Documentation
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Overview ¶
Package alphafold is the library behind the alphafold command line: the HTTP client, request shaping, and the typed data models for the EMBL-EBI AlphaFold Protein Structure Database.
The Client here is the spine every command shares. It sets a real User-Agent, paces requests so a busy session stays polite, and retries the transient failures (429 and 5xx) that any public API throws under load.
Index ¶
Constants ¶
const BaseURL = "https://" + Host
BaseURL is the root every request is built from.
const DefaultUserAgent = "alphafold-cli/dev (+https://github.com/tamnd/alphafold-cli)"
DefaultUserAgent identifies the client to AlphaFold.
const Host = "alphafold.ebi.ac.uk"
Host is the AlphaFold site this client talks to.
Variables ¶
This section is empty.
Functions ¶
This section is empty.
Types ¶
type Client ¶
type Client struct {
HTTP *http.Client
UserAgent string
// Rate is the minimum gap between requests. Zero means no pacing.
Rate time.Duration
Retries int
// contains filtered or unexported fields
}
Client talks to AlphaFold over HTTP.
func NewClient ¶
func NewClient() *Client
NewClient returns a Client with sensible defaults: a 30s timeout, a 300ms minimum gap between requests, and three retries on transient errors.
func (*Client) Get ¶
Get fetches rawURL and returns the response body. It paces and retries according to the client's settings. The body is read fully and closed here.
func (*Client) GetPrediction ¶
GetPrediction fetches all structure prediction fragments for a UniProt accession (e.g. "P04637"). Returns one Prediction per fragment entry.
type Domain ¶
type Domain struct{}
Domain is the AlphaFold driver. It carries no state; the per-run client is built by the factory Register hands kit.
func (Domain) Classify ¶
Classify turns any accepted input — a UniProt accession or an AlphaFold entry id — into the canonical (type, id). Any non-empty string is accepted.
func (Domain) Info ¶
func (Domain) Info() kit.DomainInfo
Info describes the scheme, the hostnames a pasted link is matched against, and the identity reused for the binary's help and version.
type Prediction ¶
type Prediction struct {
ID string `json:"id" kit:"id"`
UniProtID string `json:"uniprot_id,omitempty"`
Description string `json:"description,omitempty"`
Gene string `json:"gene,omitempty"`
Organism string `json:"organism,omitempty"`
TaxID int `json:"tax_id,omitempty"`
Version int `json:"version,omitempty"`
ModelDate string `json:"model_date,omitempty"`
IsReviewed bool `json:"is_reviewed,omitempty"`
GlobalScore float64 `json:"plddt_score,omitempty"`
PdbURL string `json:"pdb_url,omitempty"`
SequenceLen int `json:"sequence_length,omitempty"`
}
Prediction is a single AlphaFold predicted protein structure record.
Source Files