protex.system.ProtexTemplates

class protex.system.ProtexTemplates(states: list[dict[str, dict[str, str]]], allowed_updates: dict[frozenset[str], dict[str, float]])[source]

Bases: object

Creates the basic foundation for the Protex System.

Parameters:

states – A list of dictionary depicting the residue name and the atom name which should be changed, i.e.:

IM1H_IM1 = { "IM1H": {"atom_name": "H7", "canonical_name": "IM1"},
            "IM1": {"atom_name": "N2", "canonical_name": "IM1"} }
OAC_HOAC = { "OAC": {"atom_name": "O2", "canonical_name": "OAC"},
            "HOAC": {"atom_name": "H", "canonical_name": "OAC"} }
states = [IM1H_IM1, OAC_HOAC]

allowed_updates – A dictionary specifiying which updates are possile. Key is a frozenset with the two residue names for the update. The values is a dictionary which specifies the maximum distance (“r_max”) and the probability for this update (“prob”) r_max is in nanometer and the prob between 0 and 1

allowed_updates = {}
allowed_updates[frozenset(["IM1H", "OAC"])] = {"r_max": 0.155, "prob": 1}
allowed_updates[frozenset(["IM1", "HOAC"])] = {"r_max": 0.155, "prob": 1}
allowed_updates[frozenset(["IM1H", "IM1"])] = {"r_max": 0.155, "prob": 0.201}
allowed_updates[frozenset(["HOAC", "OAC"])] = {"r_max": 0.155, "prob": 0.684}

Variables:

pairs – A list with the pairs where the hydrogen can be transfered
states – The passed states list as a joined dictionary
names – A list with the different residue names
allowed_updates – the allowed_updates passed to the class
overall_max_distance – the longest allowed distance for a possible transfer between two updates

Methods

`dump`	Pickle the current ProtexTemplates object.
`get_atom_name_for`	Get the atom name for a specific residue.
`get_charge_template_for`	get_charge_template_for returns the charge template for a residue.
`get_equivalent_atom_for`	Get the name of the equivalent atom for a given residue name.
`get_residue_name_for_coupled_state`	get_residue_name_of_paired_ion returns the paired residue name given a reisue name.
`get_update_value_for`	Returns the value in the allowed updates dictionary.
`has_equivalent_atom`	Check if a given residue has an equivalent atom defined.
`load`	Load a pickled ProtexTemplates instance.
`set_allowed_updates`
`set_update_value_for`	Update a value in the allowed updates dictionary.

dump(fname: str) → None[source]

Pickle the current ProtexTemplates object.

Parameters:: fname (str) – The file name of the object

get_atom_name_for(resname: str) → str[source]

Get the atom name for a specific residue.

Parameters:: resname (str) – The residue name
Returns:: The atom name
Return type:: str

get_charge_template_for(name: str) → list[source]

get_charge_template_for returns the charge template for a residue.

Parameters:: name (str) – Name of the residue
Returns:: charge state of residue
Return type:: list
Raises:: RuntimeError – [description]

get_equivalent_atom_for(resname: str) → str[source]

Get the name of the equivalent atom for a given residue name.

Parameters:: resname (str) – The residue name
Returns:: The atom name
Return type:: str

get_residue_name_for_coupled_state(name: str) → str[source]

get_residue_name_of_paired_ion returns the paired residue name given a reisue name.

Parameters:: name (str) – residue name
Return type:: str
Raises:: RuntimeError – is raised if no paired residue name can be found

get_update_value_for(residue_set: frozenset[str], property: str) → float[source]

Returns the value in the allowed updates dictionary.

Parameters:

residue_set – dictionary key for residue_set, i.e [“IM1H”, “OAC”]
property – dictionary key for the property defined for the residue key, i.e. prob

Returns:

the value of the property

Return type:

float

Raises:

RuntimeError – if keys do not exist

has_equivalent_atom(resname: str) → bool[source]

Check if a given residue has an equivalent atom defined.

Parameters:: resname (str) – The residue name
Returns:: True if this residue has an equivalent atom defined, false otherwise
Return type:: bool

static load(fname: str) → ProtexTemplates[source]

Load a pickled ProtexTemplates instance.

Parameters:: fname (str) – The file name
Returns:: An instance of the ProtexTemplates
Return type:: ProtexTemplates

set_update_value_for(residue_set: frozenset[str], property: str, value: float)[source]

Update a value in the allowed updates dictionary.

Parameters:

residue – dictionary key for residue_set, i.e [“IM1H”,”OAC”]
property – dictionary key for the property defined for the residue key, i.e. prob
value – the value the property should be set to

Return type:

None

Raises:

RuntimeError – is raised if new residue_set or new property is trying to be inserted