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]
rmsds = rmsdnpy(npy, refs, selatoms)
rmsd = np.min(rmsds, axis=1)
for i in range(len(rmsd)):
print('%i %.2f' % (i + 1, rmsd[i]))
parser.add_argument('--postatoms',
nargs='+',
help="frag1-postatoms.npy frag2-postatoms.npy ...")
parser.add_argument('--rmsd',
nargs='+',
help="frag1.rmsd frag2.rmsd ...",
default=None)
args = parser.parse_args()
############
tree = json.load(open(args.graph))
max_meanrank = float(args.meanrank)
nfrag = tree["nfrags"]
postatoms = [npy2to3(np.load(f)) for f in args.postatoms]
preatoms = [npy2to3(np.load(f)) for f in args.preatoms]
meanrank_threshold = log(max_meanrank) * nfrag
lrmsds = []
if args.rmsd is not None:
for f in args.rmsd:
lrmsd = {}
lnr = 0
for l in open(f):
lnr += 1
ll = l.split()
if len(ll) != 2: continue
k = ll[0]
if k == "l-RMSD": k = lnr
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
assert len(
sys.argv) == 3, "usage: python rmsdnpy.py npy.npy Lboundr.pdb > outp"
npyfile = sys.argv[1] # npy.npy
if sys.argv[2].split(".")[-1] == "npy":
ref = np.load(sys.argv[2])
if len(ref.shape) > 2:
assert ref.shape[2] == 3
ref = ref.reshape((ref.shape[1], 3))
else:
pdb = sys.argv[2] # Lboundr.pdb
ll = [l for l in open(pdb).readlines() if l.startswith("ATOM")]
r = [[float(l[30:38]), float(l[38:46]), float(l[46:54])] for l in ll]
ref = np.array(r)
npy = npy2to3(np.load(npyfile))
nat = np.shape(npy)[1]
selatoms = range(nat)
if len(sys.argv) > 3:
selatoms = [int(i) - 1 for i in sys.argv[3:]]
RMSD = rmsdnpy(npy, ref, selatoms)
for i in range(len(RMSD)):
print('%i %.2f' % (i + 1, RMSD[i]))
#!/usr/bin/env python3
# Copyright Sjoerd J. De Vries (INSERM)
import sys, os
import numpy as np
from npy import npy2to3
npy = npy2to3(np.load(sys.argv[1]))
assert npy.ndim == 3, npy.ndim
pdb = sys.argv[2]
outpf = sys.argv[3]
dirname = os.path.dirname(os.path.abspath(__file__))
def read_forcefield(forcefieldfile):
ff = {}
aa = None
for l in open(forcefieldfile):
pound = l.find("#")
if pound > -1: l = l[:pound]
l = l.strip()
if not len(l): continue
ll = l.split()
if len(ll) == 1:
aa = ll[0]
assert len(aa) <= 3, l
ff[aa] = []
else:
assert aa is not None
try:
try:
steps = np.loadtxt(chainfile, dtype=int) - 1 ### changed 9-02_17:30
if len(steps.shape) == 1:
steps = np.reshape(steps, (1, steps.shape[0]))
except:
print("no np.loadtxt")
cc = [[int(i) - 1 for i in l.split()] for l in open(chainfile)]
steps = np.array(cc)
nfrag = steps.shape[1]
nat = args.nat
print(nat, file=sys.stderr)
assert nfrag == len(nat) + 1, (nfrag, len(nat))
coor = [npy2to3(np.load(i)) for i in args.coor] # one np.array per step
outp = args.outp
assert outp != args.chains_file, "ERROR: output is same as input"
#initialise merged structure
max_atom = sum([n.shape[1] for n in coor]) #max nb of atoms in final chain
rna = np.zeros((len(steps), max_atom, 3))
count = 0
#First atoms unchanged
len_step = coor[0].shape[1] #nb of atoms in 1st step
n = len_step - nat[0] #nb of atom to not merge in 1st step
rna[:, :n] = coor[0][steps[:, 0], :n]
count += n