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bio-nexus-api / bioai-platform /backend /app /tools

Commit History

Jul 17

21:25
fix: MolVolume -> CalcMolecularVolume + wrap optional descriptors in try/except

Samad14

3aea338
20:58
fix: ADMET import error + MD secondary structure accuracy⁠

Samad14

ec85a6b
20:38
feat: industrial-grade ADMET + detailed MD/function results⁠

Samad14

24c3fcb
19:57
debug: add OpenMM verification steps + startup check so we can see what fails

Samad14

b281340
19:42
fix: remove invalid has_anisou call from BioPython fallback

Samad14

498fe95
19:24
fix: remove invalid CaPPD import from BioPython fallback

Samad14

a623185
19:19
fix: OpenMM via micromamba + BioPython structural fallback, real error messages

Samad14

bd95b9f
19:10
feat: scientifically accurate MD simulation with OBC2 solvent, Kabsch RMSD, per-residue RMSF

Samad14

3fba508

Jul 16

20:29
Fix MD simulation: OpenMM fallback, PDB ID propagation, better error handling

Samad14

d9d71ff
20:19
Phase 3a/4/5: ADMET descriptors (RDKit), MD simulation (OpenMM), function prediction (DeepFRI-inspired) — backend + frontend

Samad14

99fb209

Jul 15

11:16
Major docking rewrite: match frontend contract (pdb_id+smiles input, nested poses/interactions output, PDB fetch from RCSB, auto grid center)

Samad14

8f9cafc
10:55
Fix docking: add pdb_to_pdbqt_receptor() for protein PDBQT conversion

Samad14

9125057
09:43
Use Dockerfile-installed Vina first, fall back to download

Samad14

dade2b6
08:55
fix: Linux Vina binary, Open Babel PDBQT, pipeline_worker utcnow⁠

Samad14

fe05da9

Jul 14

16:08
test: reduce vina timeout to 10s for faster diagnostic

Samad14

4d3a2e8
15:54
fix: indentation error at line 610

Samad14

b100aa9
15:47
fix: revert to async subprocess (no thread pool to avoid import hang), keep --cpu 1

Samad14

2a4a790
15:29
fix: use ThreadPoolExecutor with subprocess.Popen (no asyncio subprocess), add --cpu 1 and stdin=/dev/null

Samad14

d242989
15:26
fix: use asyncio.create_subprocess_exec with file handles + asyncio.wait_for (no threads, no pipes)

Samad14

48bf0d7
15:17
fix: use poll() polling loop instead of proc.wait(timeout=N) to avoid Python 3.14 pidfd-wait hang

Samad14

4a1b691
15:16
fix: use Popen + wait(timeout=N) + killpg layered kill approach

Samad14

f381b03
15:10
fix: use /usr/bin/timeout OS-level command instead of Python subprocess timeout

Samad14

8329f93
15:03
fix: use subprocess.DEVNULL for Vina output — eliminates ALL I/O blocking

Samad14

3aeb8d2
14:58
fix: use dedicated ThreadPoolExecutor(max_workers=1) + subprocess.run(file handles, timeout=N)

Samad14

1242de8
14:38
fix: use asyncio.create_subprocess_exec with file descriptors + wait_for — no threads, no pipe buffer deadlock

Samad14

6c14e2d
13:53
fix: use file handles instead of PIPE to avoid Vina pipe-buffer deadlock on Render

Samad14

88df0f4
11:33
fix: use process group kill (killpg) for reliable Vina timeout

Samad14

32957ff
11:14
debug: set Vina timeout to 60s for testing timeout mechanism

Samad14

01cccda
10:45
fix: use subprocess.run(timeout=...) instead of asyncio subprocess for reliable Vina timeout

Samad14

ab38821
09:55
fix: reliable Vina timeout via asyncio subprocess + cleanup vimontest

Samad14

ab9ad46
09:04
fix: parse CACTUS API PDB-like ATOM records instead of V2000 SDF

Samad14

80b49f1
08:31
fix: use Linux timeout command instead of subprocess timeout to reliably kill Vina

Samad14

083cf21
08:08
fix: add subprocess timeout=600, reduce exhaustiveness to 2, modes to 3

Samad14

76cecfd
07:25
fix: reorder _download_vina before module-level vina resolution

Samad14

8c7f69a
07:20
fix: detect missing Vina binary at module level and download fallback; fail early if binary not found

Samad14

058552e
07:13
fix: use asyncio.to_thread + file-based subprocess for Vina; add vina binary debug test

Samad14

d214a0c
06:57
fix: use asyncio.create_subprocess_exec for Vina to prevent pipe deadlock; fix isoformat for PostgREST

Samad14

b1d8ad7

Jul 12

18:54
feat: add progress callbacks to DockingTool.run() for real-time status tracking⁠

Samad14

8d44857
08:48
fix: add TORSDOF 0 after ENDROOT (rigid ligand)

Samad14

396bcf1
08:40
fix: right-justify charge to col 76 with {charge:>8.3f}, ad_type:>2 at 78-79

Samad14

38de281
08:20
fix: pad PDBQT to 80 cols so charge field is parseable at positions 66 or 69

Samad14

f66e99a

Jul 11

20:36
fix: correct PDBQT column alignment (atom name, coord pos, charge field)

Samad14

cdaf04c
20:27
fix: correct PDBQT column positions for atom serial number

Samad14

d29844d
20:22
fix: generate PDBQT directly from SDF (Vina binary rejects PDB/SDF input)

Samad14

3a5f903
20:18
fix: convert SDF to PDB in Python (avoids Vina SDF parser issues)

Samad14

640d93b
20:14
fix: use NCI CACTUS /mol format instead of /sdf (Vina parses MOL better)

Samad14

c11931d
20:09
fix: strip SDF data sections (Vina parser rejects >header lines)

Samad14

ecab431
19:58
fix: replace obabel CLI with NCI CACTUS API for SMILES→3D (eliminates all subprocess crashes)

Samad14

b3124a2
19:53
fix: use asyncio.to_thread(subprocess.run) instead of asyncio.create_subprocess_exec (Python 3.14 compat)

Samad14

05c77a7
19:23
fix: use obabel CLI subprocess for SMILES→3D (lightweight, no OOM) + Vina reads PDB receptor natively (no obabel PDBQT prep)

Samad14

64e0551

Commit History

Jul 17

fix: MolVolume -> CalcMolecularVolume + wrap optional descriptors in try/except

fix: ADMET import error + MD secondary structure accuracy⁠

feat: industrial-grade ADMET + detailed MD/function results⁠

debug: add OpenMM verification steps + startup check so we can see what fails

fix: remove invalid has_anisou call from BioPython fallback

fix: remove invalid CaPPD import from BioPython fallback

fix: OpenMM via micromamba + BioPython structural fallback, real error messages

feat: scientifically accurate MD simulation with OBC2 solvent, Kabsch RMSD, per-residue RMSF

Jul 16

Fix MD simulation: OpenMM fallback, PDB ID propagation, better error handling

Phase 3a/4/5: ADMET descriptors (RDKit), MD simulation (OpenMM), function prediction (DeepFRI-inspired) — backend + frontend

Jul 15

Major docking rewrite: match frontend contract (pdb_id+smiles input, nested poses/interactions output, PDB fetch from RCSB, auto grid center)

Fix docking: add pdb_to_pdbqt_receptor() for protein PDBQT conversion

Use Dockerfile-installed Vina first, fall back to download

fix: Linux Vina binary, Open Babel PDBQT, pipeline_worker utcnow⁠

Jul 14

test: reduce vina timeout to 10s for faster diagnostic

fix: indentation error at line 610

fix: revert to async subprocess (no thread pool to avoid import hang), keep --cpu 1

fix: use ThreadPoolExecutor with subprocess.Popen (no asyncio subprocess), add --cpu 1 and stdin=/dev/null

fix: use asyncio.create_subprocess_exec with file handles + asyncio.wait_for (no threads, no pipes)

fix: use poll() polling loop instead of proc.wait(timeout=N) to avoid Python 3.14 pidfd-wait hang

fix: use Popen + wait(timeout=N) + killpg layered kill approach

fix: use /usr/bin/timeout OS-level command instead of Python subprocess timeout

fix: use subprocess.DEVNULL for Vina output — eliminates ALL I/O blocking

fix: use dedicated ThreadPoolExecutor(max_workers=1) + subprocess.run(file handles, timeout=N)

fix: use asyncio.create_subprocess_exec with file descriptors + wait_for — no threads, no pipe buffer deadlock

fix: use file handles instead of PIPE to avoid Vina pipe-buffer deadlock on Render

fix: use process group kill (killpg) for reliable Vina timeout

debug: set Vina timeout to 60s for testing timeout mechanism

fix: use subprocess.run(timeout=...) instead of asyncio subprocess for reliable Vina timeout

fix: reliable Vina timeout via asyncio subprocess + cleanup vimontest

fix: parse CACTUS API PDB-like ATOM records instead of V2000 SDF

fix: use Linux timeout command instead of subprocess timeout to reliably kill Vina

fix: add subprocess timeout=600, reduce exhaustiveness to 2, modes to 3

fix: reorder _download_vina before module-level vina resolution

fix: detect missing Vina binary at module level and download fallback; fail early if binary not found

fix: use asyncio.to_thread + file-based subprocess for Vina; add vina binary debug test

fix: use asyncio.create_subprocess_exec for Vina to prevent pipe deadlock; fix isoformat for PostgREST

Jul 12

feat: add progress callbacks to DockingTool.run() for real-time status tracking⁠

fix: add TORSDOF 0 after ENDROOT (rigid ligand)

fix: right-justify charge to col 76 with {charge:>8.3f}, ad_type:>2 at 78-79

fix: pad PDBQT to 80 cols so charge field is parseable at positions 66 or 69

Jul 11

fix: correct PDBQT column alignment (atom name, coord pos, charge field)

fix: correct PDBQT column positions for atom serial number

fix: generate PDBQT directly from SDF (Vina binary rejects PDB/SDF input)

fix: convert SDF to PDB in Python (avoids Vina SDF parser issues)

fix: use NCI CACTUS /mol format instead of /sdf (Vina parses MOL better)

fix: strip SDF data sections (Vina parser rejects >header lines)

fix: replace obabel CLI with NCI CACTUS API for SMILES→3D (eliminates all subprocess crashes)

fix: use asyncio.to_thread(subprocess.run) instead of asyncio.create_subprocess_exec (Python 3.14 compat)

fix: use obabel CLI subprocess for SMILES→3D (lightweight, no OOM) + Vina reads PDB receptor natively (no obabel PDBQT prep)