Hey Max I've just tried running hippo locally (macOS) where I've created a fresh hippo env with:
- HIPPO version: 0.3.38
- molparse version: 0.0.41
- RDKit version: 2025.09.1
- Python version: 3.12.8
I try to run
import hippo
import mrich
import os
DOWNLOAD_DIR = ''
mrich.var("hippo", hippo.__file__)
# if hippo.db exists, delete it
if os.path.exists(f"{os.path.dirname(os.path.abspath(__file__))}/hippo.db"):
os.remove(f"{os.path.dirname(os.path.abspath(__file__))}/hippo.db")
animal = hippo.HIPPO("test-hippo", f"{os.path.dirname(os.path.abspath(__file__))}/hippo.db")
animal.add_hits(
target_name = 'A71EV2A',
metadata_csv = f'{DOWNLOAD_DIR}/metadata.csv',
aligned_directory = f'{DOWNLOAD_DIR}/aligned_files'
)
animal.summary()
animal.db.close()and get this output
(hippo) kate_fieseler@Kates-MacBook-Pro-2 test-hippo % python load-into-hippo_v1.py
hippo = /Users/kate_fieseler/miniconda3/envs/hippo/lib/python3.12/site-packages/hippo/__init__.py
Creating HIPPO animal
name = test-hippo
db_path = /Users/kate_fieseler/CursorProjects/TS/experiments/test-hippo/hippo.db
DEBUG: hippo.Database.__init__()
DEBUG: Database.path = /Users/kate_fieseler/CursorProjects/TS/experiments/test-hippo/hippo.db
DEBUG: hippo.Database.connect()
DEBUG: sqlite3.version='2.6.0'
Success Database connected @ /Users/kate_fieseler/CursorProjects/TS/experiments/test-hippo/hippo.db!
DEBUG: HIPPO.Database.create_table_compound()
DEBUG: HIPPO.Database.create_table_inspiration()
DEBUG: HIPPO.Database.create_table_reaction()
DEBUG: HIPPO.Database.create_table_reactant()
DEBUG: HIPPO.Database.create_table_pose()
DEBUG: HIPPO.Database.create_table_tag()
DEBUG: HIPPO.Database.create_table_quote()
DEBUG: HIPPO.Database.create_table_target()
DEBUG: HIPPO.Database.create_table_pattern_bfp()
DEBUG: HIPPO.Database.create_table_feature()
DEBUG: HIPPO.Database.create_table_route()
DEBUG: HIPPO.Database.create_table_component()
DEBUG: HIPPO.Database.create_table_interaction(table='interaction')
DEBUG: HIPPO.Database.create_table_subsite()
DEBUG: HIPPO.Database.create_table_subsite_tag()
DEBUG: HIPPO.Database.create_table_scaffold()
Success Initialised animal HIPPO("test-hippo")!
aligned_directory = /Users/kate_fieseler/Downloads/A71EV2A/aligned_files
curated_tag_cols =
[
'[Other] upload_4 2025-04-02',
'[Other] Lactam Series',
'[Other] cyclopropane',
'[Other] P2 Wave 1',
'[Other] fff_i1_design',
'[Other] New',
'[Other] upload_6_2025-02-13',
'[Other] S2 site',
'[Other] Fragment Screen',
'[Other] Covalent',
'[Other] Bogyo covalents',
'[Other] S5 site',
'[Series] Indazole series',
'[Other] S4 site',
'[Other] Sun-roof open',
'[Other] S3 site',
'[Other] upload_3 2024-12-19',
'[Other] upload_4 2025-01-06',
'[Other] upload_5 2025-02-03',
'[Other] upload_061224',
'[Other] upload_2 2024-12-12',
"[Other] S1' site",
'[Other] upload_3 2025-03-06',
'[Series] Piperidine series',
'[Other] P3 compound design',
'[Other] upload_5 2025-04-10',
'[Other] upload_1 2024-12-06',
'[Other] upload_1 2025-02-12',
'[Other] upload_2 2025-02-28',
'[Other] upload_8 2025-10-08',
'[Other] upload_6 2025-09-15',
'[Other] Active site fragment',
'[Other] S1 site',
'[Other] upload_7 2025-09-29'
]
Adding hits... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0% 0:00:00 -:--:-- {}zsh: segmentation fault python load-into-hippo_v1.pyI've looked into it a bit and I think it has something to do with iterating through all the subdirectories in the aligned file directory and parsing the PDBs with molparse. Thanks for your help
Hey Max I've just tried running hippo locally (macOS) where I've created a fresh hippo env with:
I try to run
and get this output
I've looked into it a bit and I think it has something to do with iterating through all the subdirectories in the aligned file directory and parsing the PDBs with molparse. Thanks for your help