ProtoCaller.Wrappers.modellerwrapper module

This is the wrapper responsible for handling Modeller. Here the user can add missing residues and optionally missing atoms. Note that it is not yet possible to add missing atoms if there are no missing residues. Additionally, the user can perform an optional refinement from within Modeller. More information can be found here.

Whenever PDB information is lost during the transformation, ProtoCaller automatically restores it. If the user is running Modeller outside ProtoCaller, they need to make sure that appropriate information about missing atoms, disulfide bonds and chain IDs is retained.

Note that in all cases you will need to install Modeller and have a valid license.

ProtoCaller.Wrappers.modellerwrapper.FASTA2PIR(filename_pdb, filename_fasta)

Converts a FASTA file into a PIR file using a PDB sequence.

Parameters

  • filename_pdb (str) – Name of the input PDB file.

  • filename_fasta (str) – Name of the input FASTA file.

Returns

filename_output – Name of the output PIR file.

Return type

str

ProtoCaller.Wrappers.modellerwrapper.modellerTransform(filename_pdb, filename_fasta, add_missing_atoms, pdb_code=None, refinement='very_fast')

Adds missing residues and (optionally) missing atoms to a PDB file.

Parameters

  • filename_pdb (str) – Name of the input PDB file.

  • filename_fasta (str) – Name of the input sequence FASTA file.

  • add_missing_atoms (bool) – Whether to add missing atoms.

  • pdb_code (bool) – The PDB code of the PDB file. Default: the PDB filename.

  • refinement (str, None) – Level of MD refinement. Allowed values are: None, “very_fast”, “fast”, “slow”, “very_slow”, “slow_large”.

Returns

filename_output – Absolute path to the modified file.

Return type

str