From 676142d10d97b6bdee29356aa6485e34d815b683 Mon Sep 17 00:00:00 2001 From: Josh Mitchell Date: Tue, 23 Apr 2024 22:22:17 +1000 Subject: [PATCH] link to images in colab rather than downloading them --- .../workshops/2024/vignettes/colab-vignettes.ipynb | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/source/workshops/2024/vignettes/colab-vignettes.ipynb b/source/workshops/2024/vignettes/colab-vignettes.ipynb index 20461b3f..0388d4d9 100644 --- a/source/workshops/2024/vignettes/colab-vignettes.ipynb +++ b/source/workshops/2024/vignettes/colab-vignettes.ipynb @@ -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" ] }, @@ -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)" ] }, { @@ -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)" ] }, { @@ -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)" ] }, { @@ -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)" ] }, {