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| bool | kmeans_adaptive_kernel_density_bb_dependent_rotlib.draw = False |
| | main More...
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| float | kmeans_adaptive_kernel_density_bb_dependent_rotlib.cutoff = 2.0 |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.restype = sys.argv[1] |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.ncluster = int(sys.argv[2]) |
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| string | kmeans_adaptive_kernel_density_bb_dependent_rotlib.inpfile = "./split/" + restype + ".dat" |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.inp = open(inpfile, 'r') |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.lines = inp.readlines() |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.skip = int(len(lines)/10000) |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.xyzlist = [] |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.intlist = [] |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.bblist = [] |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.dats = line.split() |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.dis = float(dats[0]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.ang = float(dats[1]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.dih = float(dats[2]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.psi = float(dats[3]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.phi = float(dats[4]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.x = dis*sin(ang)*cos(dih) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.y = dis*sin(ang)*sin(dih) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.z = dis*cos(ang) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.data = vstack(xyzlist) |
| | cluster, find the centroid More...
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.save_data = data |
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| string | kmeans_adaptive_kernel_density_bb_dependent_rotlib.fn = "refine/" + restype + ".xyz" |
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| def | kmeans_adaptive_kernel_density_bb_dependent_rotlib.centroids = load_centroid_xyz(fn, ncluster) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib._ |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.idx |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.dist |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.nd = len(data) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.savend = nd |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.colorlist = ['r', 'b', 'g', 'y', 'c', 'm', 'k', 'w', 'r'] |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.marklist = ['o', '^', '+', '>', (5,2), (5,0)] |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.fig = plt.figure() |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.ax = fig.add_subplot(111, projection='3d') |
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| float | kmeans_adaptive_kernel_density_bb_dependent_rotlib.R = 2.0 |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.c = colorlist[i] |
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| string | kmeans_adaptive_kernel_density_bb_dependent_rotlib.m = '.' |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.flag = i |
| | !!! note: it's too slow, use bined rho as an approximation Step 0 lambda_i for each data phis = np.zeros([savend]) psis = np.zeros([savend]) for nd in xrange(savend): all data phis[nd] = bblist[nd][1] psis[nd] = bblist[nd][0] More...
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.xs = save_data[flag, 0] |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.ys = save_data[flag, 1] |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.zs = save_data[flag, 2] |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.n = len(xs) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.s |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.marker |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.r = sqrt(x*x+y*y+z*z) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.t = arccos(z/r) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.p = arctan2(y,x) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.u |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.v |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.color |
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| int | kmeans_adaptive_kernel_density_bb_dependent_rotlib.kappa_scale = 50 |
| | Adaptive Kernel Desity Estimate. More...
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| int | kmeans_adaptive_kernel_density_bb_dependent_rotlib.kappa = sqrt(savend)/kappa_scale |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.prhos = [] |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.rhos = [] |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.ncs = [] |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.phis = [] |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.psis = [] |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.xphi = np.linspace(-180, 180, 36, endpoint=False) |
| | check: make sure the def is compatable with pbc !!! More...
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.ypsi = np.linspace(-180, 180, 36, endpoint=False) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.philst = np.zeros([n]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.psilst = np.zeros([n]) |
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| int | kmeans_adaptive_kernel_density_bb_dependent_rotlib.tn = 0 |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.rho = np.zeros([36,36]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.dphis = philst - phi |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.dpsis = psilst - psi |
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| def | kmeans_adaptive_kernel_density_bb_dependent_rotlib.kphis = ksr(dphis,sqrt(n)/kappa_scale) |
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| def | kmeans_adaptive_kernel_density_bb_dependent_rotlib.kpsis = ksr(dpsis,sqrt(n)/kappa_scale) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.rho_dat = np.zeros([savend]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.all_phi = np.zeros([savend]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.all_psi = np.zeros([savend]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.psi_bin |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.phi_bin |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.log_rho = np.log(rho_dat) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.log_g = np.sum(log_rho)/savend |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.lambda_i = np.exp( (log_g - log_rho)/2 ) |
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| int | kmeans_adaptive_kernel_density_bb_dependent_rotlib.kappa_i = kappa / lambda_i |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.surf |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.Pr = np.zeros([ncluster]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.sumP = np.zeros([36,36]) |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.Pr_pp = [] |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.prpp = rhos[i]*Pr[i]/sumP |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.dis_lst = [] |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.ang_lst = [] |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.dih_lst = [] |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.vdis_lst = [] |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.vang_lst = [] |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.vdih_lst = [] |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.lambda_mat = np.zeros([36,36]) |
| |
| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.g = exp(log_g) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.kappa_lst = np.zeros([n]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.dis_mat = np.zeros([36,36]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.ang_mat = np.zeros([36,36]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.dih_mat = np.zeros([36,36]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.vdis_mat = np.zeros([36,36]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.vang_mat = np.zeros([36,36]) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.vdih_mat = np.zeros([36,36]) |
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| def | kmeans_adaptive_kernel_density_bb_dependent_rotlib.kernel = kpsis*kphis |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.denominator = np.sum(kernel) |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.ddis = dis - dis_mat[x,y] |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.dang = ang - ang_mat[x,y] |
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| | kmeans_adaptive_kernel_density_bb_dependent_rotlib.ddih = dih - dih_mat[x,y] |
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| float | kmeans_adaptive_kernel_density_bb_dependent_rotlib.rr2dd = 1.0 |
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| list | kmeans_adaptive_kernel_density_bb_dependent_rotlib.dihval = dih_lst[nc][phi_bin, psi_bin]*180/pi |
| |
