I don't like the convention x-y-z for the Euler angles and we absolutely need to be consistent around IMP about them or enforce clear specification. The most used one in EM by far is ZYZ and the one that I am going to use.
Javi
> > > 2008/11/12 imp-dev-request@salilab.org: >> Send IMP-dev mailing list submissions to >> imp-dev@salilab.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://salilab.org/mailman/listinfo/imp-dev >> or, via email, send a message with subject or body 'help' to >> imp-dev-request@salilab.org >> >> You can reach the person managing the list at >> imp-dev-owner@salilab.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of IMP-dev digest..." >> >> >> Today's Topics: >> >> 1. Re: [IMP-commits] r854 - trunk/modules/misc/include >> (Dina Schneidman) >> 2. Re: [IMP-commits] r854 - trunk/modules/misc/include >> (Daniel Russel) >> 3. Re: 2D geometry ( Javier ?ngel Vel?zquez Muriel ) >> 4. Re: 2D geometry ( Javier ?ngel Vel?zquez Muriel ) >> 5. Re: 2D geometry (Daniel Russel) >> 6. Re: 2D geometry (Daniel Russel) >> 7. Re: 2D geometry (Keren Lasker) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 12 Nov 2008 15:59:13 -0800 >> From: "Dina Schneidman" duhovka@gmail.com >> Subject: Re: [IMP-dev] [IMP-commits] r854 - trunk/modules/misc/include >> To: "List for IMP development" imp-dev@salilab.org >> Message-ID: >> 55d63ce50811121559p4995f334kf9e9c1247f21d35f@mail.gmail.com >> Content-Type: text/plain; charset="iso-8859-1" >> >> I think these are Euler angles. >> http://www.euclideanspace.com/maths/algebra/matrix/orthogonal/rotation/index... >> Daniel, I agree that conceptually it is wrong to store them in Vector3D, but >> it is very convenient in practice. >> >> On Wed, Nov 12, 2008 at 10:33 PM, Keren Lasker kerenl@salilab.org wrote: >> >>> Daniel - the angles are not Euler angles but just three angles around >>> X/Y/Z axis. >>> Would you like the option to rotate around another axis, ,something >>> like: >>> (1,1,0),45 - meaning rotating around the diagonal of the XY plane in >>> 45 degrees? >>> On Nov 12, 2008, at 5:43 PM, Daniel Russel wrote: >>> >>> > I don't like having two equivalent constructors from thevsame data or >>> > using a vector to hold angles. >>> > >>> > What I had meant with my suggestion is initialization from an axis and >>> > an amount of rotation about that axis as that is a somewhat less >>> > problematic basis than Euler angles (and one I use :-) >>> > >>> > >>> > >>> > On Nov 12, 2008, at 2:31 PM, Notification of IMP commits < >>> imp-commits@salilab.org >>> >> wrote: >>> > >>> >> Author: kerenl@SALILAB.ORG >>> >> Date: 2008-11-12 14:31:59 -0800 (Wed, 12 Nov 2008) >>> >> New Revision: 854 >>> >> >>> >> Modified: >>> >> trunk/modules/misc/include/Rotation3D.h >>> >> Log: >>> >> 1. Change protected to private >>> >> 2. Add constructors from Vector3D and an angle >>> >> 3. update documentation >>> >> >>> >> Modified: trunk/modules/misc/include/Rotation3D.h >>> >> =================================================================== >>> >> --- trunk/modules/misc/include/Rotation3D.h 2008-11-12 21:15:36 >>> >> UTC (rev 853) >>> >> +++ trunk/modules/misc/include/Rotation3D.h 2008-11-12 22:31:59 >>> >> UTC (rev 854) >>> >> @@ -19,26 +19,28 @@ >>> >> >>> >> class IMPMISCEXPORT Rotation3D { >>> >> public: >>> >> - //! Initialize a rotation in x-y-z order from three angles >>> >> + Rotation3D(){ >>> >> + } >>> >> + //! Initialize a rotation in x-y-z order from three Euler angles >>> >> /** \param[in] xr Rotation around the X axis >>> >> \param[in] yr Rotation around the Y axis >>> >> \param[in] zr Rotation around the Z axis >>> >> */ >>> >> Rotation3D(Float xr, Float yr, Float zr) { >>> >> - Float cx = cos(xr); Float cy = cos(yr); Float cz = cos(zr); >>> >> - Float sx = sin(xr); Float sy = sin(yr); Float sz = sin(zr); >>> >> - Float m00 = cz*cy; >>> >> - Float m11 = -sy*sx*sz + cx*cz; >>> >> - Float m22 = cy*cx; >>> >> - quat_[0] = sqrt(1+m00+m11+m22)/2.0; >>> >> - quat_[1] = sqrt(1+m00-m11-m22)/2.0; >>> >> - quat_[2] = sqrt(1-m00+m11-m22)/2.0; >>> >> - quat_[3] = sqrt(1-m00-m11+m22)/2.0; >>> >> - if (cy*sx + sy*cx*sz + sx*cz < 0.0) quat_[1] = -quat_[1]; >>> >> - if (sz*sx - sy*cx*cz - sy < 0.0) quat_[2] = -quat_[2]; >>> >> - if (sz*cy + sy*sx*cz + sz*cx < 0.0) quat_[3] = -quat_[3]; >>> >> + init_angles(xr,yr,zr); >>> >> } >>> >> - >>> >> + //! Initialize a rotation in x-y-z order from three identical >>> >> Euler angles >>> >> + /** \param[in] e_angle Rotation around first the X axis, Y axis >>> >> and Z axis >>> >> + */ >>> >> + Rotation3D(Float e_angle){ >>> >> + init_angles(e_angle, e_angle, e_angle); >>> >> + } >>> >> + //! Initialize a rotation in x-y-z order from three Euler angles >>> >> + /** \param[in] v A vector that holds three Euler angles (x-y-z >>> >> order) >>> >> + */ >>> >> + Rotation3D(const Vector3D &v){ >>> >> + init_angles(v[0],v[1],v[2]); >>> >> + } >>> >> Matrix3D get_matrix() const { >>> >> const Float a = quat_[0]; >>> >> const Float b = quat_[1]; >>> >> @@ -76,7 +78,22 @@ >>> >> return atan2(matrix21(), matrix11()); >>> >> } >>> >> >>> >> -protected: >>> >> +private: >>> >> + void init_angles(Float xr, Float yr, Float zr) { >>> >> + Float cx = cos(xr); Float cy = cos(yr); Float cz = cos(zr); >>> >> + Float sx = sin(xr); Float sy = sin(yr); Float sz = sin(zr); >>> >> + Float m00 = cz*cy; >>> >> + Float m11 = -sy*sx*sz + cx*cz; >>> >> + Float m22 = cy*cx; >>> >> + quat_[0] = sqrt(1+m00+m11+m22)/2.0; >>> >> + quat_[1] = sqrt(1+m00-m11-m22)/2.0; >>> >> + quat_[2] = sqrt(1-m00+m11-m22)/2.0; >>> >> + quat_[3] = sqrt(1-m00-m11+m22)/2.0; >>> >> + if (cy*sx + sy*cx*sz + sx*cz < 0.0) quat_[1] = -quat_[1]; >>> >> + if (sz*sx - sy*cx*cz - sy < 0.0) quat_[2] = -quat_[2]; >>> >> + if (sz*cy + sy*sx*cz + sz*cx < 0.0) quat_[3] = -quat_[3]; >>> >> + } >>> >> + >>> >> Float matrix11() const { >>> >> return sqr(quat_[0]) + sqr(quat_[1]) - sqr(quat_[2]) - >>> >> sqr(quat_[3]); >>> >> } >>> >> >>> >> _______________________________________________ >>> >> IMP-commits mailing list >>> >> IMP-commits@salilab.org >>> >> https://salilab.org/mailman/listinfo/imp-commits >>> > _______________________________________________ >>> > IMP-dev mailing list >>> > IMP-dev@salilab.org >>> > https://salilab.org/mailman/listinfo/imp-dev >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>