Project configuration file

[iacopy]

E.g. in YAML:

---
taxa:
  - Homo sapiens
  - Mus musculus
  - Rattus norvegicus
methods:
  - X-RAY DIFFRACTION
  - SOLUTION NMR
  - ELECTRON MICROSCOPY
polymer_type:
  - Protein
results_content_type:
  - computational
  - experimental
...

Articoli di riferimento generali:

• https://hackersandslackers.com/simplify-your-python-projects-configuration/
• https://towardsdatascience.com/from-novice-to-expert-how-to-write-a-configuration-file-in-python-273e171a8eb3

Guida Yaml:

• Yaml: https://spacelift.io/blog/yaml

[iacopy]

Altre opzioni di struttura file di configurazione.

# OPZIONE 1
# queries:
#   - Homo_sapiens:
#     - entity_poly.rcsb_entity_polymer_type:
#       - Protein
#     - methods:
#       - X-RAY DIFFRACTION
#       - ELECTRON MICROSCOPY
#     - results_content_type:
#       - experimental
#   - Mus musculus:
#     - entity_poly.rcsb_entity_polymer_type:
#     - Protein
#     - methods:
#       - X-RAY DIFFRACTION
#       - ELECTRON MICROSCOPY
#     - results_content_type:
#       - experimental

## OPZIONE 2
# query:
#   - entity_poly.rcsb_entity_polymer_type:
#     - Protein
#   - methods:
#     - X-RAY DIFFRACTION
#     - ELECTRON MICROSCOPY
#   - rcsb_entity_source_organism.taxonomy_lineage.name:
#     - Homo sapiens
#     - Mus musculus
#   - results_content_type:
#     - experimental
# split_dir:
#   # crea query separate per ogni valore di questi attributi
#   # in pratica vogliamo creare una query separata per organismo
#   # in modo che i relativi file pdb siano scaricati in directory diverse
#   # solitamente vogliamo dividere anche le strutture sperimentali da quelle
#   # ottenute con metodi computazionali
#   - rcsb_entity_source_organism.taxonomy_lineage.name
#   - results_content_type

# OPZIONE 3

# project_name: Classic
# query_base:
#   - entity_poly.rcsb_entity_polymer_type:
#     - Protein
#   - methods:
#     - X-RAY DIFFRACTION
#     - ELECTRON MICROSCOPY
#     - AlphaFoldDB
# split:
#   taxa:
#     - Homo_sapiens: "Homo sapiens"
#     - Mus_musculus: "Mus musculus"
#   db_sources:
#     - experimental
#     - computational

# OPZIONE 4

taxa:
  - Rattus norvegicus
  - Mus musculus
csm: true