On Apr 27, 2010, at 7:05 AM, Mauro Truglio wrote:
> Hi,
> I got to understand the syntax to edit and even create "new"
> chemical groups for chimera to select (I successfully edited the
> file __init__.py in ChemGroups). Now I'm facing this problem with
> aromatic amines: when selecting, for example, primary aromatic
> amine, I'd like to include also che C atom in the selection - not
> only N,H,H.
> With other chemical groups this was easy, thanks to the [1,1,1,0,1]-
> like notation. But these aromatic amines are described in a
> different way, through the function findAroAmines in miscFind.py,
> and I'm finding it difficult to edit it.
> Can you help me?
Hi Mauro,
Yes, it wasn't easy (or maybe even possible) to describe aromatic
amines (and a few other groups) using the notation used for most
groups -- they required a custom function. Nonetheless the change you
desire is pretty simple. In the part of the code that finds the
aromatic carbon attached to the nitrogen, also add the carbon to the
list of atoms included in the amine. So this code:
if bonded.element.number ==
ChemGroup.C:
boundCarbons = boundCarbons + 1
if bonded.idatmType == 'Car':
boundAro = True
continue
if bonded.idatmType == 'C3':
continue
becomes:
if bonded.element.number ==
ChemGroup.C:
boundCarbons = boundCarbons + 1
if bonded.idatmType == 'Car':
boundAro = True
amine.append(bonded)
continue
if bonded.idatmType == 'C3':
continue
If you want all the bonded carbons, not just the aromatic one, put a
similar line in the "if bonded.idatmType == 'C3':" conditional.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
P.S. Directed followups to chimera-dev, since this discussion is
pretty "programmery"
On Apr 26, 2010, at 3:36 AM, Elisabeth Ortega wrote:
> Dear all,
>
> I'm trying to place a fragment in certain position. I did this (on
> Python IDLE):
>
> from BuildStructure import placeFragment
>
> placeFragment( fragment, resName, model = 'scratch', position=None)
>
>
> Where fragment = benzene and resName = RING6 but I am not sure about
> that .
> Could you give me an example of placeFragment code?
Hi Elisabeth,
This will place a benzene ring at the center of the view in a new
residue named "BZN" in a new model named "scatch":
from BuildStructure import placeFragment
from BuildStructure.Fragment import RING6, fragDict
placeFragment(fragDict[RING6]["benzene"], "BZN")
Let me know if you have more questions. Though the placeFragment
function does have some documentation, the Fragment.py file doesn't.
Sorry about that.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
P.S. I cc'ed the chimera-dev mailing list on this since that list
deals more with programming questions.
