biobb_structure_checking package

biobb_structure_checking.structure_checking module

Class for Structure Checking functionality

class biobb_structure_checking.structure_checking.StructureChecking(base_dir_path, args)[source]

Bases: object

biobb_structure_checking.StructureChecking
Main class to control structure checking functionality
Provides support for to check_structure command line
Load directly for Jupyter Notebook or python scripts.
Parameters:
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.
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
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.
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
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
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
checkall(opts=None)[source]

Predefined workflow for complete checking

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
chiral_bck()[source]

Detect/Fix Improper CA chirality. No fix.

cistransbck()[source]

Analyzes cis-trans dihedrals on backbone atoms

clashes()[source]

Detect steric clashes in groups: Severe, Apolar, Polar Donors, Polar Acceptors, Ionic Positive, Ionic Negative

command_list(opts)[source]

Manages command_list workflows

Parameters:opts (str | list(str)) – Command options as str, file or str list (‘;’ separated).
fixall(opts=None)[source]

Fix all using defaults. Not implemented (yet)

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
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
help(command=None)[source]

Provides help on StructureChecking commands

Parameters:command (str) – (None) Requested command. If empty returns all commands help
hetatm(opts=None)[source]

Manages hetero atoms. Not implemented yet. See Ligands

inscodes(opts=None)[source]

Detects residues with insertion codes.

Parameters:opts (str | dict - Options dictionary) –
  • renumber (bool): Renumber residues to remove insertion codes.
launch()[source]

Method run from the command line invocation

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
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
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
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
print_stats(prefix=None)[source]

Print statistics on the loaded structure

Parameters:prefix (str) – (None) Prefix to add to the output lines for identification.
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
revert_changes()[source]

Reload original structure. Used in Pipelines or Notebooks to revert changes.

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
sequences(opts=None)[source]

Print canonical and structure sequences in FASTA format

Parameters:opts (str | dict - Options dictionary) –
  • output_fasta (str) - File name to output (FASTA format)
water(opts=None)[source]

Detect/Select Remove Water molecules. Check only with no options. Options accepted as command-line string, or python dictionary.

Parameters:opts (str | dict - Options dictionary) –
  • remove: Yes - Remove All Water molecules