# camera_travel - Laurence Pearl, November 2003 # Pythonized by Lieven Buts, November 2003 import cmd from math import sqrt,acos,sin def quaternion(view): """ Returns a quaternion representation of a view matrix. """ nxt = [1,2,0] q = [0.0,0.0,0.0,1.0] tr = view[0]+view[4]+view[8] if tr > 0.0 : s = sqrt(tr + 1.0) qw1 = s / 2.0 s = 0.5 / s return ( (view[5] - view[7]) * s, (view[6] - view[2]) * s, (view[1] - view[3]) * s, qw1 ) else : i = 0 if (view[4] > view[0]): i = 1 if (view[8] > view[i+3*i]): i = 2 j = nxt[i] k = nxt[j] s = sqrt ((view[i+i*3] - (view[j+j*3] + view[k+k*3])) + 1.0) q[i] = s * 0.5 if (s != 0.0): s = 0.5 / s q[3] = (view[k+3*j] - view[j+3*k]) * s q[j] = (view[j+3*i] + view[i+3*j]) * s q[k] = (view[k+3*i] + view[i+3*k]) * s return q def camera_travel(first,nframes=30,sel='(all)',zflag=0,zlevel=2): """ Generate progressive view matrices to move the camera smoothly from the current view to a view defined by a PyMol selection. first - start frame nframes - duration sel - atom selection that defines the orientation at the end of the sequence zflag - flag to indicate whether the final view should be 'zoomed' or not zlevel - buffer space for zooming final view (as in cmd.zoom) """ try: first=int(first) except: print "camera_travel: first frame must be an integer" return -1 try: nframes=int(nframes) except: print "camera_travel: number of frames" ff=float(1.0/nframes) old_view = cmd.get_view(2) # print ( "view : (" + "%8.3f, "*17 + "%8.3f)" ) % (old_view) # print "oldtran : %8.3f %8.3f %8.3f" % (old_view[12], old_view[13], old_view[14]) # do orient operation on selection cmd.orient(sel,0) # if zoom to selection is required add this into view matrix if zflag: cmd.zoom(sel,zlevel,0,1) # get new view new_view = cmd.get_view() # capture new zoom/clip parameters ozc1 = new_view[11] ozc2 = new_view[15] ozc3 = new_view[16] # calculate shift in zoom/clip parameters dzc1 = (ozc1 - old_view[11]) * ff dzc2 = (ozc2 - old_view[15]) * ff dzc3 = (ozc3 - old_view[16]) * ff ozc1 = old_view[11] ozc2 = old_view[15] ozc3 = old_view[16] # capture new translation vector component ox = new_view[12] oy = new_view[13] oz = new_view[14] # calculate shift vector dx = ox - old_view[12] dy = oy - old_view[13] dz = oz - old_view[14] dx = dx*ff dy = dy*ff dz = dz*ff ox = old_view[12] oy = old_view[13] oz = old_view[14] # capture old and new rotation matrix components in quaternion form # m[0][0] = v[0] m[0][1] = v[1] m[0][2] = v[2] # m[1][0] = v[3] m[1][1] = v[4] m[1][2] = v[5] # m[2][0] = v[6] m[2][1] = v[7] m[2][2] = v[8] qx1,qy1,qz1,qw1 = quaternion(old_view) qx2,qy2,qz2,qw2 = quaternion(new_view) # calc cosine cosom = qx1 * qx2 + qy1 * qy2 + qz1 * qz2 + qw1 * qw2 limit = 0.001 if cosom>1.0+limit: raise ValueError,"Cosine of omega way out of range (positive)" elif cosom>1.0: print "Warning: cosom corrected from ",cosom,"to", cosom = 1.0 print cosom if cosom<-1.0-limit: raise ValueError,"Cosine of omega way out of range (negative)" elif cosom<-1.0: print "Warning: cosom corrected from ",cosom,"to", cosom = 1.0 print cosom # adjust signs if (cosom < 0.0): cosom = -cosom to0 = -qx2 to1 = -qy2 to2 = -qz2 to3 = -qw2 else: to0 = qx2 to1 = qy2 to2 = qz2 to3 = qw2 # calc coefficients omega = acos(cosom) sinom = sin(omega) if sinom==0.0: sinom=limit print "Warning: sinom corrected!" # restore old view cmd.set_view( ("%8.3f, " * 17 + "%8.3f") % tuple(old_view) ) # loop interpolating over nframes generating interpolated quaternion for a in range(nframes+1): scale0 = sin((1.0 - float(a*ff)) * omega) / sinom scale1 = sin(float(a*ff) * omega) / sinom rx = scale0 * qx1 + scale1 * to0; ry = scale0 * qy1 + scale1 * to1; rz = scale0 * qz1 + scale1 * to2; rw = scale0 * qw1 + scale1 * to3; # convert back to matrix x2 = rx + rx y2 = ry + ry z2 = rz + rz xx = rx * x2 xy = rx * y2 xz = rx * z2 yy = ry * y2 yz = ry * z2 zz = rz * z2 wx = rw * x2 wy = rw * y2 wz = rw * z2 nv0 = 1.0 - (yy + zz) nv3 = xy - wz nv6 = xz + wy nv1 = xy + wz nv4 = 1.0 - (xx + zz) nv7 = yz - wx nv2 = xz - wy nv5 = yz + wx nv8 = 1.0 - (xx + yy) # update translation vector ox = ox + dx oy = oy + dy oz = oz + dz # update zoom/clip parameters if required if zflag: ozc1 = ozc1 + dzc1 ozc2 = ozc2 + dzc2 ozc3 = ozc3 + dzc3 cmd.mdo("%d" % (first), ("set_view (" + "%8.3f, "*17 + "%8.3f)") % (nv0,nv1,nv2,nv3,nv4,nv5,nv6,nv7,nv8,old_view[9],old_view[10],ozc1, ox,oy,oz,ozc2,ozc3,old_view[17])) first += 1 cmd.set_view( ("%8.3f, "*17 + "%8.3f") % (nv0,nv1,nv2,nv3,nv4,nv5,nv6,nv7,nv8,old_view[9],old_view[10],ozc1, ox,oy,oz,ozc2,ozc3,old_view[17])) def camera_view_travel(first,nframes=30,new_view=(\ 1.000000000, 0.000000000, 0.000000000,\ 0.000000000, 1.000000000, 0.000000000,\ 0.000000000, 0.000000000, 1.000000000,\ 0.000000000, 0.000000000, -50.000000000,\ 0.000000000, 0.000000000, 0.000000000,\ 40.000000000, 100.000000000, 0.000000000 )): """ Generate progressive view matrices to move the camera smoothly from the current view to a new view provided as an argument. first - start frame nframes - duration new_view - PyMol view matrix that defines the view at the end of the sequence """ try: first=int(first) except: print "camera_travel: first frame must be an integer" return -1 try: nframes=int(nframes) except: print "camera_travel: number of frames" ff=float(1.0/nframes) old_view = cmd.get_view(2) # print ( "view : (" + "%8.3f, "*17 + "%8.3f)" ) % (old_view) # print "oldtran : %8.3f %8.3f %8.3f" % (old_view[12], old_view[13], old_view[14]) # capture new zoom/clip parameters ozc1 = new_view[11] ozc2 = new_view[15] ozc3 = new_view[16] # calculate shift in zoom/clip parameters dzc1 = (ozc1 - old_view[11]) * ff dzc2 = (ozc2 - old_view[15]) * ff dzc3 = (ozc3 - old_view[16]) * ff ozc1 = old_view[11] ozc2 = old_view[15] ozc3 = old_view[16] # capture new translation vector component ox = new_view[12] oy = new_view[13] oz = new_view[14] # calculate shift vector dx = ox - old_view[12] dy = oy - old_view[13] dz = oz - old_view[14] dx = dx*ff dy = dy*ff dz = dz*ff ox = old_view[12] oy = old_view[13] oz = old_view[14] # capture old and new rotation matrix components in quaternion form # m[0][0] = v[0] m[0][1] = v[1] m[0][2] = v[2] # m[1][0] = v[3] m[1][1] = v[4] m[1][2] = v[5] # m[2][0] = v[6] m[2][1] = v[7] m[2][2] = v[8] qx1,qy1,qz1,qw1 = quaternion(old_view) qx2,qy2,qz2,qw2 = quaternion(new_view) # calc cosine cosom = qx1 * qx2 + qy1 * qy2 + qz1 * qz2 + qw1 * qw2 limit = 0.001 if cosom>1.0+limit: raise ValueError,"Cosine of omega way out of range (positive)" elif cosom>1.0: print "Warning: cosom corrected from ",cosom,"to", cosom = 1.0 print cosom if cosom<-1.0-limit: raise ValueError,"Cosine of omega way out of range (negative)" elif cosom<-1.0: print "Warning: cosom corrected from ",cosom,"to", cosom = 1.0 print cosom # adjust signs if (cosom < 0.0): cosom = -cosom to0 = -qx2 to1 = -qy2 to2 = -qz2 to3 = -qw2 else: to0 = qx2 to1 = qy2 to2 = qz2 to3 = qw2 # calc coefficients omega = acos(cosom) sinom = sin(omega) if sinom==0.0: sinom=limit print "Warning: sinom corrected!" # restore old view cmd.set_view( ("%8.3f, " * 17 + "%8.3f") % tuple(old_view) ) # loop interpolating over nframes generating interpolated quaternion for a in range(nframes+1): scale0 = sin((1.0 - float(a*ff)) * omega) / sinom scale1 = sin(float(a*ff) * omega) / sinom rx = scale0 * qx1 + scale1 * to0; ry = scale0 * qy1 + scale1 * to1; rz = scale0 * qz1 + scale1 * to2; rw = scale0 * qw1 + scale1 * to3; # convert back to matrix x2 = rx + rx y2 = ry + ry z2 = rz + rz xx = rx * x2 xy = rx * y2 xz = rx * z2 yy = ry * y2 yz = ry * z2 zz = rz * z2 wx = rw * x2 wy = rw * y2 wz = rw * z2 nv0 = 1.0 - (yy + zz) nv3 = xy - wz nv6 = xz + wy nv1 = xy + wz nv4 = 1.0 - (xx + zz) nv7 = yz - wx nv2 = xz - wy nv5 = yz + wx nv8 = 1.0 - (xx + yy) # update translation vector ox = ox + dx oy = oy + dy oz = oz + dz # update zoom/clip parameters ozc1 = ozc1 + dzc1 ozc2 = ozc2 + dzc2 ozc3 = ozc3 + dzc3 cmd.mdo("%d" % (first), ("set_view (" + "%8.3f, "*17 + "%8.3f)") % (nv0,nv1,nv2,nv3,nv4,nv5,nv6,nv7,nv8,old_view[9],old_view[10],ozc1, ox,oy,oz,ozc2,ozc3,old_view[17])) first += 1 cmd.set_view( ("%8.3f, "*17 + "%8.3f") % (nv0,nv1,nv2,nv3,nv4,nv5,nv6,nv7,nv8,old_view[9],old_view[10],ozc1, ox,oy,oz,ozc2,ozc3,old_view[17])) def fly_sequence(object,first,last): """ Visit all residues in an object consecutively. Requires 15 movie frames per residue. object - first - last - """ fr=1 for ires in range(int(first),int(last)+1): res = "(" + object + (" and resi %d" % (ires,)) + ")" camera_travel(fr,9,res,1,2) fr = fr + 15 # Install new PyMol commands cmd.extend("seqfly",fly_sequence) cmd.extend("camtrav",camera_travel) cmd.extend("camvtrav",camera_view_travel) base_view = (\ 0.627689123, 0.591809154, 0.505735278,\ -0.757547379, 0.314778954, 0.571870685,\ 0.179243475, -0.742075384, 0.645906866,\ 0.000000000, -5.000000000, -293.012847900,\ 21.779773712, 60.280826569, 62.276878357,\ 246.721801758, 352.805450439, 1.000000000 ) cmd.set_view(base_view) camera_travel(1,29,'resi 300 and not n;c,n,o,ca',1,4) camera_view_travel(30,29,base_view)