I have more than 100 ligand molecules. The image I showed at the beginning of
this discussion was only an example. It had missing atoms.
See it without missing any atom in the pdb format (coordinates in Angstrom
unit):
ATOM 1 O1 LIG 1 46.050 50.290 26.860
ATOM
The center of mass of the whole ligand that I calculated is the center of
geometry (the average/mean atomic positions) from the sample input file
provided. I don't take other things into account, such as knowledge of the mass
of each atom and so on. The difference between the center of mass and
Yes, I wrote: "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." It was just an example. In fact, I don't know which atoms belong
to each half. The code should do it of course.
That is, I gav
Dear Gregory Ewing,
As I said before, I need to divide the molecule into two parts but don't know
how to do it? It seems that I need to choose/determine a plane in 3D space
which cuts the molecule in two parts. As John Ladasky suggested, I need to
describe the criteria that cut needs to satisfy
@jladasky and @Gregory:
Thanks your replies.
The code should do the steps below:
1) Calculate the center of mass (COM) of the whole ligand molecule with the
atomic coordinates (x,y,z)
2) Find the ligand heavy atom closest to the COM of the whole ligand molecule
3) Divide the ligand molecule int
@Cameron:
Thanks, I will try what you suggest. I am not sure that I'll tackle it because
I am new to python.
--
https://mail.python.org/mailman/listinfo/python-list
@Gary:
No, I don't have any algorithm. Well, I can define what I want:
1) The script will read the atom coordinates of the ligand from the input file
sent in previous message.
2) It will calculate the center of mass (COM) for all the ligand atoms and find
the ligand heavy atom closest to its COM
Hi,
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.
