I've implemented matrixget and matrixset now. It will be in the snapshot we're putting out at the beginning of December. I can provide the changed Python files to anyone who wants the matrix commands earlier. I should note that there was an error in my earlier mail (below) -- the function is chimera.Xform_xform(), not chimera.Xform(). Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Nov 1, 2004, at 12:04 PM, Eric Pettersen wrote:
On Oct 31, 2004, at 7:28 AM, Miguel Ortiz LombardÃa wrote:
Hi all,
Sorry, this question may be very simple, but I didn't manage to find an answer in the documentation.
Is it possible to read a transformation (rotation + translation) matrix so that the molecule is displayed exactly in the orientation you wish?
This is discussed a little in the programmer's FAQ, question #4 (http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html). But that question doesn't talk about how to use an _arbitrary_ rotation/translation matrix to set a model's transformation. Nonetheless, you should look at it to get the general idea of how to set a model's transformation matrix. At the end of this mail I've appended the definition of the Xform class, as our Python-wrapping program sees it (therefore, functions that are commented out [with '//'] are in the C++ code put not the Python layer). The routine you want is the constructor 'xform' that takes 12 numeric arguments defining the transformation matrix and an 'orthogonalize' boolean. So you would generate your transform with:
xf = chimera.Xform(..12 numbers..., orthogonalize=True)
You want 'orthogonalize' to be True so that Chimera will correct for any roundoff in your numeric arguments and produce an orthonormal matrix that is suitable for use as a transformation matrix. You then use the same general procedures as in FAQ question 4 to set the model transform.
Now, this would be much easier if the Midas matrixget/matrixset commands were implemented in Chimera. I will work on that and let you know when it's done. Until then, you will need to use the Xform constructor.
Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
class Xform { // WRAP CLASS // DON'T CACHE public: Xform(); // same as identity // The following static routines are the constructors: static Xform xform(Real r00, Real r01, Real r02, Real t03, Real r10, Real r11, Real r12, Real t13, Real r20, Real r21, Real r22, Real t23, bool orthogonalize = false); static Xform coordFrame(const Vector &x, const Vector &y, const Vector &z, const Point &origin, bool orthogonalize = false); static Xform identity(); static Xform translation(Real x, Real y, Real z); static Xform translation(const Vector &v); static Xform xRotation(Real angle); static Xform yRotation(Real angle); static Xform zRotation(Real angle); static Xform rotation(Real x, Real y, Real z, Real angle); static Xform rotation(const Vector &axis, Real angle); //static Xform rotation(const Real mat[3][3], bool orthogonalize = fals e); static Xform zAlign(const Point &p0, const Point &p1); static Xform zAlign(const Point &p0, const Vector &v); static Xform lookAt(const Point &eye, const Point &at, const Point &u p); static Xform lookAt(const Point &eye, const Point &at, const Vector & up); void invert(); void translate(Real x, Real y, Real z); void translate(const Vector &xyz); void xRotate(Real angle); void yRotate(Real angle); void zRotate(Real angle); void rotate(Real x, Real y, Real z, Real angle); void rotate(const Vector &xyz, Real angle); Point apply(const Point &pt) const; Vector apply(const Vector &vec) const; void premultiply(const Xform &xf); void multiply(const Xform &xf); bool isIdentity() const; void getRotation(/*OUT*/ Vector *axis, /*OUT*/ Real *angle) c onst; void getCoordFrame(/*OUT*/ Vector *x = NULL, /*OUT*/ Vector *y = NULL, /*OUT*/ Vector *z = NULL, /*OUT*/ Point *origin = NULL) const; void getTranslation(/*OUT*/ Vector *trans) const; //void get4by4(/*OUT*/ Real mat[4][4]) const; };