superpose: ReferenceError: NGL is not defined

[hainm]

(I am using code from ngl dev, just pulled)

        superpose: function(cindex0, cindex1, params){
           // superpose two components with given params (not yet)
           var component0 = this.stage.compList[cindex0];
           var component1 = this.stage.compList[cindex1];
           //component0.superpose(component1);
           console.log(component0.superpose);
           //NGL.useWorker = true;
           component0.superpose(component1);
           //NGL.useWorker = false;
        },

In console, I can see the function 'superpose' code but keep getting 'ReferenceError: NGL is not defined'.

Any idea how to fix it? thanks.

[arose]

can you try again, I made some fixes lately and just updated dist/ngl.js

[hainm]

got the same error with the newest commit: eda4864d1688c9d2eef93d16e0d9cb13414b44b1

[hainm]

just clean my cache and your commit works for me. I will double-check.

[hainm]

uhm, try again and still get the same error. Weird.

[hainm]

You can try this branch: https://github.com/arose/nglview/pull/396

[arose]

In console, I can see the function 'superpose' code but keep getting 'ReferenceError: NGL is not defined'.

In the error, can you see the code that throws it originally?

[hainm]

var C = e.getView(new NGL.Selection(r + " and .CA"))

(saw from minimized code)

[arose]

Thanks! Fixed a whole bunch of similar bugs 7d6d3c9e32b08c1d684e41eaec718f71ffbcddaf.

[hainm]

new error in here

Exception in Comm callback TypeError: Cannot read property 'getAtomSet' of undefined(…) TypeError: Cannot read property 'getAtomSet' of undefined

        getAtomSet: function(t, i) {
            e.Debug && Cu.time("StructureView.getAtomSet");
            var r = this.structure.getAtomSet(t);
            return !i && this.atomSet && (r = r.new_intersection(this.atomSet)),
            e.Debug && Cu.timeEnd("StructureView.getAtomSet"),
            r
        },

[arose]

This is odd, it suggests the StructureView has no parent structure?! Can you give some context. How are you calling this. Does the error only occurs with the superpose method?

[hainm]

Can you give some context. How are you calling this

        superpose: function(cindex0, cindex1){
           // superpose two components
           var component0 = this.stage.compList[cindex0];
           var component1 = this.stage.compList[cindex1];
           component0.superpose(component1);
        },

view._remote_call('superpose', target='Widget',
                 args=[0, 1])

Does the error only occurs with the superpose method?

Yes

[hainm]

This is the output from

c = this.stage.compList[0]

for (var i in c){
    console.log(i)
}

name
uuid
visible
signals
stage
viewer
reprList
structure
trajList
selection
structureView
defaultAssembly
constructor
type
initSelection
setSelection
setDefaultAssembly
rebuildRepresentations
rebuildTrajectories
addRepresentation
addTrajectory
removeTrajectory
dispose
centerView
getCenter
superpose
setVisibility
addBufferRepresentation
removeRepresentation
updateRepresentations
clearRepresentations
setStatus
setName
eachRepresentation
__getRepresentationComponent

[hainm]

very weird

If I wrote straight JS script, I can see the superposition. (Try to remove all cache to make sure I am using correct ngl.js file)

%%html

<script>
stage.setParameters({backgroundColor: 'white'})

stage.loadFile("./1crn.pdb", {defaultRepresentation: true})
stage.loadFile("./tz2.single.pdb", {defaultRepresentation: true})
</script>

%%html
<script>

var c0 = stage.compList[0];
var c1 = stage.compList[1];

</script>

%%html
<script>
    console.log(stage.compList)
    console.log(stage.compList[0])

    c0.superpose(c1)
</script>

[hainm]

In JS script mode

NGL.superpose(c0, c1)

TypeError: Object #

---

has no method 'getView'

BUT

c0.superpose(c1)

OK

[hainm]

LOL, weirder

If I specify

• c1.superpose(c0): work
• c0.superpose(c1): got error

[arose]

You must make sure that both molecules actually have finished loading, looking at your code, this could be the problem.

[hainm]

I only hit enter to run my code if I saw two structures.

[arose]

NGL.superpose(c0, c1)

that is not supposed to work, NGL.superpose expects Structure or StructureView objects.

[arose]

c0.superpose(c1): got error

this should definitely work

[arose]

I just did a new install from this repo and the following works for me:

import nglview
view = nglview.show_pdbid("3pqr")  # load "3pqr" from RCSB PDB and display viewer widget
view

view.add_structure(nglview.PdbIdStructure("1gzm"))

view._remote_call('superpose', target='Widget', args=[0, 1])

[hainm]

indeed. cache is evil. thanks.

[arose]

I am glad it is resolved, I was out of ideas. :-)