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installtion on read only file system #94

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installtion on read only file system #94

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d0f3d73
python consistency
EricDeveaud Apr 20, 2026
a226411
hydraconf set ouputs to HOME/.rfantibody/outputs
EricDeveaud Apr 20, 2026
2dba312
pkls saved to HOME/.rfantibody/cached_schedules
EricDeveaud Apr 20, 2026
51de79a
Revert "python consistency"
EricDeveaud Apr 20, 2026
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7 changes: 7 additions & 0 deletions scripts/config/inference/antibody.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,3 +21,10 @@ antibody:
terminate_bad_targeting: null
hotspot_termination_threshold: 10
hotspot_termination_failures_permitted: 20

hydra:
run:
dir: ${oc.env:HOME}/.rfantibody/outputs/${now:%Y-%m-%d}/${now:%H-%M-%S}
sweep:
dir: ${oc.env:HOME}/.rfantibody/multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
subdir: ${hydra.job.num}
7 changes: 7 additions & 0 deletions scripts/config/inference/base.yaml
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Expand Up @@ -168,3 +168,10 @@ scaffoldguided:
target_ss: null
target_adj: null
mask_loops: True

hydra:
run:
dir: ${oc.env:HOME}/.rfantibody/outputs/${now:%Y-%m-%d}/${now:%H-%M-%S}
sweep:
dir: ${oc.env:HOME}/.rfantibody/multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
subdir: ${hydra.job.num}
6 changes: 6 additions & 0 deletions src/rfantibody/rf2/config/base.yaml
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Expand Up @@ -54,3 +54,9 @@ model_param:
div: 4
n_heads: 4

hydra:
run:
dir: ${oc.env:HOME}/.rfantibody/outputs/${now:%Y-%m-%d}/${now:%H-%M-%S}
sweep:
dir: ${oc.env:HOME}/.rfantibody/multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
subdir: ${hydra.job.num}
11 changes: 7 additions & 4 deletions src/rfantibody/rfdiffusion/diffusion.py
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@@ -1,6 +1,7 @@
# script for diffusion protocols
import logging
import os
from pathlib import Path
import pickle
import time
from typing import List
Expand Down Expand Up @@ -49,8 +50,10 @@ def get_chi_betaT(max_timestep=100, beta_0=0.01, abar_T=1e-3, method='cosine'):
Function to precalculate beta_T for chi angles (decoded at different time steps, so T in beta_T varies).
Calculated empirically
"""
cache_dir=os.path.join(Path.home(), '.rfantibody', 'cached_schedules')
name = f'T{max_timestep}_beta_0{beta_0}_abar_T{abar_T}_method_{method}.pkl'
name=os.path.join(cache_dir, name)

name = f'./cached_schedules/T{max_timestep}_beta_0{beta_0}_abar_T{abar_T}_method_{method}.pkl'

if not os.path.exists(name):
print('Calculating chi_beta_T dictionary...')
Expand All @@ -72,8 +75,8 @@ def get_chi_betaT(max_timestep=100, beta_0=0.01, abar_T=1e-3, method='cosine'):
beta_Ts[timestep] = idx.item()

# save cached schedule
if not os.path.isdir('./cached_schedules/'):
os.makedirs('./cached_schedules/', exist_ok=True)
if not os.path.isdir(cache_dir):
os.makedirs(cache_dir, exist_ok=True)
with open(name, 'wb') as fp:
pickle.dump(beta_Ts, fp)

Expand Down Expand Up @@ -880,7 +883,7 @@ def __init__(self,
schedule_kwargs={},
chi_kwargs={},
var_scale=1.0,
cache_dir='.',
cache_dir=os.path.join(Path.home(), '.rfantibody', 'cached_schedules'),
partial_T=None,
truncation_level=2000
):
Expand Down