View source for 3D modeling

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This page is about software tools with the purpose of 3D modelling for atomically precise molecular system. <br>
Both ...
* near term nanoscale atomically precise systems and ...
* far term atomically precise systems reaching all the way up towards the macroscale.

This is about:
* Core glue software combining existing tools together (Framework). <br>
* Establishing and expanding a collection of mutually compatible software tools. <br>

One main goal here is to bring different types of structures together in the same workspace. <br>
Such that they can be worked on together in a beneficial way.

== Benefits ==

'''This can greatly aid in ...'''
* A) understanding what to aim at and ...
* B) understanding how to build it. And analyze it.
These two types of work are both boosted and are mutually synergistic.

Following in flipped order since a majority of people are <br>
working on the near term end of the spectrum.

'''Details to B)'''
* analysis of results of experiments were different things/structures have been put together
* planning of synthesis such that different things/structures will fit together
'''Details to A)'''
* determining what things/structures to synthesize in order to arrive at more advanced systems ASAP 
* determining the potential high value goals/targets

== Structures to bring together ==

* [[Structural DNA nanotechnology]]
* [[De-novo protein engineering]]
* [[Spiroligomers]]
* Design of [[transitionary structures]] like e.g. <br>[[highly polycyclic small molecule]]s, [[metal organic frameworks]], [[ceria]], [[biomineral]]s, ...
'''Still beyond experimental reach as of 2022:'''
* [[Design of crystolecules]]

=== Inclusion of structures that are not yet accessible through physical experiments ... ===

... but are accessible through reliable robust ([[molecular dynamics]]) simulation.

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This can be useful for guiding development efforts.'''See:'''
* [[Exploratory engineering]] for what can and what can't be predicted without direct & immediate physical experiments.
* [[Future-backward development]] – Backwards chaining from goals/targets

This kind of work only has to offer as product knowledge for directing R&D. <br>
As such it has little to no immediate economic value and is hard to fund. <br>
One possible way to get some of this done nonetheless may be [[gameification]] (as e.g. demonstrated in FoldIt). <br>
With the right interface the activity of building advanced namomachinery structures can maybe be made into a fun and enjoyable spare-time activity game.

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This can also provide excitement for young adults and motivation to go into a related field. <br>
In this regard noteworthy though is the [[risk of detrimental over-excitement]]. <br>
Emergence of a "fanboy/fangirl" culture nor clearly separating between 
* ideas serious proposed and by properly done low level [[exploratory engineering]] motivated and 
* ideas that are very much SciFi fantasies (like grey goo eating the whole biosphere in mere hours)
Can be more harming rather than helping.

== Existing Software (focus on open source SW tools - but not exclusive) ==

{{wikitodo|extend on these lists}}

'''Atomistic:'''
* Pymol – https://pymol.org – mostly viewing only
* Avogadro –  https://avogadro.cc/ 
* CADnano – https://cadnano.org/
* [[Rosetta]] – https://rosettacommons.org – closed source
* (FoldIt – https://fold.it/ – no actual modelling)
* [[NanoEngineer-1]]
* ...

'''Bulk limit:'''
* FreeCAD – Attempting to combine several other tools 
* [[OpenSCAD]] – programmatic denotative
* ...

== Modelling across a wide range of scales ==

Current software modelling tools are typically limited in the range of modellable scale <br>
due to usage of floating point numbers of limited range. <br>
It should be useful to lift that restriction.

For now while actual systems do not yet span many orders of magnitudes in size <br>
this is mostly useful only for far term concept visualizations. <br>
As technology will progress this will increasingly get relevant for physical experiments too.

While it may not seem urgent to solve now, if not solved early on then <br>
ugly/fragile/dangerous hacks & workarounds may creep all the way into advanced systems of the future. <br>
Not a nice prospect.

== Programming language as core ==

It's pretty much necessary as scrip-table glue. <br>
Going beyond just low performance scripting of huge high performance executed batch jobs seems quite desirable. <br>
More on that further down.

Popular suggestion for a language to use is the python programming language. <br>
A huge disadvantage (as with most of current mainstream languages) is <br>
the lack of (type level) guarantees on absence of side-effects <br>
(aka denotatveness, purity, immutable variables). <br>
More on that further below.

As of 2022 other quite revolutionary languages are juts still far from ready yet unfortunately. <br>
Content addressed programming language unison language.

=== Huge benefits of a denotative (aka purely functional) language ===

See: [[Relations of APM to purely functional programming]]

'''Just a few examples, in no way exhaustive:'''
* No errors due to wrong orderings of code lines, as it is common in imperative code.
* Easier debugging. No non-local bugs. Systematic narrowing down leads to finding the bug more reliably.
* Can serve as a basis for projectional editing which can open up huge slew of more benefits
* ...

== A Framework that is none ==

Having many standalone tools and only afterwards gluing them together is kind of a Frankenstein/Jengatower situation. <br>
The necessity of reuse of current tools mandates starting out with this kind of approach. But ... <br>

Ideally the chosen glue language is both powerful (read:fast) and expressive (read:readable) enough such, <br>
that it not only can serve as that (glue), but rather can also serve as basis for new "micro-tools". <br>

That is: Beside old very useful (but due to their size is some ways limited) <br>
monolithic batch processing monster software packages (like e.g. Rosetta) <bR>
sub-functionalities of new tools can be exposed much more fine-grainedly and user-friendly. <br>
Think e.g.: [[Tangible values (Conal Elliott)]] <br>
Think e.g.: No border between GUI applications. 

== Related ==

* [[Distorted visualization methods for convergent assembly]]
* [[Visualization methods for gemstone metamaterial factories]]
* [[Constructive solid geometry]]
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* [[Data decompression chain]]
* [[Design levels]]
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* [[Relations of APM to purely functional programming]]
* [[General software issues]]
* [[Programming languages]]

== External links ==

MSEP ... Molecular Systems Engineering Platform
* [https://www.youtube.com/watch?v=HjgjtAk-lws Youtube: 2022-10-29 – Foresight Institute – Eric Drexler | MSEP: What, Why, and How?]
Suggesting using Godot game engine as a core common base and adding python scripting glue.