From ecb59faae591c0f6b87839de552c173fb0be47db Mon Sep 17 00:00:00 2001 From: Doris Mai Date: Tue, 12 May 2026 23:26:56 +0000 Subject: [PATCH 01/14] feat: generate synthetic sf for one row with occupancy changeable using gemmi structure. --- pyproject.toml | 14 +- src/sampleworks/eval/generate_synthetic_sf.py | 389 ++++++++++++++++++ 2 files changed, 398 insertions(+), 5 deletions(-) create mode 100644 src/sampleworks/eval/generate_synthetic_sf.py diff --git a/pyproject.toml b/pyproject.toml index 16f17f7..6207d29 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,6 +18,7 @@ analysis = [ boltz = ["boltz", "cuequivariance-torch", "cuequivariance-ops-torch-cu12", "rdkit>=2025.3.6"] dev = ["pytest", "pytest-cov", "mypy", "prek", "ty", "ruff", "pytest-loguru", "python-semantic-release"] protenix = ["protenix>=0.6.3", "einx", "triton"] +sfc = ["sfcalculator-torch>=0.3", "setuptools<81"] [project] authors = [{email = "karson.chrispens@ucsf.edu", name = "Karson Chrispens"}] @@ -69,13 +70,16 @@ pyarrow = "==17.0.0" [tool.pixi.environments] analysis = {features = ["analysis"]} analysis-dev = {features = ["analysis", "dev"]} +analysis-dev-sfc = {features = ["analysis", "dev", "sfc"]} boltz = {features = ["boltz"]} boltz-analysis = {features = ["boltz", "analysis"]} boltz-dev = {features = ["boltz", "dev"]} +boltz-dev-sfc = {features = ["boltz", "dev", "sfc"]} protenix = {features = ["protenix"]} protenix-dev = {features = ["protenix", "dev"]} rf3 = {features = ["rf3"]} rf3-dev = {features = ["rf3", "dev"]} +rf3-dev-sfc = {features = ["rf3", "dev", "sfc"]} [tool.pixi.feature.protenix.pypi-options.dependency-overrides] rdkit = ">=2024.3.5,<2025.9" @@ -188,11 +192,6 @@ include = ["src/sampleworks/eval/bond_angle_and_length_outlier_eval_script.py"] possibly-missing-attribute = "ignore" [tool.ty.rules] -# Pre-existing type issues across the codebase; warn instead of error -# so ty runs in CI without blocking PRs while the team fixes them. -unresolved-import = "ignore" -unknown-argument = "warn" -unresolved-attribute = "warn" invalid-argument-type = "warn" invalid-assignment = "warn" invalid-method-override = "warn" @@ -201,6 +200,11 @@ no-matching-overload = "warn" not-iterable = "warn" not-subscriptable = "warn" too-many-positional-arguments = "warn" +unknown-argument = "warn" +unresolved-attribute = "warn" +# Pre-existing type issues across the codebase; warn instead of error +# so ty runs in CI without blocking PRs while the team fixes them. +unresolved-import = "ignore" unsupported-operator = "warn" unused-ignore-comment = "warn" unused-type-ignore-comment = "warn" diff --git a/src/sampleworks/eval/generate_synthetic_sf.py b/src/sampleworks/eval/generate_synthetic_sf.py new file mode 100644 index 0000000..fc07956 --- /dev/null +++ b/src/sampleworks/eval/generate_synthetic_sf.py @@ -0,0 +1,389 @@ +"""Generate synthetic structure factor amplitudes via SFcalculator-torch. + +Produces an MTZ file of |F_protein| (no bulk solvent, no scaling) for each input +PDB/mmCIF structure. v1 scope: protein-only structure factors, with optional +per-row override of unit cell + space group and optional R-free flag column. +""" + +import traceback +from dataclasses import dataclass, field +from pathlib import Path +from typing import Any, ClassVar + +import gemmi +import numpy as np +import reciprocalspaceship as rs +import torch +from loguru import logger +from sampleworks.utils.atom_array_utils import AltlocInfo, BLANK_ALTLOC_IDS +from SFC_Torch import SFcalculator +from SFC_Torch.io import PDBParser + + +@dataclass +class BatchRow: + """A row from the batch processing CSV file. + + Attributes + ---------- + filename + Path to the structure file (relative to base_dir) + mtzfile + Optional custom output filename for the MTZ + unit_cell + Optional unit cell to override the one in the structure file + space_group + Optional Hermann-Mauguin space group string to override the one in the + structure file (e.g., 'P 21 21 21') + occ_values + Custom list of occupancy values for altlocs, must be in range [0.0, 1.0] + """ + + VALID_EXTENSIONS: ClassVar[frozenset[str]] = frozenset({".pdb", ".cif", ".mmcif", ".ent"}) + + filename: str + mtzfile: str | None = None + unit_cell: gemmi.UnitCell | None = None + space_group: gemmi.SpaceGroup | None = None + occ_values: list[float] = field(default_factory=list) + + def __post_init__(self) -> None: + ext = Path(self.filename).suffix.lower() + if ext not in self.VALID_EXTENSIONS: + raise ValueError( + f"Invalid file extension '{ext}' for '{self.filename}'. " + f"Expected one of: {', '.join(sorted(self.VALID_EXTENSIONS))}" + ) + for i, v in enumerate(self.occ_values): + if not 0.0 <= v <= 1.0: + raise ValueError(f"Occupancy value {v} at index {i} is out of range [0.0, 1.0]") + + @classmethod + def from_dict(cls, row: dict[str, str]) -> "BatchRow": + """Create a BatchRow from a CSV row dictionary. + + CSV columns: filename (required), mtzfile, unit_cell (six floats + separated by ':' — a:b:c:alpha:beta:gamma), space_group. + """ + if "filename" not in row: + raise KeyError("CSV is missing required 'filename' column") + + unit_cell: gemmi.UnitCell | None = None + if row.get("unit_cell"): + parts = [float(v.strip()) for v in row["unit_cell"].split(":")] + if len(parts) != 6: + raise ValueError( + f"unit_cell must be 6 colon-separated values (a:b:c:alpha:beta:gamma), " + f"got {len(parts)}: {row['unit_cell']!r}" + ) + unit_cell = gemmi.UnitCell(*parts) + + space_group: gemmi.SpaceGroup | None = None + if row.get("space_group"): + space_group = row["space_group"] + if space_group.isdigit(): + space_group = int(space_group) + space_group = gemmi.SpaceGroup(space_group) + + occ_values: list[float] = [] + if row.get("occ_values"): + occ_values = [float(v.strip()) for v in row["occ_values"].split(":")] + + return cls( + filename=row["filename"], + mtzfile=row.get("mtzfile") or None, + unit_cell=unit_cell, + space_group=space_group, + occ_values=occ_values, + ) + + +def load_structure_with_cell_and_space_group( + structure_path: Path, + unit_cell: gemmi.UnitCell | None = None, + space_group: gemmi.SpaceGroup | None = None, + strip_hydrogens: bool = False, + strip_waters: bool = False, + strip_ligands_and_waters: bool = False, +) -> gemmi.Structure: + """Load a structure file and optionally override its unit cell / space group.""" + structure = gemmi.read_structure(str(structure_path)) + if unit_cell is not None: + structure.cell = unit_cell + if space_group is not None: + structure.spacegroup_hm = ( + space_group.hm if isinstance(space_group, gemmi.SpaceGroup) else space_group + ) + if strip_hydrogens: + structure.remove_hydrogens() + if strip_waters: + structure.remove_waters() + if strip_ligands_and_waters: + structure.remove_ligands_and_waters() + return structure + + +def write_amplitudes_to_mtz( + sfc: SFcalculator, + output_path: Path, + test_fraction: float = 0.05, + seed: int | None = None, + hkl_attr: str = "Hasu_array", + f_attr: str = "Ftotal_asu", + ccp4_convention: bool = False, + sigf_scale: float = 0.2, +) -> None: + """Build an rs.DataSet from SFcalculator outputs and write it as MTZ. + + Parameters + ---------- + sfc: SFcalculator + SFcalculator instance + output_path: Path + Path to the output MTZ file + test_fraction: float + Fraction of reflections to mark as R-free test set (0 disables) + seed: int | None + Optional seed for reproducible R-free flag assignment + hkl_attr: str + Attribute name in SFcalculator for hkl indices + f_attr: str + Attribute name in SFcalculator for structure factors + ccp4_convention: bool + If True, use CCP4 convention for R-free flag assignment. Default + is False, which uses Phenix convention (1 = test, 0 = working). + sigf_scale: float + Scale factor to make a fake SIGFP column from FP values so that + SFcalculator can load the output MTZ file without errors. Default + is 0.2. The actual SIGFP values only matter when computing R-factor. + """ + output_path.parent.mkdir(parents=True, exist_ok=True) + dataset = sfc.prepare_dataset(hkl_attr, f_attr) + dataset.rename(columns={"FMODEL": "FP"}, inplace=True) + dataset["SIGFP"] = dataset["FP"] * sigf_scale + dataset["SIGFP"] = dataset["SIGFP"].astype(rs.StandardDeviationDtype()) + if test_fraction > 0: + dataset = rs.utils.add_rfree( + dataset, + ccp4_convention=ccp4_convention, + fraction=test_fraction, + seed=seed, + ) + dataset.write_mtz(str(output_path)) + logger.info(f"Saved structure factors to {output_path}") + + +def detect_altlocs_from_sfcpdbparser(sfc_pdbparser: PDBParser) -> AltlocInfo: + """Detect alternate conformations from SFC's PDBParser instance. + + Mirror sampleworks.utils.atom_array_utils.detect_altlocs(). Excludes + blank values defined in BLANK_ALTLOC_IDS. + + Parameters + ---------- + sfc_pdbparser + SFcalculator instance whose internal PDBParser holds per-atom altloc labels + + Returns + ------- + AltlocInfo + Sorted list of detected altloc IDs and per-altloc boolean atom masks + """ + altloc_arr: np.ndarray[Any, np.dtype[np.str_]] = np.array(sfc_pdbparser.atom_altloc) + altloc_ids = sorted(v for v in set(altloc_arr) if v not in BLANK_ALTLOC_IDS) + atom_masks: dict[str, np.ndarray[Any, np.dtype[np.bool_]]] = { + altloc: altloc_arr == altloc for altloc in altloc_ids + } + return AltlocInfo(altloc_ids=altloc_ids, atom_masks=atom_masks) + + +def assign_occupancies( + sfc_pdbparser: PDBParser, + altloc_info: AltlocInfo, + mode: str, + occ_values: list[float] | None = None, +) -> None: + """Assign occupancy values to atoms based on their altloc membership. + + Mirror assign_occupancies in generate_synthetic_density.py. + + Parameters + ---------- + sfc_pdbparser + PDBParser (SFC's parser) instance whose atom_altloc array will be modified. + altloc_info + AltlocInfo object from detect_altlocs_from_sfcpdbparser() + mode + Assignment mode: 'default' (no change), 'uniform' (1/n_altlocs each), + or 'custom' (user-specified values) + occ_values + For 'custom' mode: list of occupancy values [0.0-1.0] assigned to altlocs + in sorted order (e.g., [0.3, 0.7] assigns 0.3 to altloc 'A', 0.7 to 'B'). + If fewer values than altlocs, remaining altlocs get occupancy 0. + + Raises + ------ + ValueError + If 'custom' mode is requested but no altlocs exist, or if occ_values + is None in custom mode, or if any occupancy value is outside [0.0, 1.0] + """ + if mode == "default": + return + + if not altloc_info.altloc_ids: + if mode == "custom": + raise ValueError( + "Custom occupancy mode was requested, but the structure has no altlocs." + ) + logger.warning("No altlocs detected, using default occupancies") + return + + if mode == "uniform": + uniform_occ = 1.0 / len(altloc_info.altloc_ids) + for altloc in altloc_info.altloc_ids: + mask = altloc_info.atom_masks[altloc] + sfc_pdbparser.atom_occ[mask] = uniform_occ + + elif mode == "custom": + if occ_values is None: + raise ValueError("occ_values required for custom mode") + for i, v in enumerate(occ_values): + if not 0.0 <= v <= 1.0: + raise ValueError(f"Occupancy value {v} at index {i} is out of range [0.0, 1.0]") + + if len(occ_values) > len(altloc_info.altloc_ids): + raise ValueError( + f"Too many occupancy values: got {len(occ_values)}, " + f"but structure has {len(altloc_info.altloc_ids)} altloc(s) " + f"({', '.join(altloc_info.altloc_ids)})." + ) + if len(occ_values) < len(altloc_info.altloc_ids): + logger.warning( + f"Expected {len(altloc_info.altloc_ids)} occupancy values, got {len(occ_values)}. " + "The missing values are automatically set to 0." + ) + occ_values = occ_values + [0.0] * (len(altloc_info.altloc_ids) - len(occ_values)) + + for altloc, occ in zip(sorted(altloc_info.altloc_ids), occ_values): + mask = altloc_info.atom_masks[altloc] + sfc_pdbparser.atom_occ[mask] = occ + else: + raise ValueError(f"Invalid occupancy mode '{mode}'") + + +def _process_single_row( + row: BatchRow, + base_dir: Path, + output_dir: Path, + dmin: float, + mode: str, + anomalous: bool, + occ_mode: str, + test_fraction: float, + seed: int | None, + device: torch.device, + strip_hydrogens: bool = False, + strip_waters: bool = False, + strip_ligands_and_waters: bool = False, + simulate_solvent_and_scale: bool = False, +) -> None: + """Compute synthetic protein structure factors for a single structure. + + Parameters + ---------- + row + BatchRow describing the input structure and optional per-row overrides + base_dir + Base directory for resolving relative structure file paths + output_dir + Directory where output MTZ files will be written + dmin + High-resolution limit in Angstroms + mode + SFcalculator mode: "xray" or "cryoem" + anomalous + If True, include anomalous scattering (keeps Friedel pairs separate) + test_fraction + Fraction of reflections to mark as R-free test set (0 disables) + seed + Optional seed for reproducible R-free flag assignment + device + PyTorch device for SFcalculator + strip_hydrogens + If True, remove hydrogen atoms before computing structure factors. Default is False. + strip_waters + If True, remove water molecules before computing structure factors. Default is False. + occ_mode + Occupancy assignment mode: 'default' (keep file values), 'uniform' (1/n_altlocs each), + or 'custom' (use per-row occ_values from BatchRow). + strip_ligands_and_waters + If True, remove ligand molecules and water molecules before computing structure factors. + Default is False. Note that this parameter is different from strip_ligands in + generate_synthetic_density.py because gemmi does not support removing only non-water + heteroatoms. + """ + structure_path = base_dir / row.filename + if not structure_path.exists(): + logger.error(f"Structure not found: {structure_path}") + return + + try: + # load structure with unit cell / space group + structure = load_structure_with_cell_and_space_group( + structure_path, + row.unit_cell, + row.space_group, + strip_hydrogens, + strip_waters, + strip_ligands_and_waters, + ) + sfc_pdbparser = PDBParser(structure) + # detect altlocs and re-assign occupancies + altloc_info = detect_altlocs_from_sfcpdbparser(sfc_pdbparser) + if row.occ_values: + if occ_mode != "custom": + logger.warning( + f"Custom occupancy values provided for {row.filename}, " + f"but occ_mode is '{occ_mode}'. Using 'custom' mode." + ) + assign_occupancies(sfc_pdbparser, altloc_info, "custom", row.occ_values) + else: + assign_occupancies(sfc_pdbparser, altloc_info, occ_mode) + # compute structure factors + sfc = SFcalculator( + pdbmodel=sfc_pdbparser, + mtzdata=None, + dmin=dmin, + mode=mode, + anomalous=anomalous, + set_experiment=False, + device=device, + ) + sfc.calc_fprotein() + if simulate_solvent_and_scale: + sfc.inspect_data() + sfc.calc_fsolvent() + sfc.init_scales(requires_grad=False) + sfc.calc_ftotal() + F_attribute = "Ftotal_asu" + else: + F_attribute = "Fprotein_asu" + logger.info(f"Computed {F_attribute} for {row.filename} on {device}") + except Exception as e: + logger.error( + f"Failed to compute for {row.filename} ({type(e).__name__}): {e}\n" + f"{''.join(traceback.format_tb(e.__traceback__))}" + ) + return + # output MTZ file + output_path = output_dir / (row.mtzfile or f"{structure_path.stem}_{dmin:.2f}A.mtz") + try: + write_amplitudes_to_mtz( + sfc, output_path, f_attr=F_attribute, test_fraction=test_fraction, seed=seed + ) + except Exception as e: + logger.error( + f"Failed to write MTZ for {row.filename} to {output_path} " + f"({type(e).__name__}): {e}\n" + f"{''.join(traceback.format_tb(e.__traceback__))}" + ) From 8373ad7ed8fe7b0b176a5de8322a0c37b634aa17 Mon Sep 17 00:00:00 2001 From: Doris Mai Date: Wed, 13 May 2026 21:41:43 +0000 Subject: [PATCH 02/14] feat: generate synthetic sf using atomarray. refactored assign_occupancies function --- src/sampleworks/eval/generate_synthetic_sf.py | 283 ++++++++---------- src/sampleworks/utils/atom_array_utils.py | 73 +++++ 2 files changed, 199 insertions(+), 157 deletions(-) diff --git a/src/sampleworks/eval/generate_synthetic_sf.py b/src/sampleworks/eval/generate_synthetic_sf.py index fc07956..dcb58a3 100644 --- a/src/sampleworks/eval/generate_synthetic_sf.py +++ b/src/sampleworks/eval/generate_synthetic_sf.py @@ -8,16 +8,26 @@ import traceback from dataclasses import dataclass, field from pathlib import Path -from typing import Any, ClassVar +from typing import ClassVar import gemmi import numpy as np import reciprocalspaceship as rs import torch +from atomworks.io.transforms.atom_array import remove_waters +from biotite.structure import AtomArray from loguru import logger -from sampleworks.utils.atom_array_utils import AltlocInfo, BLANK_ALTLOC_IDS +from sampleworks.utils.atom_array_utils import ( + assign_occupancies, + BLANK_ALTLOC_IDS, + detect_altlocs, + keep_amino_acids, + keep_polymer, + load_structure_with_altlocs, + remove_hydrogens, +) from SFC_Torch import SFcalculator -from SFC_Torch.io import PDBParser +from SFC_Torch.io import array2hier, PDBParser @dataclass @@ -33,8 +43,8 @@ class BatchRow: unit_cell Optional unit cell to override the one in the structure file space_group - Optional Hermann-Mauguin space group string to override the one in the - structure file (e.g., 'P 21 21 21') + Optional space group (in Hermann-Mauguin string format) to override the + one in the structure file. occ_values Custom list of occupancy values for altlocs, must be in range [0.0, 1.0] """ @@ -44,7 +54,7 @@ class BatchRow: filename: str mtzfile: str | None = None unit_cell: gemmi.UnitCell | None = None - space_group: gemmi.SpaceGroup | None = None + space_group: str | None = None occ_values: list[float] = field(default_factory=list) def __post_init__(self) -> None: @@ -63,7 +73,8 @@ def from_dict(cls, row: dict[str, str]) -> "BatchRow": """Create a BatchRow from a CSV row dictionary. CSV columns: filename (required), mtzfile, unit_cell (six floats - separated by ':' — a:b:c:alpha:beta:gamma), space_group. + separated by ':' — a:b:c:alpha:beta:gamma), space_group (space group number or + Hermann-Mauguin string), occ_values (colon-separated, e.g. '0.3:0.7'). """ if "filename" not in row: raise KeyError("CSV is missing required 'filename' column") @@ -78,12 +89,11 @@ def from_dict(cls, row: dict[str, str]) -> "BatchRow": ) unit_cell = gemmi.UnitCell(*parts) - space_group: gemmi.SpaceGroup | None = None + space_group: str | None = None if row.get("space_group"): space_group = row["space_group"] if space_group.isdigit(): - space_group = int(space_group) - space_group = gemmi.SpaceGroup(space_group) + space_group = gemmi.SpaceGroup(int(space_group)).hm occ_values: list[float] = [] if row.get("occ_values"): @@ -98,28 +108,53 @@ def from_dict(cls, row: dict[str, str]) -> "BatchRow": ) -def load_structure_with_cell_and_space_group( - structure_path: Path, +def atomarray_to_gemmi( + atom_array: AtomArray, unit_cell: gemmi.UnitCell | None = None, - space_group: gemmi.SpaceGroup | None = None, - strip_hydrogens: bool = False, - strip_waters: bool = False, - strip_ligands_and_waters: bool = False, + space_group: str | None = None, ) -> gemmi.Structure: - """Load a structure file and optionally override its unit cell / space group.""" - structure = gemmi.read_structure(str(structure_path)) + """Convert a biotite AtomArray to a gemmi.Structure for SFcalculator. + + Anisotropic B-factors are set to zero since biotite does not store them. + Blank altloc labels are converted from biotite's '' to gemmi's '\\x00'. + + Parameters + ---------- + atom_array + Input structure with occupancy and b_factor annotations + unit_cell + Crystallographic unit cell for the structure. If None, gemmi defaults + to (1.0, 1.0, 1.0, 90.0, 90.0, 90.0). + space_group + Space group (in Hermann-Mauguin string format) for the structure. If + empty or invalid, SFcalculator defaults to P1. + + Returns + ------- + gemmi.Structure + Structure ready to be wrapped by SFC_Torch.io.PDBParser + """ + n = len(atom_array) + cra_names = [ + f"{atom_array.chain_id[i]}-0-{atom_array.res_name[i]}-{atom_array.atom_name[i]}" + for i in range(n) + ] + # gemmi uses '\x00' for blank altloc; biotite uses '' + atom_altloc = ["\x00" if a in BLANK_ALTLOC_IDS else a for a in atom_array.altloc_id] + structure = array2hier( + atom_pos=atom_array.coord, + atom_b_aniso=np.zeros((n, 3, 3), dtype=np.float64), + atom_b_iso=atom_array.b_factor, + atom_occ=atom_array.occupancy, + atom_name=atom_array.element, + cra_name=cra_names, + atom_altloc=atom_altloc, + res_id=atom_array.res_id, + ) if unit_cell is not None: structure.cell = unit_cell if space_group is not None: - structure.spacegroup_hm = ( - space_group.hm if isinstance(space_group, gemmi.SpaceGroup) else space_group - ) - if strip_hydrogens: - structure.remove_hydrogens() - if strip_waters: - structure.remove_waters() - if strip_ligands_and_waters: - structure.remove_ligands_and_waters() + structure.spacegroup_hm = space_group return structure @@ -173,104 +208,6 @@ def write_amplitudes_to_mtz( logger.info(f"Saved structure factors to {output_path}") -def detect_altlocs_from_sfcpdbparser(sfc_pdbparser: PDBParser) -> AltlocInfo: - """Detect alternate conformations from SFC's PDBParser instance. - - Mirror sampleworks.utils.atom_array_utils.detect_altlocs(). Excludes - blank values defined in BLANK_ALTLOC_IDS. - - Parameters - ---------- - sfc_pdbparser - SFcalculator instance whose internal PDBParser holds per-atom altloc labels - - Returns - ------- - AltlocInfo - Sorted list of detected altloc IDs and per-altloc boolean atom masks - """ - altloc_arr: np.ndarray[Any, np.dtype[np.str_]] = np.array(sfc_pdbparser.atom_altloc) - altloc_ids = sorted(v for v in set(altloc_arr) if v not in BLANK_ALTLOC_IDS) - atom_masks: dict[str, np.ndarray[Any, np.dtype[np.bool_]]] = { - altloc: altloc_arr == altloc for altloc in altloc_ids - } - return AltlocInfo(altloc_ids=altloc_ids, atom_masks=atom_masks) - - -def assign_occupancies( - sfc_pdbparser: PDBParser, - altloc_info: AltlocInfo, - mode: str, - occ_values: list[float] | None = None, -) -> None: - """Assign occupancy values to atoms based on their altloc membership. - - Mirror assign_occupancies in generate_synthetic_density.py. - - Parameters - ---------- - sfc_pdbparser - PDBParser (SFC's parser) instance whose atom_altloc array will be modified. - altloc_info - AltlocInfo object from detect_altlocs_from_sfcpdbparser() - mode - Assignment mode: 'default' (no change), 'uniform' (1/n_altlocs each), - or 'custom' (user-specified values) - occ_values - For 'custom' mode: list of occupancy values [0.0-1.0] assigned to altlocs - in sorted order (e.g., [0.3, 0.7] assigns 0.3 to altloc 'A', 0.7 to 'B'). - If fewer values than altlocs, remaining altlocs get occupancy 0. - - Raises - ------ - ValueError - If 'custom' mode is requested but no altlocs exist, or if occ_values - is None in custom mode, or if any occupancy value is outside [0.0, 1.0] - """ - if mode == "default": - return - - if not altloc_info.altloc_ids: - if mode == "custom": - raise ValueError( - "Custom occupancy mode was requested, but the structure has no altlocs." - ) - logger.warning("No altlocs detected, using default occupancies") - return - - if mode == "uniform": - uniform_occ = 1.0 / len(altloc_info.altloc_ids) - for altloc in altloc_info.altloc_ids: - mask = altloc_info.atom_masks[altloc] - sfc_pdbparser.atom_occ[mask] = uniform_occ - - elif mode == "custom": - if occ_values is None: - raise ValueError("occ_values required for custom mode") - for i, v in enumerate(occ_values): - if not 0.0 <= v <= 1.0: - raise ValueError(f"Occupancy value {v} at index {i} is out of range [0.0, 1.0]") - - if len(occ_values) > len(altloc_info.altloc_ids): - raise ValueError( - f"Too many occupancy values: got {len(occ_values)}, " - f"but structure has {len(altloc_info.altloc_ids)} altloc(s) " - f"({', '.join(altloc_info.altloc_ids)})." - ) - if len(occ_values) < len(altloc_info.altloc_ids): - logger.warning( - f"Expected {len(altloc_info.altloc_ids)} occupancy values, got {len(occ_values)}. " - "The missing values are automatically set to 0." - ) - occ_values = occ_values + [0.0] * (len(altloc_info.altloc_ids) - len(occ_values)) - - for altloc, occ in zip(sorted(altloc_info.altloc_ids), occ_values): - mask = altloc_info.atom_masks[altloc] - sfc_pdbparser.atom_occ[mask] = occ - else: - raise ValueError(f"Invalid occupancy mode '{mode}'") - - def _process_single_row( row: BatchRow, base_dir: Path, @@ -284,7 +221,7 @@ def _process_single_row( device: torch.device, strip_hydrogens: bool = False, strip_waters: bool = False, - strip_ligands_and_waters: bool = False, + strip_ligands: bool = False, simulate_solvent_and_scale: bool = False, ) -> None: """Compute synthetic protein structure factors for a single structure. @@ -303,6 +240,9 @@ def _process_single_row( SFcalculator mode: "xray" or "cryoem" anomalous If True, include anomalous scattering (keeps Friedel pairs separate) + occ_mode + Occupancy assignment mode: 'default' (keep file values), 'uniform' + (1/n_altlocs each), or 'custom' (use per-row occ_values from BatchRow) test_fraction Fraction of reflections to mark as R-free test set (0 disables) seed @@ -313,45 +253,73 @@ def _process_single_row( If True, remove hydrogen atoms before computing structure factors. Default is False. strip_waters If True, remove water molecules before computing structure factors. Default is False. - occ_mode - Occupancy assignment mode: 'default' (keep file values), 'uniform' (1/n_altlocs each), - or 'custom' (use per-row occ_values from BatchRow). - strip_ligands_and_waters - If True, remove ligand molecules and water molecules before computing structure factors. - Default is False. Note that this parameter is different from strip_ligands in - generate_synthetic_density.py because gemmi does not support removing only non-water - heteroatoms. + strip_ligands + If True, keep only polymer amino-acid atoms (removes ligands and waters). + Equivalent to strip_ligands in generate_synthetic_density.py. """ structure_path = base_dir / row.filename if not structure_path.exists(): logger.error(f"Structure not found: {structure_path}") return + # Load structure and strip off unwanted atoms + try: + atom_array = load_structure_with_altlocs(structure_path) + except Exception as e: + logger.error( + f"Failed to load {row.filename} ({type(e).__name__}): {e}\n" + f"{''.join(traceback.format_tb(e.__traceback__))}" + ) + return + atom_array = remove_hydrogens(atom_array) if strip_hydrogens else atom_array + atom_array = remove_waters(atom_array) if strip_waters else atom_array + atom_array = keep_polymer(keep_amino_acids(atom_array)) if strip_ligands else atom_array + + # Altloc detection and occupancy assignment (reused from density script) + altloc_info = detect_altlocs(atom_array) # ty: ignore[invalid-argument-type] + if row.occ_values: + if occ_mode != "custom": + logger.warning( + f"Custom occupancy values provided for {row.filename}, " + f"but occ_mode is '{occ_mode}'. Using 'custom' mode." + ) + try: + atom_array = assign_occupancies(atom_array, altloc_info, "custom", row.occ_values) + except ValueError as e: + logger.error(f"Occupancy assignment error for {row.filename}: {e}") + raise + elif occ_mode in {"uniform", "default"}: + try: + atom_array = assign_occupancies(atom_array, altloc_info, occ_mode) + except ValueError as e: + logger.error(f"Occupancy assignment error for {row.filename}: {e}") + raise + else: + logger.error(f"Invalid occupancy mode '{occ_mode}' for {row.filename}") + raise ValueError(f"Invalid occupancy mode '{occ_mode}'") + + # Convert to gemmi and initialize SFcalculator try: - # load structure with unit cell / space group - structure = load_structure_with_cell_and_space_group( - structure_path, - row.unit_cell, - row.space_group, - strip_hydrogens, - strip_waters, - strip_ligands_and_waters, + unit_cell = row.unit_cell + space_group = row.space_group + if unit_cell is None or space_group is None: + gemmi_meta = gemmi.read_structure(str(structure_path)) + if unit_cell is None: + unit_cell = gemmi_meta.cell + if space_group is None: + space_group = gemmi_meta.spacegroup_hm + gemmi_structure = atomarray_to_gemmi(atom_array, unit_cell, space_group) + except Exception as e: + logger.error( + f"Failed to convert {row.filename} to gemmi ({type(e).__name__}): {e}\n" + f"{''.join(traceback.format_tb(e.__traceback__))}" ) - sfc_pdbparser = PDBParser(structure) - # detect altlocs and re-assign occupancies - altloc_info = detect_altlocs_from_sfcpdbparser(sfc_pdbparser) - if row.occ_values: - if occ_mode != "custom": - logger.warning( - f"Custom occupancy values provided for {row.filename}, " - f"but occ_mode is '{occ_mode}'. Using 'custom' mode." - ) - assign_occupancies(sfc_pdbparser, altloc_info, "custom", row.occ_values) - else: - assign_occupancies(sfc_pdbparser, altloc_info, occ_mode) - # compute structure factors + return + + # Compute structure factors + try: sfc = SFcalculator( - pdbmodel=sfc_pdbparser, + pdbmodel=PDBParser(gemmi_structure), mtzdata=None, dmin=dmin, mode=mode, @@ -375,7 +343,8 @@ def _process_single_row( f"{''.join(traceback.format_tb(e.__traceback__))}" ) return - # output MTZ file + + # Output MTZ file output_path = output_dir / (row.mtzfile or f"{structure_path.stem}_{dmin:.2f}A.mtz") try: write_amplitudes_to_mtz( diff --git a/src/sampleworks/utils/atom_array_utils.py b/src/sampleworks/utils/atom_array_utils.py index 9ea5444..e4b7c6a 100644 --- a/src/sampleworks/utils/atom_array_utils.py +++ b/src/sampleworks/utils/atom_array_utils.py @@ -243,6 +243,79 @@ def detect_altlocs(atom_array: AtomArray) -> AltlocInfo: return AltlocInfo(altloc_ids=altloc_ids, atom_masks=atom_masks) +def assign_occupancies( + atom_array: AtomArray | AtomArrayStack, + altloc_info: AltlocInfo, + mode: str, + occ_values: list[float] | None = None, +) -> AtomArray | AtomArrayStack: + """Assign occupancy values to atoms based on their altloc membership. + + Parameters + ---------- + atom_array + Structure to modify + altloc_info + Detected altloc information from detect_altlocs() + mode + Assignment mode: 'default' (no change), 'uniform' (1/n_altlocs each), + or 'custom' (user-specified values) + occ_values + For 'custom' mode: list of occupancy values [0.0-1.0] assigned to altlocs + in sorted order (e.g., [0.3, 0.7] assigns 0.3 to altloc 'A', 0.7 to 'B'). + If fewer values than altlocs, remaining altlocs get occupancy 0. + + Returns + ------- + AtomArray | AtomArrayStack + Modified structure with updated occupancies + + Raises + ------ + ValueError + If 'custom' mode is requested but no altlocs exist, or if occ_values + is None in custom mode, or if any occupancy value is outside [0.0, 1.0] + """ + if mode == "default": + return atom_array + + if not altloc_info.altloc_ids: + if mode == "custom": + raise ValueError( + "Custom occupancy mode was requested, but the structure has no altlocs." + ) + logger.warning("No altlocs detected, using default occupancies") + return atom_array + + result = atom_array.copy() + occupancy = result.occupancy + + if mode == "uniform": + n_altlocs = len(altloc_info.altloc_ids) + uniform_occ = 1.0 / n_altlocs + for altloc in altloc_info.altloc_ids: + occupancy[altloc_info.atom_masks[altloc]] = uniform_occ + + elif mode == "custom": + if occ_values is None: + raise ValueError("occ_values required for custom mode") + for i, v in enumerate(occ_values): + if not 0.0 <= v <= 1.0: + raise ValueError(f"Occupancy value {v} at index {i} is out of range [0.0, 1.0]") + + if len(occ_values) != len(altloc_info.altloc_ids): + logger.warning( + f"Expected {len(altloc_info.altloc_ids)} occupancy values, got {len(occ_values)}. " + "The missing values are automatically set to 0." + ) + occ_values = occ_values + [0.0] * (len(altloc_info.altloc_ids) - len(occ_values)) + + for altloc, occ in zip(sorted(altloc_info.altloc_ids), occ_values): + occupancy[altloc_info.atom_masks[altloc]] = occ + + return cast(AtomArray, result) + + def map_altlocs_to_stack( atom_array: AtomArray | AtomArrayStack, selection: str | None = None, From d878125c4249778f74243d676c343172e34b73ba Mon Sep 17 00:00:00 2001 From: Doris Mai Date: Thu, 14 May 2026 18:27:29 +0000 Subject: [PATCH 03/14] feat: support batch mode generation of synthetic sf --- src/sampleworks/eval/generate_synthetic_sf.py | 289 +++++++++++++++++- 1 file changed, 280 insertions(+), 9 deletions(-) diff --git a/src/sampleworks/eval/generate_synthetic_sf.py b/src/sampleworks/eval/generate_synthetic_sf.py index dcb58a3..966c2eb 100644 --- a/src/sampleworks/eval/generate_synthetic_sf.py +++ b/src/sampleworks/eval/generate_synthetic_sf.py @@ -5,10 +5,13 @@ per-row override of unit cell + space group and optional R-free flag column. """ +import argparse +import csv +import sys import traceback from dataclasses import dataclass, field from pathlib import Path -from typing import ClassVar +from typing import Any, ClassVar import gemmi import numpy as np @@ -16,6 +19,7 @@ import torch from atomworks.io.transforms.atom_array import remove_waters from biotite.structure import AtomArray +from joblib import delayed, Parallel from loguru import logger from sampleworks.utils.atom_array_utils import ( assign_occupancies, @@ -26,6 +30,7 @@ load_structure_with_altlocs, remove_hydrogens, ) +from sampleworks.utils.torch_utils import try_gpu from SFC_Torch import SFcalculator from SFC_Torch.io import array2hier, PDBParser @@ -51,7 +56,7 @@ class BatchRow: VALID_EXTENSIONS: ClassVar[frozenset[str]] = frozenset({".pdb", ".cif", ".mmcif", ".ent"}) - filename: str + filename: Path | str mtzfile: str | None = None unit_cell: gemmi.UnitCell | None = None space_group: str | None = None @@ -69,7 +74,7 @@ def __post_init__(self) -> None: raise ValueError(f"Occupancy value {v} at index {i} is out of range [0.0, 1.0]") @classmethod - def from_dict(cls, row: dict[str, str]) -> "BatchRow": + def from_dict(cls, row: dict[str, Any]) -> "BatchRow": """Create a BatchRow from a CSV row dictionary. CSV columns: filename (required), mtzfile, unit_cell (six floats @@ -214,7 +219,6 @@ def _process_single_row( output_dir: Path, dmin: float, mode: str, - anomalous: bool, occ_mode: str, test_fraction: float, seed: int | None, @@ -225,6 +229,7 @@ def _process_single_row( simulate_solvent_and_scale: bool = False, ) -> None: """Compute synthetic protein structure factors for a single structure. + Assume no anomalous scattering. Parameters ---------- @@ -238,8 +243,6 @@ def _process_single_row( High-resolution limit in Angstroms mode SFcalculator mode: "xray" or "cryoem" - anomalous - If True, include anomalous scattering (keeps Friedel pairs separate) occ_mode Occupancy assignment mode: 'default' (keep file values), 'uniform' (1/n_altlocs each), or 'custom' (use per-row occ_values from BatchRow) @@ -254,8 +257,11 @@ def _process_single_row( strip_waters If True, remove water molecules before computing structure factors. Default is False. strip_ligands - If True, keep only polymer amino-acid atoms (removes ligands and waters). - Equivalent to strip_ligands in generate_synthetic_density.py. + If True, remove ligand molecules (non-water heteroatoms) before computing structure + factors. Default is False. + simulate_solvent_and_scale + If True, compute bulk solvent and scale factors for Ftotal instead of Fprotein. + Default is False. """ structure_path = base_dir / row.filename if not structure_path.exists(): @@ -323,10 +329,15 @@ def _process_single_row( mtzdata=None, dmin=dmin, mode=mode, - anomalous=anomalous, + anomalous=False, set_experiment=False, device=device, ) + logger.info( + f"SFC info for {row.filename}: cell: {sfc.unit_cell}, " + f"space group: {sfc.space_group.hm}, " + f"n_atoms: {len(sfc.atom_pos_orth)}" + ) sfc.calc_fprotein() if simulate_solvent_and_scale: sfc.inspect_data() @@ -356,3 +367,263 @@ def _process_single_row( f"({type(e).__name__}): {e}\n" f"{''.join(traceback.format_tb(e.__traceback__))}" ) + + +def load_batch_csv(csv_path: Path) -> list[BatchRow]: + """Load and parse a CSV file for batch processing. + + Parameters + ---------- + csv_path + Path to CSV file with columns: filename (required), mtzfile, unit_cell, + space_group, occ_values (all optional) + + Returns + ------- + list[BatchRow] + List of validated batch processing rows + + Raises + ------ + KeyError + If the CSV is missing the required 'filename' column + """ + rows = [] + with open(csv_path) as f: + reader = csv.DictReader(f) + if reader.fieldnames is None or "filename" not in reader.fieldnames: + raise KeyError(f"CSV file '{csv_path}' is missing required 'filename' column") + for row in reader: + rows.append(BatchRow.from_dict(row)) + return rows + + +def process_batch( + csv_path: Path, + base_dir: Path, + output_dir: Path, + dmin: float, + mode: str, + occ_mode: str, + test_fraction: float, + seed: int | None, + device: torch.device, + n_jobs: int = -1, + strip_hydrogens: bool = False, + strip_waters: bool = False, + strip_ligands: bool = False, + simulate_solvent_and_scale: bool = False, +) -> None: + """Process multiple structures from a CSV file in batch mode. + + Parameters + ---------- + csv_path + Path to CSV file listing structures to process + base_dir + Base directory for resolving relative structure file paths + output_dir + Directory where output MTZ files will be written + dmin + High-resolution limit in Angstroms + mode + Scattering factor type: 'xray' or 'cryoem' + occ_mode + Occupancy assignment mode: 'default', 'uniform', or 'custom' + test_fraction + Fraction of reflections to mark as R-free test set (0 disables) + seed + Optional seed for reproducible R-free flag assignment + device + PyTorch device for computation + n_jobs + Number of parallel jobs. -1 means use all available CPUs. + strip_hydrogens + If True, remove hydrogen atoms before computing structure factors. + strip_waters + If True, remove water molecules before computing structure factors. + strip_ligands + If True, keep only polymer amino-acid atoms (removes ligands and waters). + simulate_solvent_and_scale + If True, compute bulk solvent and scale factors in addition to F_protein. + """ + rows = load_batch_csv(csv_path) + logger.info(f"Processing {len(rows)} structures from {csv_path} using {n_jobs} jobs") + + Parallel(n_jobs=n_jobs, backend="loky")( + delayed(_process_single_row)( + row=row, + base_dir=base_dir, + output_dir=output_dir, + dmin=dmin, + mode=mode, + occ_mode=occ_mode, + test_fraction=test_fraction, + seed=seed, + device=device, + strip_hydrogens=strip_hydrogens, + strip_waters=strip_waters, + strip_ligands=strip_ligands, + simulate_solvent_and_scale=simulate_solvent_and_scale, + ) + for row in rows + ) + + +def parse_args() -> argparse.Namespace: + parser = argparse.ArgumentParser( + description="Generate synthetic structure factor amplitudes from atomic structures" + ) + + input_group = parser.add_argument_group("Input Options") + input_group.add_argument( + "--structure", "-s", type=Path, help="Path to input structure file (mmCIF or PDB)" + ) + input_group.add_argument("--batch-csv", type=Path, help="Path to CSV file for batch processing") + input_group.add_argument( + "--base-dir", + type=Path, + default=Path("."), + help="Base directory for relative paths in CSV, not used in single-structure mode", + ) + + occ_group = parser.add_argument_group("Occupancy Options") + occ_group.add_argument( + "--occ-mode", + choices=["default", "uniform", "custom"], + default="default", + help="Occupancy assignment mode", + ) + occ_group.add_argument( + "--occ-values", + type=str, + help="Colon-separated occupancy values for custom mode (e.g., '0.3:0.7')", + ) + + sf_group = parser.add_argument_group("Structure Factor Options") + sf_group.add_argument( + "--dmin", "-r", type=float, default=1.0, help="High-resolution limit in Angstroms" + ) + sf_group.add_argument( + "--mode", + choices=["xray", "cryoem"], + default="xray", + help="Scattering factor type", + ) + sf_group.add_argument( + "--simulate-solvent-and-scale", + action="store_true", + help="Compute bulk solvent and overall scale factors (outputs Ftotal instead of Fprotein)", + ) + sf_group.add_argument( + "--remove-hydrogens", + action="store_true", + help="Remove hydrogen atoms before computing structure factors", + ) + sf_group.add_argument( + "--remove-waters", + action="store_true", + help="Remove water molecules before computing structure factors", + ) + sf_group.add_argument( + "--remove-ligands", + action="store_true", + help="Remove ligand molecules (non-water heteroatoms) before computing structure factors", + ) + + rfree_group = parser.add_argument_group("R-free Options") + rfree_group.add_argument( + "--test-fraction", + type=float, + default=0.05, + help="Fraction of reflections flagged as R-free test set (0 disables)", + ) + rfree_group.add_argument( + "--seed", + type=int, + default=None, + help="Random seed for reproducible R-free flag assignment", + ) + + crystal_group = parser.add_argument_group("Crystal Options (single-structure mode only)") + crystal_group.add_argument( + "--unit-cell", + type=str, + help="Unit cell as 'a:b:c:alpha:beta:gamma' (overrides CRYST1 record)", + ) + crystal_group.add_argument( + "--space-group", + type=str, + help="Space group as Hermann-Mauguin string or number (overrides CRYST1 record)", + ) + + output_group = parser.add_argument_group("Output Options") + output_group.add_argument("--output", "-o", type=Path, help="Output MTZ file path") + output_group.add_argument( + "--output-dir", type=Path, default=Path("."), help="Output directory for batch mode" + ) + + parallel_group = parser.add_argument_group("Parallelization Options") + parallel_group.add_argument( + "--n-jobs", + type=int, + default=-1, + help="Number of parallel jobs for batch processing (-1 uses all CPUs)", + ) + + return parser.parse_args() + + +def main() -> None: + args = parse_args() + device = try_gpu() + + if args.batch_csv: + process_batch( + csv_path=args.batch_csv, + base_dir=args.base_dir, + output_dir=args.output_dir, + dmin=args.dmin, + mode=args.mode, + occ_mode=args.occ_mode, + test_fraction=args.test_fraction, + seed=args.seed, + device=device, + n_jobs=args.n_jobs, + strip_hydrogens=args.remove_hydrogens, + strip_waters=args.remove_waters, + strip_ligands=args.remove_ligands, + simulate_solvent_and_scale=args.simulate_solvent_and_scale, + ) + elif args.structure: + row = BatchRow.from_dict( + { + "filename": args.structure.name, + "mtzfile": args.output.name if args.output else None, + "unit_cell": args.unit_cell, + "space_group": args.space_group, + "occ_values": args.occ_values, + } + ) + _process_single_row( + row=row, + base_dir=args.structure.parent, + output_dir=args.output.parent if args.output else Path("."), + dmin=args.dmin, + mode=args.mode, + occ_mode=args.occ_mode, + test_fraction=args.test_fraction, + seed=args.seed, + device=device, + strip_hydrogens=args.remove_hydrogens, + strip_waters=args.remove_waters, + strip_ligands=args.remove_ligands, + simulate_solvent_and_scale=args.simulate_solvent_and_scale, + ) + else: + logger.error("Please specify --structure or --batch-csv") + sys.exit(1) + + +if __name__ == "__main__": + main() From 08b1eed06ed8916a41e4670f9489ecdb1096f4a3 Mon Sep 17 00:00:00 2001 From: Doris Mai Date: Thu, 14 May 2026 19:07:38 +0000 Subject: [PATCH 04/14] refactor(density): remove duplicate assign_occupancies and import from utils instead --- .../eval/generate_synthetic_density.py | 78 +------------------ 1 file changed, 2 insertions(+), 76 deletions(-) diff --git a/src/sampleworks/eval/generate_synthetic_density.py b/src/sampleworks/eval/generate_synthetic_density.py index 693db47..cd5ec1c 100644 --- a/src/sampleworks/eval/generate_synthetic_density.py +++ b/src/sampleworks/eval/generate_synthetic_density.py @@ -4,17 +4,16 @@ import traceback from dataclasses import dataclass, field from pathlib import Path -from typing import cast, ClassVar +from typing import ClassVar import torch from atomworks.io.transforms.atom_array import remove_waters -from biotite.structure import AtomArray, AtomArrayStack from joblib import delayed, Parallel from loguru import logger from sampleworks.core.forward_models.xray.real_space_density import XMap_torch from sampleworks.eval.structure_utils import apply_selection from sampleworks.utils.atom_array_utils import ( - AltlocInfo, + assign_occupancies, detect_altlocs, keep_amino_acids, keep_polymer, @@ -97,79 +96,6 @@ def from_dict(cls, row: dict[str, str]) -> "BatchRow": ) -def assign_occupancies( - atom_array: AtomArray | AtomArrayStack, - altloc_info: AltlocInfo, - mode: str, - occ_values: list[float] | None = None, -) -> AtomArray | AtomArrayStack: - """Assign occupancy values to atoms based on their altloc membership. - - Parameters - ---------- - atom_array - Structure to modify - altloc_info - Detected altloc information from detect_altlocs() - mode - Assignment mode: 'default' (no change), 'uniform' (1/n_altlocs each), - or 'custom' (user-specified values) - occ_values - For 'custom' mode: list of occupancy values [0.0-1.0] assigned to altlocs - in sorted order (e.g., [0.3, 0.7] assigns 0.3 to altloc 'A', 0.7 to 'B'). - If fewer values than altlocs, remaining altlocs get occupancy 0. - - Returns - ------- - AtomArray | AtomArrayStack - Modified structure with updated occupancies - - Raises - ------ - ValueError - If 'custom' mode is requested but no altlocs exist, or if occ_values - is None in custom mode, or if any occupancy value is outside [0.0, 1.0] - """ - if mode == "default": - return atom_array - - if not altloc_info.altloc_ids: - if mode == "custom": - raise ValueError( - "Custom occupancy mode was requested, but the structure has no altlocs." - ) - logger.warning("No altlocs detected, using default occupancies") - return atom_array - - result = atom_array.copy() - occupancy = result.occupancy - - if mode == "uniform": - n_altlocs = len(altloc_info.altloc_ids) - uniform_occ = 1.0 / n_altlocs - for altloc in altloc_info.altloc_ids: - occupancy[altloc_info.atom_masks[altloc]] = uniform_occ - - elif mode == "custom": - if occ_values is None: - raise ValueError("occ_values required for custom mode") - for i, v in enumerate(occ_values): - if not 0.0 <= v <= 1.0: - raise ValueError(f"Occupancy value {v} at index {i} is out of range [0.0, 1.0]") - - if len(occ_values) != len(altloc_info.altloc_ids): - logger.warning( - f"Expected {len(altloc_info.altloc_ids)} occupancy values, got {len(occ_values)}. " - "The missing values are automatically set to 0." - ) - occ_values = occ_values + [0.0] * (len(altloc_info.altloc_ids) - len(occ_values)) - - for altloc, occ in zip(sorted(altloc_info.altloc_ids), occ_values): - occupancy[altloc_info.atom_masks[altloc]] = occ - - return cast(AtomArray, result) - - def save_density(density: torch.Tensor, xmap_torch: XMap_torch, output_path: Path) -> None: """Save a density map to disk in CCP4 format. From c9f9907a2739180308601e08d30d7c8f3319e924 Mon Sep 17 00:00:00 2001 From: Doris Mai Date: Thu, 14 May 2026 22:03:41 +0000 Subject: [PATCH 05/14] test(sfc): add atomarray_to_gemmi tests using 6b8x --- src/sampleworks/eval/generate_synthetic_sf.py | 3 +- tests/eval/test_generate_synthetic_sf.py | 122 ++++++++++++++++++ 2 files changed, 124 insertions(+), 1 deletion(-) create mode 100644 tests/eval/test_generate_synthetic_sf.py diff --git a/src/sampleworks/eval/generate_synthetic_sf.py b/src/sampleworks/eval/generate_synthetic_sf.py index 966c2eb..78c0618 100644 --- a/src/sampleworks/eval/generate_synthetic_sf.py +++ b/src/sampleworks/eval/generate_synthetic_sf.py @@ -19,7 +19,6 @@ import torch from atomworks.io.transforms.atom_array import remove_waters from biotite.structure import AtomArray -from joblib import delayed, Parallel from loguru import logger from sampleworks.utils.atom_array_utils import ( assign_occupancies, @@ -447,6 +446,8 @@ def process_batch( simulate_solvent_and_scale If True, compute bulk solvent and scale factors in addition to F_protein. """ + from joblib import delayed, Parallel + rows = load_batch_csv(csv_path) logger.info(f"Processing {len(rows)} structures from {csv_path} using {n_jobs} jobs") diff --git a/tests/eval/test_generate_synthetic_sf.py b/tests/eval/test_generate_synthetic_sf.py new file mode 100644 index 0000000..b1cb387 --- /dev/null +++ b/tests/eval/test_generate_synthetic_sf.py @@ -0,0 +1,122 @@ +"""Tests for atomarray_to_gemmi in generate_synthetic_sf, using real 6b8x structure.""" + +from pathlib import Path + +import numpy as np +import pytest +import torch + + +pytest.importorskip("SFC_Torch", reason="SFC_Torch not available; run in analysis-dev-sfc env") + +import gemmi +from atomworks.io.transforms.atom_array import remove_waters +from sampleworks.eval.generate_synthetic_sf import atomarray_to_gemmi +from sampleworks.utils.atom_array_utils import ( + assign_occupancies, + detect_altlocs, + keep_amino_acids, + keep_polymer, + load_structure_with_altlocs, + remove_hydrogens, +) +from SFC_Torch import SFcalculator +from SFC_Torch.io import PDBParser +from SFC_Torch.utils import assert_numpy + + +DMIN = 2.0 + + +@pytest.fixture(scope="module") +def stripped_gemmi(resources_dir: Path) -> gemmi.Structure: + s = gemmi.read_structure(str(resources_dir / "6b8x" / "6b8x_final.pdb")) + s.remove_hydrogens() + s.remove_ligands_and_waters() + return s + + +@pytest.fixture(scope="module") +def stripped_atom_array(resources_dir: Path): + arr = load_structure_with_altlocs(resources_dir / "6b8x" / "6b8x_final.pdb") + arr = remove_hydrogens(arr) + arr = remove_waters(arr) + return keep_polymer(keep_amino_acids(arr)) + + +@pytest.fixture(scope="module") +def gemmi_structure_from_atomarray( + stripped_atom_array, stripped_gemmi: gemmi.Structure +) -> gemmi.Structure: + return atomarray_to_gemmi( + stripped_atom_array, stripped_gemmi.cell, stripped_gemmi.spacegroup_hm + ) + + +def _compute_fprotein(gemmi_structure: gemmi.Structure, device: torch.device) -> np.ndarray: + sfc = SFcalculator( + PDBParser(gemmi_structure), + mtzdata=None, + dmin=DMIN, + mode="xray", + anomalous=False, + set_experiment=False, + device=device, + ) + sfc.calc_fprotein() + return assert_numpy(sfc.Fprotein_asu) + + +class TestAtomArrayToGemmi: + def test_cell_matches_pdb(self, gemmi_structure_from_atomarray, stripped_gemmi): + result = gemmi_structure_from_atomarray.cell + expected = stripped_gemmi.cell + assert result.a == pytest.approx(expected.a) + assert result.b == pytest.approx(expected.b) + assert result.c == pytest.approx(expected.c) + assert result.alpha == pytest.approx(expected.alpha) + assert result.beta == pytest.approx(expected.beta) + assert result.gamma == pytest.approx(expected.gamma) + + def test_space_group_matches_pdb(self, gemmi_structure_from_atomarray, stripped_gemmi): + assert gemmi_structure_from_atomarray.spacegroup_hm == stripped_gemmi.spacegroup_hm + + def test_atom_count_matches_pdb(self, gemmi_structure_from_atomarray, stripped_gemmi): + assert ( + gemmi_structure_from_atomarray[0].count_atom_sites() + == stripped_gemmi[0].count_atom_sites() + ) + + def test_occupancy_change_is_applied(self, stripped_atom_array, stripped_gemmi): + occ_values = [0.2, 0.8, 0.0] + altloc_info = detect_altlocs(stripped_atom_array) + arr = assign_occupancies(stripped_atom_array, altloc_info, "custom", occ_values) + parser = PDBParser( + atomarray_to_gemmi(arr, stripped_gemmi.cell, stripped_gemmi.spacegroup_hm) + ) + for altloc, expected in zip(altloc_info.altloc_ids, occ_values): + assert np.allclose(parser.atom_occ[altloc_info.atom_masks[altloc]], expected) + + def test_fprotein_matches_direct_gemmi( + self, gemmi_structure_from_atomarray, stripped_gemmi, device + ): + f_atomarray = _compute_fprotein(gemmi_structure_from_atomarray, device) + f_direct = _compute_fprotein(stripped_gemmi, device) + np.testing.assert_allclose(np.abs(f_atomarray), np.abs(f_direct), atol=1e-3) + + def test_fprotein_changes_with_occupancy(self, stripped_atom_array, stripped_gemmi, device): + altloc_info = detect_altlocs(stripped_atom_array) + + arr_default = assign_occupancies(stripped_atom_array, altloc_info, "default") + f_default = _compute_fprotein( + atomarray_to_gemmi(arr_default, stripped_gemmi.cell, stripped_gemmi.spacegroup_hm), + device, + ) + + arr_custom = assign_occupancies(stripped_atom_array, altloc_info, "custom", [0.2, 0.8, 0.0]) + f_custom = _compute_fprotein( + atomarray_to_gemmi(arr_custom, stripped_gemmi.cell, stripped_gemmi.spacegroup_hm), + device, + ) + + assert not np.allclose(np.abs(f_default), np.abs(f_custom), atol=1e-3) From b0280bebbd2a5e8b17a61b159ec5da4ae00255ba Mon Sep 17 00:00:00 2001 From: Doris Mai Date: Fri, 15 May 2026 23:04:45 +0000 Subject: [PATCH 06/14] refactor: extract shared structure loading in generate synthetic reward into synthetic_utils --- .../eval/generate_synthetic_density.py | 69 ++----- src/sampleworks/eval/generate_synthetic_sf.py | 108 ++++++----- src/sampleworks/eval/synthetic_utils.py | 181 ++++++++++++++++++ src/sampleworks/utils/atom_array_utils.py | 73 ------- tests/eval/test_generate_synthetic_sf.py | 2 +- 5 files changed, 250 insertions(+), 183 deletions(-) create mode 100644 src/sampleworks/eval/synthetic_utils.py diff --git a/src/sampleworks/eval/generate_synthetic_density.py b/src/sampleworks/eval/generate_synthetic_density.py index cd5ec1c..1bd1b83 100644 --- a/src/sampleworks/eval/generate_synthetic_density.py +++ b/src/sampleworks/eval/generate_synthetic_density.py @@ -7,20 +7,11 @@ from typing import ClassVar import torch -from atomworks.io.transforms.atom_array import remove_waters from joblib import delayed, Parallel from loguru import logger from sampleworks.core.forward_models.xray.real_space_density import XMap_torch -from sampleworks.eval.structure_utils import apply_selection -from sampleworks.utils.atom_array_utils import ( - assign_occupancies, - detect_altlocs, - keep_amino_acids, - keep_polymer, - load_structure_with_altlocs, - remove_hydrogens, - save_structure_to_cif, -) +from sampleworks.eval.synthetic_utils import load_structure_for_synthetic_reward +from sampleworks.utils.atom_array_utils import save_structure_to_cif from sampleworks.utils.density_utils import compute_density_from_atomarray from sampleworks.utils.torch_utils import try_gpu @@ -187,54 +178,18 @@ def _process_single_row( If True, save the processed structure to a CIF file in the input directory. Default is True. """ structure_path = base_dir / row.filename - if not structure_path.exists(): - logger.error(f"Structure not found: {structure_path}") - return - - try: - atom_array = load_structure_with_altlocs(structure_path) - except Exception as e: - logger.error( - f"Failed to load {row.filename} ({type(e).__name__}): {e}\n" - f"{''.join(traceback.format_tb(e.__traceback__))}" - ) - return - - try: - atom_array = apply_selection(atom_array, row.selection) - except ValueError as e: - logger.error(f"Selection error for {row.filename}: {e}") + atom_array = load_structure_for_synthetic_reward( + structure_path, + occ_mode=occ_mode, + occ_values=row.occ_values, + strip_hydrogens=strip_hydrogens, + strip_waters=strip_waters, + strip_ligands=strip_ligands, + selection=row.selection, + ) + if atom_array is None: return - atom_array = remove_hydrogens(atom_array) if strip_hydrogens else atom_array - atom_array = remove_waters(atom_array) if strip_waters else atom_array - # This is currently a sort of hacky way to remove ligands by keeping only polymer atoms - # TODO: there's probably a more robust way to do this - atom_array = keep_polymer(keep_amino_acids(atom_array)) if strip_ligands else atom_array - - altloc_info = detect_altlocs(atom_array) # ty: ignore[invalid-argument-type] - if row.occ_values: - if occ_mode != "custom": - logger.warning( - f"Custom occupancy values provided for {row.filename}, " - f"but occ_mode is '{occ_mode}'. Using 'custom' mode." - ) - occ_mode = "custom" - try: - atom_array = assign_occupancies(atom_array, altloc_info, "custom", row.occ_values) - except ValueError as e: - logger.error(f"Occupancy assignment error for {row.filename}: {e}") - raise - elif occ_mode in {"uniform", "default"}: - try: - atom_array = assign_occupancies(atom_array, altloc_info, occ_mode) - except ValueError as e: - logger.error(f"Occupancy assignment error for {row.filename}: {e}") - raise - else: - logger.error(f"Invalid occupancy mode '{occ_mode}' for {row.filename}") - raise ValueError(f"Invalid occupancy mode '{occ_mode}'") - try: density, xmap_torch = compute_density_from_atomarray( atom_array, resolution=resolution, em_mode=em_mode, device=device diff --git a/src/sampleworks/eval/generate_synthetic_sf.py b/src/sampleworks/eval/generate_synthetic_sf.py index 78c0618..06a4c79 100644 --- a/src/sampleworks/eval/generate_synthetic_sf.py +++ b/src/sampleworks/eval/generate_synthetic_sf.py @@ -17,18 +17,10 @@ import numpy as np import reciprocalspaceship as rs import torch -from atomworks.io.transforms.atom_array import remove_waters from biotite.structure import AtomArray from loguru import logger -from sampleworks.utils.atom_array_utils import ( - assign_occupancies, - BLANK_ALTLOC_IDS, - detect_altlocs, - keep_amino_acids, - keep_polymer, - load_structure_with_altlocs, - remove_hydrogens, -) +from sampleworks.eval.synthetic_utils import load_structure_for_synthetic_reward +from sampleworks.utils.atom_array_utils import BLANK_ALTLOC_IDS from sampleworks.utils.torch_utils import try_gpu from SFC_Torch import SFcalculator from SFC_Torch.io import array2hier, PDBParser @@ -49,6 +41,8 @@ class BatchRow: space_group Optional space group (in Hermann-Mauguin string format) to override the one in the structure file. + selection + Optional atom selection string in pyMOL-like syntax (e.g., 'chain A and resi 10-50') occ_values Custom list of occupancy values for altlocs, must be in range [0.0, 1.0] """ @@ -59,6 +53,7 @@ class BatchRow: mtzfile: str | None = None unit_cell: gemmi.UnitCell | None = None space_group: str | None = None + selection: str | None = None occ_values: list[float] = field(default_factory=list) def __post_init__(self) -> None: @@ -108,6 +103,7 @@ def from_dict(cls, row: dict[str, Any]) -> "BatchRow": mtzfile=row.get("mtzfile") or None, unit_cell=unit_cell, space_group=space_group, + selection=row.get("selection") or None, occ_values=occ_values, ) @@ -193,8 +189,9 @@ def write_amplitudes_to_mtz( is False, which uses Phenix convention (1 = test, 0 = working). sigf_scale: float Scale factor to make a fake SIGFP column from FP values so that - SFcalculator can load the output MTZ file without errors. Default - is 0.2. The actual SIGFP values only matter when computing R-factor. + SFcalculator can load the output MTZ file as synthetic reward + without errors. The actual SIGFP values only matter when + computing R-factor. """ output_path.parent.mkdir(parents=True, exist_ok=True) dataset = sfc.prepare_dataset(hkl_attr, f_attr) @@ -226,6 +223,7 @@ def _process_single_row( strip_waters: bool = False, strip_ligands: bool = False, simulate_solvent_and_scale: bool = False, + save_structure: bool = False, ) -> None: """Compute synthetic protein structure factors for a single structure. Assume no anomalous scattering. @@ -261,49 +259,24 @@ def _process_single_row( simulate_solvent_and_scale If True, compute bulk solvent and scale factors for Ftotal instead of Fprotein. Default is False. + save_structure + If True, save the processed structure (after selection and occupancy assignment) + as mmCIF to output_dir. Unit cell and space group are preserved. Default is False. """ structure_path = base_dir / row.filename - if not structure_path.exists(): - logger.error(f"Structure not found: {structure_path}") + atom_array = load_structure_for_synthetic_reward( + structure_path, + occ_mode=occ_mode, + occ_values=row.occ_values, + strip_hydrogens=strip_hydrogens, + strip_waters=strip_waters, + strip_ligands=strip_ligands, + selection=row.selection, + ) + if atom_array is None: return - # Load structure and strip off unwanted atoms - try: - atom_array = load_structure_with_altlocs(structure_path) - except Exception as e: - logger.error( - f"Failed to load {row.filename} ({type(e).__name__}): {e}\n" - f"{''.join(traceback.format_tb(e.__traceback__))}" - ) - return - atom_array = remove_hydrogens(atom_array) if strip_hydrogens else atom_array - atom_array = remove_waters(atom_array) if strip_waters else atom_array - atom_array = keep_polymer(keep_amino_acids(atom_array)) if strip_ligands else atom_array - - # Altloc detection and occupancy assignment (reused from density script) - altloc_info = detect_altlocs(atom_array) # ty: ignore[invalid-argument-type] - if row.occ_values: - if occ_mode != "custom": - logger.warning( - f"Custom occupancy values provided for {row.filename}, " - f"but occ_mode is '{occ_mode}'. Using 'custom' mode." - ) - try: - atom_array = assign_occupancies(atom_array, altloc_info, "custom", row.occ_values) - except ValueError as e: - logger.error(f"Occupancy assignment error for {row.filename}: {e}") - raise - elif occ_mode in {"uniform", "default"}: - try: - atom_array = assign_occupancies(atom_array, altloc_info, occ_mode) - except ValueError as e: - logger.error(f"Occupancy assignment error for {row.filename}: {e}") - raise - else: - logger.error(f"Invalid occupancy mode '{occ_mode}' for {row.filename}") - raise ValueError(f"Invalid occupancy mode '{occ_mode}'") - - # Convert to gemmi and initialize SFcalculator + # Convert to gemmi for SFcalculator try: unit_cell = row.unit_cell space_group = row.space_group @@ -321,6 +294,18 @@ def _process_single_row( ) return + if save_structure: + structure_output_path = output_dir / f"{structure_path.stem}_sf_input.cif" + structure_output_path.parent.mkdir(parents=True, exist_ok=True) + try: + gemmi_structure.make_mmcif_document().write_file(str(structure_output_path)) + logger.info(f"Saved processed structure to {structure_output_path}") + except Exception as e: + logger.error( + f"Failed to save structure for {row.filename} ({type(e).__name__}): {e}\n" + f"{''.join(traceback.format_tb(e.__traceback__))}" + ) + # Compute structure factors try: sfc = SFcalculator( @@ -375,7 +360,7 @@ def load_batch_csv(csv_path: Path) -> list[BatchRow]: ---------- csv_path Path to CSV file with columns: filename (required), mtzfile, unit_cell, - space_group, occ_values (all optional) + space_group, selection, occ_values (all optional) Returns ------- @@ -412,6 +397,7 @@ def process_batch( strip_waters: bool = False, strip_ligands: bool = False, simulate_solvent_and_scale: bool = False, + save_structure: bool = False, ) -> None: """Process multiple structures from a CSV file in batch mode. @@ -445,6 +431,8 @@ def process_batch( If True, keep only polymer amino-acid atoms (removes ligands and waters). simulate_solvent_and_scale If True, compute bulk solvent and scale factors in addition to F_protein. + save_structure + If True, save each processed structure as mmCIF to output_dir. """ from joblib import delayed, Parallel @@ -466,6 +454,7 @@ def process_batch( strip_waters=strip_waters, strip_ligands=strip_ligands, simulate_solvent_and_scale=simulate_solvent_and_scale, + save_structure=save_structure, ) for row in rows ) @@ -488,6 +477,13 @@ def parse_args() -> argparse.Namespace: help="Base directory for relative paths in CSV, not used in single-structure mode", ) + selection_group = parser.add_argument_group("Selection Options") + selection_group.add_argument( + "--selection", + type=str, + help="Atom selection (e.g., 'chain A and resi 10-50' or 'chain A and resi 10')", + ) + occ_group = parser.add_argument_group("Occupancy Options") occ_group.add_argument( "--occ-mode", @@ -559,6 +555,11 @@ def parse_args() -> argparse.Namespace: ) output_group = parser.add_argument_group("Output Options") + output_group.add_argument( + "--save-structure", + action="store_true", + help="Save the processed structure (after selection, occupancy assignment) to CIF", + ) output_group.add_argument("--output", "-o", type=Path, help="Output MTZ file path") output_group.add_argument( "--output-dir", type=Path, default=Path("."), help="Output directory for batch mode" @@ -595,6 +596,7 @@ def main() -> None: strip_waters=args.remove_waters, strip_ligands=args.remove_ligands, simulate_solvent_and_scale=args.simulate_solvent_and_scale, + save_structure=args.save_structure, ) elif args.structure: row = BatchRow.from_dict( @@ -603,6 +605,7 @@ def main() -> None: "mtzfile": args.output.name if args.output else None, "unit_cell": args.unit_cell, "space_group": args.space_group, + "selection": args.selection, "occ_values": args.occ_values, } ) @@ -620,6 +623,7 @@ def main() -> None: strip_waters=args.remove_waters, strip_ligands=args.remove_ligands, simulate_solvent_and_scale=args.simulate_solvent_and_scale, + save_structure=args.save_structure, ) else: logger.error("Please specify --structure or --batch-csv") diff --git a/src/sampleworks/eval/synthetic_utils.py b/src/sampleworks/eval/synthetic_utils.py new file mode 100644 index 0000000..6e12f87 --- /dev/null +++ b/src/sampleworks/eval/synthetic_utils.py @@ -0,0 +1,181 @@ +"""Shared utilities for synthetic structure factor and density generation.""" + +import traceback +from pathlib import Path +from typing import cast + +from atomworks.io.transforms.atom_array import remove_waters +from biotite.structure import AtomArray, AtomArrayStack +from loguru import logger +from sampleworks.eval.structure_utils import apply_selection +from sampleworks.utils.atom_array_utils import ( + AltlocInfo, + detect_altlocs, + keep_amino_acids, + keep_polymer, + load_structure_with_altlocs, + remove_hydrogens, +) + + +def assign_occupancies( + atom_array: AtomArray | AtomArrayStack, + altloc_info: AltlocInfo, + mode: str, + occ_values: list[float] | None = None, +) -> AtomArray | AtomArrayStack: + """Assign occupancy values to atoms based on their altloc membership. + + Parameters + ---------- + atom_array + Structure to modify + altloc_info + Detected altloc information from detect_altlocs() + mode + Assignment mode: 'default' (no change), 'uniform' (1/n_altlocs each), + or 'custom' (user-specified values) + occ_values + For 'custom' mode: list of occupancy values [0.0-1.0] assigned to altlocs + in sorted order (e.g., [0.3, 0.7] assigns 0.3 to altloc 'A', 0.7 to 'B'). + If fewer values than altlocs, remaining altlocs get occupancy 0. + + Returns + ------- + AtomArray | AtomArrayStack + Modified structure with updated occupancies + + Raises + ------ + ValueError + If 'custom' mode is requested but no altlocs exist, or if occ_values + is None in custom mode, or if any occupancy value is outside [0.0, 1.0] + """ + if mode == "default": + return atom_array + + if not altloc_info.altloc_ids: + if mode == "custom": + raise ValueError( + "Custom occupancy mode was requested, but the structure has no altlocs." + ) + logger.warning("No altlocs detected, using default occupancies") + return atom_array + + result = atom_array.copy() + occupancy = result.occupancy + + if mode == "uniform": + n_altlocs = len(altloc_info.altloc_ids) + uniform_occ = 1.0 / n_altlocs + for altloc in altloc_info.altloc_ids: + occupancy[altloc_info.atom_masks[altloc]] = uniform_occ + + elif mode == "custom": + if occ_values is None: + raise ValueError("occ_values required for custom mode") + for i, v in enumerate(occ_values): + if not 0.0 <= v <= 1.0: + raise ValueError(f"Occupancy value {v} at index {i} is out of range [0.0, 1.0]") + + if len(occ_values) != len(altloc_info.altloc_ids): + logger.warning( + f"Expected {len(altloc_info.altloc_ids)} occupancy values, got {len(occ_values)}. " + "The missing values are automatically set to 0." + ) + occ_values = occ_values + [0.0] * (len(altloc_info.altloc_ids) - len(occ_values)) + + for altloc, occ in zip(sorted(altloc_info.altloc_ids), occ_values): + occupancy[altloc_info.atom_masks[altloc]] = occ + + return cast(AtomArray, result) + + +def load_structure_for_synthetic_reward( + structure_path: Path, + occ_mode: str, + occ_values: list[float], + strip_hydrogens: bool = False, + strip_waters: bool = False, + strip_ligands: bool = False, + selection: str | None = None, +) -> AtomArray | None: + """Load and prepare a structure for synthetic reward generation. + + Handles loading, optional atom selection, stripping of unwanted atom classes, + and occupancy assignment. Returns None on load or selection errors (logged); + raises ValueError on invalid occ_mode or occupancy assignment errors (logged + before raising). + + Parameters + ---------- + structure_path + Absolute path to the structure file + occ_mode + Occupancy assignment mode: 'default' (keep file values), 'uniform' + (1/n_altlocs each), or 'custom' (use occ_values) + occ_values + Occupancy values for custom mode. If non-empty and occ_mode is not + 'custom', occ_mode is overridden with a warning. + strip_hydrogens + If True, remove hydrogen atoms + strip_waters + If True, remove water molecules + strip_ligands + If True, keep only polymer amino-acid atoms + selection + Optional atom selection string. If None, the full structure is used. + + Returns + ------- + AtomArray | None + Prepared structure, or None if loading or selection failed + """ + if not structure_path.exists(): + logger.error(f"Structure not found: {structure_path}") + return None + + try: + atom_array = load_structure_with_altlocs(structure_path) + except Exception as e: + logger.error( + f"Failed to load {structure_path} ({type(e).__name__}): {e}\n" + f"{''.join(traceback.format_tb(e.__traceback__))}" + ) + return None + + try: + atom_array = apply_selection(atom_array, selection) + except ValueError as e: + logger.error(f"Selection error for {structure_path}: {e}") + return None + + atom_array = remove_hydrogens(atom_array) if strip_hydrogens else atom_array + atom_array = remove_waters(atom_array) if strip_waters else atom_array + atom_array = keep_polymer(keep_amino_acids(atom_array)) if strip_ligands else atom_array + # This is currently a sort of hacky way to remove ligands by keeping only polymer atoms + # TODO: there's probably a more robust way to do this + altloc_info = detect_altlocs(atom_array) # ty: ignore[invalid-argument-type] + if occ_values: + if occ_mode != "custom": + logger.warning( + f"Custom occupancy values provided for {structure_path}, " + f"but occ_mode is '{occ_mode}'. Using 'custom' mode." + ) + occ_mode = "custom" + try: + atom_array = assign_occupancies(atom_array, altloc_info, "custom", occ_values) + except ValueError as e: + logger.error(f"Occupancy assignment error for {structure_path}: {e}") + raise + elif occ_mode in {"uniform", "default"}: + try: + atom_array = assign_occupancies(atom_array, altloc_info, occ_mode) + except ValueError as e: + logger.error(f"Occupancy assignment error for {structure_path}: {e}") + raise + else: + logger.error(f"Invalid occupancy mode '{occ_mode}' for {structure_path}") + raise ValueError(f"Invalid occupancy mode '{occ_mode}'") + + return cast(AtomArray, atom_array) diff --git a/src/sampleworks/utils/atom_array_utils.py b/src/sampleworks/utils/atom_array_utils.py index e4b7c6a..9ea5444 100644 --- a/src/sampleworks/utils/atom_array_utils.py +++ b/src/sampleworks/utils/atom_array_utils.py @@ -243,79 +243,6 @@ def detect_altlocs(atom_array: AtomArray) -> AltlocInfo: return AltlocInfo(altloc_ids=altloc_ids, atom_masks=atom_masks) -def assign_occupancies( - atom_array: AtomArray | AtomArrayStack, - altloc_info: AltlocInfo, - mode: str, - occ_values: list[float] | None = None, -) -> AtomArray | AtomArrayStack: - """Assign occupancy values to atoms based on their altloc membership. - - Parameters - ---------- - atom_array - Structure to modify - altloc_info - Detected altloc information from detect_altlocs() - mode - Assignment mode: 'default' (no change), 'uniform' (1/n_altlocs each), - or 'custom' (user-specified values) - occ_values - For 'custom' mode: list of occupancy values [0.0-1.0] assigned to altlocs - in sorted order (e.g., [0.3, 0.7] assigns 0.3 to altloc 'A', 0.7 to 'B'). - If fewer values than altlocs, remaining altlocs get occupancy 0. - - Returns - ------- - AtomArray | AtomArrayStack - Modified structure with updated occupancies - - Raises - ------ - ValueError - If 'custom' mode is requested but no altlocs exist, or if occ_values - is None in custom mode, or if any occupancy value is outside [0.0, 1.0] - """ - if mode == "default": - return atom_array - - if not altloc_info.altloc_ids: - if mode == "custom": - raise ValueError( - "Custom occupancy mode was requested, but the structure has no altlocs." - ) - logger.warning("No altlocs detected, using default occupancies") - return atom_array - - result = atom_array.copy() - occupancy = result.occupancy - - if mode == "uniform": - n_altlocs = len(altloc_info.altloc_ids) - uniform_occ = 1.0 / n_altlocs - for altloc in altloc_info.altloc_ids: - occupancy[altloc_info.atom_masks[altloc]] = uniform_occ - - elif mode == "custom": - if occ_values is None: - raise ValueError("occ_values required for custom mode") - for i, v in enumerate(occ_values): - if not 0.0 <= v <= 1.0: - raise ValueError(f"Occupancy value {v} at index {i} is out of range [0.0, 1.0]") - - if len(occ_values) != len(altloc_info.altloc_ids): - logger.warning( - f"Expected {len(altloc_info.altloc_ids)} occupancy values, got {len(occ_values)}. " - "The missing values are automatically set to 0." - ) - occ_values = occ_values + [0.0] * (len(altloc_info.altloc_ids) - len(occ_values)) - - for altloc, occ in zip(sorted(altloc_info.altloc_ids), occ_values): - occupancy[altloc_info.atom_masks[altloc]] = occ - - return cast(AtomArray, result) - - def map_altlocs_to_stack( atom_array: AtomArray | AtomArrayStack, selection: str | None = None, diff --git a/tests/eval/test_generate_synthetic_sf.py b/tests/eval/test_generate_synthetic_sf.py index b1cb387..c460340 100644 --- a/tests/eval/test_generate_synthetic_sf.py +++ b/tests/eval/test_generate_synthetic_sf.py @@ -12,8 +12,8 @@ import gemmi from atomworks.io.transforms.atom_array import remove_waters from sampleworks.eval.generate_synthetic_sf import atomarray_to_gemmi +from sampleworks.eval.synthetic_utils import assign_occupancies from sampleworks.utils.atom_array_utils import ( - assign_occupancies, detect_altlocs, keep_amino_acids, keep_polymer, From 365b1cced515761913fe3cda97dd3fc62171d80e Mon Sep 17 00:00:00 2001 From: Doris Mai Date: Wed, 27 May 2026 02:04:59 +0000 Subject: [PATCH 07/14] refactor(sfc): improve naming, documentation, and validation in synthetic sf script --- pixi.lock | 6551 ++++++++++------- .../eval/generate_synthetic_density.py | 4 +- src/sampleworks/eval/generate_synthetic_sf.py | 234 +- src/sampleworks/eval/synthetic_utils.py | 97 +- 4 files changed, 4223 insertions(+), 2663 deletions(-) diff --git a/pixi.lock b/pixi.lock index 42e211c..ebcb77c 100644 --- a/pixi.lock +++ b/pixi.lock @@ -35,7 +35,7 @@ environments: - 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The MTZ file has dummy values for +SIGFP and optionally R-free flag column. Each structure can be optionally +overridden with unit cell, space group, atom selection, and occupancy. """ import argparse @@ -19,7 +20,10 @@ import torch from biotite.structure import AtomArray from loguru import logger -from sampleworks.eval.synthetic_utils import load_structure_for_synthetic_reward +from sampleworks.eval.synthetic_utils import ( + load_structure_for_synthetic_reward, + validate_occupancy_values, +) from sampleworks.utils.atom_array_utils import BLANK_ALTLOC_IDS from sampleworks.utils.torch_utils import try_gpu from SFC_Torch import SFcalculator @@ -27,53 +31,67 @@ @dataclass -class BatchRow: - """A row from the batch processing CSV file. +class BatchRowForMTZ: + """A row from the batch processing CSV file. Each row represents one structure. Attributes ---------- filename - Path to the structure file (relative to base_dir) + Path to the structure file (relative to base_dir, which is meant to be the + parent directory of all structures.) mtzfile Optional custom output filename for the MTZ unit_cell Optional unit cell to override the one in the structure file space_group - Optional space group (in Hermann-Mauguin string format) to override the - one in the structure file. + Optional space group to override the one in the structure file. Accepts any + string (e.g. "P 21 21 2") or integer (space group number, e.g. 18) that gemmi + can convert to a SpaceGroup object, which is then converted to the international + notation (Hermann-Mauguin string). See gemmi documentation for more details + (https://gemmi.readthedocs.io/en/latest/symmetry.html#spacegroup). selection Optional atom selection string in pyMOL-like syntax (e.g., 'chain A and resi 10-50') - occ_values + occupancy_values Custom list of occupancy values for altlocs, must be in range [0.0, 1.0] """ - VALID_EXTENSIONS: ClassVar[frozenset[str]] = frozenset({".pdb", ".cif", ".mmcif", ".ent"}) + VALID_EXTENSIONS: ClassVar[frozenset[str]] = frozenset({".cif", ".mmcif"}) + LEGACY_EXTENSIONS: ClassVar[frozenset[str]] = frozenset({".pdb", ".ent"}) filename: Path | str mtzfile: str | None = None unit_cell: gemmi.UnitCell | None = None space_group: str | None = None selection: str | None = None - occ_values: list[float] = field(default_factory=list) + occupancy_values: list[float] = field(default_factory=list) def __post_init__(self) -> None: ext = Path(self.filename).suffix.lower() - if ext not in self.VALID_EXTENSIONS: + all_supported = self.VALID_EXTENSIONS | self.LEGACY_EXTENSIONS + if ext not in all_supported: raise ValueError( f"Invalid file extension '{ext}' for '{self.filename}'. " - f"Expected one of: {', '.join(sorted(self.VALID_EXTENSIONS))}" + f"Expected one of: {', '.join(sorted(all_supported))}" ) - for i, v in enumerate(self.occ_values): - if not 0.0 <= v <= 1.0: - raise ValueError(f"Occupancy value {v} at index {i} is out of range [0.0, 1.0]") + if ext in self.LEGACY_EXTENSIONS: + logger.warning( + f"'{ext}' is a legacy PDB format and support may be removed in a future version. " + "Prefer .cif or .mmcif (mmCIF format)." + ) + validate_occupancy_values(self.occupancy_values) @classmethod - def from_dict(cls, row: dict[str, Any]) -> "BatchRow": - """Create a BatchRow from a CSV row dictionary. - - CSV columns: filename (required), mtzfile, unit_cell (six floats - separated by ':' — a:b:c:alpha:beta:gamma), space_group (space group number or - Hermann-Mauguin string), occ_values (colon-separated, e.g. '0.3:0.7'). + def from_dict(cls, row: dict[str, Any]) -> "BatchRowForMTZ": + """Create a BatchRowForMTZ from a CSV row dictionary. + + CSV columns: + - filename (required): e.g. '1abc.cif', relative to base_dir + - mtzfile: e.g. 'output/1abc.mtz' + - unit_cell (six floats separated by ':'): e.g. '1.0:1.0:1.0:90.0:90.0:90.0' + in units of Angstroms and degrees + - space_group (number or Hermann-Mauguin string): e.g. '18' or 'P 21 21 2' + - occupancy_values (colon-separated floats summing to 1.0): e.g. '0.3:0.7' + - selection (PyMOL-like syntax): e.g. 'chain A' """ if "filename" not in row: raise KeyError("CSV is missing required 'filename' column") @@ -94,9 +112,9 @@ def from_dict(cls, row: dict[str, Any]) -> "BatchRow": if space_group.isdigit(): space_group = gemmi.SpaceGroup(int(space_group)).hm - occ_values: list[float] = [] - if row.get("occ_values"): - occ_values = [float(v.strip()) for v in row["occ_values"].split(":")] + occupancy_values: list[float] = [] + if row.get("occupancy_values"): + occupancy_values = [float(v.strip()) for v in row["occupancy_values"].split(":")] return cls( filename=row["filename"], @@ -104,7 +122,7 @@ def from_dict(cls, row: dict[str, Any]) -> "BatchRow": unit_cell=unit_cell, space_group=space_group, selection=row.get("selection") or None, - occ_values=occ_values, + occupancy_values=occupancy_values, ) @@ -124,7 +142,7 @@ def atomarray_to_gemmi( Input structure with occupancy and b_factor annotations unit_cell Crystallographic unit cell for the structure. If None, gemmi defaults - to (1.0, 1.0, 1.0, 90.0, 90.0, 90.0). + to (1.0, 1.0, 1.0, 90.0, 90.0, 90.0) in units of Angstroms and degrees. space_group Space group (in Hermann-Mauguin string format) for the structure. If empty or invalid, SFcalculator defaults to P1. @@ -139,9 +157,9 @@ def atomarray_to_gemmi( f"{atom_array.chain_id[i]}-0-{atom_array.res_name[i]}-{atom_array.atom_name[i]}" for i in range(n) ] - # gemmi uses '\x00' for blank altloc; biotite uses '' + # gemmi uses '\x00' for blank altloc atom_altloc = ["\x00" if a in BLANK_ALTLOC_IDS else a for a in atom_array.altloc_id] - structure = array2hier( + structure: gemmi.Structure = array2hier( atom_pos=atom_array.coord, atom_b_aniso=np.zeros((n, 3, 3), dtype=np.float64), atom_b_iso=atom_array.b_factor, @@ -158,46 +176,49 @@ def atomarray_to_gemmi( return structure -def write_amplitudes_to_mtz( +def process_amplitudes_to_dataset( sfc: SFcalculator, - output_path: Path, test_fraction: float = 0.05, seed: int | None = None, - hkl_attr: str = "Hasu_array", - f_attr: str = "Ftotal_asu", + miller_index_column: str = "Hasu_array", + structure_factor_column: str = "Ftotal_asu", ccp4_convention: bool = False, - sigf_scale: float = 0.2, -) -> None: - """Build an rs.DataSet from SFcalculator outputs and write it as MTZ. + sigma_f_scale: float = 0.2, + output_path: Path | None = None, +) -> rs.DataSet: + """Build an rs.DataSet from SFcalculator outputs, optionally writing it as MTZ. Parameters ---------- sfc: SFcalculator SFcalculator instance - output_path: Path - Path to the output MTZ file test_fraction: float Fraction of reflections to mark as R-free test set (0 disables) seed: int | None Optional seed for reproducible R-free flag assignment - hkl_attr: str + miller_index_column: str Attribute name in SFcalculator for hkl indices - f_attr: str + structure_factor_column: str Attribute name in SFcalculator for structure factors ccp4_convention: bool If True, use CCP4 convention for R-free flag assignment. Default is False, which uses Phenix convention (1 = test, 0 = working). - sigf_scale: float - Scale factor to make a fake SIGFP column from FP values so that - SFcalculator can load the output MTZ file as synthetic reward - without errors. The actual SIGFP values only matter when - computing R-factor. + sigma_f_scale: float + Scale factor to make a fake sigma column from the structure factor amplitude + values so that SFcalculator can load the output MTZ file as synthetic reward + without errors. The actual sigma values only matter when computing R-factor. + output_path: Path | None + If provided, write the dataset to this MTZ file path. """ - output_path.parent.mkdir(parents=True, exist_ok=True) - dataset = sfc.prepare_dataset(hkl_attr, f_attr) - dataset.rename(columns={"FMODEL": "FP"}, inplace=True) - dataset["SIGFP"] = dataset["FP"] * sigf_scale - dataset["SIGFP"] = dataset["SIGFP"].astype(rs.StandardDeviationDtype()) + dataset: rs.DataSet = sfc.prepare_dataset(miller_index_column, structure_factor_column) + # assumes the first detected column of dtype F is the structure factor amplitude column + # avoids hardcoding unexposed column name "FMODEL" from sfc.prepare_dataset(). + structure_factor_amplitude_column = dataset.select_mtzdtype( + rs.StructureFactorAmplitudeDtype() + ).columns[0] + sigma_f_column = f"SIG{structure_factor_amplitude_column}" + dataset[sigma_f_column] = dataset[structure_factor_amplitude_column] * sigma_f_scale + dataset[sigma_f_column] = dataset[sigma_f_column].astype(rs.StandardDeviationDtype()) if test_fraction > 0: dataset = rs.utils.add_rfree( dataset, @@ -205,17 +226,20 @@ def write_amplitudes_to_mtz( fraction=test_fraction, seed=seed, ) - dataset.write_mtz(str(output_path)) - logger.info(f"Saved structure factors to {output_path}") + if output_path is not None: + output_path.parent.mkdir(parents=True, exist_ok=True) + dataset.write_mtz(str(output_path)) + logger.info(f"Saved structure factors to {output_path}") + return dataset def _process_single_row( - row: BatchRow, + row: BatchRowForMTZ, base_dir: Path, output_dir: Path, - dmin: float, - mode: str, - occ_mode: str, + resolution: float, + scattering_factor_mode: str, + occupancy_mode: str, test_fraction: float, seed: int | None, device: torch.device, @@ -231,18 +255,18 @@ def _process_single_row( Parameters ---------- row - BatchRow describing the input structure and optional per-row overrides + BatchRowForMTZ describing the input structure and optional per-row overrides base_dir Base directory for resolving relative structure file paths output_dir Directory where output MTZ files will be written - dmin - High-resolution limit in Angstroms - mode + resolution + High-resolution (dmin) limit in Angstroms + scattering_factor_mode SFcalculator mode: "xray" or "cryoem" - occ_mode + occupancy_mode Occupancy assignment mode: 'default' (keep file values), 'uniform' - (1/n_altlocs each), or 'custom' (use per-row occ_values from BatchRow) + (1/n_altlocs each), or 'custom' (use per-row occupancy_values from BatchRowForMTZ) test_fraction Fraction of reflections to mark as R-free test set (0 disables) seed @@ -266,8 +290,8 @@ def _process_single_row( structure_path = base_dir / row.filename atom_array = load_structure_for_synthetic_reward( structure_path, - occ_mode=occ_mode, - occ_values=row.occ_values, + occupancy_mode=occupancy_mode, + occupancy_values=row.occupancy_values, strip_hydrogens=strip_hydrogens, strip_waters=strip_waters, strip_ligands=strip_ligands, @@ -311,13 +335,13 @@ def _process_single_row( sfc = SFcalculator( pdbmodel=PDBParser(gemmi_structure), mtzdata=None, - dmin=dmin, - mode=mode, + dmin=resolution, + mode=scattering_factor_mode, anomalous=False, set_experiment=False, device=device, ) - logger.info( + logger.debug( f"SFC info for {row.filename}: cell: {sfc.unit_cell}, " f"space group: {sfc.space_group.hm}, " f"n_atoms: {len(sfc.atom_pos_orth)}" @@ -331,7 +355,7 @@ def _process_single_row( F_attribute = "Ftotal_asu" else: F_attribute = "Fprotein_asu" - logger.info(f"Computed {F_attribute} for {row.filename} on {device}") + logger.debug(f"Computed {F_attribute} for {row.filename} on {device}") except Exception as e: logger.error( f"Failed to compute for {row.filename} ({type(e).__name__}): {e}\n" @@ -340,10 +364,14 @@ def _process_single_row( return # Output MTZ file - output_path = output_dir / (row.mtzfile or f"{structure_path.stem}_{dmin:.2f}A.mtz") + output_path = output_dir / (row.mtzfile or f"{structure_path.stem}_{resolution:.2f}A.mtz") try: - write_amplitudes_to_mtz( - sfc, output_path, f_attr=F_attribute, test_fraction=test_fraction, seed=seed + process_amplitudes_to_dataset( + sfc, + structure_factor_column=F_attribute, + test_fraction=test_fraction, + seed=seed, + output_path=output_path, ) except Exception as e: logger.error( @@ -353,18 +381,18 @@ def _process_single_row( ) -def load_batch_csv(csv_path: Path) -> list[BatchRow]: +def load_batch_csv(csv_path: Path) -> list[BatchRowForMTZ]: """Load and parse a CSV file for batch processing. Parameters ---------- csv_path Path to CSV file with columns: filename (required), mtzfile, unit_cell, - space_group, selection, occ_values (all optional) + space_group, selection, occupancy_values (all optional) Returns ------- - list[BatchRow] + list[BatchRowForMTZ] List of validated batch processing rows Raises @@ -378,7 +406,7 @@ def load_batch_csv(csv_path: Path) -> list[BatchRow]: if reader.fieldnames is None or "filename" not in reader.fieldnames: raise KeyError(f"CSV file '{csv_path}' is missing required 'filename' column") for row in reader: - rows.append(BatchRow.from_dict(row)) + rows.append(BatchRowForMTZ.from_dict(row)) return rows @@ -386,9 +414,9 @@ def process_batch( csv_path: Path, base_dir: Path, output_dir: Path, - dmin: float, - mode: str, - occ_mode: str, + resolution: float, + scattering_factor_mode: str, + occupancy_mode: str, test_fraction: float, seed: int | None, device: torch.device, @@ -409,11 +437,11 @@ def process_batch( Base directory for resolving relative structure file paths output_dir Directory where output MTZ files will be written - dmin - High-resolution limit in Angstroms - mode + resolution + High-resolution (dmin) limit in Angstroms + scattering_factor_mode Scattering factor type: 'xray' or 'cryoem' - occ_mode + occupancy_mode Occupancy assignment mode: 'default', 'uniform', or 'custom' test_fraction Fraction of reflections to mark as R-free test set (0 disables) @@ -444,9 +472,9 @@ def process_batch( row=row, base_dir=base_dir, output_dir=output_dir, - dmin=dmin, - mode=mode, - occ_mode=occ_mode, + resolution=resolution, + scattering_factor_mode=scattering_factor_mode, + occupancy_mode=occupancy_mode, test_fraction=test_fraction, seed=seed, device=device, @@ -484,25 +512,29 @@ def parse_args() -> argparse.Namespace: help="Atom selection (e.g., 'chain A and resi 10-50' or 'chain A and resi 10')", ) - occ_group = parser.add_argument_group("Occupancy Options") - occ_group.add_argument( - "--occ-mode", + occupancy_group = parser.add_argument_group("Occupancy Options") + occupancy_group.add_argument( + "--occupancy-mode", choices=["default", "uniform", "custom"], default="default", help="Occupancy assignment mode", ) - occ_group.add_argument( - "--occ-values", + occupancy_group.add_argument( + "--occupancy-values", type=str, help="Colon-separated occupancy values for custom mode (e.g., '0.3:0.7')", ) sf_group = parser.add_argument_group("Structure Factor Options") sf_group.add_argument( - "--dmin", "-r", type=float, default=1.0, help="High-resolution limit in Angstroms" + "--resolution", + "-r", + type=float, + default=1.0, + help="High-resolution (dmin) limit in Angstroms", ) sf_group.add_argument( - "--mode", + "--scattering-factor-mode", choices=["xray", "cryoem"], default="xray", help="Scattering factor type", @@ -585,9 +617,9 @@ def main() -> None: csv_path=args.batch_csv, base_dir=args.base_dir, output_dir=args.output_dir, - dmin=args.dmin, - mode=args.mode, - occ_mode=args.occ_mode, + resolution=args.resolution, + scattering_factor_mode=args.scattering_factor_mode, + occupancy_mode=args.occupancy_mode, test_fraction=args.test_fraction, seed=args.seed, device=device, @@ -599,23 +631,23 @@ def main() -> None: save_structure=args.save_structure, ) elif args.structure: - row = BatchRow.from_dict( + row = BatchRowForMTZ.from_dict( { "filename": args.structure.name, "mtzfile": args.output.name if args.output else None, "unit_cell": args.unit_cell, "space_group": args.space_group, "selection": args.selection, - "occ_values": args.occ_values, + "occupancy_values": args.occupancy_values, } ) _process_single_row( row=row, base_dir=args.structure.parent, output_dir=args.output.parent if args.output else Path("."), - dmin=args.dmin, - mode=args.mode, - occ_mode=args.occ_mode, + resolution=args.resolution, + scattering_factor_mode=args.scattering_factor_mode, + occupancy_mode=args.occupancy_mode, test_fraction=args.test_fraction, seed=args.seed, device=device, diff --git a/src/sampleworks/eval/synthetic_utils.py b/src/sampleworks/eval/synthetic_utils.py index 6e12f87..7e40fd9 100644 --- a/src/sampleworks/eval/synthetic_utils.py +++ b/src/sampleworks/eval/synthetic_utils.py @@ -1,5 +1,6 @@ """Shared utilities for synthetic structure factor and density generation.""" +import math import traceback from pathlib import Path from typing import cast @@ -18,11 +19,20 @@ ) +def validate_occupancy_values(occupancy_values: list[float]) -> None: + """Raise ValueError if any value is outside [0.0, 1.0] or values don't sum to 1.0.""" + for i, v in enumerate(occupancy_values): + if not 0.0 <= v <= 1.0: + raise ValueError(f"Occupancy value {v} at index {i} is out of range [0.0, 1.0]") + if occupancy_values and not math.isclose(sum(occupancy_values), 1.0): + raise ValueError(f"Occupancy values must sum to 1.0, got {sum(occupancy_values)}") + + def assign_occupancies( atom_array: AtomArray | AtomArrayStack, altloc_info: AltlocInfo, - mode: str, - occ_values: list[float] | None = None, + occupancy_mode: str, + occupancy_values: list[float] | None = None, ) -> AtomArray | AtomArrayStack: """Assign occupancy values to atoms based on their altloc membership. @@ -32,10 +42,10 @@ def assign_occupancies( Structure to modify altloc_info Detected altloc information from detect_altlocs() - mode + occupancy_mode Assignment mode: 'default' (no change), 'uniform' (1/n_altlocs each), or 'custom' (user-specified values) - occ_values + occupancy_values For 'custom' mode: list of occupancy values [0.0-1.0] assigned to altlocs in sorted order (e.g., [0.3, 0.7] assigns 0.3 to altloc 'A', 0.7 to 'B'). If fewer values than altlocs, remaining altlocs get occupancy 0. @@ -48,14 +58,14 @@ def assign_occupancies( Raises ------ ValueError - If 'custom' mode is requested but no altlocs exist, or if occ_values + If 'custom' mode is requested but no altlocs exist, or if occupancy_values is None in custom mode, or if any occupancy value is outside [0.0, 1.0] """ - if mode == "default": + if occupancy_mode == "default": return atom_array if not altloc_info.altloc_ids: - if mode == "custom": + if occupancy_mode == "custom": raise ValueError( "Custom occupancy mode was requested, but the structure has no altlocs." ) @@ -65,36 +75,39 @@ def assign_occupancies( result = atom_array.copy() occupancy = result.occupancy - if mode == "uniform": + if occupancy_mode == "uniform": n_altlocs = len(altloc_info.altloc_ids) uniform_occ = 1.0 / n_altlocs for altloc in altloc_info.altloc_ids: occupancy[altloc_info.atom_masks[altloc]] = uniform_occ - elif mode == "custom": - if occ_values is None: - raise ValueError("occ_values required for custom mode") - for i, v in enumerate(occ_values): - if not 0.0 <= v <= 1.0: - raise ValueError(f"Occupancy value {v} at index {i} is out of range [0.0, 1.0]") - - if len(occ_values) != len(altloc_info.altloc_ids): + elif occupancy_mode == "custom": + if occupancy_values is None: + raise ValueError("occupancy_values required for custom mode") + n_altlocs = len(altloc_info.altloc_ids) + if len(occupancy_values) > n_altlocs: logger.warning( - f"Expected {len(altloc_info.altloc_ids)} occupancy values, got {len(occ_values)}. " - "The missing values are automatically set to 0." + f"Got {len(occupancy_values)} occupancy values but structure " + f"has {n_altlocs} altlocs. Extra values will be ignored." ) - occ_values = occ_values + [0.0] * (len(altloc_info.altloc_ids) - len(occ_values)) - - for altloc, occ in zip(sorted(altloc_info.altloc_ids), occ_values): - occupancy[altloc_info.atom_masks[altloc]] = occ + occupancy_values = occupancy_values[:n_altlocs] + elif len(occupancy_values) < n_altlocs: + logger.warning( + f"Got {len(occupancy_values)} occupancy values but structure " + f"has {n_altlocs} altlocs. Missing values are automatically set to 0." + ) + occupancy_values = occupancy_values + [0.0] * (n_altlocs - len(occupancy_values)) + validate_occupancy_values(occupancy_values) + for altloc, occupancy_value in zip(sorted(altloc_info.altloc_ids), occupancy_values): + occupancy[altloc_info.atom_masks[altloc]] = occupancy_value return cast(AtomArray, result) def load_structure_for_synthetic_reward( structure_path: Path, - occ_mode: str, - occ_values: list[float], + occupancy_mode: str, + occupancy_values: list[float], strip_hydrogens: bool = False, strip_waters: bool = False, strip_ligands: bool = False, @@ -104,19 +117,19 @@ def load_structure_for_synthetic_reward( Handles loading, optional atom selection, stripping of unwanted atom classes, and occupancy assignment. Returns None on load or selection errors (logged); - raises ValueError on invalid occ_mode or occupancy assignment errors (logged + raises ValueError on invalid occupancy_mode or occupancy assignment errors (logged before raising). Parameters ---------- structure_path Absolute path to the structure file - occ_mode + occupancy_mode Occupancy assignment mode: 'default' (keep file values), 'uniform' - (1/n_altlocs each), or 'custom' (use occ_values) - occ_values - Occupancy values for custom mode. If non-empty and occ_mode is not - 'custom', occ_mode is overridden with a warning. + (1/n_altlocs each), or 'custom' (use occupancy_values) + occupancy_values + Occupancy values for custom mode. If non-empty and occupancy_mode is not + 'custom', occupancy_mode is overridden with a warning. strip_hydrogens If True, remove hydrogen atoms strip_waters @@ -150,32 +163,34 @@ def load_structure_for_synthetic_reward( logger.error(f"Selection error for {structure_path}: {e}") return None + # This is currently a sort of hacky way to remove ligands by keeping only polymer atoms + # TODO: there's probably a more robust way to do this atom_array = remove_hydrogens(atom_array) if strip_hydrogens else atom_array atom_array = remove_waters(atom_array) if strip_waters else atom_array atom_array = keep_polymer(keep_amino_acids(atom_array)) if strip_ligands else atom_array - # This is currently a sort of hacky way to remove ligands by keeping only polymer atoms - # TODO: there's probably a more robust way to do this altloc_info = detect_altlocs(atom_array) # ty: ignore[invalid-argument-type] - if occ_values: - if occ_mode != "custom": + if occupancy_values: + if occupancy_mode != "custom": logger.warning( f"Custom occupancy values provided for {structure_path}, " - f"but occ_mode is '{occ_mode}'. Using 'custom' mode." + f"but occupancy_mode is '{occupancy_mode}'. Using 'custom' mode." ) - occ_mode = "custom" + occupancy_mode = "custom" try: - atom_array = assign_occupancies(atom_array, altloc_info, "custom", occ_values) + atom_array = assign_occupancies( + atom_array, altloc_info, occupancy_mode, occupancy_values + ) except ValueError as e: logger.error(f"Occupancy assignment error for {structure_path}: {e}") raise - elif occ_mode in {"uniform", "default"}: + elif occupancy_mode in {"uniform", "default"}: try: - atom_array = assign_occupancies(atom_array, altloc_info, occ_mode) + atom_array = assign_occupancies(atom_array, altloc_info, occupancy_mode) except ValueError as e: logger.error(f"Occupancy assignment error for {structure_path}: {e}") raise else: - logger.error(f"Invalid occupancy mode '{occ_mode}' for {structure_path}") - raise ValueError(f"Invalid occupancy mode '{occ_mode}'") + logger.error(f"Invalid occupancy mode '{occupancy_mode}' for {structure_path}") + raise ValueError(f"Invalid occupancy mode '{occupancy_mode}'") return cast(AtomArray, atom_array) From 480d3833210971938cc99eb7a43e83627ec77293 Mon Sep 17 00:00:00 2001 From: Doris Mai Date: Wed, 27 May 2026 21:57:25 +0000 Subject: [PATCH 08/14] test(sfc): add more tests on atomarray_to_gemmi and occupancy reassignment, document GPU memory issue in both synthetic scripts --- .../eval/generate_synthetic_density.py | 3 ++ src/sampleworks/eval/generate_synthetic_sf.py | 9 ++++ tests/eval/test_generate_synthetic_sf.py | 42 +++++++++++++++---- 3 files changed, 46 insertions(+), 8 deletions(-) diff --git a/src/sampleworks/eval/generate_synthetic_density.py b/src/sampleworks/eval/generate_synthetic_density.py index a9cd1ea..755ee2d 100644 --- a/src/sampleworks/eval/generate_synthetic_density.py +++ b/src/sampleworks/eval/generate_synthetic_density.py @@ -276,6 +276,9 @@ def process_batch( rows = load_batch_csv(csv_path) logger.info(f"Processing {len(rows)} structures from {csv_path} using {n_jobs} jobs") + # TODO(`#242`): When device is CUDA and n_jobs > 1, each loky worker gets its own + # CUDA context, risking GPU memory contention or OOM errors. Consider explicit + # per-worker device assignment and/or n_jobs capping. Same issue in SF script. Parallel(n_jobs=n_jobs, backend="loky")( delayed(_process_single_row)( row=row, diff --git a/src/sampleworks/eval/generate_synthetic_sf.py b/src/sampleworks/eval/generate_synthetic_sf.py index 37f1964..0b28f54 100644 --- a/src/sampleworks/eval/generate_synthetic_sf.py +++ b/src/sampleworks/eval/generate_synthetic_sf.py @@ -209,6 +209,12 @@ def process_amplitudes_to_dataset( without errors. The actual sigma values only matter when computing R-factor. output_path: Path | None If provided, write the dataset to this MTZ file path. + + Returns + ------- + rs.DataSet + Dataset with structure factor amplitudes, fake sigma column, and optionally + R-free flags. """ dataset: rs.DataSet = sfc.prepare_dataset(miller_index_column, structure_factor_column) # assumes the first detected column of dtype F is the structure factor amplitude column @@ -467,6 +473,9 @@ def process_batch( rows = load_batch_csv(csv_path) logger.info(f"Processing {len(rows)} structures from {csv_path} using {n_jobs} jobs") + # TODO(`#242`): When device is CUDA and n_jobs > 1, each loky worker gets its own + # CUDA context, risking GPU memory contention or OOM errors. Consider explicit + # per-worker device assignment and/or n_jobs capping. Same issue in density script. Parallel(n_jobs=n_jobs, backend="loky")( delayed(_process_single_row)( row=row, diff --git a/tests/eval/test_generate_synthetic_sf.py b/tests/eval/test_generate_synthetic_sf.py index c460340..8caf22b 100644 --- a/tests/eval/test_generate_synthetic_sf.py +++ b/tests/eval/test_generate_synthetic_sf.py @@ -1,5 +1,6 @@ """Tests for atomarray_to_gemmi in generate_synthetic_sf, using real 6b8x structure.""" +import logging from pathlib import Path import numpy as np @@ -81,10 +82,13 @@ def test_cell_matches_pdb(self, gemmi_structure_from_atomarray, stripped_gemmi): def test_space_group_matches_pdb(self, gemmi_structure_from_atomarray, stripped_gemmi): assert gemmi_structure_from_atomarray.spacegroup_hm == stripped_gemmi.spacegroup_hm - def test_atom_count_matches_pdb(self, gemmi_structure_from_atomarray, stripped_gemmi): - assert ( - gemmi_structure_from_atomarray[0].count_atom_sites() - == stripped_gemmi[0].count_atom_sites() + def test_atoms_match_pdb(self, gemmi_structure_from_atomarray, stripped_gemmi): + # atom order is preserved: biotite keeps PDB file order, array2hier reconstructs it + parser_from_atomarray = PDBParser(gemmi_structure_from_atomarray) + parser_from_gemmi = PDBParser(stripped_gemmi) + assert np.array_equal(parser_from_atomarray.atom_name, parser_from_gemmi.atom_name) + np.testing.assert_allclose( + parser_from_atomarray.atom_pos, parser_from_gemmi.atom_pos, atol=1e-3 ) def test_occupancy_change_is_applied(self, stripped_atom_array, stripped_gemmi): @@ -104,12 +108,34 @@ def test_fprotein_matches_direct_gemmi( f_direct = _compute_fprotein(stripped_gemmi, device) np.testing.assert_allclose(np.abs(f_atomarray), np.abs(f_direct), atol=1e-3) + def test_occupancy_warns_on_extra_values(self, stripped_atom_array, caplog): + altloc_info = detect_altlocs(stripped_atom_array) + with caplog.at_level(logging.WARNING): + assign_occupancies(stripped_atom_array, altloc_info, "custom", [0.2, 0.8, 0.0, 0.0]) + assert "Extra values will be ignored" in caplog.text + + def test_occupancy_warns_on_missing_values(self, stripped_atom_array, caplog): + altloc_info = detect_altlocs(stripped_atom_array) + with caplog.at_level(logging.WARNING): + assign_occupancies(stripped_atom_array, altloc_info, "custom", [0.5, 0.5]) + assert "Missing values are automatically set to 0" in caplog.text + + def test_occupancy_raises_on_out_of_range(self, stripped_atom_array): + altloc_info = detect_altlocs(stripped_atom_array) + with pytest.raises(ValueError, match="out of range"): + assign_occupancies(stripped_atom_array, altloc_info, "custom", [1.5, 0.0, 0.0]) + + def test_occupancy_raises_on_bad_sum(self, stripped_atom_array): + altloc_info = detect_altlocs(stripped_atom_array) + with pytest.raises(ValueError, match="sum to 1.0"): + assign_occupancies(stripped_atom_array, altloc_info, "custom", [0.3, 0.3, 0.3]) + def test_fprotein_changes_with_occupancy(self, stripped_atom_array, stripped_gemmi, device): altloc_info = detect_altlocs(stripped_atom_array) - arr_default = assign_occupancies(stripped_atom_array, altloc_info, "default") - f_default = _compute_fprotein( - atomarray_to_gemmi(arr_default, stripped_gemmi.cell, stripped_gemmi.spacegroup_hm), + arr_uniform = assign_occupancies(stripped_atom_array, altloc_info, "uniform") + f_uniform = _compute_fprotein( + atomarray_to_gemmi(arr_uniform, stripped_gemmi.cell, stripped_gemmi.spacegroup_hm), device, ) @@ -119,4 +145,4 @@ def test_fprotein_changes_with_occupancy(self, stripped_atom_array, stripped_gem device, ) - assert not np.allclose(np.abs(f_default), np.abs(f_custom), atol=1e-3) + assert not np.allclose(np.abs(f_uniform), np.abs(f_custom), atol=1e-3) From 4d81fe06206ddcb7471a125eefc16c93d01d70c3 Mon Sep 17 00:00:00 2001 From: Doris Mai Date: Wed, 27 May 2026 23:34:43 +0000 Subject: [PATCH 09/14] build(deps): add protenix-dev-sfc env and relax setuptools pin and add tests docstring --- pixi.lock | 491 ++++++++++++++++++++++- pyproject.toml | 4 +- tests/eval/test_generate_synthetic_sf.py | 13 + 3 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["sfcalculator-torch>=0.3", "setuptools<81"] +sfc = ["sfcalculator-torch>=0.3.2"] [project] authors = [{email = "karson.chrispens@ucsf.edu", name = "Karson Chrispens"}] @@ -77,11 +77,13 @@ boltz-dev = {features = ["boltz", "dev"]} boltz-dev-sfc = {features = ["boltz", "dev", "sfc"]} protenix = {features = ["protenix"]} protenix-dev = {features = ["protenix", "dev"]} +protenix-dev-sfc = {features = ["protenix", "dev", "sfc"]} rf3 = {features = ["rf3"]} rf3-dev = {features = ["rf3", "dev"]} rf3-dev-sfc = {features = ["rf3", "dev", "sfc"]} [tool.pixi.feature.protenix.pypi-options.dependency-overrides] +pandas = "==2.3.1" rdkit = ">=2024.3.5,<2025.9" [tool.pixi.feature.rf3.pypi-dependencies] diff --git a/tests/eval/test_generate_synthetic_sf.py b/tests/eval/test_generate_synthetic_sf.py index 8caf22b..0b04a40 100644 --- a/tests/eval/test_generate_synthetic_sf.py +++ b/tests/eval/test_generate_synthetic_sf.py @@ -69,7 +69,10 @@ def _compute_fprotein(gemmi_structure: gemmi.Structure, device: torch.device) -> class TestAtomArrayToGemmi: + """Tests for atomarray_to_gemmi using the 6b8x structure.""" + def test_cell_matches_pdb(self, gemmi_structure_from_atomarray, stripped_gemmi): + """Unit cell parameters are preserved through the biotite→gemmi conversion.""" result = gemmi_structure_from_atomarray.cell expected = stripped_gemmi.cell assert result.a == pytest.approx(expected.a) @@ -80,9 +83,11 @@ def test_cell_matches_pdb(self, gemmi_structure_from_atomarray, stripped_gemmi): assert result.gamma == pytest.approx(expected.gamma) def test_space_group_matches_pdb(self, gemmi_structure_from_atomarray, stripped_gemmi): + """Space group is preserved through the biotite→gemmi conversion.""" assert gemmi_structure_from_atomarray.spacegroup_hm == stripped_gemmi.spacegroup_hm def test_atoms_match_pdb(self, gemmi_structure_from_atomarray, stripped_gemmi): + """Atom names and positions match the original PDB, in the same order.""" # atom order is preserved: biotite keeps PDB file order, array2hier reconstructs it parser_from_atomarray = PDBParser(gemmi_structure_from_atomarray) parser_from_gemmi = PDBParser(stripped_gemmi) @@ -92,6 +97,7 @@ def test_atoms_match_pdb(self, gemmi_structure_from_atomarray, stripped_gemmi): ) def test_occupancy_change_is_applied(self, stripped_atom_array, stripped_gemmi): + """Custom occupancy values are correctly written to each altloc group.""" occ_values = [0.2, 0.8, 0.0] altloc_info = detect_altlocs(stripped_atom_array) arr = assign_occupancies(stripped_atom_array, altloc_info, "custom", occ_values) @@ -104,33 +110,40 @@ def test_occupancy_change_is_applied(self, stripped_atom_array, stripped_gemmi): def test_fprotein_matches_direct_gemmi( self, gemmi_structure_from_atomarray, stripped_gemmi, device ): + """Fprotein amplitudes from the converted structure match those from + the original gemmi structure.""" f_atomarray = _compute_fprotein(gemmi_structure_from_atomarray, device) f_direct = _compute_fprotein(stripped_gemmi, device) np.testing.assert_allclose(np.abs(f_atomarray), np.abs(f_direct), atol=1e-3) def test_occupancy_warns_on_extra_values(self, stripped_atom_array, caplog): + """A warning is logged when more occupancy values are provided than there are altlocs.""" altloc_info = detect_altlocs(stripped_atom_array) with caplog.at_level(logging.WARNING): assign_occupancies(stripped_atom_array, altloc_info, "custom", [0.2, 0.8, 0.0, 0.0]) assert "Extra values will be ignored" in caplog.text def test_occupancy_warns_on_missing_values(self, stripped_atom_array, caplog): + """A warning is logged when fewer occupancy values are provided than there are altlocs.""" altloc_info = detect_altlocs(stripped_atom_array) with caplog.at_level(logging.WARNING): assign_occupancies(stripped_atom_array, altloc_info, "custom", [0.5, 0.5]) assert "Missing values are automatically set to 0" in caplog.text def test_occupancy_raises_on_out_of_range(self, stripped_atom_array): + """ValueError is raised when an occupancy value is outside [0.0, 1.0].""" altloc_info = detect_altlocs(stripped_atom_array) with pytest.raises(ValueError, match="out of range"): assign_occupancies(stripped_atom_array, altloc_info, "custom", [1.5, 0.0, 0.0]) def test_occupancy_raises_on_bad_sum(self, stripped_atom_array): + """ValueError is raised when occupancy values do not sum to 1.0.""" altloc_info = detect_altlocs(stripped_atom_array) with pytest.raises(ValueError, match="sum to 1.0"): assign_occupancies(stripped_atom_array, altloc_info, "custom", [0.3, 0.3, 0.3]) def test_fprotein_changes_with_occupancy(self, stripped_atom_array, stripped_gemmi, device): + """Fprotein amplitudes differ when occupancies changes from uniform to custom values.""" altloc_info = detect_altlocs(stripped_atom_array) arr_uniform = assign_occupancies(stripped_atom_array, altloc_info, "uniform") From 88be51795bf0d01bb49a3e94026750e2844f80e7 Mon Sep 17 00:00:00 2001 From: Doris Mai Date: Thu, 28 May 2026 22:53:06 +0000 Subject: [PATCH 10/14] build(deps): 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gcsfs>=2022.11.0 ; extra == 'all' - - html5lib>=1.1 ; extra == 'all' - - hypothesis>=6.46.1 ; extra == 'all' - - jinja2>=3.1.2 ; extra == 'all' - - lxml>=4.9.2 ; extra == 'all' - - matplotlib>=3.6.3 ; extra == 'all' - - numba>=0.56.4 ; extra == 'all' - - numexpr>=2.8.4 ; extra == 'all' - - odfpy>=1.4.1 ; extra == 'all' - - openpyxl>=3.1.0 ; extra == 'all' - - pandas-gbq>=0.19.0 ; extra == 'all' - - psycopg2>=2.9.6 ; extra == 'all' - - pyarrow>=10.0.1 ; extra == 'all' - - pymysql>=1.0.2 ; extra == 'all' - - pyqt5>=5.15.9 ; extra == 'all' - - pyreadstat>=1.2.0 ; extra == 'all' - - pytest>=7.3.2 ; extra == 'all' - - pytest-xdist>=2.2.0 ; extra == 'all' - - python-calamine>=0.1.7 ; extra == 'all' - - pyxlsb>=1.0.10 ; extra == 'all' - - qtpy>=2.3.0 ; extra == 'all' - - scipy>=1.10.0 ; extra == 'all' - - s3fs>=2022.11.0 ; extra == 'all' - - sqlalchemy>=2.0.0 ; extra == 'all' - - tables>=3.8.0 ; extra == 'all' - - tabulate>=0.9.0 ; extra == 'all' - - xarray>=2022.12.0 ; extra == 'all' - - xlrd>=2.0.1 ; extra == 'all' - - xlsxwriter>=3.0.5 ; extra == 'all' - - zstandard>=0.19.0 ; extra == 'all' - requires_python: '>=3.9' - pypi: https://files.pythonhosted.org/packages/e7/05/c19819d5e3d95294a6f5947fb9b9629efb316b96de511b418c53d245aae6/cycler-0.12.1-py3-none-any.whl name: cycler version: 0.12.1 diff --git a/pyproject.toml b/pyproject.toml index e6fa3e2..3166922 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,6 +5,7 @@ requires = ["hatchling"] [dependency-groups] analysis = [ "ipython", + "joblib", "marimo", "matplotlib", "mdtraj", @@ -18,7 +19,6 @@ analysis = [ boltz = ["boltz", "cuequivariance-torch", "cuequivariance-ops-torch-cu12", "rdkit>=2025.3.6"] dev = ["pytest", "pytest-cov", "mypy", "prek", "ty", "ruff", "pytest-loguru", "python-semantic-release"] protenix = ["protenix>=0.6.3", "einx", "triton"] -sfc = ["sfcalculator-torch>=0.3.2"] [project] authors = [{email = "karson.chrispens@ucsf.edu", name = "Karson Chrispens"}] @@ -30,7 +30,8 @@ dependencies = [ "einx<0.4", "hydra-core", "loguru", - "omegaconf" + "omegaconf", + "sfcalculator-torch>=0.3.2" ] name = "sampleworks" requires-python = ">= 3.11, <3.14" @@ -70,20 +71,15 @@ pyarrow = "==17.0.0" [tool.pixi.environments] analysis = {features = ["analysis"]} analysis-dev = {features = ["analysis", "dev"]} -analysis-dev-sfc = {features = ["analysis", "dev", "sfc"]} boltz = {features = ["boltz"]} boltz-analysis = {features = ["boltz", "analysis"]} boltz-dev = {features = ["boltz", "dev"]} -boltz-dev-sfc = {features = ["boltz", "dev", "sfc"]} protenix = {features = ["protenix"]} protenix-dev = {features = ["protenix", "dev"]} -protenix-dev-sfc = {features = ["protenix", "dev", "sfc"]} rf3 = {features = ["rf3"]} rf3-dev = {features = ["rf3", "dev"]} -rf3-dev-sfc = {features = ["rf3", "dev", "sfc"]} [tool.pixi.feature.protenix.pypi-options.dependency-overrides] -pandas = "==2.3.1" rdkit = ">=2024.3.5,<2025.9" [tool.pixi.feature.rf3.pypi-dependencies] @@ -92,6 +88,12 @@ rc-foundry = {editable = true, extras = ["rf3"], git = "https://github.com/k-chr [tool.pixi.pypi-dependencies] sampleworks = {editable = true, path = "."} +# Workspace-level override: reciprocalspaceship (sfcalculator-torch transitive dep) +# caps pandas<=2.2.3 in its metadata, but runs fine on 2.3.1; protenix hard-pins +# pandas==2.3.1. Standardize all envs on 2.3.1 to avoid silent downgrades. +[tool.pixi.pypi-options.dependency-overrides] +pandas = "==2.3.1" + [tool.pixi.system-requirements] cuda = "12" diff --git a/tests/eval/test_generate_synthetic_sf.py b/tests/eval/test_generate_synthetic_sf.py index 0b04a40..043d694 100644 --- a/tests/eval/test_generate_synthetic_sf.py +++ b/tests/eval/test_generate_synthetic_sf.py @@ -3,14 +3,10 @@ import logging from pathlib import Path +import gemmi import numpy as np import pytest import torch - - -pytest.importorskip("SFC_Torch", reason="SFC_Torch not available; run in analysis-dev-sfc env") - -import gemmi from atomworks.io.transforms.atom_array import remove_waters from sampleworks.eval.generate_synthetic_sf import atomarray_to_gemmi from sampleworks.eval.synthetic_utils import assign_occupancies From 27691dba3c5bb940afdbe4ed5ae18f7eb22e07d1 Mon Sep 17 00:00:00 2001 From: Doris Mai Date: Thu, 28 May 2026 23:13:04 +0000 Subject: [PATCH 11/14] refactor(sfc): tighten AtomArray typing in synthetic helpers Narrow `assign_occupancies` to `AtomArray -> AtomArray` and replace two `cast(AtomArray, ...)` calls in `synthetic_utils.py` with a single `assert isinstance(atom_array, AtomArray)` after the broadening transforms. Drop a now-redundant `# ty: ignore[invalid-argument-type]` on `detect_altlocs`. Add `import reciprocalspaceship.utils` so ty resolves `rs.utils.add_rfree`. Apply the same narrowing pattern to the `stripped_atom_array` test fixture. Resolves 4 ty warnings in the protenix-dev typecheck. Co-Authored-By: Claude Opus 4.7 --- src/sampleworks/eval/generate_synthetic_sf.py | 1 + src/sampleworks/eval/synthetic_utils.py | 16 ++++++++-------- tests/eval/test_generate_synthetic_sf.py | 7 +++++-- 3 files changed, 14 insertions(+), 10 deletions(-) diff --git a/src/sampleworks/eval/generate_synthetic_sf.py b/src/sampleworks/eval/generate_synthetic_sf.py index 0b28f54..6b64d36 100644 --- a/src/sampleworks/eval/generate_synthetic_sf.py +++ b/src/sampleworks/eval/generate_synthetic_sf.py @@ -17,6 +17,7 @@ import gemmi import numpy as np import reciprocalspaceship as rs +import reciprocalspaceship.utils import torch from biotite.structure import AtomArray from loguru import logger diff --git a/src/sampleworks/eval/synthetic_utils.py b/src/sampleworks/eval/synthetic_utils.py index 7e40fd9..7765bbe 100644 --- a/src/sampleworks/eval/synthetic_utils.py +++ b/src/sampleworks/eval/synthetic_utils.py @@ -3,10 +3,9 @@ import math import traceback from pathlib import Path -from typing import cast from atomworks.io.transforms.atom_array import remove_waters -from biotite.structure import AtomArray, AtomArrayStack +from biotite.structure import AtomArray from loguru import logger from sampleworks.eval.structure_utils import apply_selection from sampleworks.utils.atom_array_utils import ( @@ -29,11 +28,11 @@ def validate_occupancy_values(occupancy_values: list[float]) -> None: def assign_occupancies( - atom_array: AtomArray | AtomArrayStack, + atom_array: AtomArray, altloc_info: AltlocInfo, occupancy_mode: str, occupancy_values: list[float] | None = None, -) -> AtomArray | AtomArrayStack: +) -> AtomArray: """Assign occupancy values to atoms based on their altloc membership. Parameters @@ -52,7 +51,7 @@ def assign_occupancies( Returns ------- - AtomArray | AtomArrayStack + AtomArray Modified structure with updated occupancies Raises @@ -101,7 +100,7 @@ def assign_occupancies( for altloc, occupancy_value in zip(sorted(altloc_info.altloc_ids), occupancy_values): occupancy[altloc_info.atom_masks[altloc]] = occupancy_value - return cast(AtomArray, result) + return result def load_structure_for_synthetic_reward( @@ -168,7 +167,8 @@ def load_structure_for_synthetic_reward( atom_array = remove_hydrogens(atom_array) if strip_hydrogens else atom_array atom_array = remove_waters(atom_array) if strip_waters else atom_array atom_array = keep_polymer(keep_amino_acids(atom_array)) if strip_ligands else atom_array - altloc_info = detect_altlocs(atom_array) # ty: ignore[invalid-argument-type] + assert isinstance(atom_array, AtomArray) + altloc_info = detect_altlocs(atom_array) if occupancy_values: if occupancy_mode != "custom": logger.warning( @@ -193,4 +193,4 @@ def load_structure_for_synthetic_reward( logger.error(f"Invalid occupancy mode '{occupancy_mode}' for {structure_path}") raise ValueError(f"Invalid occupancy mode '{occupancy_mode}'") - return cast(AtomArray, atom_array) + return atom_array diff --git a/tests/eval/test_generate_synthetic_sf.py b/tests/eval/test_generate_synthetic_sf.py index 043d694..030bd55 100644 --- a/tests/eval/test_generate_synthetic_sf.py +++ b/tests/eval/test_generate_synthetic_sf.py @@ -8,6 +8,7 @@ import pytest import torch from atomworks.io.transforms.atom_array import remove_waters +from biotite.structure import AtomArray from sampleworks.eval.generate_synthetic_sf import atomarray_to_gemmi from sampleworks.eval.synthetic_utils import assign_occupancies from sampleworks.utils.atom_array_utils import ( @@ -34,11 +35,13 @@ def stripped_gemmi(resources_dir: Path) -> gemmi.Structure: @pytest.fixture(scope="module") -def stripped_atom_array(resources_dir: Path): +def stripped_atom_array(resources_dir: Path) -> AtomArray: arr = load_structure_with_altlocs(resources_dir / "6b8x" / "6b8x_final.pdb") arr = remove_hydrogens(arr) arr = remove_waters(arr) - return keep_polymer(keep_amino_acids(arr)) + arr = keep_polymer(keep_amino_acids(arr)) + assert isinstance(arr, AtomArray) + return arr @pytest.fixture(scope="module") From e9fefb30b4c349b265f2eefe9f2e7567bba60f87 Mon Sep 17 00:00:00 2001 From: Doris Mai Date: Fri, 29 May 2026 00:28:23 +0000 Subject: [PATCH 12/14] chore(types): fix easy ty warnings shared across boltz/protenix/rf3 envs --- scripts/eval/classify_altloc_regions.py | 2 +- src/sampleworks/metrics/metric.py | 4 +++- src/sampleworks/utils/guidance_script_utils.py | 2 +- src/sampleworks/utils/mmseqs2.py | 4 ++++ tests/cli/test_guidance_cli.py | 2 +- tests/rewards/test_real_space_density_reward.py | 12 ++++++------ tests/utils/test_framework_utils.py | 4 ++-- 7 files changed, 18 insertions(+), 12 deletions(-) diff --git a/scripts/eval/classify_altloc_regions.py b/scripts/eval/classify_altloc_regions.py index 814d851..5cb6d1f 100644 --- a/scripts/eval/classify_altloc_regions.py +++ b/scripts/eval/classify_altloc_regions.py @@ -415,7 +415,7 @@ def main(args: argparse.Namespace) -> None: ) ) - out_df = pd.DataFrame(all_rows, columns=OUTPUT_COLUMNS) + out_df = pd.DataFrame(all_rows, columns=pd.Index(OUTPUT_COLUMNS)) args.output_file.parent.mkdir(parents=True, exist_ok=True) out_df.to_csv(args.output_file, index=False) logger.info(f"Wrote {len(out_df)} classified spans to {args.output_file}") diff --git a/src/sampleworks/metrics/metric.py b/src/sampleworks/metrics/metric.py index 08e6a5b..78577eb 100644 --- a/src/sampleworks/metrics/metric.py +++ b/src/sampleworks/metrics/metric.py @@ -26,8 +26,10 @@ def instantiate_metric_manager( A dictionary where keys are metric names and values are Hydra configurations for the metrics. """ - metrics = {} + metrics: dict[str, Metric] = {} for name, cfg in metrics_cfg.items(): + if not isinstance(name, str): + raise TypeError(f"metrics_cfg key must be a str, got {type(name).__name__}: {name!r}") metric = hydra.utils.instantiate(cfg) if not isinstance(metric, Metric): raise TypeError(f"{name} must be a Metric instance") diff --git a/src/sampleworks/utils/guidance_script_utils.py b/src/sampleworks/utils/guidance_script_utils.py index 410ad2e..45476f1 100644 --- a/src/sampleworks/utils/guidance_script_utils.py +++ b/src/sampleworks/utils/guidance_script_utils.py @@ -164,7 +164,7 @@ def save_losses(losses, output_dir): def get_model_and_device( device_str: str, - model_checkpoint_path: str, + model_checkpoint_path: str | None, model_type: str, method: str | None = None, model: Any = None, diff --git a/src/sampleworks/utils/mmseqs2.py b/src/sampleworks/utils/mmseqs2.py index 0babd49..3486627 100644 --- a/src/sampleworks/utils/mmseqs2.py +++ b/src/sampleworks/utils/mmseqs2.py @@ -297,6 +297,10 @@ def download(ID, path): update_M = False if M not in a3m_lines: a3m_lines[M] = [] + if M is None: + # Well-formed A3M files always begin with a `>` header that sets M, + # so this only triggers on malformed input. Skip rather than KeyError. + continue a3m_lines[M].append(line) # we run all the sequences together in one string, so this is really just a list of file dumps diff --git a/tests/cli/test_guidance_cli.py b/tests/cli/test_guidance_cli.py index 3d4b496..5e5cf6c 100644 --- a/tests/cli/test_guidance_cli.py +++ b/tests/cli/test_guidance_cli.py @@ -66,7 +66,7 @@ def test_model_specific_args_rf3_msa(self): "/data/msa.a3m", ] + COMMON_ARGS config = GuidanceConfig.from_cli(argv) - assert config.msa_path == "/data/msa.a3m" + assert config.msa_path == "/data/msa.a3m" # ty: ignore[unresolved-attribute] def test_guidance_specific_args_fk(self): argv = [ diff --git a/tests/rewards/test_real_space_density_reward.py b/tests/rewards/test_real_space_density_reward.py index 66a27cd..dc3c622 100644 --- a/tests/rewards/test_real_space_density_reward.py +++ b/tests/rewards/test_real_space_density_reward.py @@ -476,8 +476,8 @@ def test_vmap_output_shape(self, reward_function_1vme, test_coordinates_1vme, de unique_combinations, inverse_indices = ( reward_function_1vme.precompute_unique_combinations( - elements_batch[0, 0], # ty: ignore[no-matching-overload, invalid-argument-type] - b_factors_batch[0, 0], # ty: ignore[no-matching-overload, invalid-argument-type] + elements_batch[0, 0], + b_factors_batch[0, 0], ) ) @@ -496,7 +496,7 @@ def test_vmap_output_shape(self, reward_function_1vme, test_coordinates_1vme, de op=rf_partial, ) - assert result.shape == torch.Size([num_particles]) # ty: ignore[unresolved-attribute] + assert result.shape == torch.Size([num_particles]) def test_vmap_consistency(self, reward_function_1vme, test_coordinates_1vme, device): """Test vmap results match sequential calls.""" @@ -520,8 +520,8 @@ def test_vmap_consistency(self, reward_function_1vme, test_coordinates_1vme, dev occupancies_batch = einx.rearrange("n -> p e n", occupancies, p=num_particles, e=1) unique_combinations, inverse_indices = reward_function_1vme.precompute_unique_combinations( - elements_batch[0, 0], # ty: ignore[no-matching-overload, invalid-argument-type] - b_factors_batch[0, 0], # ty: ignore[no-matching-overload, invalid-argument-type] + elements_batch[0, 0], + b_factors_batch[0, 0], ) rf_partial = partial( @@ -549,7 +549,7 @@ def test_vmap_consistency(self, reward_function_1vme, test_coordinates_1vme, dev ) result_sequential.append(loss.item()) - result_sequential = torch.tensor(result_sequential, device=result_vmap.device) # ty: ignore[unresolved-attribute] + result_sequential = torch.tensor(result_sequential, device=result_vmap.device) # GPU vmap and sequential loops accumulate floating-point reductions in # different orders, yielding abs diffs up to ~1.3e-4 and rel diffs up to diff --git a/tests/utils/test_framework_utils.py b/tests/utils/test_framework_utils.py index e052c3b..1738b6a 100644 --- a/tests/utils/test_framework_utils.py +++ b/tests/utils/test_framework_utils.py @@ -527,7 +527,7 @@ def test_raises_on_incompatible_batch_sizes(self): def test_raises_on_scalar_input(self): scalar = np.float64(1.0) with pytest.raises(ValueError, match="ndim >= 1"): - match_batch(scalar, target_batch_size=2) # type: ignore[no-matching-overload] + match_batch(scalar, target_batch_size=2) # ty: ignore[no-matching-overload] def test_1d_array(self): array = np.array([42.0]) @@ -549,4 +549,4 @@ def test_preserves_dtype(self): def test_raises_on_unsupported_type(self): with pytest.raises(TypeError, match="unsupported array type"): - match_batch([1, 2, 3], target_batch_size=2) # type: ignore[no-matching-overload] + match_batch([1, 2, 3], target_batch_size=2) # ty: ignore[no-matching-overload] From baedd4076b8afd8cd9fb01a677eaa7419bf5572d Mon Sep 17 00:00:00 2001 From: Doris Mai Date: Fri, 29 May 2026 01:00:54 +0000 Subject: [PATCH 13/14] chore(doc): add docstring in tests --- tests/eval/test_generate_synthetic_sf.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/tests/eval/test_generate_synthetic_sf.py b/tests/eval/test_generate_synthetic_sf.py index 030bd55..39534b3 100644 --- a/tests/eval/test_generate_synthetic_sf.py +++ b/tests/eval/test_generate_synthetic_sf.py @@ -28,6 +28,7 @@ @pytest.fixture(scope="module") def stripped_gemmi(resources_dir: Path) -> gemmi.Structure: + """gemmi.Structure with hydrogens, ligands, and waters removed using gemmi methods.""" s = gemmi.read_structure(str(resources_dir / "6b8x" / "6b8x_final.pdb")) s.remove_hydrogens() s.remove_ligands_and_waters() @@ -36,6 +37,8 @@ def stripped_gemmi(resources_dir: Path) -> gemmi.Structure: @pytest.fixture(scope="module") def stripped_atom_array(resources_dir: Path) -> AtomArray: + """AtomArray with hydrogens, waters, and non-polymer/non-amino-acid atoms + removed using existing utils.""" arr = load_structure_with_altlocs(resources_dir / "6b8x" / "6b8x_final.pdb") arr = remove_hydrogens(arr) arr = remove_waters(arr) @@ -48,12 +51,15 @@ def stripped_atom_array(resources_dir: Path) -> AtomArray: def gemmi_structure_from_atomarray( stripped_atom_array, stripped_gemmi: gemmi.Structure ) -> gemmi.Structure: + """gemmi.Structure converted from the stripped AtomArray.""" return atomarray_to_gemmi( stripped_atom_array, stripped_gemmi.cell, stripped_gemmi.spacegroup_hm ) def _compute_fprotein(gemmi_structure: gemmi.Structure, device: torch.device) -> np.ndarray: + """Compute |Fprotein| amplitudes from a gemmi structure via SFcalculator at ``DMIN`` + resolution. The final assert_numpy converts any tensor or list to a numpy array.""" sfc = SFcalculator( PDBParser(gemmi_structure), mtzdata=None, From c75d08bbd086abbfb3b4f986d5b3941454123049 Mon Sep 17 00:00:00 2001 From: Doris Mai Date: Fri, 12 Jun 2026 11:54:16 -0700 Subject: [PATCH 14/14] fix(msa): normalize protenix MSA paths to Path in get_msa --- src/sampleworks/utils/msa.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/sampleworks/utils/msa.py b/src/sampleworks/utils/msa.py index e5b948e..83e2805 100644 --- a/src/sampleworks/utils/msa.py +++ b/src/sampleworks/utils/msa.py @@ -397,7 +397,9 @@ def get_msa( else: self._cache_hits += 1 - msa_path_dict = {key: path for key, path in zip(data_keys, msa_directories)} + # protenix_msa_search returns string-style paths; normalize to Path so the + # return type matches the declared dict[str | int, Path] (idempotent on Paths). + msa_path_dict = {key: Path(path) for key, path in zip(data_keys, msa_directories)} else: raise ValueError(f"Unknown structure predictor: {structure_predictor}")