[chimera-dev] 1.2199 and BILD

[Eric Pettersen]

On Feb 28, 2006, at 9:28 AM, Thomas Goddard wrote:

>   The PDB file reader is implemented in C++ and I believe there is no
> Python interface to read from a string.  The C++ code can read from a
> C++ stream (which could be a string stream), but there does not appear
> to be a Python interface.  I'd suggest requesting this feature in an
> email to chimera-bugs at cgl.ucsf.edu (also used for new feature  
> requests).

I second Tom's idea of requesting the feature via chimera-bugs.

It would seem that you have the molecular data of interest internal  
to your extension rather than in an external file.  What you can do  
is construct a Molecule directly rather than via a PDB file.  Here's  
example code that constructs a model of a single water molecule:

---
import chimera
H = chimera.Element("H")
O = chimera.Element("O")

m = chimera.Molecule()
m.name = "my water" # used by the Model Panel

r = m.newResidue("HOH", "water", 1, "")  # name, chain, position,  
insertion code

o = m.newAtom("O", O) # name, element
h1 = m.newAtom("H1", H)
h2 = m.newAtom("H2", H)
for a in [o, h1, h2]:
	r.addAtom(a)

o.setCoord(chimera.Point(35.713, 15.029, 104.298))
h1.setCoord(chimera.Point(36.2803, 15.2855, 105.025))
h2.setCoord(chimera.Point(34.848, 15.4221, 104.414))

m.newBond(o, h1)
m.newBond(o, h2)

chimera.openModels.add([m])
---

If you didn't want to have to explicitly specify connectivity, you  
could call "chimera.connectMolecule(m)" in place of the newBond()  
calls, which would have Chimera add bonds based on distance.

--Eric



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