Skip to content

Commit

Permalink
link to images in colab rather than downloading them
Browse files Browse the repository at this point in the history
  • Loading branch information
Yoshanuikabundi committed Apr 23, 2024
1 parent 40c70a2 commit 676142d
Showing 1 changed file with 4 additions and 8 deletions.
12 changes: 4 additions & 8 deletions source/workshops/2024/vignettes/colab-vignettes.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -29,10 +29,6 @@
"!wget -qN -P inputs https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/inputs/PT2385.sdf\n",
"!wget -qN -P inputs https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/inputs/solvated_complex.pdb\n",
"!wget -qN -P inputs https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/inputs/ribozymes.pdb\n",
"!wget -qN -P images https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/images/vsites_bondcharge.jpg\n",
"!wget -qN -P images https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/images/vsites_divalent.jpg\n",
"!wget -qN -P images https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/images/vsites_monovalent.jpg\n",
"!wget -qN -P images https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/images/vsites_trivalent.jpg\n",
"!mamba env update -q --name=base --file=colab-env.yml"
]
},
Expand Down Expand Up @@ -300,7 +296,7 @@
"\n",
"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",
"\n",
"![](images/vsite_bondcharge.jpg)"
"![](https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/images/vsite_bondcharge.jpg)"
]
},
{
Expand Down Expand Up @@ -334,7 +330,7 @@
"\n",
"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",
"\n",
"![](images/vsite_monovalent.jpg)"
"![](https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/images/vsite_monovalent.jpg)"
]
},
{
Expand Down Expand Up @@ -368,7 +364,7 @@
"\n",
"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",
"\n",
"![](images/vsite_divalent.jpg)"
"![](https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/images/vsite_divalent.jpg)"
]
},
{
Expand Down Expand Up @@ -424,7 +420,7 @@
"\n",
"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",
"\n",
"![](images/vsite_trivalent.jpg)"
"![](https://raw.githubusercontent.com/openforcefield/openff-docs/main/source/workshops/2024/vignettes/images/vsite_trivalent.jpg)"
]
},
{
Expand Down

0 comments on commit 676142d

Please sign in to comment.