`pyqmmm.md.quickcsa`¶

Performs charge shift analysis (CSA) form TeraChem output.

Module Contents¶

`clean_dir`(→ str)	Searches the current directory for files, prints missing file alerts.
`file_mover`(→ None)	Check the current directory for the five required files and move them.
`get_mask_res`(→ List)	Create a list of the residues that should belong to the holo/apo regions.
`mask_maker`(→ None)	Create the apo and holo masks from the original PDB file.
`collect_charges`(→ None)	Collect the charges from the charge.xls file.
`get_res_diff`(→ List)	Calculate the charge difference for the apo and holo residue list files.
`charge_diff`(→ None)	Calculate the difference in the charges for the apo and holo residue lists.
`quick_csa_intro`(→ None)	Introduces the user to Quick CSA and provides information on how it is run.
`quick_csa`(→ None)	The central handler funtion for the Quick CSA program.

pyqmmm.md.quickcsa.clean_dir() → str[source]¶

Searches the current directory for files, prints missing file alerts.

Cleans the directory into a three-folder system: 1_input, 2_temp, and 3_out.

Parameters:: pdb_name (str) – The name of the PDB that the user would like processed.
Returns:: pdb_name – The name of the PDB that the user would like processed.
Return type:: str

pyqmmm.md.quickcsa.file_mover(file_system_exists, pdb_name) → None[source]¶

Check the current directory for the five required files and move them.

Parameters:: file_system_exists (boolean) – The path of the user’s full PDB.

pyqmmm.md.quickcsa.get_mask_res(type) → List[source]¶

Create a list of the residues that should belong to the holo/apo regions.

Parameters:: type (str) – Tell function if it is the holo or apo list.
Returns:: mask_list – An array of all the residues that the user wants included in their mask.
Return type:: List[]

pyqmmm.md.quickcsa.mask_maker(mask, pdb_name, type) → None[source]¶

Create the apo and holo masks from the original PDB file.

Parameters:

raw_mask (str) – A list of residues that the user wants pulled from the original PDB.
pdb_name (str) – The name of the user’s original PDB file from which we create the mask.
type (str) – Tell function if it is the holo or apo mask.

pyqmmm.md.quickcsa.collect_charges(type) → None[source]¶

Collect the charges from the charge.xls file.

Parameters:: type (str) – Tell function if it is the holo or apo mask.

pyqmmm.md.quickcsa.get_res_diff() → List[source]¶

Calculate the charge difference for the apo and holo residue list files.

Returns:: res_diff – A list of the residues that were removed in the holo structure.
Return type:: list

pyqmmm.md.quickcsa.charge_diff(cutoff) → None[source]¶

Calculate the difference in the charges for the apo and holo residue lists.

Parameters:: ns_res_list (list) – A list of the residues that were removed in the holo structure.

pyqmmm.md.quickcsa.quick_csa_intro() → None[source]¶: Introduces the user to Quick CSA and provides information on how it is run. Contains information about the required files and the naming conventions.

pyqmmm.md.quickcsa.quick_csa() → None[source]¶: The central handler funtion for the Quick CSA program. This function is also provided as a module in the pyQM/MM package.