.. Note on large code blocks: keep max. width to 100 or it will look bad on webpage! .. TODO: look at argparse directive to autogenerate --help output! .. ost-actions: OST Actions ================================================================================ A pure command line interface of OST is provided by actions. You can execute ``ost -h`` for a list of possible actions and for every action, you can type ``ost -h`` to get a description on its usage. Here we list the most prominent actions with simple examples. .. ost-compare-structures: Comparing two structures -------------------------------------------------------------------------------- You can compare two structures in terms of quaternary structure score and lDDT scores between two complexes from the command line with the ``ost compare-structures`` action. In summary it performs the following steps: - Read structures (PDB or mmCIF format, can be gzipped) and split into biological assemblies (all possible pairs are scored). - Mandatory cleanup of hydrogen atoms, ligand and water chains, small (< 20 residues) peptides or chains with no amino acids as described in :attr:`QSscoreEntity.ent ` and :attr:`QSscoreEntity.removed_chains `. - Optional cleanup of structures with :func:`~ost.mol.alg.Molck`. - Optional structural checks with :func:`~ost.mol.alg.CheckStructure`. - Unless user-provided, find chain mapping between complexes (see :attr:`here ` for details) - Perform sequence alignment of chain pairs (unless user asks for alignment based on residue numbers). Alignment can optionally checked for consistency if 100% sequence identity is expected. - Compute scores requested by user (CA-RMSD of oligomer, :mod:`QS scores of oligomer `, :class:`single chain lDDT scores `, :attr:`weighted average of single chain lDDT scores `, :attr:`lDDT score of oligomer `). Note that while the QS score is symmetric (same result when swapping reference and model), the lDDT scores are not. Extra atoms in the model for mapped chains have no effect on the score, while extra atoms in the reference reduce the score. For the oligomeric variants (weighted-lDDT & oligo-lDDT), we do :attr:`penalize for extra chains ` in both reference and model. .. note :: The action relies on OST's :mod:`~ost.mol.alg.qsscoring` module and has the same requirements on your OST installation (needs compound library, ClustalW, numpy and scipy). Details on the usage (output of ``ost compare-structures --help``): .. code-block:: console usage: ost compare-structures [-h] -m MODEL -r REFERENCE [-v VERBOSITY] [-o OUTPUT] [-d] [-ds DUMP_SUFFIX] [-rs REFERENCE_SELECTION] [-ms MODEL_SELECTION] [-ca] [-ft] [-cl COMPOUND_LIBRARY] [-ml] [-rm REMOVE [REMOVE ...]] [-ce] [-mn] [-sc] [-p PARAMETER_FILE] [-bt BOND_TOLERANCE] [-at ANGLE_TOLERANCE] [-c CHAIN_MAPPING [CHAIN_MAPPING ...]] [--qs-max-mappings-extensive QS_MAX_MAPPINGS_EXTENSIVE] [-cc] [-rna] [-qs] [--qs-rmsd] [-l] [-ir INCLUSION_RADIUS] [-ss SEQUENCE_SEPARATION] [-spr] Evaluate model structure against reference. eg. ost compare-structures \ --model \ --reference \ --output output.json \ --lddt \ --structural-checks \ --consistency-checks \ --molck \ --remove oxt hyd \ --map-nonstandard-residues Here we describe how the parameters can be set to mimick a CAMEO evaluation (as of August 2018). CAMEO calls the lddt binary as follows: lddt \ -p \ -f \ -a 15 \ -b 15 \ -r 15 \ \ Only model structures are "Molck-ed" in CAMEO. The call to molck is as follows: molck \ --complib= \ --rm=hyd,oxt,unk,nonstd \ --fix-ele \ --map-nonstd \ --out= \ To be as much compatible with with CAMEO as possible one should call compare-structures as follows: ost compare-structures \ --model \ --reference \ --output output.json \ --molck \ --remove oxt hyd unk nonstd \ --clean-element-column \ --map-nonstandard-residues \ --structural-checks \ --bond-tolerance 15.0 \ --angle-tolerance 15.0 \ --residue-number-alignment \ --consistency-checks \ --qs-score \ --lddt \ --inclusion-radius 15.0 optional arguments: -h, --help show this help message and exit required arguments: -m MODEL, --model MODEL Path to the model file. -r REFERENCE, --reference REFERENCE Path to the reference file. general arguments: -v VERBOSITY, --verbosity VERBOSITY Set verbosity level. Defaults to 3. -o OUTPUT, --output OUTPUT Output file name. The output will be saved as a JSON file. -d, --dump-structures Dump cleaned structures used to calculate all the scores as PDB files using specified suffix. Files will be dumped to the same location as original files. -ds DUMP_SUFFIX, --dump-suffix DUMP_SUFFIX Use this suffix to dump structures. Defaults to .compare.structures.pdb. -rs REFERENCE_SELECTION, --reference-selection REFERENCE_SELECTION Selection performed on reference structures. -ms MODEL_SELECTION, --model-selection MODEL_SELECTION Selection performed on model structures. -ca, --c-alpha-only Use C-alpha atoms only. Equivalent of calling the action with '--model-selection="aname=CA" --reference-selection="aname=CA"' options. -ft, --fault-tolerant Fault tolerant parsing. -cl COMPOUND_LIBRARY, --compound-library COMPOUND_LIBRARY Location of the compound library file (compounds.chemlib). If not provided, the following locations are searched in this order: 1. Working directory, 2. OpenStructure standard library location. molecular check arguments: -ml, --molck Run molecular checker to clean up input. -rm REMOVE [REMOVE ...], --remove REMOVE [REMOVE ...] Remove atoms and residues matching some criteria: * zeroocc - Remove atoms with zero occupancy * hyd - remove hydrogen atoms * oxt - remove terminal oxygens * nonstd - remove all residues not one of the 20 standard amino acids * unk - Remove unknown and atoms not following the nomenclature Defaults to hyd. -ce, --clean-element-column Clean up element column -mn, --map-nonstandard-residues Map modified residues back to the parent amino acid, for example MSE -> MET, SEP -> SER. structural check arguments: -sc, --structural-checks Perform structural checks and filter input data. -p PARAMETER_FILE, --parameter-file PARAMETER_FILE Location of the stereochemical parameter file (stereo_chemical_props.txt). If not provided, the following locations are searched in this order: 1. Working directory, 2. OpenStructure standard library location. -bt BOND_TOLERANCE, --bond-tolerance BOND_TOLERANCE Tolerance in STD for bonds. Defaults to 12. -at ANGLE_TOLERANCE, --angle-tolerance ANGLE_TOLERANCE Tolerance in STD for angles. Defaults to 12. chain mapping arguments: -c CHAIN_MAPPING [CHAIN_MAPPING ...], --chain-mapping CHAIN_MAPPING [CHAIN_MAPPING ...] Mapping of chains between the reference and the model. Each separate mapping consist of key:value pairs where key is the chain name in reference and value is the chain name in model. --qs-max-mappings-extensive QS_MAX_MAPPINGS_EXTENSIVE Maximal number of chain mappings to test for 'extensive' chain mapping scheme which is used as a last resort if other schemes failed. The extensive chain mapping search must in the worst case check O(N!) possible mappings for complexes with N chains. Two octamers without symmetry would require 322560 mappings to be checked. To limit computations, no scores are computed if we try more than the maximal number of chain mappings. Defaults to 1000000. sequence alignment arguments: -cc, --consistency-checks Take consistency checks into account. By default residue name consistency between a model-reference pair would be checked but only a warning message will be displayed and the script will continue to calculate scores. If this flag is ON, checks will not be ignored and if the pair does not pass the test all the scores for that pair will be marked as a FAILURE. -rna, --residue-number-alignment Make alignment based on residue number instead of using a global BLOSUM62-based alignment. QS score arguments: -qs, --qs-score Calculate QS-score. --qs-rmsd Calculate CA RMSD between shared CA atoms of mapped chains. This uses a superposition using all mapped chains which minimizes the CA RMSD. lDDT score arguments: -l, --lddt Calculate lDDT. -ir INCLUSION_RADIUS, --inclusion-radius INCLUSION_RADIUS Distance inclusion radius for lDDT. Defaults to 15 A. -ss SEQUENCE_SEPARATION, --sequence-separation SEQUENCE_SEPARATION Sequence separation. Only distances between residues whose separation is higher than the provided parameter are considered when computing the score. Defaults to 0. -spr, --save-per-residue-scores 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. 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:: none { "options": { ... }, # Options used to run the script "result": { "": { # Model name extracted from the file name "": { # Reference name extracted from the file name "info": { "mapping": { "alignments": , "chain_mapping": , "chain_mapping_scheme": }, "residue_names_consistent": }, "lddt": { # calculated when --lddt (-l) option is selected "oligo_lddt": { "error": , "global_score": , "status": }, "single_chain_lddt": [ # a list of chain-chain lDDTs { "conserved_contacts": , "error": , "global_score": , "model_chain": , "reference_chain": , "status": , "total_contacts": , "per_residue_scores": [ # per-residue lDDT scores # only calculated when --save-per-residue-scores (-spr) option is selected { "residue_name": , "residue_number": , "lddt": , "conserved_contacts": , "total_contacts": }, . . . ] } ], "weighted_lddt": { "error": , "global_score": , "status": } }, "qs_score": { # calculated when --qs-score (-q) option is selected "best_score": , "error": , "global_score": , "status": } } } } } 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: .. code-block:: console $ CAMEO_TARGET_URL=https://www.cameo3d.org/static/data/modeling/2019.07.13/6PO4_F $ curl $CAMEO_TARGET_URL/bu_target_01.pdb > reference.pdb $ curl $CAMEO_TARGET_URL/servers/server20/oligomodel-1/oligomodel-1.pdb > model.pdb $ $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 nonstd \ --clean-element-column --map-nonstandard-residues ################################################################################ Reading input files (fault_tolerant=False) --> reading model from model.pdb imported 2 chains, 462 residues, 3400 atoms; with 0 helices and 0 strands --> reading reference from reference.pdb imported 3 chains, 471 residues, 3465 atoms; with 0 helices and 0 strands ################################################################################ Cleaning up input with Molck removing hydrogen atoms --> removed 0 hydrogen atoms removing OXT atoms --> removed 3 OXT atoms _.HCS1 is not a standard amino acid --> removed _.ADE2 is not a standard amino acid --> removed _.BO33 is not a standard amino acid --> removed _.ADE4 is not a standard amino acid --> removed _.HCS5 is not a standard amino acid --> removed _.BO36 is not a standard amino acid --> removed removing hydrogen atoms --> removed 0 hydrogen atoms removing OXT atoms --> removed 0 OXT atoms ################################################################################ Performing structural checks --> for reference(s) Checking reference.pdb Checking stereo-chemistry Average Z-Score for bond lengths: 0.33163 Bonds outside of tolerance range: 0 out of 2993 Bond Avg Length Avg zscore Num Bonds C-C 1.51236 0.03971 1682 C-N 1.46198 0.96819 603 C-O 1.25794 0.49967 674 C-S 1.80242 0.15292 34 Average Z-Score angle widths: -0.12077 Angles outside of tolerance range: 0 out of 3260 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 model.pdb Checking stereo-chemistry Average Z-Score for bond lengths: 0.23693 Bonds outside of tolerance range: 0 out of 2976 Bond Avg Length Avg zscore Num Bonds C-C 1.52020 0.40359 1674 C-N 1.43936 -0.19949 598 C-O 1.25221 0.20230 670 C-S 1.81182 0.38936 34 Average Z-Score angle widths: 0.04946 Angles outside of tolerance range: 0 out of 3241 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 model.pdb to reference.pdb Chains in reference.pdb: AB Chains in model.pdb: AB Chemically equivalent chain-groups in reference.pdb: [['A', 'B']] Chemically equivalent chain-groups in model.pdb: [['A', 'B']] Chemical chain-groups mapping: {('A', 'B'): ('A', 'B')} Identifying Symmetry Groups... 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 reference.pdb: [('A',), ('B',)] Symmetry-groups used in model.pdb: [('A',), ('B',)] Closed Symmetry with strict parameters Mapping found: {'A': 'A', 'B': 'B'} -------------------------------------------------------------------------------- Checking consistency between model.pdb and reference.pdb Consistency check: OK -------------------------------------------------------------------------------- Computing QS-score QSscore reference.pdb, model.pdb: best: 0.96, global: 0.96 -------------------------------------------------------------------------------- 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 A and reference chain A Coverage: 0.991416 (231 out of 233 residues) Global LDDT score: 0.8955 (1194245 conserved distances out of 1333644 checked, over 4 thresholds) --> Computing lDDT between model chain B and reference chain B Coverage: 0.991379 (230 out of 232 residues) Global LDDT score: 0.8998 (1200391 conserved distances out of 1334056 checked, over 4 thresholds) --> Computing oligomeric lDDT score Reference reference.pdb has: 2 chains Model model.pdb has: 2 chains Coverage: 0.991398 (461 out of 465 residues) Oligo lDDT score: 0.8977 --> Computing weighted lDDT score Weighted lDDT score: 0.8976 ################################################################################ Saving output into output.json This reads the model and reference file and calculates QS- and lDDT-scores between them. In the example above the output file looks as follows (FASTA alignments were cut in display here for readability): .. code snippet to fix output.json generated above import json json_data = json.load(open("output.json")) mapping = json_data["result"]["model.pdb"]["reference.pdb"]["info"]["mapping"] new_alns = list() for aln in mapping["alignments"]: aln_lines = aln.splitlines() aln_lines[1] = aln_lines[1][:15] + "..." aln_lines[3] = aln_lines[3][:15] + "..." new_alns.append("\n".join(aln_lines)) mapping["alignments"] = new_alns json_data["options"]["parameter_file"] = "Path to stage/share/openstructure/stereo_chemical_props.txt" json_data["options"]["compound_library"] = "Path to stage/share/openstructure/compounds.chemlib" json_data["options"]["cwd"] = "Path to current working directory" with open("output_fixed.json", "w") as outfile: json.dump(json_data, outfile, indent=2, sort_keys=True) .. code-block:: json { "options": { "angle_tolerance": 15.0, "bond_tolerance": 15.0, "c_alpha_only": false, "chain_mapping": null, "clean_element_column": true, "compound_library": "Path to stage/share/openstructure/compounds.chemlib", "consistency_checks": true, "cwd": "Path to current working directory", "dump_structures": false, "dump_suffix": ".compare.structures.pdb", "fault_tolerant": false, "inclusion_radius": 15.0, "lddt": true, "map_nonstandard_residues": true, "model": "model.pdb", "model_selection": "", "molck": true, "output": "output.json", "parameter_file": "Path to stage/share/openstructure/stereo_chemical_props.txt", "qs_max_mappings_extensive": 1000000, "qs_rmsd": false, "qs_score": true, "reference": "reference.pdb", "reference_selection": "", "remove": [ "oxt", "hyd", "unk", "nonstd" ], "residue_number_alignment": true, "save_per_residue_scores": false, "sequence_separation": 0, "structural_checks": true, "verbosity": 3 }, "result": { "model.pdb": { "reference.pdb": { "info": { "mapping": { "alignments": [ ">reference:A\n-NAMKIGIVGAMAQE...\n>model:A\n---MKIGIVGAMAQE...", ">reference:B\n-NAMKIGIVGAMAQE...\n>model:B\n---MKIGIVGAMAQE..." ], "chain_mapping": { "A": "A", "B": "B" }, "chain_mapping_scheme": "strict" }, "residue_names_consistent": true }, "lddt": { "oligo_lddt": { "error": "", "global_score": 0.8977285786061329, "status": "SUCCESS" }, "single_chain_lddt": [ { "conserved_contacts": 1194245, "error": "", "global_score": 0.8954750895500183, "model_chain": "A", "reference_chain": "A", "status": "SUCCESS", "total_contacts": 1333644 }, { "conserved_contacts": 1200391, "error": "", "global_score": 0.8998055458068848, "model_chain": "B", "reference_chain": "B", "status": "SUCCESS", "total_contacts": 1334056 } ], "weighted_lddt": { "error": "", "global_score": 0.8976406520766181, "status": "SUCCESS" } }, "qs_score": { "best_score": 0.9619749105661133, "error": "", "global_score": 0.9619749105661133, "status": "SUCCESS" } } } } } If all the structures are clean and have matching residue numbers, one can omit all the checking steps and calculate scores directly as here: .. 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, 462 residues, 3400 atoms; with 0 helices and 0 strands --> reading reference from reference.pdb imported 3 chains, 471 residues, 3465 atoms; with 0 helices and 0 strands ################################################################################ Comparing model.pdb to reference.pdb Chains removed from reference.pdb: _ Chains in reference.pdb: AB Chains in model.pdb: AB Chemically equivalent chain-groups in reference.pdb: [['A', 'B']] Chemically equivalent chain-groups in model.pdb: [['A', 'B']] Chemical chain-groups mapping: {('A', 'B'): ('A', 'B')} Identifying Symmetry Groups... 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 reference.pdb: [('A',), ('B',)] Symmetry-groups used in model.pdb: [('A',), ('B',)] Closed Symmetry with strict parameters Mapping found: {'A': 'A', 'B': 'B'} -------------------------------------------------------------------------------- Checking consistency between model.pdb and reference.pdb Consistency check: OK -------------------------------------------------------------------------------- Computing QS-score QSscore reference.pdb, model.pdb: best: 0.96, global: 0.96 ################################################################################ Saving output into output_qs.json