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, use_wat=False)[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