Usage

Importing promoe into your own project:

import promoe

promoe’s commandline interface:

Promoe offers three not necessarily distinct entry points:

 ____  ____   ___  __  __  ___  _____
|  _ \|  _ \ / _ \|  \/  |/ _ \| ____|
| |_) | |_) | | | | |\/| | | | |  _|
|  __/|  _ <| |_| | |  | | |_| | |___
|_|   |_| \_ \___/|_|  |_|\___/|_____|

Usage: promoe [OPTIONS] COMMAND [ARGS]…

Options:

-v, --verbose	Verbose output (print debug statements)
--help	Show this message and exit.

Commands:

protonize

protonize-selected

clean-hydrogens

The help menus of the respective commands can be requested via:

promoe <command> --help
e.g. promoe protonize --help

promoe protonize

Help menu:

|  _ \|  _ \ / _ \|  \/  |/ _ \| ____|
| |_) | |_) | | | | |\/| | | | |  _|
|  __/|  _ <| |_| | |  | | |_| | |___
|_|   |_| \_ \___/|_|  |_|\___/|_____|

Usage: promoe protonize [OPTIONS]

Options:

--pdbs TEXT	pdb identifier to protonize -> binding site will be extracted automatically [required]
--keep_hydrogens
	Specify if all hydrogens after protonization should be kept.
--remove_hydrogens
	Specify if hydrogens that are not within a specific distance should be deleted.
--distance INTEGER
	The maximal distance of the ligand to the surrounding water atoms after protonization, that should be kept. Default is 4. Hence, all water atoms within distance 4 to the ligand are not removed!
--help	Show this message and exit

Multiple pdbs can be specified by repeating the –pdb parameter.

The workflow is as follows:

The results include several folders separating the generated results.

The pdb, as well as mol2 files for the full protein, the binding sites, as well as the ligands can be found in the pdb_files and mol2_files folders.

Additionally, the protonated binding sites are contained in the mol2 folder.

All distances from the atoms to the ligand that are below the specified distance are in the distances_files folder.

Moreover, the calculated charges for all residues are contained in the charge_files folder.

promoe protonize-selected

Help menu:

 ____  ____   ___  __  __  ___  _____
|  _ \|  _ \ / _ \|  \/  |/ _ \| ____|
| |_) | |_) | | | | |\/| | | | |  _|
|  __/|  _ <| |_| | |  | | |_| | |___
|_|   |_| \_ \___/|_|  |_|\___/|_____|

Usage: promoe protonize-selected [OPTIONS]

Options:

--pdb TEXT	Path to a pdb file [required]
--atoms TEXT	A list of atoms in the following format: –atoms ‘[‘GLN’, ‘144’, ‘N’], [‘LEU’, ‘145’, ‘N’]’ [required]
--chain TEXT	A chain specifier such as ‘A’ or ‘B’ or ‘all’
--keep_hydrogens
	Specify if all hydrogens after protonization should be kept.
--remove_hydrogens
	Specify if hydrogens that are not within a specific distance should be deleted.
--distance INTEGER
	The maximal distance of the ligand to the surrounding water atoms after protonization, that should be kept. Default is 4. Hence, all water atoms within distance 4 to the ligand are not removed!
--help	Show this message and exit.

Please ensure, that the atoms are specified in the following format: ‘[‘GLN’, ‘144’, ‘N’], [‘LEU’, ‘145’, ‘N’]’

The quote are required! This is due to the forwarding of parameters to a svl script via a process, which unfortunately requires a very specific format. It is a non-trivial task to fix this dynamically in python. Thank the svl developers for this one.

The generated results are very similar to the ones mentioned for protonize

promoe clean-hydrogens

Help menu:

 ____  ____   ___  __  __  ___  _____
|  _ \|  _ \ / _ \|  \/  |/ _ \| ____|
| |_) | |_) | | | | |\/| | | | |  _|
|  __/|  _ <| |_| | |  | | |_| | |___
|_|   |_| \_ \___/|_|  |_|\___/|_____|

Usage: promoe clean-hydrogens [OPTIONS]

Options:

--mol2 TEXT	Path to the mol2 file[required]
--distance INTEGER
	The maximal distance of the ligand to the surrounding water atoms after protonization, that should be kept. Default is 4. Hence, all water atoms within distance 4 to the ligand are not removed!
--help	Show this message and exit.

clean-hydrogens only generates distance files and the modified mol2 file.