configuration package

Submodules

model.mutate module

Module containing the Mutate class and the command line interface.

class model.mutate.Mutate(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs)[source]

Bases: object

Class to mutate one amino acid by another in a 3d structure.

Parameters:
  • input_pdb_path (str) – Input PDB file path. File type: input. Sample file. Accepted formats: pdb.
  • output_pdb_path (str) –

    Output PDB file path. File type: output. Sample file. Accepted formats: pdb.

  • properties (dic) –
    • mutation_list (str): (“A:Val2Ala”) Mutation list in the format “Chain:WT_AA_ThreeLeterCode Resnum MUT_AA_ThreeLeterCode” (no spaces between the elements) separated by commas. If no chain is provided as chain code all the chains in the pdb file will be mutated. ie: “A:ALA15CYS”
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.
launch() → int[source]

Mutate one or more amino acids.

model.mutate.main()[source]

model.fix_side_chain module

Module containing the FixSideChain class and the command line interface.

class model.fix_side_chain.FixSideChain(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs)[source]

Bases: object

Class to model the missing atoms in amino acid side chains of a PDB.

Parameters:
  • input_pdb_path (str) –

    Input PDB file path. File type: input. Sample file. Accepted formats: pdb.

  • output_pdb_path (str) –

    Output PDB file path. File type: output. Sample file. Accepted formats: pdb.

  • properties (dic) –
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.
launch() → int[source]

Model the missing atoms in side chains.

model.fix_side_chain.main()[source]