On Feb 23, 2010, at 4:16 AM, Mauro Truglio wrote:
Hi,
I'm a newbie, and I'd like to use Chimera to recognize functional groups on a structure or a ligand, and I need it to write a file with the atoms involved. Now, if I do Select>Chemistry>functional group , search for one, and export the results through "write list", it exports a raw list of atoms without any specification of which atom is involved in which f.g..
It could be useful to add some sort of identifier, like:
FG1:
atom
atom
atom
FG2:
atom
atom
atom
How can I do that? Already tried to modify __init__.py in ChemGroups, but all I obtain is a list of physical addresses of atoms, e.g.:
Group number 1 :
[<_chimera.Atom object at 0xa455db8>, <_chimera.Atom object at 0xa455dd0>, <_chimera.Atom object at 0xa455de8>, <_chimera.Atom object at 0xa455e00>, <_chimera.Atom object at 0xa455e18>]
Group number 2 :
[<_chimera.Atom object at 0xa455e30>, <_chimera.Atom object at 0xa455e48>, <_chimera.Atom object at 0xa455e60>, <_chimera.Atom object at 0xa455e78>, <_chimera.Atom object at 0xa455e90>]
Oooh, you were so close! It's seems you're Python savvy, so here's what you need to know: printing a list of Atoms prints their repr()s -- you need to print their str()s. Assuming that your list of Atoms was in a variable called 'grp', then either:
for a in grp:
print a,
print
or:
print [str(a) for a in grp]
The latter will have surrounding brackets whereas the former won't. Let me know if you need more info than this.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab