oedepict flattens molecules

[bannanc]

@cbayly13 pointed out an internal issue with oedepict today. When it is used to depict a molecule it flattens it. So the coordinates are lost.

This is used in a few places in this repository:
SmartsDepict.py
substructRemove.py
smiAmberize.py
oebHasAmberParams.py
oebToAmberMol2TopCrd.py
smartsDepict.ipynb
substrucDepict.ipynb

Instead a copy of the molecule should be used for the depiction, for example:

def depict(input_mol):
   mol = OEGraphMol(input_mol)

[bannanc]

There is a follow up on this very old issue. Today I tried changing the depictMatch method in substrucDepict.ipynb

I tried changing the first line from

def depictMatch(mol, match, width=500, height = 200):
...

to

def depictMatch(input_mol, match, width=500, height=200):
mol = oechem.OEGraphMol(input_mol) 
....

After doing this the 2D depiction didn't show the color change on the molecule anymore, I think this has something to do with the match being for the origin molecule instead of the copy.

I don't think this is serious right now because all of these scripts are targeted at depicting molecules so we're not trying to access the 3D coordinates after depicting it.