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Commit f5bb95d8 authored by Gerardo Tauriello's avatar Gerardo Tauriello
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Doc update.

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modules/doc/actions.rst
+ 42
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View file @ f5bb95d8
......@@ -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,
......
modules/mol/alg/pymod/qsscoring.py
+ 6
− 6
View file @ f5bb95d8
......@@ -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
......
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