diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index 81813ef34e8c25076fda96bc0e45ee5d13f91a61..fb2f882d86d64700652cdf26921ecbd133ec277a 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -44,8 +44,10 @@ The output file has following format:
"<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"}>,
+ "residue_names_consistent": <Are the residue numbers consistent? true or false>,
+ "mapping": {
+ "chain_mapping": <Mapping of chains eg. {"A": "B", "B": "A"}>,
+ "chain_mapping_scheme": <Scheme used to get mapping, check mapping manually if "permissive" or "extensive">,
"alignments": <list of chain-chain alignments in FASTA format>
}
},
@@ -72,10 +74,10 @@ The output file has following format:
"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>,
+ "residue_name": <three letter code of the residue in reference chain>,
"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>
+ "residue_number": <residue number in reference chain>
},
.
.
@@ -164,51 +166,57 @@ Example usage:
################################################################################
Performing structural checks
--> for reference(s)
- Checking
+ Checking reference.pdb
Checking stereo-chemistry
- Average Z-Score for bond lengths: -nan
- Bonds outside of tolerance range: 0 out of 0
+ Average Z-Score for bond lengths: 0.13694
+ Bonds outside of tolerance range: 0 out of 2654
Bond Avg Length Avg zscore Num Bonds
- Average Z-Score angle widths: 0.00000
- Angles outside of tolerance range: 0 out of 1
+ C-C 1.50876 0.09299 1501
+ C-N 1.42978 0.17690 635
+ C-O 1.25079 0.21528 518
+ Average Z-Score angle widths: 0.07562
+ Angles outside of tolerance range: 0 out of 2941
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 model.pdb
Checking stereo-chemistry
- Average Z-Score for bond lengths: -nan
- Bonds outside of tolerance range: 0 out of 0
+ Average Z-Score for bond lengths: -0.22524
+ Bonds outside of tolerance range: 0 out of 2774
Bond Avg Length Avg zscore Num Bonds
- Average Z-Score angle widths: 0.00000
- Angles outside of tolerance range: 0 out of 1
+ C-C 1.50225 -0.20158 1558
+ C-N 1.42294 -0.12261 666
+ C-O 1.24232 -0.42115 546
+ C-S 1.80215 0.20858 4
+ Average Z-Score angle widths: -0.06767
+ Angles outside of tolerance range: 0 out of 3079
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']]
+ Comparing model.pdb to reference.pdb
+ Chains in reference.pdb: AB
+ Chains in model.pdb: AB
+ Chemically equivalent chain-groups in reference.pdb: [['B', 'A']]
+ Chemically equivalent chain-groups in model.pdb: [['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
+ Symmetry threshold 0.1 used for angles of reference.pdb
+ Symmetry threshold 0.1 used for axis of reference.pdb
+ Symmetry threshold 0.1 used for angles of model.pdb
+ Symmetry threshold 0.1 used for axis of model.pdb
Selecting Symmetry Groups...
- Symmetry-groups used in pdb_1: [('B',), ('A',)]
- Symmetry-groups used in pdb_2: [('A',), ('B',)]
+ Symmetry-groups used in reference.pdb: [('B',), ('A',)]
+ Symmetry-groups used in model.pdb: [('A',), ('B',)]
Closed Symmetry with strict parameters
Mapping found: {'A': 'B', 'B': 'A'}
--------------------------------------------------------------------------------
- Checking consistency between and
+ Checking consistency between model.pdb and reference.pdb
Consistency check: OK
--------------------------------------------------------------------------------
Computing QS-score
- QSscore pdb_1, pdb_2: best: 0.90, global: 0.90
+ QSscore reference.pdb, model.pdb: best: 0.90, global: 0.90
--------------------------------------------------------------------------------
Computing lDDT scores
lDDT settings:
@@ -226,8 +234,8 @@ Example usage:
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
+ Reference reference.pdb has: 2 chains
+ Model model.pdb has: 2 chains
Coverage: 1 (384 out of 384 residues)
Oligo lDDT score: 0.8025
--> Computing weighted lDDT score
@@ -251,8 +259,8 @@ In the example above the output file looks as follows:
"chain_mapping": {
"A": "B",
"B": "A"
- },
- "chain_mapping_scheme": "strict",
+ },
+ "chain_mapping_scheme": "strict",
"alignments": [
">reference:A\n-PGLFLTLEGLDGSGKTTQARRLAAFLEAQGRPVLLTREPGGGLPEVRSL---QELSPEAEYLLFSADRAEHVRKVILPGLAAGKVVISDRYLDSSLAYQGYGRGLPLPWLREVAREATRGLKPRLTFLLDLPPEAALRRVR-------LGLEFFRRVREGYLALARAEPGRFVVLDATLPEEEIARAIQAHLRPLLP\n>model:B\nMPGLFLTLEGLDGSGKTTQARRLAAFLEAQGRPVLLTREPGGGLPEVRSLLLTQELSPEAEYLLFSADRAEHVRKVILPGLAAGKVVISDRYLDSSLAYQGYGRGLPLPWLREVAREATRGLKPRLTFLLDLPPEAALRRVRRPDRLEGLGLEFFRRVREGYLALARAEPGRFVVLDATLPEEEIARAIQAHLRPLLP",
">reference:B\n-PGLFLTLEGLDGSGKTTQARRLAAFLEAQGRPVLLTREPGGGLPEVRSLLLTQELSPEAEYLLFSADRAEHVRKVILPGLAAGKVVISDRYLDSSLAYQGYGRGLPLPWLREVAREATRGLKPRLTFLLDLPPEAALRRVRRPDRLEGLGLEFFRRVREGYLALARAEPGRFVVLDATLPEEEIARAIQAHLRPLLP\n>model:A\nMPGLFLTLEGLDGSGKTTQARRLAAFLEAQGRPVLLTREPGGGLPEVRSLLLTQELSPEAEYLLFSADRAEHVRKVILPGLAAGKVVISDRYLDSSLAYQGYGRGLPLPWLREVAREATRGLKPRLTFLLDLPPEAALRRVRRPDRLEGLGLEFFRRVREGYLALARAEPGRFVVLDATLPEEEIARAIQAHLRPLLP"
@@ -262,7 +270,7 @@ In the example above the output file looks as follows:
"lddt": {
"oligo_lddt": {
"status": "SUCCESS",
- "global_score": 0.8025223016738892,
+ "global_score": 0.8025223275721413,
"error": ""
},
"weighted_lddt": {
@@ -312,6 +320,7 @@ In the example above the output file looks as follows:
"save_per_residue_scores": false,
"fault_tolerant": false,
"reference_selection": "",
+ "qs_rmsd": false,
"cwd": "CWD",
"inclusion_radius": 15.0,
"angle_tolerance": 15.0,
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index b67746f6f2f2b8357288a607023277e008116601..228fbb43208b9fee2b1b763275636e6a64849945 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -208,9 +208,8 @@ class QSscorer:
:attr:`qs_ent_1` and value = :class:`tuple` of chain names in
:attr:`qs_ent_2`.
- :raises: :class:`QSscoreError` if we end up having less than 2 chains for
- either entity in the mapping (can happen if chains do not have CA
- atoms).
+ :raises: :class:`QSscoreError` if we end up having no chains for either
+ entity in the mapping (can happen if chains do not have CA atoms).
"""
if self._chem_mapping is None:
self._chem_mapping = _GetChemGroupsMapping(self.qs_ent_1, self.qs_ent_2)
@@ -389,8 +388,7 @@ class QSscorer:
:getter: Computed with :attr:`chain_mapping` on first use (cached)
:type: :class:`str`
- :raises: :class:`QSscoreError` if there are too many combinations to check
- to find a chain mapping.
+ :raises: :class:`QSscoreError` as in :attr:`chain_mapping`.
"""
if self._chain_mapping_scheme is None:
# default: user provided
@@ -455,6 +453,7 @@ class QSscorer:
:getter: Computed on first use (cached)
:type: :class:`float`
+ :raises: :class:`QSscoreError` if only one chain is mapped
"""
if self._global_score is None:
self._ComputeScores()
@@ -470,6 +469,7 @@ class QSscorer:
:getter: Computed on first use (cached)
:type: :class:`float`
+ :raises: :class:`QSscoreError` if only one chain is mapped
"""
if self._best_score is None:
self._ComputeScores()
@@ -1339,7 +1339,7 @@ class MappedLDDTScorer(object):
existing in model and reference:
- "residue_number": Residue number in reference chain
- - "residue_name": Residue number in reference chain
+ - "residue_name": Residue name in reference chain
- "lddt": local lDDT
- "conserved_contacts": number of conserved contacts
- "total_contacts": total number of contacts