def _get_gly_cb_vector(self, residue):
"""
Return a pseudo CB vector for a Gly residue.
The pseudoCB vector is centered at the origin.
CB coord=N coord rotated over -120 degrees
along the CA-C axis.
"""
try:
n_v = residue["N"].get_vector()
c_v = residue["C"].get_vector()
ca_v = residue["CA"].get_vector()
except:
return None
# center at origin
n_v = n_v - ca_v
c_v = c_v - ca_v
# rotation around c-ca over -120 deg
rot = rotaxis(-pi * 120.0 / 180.0, c_v)
cb_at_origin_v = n_v.left_multiply(rot)
# move back to ca position
cb_v = cb_at_origin_v + ca_v
# This is for PyMol visualization
self.ca_cb_list.append((ca_v, cb_v))
return cb_at_origin_v
def _get_gly_cb_vector(self, residue):
"""
Return a pseudo CB vector for a Gly residue.
The pseudoCB vector is centered at the origin.
CB coord=N coord rotated over -120 degrees
along the CA-C axis.
"""
try:
n_v=residue["N"].get_vector()
c_v=residue["C"].get_vector()
ca_v=residue["CA"].get_vector()
except:
return None
# center at origin
n_v=n_v-ca_v
c_v=c_v-ca_v
# rotation around c-ca over -120 deg
rot=rotaxis(-pi*120.0/180.0, c_v)
cb_at_origin_v=n_v.left_multiply(rot)
# move back to ca position
cb_v=cb_at_origin_v+ca_v
# This is for PyMol visualization
self.ca_cb_list.append((ca_v, cb_v))
return cb_at_origin_v
def calculateCoordinates(refA, refB, refC, L, ang, di):
AV=refA.get_vector()
BV=refB.get_vector()
CV=refC.get_vector()
CA=AV-CV
CB=BV-CV
##CA vector
AX=CA[0]
AY=CA[1]
AZ=CA[2]
##CB vector
BX=CB[0]
BY=CB[1]
BZ=CB[2]
##Plane Parameters
A=(AY*BZ)-(AZ*BY)
B=(AZ*BX)-(AX*BZ)
G=(AX*BY)-(AY*BX)
##Dot Product Constant
F= math.sqrt(BX*BX + BY*BY + BZ*BZ) * L * math.cos(ang*(math.pi/180.0))
##Constants
const=math.sqrt( math.pow((B*BZ-BY*G),2) *(-(F*F)*(A*A+B*B+G*G)+(B*B*(BX*BX+BZ*BZ) + A*A*(BY*BY+BZ*BZ)- (2*A*BX*BZ*G) + (BX*BX+ BY*BY)*G*G - (2*B*BY)*(A*BX+BZ*G))*L*L))
denom= (B*B)*(BX*BX+BZ*BZ)+ (A*A)*(BY*BY+BZ*BZ) - (2*A*BX*BZ*G) + (BX*BX+BY*BY)*(G*G) - (2*B*BY)*(A*BX+BZ*G)
X= ((B*B*BX*F)-(A*B*BY*F)+(F*G)*(-A*BZ+BX*G)+const)/denom
if((B==0 or BZ==0) and (BY==0 or G==0)):
const1=math.sqrt( G*G*(-A*A*X*X+(B*B+G*G)*(L-X)*(L+X)))
Y= ((-A*B*X)+const1)/(B*B+G*G)
Z= -(A*G*G*X+B*const1)/(G*(B*B+G*G))
else:
Y= ((A*A*BY*F)*(B*BZ-BY*G)+ G*( -F*math.pow(B*BZ-BY*G,2) + BX*const) - A*( B*B*BX*BZ*F- B*BX*BY*F*G + BZ*const)) / ((B*BZ-BY*G)*denom)
Z= ((A*A*BZ*F)*(B*BZ-BY*G) + (B*F)*math.pow(B*BZ-BY*G,2) + (A*BX*F*G)*(-B*BZ+BY*G) - B*BX*const + A*BY*const) / ((B*BZ-BY*G)*denom)
#GET THE NEW VECTOR from the orgin
D=Vector(X, Y, Z) + CV
with warnings.catch_warnings():
# ignore inconsequential warning
warnings.simplefilter("ignore")
temp=calc_dihedral(AV, BV, CV, D)*(180.0/math.pi)
di=di-temp
rot= rotaxis(math.pi*(di/180.0), CV-BV)
D=(D-BV).left_multiply(rot)+BV
return D.get_array()
def get_expected_cb_pos(aa):
n = aa['N'].get_vector()
c = aa['C'].get_vector()
ca = aa['CA'].get_vector()
# center at origin
n = n - ca
c = c - ca
# find rotation matrix that rotates n -120 degrees along the ca-c vector
rot = rotaxis(-math.pi * 120.0 / 180.0, c)
# apply rotation to ca-n vector
cb_at_origin = n.left_multiply(rot)
# put on top of ca atom
return (cb_at_origin + ca)
def get_gly_cb_coords(residue):
try:
n_v = residue["N"].get_vector()
c_v = residue["C"].get_vector()
ca_v = residue["CA"].get_vector()
except:
return None
n_v = n_v - ca_v
c_v = c_v - ca_v
rot = rotaxis(-np.pi * 120.0 / 180.0, c_v)
cb_at_origin_v = n_v.left_multiply(rot)
cb_v = cb_at_origin_v + ca_v
return cb_v.get_array()
def get_expected_cb_pos(aa): n = aa['N'].get_vector() c = aa['C'].get_vector() ca = aa['CA'].get_vector() # center at origin n = n - ca c = c - ca # find rotation matrix that rotates n -120 degrees along the ca-c vector rot = rotaxis(-math.pi*120.0/180.0, c) # apply rotation to ca-n vector cb_at_origin = n.left_multiply(rot) # put on top of ca atom return (cb_at_origin + ca)
