def rotateTranslatePdb(fname,
rotX,
rotY,
rotZ,
transX,
transY,
transZ,
fnameOut=None):
print(fname, rotX, rotY, rotZ, transX, transY, transZ, fnameOut)
struct = myPDBParser(QUIET=True).get_structure(fname)
rotationX = rotaxis(-rotX, Vector(1, 0, 0))
rotationY = rotaxis(rotY, Vector(0, 1, 0))
rotationZ = rotaxis(-rotZ, Vector(0, 0, 1))
translation = np.array((transX, transY, transZ), 'f')
rotation = rotationX.dot(rotationY).dot(rotationZ)
struct.transform(rotation, translation)
if fnameOut is not None:
fnameOut = fnameOut
pdbWriter = PDBIO()
pdbWriter.set_structure(struct)
pdbWriter.save(fnameOut)
return struct
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(-math.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(-math.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 BuildVirtualCB(residue):
if residue.get_resname().upper() != 'GLY':
print 'ERROR: you shall not build a virtual Cb atom for non-Glycine residue'
exit(1)
# get atom coordinates as vectors
try:
n = residue['N'].get_vector()
c = residue['C'].get_vector()
ca = residue['CA'].get_vector()
except:
print 'WARNING: failed to obtain all of N, C and CA atoms in building a virtual Cb atom for residue ', residue.get_full_id(
)
return None
# center at origin
n = n - ca
c = c - ca
# find rotation matrix that rotates n -120 degrees along the ca-c vector
rot = rotaxis(-np.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
cb = cb_at_origin + ca
return cb
def _virtual_cb_vector(residue):
# get atom coordinates as vectors
n = residue['N'].get_vector()
c = residue['C'].get_vector()
ca = residue['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(-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
cb = cb_at_origin + ca
return cb
def virtual_cbeta(residue):
"""Copied from: https://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ
Function Calculates Atomic coordinates of virtual C-beta atom for glycine residue
"""
# get atom coordinates as vectors
n = residue['N'].get_vector()
c = residue['C'].get_vector()
ca = residue['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(-np.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
cb = cb_at_origin + ca
return [round(i, 3) for i in cb]
def build_coords_2xSP3(dst, at0, at1, at2):
"""
Generates coordinates for two SP3 bonds given the other two
**dst** Bond distance
**at0** Central atom
**at1** atom with existing bond
**at2** atom with existing bond
"""
cr0 = Vector(at0.get_coord())
cr1 = Vector(at1.get_coord())
cr2 = Vector(at2.get_coord())
axe = cr0 - cr1
mat = rotaxis(120. * pi / 180., axe)
bond = cr2 - cr0
bond.normalize()
bond._ar = bond._ar * dst
cr3 = cr0 + bond.left_multiply(mat)
cr4 = cr0 + bond.left_multiply(mat).left_multiply(mat)
crs = []
crs.append(cr3._ar)
crs.append(cr4._ar)
return crs
n_atoms = list(filter(lambda a: a.name == 'N',
input_structure.get_atoms()))
c_atoms = list(filter(lambda a: a.name == 'C',
input_structure.get_atoms()))
ca_atoms = list(
filter(lambda a: a.name == 'CA', input_structure.get_atoms()))
cb_xyz = []
for n_at, c_at, ca_at in zip(n_atoms, c_atoms, ca_atoms):
n = n_at.get_vector()
c = c_at.get_vector()
ca = ca_at.get_vector()
n = n - ca
c = c - ca
rot = rotaxis(-1 * np.pi * 120.0 / 180.0, c)
cb_at_origin = n.left_multiply(rot)
cb = cb_at_origin + ca
cb_xyz.append(cb)
input_distance_matrix = pd.DataFrame(
np.array([[np.linalg.norm(at2 - at1) for at2 in cb_xyz]
for at1 in cb_xyz]))
input_distance_matrix[input_distance_matrix > 20] = 0
ppb = PDB.Polypeptide.PPBuilder()
input_sequence = ppb.build_peptides(input_structure).pop().get_sequence()
# dump input sequence into a temporary file and run TrRosetta
with NamedTemporaryFile('+w') as fasta:
fasta.write('> input\n{}'.format(input_sequence))
def calculateCoordinates(refA: Residue, refB: Residue, refC: Residue, L: float,
ang: float, di: float) -> np.ndarray:
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 origin
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 protein_synthesis(l,t,d,t5,t95,d5,d95):
"""
protein_synthesis takes all the lengths, angles and dihedrals and returns points in 3-D space using rotation matrices, as well as returning the points
in space of the 5th and 95th percentiles of the angles and dihedrals
"""
V=[]
VA5=[]
VA95=[]
VD5=[]
VD95=[]
#rotation matrices for the second vector, rotating about a vector perpendicular to the first vector
if (t[0] >= 0):
RT = rotaxis(math.pi - t[0], Vector(0, 1, 0))
elif (t[0] < 0):
RT = rotaxis(-(math.pi - t[0]), Vector(0, 1, 0))
if (t5[0] >= 0):
RT5 = rotaxis(math.pi - t5[0], Vector(0, 1, 0))
elif (t[0] < 0):
RT5 = rotaxis(-(math.pi - t5[0]), Vector(0, 1, 0))
if (t5[0] >= 0):
RT95 = rotaxis(math.pi - t95[0], Vector(0, 1, 0))
elif (t[0] < 0):
RT95 = rotaxis(-(math.pi - t95[0]), Vector(0, 1, 0))
#First 3 points for the representation
#point 0
V.append(Vector(0,0,0))
#point 1
V.append(Vector(l[0],0,0))
#point 2, found by rotating the original vector and changing the length
V.append(V[1]+(V[1].left_multiply(RT)).normalized()**l[1])
#Points for the 5th and 95th percentiles
# point 0
VA5.append(Vector(0, 0, 0))
# point 1
VA5.append(Vector(l[0], 0, 0))
# point 2
VA5.append(V[1] + (V[1].left_multiply(RT5)).normalized() ** l[1])
# point 0
VA95.append(Vector(0, 0, 0))
# point 1
VA95.append(Vector(l[0], 0, 0))
# point 2
VA95.append(V[1] + (V[1].left_multiply(RT95)).normalized() ** l[1])
# point 0
VD5.append(Vector(0, 0, 0))
# point 1
VD5.append(Vector(l[0], 0, 0))
# point 2
VD5.append(V[1] + (V[1].left_multiply(RT)).normalized() ** l[1])
# point 0
VD95.append(Vector(0, 0, 0))
# point 1
VD95.append(Vector(l[0], 0, 0))
# point 2
VD95.append(V[1] + (V[1].left_multiply(RT)).normalized() ** l[1])
#loops through all the lengths, angles and dihedrals, creating new vectors and points in 3-D space
i=2
while (i<=len(l)-1):
#New angle rotation matrices
if (t[i-1] >= 0):
RT = rotaxis(math.pi - t[i-1], (V[i] - V[i-1]) ** (V[i-1]-V[i-2]))
elif (t[i-1] < 0):
RT = rotaxis(-(math.pi - t[i-1]), (V[i] - V[i-1]) ** (V[i-1]-V[i-2]))
if (t5[i-1] >= 0):
RT5 = rotaxis(math.pi - t5[i-1], (V[i] - V[i-1]) ** (V[i-1]-V[i-2]))
elif (t5[i-1] < 0):
RT5 = rotaxis(-(math.pi - t5[i-1]), (V[i] - V[i-1]) ** (V[i-1]-V[i-2]))
if (t95[i-1] >= 0):
RT95 = rotaxis(math.pi - t95[i-1], (V[i] - V[i-1]) ** (V[i-1]-V[i-2]))
elif (t95[i-1] < 0):
RT95 = rotaxis(-(math.pi - t95[i-1]), (V[i] - V[i-1]) ** (V[i-1]-V[i-2]))
#New dihedral rotation matrices
if (d[i-2] >= 0):
RD = rotaxis((math.pi - d[i-2]), V[i] - V[i-1])
elif (d[i-2] < 0):
RD = rotaxis(-(math.pi - d[i-2]), V[i] - V[i-1])
if (d5[i-2] >= 0):
RD5 = rotaxis((math.pi - d5[i-2]), V[i] - V[i-1])
elif (d5[i-2] < 0):
RD5 = rotaxis(-(math.pi - d5[i-2]), V[i] - V[i-1])
if (d95[i-2] >= 0):
RD95 = rotaxis((math.pi - d95[i-2]), V[i] - V[i-1])
elif (d95[i-2] < 0):
RD95 = rotaxis(-(math.pi - d95[i-2]), V[i] - V[i-1])
#point i+1
#rotates by angles and by dihedral
V.append(V[i]+(((V[i]-V[i-1]).left_multiply(RT)).left_multiply(RD)).normalized()**l[i])
VA5.append(V[i] + (((V[i] - V[i - 1]).left_multiply(RT5)).left_multiply(RD)).normalized() ** l[i])
VA95.append(V[i] + (((V[i] - V[i - 1]).left_multiply(RT95)).left_multiply(RD)).normalized() ** l[i])
VD5.append(V[i] + (((V[i] - V[i - 1]).left_multiply(RT)).left_multiply(RD5)).normalized() ** l[i])
VD95.append(V[i] + (((V[i] - V[i - 1]).left_multiply(RT)).left_multiply(RD95)).normalized() ** l[i])
i=i+1
return V,VA5,VA95,VD5,VD95
