Calculate center of geometry

[ghutchis]

A lot of interaction needs to calculate the center of a set of selected atoms or the molecule as a whole.

We need a few methods added to the molecule classes:

• centerOfGeometry() - calculate the center of the molecule or a set of selected atoms
• centerOfMass() - calculate the mass-weighted center of the molecule or set of selected atoms
• radius() - calculate the approximate radius of a sphere surrounding the molecule (e.g., square root of the distance between the furthest atom and the center of geometry)
• bestFitPlane() - use Eigen to calculate the normal to the plane of best fit

[HeyAEE]

I would like to work on this as my first issue.

[ghutchis]

Great - you'll want to start with core/molecule.* and look at the mass() and formula() methods and add similar methods that loop through the atoms.

[HeyAEE]

That sounds good. I'm sort of struggling to compile it on Windows. Would it be preferable to run on Linux?

…

On Thu, Mar 15, 2018 at 11:20 AM, Geoff Hutchison ***@***.***> wrote: Great - you'll want to start with core/molecule.* and look at the mass() and formula() methods and add similar methods that loop through the atoms. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#223 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB3HysISkZlqCelOEkViRV8MVp8S1aLpks5terDRgaJpZM4Srbd6> .

-- *Adam Even Engel, M.A.T.* *Lab2Class Fellow* *101 Advisor and Science Specialist* *Highline Big Picture High School* "Science is organized knowledge. Wisdom is organized life." -Immanuel Kant

[cryos]

It should work on Windows, but Windows is often a little more difficult. Happy to help out if you want to get in touch, Linux and macOS should also work fine.

[HeyAEE]

That would be great, Marcus. Can you message me through Github? Alternately, can you see my email?

…

On Sun, Mar 18, 2018 at 7:20 PM, Marcus D. Hanwell ***@***.*** > wrote: It should work on Windows, but Windows is often a little more difficult. Happy to help out if you want to get in touch, Linux and macOS should also work fine. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#223 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB3Hyjsqt79V_WE5BVwSN2hCWRn48RCyks5tfxYGgaJpZM4Srbd6> .

-- *Adam Even Engel, M.A.T.* *Lab2Class Fellow* *101 Advisor and Science Specialist* *Highline Big Picture High School* "Science is organized knowledge. Wisdom is organized life." -Immanuel Kant

[0xrushi]

Is this solved ? i would like to work on this

[ghutchis]

@rushic24 - no, this has not been completed. If you'd like to do it, that would be great.

[0xrushi]

what does Array m_atomicNumbers; contain ? could you give an example say c6h6 or something else

[vsomnath]

Is this task complete? I couldn't find any PR raised.
Also, @rushic24: I think m_atomicNumbers contains the atomic_numbers of each atom in the molecule. This can be seen from:

inline bool Molecule::setAtomicNumbers(const Core::Array<unsigned char>& nums)
{
  if (nums.size() == atomCount()) {
    m_atomicNumbers = nums;
    return true;
  }
  return false;
}

[ghutchis]

This task is not complete, no.

[dvermd]

I partially implemented the requested methods. I don't know how to compute bestFitPlane. Can you give me some hints ?

[ghutchis]

There are a few links on how to do this with eigen, e.g.
https://stackoverflow.com/a/39374496/131896
https://stackoverflow.com/q/40589802/131896

I'd particularly look at the last link. Ideally, the method should allow passing a set of atoms / points (e.g. find the best fit plane for the selected atoms).