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@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