getting the center of mass of each part of a molecule
On 15May2017 13:29, qasimpars at gmail.com <qasimpars at gmail.com> wrote:
>I need to get the center of mass (COM) of each half of the ligand shown in the
>figure (https://i.stack.imgur.com/dtdul.png). I get the main COM all the
>ligand, lets say it is close to C1 atom. In addition to the main COM of all
>the ligand, I need to find the COM of each half of the ligand. The atoms of
>the first part/half according to the main COM of the ligand are C2, C7, C8 and
>C9. As for the second part they are C3, C4, C5 and C6 atoms. The question is
>how can I divide the ligand in two parts according to the main COM and
>calculate the COM of each divided part (except for the atom closest to the
>main COM, C1)? By the way I have multiple ligands. The code should be user
Leaving aside that you are using numpy arrays, if sources like you need to
partition an existing array into 2 parts around the dividing element (C1).
Figure out how to find the position of C1 in the array. If your atoms are
unique in the sense that C1 != C2 even if they are both carbon atoms) you could
use the .index method of a list (hoping numpy array support that). But
otherwise, loop over the array until you find the element C1 and return the
index. Write a short function for this purpose, eg (incomplete):
def find_atom(atom, atoms):
for i, a in enumerate(atoms):
if a is the target atom "atom":
raise IndexError("no such atom")
Then all you need to do is:
- figure out _which_ atom is your "C1"
- locate it in the main array of atoms
- extract the left and half subarrays
For the last part, remember that to get a sublist you can write L[a:b] to get
all the elements of L from a up to but excluding b. And that omitting "a"
implies index 0 and omitting "b" implies len(L).
The homework suggestion that the "code should be user firendly" I would take to
imply that the last step should itself be a function, eg:
def partition_atoms(atom, atoms):
which takes your target atom (C1) and the original array, calls find_atom to
locate C1, and returns the left and right sublists.
Cameron Simpson <cs at zip.com.au>