Having methods to create standard bits of molecules would be great. I
think they are on the list I high level functionality I proposed some
time back :-)
That said, creating a single coordinate in PDB format is kind of an
odd end goal, and if you just want to do that, printf seems the right
way to go :-)
Without such methods, you can't do much better although Chain and
Residue and Atom all inherit from Hierarchy and so the casts are not
needed. Nor are the separate creation of the Particles:
On Aug 7, 2009, at 11:24 AM, Dina Schneidman wrote:
atom = IMP::atom::Atom::create(p,IMP::atom::AT_CA)
connecting this atom to a molecule ( with residue and chain of
course)
I tried to do the same thing now, i.e. print single coordinate in
PDB format.
something that normally should take 2 lines of code and ended up
with 14 lines.
m = IMP.Model()
rp = IMP.Particle(m)
ap = IMP.Particle(m)
cp = IMP.Particle(m);
chain = IMP.atom.Chain.create(cp, 'A')
residue = IMP.atom.Residue.create(rp)
atom = IMP.atom.Atom.create(ap, IMP.atom.AT_CA)
xyz = IMP.core.XYZ.create(ap)
hcd = IMP.atom.Hierarchy.cast(cp)
hrd = IMP.atom.Hierarchy.cast(rp)
had = IMP.atom.Hierarchy.cast(ap)
hcd.add_child(hrd)
hrd.add_child(had)
print atom.get_pdb_string()
Is there a way to make it simpler?
Am I the only one who thinks it should be simpler?
Dina
On Aug 6, 2009, at 7:05 PM, Daniel Russel wrote:
It should get it from the aromtype for all properly initialized atom
types. If it isn't currently doing that blame Dina :-) we should
be able to
fix it easily.
I'm not sure there is a reason to store the element in the
particle rather
than just look it up from the atomtype when get_element is called.
Is there?
On Aug 6, 2009, at 6:31 PM, Keren Lasker <> wrote:
seems that now element is needed for writing atoms in pdb format.
Would not it make sense to set the value of element in
Atom::create()?