biobb_structure_checking package¶
biobb_structure_checking.structure_checking module¶
Class for Structure Checking functionality
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class
biobb_structure_checking.structure_checking.
StructureChecking
(base_dir_path, args)[source]¶ Bases:
object
biobb_structure_checking.StructureCheckingMain class to control structure checking functionalityProvides support for to check_structure command lineLoad directly for Jupyter Notebook or python scripts.Parameters: - base_dir_path (str) – Base directory path where application resides.
- args (dict) – Arguments dictionary see https://biobb-structure-checking.readthedocs.io/en/latest/command_line_usage.html.
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add_hydrogen
(opts=None)[source]¶ Add Hydrogen Atoms to the structure. Check only with no options. Options accepted as command-line string, or python dictionary.
Parameters: opts (str | dict - Options dictionary) – - add_mode:
- auto - Add hydrogen atom considering pH 7.0.
- pH (float) - Set explicit pH value.
- list (str) - Explicit residue list as [*:]HisXXHid.
- no_fix_side (bool) - (False) Do not fix side chains.
- keep_h (bool) - (False) Keep original Hydrigen atoms.
- add_charges FF (str) - Add charges and atom types for the selected FF.
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altloc
(opts=None)[source]¶ Detect/Select Alternative Locations. Check only with no options. Options accepted as command-line string, or python dictionary.
Parameters: opts (str | dict - Options dictionary) – - select:
- occupancy - select higher occupancy,
- alt_id - All atoms of the indicated alternative
- list of res_id:alt_id - Indicate selection per atom
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amide
(opts=None)[source]¶ Detect/Fix Amide atoms Assignment. Check only with no options. Options accepted as command-line string, or python dictionary.
Parameters: opts (str | dict - Options dictionary) – - fix:
- all - Fix all residues,
- residue_list - Fix indicated residues
- auto - Find the best combination to minimize amide contacts .
- no_recheck (bool) - (False) Do not recheck amide residues after modification.
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backbone
(opts=None)[source]¶ Analyze/Fix main chain missing atoms and fragments (protein only). Check only with no options. Options accepted as command-line string, or python dictionary.
Parameters: opts (str | dict - Options dictionary) – - fix_atoms (str - Fix missing O, OXT backbone atoms):
- all - Fix all residues
- residue List - Fix indicated residues
- fix_chain (str - Fix backbone main chain):
- all - All detected breaks
- break list - Indicated breaks
- add_caps (str - Add ACE and NME residues):
- all - All detected terminals
- residue_list - Indicated terminals
- breaks - Add caps to backbone breaks
- terms - Add caps to true terminals
- extra_gap (int) - (‘0’) Recover addiciontal residues from the model to improve match (experimental)
- no_recheck (bool) - (False) Do not recheck backbone after fixing
- no_check_clashes (bool) - (False) Do not check for generated clashes
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chains
(opts=None)[source]¶ Detect/Select Chains. Check only with no options. Options accepted as command-line string, or python dictionary.
Parameters: opts (str | dict - Options dictionary) – - select:
- chain_id_list - List of chains to retain (comma separated, case sensitive),
- protein - Select all protein chains,
- na - Select all NA chains,
- rna - Select all RNA chains,
- dna - Select all DNA chains.
- rename:
- auto - Add first possible label staring on A to unlabeled chains
- label - Use indicated label
- renumber:
- auto - Renumbers all residues from 1 without repeating residue numbers. Chains are preserved but relabelled from A
- str - Specific renumbering recipe indicated as a list of tasks: [OldChain:]i0[-j0]=[NewChain:]i1. No j0 implies to the end of chain. No chain implies do the transformation in all chains.
- rebuild: - Creates chain labels and renumbers residues based on backbone connectivity
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check_report_clashes
(residue_list=None, contact_types=None)[source]¶ Check and reports clashes
Parameters: - residue_list (res (list)) – Residues to check
- contact_types (int (list)) – Types of contacts to consider
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chiral
(opts=None)[source]¶ Detect/Fix Improper side chain chirality. Check only with no options. Options accepted as command-line string, or python dictionary.
Parameters: opts (str | dict - Options dictionary) – - fix:
- All - Fix all residues
- residue_list - Fix indicates residues
- no_check_clashes (bool) - (False) Do not check generated clashes
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clashes
()[source]¶ Detect steric clashes in groups: Severe, Apolar, Polar Donors, Polar Acceptors, Ionic Positive, Ionic Negative
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command_list
(opts)[source]¶ Manages command_list workflows
Parameters: opts (str | list(str)) – Command options as str, file or str list (‘;’ separated).
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fixside
(opts=None)[source]¶ Complete side chains (heavy atoms, protein only). Check only with no options. Options accepted as command-line string, or python dictionary.
Parameters: opts (str | dict - Options dictionary) – - fix:
- all - Fix all residues
- residue_list - Fix indicated residues
- no_check_clashes (bool) - (False) Do not check for generated clashes
- rebuild (bool) - (False) Rebuild side chains using Modeller
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getss
(opts=None)[source]¶ Detect SS Bonds. Check only with no options. Options accepted as command-line string, or python dictionary.
Parameters: opts (str | dict - Options dictionary) – - mark:
- all - Rename all reported cys residues as CYX,
- residue_list - Rename indicated residues
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help
(command=None)[source]¶ Provides help on StructureChecking commands
Parameters: command (str) – (None) Requested command. If empty returns all commands help
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inscodes
(opts=None)[source]¶ Detects residues with insertion codes.
Parameters: opts (str | dict - Options dictionary) – - renumber (bool): Renumber residues to remove insertion codes.
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ligands
(opts=None)[source]¶ Detect/Remove Ligands. Check only with no options. Options accepted as command-line string, or python dictionary.
Parameters: opts (str | dict - Options dictionary) – - remove:
- all - Remove all hetatm,
- res_type_list - Remove Hetatm of given types,
- residue_list - Remove indicated residues
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metals
(opts=None)[source]¶ Detect/Remove Metals. Check only with no options. Options accepted as command-line string, or python dictionary.
Parameters: opts (str | dict - Options dictionary) – - remove:
- all - Remove all metal atoms,
- atom_type_list: Remove all Metals of listed types
- residue_list: Remove indicated residues
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models
(opts=None)[source]¶ Detect/Select Models. Check only with no options. Options accepted as command-line string, or python dictionary.
Parameters: opts (str | dict - Options dictionary) – - select (int) - model(s) to select
- superimpose (bool) - superimpose models
- build_complex (bool) - Build a complex from selected models
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mutateside
(mut_list)[source]¶ Mutate side chain with minimal atom replacement. Check only with no options. Options accepted as command-line string, or python dictionary.
Parameters: opts (str | dict - Options dictionary) – - mut (str) - List of mutations
- no_check_clashes (bool) - (False) Do not check for generated clashes
- rebuild (bool) - (False) - Optimize new side chains using Modeller
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print_stats
(prefix=None)[source]¶ Print statistics on the loaded structure
Parameters: prefix (str) – (None) Prefix to add to the output lines for identification.
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rem_hydrogen
(opts=None)[source]¶ StructureChecking.add_hydrogen Remove Hydrogen atoms from structure. Check only with no options. Options accepted as command-line string, or python dictionary.
Parameters: opts (str | dict - Options dictionary) – - remove (str): Yes - remove all hydrogen atoms
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revert_changes
()[source]¶ Reload original structure. Used in Pipelines or Notebooks to revert changes.
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save_structure
(output_structure_path, rename_terms=False, split_models=False)[source]¶ Saving the current structure in a the output file
Parameters: - output_structure_path (str) – Path to saved File
- rename_terms (bool) – (False) Rename terminal residues as NXXX, CXXX
- split_models (bool) – (False) Save models in separated output files