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29 | 29 | "!wget -qN -P inputs https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/inputs/PT2385.sdf\n",
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30 | 30 | "!wget -qN -P inputs https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/inputs/solvated_complex.pdb\n",
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31 | 31 | "!wget -qN -P inputs https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/inputs/ribozymes.pdb\n",
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32 |
| - "!wget -qN -P images https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/images/vsites_bondcharge.jpg\n", |
33 |
| - "!wget -qN -P images https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/images/vsites_divalent.jpg\n", |
34 |
| - "!wget -qN -P images https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/images/vsites_monovalent.jpg\n", |
35 |
| - "!wget -qN -P images https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/images/vsites_trivalent.jpg\n", |
36 | 32 | "!mamba env update -q --name=base --file=colab-env.yml"
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37 | 33 | ]
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38 | 34 | },
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300 | 296 | "\n",
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301 | 297 | "This supports placement of a virtual site S along a vector between two specified atoms, e.g. to allow for a sigma hole for halogens or similar contexts. With positive values of the distance, the virtual site lies outside the first indexed atom (cyan in this image).\n",
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302 | 298 | "\n",
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303 |
| - "" |
| 299 | + "" |
304 | 300 | ]
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305 | 301 | },
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306 | 302 | {
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334 | 330 | "\n",
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335 | 331 | "This is originally intended for situations like a carbonyl, and allows placement of a virtual site `S` at a specified distance `d` from the first indexed atom, with angles `inPlaneAngle` (θ₁ in the diagram) and `outOfPlaneAngle` (θ₂ in the diagram) relative to the plane defined by the three indexed atoms. The atom labeled `w` is not used to place the virtual site.\n",
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336 | 332 | "\n",
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337 |
| - "" |
| 333 | + "" |
338 | 334 | ]
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339 | 335 | },
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340 | 336 | {
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368 | 364 | "\n",
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369 | 365 | "This is suitable for cases like four-point and five-point water models as well as pyrimidine; a virtual site `S` lies a specified distance `d` from the atom indexed 1 (blue) along the bisector of the angle between the three indexed atoms (if `outOfPlaneAngle` is zero) or out of the plane by the specified angle (if `outOfPlaneAngle` is nonzero) with its projection along the bisector. For positive values of the distance `d` the virtual site lies outside the 2-1-3 angle and for negative values it lies inside.\n",
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370 | 366 | "\n",
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371 |
| - "" |
| 367 | + "" |
372 | 368 | ]
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373 | 369 | },
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374 | 370 | {
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424 | 420 | "\n",
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425 | 421 | "This is suitable for planar or tetrahedral nitrogen lone pairs; a charge site `S` lies above the central atom (blue) a distance `d` along the vector perpendicular to the plane of the other three indexed atoms (2,3,4). With positive values of `d` the site lies above the central atom and with negative values it lies below.\n",
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426 | 422 | "\n",
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427 |
| - "" |
| 423 | + "" |
428 | 424 | ]
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429 | 425 | },
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430 | 426 | {
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