Templates

class enzymm.template.AnnotatedResidue(_atoms: Tuple[TemplateAtom, TemplateAtom, TemplateAtom], _vec: Vec3, _indices: Tuple[int, int], reference_idx: int, reference_pdb: HomologousPDB, reference_residue: ReferenceCatalyticResidue)

Child class inheriting from Residue for M-CSA annotated template residues.

reference_idx

int Residue indentifier of the reference residue.

Type:: int

reference_pdb

HomologousPDB The PDB reference of the residue.

Type:: enzymm.mcsa_info.HomologousPDB

reference_residue

ReferenceCatalyticResidue The reference residue.

Type:: enzymm.mcsa_info.ReferenceCatalyticResidue

__init__(_atoms: Tuple[TemplateAtom, TemplateAtom, TemplateAtom], _vec: Vec3, _indices: Tuple[int, int], reference_idx: int, reference_pdb: HomologousPDB, reference_residue: ReferenceCatalyticResidue) → None

Initilaize a Residue instance from a triplet of TemplateAtom objects.

Parameters:: atoms – tuple of 3 TemplateAtom instances
Returns:: Residue

property has_ptm: bool: Wether the residue in the M-CSA reference PDB structure was post-translationally modified

property is_metal_ligand: bool: Wether the residue in the M-CSA reference PDB structure was metal coordinating

property is_mutated: bool: Wether the residue in the M-CSA reference PDB structure was mutated

property roles: List[str]: list of str of EMO (Enyzme Mechanism Ontology) terms of catalytic roles

property roles_summary: List[str]: list of str describing catalytic roles

class enzymm.template.AnnotatedTemplate(*, residues: Sequence[AnnotatedResidue], pdb_id: str, mcsa_id: int, number_of_mutated_residues: int, number_of_metal_ligands: Tuple[int, int], number_of_ptm_residues: Tuple[int, int], number_of_side_chain_residues: Tuple[int, int], total_reference_residues: int, assembly: int, id: str | None = None, template_id_string: str | None = None, cluster: Cluster | None = None, uniprot_id: str | None = None, organism: str | None = None, organism_id: str | None = None, resolution: float | None = None, experimental_method: str | None = None, enzyme_discription: str | None = None, represented_sites: int | None = None, ec: Iterable[str] = (), cath: Iterable[str] = ())

Child class inheriting from Template for M-CSA annotated catalytic site templates.

__init__(*, residues: Sequence[AnnotatedResidue], pdb_id: str, mcsa_id: int, number_of_mutated_residues: int, number_of_metal_ligands: Tuple[int, int], number_of_ptm_residues: Tuple[int, int], number_of_side_chain_residues: Tuple[int, int], total_reference_residues: int, assembly: int, id: str | None = None, template_id_string: str | None = None, cluster: Cluster | None = None, uniprot_id: str | None = None, organism: str | None = None, organism_id: str | None = None, resolution: float | None = None, experimental_method: str | None = None, enzyme_discription: str | None = None, represented_sites: int | None = None, ec: Iterable[str] = (), cath: Iterable[str] = ())

Initialize an annotated template with descriptions of catalytic activity from the M-CSA.

Keyword Arguments:

residues – Sequence of Residue instances
id – str Internal Template ID string. Default None
pdb_id – str The PDB ID of the template
template_id_string – str String in the ID line of a template
mcsa_id – int The M-CSA entry index form which the template was generated
cluster – Cluster Instance of the template
uniprot_id – str UniProt Identifier of the Protein from which the template was generated
organism – str Organism name of the Protein from which the template was generated
organism_id – str Taxonomic Identifier of the Organism of the Protein from which the template was generated
resolution – float Resolution of the Protein Structure from which the template was generated
experimental_method – str Experimental method by which the Protein Structure of the template was resolved
enzyme_description – str Text Discription of the Protein from which the template was generated
represented_sites – int The number of Enzymes which this template is representative for
ec – list of str of EC numbers associated with Enzymes this template represents
cath – list of str of CATH numbers associated with Enzymes this template represents
number_of_mutated_residues – int The number of side chain specific residues which have been mutated relative to the reference
number_of_metal_ligands – tuple of (int , int) Number of metal chelating residues in the template and the reference
number_of_ptm_residues – tuple of (int , int) Number of post translationally modified residues in the template and the reference
number_of_side_chain_residues – tuple of (int, int) Number of side chain interacting residues in the template and the reference
total_reference_residues – int Total number of residues (main and side chain) in the reference structure

Note

In order for a template file to be loaded as an AnnotatedTemplate, it must have both an mcsa_id and a pdb_id. This pdb_id must be found in the PDB-homologs of the M-CSA!

Note

It is recommended to not pass an id string. If id is None, the id will be set to

> {effective_size}-Residues_{template_id_string}_Cluster_{Cluster.id}-{Cluster.member}-{Cluster.size}

This identifier string should be unique.

Returns:: AnnotatedTemplate

copy() → AnnotatedTemplate

Create a copy of the template.

Returns:: A new template object with identical attributes and a copy of the TemplateAtom it contains.
Return type:: Template

Overloaded load to parse a pyjess.Template and its associated info into a Template object

Parameters:

file – file-like object or str or path-like from which to load
id – str or None Internal pyjess string which will superseed the ID string parsed from the template file. Default None
warn – bool If warnings should be printed. Default False
with_annotations – bool If True (default) M-CSA derived templates with a PDB-id and M-CSA id will be annotated with extra information.

Returns:

Template | AnnotatedTemplate

classmethod loads(text: str, id: str | None = None, warn: bool = False, with_annotations: bool = True) → Template | AnnotatedTemplate

Load Template from str. Calls Template.load()

Parameters:

text – str of Template to load
id – str or None Internal pyjess string which will superseed the ID string parsed from the template file. Default None
warn – bool If warnings should be printed. Default False
with_annotations – bool If True (default) M-CSA derived templates with a PDB-id and M-CSA id will be annotated with extra information.

Returns:

Template | AnnotatedTemplate

class enzymm.template.Cluster(id: int, member: int, size: int)

Class for storing template cluster information.

id

int Index of the template cluster

Type:: int

member

int Member index within the template cluster

Type:: int

size

int Total number of members in the template cluster

Type:: int

__init__(id: int, member: int, size: int) → None

class enzymm.template.Residue(atoms: Tuple[TemplateAtom, TemplateAtom, TemplateAtom])

Class for storing template residues (defined as 3 atoms) with relevant information.

__init__(atoms: Tuple[TemplateAtom, TemplateAtom, TemplateAtom])

Initilaize a Residue instance from a triplet of TemplateAtom objects.

Parameters:: atoms – tuple of 3 TemplateAtom instances
Returns:: Residue

property allowed_residues: str

Get the allowed residue types as string of single letter codes.

Type:: str

property atoms: Tuple[TemplateAtom, TemplateAtom, TemplateAtom]: Get the tuple of three TemplateAtom describing the residue.

property backbone: bool

True if an atom may match a backbone atom.

True if the atom may match backbone atoms. Check if the atom has ‘ANY’ or ‘XXX’ in its residue_names attribute

Type:: bool

static calc_residue_orientation(atoms: Tuple[TemplateAtom, TemplateAtom, TemplateAtom]) → Tuple[Vec3, Tuple[int, int]]

Method to calculate the residue orientation depending on the residue type.

Parameters:: atoms – tuple of 3 TemplateAtom

Note

For symmetric atom triplets, the angle is calculated from the central atom to the midpoint between the two identical atom types. For non-symetric atom triplets, the angle is calculated between two atoms following the axis of polarization.

Returns:: of Residue.orientation_vector and Residue.orientation_vector_indices
Return type:: tuple

property chain_id: str

Get the pdb chain_id from the first atom.

Type:: str

classmethod construct_residues_from_atoms(atoms: Iterable[TemplateAtom]) → List[Residue]

Classmethod to construct a List of Residue from an interable of TemplateAtom

Parameters:: atoms – iterable of TemplateAtom modulo 3

Note

The atoms are chunked into residues of 3 atoms. Ensure the atoms are in order of residues!

Returns:: of Residue
Return type:: List

classmethod from_molecule_residue(molecule: Molecule, residue_idx: int, chain_name: str, distance_weight: float = 0, match_mode: Literal[-1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 100, 101, 102, 103, 104, 105, 106, 107] = 0) → Residue

Classmethod to construct a residue from a Molecule and residue indices

Parameters:

molecule – Molecule
residue_idx – int
chain_name – str
distance_weight – float tolerance in Angstrom for this atom
match_mode – Literal of int usually one of 0, 1, 3, or 8

Note

Technically each atom in the residue could have a different match mode and distance weight. This behaviour is currently unsupported for this constructor. Raise an issue/pr if you desire this behaviour

Returns:: Residue

property name: str

Get the amino-acid type as three letter code from the first atom.

Type:: str

property number: int

Get the pdb residue number from the first atom.

Type:: int

property orientation_vector: Vec3

Calculate the residue orientation vector according to the residue type.

Type:: Vec3

property orientation_vector_indices: Tuple[int, int]

Return the indices of the atoms between which the orientation vector was calculated according to the residue type.

Type:: tuple of (int, int)

property specific: bool

Atoms with a match_mode greater 100 are unspecific. <100 is specific.

Type:: bool

Class for storing templates and associated information.

Inherits and extends from Template

Initialize a template.

Keyword Arguments:

residues – sequence of Residue instances
id – str Internal Template ID string. Default None
pdb_id – str The PDB ID of the template
template_id_string – str String in the ID line of a template
mcsa_id – int The M-CSA entry index form which the template was generated
cluster – Cluster Instance of the template
uniprot_id – str UniProt Identifier of the Protein from which the template was generated
organism – str Organism name of the Protein from which the template was generated
organism_id – str Taxonomic Identifier of the Organism of the Protein from which the template was generated
resolution – float Resolution of the Protein Structure from which the template was generated
experimental_method – str Experimental method by which the Protein Structure of the template was resolved
enzyme_description – str Text Discription of the Protein from which the template was generated
represented_sites – int The number of Enzymes which this template is representative for
ec – list of str of EC numbers associated with Enzymes this template represents
cath – list of str of CATH numbers associated with Enzymes this template represents

Note

It is recommended not to pass an id string. If id is None, the id string will be set to:

> {Template.dimension}-residues_{Template.template_id_string}_Cluster_{Cluster.id}-{Cluster.member}-{Cluster.size}

This identifier string should be unique.

Note

residues can be constructed from a list of TemplateAtoms via the staticmethod Residue.construct_residues_from_atoms(atoms=atoms)

Note

Iterating over Template gives TemplateAtom. If you want to get Residue, iterate over Template.residues

Returns:: Template

copy() → Template

Create a copy of the template.

Returns:: A new template object with identical attributes and a copy of the TemplateAtom it contains.
Return type:: Template

dump(file: TextIO)

Dump Template to file-like object.

Parameters:: file – file-like object to write to

dumps() → str: Dump Template to a str. Calls Template.dump()

property effective_size: int

The number of unique residues in the template, excluding backbone residues and unspecific residues.

Type:: int

Classmethod to construct a template from a Molecule and a list of residue specifications

Parameters:

molecule – Molecule
residue_ids – list of tuple of str and int for the chain_name and residue_index
cluster – Cluster Instance of the template
organism – str Organism name of the Protein from which the template was generated
organism_id – str Taxonomic Identifier of the Organism of the Protein from which the template was generated
resolution – float Resolution of the Protein Structure from which the template was generated
experimental_method – str Experimental method by which the Protein Structure of the template was resolved
enzyme_description – str Text Discription of the Protein from which the template was generated
uniprot_id – str UniProt Identifier of the Protein from which the template was generated
represented_sites – int The number of Enzymes which this template is representative for
ec – list of str of EC numbers associated with Enzymes this template represents
cath – list of str of CATH numbers associated with Enzymes this template represents

Note

A template generated through this method will not specify an M-CSA id.

Returns:: Template

classmethod from_structure_file(path: Path | TextIO | str, residue_ids: List[Tuple[str, int]]) → Template

Classmethod to construct a template from a filepath to a structure and a list of residue specifications

Parameters:

path – path-like or str to a structure file
residue_ids – list of tuple of str and int for the chain_name and residue_index
uniprot_id – str UniProt Identifier of the Protein from which the template was generated
ec – list of str of EC numbers associated with Enzymes this template represents
cath – list of str of CATH numbers associated with Enzymes this template represents

Note

A template generated through this method will represent a single site and will not specify an M-CSA id or any other meta data.

Returns:: Template

classmethod load(file: TextIO | Iterator[str] | str | PathLike[str], id: str | None = None, warn: bool = False) → Template

Overloaded load to parse a pyjess.Template and its associated info into an Template object

Parameters:

file – file-like object or str or path-like from which to load
id – str or None Internal pyjess string which will superseed the ID string parsed from the template file. Default None
warn – bool If warnings should be printed. Default False

Returns:

Template

classmethod loads(text: str, id: str | None = None, warn: bool = False) → Template

Load Template from str. Calls Template.load()

Parameters:

text – str of Template to load
id – str or None Internal pyjess string which will superseed the ID string parsed from the template file. Default None
warn – bool If warnings should be printed. Default False

Returns:

Template

property multimeric: bool

True if the template contains residues from multiple protein chains.

Type:: bool

property relative_order: List[int]

Relative order of residues in the template sorted by the pdb residue number.

Note

This only works for non-multimeric templates. In this case returns ‘[0]’.

Type:: list of int

class enzymm.template.Vec3(x: float, y: float, z: float)

Class for storing 3D vectors in XYZ.

x

float X-Coordinate value

Type:: float

y

float Y-Coordinate value

Type:: float

z

float Z-Coordinate value

Type:: float

__add__(other: int | float | Vec3) → Vec3

Overloads the + operator to add either an int, float or other Vec3 to a Vec3.

Parameters:: other – int | float | Vec3 argument to add
Returns:: Vec3

__init__(x: float, y: float, z: float) → None

__matmul__(other: Vec3) → float

Overloads the @ operator to perform dot product between two Vec3 vectors.

Parameters:: other – Vec3 instance
Returns:: Vec3

__sub__(other: int | float | Vec3) → Vec3

Overloads the - operator to subtract either an int, float or other Vec3 from a Vec3.

Parameters:: other – int | float | Vec3 argument to subtract
Returns:: Vec3

__truediv__(other: int | float | Vec3) → Vec3

Overloads the / operator to divide a Vec3 object by either an int, float or other Vec3.

Parameters:: other – int | float | Vec3 argument to divide by
Returns:: Vec3

angle_to(other: Vec3) → float

Returns the angle in radians between two Vec3 vectors.

Parameters:: other – Vec3 to which to calculate the angle
Returns:: angle in radians
Return type:: float

classmethod from_xyz(item: Any) → Vec3

Create a Vec3 instance from an object with x,y,z attributes.

Parameters:: any (item) – Any object with x, y, z attributes
Returns:: Vec3 instance

property norm: float

The vector norm (root of sum of squares)

Type:: float

normalize() → Vec3: Vec3: The vector devided by its norm

enzymm.template.load_templates(template_dir: Path | None = None, warn: bool = False, verbose: bool = False, with_annotations: bool = True) → Iterator[Template | AnnotatedTemplate]

Load templates from a given directory, recursively.

Parameters:

template_dir – Path | None Directory which to search recursively for files with the ‘.pdb’ extension. By default, set to None, it will load templates included in this library.
warn – bool If warnings about annoation issues in templates should be printed. Default False
verbose – bool If loading should be verbose. Default False
with_annotations – bool If True (default) M-CSA derived templates with a PDB-id and M-CSA id will be annotated with extra information.

Yields:

Template | AnnotatedTemplate