File size: 2,272 Bytes
96f168d | 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 | import numpy as np
from itertools import permutations
import MDAnalysis as mda
# from MDAnalysis.analysis import dihedrals
from MDAnalysis.analysis import distances
def obtain_self_dist(res):
try:
#xx = res.atoms.select_atoms("not name H*")
xx = res.atoms
dists = distances.self_distance_array(xx.positions)
ca = xx.select_atoms("name CA")
c = xx.select_atoms("name C")
n = xx.select_atoms("name N")
o = xx.select_atoms("name O")
return [dists.max()*0.1, dists.min()*0.1, distances.dist(ca,o)[-1][0]*0.1, distances.dist(o,n)[-1][0]*0.1, distances.dist(n,c)[-1][0]*0.1]
except:
return [0, 0, 0, 0, 0]
def obtain_dihediral_angles(res):
try:
if res.phi_selection() is not None:
phi = res.phi_selection().dihedral.value()
else:
phi = 0
if res.psi_selection() is not None:
psi = res.psi_selection().dihedral.value()
else:
psi = 0
if res.omega_selection() is not None:
omega = res.omega_selection().dihedral.value()
else:
omega = 0
if res.chi1_selection() is not None:
chi1 = res.chi1_selection().dihedral.value()
else:
chi1 = 0
return [phi*0.01, psi*0.01, omega*0.01, chi1*0.01]
except:
return [0, 0, 0, 0]
##'FE', 'SR', 'GA', 'IN', 'ZN', 'CU', 'MN', 'SR', 'K' ,'NI', 'NA', 'CD' 'MG','CO','HG', 'CS', 'CA',
def obatin_edge(u, cutoff=10.0):
edgeids = []
dismin = []
dismax = []
for res1, res2 in permutations(u.residues, 2):
dist = calc_dist(res1, res2)
if dist.min() <= cutoff:
edgeids.append([res1.ix, res2.ix])
dismin.append(dist.min()*0.1)
dismax.append(dist.max()*0.1)
return edgeids, np.array([dismin, dismax]).T
def check_connect(u, i, j):
if abs(i-j) != 1:
return 0
else:
if i > j:
i = j
nb1 = len(u.residues[i].get_connections("bonds"))
nb2 = len(u.residues[i+1].get_connections("bonds"))
nb3 = len(u.residues[i:i+2].get_connections("bonds"))
if nb1 + nb2 == nb3 + 1:
return 1
else:
return 0
def calc_dist(res1, res2):
#xx1 = res1.atoms.select_atoms('not name H*')
#xx2 = res2.atoms.select_atoms('not name H*')
#dist_array = distances.distance_array(xx1.positions,xx2.positions)
dist_array = distances.distance_array(res1.atoms.positions,res2.atoms.positions)
return dist_array
#return dist_array.max()*0.1, dist_array.min()*0.1
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