Commit 58195eb7 authored by Jacob Durrant's avatar Jacob Durrant

Update to 1.0.1.

parent 0202e3c7
Pipeline #263 failed with stages
......@@ -33,3 +33,6 @@ biotite_app/build/
dist/environs/**/*.log
dist/environs/**/*.txt
scene.log
update_node_etc.sh
TODO.md
*.old
CHANGES
=======
1.0.1
-----
* Hydrogens are now displayed on PDB files, just like SDF files.
* Improved license visibility in source and compiled code.
1.0.0
-----
......
The 3-Clause BSD License
========================
Copyright 2019 Jacob D. Durrant
Copyright 2019 Jacob D. Durrant.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
......
# ProteinVR 1.0.0 #
# ProteinVR 1.0.1 #
## Introduction ##
......
......@@ -91,6 +91,6 @@
<script src="js/jsfile.4.babylonjs.materials.min.js"></script>
<script src="js/jsfile.5.babylon.gui.min.js"></script>
<script src="js/peer.min.js" async></script>
<script type="text/javascript" src="runtime.3a0a2cd98eaecc17ab2f.js"></script><script type="text/javascript" src="vendors.3a0a2cd98eaecc17ab2f.js"></script><script type="text/javascript" src="app.3a0a2cd98eaecc17ab2f.js"></script></body>
<script type="text/javascript" src="runtime.3f41f9afe78453dc3ff2.js"></script><script type="text/javascript" src="vendors.3f41f9afe78453dc3ff2.js"></script><script type="text/javascript" src="app.3f41f9afe78453dc3ff2.js"></script></body>
</html>
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
(function(context) {
// Get the URL for following.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
(function(context) {
// Determine whether warning should be displayed. Do this fast.
......
importScripts("https://storage.googleapis.com/workbox-cdn/releases/4.3.1/workbox-sw.js");importScripts("precache-manifest.c38a7c567da8016b56fa6c2884cf27fa.js");workbox.core.skipWaiting();workbox.core.clientsClaim();self.__precacheManifest=[].concat(self.__precacheManifest||[]);workbox.precaching.precacheAndRoute(self.__precacheManifest,{});workbox.routing.registerRoute(/\./,new workbox.strategies.NetworkFirst,"GET");
importScripts("https://storage.googleapis.com/workbox-cdn/releases/4.3.1/workbox-sw.js");importScripts("precache-manifest.2c864dfdc2426ab470df6f66f95e5fe8.js");workbox.core.skipWaiting();workbox.core.clientsClaim();self.__precacheManifest=[].concat(self.__precacheManifest||[]);workbox.precaching.precacheAndRoute(self.__precacheManifest,{});workbox.routing.registerRoute(/\./,new workbox.strategies.NetworkFirst,"GET");
{
"name": "protein-vr",
"version": "1.0.0",
"version": "1.0.1",
"lockfileVersion": 1,
"requires": true,
"dependencies": {
......
{
"name": "protein-vr",
"version": "1.0.0",
"version": "1.0.1",
"description": "",
"private": true,
"scripts": {
......
No preview for this file type
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// These functions include camera functions common to all kinds of cameras.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// This sets up the non vr camera. Not everyone has a vr headset.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
import * as Vars from "../Vars/Vars";
import * as NonVRCamera from "./NonVRCamera";
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// This module sets up the VR camera.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
import * as Navigation from "../Navigation/Navigation";
import * as Pickables from "../Navigation/Pickables";
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
import * as Optimizations from "../../Scene/Optimizations";
import * as Vars from "../../Vars/Vars";
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// Functions from loading molecules directly from a 3Dmol.js instance. See
// VRML.ts for additional functions related to the mesh itself.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// An module to manage VRML data obtained from 3Dmol.js. Assumes the 3Dmol.js
// javascript file is already loaded.
......@@ -92,7 +95,7 @@ export function resetAll(): void {
// whole thing.
viewer = null;
setup(() => {
viewer.addModel(molTxt, "pdb");
viewer.addModel(molTxt, "pdb", {"keepH": true});
});
}
......@@ -124,7 +127,7 @@ export function loadPDBURL(url: string, callBack: any): void {
molTxtType = "sdf";
}
const mdl = viewer.addModel(data, molTxtType);
const mdl = viewer.addModel(data, molTxtType, {"keepH": true});
callBack(mdl);
},
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// import { groundPointBelowCamera } from "../../Navigation/Points";
// import * as VRML from "./VRML";
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// Functions to create a protein visualization using 3DMol.js
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
import * as Optimizations from "../Scene/Optimizations";
import * as Menu3D from "../UI/Menu3D/Menu3D";
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// Functions to handle molecule shadows.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// This module handles all things navigation related.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// This module includes functions to manage which meshes in the scene are
// pickable.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// This module has functions for storing various important points in the
// scene. Note that the camera location is in CommonCamera, not here.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// VOICE COMMANDS CURRENTLY DEPRECIATED. BUT PERHAPS IN A FUTURE RELEASE, SO
// I'M GOING TO LEAVE THIS VESTIGIAL CODE HERE...
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
import * as CamerasSetup from "../Cameras/Setup";
import * as VRCamera from "../Cameras/VRCamera";
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
import * as MolShadows from "../Mols/MolShadows";
import * as Vars from "../Vars/Vars";
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// Functions to display messages in the VR world. To make debugging easier on
// devices like Oculus Go.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
import * as Vars from "../Vars/Vars";
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
import * as Pickables from "../../Navigation/Pickables";
import * as Vars from "../../Vars/Vars";
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
import * as CommonCamera from "../../Cameras/CommonCamera";
import * as VRPoints from "../../Navigation/Points";
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
import * as PositionInScene from "../../Mols/3DMol/PositionInScene";
import * as VRML from "../../Mols/3DMol/VRML";
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
import * as ThreeDMol from "../../Mols/3DMol/ThreeDMol";
import * as VisStyles from "../../Mols/3DMol/VisStyles";
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
declare var jQuery: any;
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
(function(context) {
// Get the URL for following.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
(function(context) {
// Determine whether warning should be displayed. Do this fast.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// Sets up tweaks to the UI.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
import * as ThreeDMol from "../Mols/3DMol/ThreeDMol";
import * as VisStyles from "../Mols/3DMol/VisStyles";
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// A place to put variables that need to be accessed from multiple places.
// This module is a place to store "global" variables.
......@@ -19,7 +22,7 @@ export interface IVRSetup {
menuActive?: boolean;
}
export const VERSION = "1.0.0";
export const VERSION = "1.0.1";
export let canvas: any;
export let engine: any;
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// Functions for leader mode, that the leader (lecturer) uses.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// Functions for leader mode, that the follower (student) uses.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
// Functions that are common to the main classes of Lecturer.ts and
// Student.ts.
......
// Copyright 2019 Jacob D. Durrant
// This file is part of ProteinVR, released under the 3-Clause BSD License.
// See LICENSE.md or go to https://opensource.org/licenses/BSD-3-Clause for
// full details. Copyright 2019 Jacob D. Durrant.
import * as LoadAndSetup from "./components/Scene/LoadAndSetup";
import 'bootstrap';
......
......@@ -39,6 +39,14 @@ mv t service-worker.js
cd -
# Add the license to the top of the app..js file. Tries using @license, but
# closure compiler didn't put it right at the top.
cd dist
echo "/**" > t; cat ../LICENSE.md | grep -v "\=\=\=\=" | sed "s/The 3-Clause BSD License/ProteinVR (The 3-Clause BSD License)/g" | awk '{print " * " $0}' >> t; echo " */" >> t
ls app*.js | awk '{print "cat t > t2; cat " $1 " >> t2; mv t2 " $1}' | bash
rm t
cd -
# All babylon files should use jpg, not png. It downloads faster for phones.
# So note that transparent textures aren't allowed. Also, ImageMagik must be
# installed to make this part work.
......
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