[chimera-dev] [Chimera-users] Parsing a new 3D file format
ros
rodrigogalindo at gmail.com
Tue Jan 6 08:24:35 PST 2015
Dear Eric! Thank you for your detailed explanation and the time to write it!
It will be my first time messing with the inner workings of chimera,
but I will try it.
I will use your advice as my starting point and ask following
questions in the chimera-dev list.
Thank you again and have a good day,
Rodrigo.
On Mon, Jan 5, 2015 at 8:43 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Hi Rodrigo,
> There is code in Chimera to read XYZ files, which are somewhat similar, so
> you could base you code off of that. The XYZ-reading code is in <your
> Chimera>/share/ReadXYZ/__init__.py, the readXYZ() function. On a Mac,
> "<your Chimera>" is actually Chimera.app/Contents/Resources. Anyway, there
> is a lot of error-checking in that code so it may be hard to see the most
> relevant parts for your purposes. Here's a digest version:
>
> import objects/functions we will be using
> from chimera import Molecule, Element, Coord, connectMolecule
>
> create a new empty molecule
> m = Molecule()
>
> create a residue named UNK in that molecule, with sequence position 1, no
> chain ID, and no insertion code
> r = m.newResidue("UNK", " ", 1, " ")
>
> assign a name to the molecule for display in the model panel and so forth
> m.name = "molecule_name"
>
> create the appropriate chemical element
> element = Element(text or integer)
>
> make a new atom with the appropriate name and element
> a = m.newAtom("atom_name", element)
>
> add the atom to the residue
> r.addAtom(a)
>
> assign the atom's xyz coordinate
> a.setCoord(Coord(x, y, z))
>
> assign a serial number to the atom
> a.serialNumber = serial
>
> make appropriate bonds between the atoms
> connectMolecule(m)
>
> return a list of models (Molecules) to open
> return [m]
>
> Geez, that already was a lot. Anyway, let's ignore the file's "critical
> points" for a second so that we can finish with getting this open in
> Chimera. Basically, you will package this as an extension to Chimera that
> doesn't put anything in the Tools menu (or model panel) but just adds to the
> file types that Chimera knows how to open with the File->Open dialog and
> with the "open" command (ala "open coords.xyz"). To do so, in the same
> folder as your file-reading code you will need a file named
> ChimeraExtension.py that has this in it:
>
> ----
> 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 above code assumes that the folder containing your code is named
> "ReadAimall", that the file-reading function is named "readAimall", that it
> is in a file named "__init__.py" in the folder, and that the files are
> ".mgpviz" files. The second list in the register call (["mpgviz"]) allows
> the file type to be specified with a "mpgviz:" prefix in an "open" command
> should the file not actually have a .mgpviz suffix.
> You can then get Chimera to find this extension by adding the folder above
> the ReadAimall folder to the list in the Locations section of Chimera's
> Tools preferences (remember to click Save afterward), i.e. you add the
> folder containing new tools (in this case, the folder above ReadAimall)
> rather than each tool folder itself.
>
> Okay, back to the critical points. Depending somewhat on what you want to
> learn from them, I see four possible options: 1) fake atoms; 2) markers;
> 3) sphere shapes; 4) bond colors. In the below, I tend to put the critical
> points in their own model, since having fake atoms mixed into a real
> molecule will mess up things like hydrogen bond finding, aromatic ring
> determination, etc.
>
> Fake Atoms
> In this scenario, you would create a second Molecule as you read the file
> and add the critical points as atoms to that. You include the additional
> Molecule in the list of models you return ("return [m, m2]"). You would
> not call connectMolecule() on the second Molecule, but might add pseudobonds
> from the critical points to the appropriate atoms (you can't add regular
> bonds between models). The second molecule will have the same ID and sub-ID
> # as the first one, and will move in tandem with it. It will show up in the
> model panel.
>
> Markers
> Markers are what the Volume Tracer tool uses to mark volume data. They're
> really fake atoms, but have their own little support infrastructure. A
> simple example of using them is in the markeruse.py script on our Scripts
> page: http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts . They would have
> the same limitation in that they could only connect to the "real" atoms via
> pseudobonds. Also, they would only move in tandem with the real molecule as
> long as both models are "active" (which is usually the case unless you
> specifically do something to make their active states different).
>
> Sphere Shapes
> These are shapes (surfaces, really) created by the "shape" command.
> Probably the easiest way to create them is something like:
>
> from chimera import runCommand
> runCommand("shape sphere radius rad center x,y,z modelName 'critical points'
> modelId 100")
>
> which would put them all in model #100. If you wanted them in the same
> model number as the molecule, that would require fancier code. You could
> look at Aniso/__init__.py or at sphere_shape() in Shape/shapecmd.py for
> examples of that.
>
> Bond Colors
> If the critical points are really associated with bonds and are trying to
> convey properties of the bonds, you could vary the thickness or color of the
> bonds instead. To find the Bond object b between Atoms a1 and a2, you would
> do this:
>
> b = a1.atomsMap(a2)
>
> To change the bond radius, you would show it as stick and change the radius:
>
> b.drawMode = chimera.Bond.Stick
> b.radius = radius
>
> To change the color, you would make sure it wasn't in "halfbond" mode (each
> half colored the same as its endpoint atom) and then set the color:
>
> b.halfbond = False
> b.color = chimera.MaterialColor(red, green, blue, opacity)
>
> red / green / blue / opacity all in the range 0-1.
> So finally, this is really a developer-oriented subject, so I have directed
> follow ups to chimera-dev instead of chimera-users. Feel free to ask
> additional questions there…
>
> --Eric
>
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
>
> On Jan 5, 2015, at 1:33 PM, ros <rodrigogalindo at gmail.com> wrote:
>
> Hello!
>
> I would like to ask for advice and starting directions to be able to
> parse a new file format in Chimera so I can use Chimera's tools and
> generate images.
>
> The file format that I want to be able to open is generated from the
> Atoms in Molecules program AIMAll ( http://aim.tkgristmill.com/ )
>
> The AIMAll program of course can also do visualization and is very
> good at it. I am attaching an example of how a molecule looks. The
> problem is that if you want to work with big biomolecules (like DNA),
> the program is not very good to cloak/hide/select atoms so you have to
> click atom by atom to hide it and make some sense of the
> visualization. So, I will try to make a parser (or something that you
> would recommend) to open the file in Chimera and use Chimera's masking
> rules to select/deselect, hide/show atoms, which is very powerful.
>
> The text output generated by AIMAll has an XYZ list for each atom like this:
>
> Nuclear Charges and Cartesian Coordinates:
> -------------------------------------------------------------------------------
> Atom Charge X Y Z
> -------------------------------------------------------------------------------
> C1 6.0 0.0000000000E+00 2.3265459100E+00
> 0.0000000000E+00
> C2 6.0 0.0000000000E+00 0.0000000000E+00
> 1.7647056500E+00
> C3 6.0 0.0000000000E+00 0.0000000000E+00
> -1.7647056500E+00
> H4 1.0 1.6866221200E+00 3.4814514700E+00
> 0.0000000000E+00
> H5 1.0 -1.6866221200E+00 3.4814514700E+00
> 0.0000000000E+00
> C6 6.0 -2.0148478600E+00 -1.1632729600E+00
> 0.0000000000E+00
> H7 1.0 -2.1717143500E+00 -3.2013833400E+00
> 0.0000000000E+00
> H8 1.0 -3.8583364700E+00 -2.8006813000E-01
> 0.0000000000E+00
> C9 6.0 2.0148478600E+00 -1.1632729600E+00
> 0.0000000000E+00
> H10 1.0 2.1717143500E+00 -3.2013833400E+00
> 0.0000000000E+00
> H11 1.0 3.8583364700E+00 -2.8006813000E-01
> 0.0000000000E+00
> H12 1.0 0.0000000000E+00 0.0000000000E+00
> 3.8040484300E+00
> H13 1.0 0.0000000000E+00 0.0000000000E+00
> -3.8040484300E+00
>
>
> That is easy, I think. But as you can see from the attached image, I
> want to be able to visualize the green spheres (which are called
> critical points and represents special properties of the electron
> density, extracted from quantum mechanical calculations). Those
> points are represented in the output file as:
>
> CP# 16 Coords = 5.97894312844235E-20 1.21974356425640E+00
> -9.60854463947958E-01
> Type = (3,-1) BCP C1 C3
> Rho = 2.4067790431E-01
> GradRho = 3.5016504866E-18 -2.7948129921E-14 1.7716730860E-14
> HessRho_EigVals = -4.4278076226E-01 -4.3836581782E-01
> 3.5682199801E-01
> HessRho_EigVec1 = 1.0000000000E+00 0.0000000000E+00
> 0.0000000000E+00
> HessRho_EigVec2 = 0.0000000000E+00 -6.1321358320E-01
> 7.8991714842E-01
> HessRho_EigVec3 = 0.0000000000E+00 7.8991714842E-01
> 6.1321358320E-01
> DelSqRho = -5.2432458207E-01
> Bond Ellipticity = 1.0071370222E-02
> V = -2.5219393995E-01
> G = 6.0556397216E-02
> CP# 18 Coords = 1.05289204670721E+00 3.04112062239339E+00
> 1.96757752864282E-18
> Type = (3,-1) BCP H4 C1
> Rho = 2.9524693796E-01
> GradRho = 1.0061396161E-16 -1.6479873022E-16 1.6660693347E-18
> HessRho_EigVals = -7.9444808957E-01 -7.8708168641E-01
> 4.1039750300E-01
> HessRho_EigVec1 = -5.7017191910E-01 8.2152539989E-01
> 0.0000000000E+00
> HessRho_EigVec2 = 0.0000000000E+00 0.0000000000E+00
> 1.0000000000E+00
> HessRho_EigVec3 = 8.2152539989E-01 5.7017191910E-01
> 0.0000000000E+00
> DelSqRho = -1.1711322730E+00
> Bond Ellipticity = 9.3591342377E-03
> V = -3.7782718105E-01
> G = 4.2522056404E-02
>
> etc etc etc
>
> First line indicates the critical point number followed by the XYZ
> coordinate of the point, and the second line shows which atoms are
> involved between that critical point. The rest is the electronic
> properties of the critical point (nothing to visualize there)
>
> So, I am guessing that the critical points can be represented as dummy
> atoms in Chimera following the XYZ coordinates?
>
> The idea is that first the molecule coordinates are parsed and the
> molecule is displayed and then display the critical points of each
> atom. If possible, show lines joining atoms that have a critical
> point between them...
>
> I know it is a difficult task, but maybe you can provide some starting
> directions? Anything will help because right now is double clicking
> 1000+ atoms!
>
> Thank you so much and have a good day,
>
> Rodrigo.
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