Sunset Lake Software - Comments for "A few very useful features"

Brad Larson wrote:As far as

Brad Larson wrote:

As far as the inertia-based rotation, I think what you're looking for is if you flick the display you want the molecule to spin for a short duration after the flick, with the degree of rotation determined by the speed of the flick. This would be similar to the scrolling effect of the lists on the iPhone. Right now, rotation is determined by the instantaneous differences in position of your finger as it moves across the screen. To implement this suggestion, I'd need to differentiate between a slow and fast moving gesture, as well as one that stops before the finger is picked up or one where the finger leaves the surface as it is still moving. Then, I'd need to add a timing routine that moves the molecule at a set rotational velocity determined by the flick speed, and decelerating for a set period of time. This timing routine would need to be interruptible in case you wanted to stop the rotation before it was finished and move it a different direction.

I need this. Exactly this. For another model/app in development.

Appreciate tips and points toward this direction. Or... if anyone would like to develop this behavior for me, give a holler.

steve at madmadmad dot com

Adding small molecule

Adding small molecule database support is one of the new features I have planned for the next couple of versions. I just need to settle on which databases to use and then implement the various file formats needed. Also, I'll be tweaking the rendering to provide better quality views of these small molecules (more faces on the spheres, etc.).

I'm just a little behind schedule with my other application, so that's taken priority lately.

I love this app, but... I

I love this app, but... I know this app is aimed at a specific group, but is there a way to find simpler molecules? i.e. Water, Carbon Dioxide, Ammonia etc. rather than macromolecules. As a biochemical engineering student I can definitely appreciate the time and effort taken to produce these complex macromolecules, but Having access to simpler molecules could be integral to seeing how those simple molecules function in the macromolecules.
Thank you for your consideration.

Are there any "simple molecules" databases to download from?

Accelerometer to pan around...

The user interface I'm imagining would allow one to position the molecule using the current touch gestures. Once that was done, the accelerometer would then allow Molecules to hold the model in the same "virtual" orientation while the iPhone moved around.

For example, imagine an iPhone lying on a table with the DNA model oriented (using existing touch gestures) with the axis of the helix sticking up vertically out of the table. Now lift the top of the iPhone to tilt the screen up 45 degrees from the table; could Molecules use the accelerometer to dynamically reorient the DNA model so that the helix' axis continued to stick straight up from the table even though the iPhone changed position? Using the accelerometer in this way would, I think, make the model seem somewhat independent of the iPhone and thus a bit more "real".

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kgutwin wrote:

Christoph wrote:

It's not inertia really, it's simple detection of orientation of the device relative to the gravity field, AFAIK. But I agree, a potentially complex app like Molecules needs to take advantage of all features of the iPhone to remain simple to use. I imagine translation of the displayed object could be dependent on how you hold the device, i.e. letting the molecule "slide" across the screen under the influence of gravity. Maybe this needs a "button" for activation to control when we want it and when not.

Maybe we're thinking of different things :) I'm not talking about any accelerometer-based effect; instead, when you swipe your finger, the molecule keeps spinning for a bit. Like how when you scroll a list, it'll keep scrolling, gradually slowing down.

But the accelerometer would add a unique twist to this app... You mentioned translation -- I think rotation might be more interesting. Kind of like the iPhone was a window into a virtual world, you imagine the iPhone being on the surface of a virtual sphere, and rotation of the phone in the gravitational field moves the camera on that sphere appropriately. Then, if you wanted to look at the top of the molecule, you would hold the phone flat and look down; if you wanted to look at the bottom, you would hold the phone over your head and look up :)

Like many iPhone developers, I thought the accelerometer was really cool and wanted to use it as an input method. Unfortunately, I tried it and it doesn't work too well in practice for this kind of application. It just doesn't provide you the same sort of precise control over rotation that a direct touch does. Besides, you'd have to hold the device perfectly flat in order to maintain a specific view angle on the molecule or do weird contortions to look at it from different angles.

That said, maybe rotating the view on a switch to landscape might have some advantages. I'll take a look at it.

It's doable, but It'd take a bit of time, so I don't think it will be a high priority until I've addressed the more important issues, like multiple data sources, ribbon visualization, overall performance, etc. Once you think about it, you start to appreciate all the stuff that Apple is doing under the hood for you in their control elements.

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jhoch wrote:

Also - many PDB files (e.g. NMR structures) contain more than one instance of the molecule. At present Molecules loads all of these and superimposes them. A way to select a single instance would be helpful. An example of the syntax used by some other applications is 1RW5:3

Yeah, this was one of those things that I discovered after I submitted the application. I had just been looking at the X-ray structures and forgot about the NMR ones. It's also a tricky UI problem. Where would you suggest the choice of alternate structures be presented to the user? I'm thinking that it could be under the detail view for the molecule as a "Currently visible structure" item that, when tapped, slides over to a list where you can pick the structure to show. I haven't looked, but are the different structures identified by anything other than number in the PDB format? If so, that could be used as the labels in that list.

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Will-WAC wrote:

This is a fantastic app; thanks! Ball and sticks is best for me too!

kgutwin wrote:

- Loading structures from personal files would be nice.

As a chemist this would be extremely useful. I am not so interested in proteins and would love to be able to somehow put normal molecules on there. I have no idea how the software works, and whether it makes a difference, but I am able to save them as a .pdb file, or any other 3D file.

The tricky part of this is getting the structures on the device. Apple did not provide a means of syncing data through the tether via iTunes like it has for all its applications (with the weird exception of Notes). This is why I went with the direct download via the PDB, as kludgy as it is right now, because the PDB is an always-on, network-accessible source.

However, a couple of developers have put out applications that use Bonjour and a local network to transfer data, one or two even making the device look like a network-attached drive. If I can figure out how to do that, then it should be possible to let users load custom structures. In the worst case it might require a client program on the user's computer to transfer the files, but I was planning on porting Molecules across to the Mac anyways (a little UI work is needed, but the core Cocoa code would stay the same), so this could just be another function of that port.

superimposed

jhoch wrote:

ohhh that's good, I thought it was just me. I tried openeing some calicheamicin thing and it had all 6 structures all displayed on top of one another. I hope that isn't too hard a problem to fix.

more features...

The ability to load structures that are not yet deposited in the PDB would be awesome - and structural biologists like myself would use it as a research tool.

This is a fantastic app;

This is a fantastic app; thanks! Ball and sticks is best for me too!

kgutwin wrote:

- Loading structures from personal files would be nice.