R/chembl_helpers.R

In bhklab/AnnotationGx: AnnotationGx: A package for building, updating and querying an annotation database for pharmaco-genomic data

#' Internal function that returns all possible chembl resources
#' @keywords internal
#' @noRd
.chembl_resources <- function() {
  c(
    "activity", "assay", "atc_class", "binding_site", "biotherapeutic", "cell_line",
    "chembl_id_lookup", "compound_record", "compound_structural_alert", "document",
    "document_similarity", "document_term", "drug", "drug_indication", "drug_warning",
    "go_slim", "image", "mechanism", "metabolism", "molecule", "molecule_form",
    "organism", "protein_classification", "similarity", "source", "status", "substructure",
    "target", "target_component", "target_relation", "tissue", "xref_source"
  )
}

#' Internal function that returns all possible chembl filter types
#' @keywords internal
#' @noRd
.chembl_filter_types <- function() {
  c(
    "exact", "iexact", "contains", "icontains", "startswith", "istartswith",
    "endswith", "iendswith", "regex", "iregex", "gt", "gte", "lt", "lte",
    "range", "in", "isnull", "search", "only"
  )
}

#' Internal function that returns all possible chembl mechanism columns
#' @keywords internal
#' @noRd
.chembl_mechanism_cols <- function() {
  c(
    "action_type", "binding_site_comment", "direct_interaction", "disease_efficacy",
    "max_phase", "mec_id", "mechanism_comment", "mechanism_of_action",
    "mechanism_refs", "molecular_mechanism", "molecule_chembl_id",
    "parent_molecule_chembl_id", "record_id", "selectivity_comment",
    "site_id", "target_chembl_id", "variant_sequence"
  )
}

#' Internal function that returns the complete schema for a Chembl resource
#' @keywords internal
#' @noRd
.chembl_resource_schema <- function(resource) {
  .build_chembl_request(paste0(resource, "/schema")) |>
    .perform_request() |>
    .parse_resp_json()
}