restraintmaker.interface_Pymol.pymol_utilities package
Submodules
restraintmaker.interface_Pymol.pymol_utilities.program_states module
restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities module
contains functions that are useful to the restraintmaker_PyMOL module, but do not need to be within the Distance_restraints class This also includes functions that are only usefull for debugging and testing
- restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities._atom_list_to_pymol_selection(atom_list: List[restraintmaker.utils.Utilities.Atom]) str[source]
atom_list_to_pymol_selection converts a List of Atoms to a string that pymool can understand. @warning Pymol can only handle a string with a length of ca 1000. (ca 200 atoms.) Consider using help_pymol_with_big_atoms_List
- Parameters
atom_list (t.List[u.Atom]) – A List of Atoms
- Returns
A interface_Pymol selection expression, containing all those Atoms
- Return type
str
- restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities._convert_molecules_to_pdb() List[str][source]
- convert_molecules_to_pdb gives a list containing one pdb string for each molecule
@Warnings atoms willbeassigned different IDS than they currently have in interface_Pymol!!!!!
- Returns
List of pdb string for each molecule in interface_Pymol
- Return type
t.List[str]
- restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities.colorize(atoms)[source]
sets the pymol colors - FOOLING AROUND :) colorize_atoms: Some tests for different ways of colouring atoms.
When using the predefinied names (e.g. “gray”) PyMol raises a Quiet Error. With this method I can test, that Pymol does accept the different colour numbering schemes (s for spectrum, c for complementary etc.) :Parameters: atoms (Atoms)
- restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities.create_pymol_objects_for_molecules(exclude: List[str] = [])[source]
creates separate selecetions for all molecules in interface_Pymol
TODO; WRITE THE NAME OF THE MOLECULE IN TO THE ATOM SOMEHOW TODO: make more stable if protein is present!
- Parameters
exclude (t.List[str]) – A list of molecules that should not be considered, e.g. ‘solv;, ‘protein’, etc
- Returns
The list of the molecule object names
- Return type
t.List[u.Atom]
- restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities.help_pymol_with_big_atom_list(pymol_function: Callable, atom_list: List[restraintmaker.utils.Utilities.Atom], *args, **kw_args)[source]
help_pymol_with_big_atom_list can be wrapped around any interface_Pymol function, that takes ‘selection’ as an argument.
help_pymol_with_big_atom_list will call pymol_function several times with small enough parts of the list
- Parameters
pymol_function (t.Callable) – Any funciton from one of the interface_Pymol modules, who takes ‘selection’ as an argument
atom_list (t.List[u.Atom]) – A list of atoms
args (list) – arguments for the interface_Pymol function
kw_args (dict) – keyword argument for the interface_Pymol functiom
- Returns
a list of all return values of the seperate calls
- Return type
t.List
- Raises
ValueError – if interface_Pymol function is not passed the correct arguments
- restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities.pymol_selection_to_atom_list(sele: str) List[restraintmaker.utils.Utilities.Atom][source]
converts a interface_Pymol selection and returns a list of restraintmaker_Logic.utilities.Atom
- Parameters
sele (str) – pymol selection string
- Returns
A list of Atoms
- Return type
t.List[u.Atom]
- restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities.try_to_get_args(my_x, input_function) bool[source]
wrapper function for get_args. Takes care of the error handling
- Parameters
my_x (_Importer,_Restraint,_Selection,_Filter,_Optimzer or _Exporter) – An Object that should call get args
input_function (t.Callable[str]) – The input_function argument of get_args
- Returns
Could get_args be executed without errors?
- Return type
bool
restraintmaker.interface_Pymol.pymol_utilities.qt_dialogs module
- restraintmaker.interface_Pymol.pymol_utilities.qt_dialogs.create_file_open_dialog()[source]
create_file_dialog returns a function which: Opens a pyQt5 file Dialog with the speciefed message. In this format it can be provided to the get_args functions
- Returns
Returns a function, that opens an input dialog, with the specified title, and is centered at the interface_Pymol window.
- Return type
t.Callable[str,[str])
- restraintmaker.interface_Pymol.pymol_utilities.qt_dialogs.create_file_save_dialog()[source]
create_file_dialog returns a function which: Opens a pyQt5 file Dialog with the speciefed message. In this format it can be provided to the get_args functions
- Returns
Returns a function, that opens an input dialog, with the specified title, and is centered at the interface_Pymol window.
- Return type
t.Callable[str,[str]]
- restraintmaker.interface_Pymol.pymol_utilities.qt_dialogs.create_input_dialog(parent_window, title: str) Callable[[str], str][source]
create_input_dialog returns a function which:
Opens a pyQt5 input Dialog with the speciefed message. In this format it can be provided to the get_args functions
- Parameters
parent_window – parent QT window of the sub dialog
title (str) – dialog title
- Returns
Returns a function, that opens an input dialog, with the specified title, and is centered at the interface_Pymol window.
- Return type
t.Callable[str,[str])
- restraintmaker.interface_Pymol.pymol_utilities.qt_dialogs.create_multi_dialog(title, inputs: List[str], options: Dict[str, List[str]] = {}, default: Dict = {}) Callable[[str], List[str]][source]
create_multi_dialog return
- TODO get_args: I am not happpy with the create_multi_dialog solution: Now we have to ‘prepare’ the input function in set_x_type by checking what x(optimizer, filter…) type we want to create.
The initial idea was that input_function is passed to get_args, which can then call it as needed, without having to know the format of its arguments We have to choose either:1) input function returns exactly one str. if more inputs are required, input fkt is called several times. => Does not allow to ask for all in one dialog
or :2) Abolish get_args. Each type has a list required_args. the logic handler will read that list and then get them all from the user. The Optimizer?Filter… then only has to check the type
- Warning
Do not call before the constructor o f the Pymol module has finished, or pyumol will hate you.
- Warning
Will not throw an error if close button is pressed. Just return an enmpty list
- Parameters
title (str) – Title of theDialog
:param inputs; all inputs that should be asked for :type inputs: t.List[str] :param options: optional, specifies the options an input can have. (input as key, list of acceptable values as values) :type options: t.dict[str,t.List[str]] :param default: Specifies the options an input can have. (input as key, list of acceptable values as value0 :type default: t.dict[str,t.Any] :return: A function which will open a dialog, asking for the inputs specified in inputs :rtype: t.Callable[[str],t.List[str or t.List[str]]]