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update docker
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@ndonyapour
ndonyapour committed Dec 23, 2024
1 parent 4f69b52 commit 8ce3b24
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Showing 8 changed files with 21 additions and 4,176 deletions.
3 changes: 3 additions & 0 deletions utils/autodock-vina-filter-plugin/.gitattributes
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*.pdb filter=lfs diff=lfs merge=lfs -text
*.pdbqt filter=lfs diff=lfs merge=lfs -text
*.txt filter=lfs diff=lfs merge=lfs -text
2 changes: 1 addition & 1 deletion ...na-filter-plugin/autodock_vina_filter.cwl → ...ter-plugin/autodock_vina_filter_0@[email protected]
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Expand Up @@ -13,7 +13,7 @@ baseCommand: ["python3", "-m", "polus.mm.utils.autodock_vina_filter"]

hints:
DockerRequirement:
dockerPull: ndonyapour/autodock_vina_filter
dockerPull: polusai/autodock-vina-filter-tool@sha256:ca69ac31ed3733d544abc6424646a9b508e6e886a7a08ffef7a902490b7fca61

requirements:
InlineJavascriptRequirement: {}
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4 changes: 4 additions & 0 deletions utils/autodock-vina-filter-plugin/build-docker.sh
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#!/bin/bash

version=$(<VERSION)
docker build . -t polusai/autodock-vina-filter-tool:${version}
7 changes: 3 additions & 4 deletions utils/autodock-vina-filter-plugin/pyproject.toml
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Expand Up @@ -2,15 +2,14 @@
name = "polus-mm-utils-autodock-vina-filter"
version = "0.1.0"
description = "Filters results of the AutoDock Vina software."
authors = ["Data Scientist <[email protected]>"]
authors = ["Nazanin Donyapour <[email protected]>", "Brandon Walker <[email protected]>"]
readme = "README.md"
packages = [{include = "polus", from = "src"}]

[tool.poetry.dependencies]
python = ">=3.9,<3.12"
python = ">=3.9,<3.13"
typer = "^0.7.0"
cwl-utils = "0.33"
cwltool = "3.1.20240404144621"
sophios = "0.1.4"

[tool.poetry.group.dev.dependencies]
bump2version = "^1.0.1"
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65 changes: 3 additions & 62 deletions utils/autodock-vina-filter-plugin/tests/1e3g.pdbqt
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REMARK Name = 1e3g_ligand
REMARK 3 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C_13 and C_18
REMARK 2 A between atoms: C_17 and C_19
REMARK 3 A between atoms: C_17 and O_21
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 C UNL A 1 0.414 28.070 4.103 0.00 0.00 -0.020 C
ATOM 2 C UNL A 1 1.195 26.999 4.832 0.00 0.00 +0.014 C
ATOM 3 C UNL A 1 2.661 27.140 4.532 0.00 0.00 +0.157 C
ATOM 4 C UNL A 1 3.174 28.457 4.794 0.00 0.00 -0.016 C
ATOM 5 C UNL A 1 2.367 29.553 4.780 0.00 0.00 -0.041 C
ATOM 6 C UNL A 1 2.973 30.906 5.116 0.00 0.00 -0.027 C
ATOM 7 C UNL A 1 2.207 32.030 4.457 0.00 0.00 -0.042 C
ATOM 8 C UNL A 1 0.733 31.962 4.898 0.00 0.00 -0.012 C
ATOM 9 C UNL A 1 0.124 30.597 4.514 0.00 0.00 -0.041 C
ATOM 10 C UNL A 1 0.912 29.480 4.476 0.00 0.00 -0.040 C
ATOM 11 C UNL A 1 -1.316 30.583 4.251 0.00 0.00 -0.061 C
ATOM 12 C UNL A 1 -2.102 31.675 4.310 0.00 0.00 -0.075 C
ATOM 13 C UNL A 1 -1.535 33.039 4.664 0.00 0.00 +0.018 C
ATOM 14 C UNL A 1 -0.056 33.066 4.261 0.00 0.00 -0.023 C
ATOM 15 C UNL A 1 0.387 34.509 4.572 0.00 0.00 -0.046 C
ATOM 16 C UNL A 1 -0.899 35.299 4.311 0.00 0.00 -0.023 C
ATOM 17 C UNL A 1 -2.001 34.282 3.900 0.00 0.00 +0.072 C
ATOM 18 O UNL A 1 3.375 26.212 4.162 0.00 0.00 -0.293 OA
ATOM 19 H UNL A 1 -0.635 27.987 4.386 0.00 0.00 +0.032 HD
ATOM 20 H UNL A 1 0.548 27.927 3.031 0.00 0.00 +0.032 HD
ATOM 21 H UNL A 1 0.854 26.018 4.502 0.00 0.00 +0.035 HD
ATOM 22 H UNL A 1 1.036 27.106 5.905 0.00 0.00 +0.035 HD
ATOM 23 H UNL A 1 4.235 28.581 5.009 0.00 0.00 +0.066 HD
ATOM 24 H UNL A 1 4.000 30.926 4.752 0.00 0.00 +0.031 HD
ATOM 25 H UNL A 1 2.933 31.046 6.196 0.00 0.00 +0.031 HD
ATOM 26 H UNL A 1 2.270 31.931 3.373 0.00 0.00 +0.027 HD
ATOM 27 H UNL A 1 2.634 32.988 4.753 0.00 0.00 +0.027 HD
ATOM 28 H UNL A 1 0.692 32.079 5.981 0.00 0.00 +0.035 HD
ATOM 29 H UNL A 1 -1.780 29.631 3.992 0.00 0.00 +0.062 HD
ATOM 30 H UNL A 1 -3.167 31.578 4.099 0.00 0.00 +0.058 HD
ATOM 31 H UNL A 1 0.123 32.850 3.208 0.00 0.00 +0.032 HD
ATOM 32 H UNL A 1 1.229 34.842 3.966 0.00 0.00 +0.027 HD
ATOM 33 H UNL A 1 0.773 34.634 5.584 0.00 0.00 +0.027 HD
ATOM 34 H UNL A 1 -0.742 36.030 3.518 0.00 0.00 +0.029 HD
ATOM 35 H UNL A 1 -1.199 35.843 5.207 0.00 0.00 +0.029 HD
ENDROOT
BRANCH 13 36
ATOM 36 C UNL A 1 -1.725 33.228 6.189 0.00 0.00 -0.053 C
ATOM 37 H UNL A 1 -2.787 33.178 6.431 0.00 0.00 +0.024 HD
ATOM 38 H UNL A 1 -1.192 32.440 6.721 0.00 0.00 +0.024 HD
ATOM 39 H UNL A 1 -1.329 34.199 6.486 0.00 0.00 +0.024 HD
ENDBRANCH 13 36
BRANCH 17 40
ATOM 40 C UNL A 1 -2.034 34.050 2.412 0.00 0.00 -0.035 C
ATOM 41 H UNL A 1 -1.034 33.791 2.064 0.00 0.00 +0.026 HD
ATOM 42 H UNL A 1 -2.721 33.234 2.188 0.00 0.00 +0.026 HD
ATOM 43 H UNL A 1 -2.370 34.958 1.911 0.00 0.00 +0.026 HD
ENDBRANCH 17 40
BRANCH 17 44
ATOM 44 O UNL A 1 -3.257 34.797 4.345 0.00 0.00 -0.388 OA
ATOM 45 H UNL A 1 -3.486 35.571 3.826 0.00 0.00 +0.210 HD
ENDBRANCH 17 44
TORSDOF 3
version https://git-lfs.github.com/spec/v1
oid sha256:24bf6ec9386d191d5c680bf100af549c86957d6f6229533a2b4dbad7860468c5
size 4119
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