-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
get biojs-sniper snippets working again
- Loading branch information
Showing
15 changed files
with
216 additions
and
193 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,15 +1,6 @@ | ||
| #!/bin/bash | ||
|
|
||
| set -e | ||
| grunt | ||
| RELEASE_VERSION=`git tag | tail -n 1` | ||
| DIR="pv-$RELEASE_VERSION" | ||
| echo $DIR | ||
| rm -rf $DIR | ||
| mkdir $DIR | ||
| cp js/pv.dbg.js $DIR/pv-$RELEASE_VERSION.dbg.js | ||
| cp js/pv.rel.js $DIR/pv-$RELEASE_VERSION.rel.js | ||
| cp js/pv.min.js $DIR/pv-$RELEASE_VERSION.min.js | ||
| cp LICENSE.txt $DIR | ||
| rm -rf $DIR.zip | ||
| zip -r $DIR.zip $DIR | ||
| env | ||
| cp js/pv.dbg.js pv.js | ||
| python scripts/mangle-private-identifiers.py js/pv.min.js pv.min.js |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,64 +1,74 @@ | ||
| var app = require("bio-pv"); | ||
| var pv = app.Viewer(document.getElementById('gl'), | ||
| var viewer = pv.Viewer(document.getElementById('gl'), | ||
| { quality : 'high', width: 'auto', height : 'auto', | ||
| antialias : true, outline : true}); | ||
|
|
||
| var structure; | ||
|
|
||
| function lines() { | ||
| pv.clear(); | ||
| pv.lines('structure', structure); | ||
| viewer.clear(); | ||
| viewer.lines('structure', structure); | ||
| } | ||
|
|
||
| function cartoon() { | ||
| pv.clear(); | ||
| pv.cartoon('structure', structure, { color: color.ssSuccession() }); | ||
| viewer.clear(); | ||
| viewer.cartoon('structure', structure, { color: color.ssSuccession() }); | ||
| } | ||
|
|
||
| function lineTrace() { | ||
| pv.clear(); | ||
| pv.lineTrace('structure', structure); | ||
| viewer.clear(); | ||
| viewer.lineTrace('structure', structure); | ||
| } | ||
|
|
||
| function sline() { | ||
| pv.clear(); | ||
| pv.sline('structure', structure); | ||
| viewer.clear(); | ||
| viewer.sline('structure', structure); | ||
| } | ||
|
|
||
| function tube() { | ||
| pv.clear(); | ||
| pv.tube('structure', structure); | ||
| viewer.clear(); | ||
| viewer.tube('structure', structure); | ||
| } | ||
|
|
||
| function trace() { | ||
| pv.clear(); | ||
| pv.trace('structure', structure); | ||
| viewer.clear(); | ||
| viewer.trace('structure', structure); | ||
| } | ||
|
|
||
| function preset() { | ||
| pv.clear(); | ||
| viewer.clear(); | ||
| var ligand = structure.select({rnames : ['RVP', 'SAH']}); | ||
| pv.ballsAndSticks('ligand', ligand); | ||
| pv.cartoon('protein', structure); | ||
| viewer.ballsAndSticks('ligand', ligand); | ||
| viewer.cartoon('protein', structure); | ||
| } | ||
| function load(pdb_id) { | ||
| document.getElementById('status').innerHTML ='loading '+pdb_id; | ||
| var xhr = new XMLHttpRequest(); | ||
| xhr.open('GET', '../pdbs/'+pdb_id+'.pdb'); | ||
| xhr.setRequestHeader('Content-type', 'application/x-pdb'); | ||
| xhr.onreadystatechange = function() { | ||
| if (xhr.readyState == 4) { | ||
| structure = io.pdb(xhr.responseText); | ||
| preset(); | ||
| pv.centerOn(structure); | ||
| } | ||
| document.getElementById('status').innerHTML = ''; | ||
| } | ||
| xhr.send(); | ||
| } | ||
| function transferase() { | ||
| load('1r6a'); | ||
|
|
||
| function loadTransferase() { | ||
| document.getElementById('status').innerHTML ='loading transferase'; | ||
| pv.io.fetchPdb('../pdbs/1r6a.pdb', function(molecule) { | ||
| structure = molecule; | ||
| preset(); | ||
| // set camera orientation to pre-determined rotation, zoom and | ||
| // center values that are optimal for this very molecule | ||
| var rotation = [ | ||
| 0.1728139370679855, 0.1443438231945038, 0.974320650100708, | ||
| 0.0990324765443802, 0.9816440939903259, -0.162993982434272, | ||
| -0.9799638390541077, 0.1246569454669952, 0.155347332358360 | ||
| ]; | ||
| var center = [6.514, -45.571, 2.929]; | ||
| viewer.setCamera(rotation, center, 73); | ||
| document.getElementById('status').innerHTML = ' '; | ||
| }); | ||
| } | ||
|
|
||
| document.getElementById('cartoon').onclick = cartoon; | ||
| document.getElementById('line-trace').onclick = lineTrace; | ||
| document.getElementById('preset').onclick = preset; | ||
| document.getElementById('lines').onclick = lines; | ||
| document.getElementById('trace').onclick = trace; | ||
| document.getElementById('sline').onclick = sline; | ||
| document.getElementById('tube').onclick = tube; | ||
|
|
||
| window.onresize = function(event) { | ||
| pv.fitParent(); | ||
| viewer.fitParent(); | ||
| } | ||
| document.addEventListener('DOMContentLoaded', transferase); | ||
|
|
||
| viewer.on('viewerReady', loadTransferase); |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.