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WebGL accelerated JavaScript molecular graphics library

License: Other

JavaScript 9.25% CSS 0.21% Python 0.05% HTML 3.30% TeX 0.05% Jupyter Notebook 86.13% TypeScript 0.98% GLSL 0.03%

molecular-graphics molecular-modeling computational-biology computational-chemistry

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nrego armish sky1e mattragoza jlc206 racingtadpole souvik1997 khoama killsos kamladi prabhjotsl xtmgah victor-gil-sepulveda jstopchick jenny19880324 rschaeff kaulkie csera vasek111 geoffrowland yuhangwang sbliven mcanthony avirshup sunbc0120 medici hainm onursumer adamskiredj athemis cs76 yxngl joeskinov alejandrogallo yaoxiaoge jturney zhou5852 cihankayacihan silky manohar-94 helblazer811 bennyyu686 mammmals dllahr galnova justinmc sillitoe bjodah tslmy dolittle007 gaoktp corefan mkhorton malithakabir lirenfish wsl1107073609 foowhiz irista56 bas164 johan-westin-work yfyh2013 redgene m-vaishnavi crane-may chemphy sbrudz ewail haoziyeung cjh1 openchemistry aspirincode thaneacheron mengwuxiao xtylovesyj cienciascontic mofplus qcgm1978 andytengca drc007 k7s3 arpit-24 addictedcoder0 pablowatson gravitypersists xiaofeihui bassemhermina jinyoungan85 fongchun dgasmith mori0711 klklklzzd xiaohong23 matuskalas rowbottomn c4pt000 naveen584 jalees-jahanzaib jamesmkrieger bistaastha laura-lc

3dmol.js's Issues

Background Alpha Not Working

The alpha value doesn't change the background color with setBackgroundColor. I am trying to make the viewer completely transparent but it doesn't seem to change regardless of the alpha value. The color does change but not the transparency.

viewer.setBackgroundColor(0x0d0ddd, 0);
viewer.render();

Is there an option to set the alpha value through a data attribute?

data-surface in embeded changes nothing(test7)

Events

Does the viewer fire events when rotating, translating and zooming the model?
I don't see events in the docs.
http://3dmol.csb.pitt.edu/doc/$3Dmol.GLViewer.html

Support expand and within selector keywords

These can be used to efficiently expand a provided solution to all atoms within a specified distance. Expand is basic expansion. Within takes a selection object and distance and then the result can be combined with the rest of a selection object. Will work nicely with byres.

Matt is working on this.

addIsoSurface framework opacity doesn't work

viewer.addIsosurface(voldata, {isoval: -0.01, color: "red", alpha: 0.95, smoothness: 5,
opacity:1.0, wireframe:true,linewidth:0.1,clickable:true, callback:
function() {
this.opacity = 1.;
viewer.render();
}});

Problem reading mmCIF file

I've read in some old issues that mmCIF support is implemented already into 3dmol.js. Is that right?

I wanted to try a very simple case with a file downloaded straight from the PDB (PDB id 1smt). This is what I do:

<html>

<head>
 <script src="http://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script> 
</head>

<div style="height: 800px; width: 800px; position: relative;" class='viewer_3Dmoljs' data-href='1smt.cif'>
</div>

</html>

I only get an empty page and this in the js console:

Uncaught TypeError: Cannot read property 'id' of undefined (3Dmol-min.js:529)

I've also tried removing all headers from the mmCIF file and keeping only the _atom_site lines, but the error is the same. Also if I specify the file format as data-type='cif' the error is the same.

Any ideas what am I doing wrong?

Thanks by the way for such a great piece of software :)

Crystal support?

Hi,

I was recently forwarded a link to this project - it looks great! I work with crystals, and I was wondering if there are any plans to support unit cell drawing or CIF unpacking.

If this isn't on the priority list, I could try implementing it myself and sending over a PR (likely on an upcoming slow Sunday). Let me know either way!

improve support for multi-model file formats

eg. 1MO7 and 1MO8 from pdb

provide support for integrating with javascript openbabel

http://baoilleach.blogspot.co.uk/2015/02/cheminformaticsjs-open-babel.html

Noel is a crazy guy.

Add GLViewer.addLine()

I'd like to draw a line between two atoms.

I'm currently using viewer.addCylinder, with a radius of 0.05.

I'd like to have a command like addLine (perhaps even allowing dotted lines...?).

Implement efficient display of symmetric assemblies

As long as we don't mind applying exactly the same style to each subunit, this can be done very efficiently by just applying a transformation matrix. Probably would be nice to have an API that let the user turn the implicit assembly into an explicit model too.

add built-in gzip support

Probably with pako

addIsoSurface callback doesn't work

support pse format

pse is just a pickled format, but in binary. Here's a library for text pickle:
https://github.com/lalanotlistening/pickle-js
Couldn't find a binary unpickler.

jquery dependency

It seems that jquery is used only in few places to load pdf from a server and read data attributes.
Will you consider removing the jquery dependency and use plain javascript?

I also think that 3Dmol is easier to remember than $3Dmol for the API.

enable spectrum coloring for all styles

probably implement this by interpreting spectrum is a property map of the resi with a gradient from the smallest to largest resi in the selection

support for mmCIF

http://www.ebi.ac.uk/pdbe/docs/documentation/mmcif.html

rna cartoon rendering broken

1J5E for example

expand has questionable behavior

http://3dmol.csb.pitt.edu/viewer.html?pdb=1eqg&style=cartoon&select=resn:IBP;expand:20&addstyle=stick:colorscheme~greenCarbon

expand value needs to be wrapped in parseInt.

The box expansion does not seem to have the selection in the middle.

documentation has broken links to shape specs

Hi - I'm sure you know this, but just in case...

doc/$3Dmol.GLViewer.html (eg. on http://3dmol.csb.pitt.edu/doc/$3Dmol.GLViewer.html ) has links like: <a href="SphereSpec.html">SphereSpec</a> and similarly for ArrowSpec and ShapeSpec - but there is no SphereSpec.html file.

Offer CDN usage through JSDelivr

http://www.jsdelivr.com is a free versioned CDN for GitHub hosted (and other) JS libraries, CSS, etc. To add resources, you create a pull request at GitHub and ideally add an update.json file, e.g.

{
"packageManager": "github",
"name": "morris.js",
"repo": "morrisjs/morris.js",
"files": {
"include": ["morris.css", "morris.js", "morris.min.js"]
}
}

At that point, when 3Dmol.js releases are tagged on GitHub, JSDelivr will auto-update.

It seems natural to offer releases of 3Dmol.js through the service for distributed world-wide use.

addsurface adds only part of the surface

test 19
viewer.addSurface($3Dmol.SurfaceType.VDW, {opacity:0.85, colorscheme:'greenCarbon'},{chain:'D'});

Build instructions

Can you please add build instructions and dependencies to the README and docs?
Java, node, npm, grunt...
https://github.com/dkoes/3Dmol.js/blob/master/README.md
http://3dmol.csb.pitt.edu/doc/index.html

Thanks

Different display with Mol2 and SDF

When we use 3DMol for the same file in either Mol2 or SDF format, we see two very different geometries. Also, with Mol2 files, hydrogens aren't shown, but they are with SDF.
https://gist.github.com/ghutchis/4243c0242423770d58a3

Is it possible to make showing explicit hydrogens a setting (i.e., so it can be the default for us even with Mol2 files)?
Why is the geometry so different with Mol2 - the Cartesian coordinates are the same and Open Babel generates the same InChI as far as I can tell..

can't change color of other parts after specity it to spectrum

test12
viewer.setStyle({chain:'A'},{cartoon:{color:'spectrum'}});
viewer.setStyle({chain:'C'},{cartoon:{color:'red'}});

//all the chains are of color spectrum

drawCustom has limitation on size of mesh

since webgl is limited to 2^16.. I have the code to breakup big meshes, just have to port it over..

support imposters

As far as I can tell, no browsers properly support gl_fragdepth at the moment, although some lie about it. But once they do..

embeded 'data-style='cross:radius=1.0' doesn't work while data-style='{"cross":{"radius":1.0}} works

test4

Accelerate rendering with ANGLE_instanced_arrays

Most browsers seem to support this. Should be useful for accelerating spheres and possibly cylinders, but requires a revamp of the rendering code..

Integrate with JSmol for file parsing

Use JSmol as a subcomponent to translate different file types.

Support for PaperChain / Twister carbohydrate cartoons

VMD has support for "PaperChain" and "Twister" cartoons for carbohydrates:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158682/#!po=53.7037

Can't use MOL2 files with embedded JS element

There is no tag to add to the embedded js viewer to use a MOL2 file to display the molecule. This functionality exists in the online, URL controlled version.

add an outlining render mode

Similar to ray_trace_mode=1 in pymol. Some people who are not me like this...

need better documentation of shapes

define and support json format

this should be trivial.. basically just documentation and not dumping unnecessary stuff

support for multiple cartoon formats

edged (current), oval (jmol/pymol), flat, basic (cylinders for helices)
also thickness and height
nucliec sticks

Hexadecimal color codes not working

From some commits to now, it seems that hexadecimal color codes are not working anymore when using them in selections:

<html>

<head>
<script src="http://3Dmol.csb.pitt.edu/build/3Dmol.js"></script>
</head>

<div style="height: 800px; width: 800px; position: relative;" class='viewer_3Dmoljs' 
 data-href='1smt.pdb' 
 data-backgroundcolor='0xffffff'
 data-select1='chain:A' data-style1='cartoon:color=0x00ff00'  
 data-select2='chain:B' data-style2='cartoon:color=0x00ffff'
> 
</div>

</html>

What I get now is both chains colored in black, whilst that kind of thing used to work a few commits ago. If I specify color strings like 'red' or 'cyan' everything works fine.

addStyle behavior

addStyle seems to add style to the invert of the selection, not the selection itself

Spectrum coloring based on b-factors

If I understand it, the current spectrum coloring will color things based on residue or atom indices. For instance I can see that applying spectrum on a chain, I get an n-terminal to c-terminal spectrum.

It would be really cool to have the pymol-like feature, where spectrum can use the b-factors for the coloring. In fact the spectrum command in pymol can do quite a lot of things, all of those could be really useful.

Another very nice feature would be that spectrum worked also in surface representation (it looks like that's already in issue #79 ). Spectrum on b-factors (temperature factors or whatever property is actually written in the b-factors column) is especially useful in surface representation.

support for Gaussian fchk file

gzipped even
Format specification:
http://www.gaussian.com/g_tech/g_ur/f_formchk.htm

Will most certainly have read jmol code to understand how to interpret this quantum data.

Add support for X-ray density maps

Takanori has some really cool looking volume rendering. Adding simple meshes shouldn't be too hard.

Extract partial charges from Mol2 files

Most mol2 files include atomic partial charges. It would be awesome to use the potentials defined by the file rather than residue-based charges, e.g.:

  1 O          -3.9862   -0.0915   -0.4753 O.2     1  UNL11111   -0.4322
  2 C          -3.1086   -0.7606    0.0104 C.2     1  UNL11111    0.3255
  3 C          -1.9542   -0.0724    0.7328 C.3     1  UNL11111   -0.0217
  4 H          -2.0091   -0.2416    1.8344 H       1  UNL11111    0.1622
  5 O          -2.0231    1.3296    0.5822 O.3     1  UNL11111   -0.5655

The last column is always the partial charge. Open Babel's parser looks like this:

   sscanf(buffer," %*s %1024s %lf %lf %lf %1024s %d %1024s %lf",
           atmid, &x,&y,&z, temp_type, &resnum, resname, &pcharge);

This would imply that there's always(?) a token[8] entry with the floating-point partial charge.