[chimera-dev] AIMAll extension update 1

6 Jan 2015

      Hello!

Thanks to the recommendations from Dr. Eric, I was able to code an
extension for Chimera that reads mgpviz files generated from the
AIMAll program.  Right now, only the XYZ and atom type information is
parsed and the molecule is displayed.  Although, I do not know why it
shows no connectivity.  I am including a screenshot that shows how
Chimera displays the molecule (left) and how does it look in AIMAll
(right).

I do use the command connectMolecule() but I do not know if I have to
include some other argument for that function.  I based the code from
the ReadXYZ extension.

My code (I am no coder, so it might be super ugly  (: )

ChimeraExtension.py
------------------------------------------------------------------------------
def aimallOpen(fileName):
    from ReadAimall import readAimall
    return readAimall(fileName)

import chimera
chimera.fileInfo.register("AIMAll mgpviz", aimallOpen, [".mgpviz"], ["mpgviz"],
                          category=chimera.FileInfo.STRUCTURE)

the readAimall function:
-----------------------------------------------------------------------------------
## Extension to read a file output from AIMALL
## based on the code ReadXYZ
def readAimall(fileName):
from OpenSave import osOpen
from chimera import UserError, Molecule, Element, openModels, replyobj
from chimera import Coord, connectMolecule
        anums = {}

        ## Open the file
getatoms = osOpen(fileName)

        ## Search for the string:
        ## 'Number of NACPs'
        ## which gives us the number of atoms
        ## and store it in numAtoms
        for data in getatoms:
                data = data.strip()
                if data.startswith("Number of NACPs"):
                        a,b,c,d,e = data.split()
                        numAtoms = int(e)

        getatoms.close()

f = osOpen(fileName)
        readAtoms = 1
        state = "init"

        ## Skip the 26 header lines from the mpgviz file
        f = f.readlines()[26:]

        ## cycle through the file until it reaches
        ## the number of Atoms
        for line in f:
                if readAtoms == numAtoms:
                        break
                line = line.strip()
                if state == "init":
                        state = "post"
                        m = Molecule()
                        r = m.newResidue("UNK", " ", 1, " ")
                        state = "atoms"
                        serial = 1
                if not line: continue

                elem, charge, x, y, z = line.split()
                x, y, z = [float(c) for c in [x,y,z]]
                ## Remove the number from the atomic symbol
                elem = filter(lambda x: x.isalpha(), elem)
                element = Element(elem)
                anum = anums.get(element.name, 0) + 1
                anums[element.name] = anum
                a = m.newAtom("%s%d" % (element.name, anum), element)
                r.addAtom(a)
                a.setCoord(Coord(x, y, z))
                a.serialNumber = serial
                serial += 1
                readAtoms += 1
        #f.close()
        connectMolecule(m)
        return [m]

---------------------------------------------------------------------------------------------------

I couple of questions:

1- Do I have to include something in the connectMolecule function to
enable the display of bonds?
2- At the end, what would be your recommendation, based on your
experience, to display the critical points and bonds between atoms?
We were considering: Fake atoms, Markers, Sphere shapes and bond
colors.  What we are trying to achieve is to be able to turn off
certain critical points and leave some  on to show how molecules
interact.

Thank you for your help and let me know what you think!!

Rodrigo.

[chimera-dev] AIMAll extension update 1

ros