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d766458 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 | import matplotlib
import matplotlib.pyplot as plt
from matplotlib import animation
from colabdesign.shared.plot import plot_pseudo_3D, pymol_cmap, _np_kabsch
from string import ascii_uppercase, ascii_lowercase
alphabet_list = list(ascii_uppercase+ascii_lowercase)
import numpy as np
def sym_it(coords, center, cyclic_symmetry_axis, reflection_axis=None):
def rotation_matrix(axis, theta):
axis = axis / np.linalg.norm(axis)
a = np.cos(theta / 2)
b, c, d = -axis * np.sin(theta / 2)
return np.array([[a*a+b*b-c*c-d*d, 2*(b*c-a*d), 2*(b*d+a*c)],
[2*(b*c+a*d), a*a+c*c-b*b-d*d, 2*(c*d-a*b)],
[2*(b*d-a*c), 2*(c*d+a*b), a*a+d*d-b*b-c*c]])
def align_axes(coords, source_axis, target_axis):
rotation_axis = np.cross(source_axis, target_axis)
rotation_angle = np.arccos(np.dot(source_axis, target_axis))
rot_matrix = rotation_matrix(rotation_axis, rotation_angle)
return np.dot(coords, rot_matrix)
# Center the coordinates
coords = coords - center
# Align cyclic symmetry axis with Z-axis
z_axis = np.array([0, 0, 1])
coords = align_axes(coords, cyclic_symmetry_axis, z_axis)
if reflection_axis is not None:
# Align reflection axis with X-axis
x_axis = np.array([1, 0, 0])
coords = align_axes(coords, reflection_axis, x_axis)
return coords
def fix_partial_contigs(contigs, parsed_pdb):
INF = float("inf")
# get unique chains
chains = []
for c, i in parsed_pdb["pdb_idx"]:
if c not in chains: chains.append(c)
# get observed positions and chains
ok = []
for contig in contigs:
for x in contig.split("/"):
if x[0].isalpha:
C,x = x[0],x[1:]
S,E = -INF,INF
if x.startswith("-"):
E = int(x[1:])
elif x.endswith("-"):
S = int(x[:-1])
elif "-" in x:
(S,E) = (int(y) for y in x.split("-"))
elif x.isnumeric():
S = E = int(x)
for c, i in parsed_pdb["pdb_idx"]:
if c == C and i >= S and i <= E:
if [c,i] not in ok: ok.append([c,i])
# define new contigs
new_contigs = []
for C in chains:
new_contig = []
unseen = []
seen = []
for c,i in parsed_pdb["pdb_idx"]:
if c == C:
if [c,i] in ok:
L = len(unseen)
if L > 0:
new_contig.append(f"{L}-{L}")
unseen = []
seen.append([c,i])
else:
L = len(seen)
if L > 0:
new_contig.append(f"{seen[0][0]}{seen[0][1]}-{seen[-1][1]}")
seen = []
unseen.append([c,i])
L = len(unseen)
if L > 0:
new_contig.append(f"{L}-{L}")
L = len(seen)
if L > 0:
new_contig.append(f"{seen[0][0]}{seen[0][1]}-{seen[-1][1]}")
new_contigs.append("/".join(new_contig))
return new_contigs
def fix_contigs(contigs,parsed_pdb):
def fix_contig(contig):
INF = float("inf")
X = contig.split("/")
Y = []
for n,x in enumerate(X):
if x[0].isalpha():
C,x = x[0],x[1:]
S,E = -INF,INF
if x.startswith("-"):
E = int(x[1:])
elif x.endswith("-"):
S = int(x[:-1])
elif "-" in x:
(S,E) = (int(y) for y in x.split("-"))
elif x.isnumeric():
S = E = int(x)
new_x = ""
c_,i_ = None,0
for c, i in parsed_pdb["pdb_idx"]:
if c == C and i >= S and i <= E:
if c_ is None:
new_x = f"{c}{i}"
else:
if c != c_ or i != i_+1:
new_x += f"-{i_}/{c}{i}"
c_,i_ = c,i
Y.append(new_x + f"-{i_}")
elif "-" in x:
# sample length
s,e = x.split("-")
m = np.random.randint(int(s),int(e)+1)
Y.append(f"{m}-{m}")
elif x.isnumeric() and x != "0":
Y.append(f"{x}-{x}")
return "/".join(Y)
return [fix_contig(x) for x in contigs]
def fix_pdb(pdb_str, contigs):
def get_range(contig):
L_init = 1
R = []
sub_contigs = [x.split("-") for x in contig.split("/")]
for n,(a,b) in enumerate(sub_contigs):
if a[0].isalpha():
if n > 0:
pa,pb = sub_contigs[n-1]
if pa[0].isalpha() and a[0] == pa[0]:
L_init += int(a[1:]) - int(pb) - 1
L = int(b)-int(a[1:]) + 1
else:
L = int(b)
R += range(L_init,L_init+L)
L_init += L
return R
contig_ranges = [get_range(x) for x in contigs]
R,C = [],[]
for n,r in enumerate(contig_ranges):
R += r
C += [alphabet_list[n]] * len(r)
pdb_out = []
r_, c_,n = None, None, 0
for line in pdb_str.split("\n"):
if line[:4] == "ATOM":
c = line[21:22]
r = int(line[22:22+5])
if r_ is None: r_ = r
if c_ is None: c_ = c
if r != r_ or c != c_:
n += 1
r_,c_ = r,c
pdb_out.append("%s%s%4i%s" % (line[:21],C[n],R[n],line[26:]))
if line[:5] == "MODEL" or line[:3] == "TER" or line[:6] == "ENDMDL":
pdb_out.append(line)
r_, c_,n = None, None, 0
return "\n".join(pdb_out)
def get_ca(pdb_filename, get_bfact=False):
xyz = []
bfact = []
for line in open(pdb_filename, "r"):
line = line.rstrip()
if line[:4] == "ATOM":
atom = line[12:12+4].strip()
if atom == "CA":
x = float(line[30:30+8])
y = float(line[38:38+8])
z = float(line[46:46+8])
xyz.append([x, y, z])
if get_bfact:
b_factor = float(line[60:60+6].strip())
bfact.append(b_factor)
if get_bfact:
return np.array(xyz), np.array(bfact)
else:
return np.array(xyz)
def get_Ls(contigs):
Ls = []
for contig in contigs:
L = 0
for n,(a,b) in enumerate(x.split("-") for x in contig.split("/")):
if a[0].isalpha():
L += int(b)-int(a[1:]) + 1
else:
L += int(b)
Ls.append(L)
return Ls
def make_animation(pos, plddt=None, Ls=None, ref=0, line_w=2.0, dpi=100):
if plddt is None:
plddt = [None] * len(pos)
# center inputs
pos = pos - pos[ref,None].mean(1,keepdims=True)
# align to best view
best_view = _np_kabsch(pos[ref], pos[ref], return_v=True, use_jax=False)
pos = np.asarray([p @ best_view for p in pos])
fig, (ax1) = plt.subplots(1)
fig.set_figwidth(5)
fig.set_figheight(5)
fig.set_dpi(dpi)
xy_min = pos[...,:2].min() - 1
xy_max = pos[...,:2].max() + 1
z_min = None #pos[...,-1].min() - 1
z_max = None #pos[...,-1].max() + 1
for ax in [ax1]:
ax.set_xlim(xy_min, xy_max)
ax.set_ylim(xy_min, xy_max)
ax.axis(False)
ims=[]
for pos_,plddt_ in zip(pos,plddt):
if plddt_ is None:
if Ls is None:
img = plot_pseudo_3D(pos_, ax=ax1, line_w=line_w, zmin=z_min, zmax=z_max)
else:
c = np.concatenate([[n]*L for n,L in enumerate(Ls)])
img = plot_pseudo_3D(pos_, c=c, cmap=pymol_cmap, cmin=0, cmax=39, line_w=line_w, ax=ax1, zmin=z_min, zmax=z_max)
else:
img = plot_pseudo_3D(pos_, c=plddt_, cmin=50, cmax=90, line_w=line_w, ax=ax1, zmin=z_min, zmax=z_max)
ims.append([img])
ani = animation.ArtistAnimation(fig, ims, blit=True, interval=120)
plt.close()
return ani.to_html5_video() |