feat(synthetic-sf): add script to generate synthetic structure factors#234

Merged

DorisMai merged 14 commits into

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dm/add-sfc-synthetic

Jun 12, 2026

Commits on Jun 12, 2026

feat: generate synthetic sf for one row with occupancy changeable using gemmi structure.

DorisMai
authored and
Doris Mai
committed
feat: generate synthetic sf using atomarray. refactored assign_occupancies function

DorisMai
authored and
Doris Mai
committed
feat: support batch mode generation of synthetic sf

DorisMai
authored and
Doris Mai
committed
refactor(density): remove duplicate assign_occupancies and import from utils instead

DorisMai
authored and
Doris Mai
committed
test(sfc): add atomarray_to_gemmi tests using 6b8x

DorisMai
authored and
Doris Mai
committed
refactor: extract shared structure loading in generate synthetic reward into synthetic_utils

DorisMai
authored and
Doris Mai
committed
refactor(sfc): improve naming, documentation, and validation in synthetic sf script

DorisMai
authored and
Doris Mai
committed
test(sfc): add more tests on atomarray_to_gemmi and occupancy reassignment, document GPU memory issue in both synthetic scripts

DorisMai
authored and
Doris Mai
committed
build(deps): add protenix-dev-sfc env and relax setuptools pin and add tests docstring

DorisMai
authored and
Doris Mai
committed
build(deps): promote sfcalculator-torch to core dependency, add joblib to analysis dependency

DorisMai
authored and
Doris Mai
committed
refactor(sfc): tighten AtomArray typing in synthetic helpers

authored and
Doris Mai
committed
chore(types): fix easy ty warnings shared across boltz/protenix/rf3 envs

DorisMai
authored and
Doris Mai
committed
chore(doc): add docstring in tests

DorisMai
authored and
Doris Mai
committed
fix(msa): normalize protenix MSA paths to Path in get_msa

Doris Mai
authored and
Doris Mai
committed

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feat(synthetic-sf): add script to generate synthetic structure factors#234

feat(synthetic-sf): add script to generate synthetic structure factors#234
DorisMai merged 14 commits into
mainfrom
dm/add-sfc-synthetic

Commits on Jun 12, 2026

feat: generate synthetic sf for one row with occupancy changeable using gemmi structure.

feat: generate synthetic sf using atomarray. refactored assign_occupancies function

feat: support batch mode generation of synthetic sf

refactor(density): remove duplicate assign_occupancies and import from utils instead

test(sfc): add atomarray_to_gemmi tests using 6b8x

refactor: extract shared structure loading in generate synthetic reward into synthetic_utils

refactor(sfc): improve naming, documentation, and validation in synthetic sf script

test(sfc): add more tests on atomarray_to_gemmi and occupancy reassignment, document GPU memory issue in both synthetic scripts

build(deps): add protenix-dev-sfc env and relax setuptools pin and add tests docstring

build(deps): promote sfcalculator-torch to core dependency, add joblib to analysis dependency

refactor(sfc): tighten AtomArray typing in synthetic helpers

chore(types): fix easy ty warnings shared across boltz/protenix/rf3 envs

chore(doc): add docstring in tests

fix(msa): normalize protenix MSA paths to Path in get_msa