Dear PyMOL-ers,
I have just started dabbling in the chempy module, and I have a couple
of questions:
1. If I load in a molecule using the following code...
from chempy import io
from chempy import protein
m = io.pdb.fromFile("/tmp/x.pdb")
# Use the load_object call, specifying the type of object as a chempy
# model (index 8)
cmd.load_object(8,m,"protein")
...there are no bonds displayed. Is there a chempy call I can make on
the model object (m) to calculate covalent bonds?
2. I can happily iterate over, or select by index, atoms in a chempy
model, using either of the following
# Iterate over all atoms
for a in m.atom:
# do something
# Random access
a = m.atom[10]
Are there corresponding residue and atom arrays, or does chempy
represent these aggregates simply by the fields of the Atom object
(resn, resi, chain etc)? As far as I can see, the latter is true, but
like I said, so far I am only a dabbler.
I should mention why I'm doing this, in case anyone has a more elegant
solution. Basically I have a C++ library which handles molecules,
making selections, identifying h-bonds etc. I wanted a way to dump out
a molecule object from my library, and display it in PyMOL with all of
its associated selections and bonds. So basically what I do is:
1. Write out a PDB file for my molecule
2. Write out a short Python program which creates PyMOL selections
corresponding to my selections, by way of atom indices. Basically this
works by grabbing the 'nth' atom from the chempy model, then composing a
selection string which is passed to the cmd.select function. Missing
out some detail, here is the bare bones:
# Function 1: get a PyMOL selection string from a ChemPy atom
def atom_sel(a,obj_name):
return "/" + obj_name + "//" + a.chain + "/" + a.resi + "/" + a.name
# Function 2: create a PyMOL selection from an array of atom indices
def make_atom_sel(sel_name,array,model,obj_name):
sel_str = ""
for i in range(len(array)):
sel = atom_sel(model.atom[array[i]],obj_name)
sel_str += sel
if(i < len(array)-1):
sel_str += " or "
cmd.select(sel_name, sel_str)
# Similar functions exist for creating an h-bond between ith and jth
# atoms
So to put it all together, given these two functions, the program I
execute in order to reconstitute my molecule in PyMOL looks like
m = io.pdb.fromFile("/tmp/x.pdb")
cmd.load_object(8,m,"protein")
make_atom_sel("my_sel", [0,2,5,8,18,22], m, "protein")
Gareth
--
Gareth Stockwell <[email protected]>
European Bioinformatics Institute
