def pairwise_rmsdnpy(a, b):
a = npy3to2(a)
b = npy3to2(b)
ncoord = np.shape(a[0])[0]
RMSD = np.array([[(sum([(a1[i] - b1[i])**2
for i in range(ncoord)]) / (ncoord / 3))**0.5
for b1 in b] for a1 in a])
return RMSD
def rmsdnpy(npy, ref, selatoms):
ref = ref.reshape(ref.shape[0] * ref.shape[1])
struc = npy3to2(npy[:, selatoms, :])
nat = len(selatoms)
RMSD = [(sum([(s[i] - ref[i])**2 for i in range(nat * 3)]) / nat)**0.5
for s in struc]
return RMSD
nfrag = int((len(c) - 3) * 0.5)
chains = np.array([[int(i) - 1 for i in l.split()[3:3 + nfrag]]
for l in cc])
if args.nfrag is None:
nfrag = len(chains[0])
else:
nfrag = args.nfrag
assert nfrag == len(chains[0])
nat = args.nat[:nfrag + 2] # 7666 for AUUU
m = [int(i) - 1 for i in args.motifs[:nfrag]] # motifs: 1 1 2 for AUU+UUU+UUU
#assert nfrag == len(nat) - 2
assert len(m) == nfrag, (m, nfrag)
struct = [npy3to2(np.load(i)) for i in args.npy] # one np.array per motif
outp = args.outp
assert outp != args.chains_file, "outp is same as input"
c = [3 * n_atoms for n_atoms in nat]
for i in range(nfrag):
assert struct[m[i]].shape[1] == sum(c[i:i + 3]), (i, struct[m[i]].shape,
sum(c[i:i + 3]))
rna = np.zeros((len(chains), 3 * sum(nat)))
#First nucleotide unchanged
rna[:, :c[0]] = struct[m[0]][chains[:, 0], :c[0]]
#Merge pairs of overlapping atoms in 1st overlap
coor1 = struct[m[0]][chains[:, 0], c[0]:sum(c[:2])]
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('npy', help="numpy coordinates")
parser.add_argument("--ref", help="reference pdb structures", nargs='+')
parser.add_argument("--sym", default=None, help="indices of symetrical atoms")
parser.add_argument("--atoms",
default=None,
help="indices of atoms to consider")
args = parser.parse_args()
#######################################
refs = args.ref
# convert references into lists of coordinates
if refs[0].split(".")[-1] == "npy":
refs = [npy3to2(np.load(r)) for r in refs]
else:
coors = []
for r in refs:
ll = [l for l in open(r).readlines() if l.startswith("ATOM")]
coor = [[float(l[30:38]),
float(l[38:46]),
float(l[46:54])] for l in ll]
coors.append(coor)
refs = np.array(coors)
npy = npy2to3(np.load(args.npy))
nat = np.shape(npy)[1]
selatoms = range(nat)
if args.atoms:
selatoms = [int(i) - 1 for i in args.atoms]
outp = name + '-dr' + str(args.cutoff) + '.npy'
else:
outp = args.outp
if args.fit:
print("fitting", file=sys.stderr)
from rmsdlib import multifit
rotation, translation, RMSD = multifit(npy, npy[0])
rot = np.transpose(rotation, axes=(0, 2, 1))
COM = npy.sum(axis=1) / npy.shape[1]
translated = npy - COM[:, None, :]
#print(rot.shape, file=sys.stderr)
#print(translated.shape, file=sys.stderr)
npy = np.einsum('...ij,...jk->...ik', translated, rot)
npy = npy[[i for i in range(len(RMSD)) if RMSD[i] > args.cutoff or i == 0]]
if not args.center:
COM1 = npy[0].sum(axis=0)
npy = npy + COM1
from cluster import cluster
nn = npy3to2(npy)
c = cluster(npy3to2(npy), args.cutoff, args.chunksize)
centers = np.array([c[k][0] for k in list(c.keys())])
npclust = npy[centers]
clustlist = open('%s-clust%.1f.list' % (name, args.cutoff), "w")
print(name + "-clust" + str(args.cutoff))
for k in centers:
print("%i " % (k + 1), file=clustlist)
np.save(outp, npclust)
clustlist.close()