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bio-nexus-api / bioai-platform /backend /app /tools /docking.py

Commit History

Aug 6

08:09
Docking: flatten multi-chain obabel receptor output to a single model

Samad14

033c1d2
07:59
Fix docking on Windows: resolve obabel from venv, use Windows Vina binary⁠

Samad14

0c3a0da
07:39
Fix pipeline MSA/AI stall, add SwissADME-parity ADMET panel, PubChem search, docking ligand data⁠

Samad14

5bb077e

Aug 4

20:07
feat(docking): Vina full-detail — parse 1.2.7 log (RMSD l.b./u.b., version, seed), RMSD table + run-config UI (3e)

Samad14

4320faf

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
18:46
fix: use PDB instead of SDF for ligand (Vina SDF parser rejects RDKit tag)

Samad14

36897bb
18:42
fix: eliminate obabel entirely — use RDKit for SMILES→3D + Vina PDB/SDF input (avoids OOM from obabel C++ subprocess)

Samad14

618a4e0
18:25
fix: add import subprocess and use subprocess.PIPE instead of asyncio.subprocess.PIPE (Python 3.14 compat)

Samad14

6d68d15
18:16
fix: revert to BackgroundTasks + async DockingTool.run (no threads, no pybel); pre-download vina in build.sh

Samad14

538a17a
18:11
fix: fully sync _worker_sync — replaces asyncio.run with subprocess.run + httpx.Client to avoid Python 3.14 thread crash

Samad14

890c537
17:55
fix: remove pybel bindings (causes segfault on Render), use obabel CLI subprocess only

Samad14

0ed4824

Commit History

Aug 6

Docking: flatten multi-chain obabel receptor output to a single model

Fix docking on Windows: resolve obabel from venv, use Windows Vina binary⁠

Fix pipeline MSA/AI stall, add SwissADME-parity ADMET panel, PubChem search, docking ligand data⁠

Aug 4

feat(docking): Vina full-detail — parse 1.2.7 log (RMSD l.b./u.b., version, seed), RMSD table + run-config UI (3e)

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)

fix: use PDB instead of SDF for ligand (Vina SDF parser rejects RDKit tag)

fix: eliminate obabel entirely — use RDKit for SMILES→3D + Vina PDB/SDF input (avoids OOM from obabel C++ subprocess)

fix: add import subprocess and use subprocess.PIPE instead of asyncio.subprocess.PIPE (Python 3.14 compat)

fix: revert to BackgroundTasks + async DockingTool.run (no threads, no pybel); pre-download vina in build.sh

fix: fully sync _worker_sync — replaces asyncio.run with subprocess.run + httpx.Client to avoid Python 3.14 thread crash

fix: remove pybel bindings (causes segfault on Render), use obabel CLI subprocess only