict parameters
+ Mapping found: {'A': 'B', 'B': 'A'}
+ --------------------------------------------------------------------------------
+ Checking consistency between and
+ Consistency check: OK
+ --------------------------------------------------------------------------------
+ Computing QS-score
+ QSscore pdb_1, pdb_2: best: 0.90, global: 0.90
+ --------------------------------------------------------------------------------
+ Computing lDDT scores
+ lDDT settings:
+ Inclusion Radius: 15
+ Sequence separation: 0
+ Cutoffs: 0.5, 1, 2, 4
+ Residue properties label: lddt
+ ===
+ --> Computing lDDT between model chain B and reference chain A
+ Coverage: 1 (187 out of 187 residues)
+ Global LDDT score: 0.8257
+ (877834 conserved distances out of 1063080 checked, over 4 thresholds)
+ --> Computing lDDT between model chain A and reference chain B
+ Coverage: 1 (197 out of 197 residues)
+ Global LDDT score: 0.7854
+ (904568 conserved distances out of 1151664 checked, over 4 thresholds)
+ --> Computing oligomeric lDDT score
+ Reference pdb_1 has: 2 chains
+ Model pdb_2 has: 2 chains
+ Coverage: 1 (384 out of 384 residues)
+ Oligo lDDT score: 0.8025
+ --> Computing weighted lDDT score
+ Weighted lDDT score: 0.8048
+ ################################################################################
+ Saving output into output.json
+
+
+This reads the model and reference file and calculates QS-score between them.
+In the example above the output file looks as follows:
+
+.. code-block:: python
- Reading model from model.pdb
+ {
+ "result": {
+ "": {
+ "": {
+ "info": {
+ "residue_names_consistent": true,
+ "mapping": {
+ "chain_mapping": {
+ "A": "B",
+ "B": "A"
+ },
+ "alignments": [
+ ">reference:A\n-PGLFLTLEGLDGSGKTTQARRLAAFLEAQGRPVLLTREPGGGLPEVRSL---QELSPEAEYLLFSADRAEHVRKVILPGLAAGKVVISDRYLDSSLAYQGYGRGLPLPWLREVAREATRGLKPRLTFLLDLPPEAALRRVR-------LGLEFFRRVREGYLALARAEPGRFVVLDATLPEEEIARAIQAHLRPLLP\n>model:B\nMPGLFLTLEGLDGSGKTTQARRLAAFLEAQGRPVLLTREPGGGLPEVRSLLLTQELSPEAEYLLFSADRAEHVRKVILPGLAAGKVVISDRYLDSSLAYQGYGRGLPLPWLREVAREATRGLKPRLTFLLDLPPEAALRRVRRPDRLEGLGLEFFRRVREGYLALARAEPGRFVVLDATLPEEEIARAIQAHLRPLLP",
+ ">reference:B\n-PGLFLTLEGLDGSGKTTQARRLAAFLEAQGRPVLLTREPGGGLPEVRSLLLTQELSPEAEYLLFSADRAEHVRKVILPGLAAGKVVISDRYLDSSLAYQGYGRGLPLPWLREVAREATRGLKPRLTFLLDLPPEAALRRVRRPDRLEGLGLEFFRRVREGYLALARAEPGRFVVLDATLPEEEIARAIQAHLRPLLP\n>model:A\nMPGLFLTLEGLDGSGKTTQARRLAAFLEAQGRPVLLTREPGGGLPEVRSLLLTQELSPEAEYLLFSADRAEHVRKVILPGLAAGKVVISDRYLDSSLAYQGYGRGLPLPWLREVAREATRGLKPRLTFLLDLPPEAALRRVRRPDRLEGLGLEFFRRVREGYLALARAEPGRFVVLDATLPEEEIARAIQAHLRPLLP"
+ ]
+ }
+ },
+ "lddt": {
+ "oligo_lddt": {
+ "status": "SUCCESS",
+ "global_score": 0.8025223016738892,
+ "error": ""
+ },
+ "weighted_lddt": {
+ "status": "SUCCESS",
+ "global_score": 0.804789180710712,
+ "error": ""
+ },
+ "single_chain_lddt": [
+ {
+ "status": "SUCCESS",
+ "global_score": 0.8257459402084351,
+ "conserved_contacts": 877834,
+ "reference_chain": "A",
+ "total_contacts": 1063080,
+ "error": "",
+ "model_chain": "B"
+ },
+ {
+ "status": "SUCCESS",
+ "global_score": 0.7854443788528442,
+ "conserved_contacts": 904568,
+ "reference_chain": "B",
+ "total_contacts": 1151664,
+ "error": "",
+ "model_chain": "A"
+ }
+ ]
+ },
+ "qs_score": {
+ "status": "SUCCESS",
+ "global_score": 0.8974384796108209,
+ "best_score": 0.9022811630070536,
+ "error": ""
+ }
+ }
+ }
+ },
+ "options": {
+ "reference": "reference.pdb",
+ "structural_checks": true,
+ "chain_mapping": null,
+ "bond_tolerance": 15.0,
+ "parameter_file": "Path to stage/share/openstructure/stereo_chemical_props.txt",
+ "consistency_checks": true,
+ "qs_score": true,
+ "map_nonstandard_residues": true,
+ "save_per_residue_scores": false,
+ "fault_tolerant": false,
+ "reference_selection": "",
+ "cwd": "CWD",
+ "inclusion_radius": 15.0,
+ "angle_tolerance": 15.0,
+ "c_alpha_only": false,
+ "clean_element_column": true,
+ "dump_suffix": ".compare.structures.pdb",
+ "compound_library": "Path to stage/share/openstructure/compounds.chemlib",
+ "dump_structures": false,
+ "residue_number_alignment": true,
+ "verbosity": 3,
+ "remove": [
+ "oxt",
+ "hyd",
+ "unk"
+ ],
+ "molck": true,
+ "sequence_separation": 0,
+ "output": "output.json",
+ "model": "model.pdb",
+ "lddt": true,
+ "model_selection": ""
+ }
+ }
+
+If only all the structures are clean one can omit all the checking steps and
+calculate eg. QS-score directly:
+
+.. code:: console
+
+ $OST_ROOT/bin/ost compare-structures --model model.pdb --reference reference.pdb --output output_qs.json --qs-score --residue-number-alignment
+ ################################################################################
+ Reading input files (fault_tolerant=False)
+ --> reading model from model.pdb
imported 2 chains, 396 residues, 3106 atoms; with 0 helices and 0 strands
- Reading reference from reference.pdb
+ --> reading reference from reference.pdb
imported 3 chains, 408 residues, 3011 atoms; with 0 helices and 0 strands
- #
+ ################################################################################
Comparing model.pdb to reference.pdb
Chains removed from reference.pdb: _
Chains in reference.pdb: AB
@@ -77,34 +365,12 @@ Example usage:
Symmetry-groups used in model.pdb: [('A',), ('B',)]
Closed Symmetry with strict parameters
Mapping found: {'A': 'B', 'B': 'A'}
- QSscore reference.pdb, model.pdb: best: 0.90, global: 0.86
- Computing lDDT score
- Reference reference.pdb has: 2 chains
- Model model.pdb has: 2 chains
- Reference reference.pdb has: 384 residues
- Model model.pdb has: 396 residues
- lDDT score: 0.924
-
-This reads the model and reference file and calculates QS-score between them.
-In the example above the output file looks as follows:
-
-.. code-block:: python
-
- {
- "result": [
- {
- "status": "SUCCESS",
- "chain_mapping": {
- "A": "B",
- "B": "A"
- },
- "global_score": 0.8649009937090414,
- "error": "",
- "reference_name": "reference.pdb",
- "best_score": 0.8979578363524581,
- "model_name": "model.pdb",
- "lddt_score": 0.924271821975708
- }
- ]
- }
+ --------------------------------------------------------------------------------
+ Checking consistency between model.pdb and reference.pdb
+ Consistency check: OK
+ --------------------------------------------------------------------------------
+ Computing QS-score
+ QSscore reference.pdb, model.pdb: best: 0.90, global: 0.90
+ ################################################################################
+ Saving output into output_qs.json