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Code documentation and restructuring, example files from manuscript, … 
…etc.
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@jacobdurrant
jacobdurrant committed Apr 14, 2020
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6 changes: 3 additions & 3 deletions CHANGELOG.md
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* Modified Webina so users can optionally use PDBQTConvert to convert their
files. Webina communicates with PDBQTConvert at "arms length," via an
iframe.
* Added the ability to draw small-molecule ligands using the [PubChem
Sketcher](https://pubchem.ncbi.nlm.nih.gov/edit3/index.html) provided by the
NIH (embedded via an iframe).
* Added the ability to draw small-molecule ligands.
* Added technical documentation (see `docs/`).
* Added link to optionally remove non-protein residues from the receptor.

1.0.0
-----
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4 changes: 2 additions & 2 deletions dist/index.html
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<meta charset="utf-8">
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
<title>Webina</title>
<link rel="shortcut icon" href="favicon.ico"><link href="vendors.bada13cfacf3ef663f74.css" rel="stylesheet"><link href="styles.css.bada13cfacf3ef663f74.css" rel="stylesheet"></head>
<link rel="shortcut icon" href="favicon.ico"><link href="vendors.9c89844bce1d7efcb659.css" rel="stylesheet"><link href="styles.9c89844bce1d7efcb659.css" rel="stylesheet"></head>

<body>
<div id="app"></div>
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<script src="vue.min.js"></script>
<script src="vuex.min.js"></script>
<script src="bootstrap-vue.min.js"></script>
<script type="text/javascript" src="runtime.bada13cfacf3ef663f74.js"></script><script type="text/javascript" src="vendors.bada13cfacf3ef663f74.js"></script><script type="text/javascript" src="app.bada13cfacf3ef663f74.js"></script><script type="text/javascript" src="styles.css.bada13cfacf3ef663f74.js"></script></body>
<script type="text/javascript" src="runtime.9c89844bce1d7efcb659.js"></script><script type="text/javascript" src="vendors.9c89844bce1d7efcb659.js"></script><script type="text/javascript" src="app.9c89844bce1d7efcb659.js"></script><script type="text/javascript" src="styles.9c89844bce1d7efcb659.js"></script><script type="text/javascript" src="styles.css.9c89844bce1d7efcb659.js"></script></body>

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8 changes: 8 additions & 0 deletions docking_files/benchmarks/1HWL_docking_params.txt
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center_x: 17.35687879
center_y: 7.5200303
center_z: 14.92545455
size_x: 20
size_y: 20
size_z: 20
exhaustiveness: 8
seed: 123456789
76 changes: 76 additions & 0 deletions docking_files/benchmarks/1HWL_ligand_rosuvastatin.pdbqt
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REMARK 12 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: O1_2 and C1_3
REMARK 2 A between atoms: C1_3 and C2_4
REMARK 3 A between atoms: C1_3 and C19_28
REMARK 4 A between atoms: C3_5 and C4_6
REMARK 5 A between atoms: C5_7 and C6_8
REMARK 6 A between atoms: C12_16 and N2_17
REMARK 7 A between atoms: N2_17 and S1_19
REMARK 8 A between atoms: C15_24 and C16_25
REMARK 9 A between atoms: C19_28 and C20_29
REMARK 10 A between atoms: C20_29 and O4_30
REMARK 11 A between atoms: C20_29 and C21_32
REMARK 12 A between atoms: C21_32 and C22_33
ROOT
HETATM 1 C4 UNL 1 -0.594 0.200 -0.340 1.00 0.00 0.020 A
HETATM 2 C5 UNL 1 -1.430 0.886 -1.250 1.00 0.00 0.098 A
HETATM 3 N1 UNL 1 -2.705 0.456 -1.443 1.00 0.00 -0.060 NA
HETATM 4 C12 UNL 1 -3.208 -0.614 -0.779 1.00 0.00 0.738 A
HETATM 5 N3 UNL 1 -2.418 -1.284 0.098 1.00 0.00 -0.065 NA
HETATM 6 C15 UNL 1 -1.135 -0.914 0.351 1.00 0.00 0.069 A
ENDROOT
BRANCH 1 7
HETATM 7 C3 UNL 1 0.831 0.574 -0.214 1.00 0.00 0.014 C
HETATM 8 C2 UNL 1 1.318 1.101 0.914 1.00 0.00 0.006 C
BRANCH 8 9
HETATM 9 C1 UNL 1 2.764 1.509 1.031 1.00 0.00 0.143 C
BRANCH 9 10
HETATM 10 O1 UNL 1 2.952 2.281 2.192 1.00 0.00 -0.392 OA
HETATM 11 H1 UNL 1 2.759 1.700 2.975 1.00 0.00 0.210 HD
ENDBRANCH 9 10
BRANCH 9 12
HETATM 12 C19 UNL 1 3.688 0.270 1.030 1.00 0.00 0.068 C
BRANCH 12 13
HETATM 13 C20 UNL 1 5.182 0.648 1.008 1.00 0.00 0.130 C
BRANCH 13 14
HETATM 14 O4 UNL 1 5.538 1.268 2.217 1.00 0.00 -0.395 OA
HETATM 15 H25 UNL 1 6.395 1.744 2.055 1.00 0.00 0.210 HD
ENDBRANCH 13 14
BRANCH 13 16
HETATM 16 C21 UNL 1 6.074 -0.585 0.758 1.00 0.00 0.144 C
BRANCH 16 17
HETATM 17 C22 UNL 1 5.955 -1.618 1.839 1.00 0.00 0.175 C
HETATM 18 O5 UNL 1 6.341 -1.363 3.010 1.00 0.00 -0.648 OA
HETATM 19 O6 UNL 1 5.428 -2.870 1.548 1.00 0.00 -0.648 OA
ENDBRANCH 16 17
ENDBRANCH 13 16
ENDBRANCH 12 13
ENDBRANCH 9 12
ENDBRANCH 8 9
ENDBRANCH 1 7
BRANCH 2 20
HETATM 20 C6 UNL 1 -0.971 2.063 -2.023 1.00 0.00 -0.006 A
HETATM 21 C7 UNL 1 -1.182 2.112 -3.411 1.00 0.00 0.017 A
HETATM 22 C8 UNL 1 -0.770 3.226 -4.149 1.00 0.00 0.043 A
HETATM 23 C9 UNL 1 -0.158 4.305 -3.506 1.00 0.00 0.116 A
HETATM 24 F1 UNL 1 0.239 5.386 -4.223 1.00 0.00 -0.206 F
HETATM 25 C10 UNL 1 0.037 4.275 -2.123 1.00 0.00 0.043 A
HETATM 26 C11 UNL 1 -0.375 3.164 -1.381 1.00 0.00 0.017 A
ENDBRANCH 2 20
BRANCH 6 27
HETATM 27 C16 UNL 1 -0.301 -1.808 1.253 1.00 0.00 0.031 C
HETATM 28 C17 UNL 1 -1.112 -2.284 2.466 1.00 0.00 0.016 C
HETATM 29 C18 UNL 1 0.227 -3.002 0.455 1.00 0.00 0.016 C
ENDBRANCH 6 27
BRANCH 4 30
HETATM 30 N2 UNL 1 -4.563 -1.042 -1.009 1.00 0.00 -0.109 N
HETATM 31 C13 UNL 1 -5.445 -0.239 -1.857 1.00 0.00 0.189 C
BRANCH 30 32
HETATM 32 S1 UNL 1 -5.173 -2.472 -0.222 1.00 0.00 0.242 S
HETATM 33 O2 UNL 1 -6.429 -2.945 -0.899 1.00 0.00 -0.205 OA
HETATM 34 O3 UNL 1 -4.149 -3.568 -0.298 1.00 0.00 -0.205 OA
HETATM 35 C14 UNL 1 -5.530 -2.105 1.480 1.00 0.00 0.186 C
ENDBRANCH 30 32
ENDBRANCH 4 30
TORSDOF 12

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