As a disclaimer, I'm an amazingly poor excuse for a chemist. In this
case, I'm simply a programming resource in a research project so
please forgive any amateur mistakes or abuses of terminology. The
project is being done in Python using pybel.
As part of our process, we will be doing a scf calculation in NWChem
of both a metal ligand complex and the host portion (the ligand in
this case). I'm getting a file with the guest metal and another file
with a series of metal ligand complexes, but I am not provided the
host portion directly. The goal is to extract the metal portion from
the complex and then generate NWChem input files.
For example, I might have RhCl3 as the metal and C9H21Cl3N3Rh as the
complex. I'm reading those two out of .xyz files so I have coordinate
data as well. I would like to end up with C9H21N3. Assuming that the
ligand might also contain Cl, it's probably not sufficient to just
randomly remove a couple Cl and a Rh. My somewhat naive approach was
to find atoms that shared both atomic number and coordinates. Is that
an accurate approach?
When doing that, I discovered that the coordinates of the data read in
from file would change when I made a copy of the molecule. I need to
hold onto the complex as well as extract/calculate the host so I
copied the molecule first by doing something like copy_of_complex =
pybel.Molecule(complex_molecule). I then iterated over the guest
atoms and removed the matching atoms in the copy of the complex.
Because the coordinates of the copy did not match what I read in from
the file, it couldn't find the matching atoms. Done against the
original metal ligand complex read from file, it found matching atoms.
In the example code/output below, note that the coordinates of the
copy are different for the first atom.
Is this occurring because openbabel is storing the coordinates in
floating point numbers instead of "decimal" style numbers? If I
remember correctly from looking at the API earlier, they are stored as
doubles. Any way around this? Or is this unexpected behavior?
Also, is my entire approach flawed? Should I be trying to split the
complex prior to loading it into openbabel? Should I be reading the
complex in twice as it seems to be consistent on read? Is there a
better method available in openbabel to accomplish this?
Finally, one other oddity I've noticed. Even when removing the atoms
from the original complex, the formula attribute of the pybel molecule
does not update even tthough the atoms are indeed gone. I'm removing
them using complex_molecule.OBMol.DeleteAtom(atom_from_complex_to_remove,
True). In the output below, note that the formula does not change,
but the number of atoms show that 4 have been removed (as expected).
Thanks in advance for any insights you can provide,
Greg Fortune
--------------
Code
--------------
import pybel
def molecule_diff(minuend, subtrahend):
for sub_atom in subtrahend.atoms:
for min_atom in minuend.atoms:
if(sub_atom.atomicnum == min_atom.atomicnum and
sub_atom.coords == min_atom.coords):
t = minuend.OBMol.DeleteAtom(min_atom.OBAtom, True)
def print_atom(atom, indent='\t'):
print(indent + '%s: %s'% (pybel.ob.etab.GetSymbol(atom.atomicnum),
str(atom.coords)))
guest = [mol for mol in pybel.readfile('xyz', 'guest.xyz')][0]
comp = [mol for mol in pybel.readfile('xyz', 'amine.xyz')][0]
host = pybel.Molecule(comp)
print('guest: ' + guest.formula)
print_atom(guest.atoms[0], '')
print('complex: ' + comp.formula)
print_atom(comp.atoms[0], '')
print('host: ' + host.formula)
print_atom(host.atoms[0], '')
molecule_diff(comp, guest)
print(comp.formula) #This should give back the formula without RhCl3,
but it gives the full formula of the original complex
print(len(comp.atoms)) #The original total is 37 atoms so 33 makes
sense assuming we removed the 4 atoms from the guest.
--------------
Output
--------------
guest: Cl3Rh
Rh: (0.06029, -2.22815, 0.03786)
complex: C9H21Cl3N3Rh
Rh: (0.06029, -2.22815, 0.03786)
host: C9H21Cl3N3Rh
Rh: (0.0603, -2.2281, 0.0379)
C9H21Cl3N3Rh
33
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