restraintmaker.utils package

Submodules

restraintmaker.utils.Types module

restraintmaker.utils.Utilities module

Utilities utilities contains functions and definitions that are usefull to all modules in the restraintmaker project

class restraintmaker.utils.Utilities.Atom(elem, id, name, x, y, z, chain, resn, resi, alt, b, label)

Bases: tuple

alt

Alias for field number 9

b

Alias for field number 10

chain

Alias for field number 6

elem

Alias for field number 0

id

Alias for field number 1

label

Alias for field number 11

name

Alias for field number 2

resi

Alias for field number 8

resn

Alias for field number 7

x

Alias for field number 3

y

Alias for field number 4

z

Alias for field number 5

exception restraintmaker.utils.Utilities.BadArgumentException(*args)[source]

Bases: Exception

A BadArgumentException will be raised by the Filter, Selection and Optimizer classes if their function get-args(…) does not produce arguments in the desired format.

exception restraintmaker.utils.Utilities.NoOptimalSolutionException(args)[source]

Bases: Exception

A no optimal solution excpetion will be raised by an Optimizer, if it can not find a solution fulfilling its criteria.

class restraintmaker.utils.Utilities.RestraintPair(r1, r2, distance)

Bases: tuple

distance

Alias for field number 2

r1

Alias for field number 0

r2

Alias for field number 1

restraintmaker.utils.Utilities.check_for_doubles(list: List) → bool[source]

Just used for debbuging Checks if a List contains doubles

Parameters

list (t.List) – Any list

Returns

Does the list contain doubles?

Return type

bool

restraintmaker.utils.Utilities.check_or_convert_argument(input, desired_type, acceptable_values=None)[source]

try to convert should be used in all get_args functions to check the input from the input function and try to convert it if necessary

TODO: Might be even nicer if we do not pass a list of acceptable values but a bool function TODO: Pass name of the variable as arg, so we can get better Error messages ()

Parameters

  • input (t.Any) – input as received from the function

  • desired_type (type) – the needed type

  • acceptable_values (t.List) – Optional. a List of set Values the input must have.

Returns

converted input to desired_type

Return type

type

Raises

u.BadArgument_Exception – if conversion is not possible or the input is not an acceptable value

restraintmaker.utils.Utilities.check_restraint_pairs_for_doubles(list)[source]

check_restraint_pairs_for_doubles checks a list of pairs for doubles. Pairs count as doubles if the order of elements is changed.

Parameters

list (t.List[t.Tuple]) – A list of tuples

Returns

Does the list contain doubles?

Return type

bool

restraintmaker.utils.Utilities.convert_atoms_to_pdb_molecules(atoms: List[restraintmaker.utils.Utilities.Atom]) → List[str][source]

This function converts the atom list into pdb blocks.

Parameters

atoms (t.List[Atom]) – List of atoms

Returns

pdb strings of that molecule

Return type

t.List[str]

restraintmaker.utils.Utilities.do_nothing(dummy_string: str = '')[source]

does nothing. Can be passed to the *.get_args functions which require a function of a string as parameter. Because it is more readable than lambda x: None

Parameters

dummy_string (str) – Dummy String to satisfy format

Return type

NoReturn

restraintmaker.utils.Utilities.execute_at_different_verbosity(new_verbosity_threshold, func, *args, **kwargs)[source]
Wrapper function to change the program verbosity during the execution of one function.

@Warning All Errors will be passed on to the calling function. But the verbosity_thresheold will be reset to the previous value in any case.

Parameters

  • new_verbosity_threshold (int) – verbosity threshold to be applied duribng the execution of func

  • func (t.Callable) – Function which should be executed

  • args (Any)

  • kwargs (Any)

Returns

return value of func

Return type

Any

restraintmaker.utils.Utilities.find_atom_by_property(atoms: List[restraintmaker.utils.Utilities.Atom], property_value: any, property_name: str = 'id') → restraintmaker.utils.Utilities.Atom[source]

find_atom will look for the first atom with the specified property and value

Parameters

  • property_value (Any) – value of the property

  • property_name (str, optional) – name of the property (default: id)

Returns

returns the atom

Return type

u.Atom

Raises

ValueError – if there is no or more than one atom with that id

restraintmaker.utils.Utilities.get_all_subclasses(parent: type, include_private_sublcasses=False) → List[type][source]

get_all_subclasses returns ALL subclasses of a type, including grandchilder etc.

Parameters

  • parent (type) – Parentn class

  • include_private_sublcasses (bool, optional) – shall privates be included? (default: False)

Returns

List of all subclasses

Return type

t.List[type]

restraintmaker.utils.Utilities.order_atoms_by_molecule(atoms: List[restraintmaker.utils.Utilities.Atom]) → Dict[str, List[restraintmaker.utils.Utilities.Atom]][source]
Parameters

atoms (t.List[Atom]) – A list of atoms

Returns

A Dictionary: Molecules names as keys, List of atoms in the molecule as entry

Return type

t.Dict[t.List[Atom]]

restraintmaker.utils.Utilities.print(*x: str, mv: int = 0, **kargs)[source]
print is overridden for the restraintmaker project:

The parameter mv indicates the minimal verbosity at which the statement will still be printed.

The verobsity threshold of the program can be chagned in utilities.

0 = Print everything, 1 = Debug, 2 = Develop, 3 = Interested user, 4 = disinterested user (Error messages only)

Parameters

  • x (Any) – Arguments to be printed

  • mv (int) – Minimal verbosity at which this statement will still be printed.

Return type

NoReturn

Module contents