`pyqmmm.md.modeller_automator`¶

Automates the process of replacing missing residues with Modeller.

Module Contents¶

`get_pdb_name`()	Identify the user's primary PDB file.
`get_fasta`(pdb_name)	Get sequences from provided fasta file deposited in 1_in.
`step_1`(pdb_name, pdb_file)	Generate the modeller seq file.
`get_mod_seq`(pdb_name, pdb_file, aa_lookup)	Using the Modeller seq file, create a list of the extracted residues.
`get_pdb_seq`(pdb_name, pdb_file, fasta_seq, aa_lookup)	Using the PDB, create a dict with keys as res IDs and values as amino acids.
`get_ali`(pdb_seq, fasta_seq, pdb_name, header)	Compare fasta and modeller seq files.
`step_2`(pdb_name, pdb_file)	The second step of Modeller software.
`clean_up`(pdb_name)	To address messy and strange file and naming conventions of Modeller,
`modeller_automator`(aa_lookup)

pyqmmm.md.modeller_automator.get_pdb_name()¶

Identify the user’s primary PDB file.

Returns:

pdb_name (str) – The file name of the users PDB that will be used to create masks.
pdb_file (str) – The pdb name and the extenstion.

pyqmmm.md.modeller_automator.get_fasta(pdb_name)¶

Get sequences from provided fasta file deposited in 1_in.

Parameters:: pdb_name (str) – The name of the user’s PDB.
Returns:: fasta – The fasta seq with the index as the key and amino acid as the value.
Return type:: dict

pyqmmm.md.modeller_automator.step_1(pdb_name, pdb_file)¶

Generate the modeller seq file.

Parameters:

pyqmmm.md.modeller_automator.get_mod_seq(pdb_name, pdb_file, aa_lookup)¶

Using the Modeller seq file, create a list of the extracted residues.

Parameters:

Returns:

mod_seq – The modeller seq as a list with one-letter codes as elements. Missing residues are delineated with a - character.

Return type:

list

pyqmmm.md.modeller_automator.get_pdb_seq(pdb_name, pdb_file, fasta_seq, aa_lookup)¶

Using the PDB, create a dict with keys as res IDs and values as amino acids.

Parameters:

Returns:

pdb_seq – Res IDs keys and amino acid values with missing residues with None type.

Return type:

dict

pyqmmm.md.modeller_automator.get_ali(pdb_seq, fasta_seq, pdb_name, header)¶

Compare fasta and modeller seq files.

Create the .ali file that Modeller needs for part 2.

Parameters:

pdb_name (str) – The name of the user’s PDB.
fasta (list) – The fasta seq in list form with one-letter codes as elements.

pyqmmm.md.modeller_automator.step_2(pdb_name, pdb_file)¶: The second step of Modeller software.

pyqmmm.md.modeller_automator.clean_up(pdb_name)¶: To address messy and strange file and naming conventions of Modeller, we will clean up the output files for the user to save time.