haddock.clis.restraints.webservice module

Webservice for the haddock3 restraints module.

Exposes the haddock3-restraints CLI subcommands as a RESTful webservice. Also includes endpoint for PDB preprocessing.

Run with:

`shell uvicorn --port 5000 haddock.clis.restraints.webservice:app `

The Swagger UI is running at http://127.0.0.1:5000/docs .

To pass a PDB file in the JSON body of a request, it needs to be gzipped and then base64 encoded.

A base64 encoded gzipped PDB file can made with:

`shell cat examples/data/2oob.pdb | gzip | base64 -w 0 > 2oob.pdb.gz.base64 `

Background for PDB file handling:

To store a multiline string, like a pdb file, in JSON we need to encode it in base64. Base64 encoding make things 1.33 times bigger. A pdb is text which can be compressed a lot. To transfer less data we can compress the pdb with gzip before base64 encoding. For example the 2oob.pdb 74.8Kb becomes 101Kb when base64 encoded while first gzip and then base64 encode it is 25.4Kb.

class haddock.clis.restraints.webservice.ActPassToAmbigRequest(*, active1: list[int], active2: list[int], passive1: list[int], passive2: list[int], segid1: str = 'A', segid2: str = 'B')

Bases: BaseModel

active1: list[int]

active2: list[int]

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

passive1: list[int]

passive2: list[int]

segid1: str

segid2: str

class haddock.clis.restraints.webservice.CalcAccessibilityRequest(*, structure: str, cutoff: float)

Bases: BaseModel

cutoff: float

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

structure: ', json_schema_extra={'contentMediaType': 'text/plain', 'contentEncoding': 'base64'})]

class haddock.clis.restraints.webservice.PDBPreprocessRequest(*, structure: str, from_chain: str, to_chain: str, delhetatm: bool = False, keepcoord: bool = False)

Bases: BaseModel

delhetatm: bool

from_chain: str

keepcoord: bool

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

structure: ', json_schema_extra={'contentMediaType': 'text/plain', 'contentEncoding': 'base64'})]

to_chain: str

class haddock.clis.restraints.webservice.PassiveFromActiveRequest(*, structure: str, active: list[int], chain: str = 'A', surface: list[int] = [], radius: float = 6.5)

Bases: BaseModel

active: list[int]

chain: str

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

radius: float

structure: ', json_schema_extra={'contentMediaType': 'text/plain', 'contentEncoding': 'base64'})]

surface: list[int]

class haddock.clis.restraints.webservice.RestrainBodiesRequest(*, structure: str, exclude: list[str] = [])

Bases: BaseModel

exclude: list[str]

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

structure: ', json_schema_extra={'contentMediaType': 'text/plain', 'contentEncoding': 'base64'})]

class haddock.clis.restraints.webservice.ValidateTblRequest(*, tbl: str, pcs: bool = False, quick: bool = False)

Bases: BaseModel

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

pcs: bool

quick: bool

tbl: ', json_schema_extra={'contentMediaType': 'text/plain', 'contentEncoding': 'base64'})]

haddock.clis.restraints.webservice.calculate_accessibility(request: CalcAccessibilityRequest) → dict[str, list[int]]

Calculate the accessibility of the side chains and apply a cutoff.

haddock.clis.restraints.webservice.calculate_actpass_to_ambig(request: ActPassToAmbigRequest) → str

Get the passive residues.

haddock.clis.restraints.webservice.calculate_passive_from_active(request: PassiveFromActiveRequest) → list[int]

Calculate active restraints to passive restraints.

haddock.clis.restraints.webservice.preprocess_pdb(request: PDBPreprocessRequest) → str

Preprocess a PDB file.

Runs the following [pdbtools](http://www.bonvinlab.org/pdb-tools/) pipeline:

`shell cat pdb | pdb_tidy -strict | pdb_selchain -<from_chain> | pdb_chain -<to_chain> | pdb_fixinsert | pdb_selaltloc | pdb_tidy -strict `

or with delhetatm and keepcoord set to true:

`shell cat pdb | pdb_tidy -strict | pdb_selchain -<from_chain> | pdb_chain -<to_chain> | pdb_delhetatm |         pdb_fixinsert | pdb_keepcoord | pdb_selaltloc | pdb_tidy -strict `

haddock.clis.restraints.webservice.restrain_bodies(request: RestrainBodiesRequest) → str

Create distance restraints to lock several chains together.

haddock.clis.restraints.webservice.unpacked_structure(structure: str) → bytes

Gunzips a base64 encoded string.

haddock.clis.restraints.webservice.unpacked_tbl(tbl: str) → str

Gunzips a base64 encoded tbl file contents.

haddock.clis.restraints.webservice.validate_tbl(request: ValidateTblRequest) → str