def _construct_ideal_balls_(self):
# load residues
residues = np.loadtxt('inputs/{pdb}/{pdb}.res'.format(pdb=self.pdb)).astype(int).tolist()
residues = [200]+residues
# load regs and peris got from reg adjustment
periregs = np.loadtxt('{inputdirn}/regs/{pdb}.regs'.format(inputdirn=self.inputdirn, pdb=self.pdb)).astype(int)
peris = np.loadtxt('{inputdirn}/peris/{pdb}.peris'.format(inputdirn=self.inputdirn, pdb=self.pdb)).astype(int)
# load facings got from reg adjustment
with open('{inputdirn}/facings/{pdb}.facings'.format(inputdirn=self.inputdirn, pdb=self.pdb)) as f:
lines = f.readlines()
firstfacings = [ line.strip() for line in lines ]
# load strandends
strandends = np.loadtxt('inputs/{pdb}/{pdb}.strands'.format(pdb=self.pdb)).astype(int)
# the strand ranges here may not be the ranges used for reg prediction
# correct reg according to the difference between strandends to construct barrel and peris used in reg pred
# after this loop, array periregs will be the predicted regs of strandends
for strdi in range(len(strandends)):
strdim1 = (strdi-1)%len(strandends)
if strdi%2==0:
periregs[strdi] -= strandends[strdi][0]-peris[strdi]
periregs[strdim1] += strandends[strdi][0]-peris[strdi]
else:
periregs[strdi] += strandends[strdi][1]-peris[strdi]
periregs[strdim1] -= strandends[strdi][1]-peris[strdi]
# correct facing according to the difference between strandends to construct barrel and peris used in reg pred
for strdi in range(len(strandends)):
if strdi%2==0:
if (strandends[strdi][0]-peris[strdi])%2!=0:
if firstfacings[strdi]=='OUT':
firstfacings[strdi]='IN'
else:
firstfacings[strdi]='OUT'
else:
if (strandends[strdi][1]-peris[strdi])%2!=0:
if firstfacings[strdi]=='OUT':
firstfacings[strdi]='IN'
else:
firstfacings[strdi]='OUT'
# add extra residues for bbq
for strdi in range(len(strandends)):
strandends[strdi][0]-=Barrel.extra_ball_num
strandends[strdi][1]+=Barrel.extra_ball_num
# construct facing arrays for all residues (including extra residues)
facings = []
for fac in firstfacings:
if fac == 'OUT':
facings.append([Ball.Facing.OUT])
else:
facings.append([Ball.Facing.IN])
for strdi in range(len(strandends)):
for resi in range(strandends[strdi][1]-strandends[strdi][0]):
if facings[strdi][resi] == Ball.Facing.OUT:
facings[strdi].append(Ball.Facing.IN)
else:
facings[strdi].append(Ball.Facing.OUT)
peripositions = np.cumsum( np.hstack( ([0], -periregs) ) )
N = len(strandends) # strand num
A = self.A # intrastrand Ca distance
B = self.B # interstrand Ca distance
S = sum(periregs) # shear number
## circle formula
#a = math.sqrt( (N*B)**2+(S*A)**2 ) / 2.0 / math.pi # tilt angle
#theta = math.asin(S*A/2.0/math.pi/a) # radius
## polygan formula
theta = math.atan( S*A / (N*B) ) # tilt angle
a = B / ( 2*math.sin(math.pi/N) * math.cos(theta) ) # radius
self.radius = a
b = a / math.tan(theta) # vertical speed
c = math.sqrt( a*a + b*b )
delta = 2 * math.pi * a * a / (c*N) # offset on the neigbouring strand to ensure inter H-bond is perpendicular to the strand
currid = 0
ids = []
seqids = []
restypes = []
cacoords = []
# construct the barrel
for strdi in range(N):
# seq ids
if strdi%2==0:
seqids.append( range( strandends[strdi][0], strandends[strdi][1]+1 ) )
else:
seqids.append( range( strandends[strdi][0], strandends[strdi][1]+1 )[::-1] )
ids.append( range( currid, currid+len(seqids[strdi]) ) )
currid += len(seqids[strdi])
# residue types
restypes.append([])
for seqid in seqids[strdi]:
try:
restypes[strdi].append(AA.index_to_one(residues[seqid]))
except:
restypes[strdi].append('C')
cacoords.append([])
for resi in range(strandends[strdi][1]-strandends[strdi][0]+1):
# zigzag deviation
if facings[strdi][resi] == Ball.Facing.OUT:
dr = self.dr
# righthand side of out facing residue is always SH
# lefthand side NH
if strdi%2==0:
dw = self.dw
else:
dw = -self.dw
if self.np1_right: #test TODO
if strdi%2==0:
dw = -self.dw
else:
dw = self.dw
else:
dr = -self.dr
if strdi%2==0:
dw = -self.dw
else:
dw = self.dw
if self.np1_right: #test TODO
if strdi%2==0:
dw = self.dw
else:
dw = -self.dw
s = ( peripositions[strdi] + resi ) * A + strdi * delta
x = (a+dr) * math.cos(s/c-2*math.pi*strdi/N);
y = (a+dr) * math.sin(s/c-2*math.pi*strdi/N);
if self.np1_right: #test TODO
s = ( peripositions[strdi] + resi ) * A + (N-strdi) * delta
x = (a+dr) * math.sin(s/c+2*math.pi*strdi/N);
y = (a+dr) * math.cos(s/c+2*math.pi*strdi/N);
z = b * s/c;
xn1 = (a+dr) * ( - math.cos(s/c-2*math.pi*strdi/N) + math.cos((s+delta)/c-2*math.pi*(strdi+1)/N) );
yn1 = (a+dr) * ( - math.sin(s/c-2*math.pi*strdi/N) + math.sin((s+delta)/c-2*math.pi*(strdi+1)/N) );
zn1 = b*delta/c
if (strdi%2==1 and facings[strdi][resi] == Ball.Facing.OUT) or (strdi%2==0 and facings[strdi][resi] == Ball.Facing.IN):
xn1 = (a+dr) * ( - math.cos(s/c-2*math.pi*(strdi-1)/N) + math.cos((s+delta)/c-2*math.pi*strdi/N) );
yn1 = (a+dr) * ( - math.sin(s/c-2*math.pi*(strdi-1)/N) + math.sin((s+delta)/c-2*math.pi*strdi/N) );
zn1 = b*delta/c
if self.np1_right: #test TODO
xn1 = (a+dr) * ( - math.sin(s/c+2*math.pi*strdi/N) + math.sin((s+delta)/c+2*math.pi*(strdi+1)/N) );
yn1 = (a+dr) * ( - math.cos(s/c+2*math.pi*strdi/N) + math.cos((s+delta)/c+2*math.pi*(strdi+1)/N) );
if (strdi%2==1 and facings[strdi][resi] == Ball.Facing.OUT) or (strdi%2==0 and facings[strdi][resi] == Ball.Facing.IN):
xn1 = (a+dr) * ( - math.sin(s/c+2*math.pi*(strdi-1)/N) + math.sin((s+delta)/c+2*math.pi*strdi/N) );
yn1 = (a+dr) * ( - math.cos(s/c+2*math.pi*(strdi-1)/N) + math.cos((s+delta)/c+2*math.pi*strdi/N) );
n1norm = math.sqrt(xn1*xn1+yn1*yn1+zn1*zn1)
xn1 = xn1/n1norm
yn1 = yn1/n1norm
zn1 = zn1/n1norm
x+=dw*xn1
y+=dw*yn1
z+=dw*zn1
cacoords[strdi].append(np.array([x,y,z]))
self.strandlens.append(len(ids[strdi]))
for i in range(len(ids)):
for j in range(len(ids[i])):
## following line is for model/param selections
#ball = Ball([ ids[i][j], seqids[i][j], cacoords[i][j][0], cacoords[i][j][1], cacoords[i][j][2], AA.one_to_index(restypes[i][j]), facings[i][j] ])
## store ballids instead of seqids. needs to be correted after bbq
## if using seqids, bbq will have problems
if i%2!=0:
ball = Ball([ ids[i][j], ids[i][len(ids[i])-j-1], cacoords[i][j][0], cacoords[i][j][1], cacoords[i][j][2], AA.one_to_index(restypes[i][j]), facings[i][j] ])
if j >= Barrel.extra_ball_num and j < len(ids[i])-Barrel.extra_ball_num:
self.reindexmap.append( (ids[i][len(ids[i])-j-1], seqids[i][j]) )
else:
ball = Ball([ ids[i][j], ids[i][j], cacoords[i][j][0], cacoords[i][j][1], cacoords[i][j][2], AA.one_to_index(restypes[i][j]), facings[i][j] ])
if j >= Barrel.extra_ball_num and j < len(ids[i])-Barrel.extra_ball_num:
self.reindexmap.append( (ids[i][j], seqids[i][j]) )
self.balls.append(ball)
def __str__(self): return str(self[Ball.p_ballid]) +" "+ str(self[Ball.p_resseqid]) +" " +\ str(self.getcoord())+" "+\ AA.index_to_one(self[Ball.p_aaid]) +" "+ str(self[Ball.p_facing])