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Save diffusion trajectory in mmCIF format instead of PDB #75

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Save diffusion trajectory in mmCIF format instead of PDB #75

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8af9bf8
Save diffusion trajectory in mmCIF format.
MrGreyfun Nov 21, 2025
07abf8e
Merge branch 'main' into ciftacj
MrGreyfun Nov 21, 2025
9f03d3b
Move gemmi import to head
MrGreyfun Nov 21, 2025
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36 changes: 17 additions & 19 deletions src/boltzgen/task/predict/writer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@

import numpy as np
import torch
import gemmi
from pytorch_lightning import LightningModule, Trainer
from pytorch_lightning.callbacks import BasePredictionWriter
from torch import Tensor
Expand Down Expand Up @@ -431,7 +432,7 @@ def write_on_batch_end( # noqa: PLR0915
.squeeze()
)

pdbs = []
mmcifs = []
all_coords = []
ensemble = []
atom_idx = 0
Expand All @@ -447,7 +448,7 @@ def write_on_batch_end( # noqa: PLR0915
raise ValueError("Either atom14 or atom37 must be true")

str_frame, _, _ = Structure.from_feat(sample)
pdbs.append(to_pdb(str_frame))
mmcifs.append(to_mmcif(str_frame))
all_coords.append(str_frame.coords)
ensemble.append(
(
Expand All @@ -457,8 +458,8 @@ def write_on_batch_end( # noqa: PLR0915
)
atom_idx += len(str_frame.coords)

open(self.outdir / f"{file_name}_traj.pdb", "w").write(
self.combine_pdb_models(pdbs)
open(self.outdir / f"{file_name}_traj.cif", "w").write(
self.combine_mmcif_models(mmcifs)
)

# Write x0 trajectories
Expand All @@ -479,7 +480,7 @@ def write_on_batch_end( # noqa: PLR0915
.squeeze()
)

pdbs = []
mmcifs = []
all_coords = []
ensemble = []
atom_idx = 0
Expand All @@ -495,7 +496,7 @@ def write_on_batch_end( # noqa: PLR0915
raise ValueError("Either atom14 or atom37 must be true")

str_frame, _, _ = Structure.from_feat(sample)
pdbs.append(to_pdb(str_frame))
mmcifs.append(to_mmcif(str_frame))
all_coords.append(str_frame.coords)
ensemble.append(
(
Expand All @@ -505,8 +506,8 @@ def write_on_batch_end( # noqa: PLR0915
)
atom_idx += len(str_frame.coords)

open(self.outdir / f"{file_name}_x0_traj.pdb", "w").write(
self.combine_pdb_models(pdbs)
open(self.outdir / f"{file_name}_x0_traj.cif", "w").write(
self.combine_mmcif_models(mmcifs)
)

except Exception as e: # noqa: BLE001
Expand All @@ -516,18 +517,15 @@ def write_on_batch_end( # noqa: PLR0915
msg = f"predict/writer.py: Validation structure writing failed on {batch['id'][0]} with error {e}. Skipping."
print(msg)

def combine_pdb_models(self, pdb_strings):
combined_pdb = ""
model_number = 1
def combine_mmcif_models(self, mmcif_strings):
gemmi_structure = gemmi.Structure()
for model_number, mmcif_string in enumerate(mmcif_strings, start=1):
block = gemmi.cif.read_string(mmcif_string).sole_block()
gemmi_model = gemmi.make_structure_from_block(block)[0]
gemmi_model.name = str(model_number)
gemmi_structure.add_model(gemmi_model)

for pdb in pdb_strings:
# Add a model number at the start of each model
combined_pdb += f"MODEL {model_number}\n"
combined_pdb += pdb.split("\nEND")[0]
combined_pdb += "\nENDMDL\n" # End of model marker
model_number += 1

return combined_pdb
return gemmi_structure.make_mmcif_document().as_string()

def on_predict_epoch_end(
self,
Expand Down