Template

class pyjess.TemplateAtom

A single template atom.

__init__(*, chain_id, residue_number, x, y, z, residue_names, atom_names, distance_weight=0.0, match_mode=0)

Create a new template atom.

Raises:

MemoryError – When the system allocator fails to allocate enough memory for the template atom storage.

classmethod load(file)

Load a template atom from the given file.

Parameters:

file (file-like object) – A file-like object opened in text mode to read the template atom from.

classmethod loads(text)

Load a template atom from the given string.

Parameters:

text (str, bytes or bytearray) – The atom line to read the atom metadata from.

atom_names

The different atom names for this atom.

Type:

list of str

chain_id

The identifier of the chain the atom belongs to.

Type:

str

distance_weight

The distance weight for this atom.

Type:

float

match_mode

The match mode for this particular atom.

Type:

int

residue_names

The different residue names for this atom.

Type:

list of str

residue_number

The residue sequence number.

Type:

int

x

The x coordinate of the atom.

Type:

float

y

The y coordinate of the atom.

Type:

float

z

The z coordinate of the atom.

Type:

float

class pyjess.Template

A template, as a sequence of TemplateAtom objects.

__getitem__(key, /)

Return self[key].

__init__(atoms=(), id=None)

Create a new template.

Parameters:

• atoms (sequence of TemplateAtom) – The atoms of the templates.

• id (str, optional) – The identifier of the template.

Raises:

MemoryError – When the system allocator fails to allocate enough memory for the template storage.

__len__()

Return len(self).

dimension

The dimension of the template (i.e. number of residues).

Type:

int