def rmsdQCP3(previous_smotif, csmotif, direction):
"""
:param previous_smotif:
:param csmotif:
:param direction:
:return:
"""
for entry in previous_smotif:
if 'qcp_rmsd' == entry[0]:
temp_holder = entry[1]
presse = temp_holder[:]
#print csmotif
if direction == 'left':
frag_b = getcoo(csmotif[2])
native_fragb_2ndsse = copy.copy(csmotif[1])
frag_a = copy.deepcopy(presse[0])
else:
try:
frag_a = copy.deepcopy(presse[-1])
frag_b = getcoo(csmotif[1])
native_fragb_2ndsse = copy.copy(csmotif[2])
except:
print previous_smotif
frag_a, a_cen = centerCoo(frag_a)
frag_b, b_cen = centerCoo(frag_b)
frag_aca = getCAcoo(frag_a)
frag_bca = getCAcoo(frag_b)
fraglen = len(frag_aca[0])
xyz1 = qcprot.MakeDMatrix(3, fraglen)
xyz2 = qcprot.MakeDMatrix(3, fraglen)
for i in range(0, fraglen):
qcprot.SetDArray(0, i, xyz1, frag_aca[0][i])
qcprot.SetDArray(1, i, xyz1, frag_aca[1][i])
qcprot.SetDArray(2, i, xyz1, frag_aca[2][i])
for i in range(0, fraglen):
qcprot.SetDArray(0, i, xyz2, frag_bca[0][i])
qcprot.SetDArray(1, i, xyz2, frag_bca[1][i])
qcprot.SetDArray(2, i, xyz2, frag_bca[2][i])
rot = qcprot.MakeDvector(9)
# *********
rmsd = qcprot.CalcRMSDRotationalMatrix(xyz1, xyz2, fraglen, rot)
# *********
# print rmsd
rotmat = []
for i in range(0, 9):
rotmat.append(qcprot.GetDvector(i, rot))
# translate the other SSE of the current smotif
sse_2nd_coos = getcoo(native_fragb_2ndsse)
cm_sse2nd = translateCM(sse_2nd_coos, b_cen)
rot_sse_2nd = applyRot(cm_sse2nd, rotmat)
trans_sse2nd = applyTranslation(rot_sse_2nd, a_cen)
# append the translated coordinates
temp_holder = copy.deepcopy(presse)
if direction == 'left':
temp_holder.insert(0, trans_sse2nd)
else:
temp_holder.append(trans_sse2nd)
qcprot.FreeDMatrix(xyz1)
qcprot.FreeDMatrix(xyz2)
qcprot.FreeDArray(rot)
return rmsd, temp_holder
def rmsdQCP(psmotif, csmotif, direction):
"""
use rmsdQCP
:param psmotif:
:param csmotif:
:param direction:
:return:
"""
psmotif = copy.copy(psmotif[1])
if direction == 'left':
native_fraga = getcoo(psmotif[1])
frag_a = getcoo(psmotif[1])
frag_b = getcoo(csmotif[2])
native_fragb_2ndsse = copy.copy(csmotif[1])
native_fraga_2ndsse = getcoo(psmotif[2])
else:
native_fraga = getcoo(psmotif[2])
frag_a = getcoo(psmotif[2])
frag_b = getcoo(csmotif[1])
native_fragb_2ndsse = copy.copy(csmotif[2])
native_fraga_2ndsse = getcoo(psmotif[1])
frag_a, a_cen = centerCoo(frag_a)
frag_b, b_cen = centerCoo(frag_b)
frag_aca = getCAcoo(frag_a)
frag_bca = getCAcoo(frag_b)
fraglen = len(frag_aca[0])
xyz1 = qcprot.MakeDMatrix(3, fraglen)
xyz2 = qcprot.MakeDMatrix(3, fraglen)
for i in range(0, fraglen):
qcprot.SetDArray(0, i, xyz1, frag_aca[0][i])
qcprot.SetDArray(1, i, xyz1, frag_aca[1][i])
qcprot.SetDArray(2, i, xyz1, frag_aca[2][i])
for i in range(0, fraglen):
qcprot.SetDArray(0, i, xyz2, frag_bca[0][i])
qcprot.SetDArray(1, i, xyz2, frag_bca[1][i])
qcprot.SetDArray(2, i, xyz2, frag_bca[2][i])
rot = qcprot.MakeDvector(9)
# *********
rmsd = qcprot.CalcRMSDRotationalMatrix(xyz1, xyz2, fraglen, rot)
# *********
rotmat = []
for i in range(0, 9):
rotmat.append(qcprot.GetDvector(i, rot))
rotated_fragb = applyRot(frag_b, rotmat)
# trans_fragb = applyTranslation(rotated_fragb, a_cen)
# translate the other SSE of the current smotif
sse_2nd_coos = getcoo(native_fragb_2ndsse)
# sse_2nd_coos, sec_cm = centerCoo(sse_2nd_coos)
cm_sse2nd = translateCM(sse_2nd_coos,b_cen)
rot_sse_2nd = applyRot(cm_sse2nd, rotmat)
trans_sse2nd = applyTranslation(rot_sse_2nd, a_cen)
#return 3 arrays of coordinates
if direction == 'left':
#transformed_coor = [native_fraga, native_fraga_2ndsse, trans_sse2nd]
transformed_coor = [trans_sse2nd, native_fraga, native_fraga_2ndsse]
#
else:
transformed_coor = [native_fraga_2ndsse, native_fraga, trans_sse2nd]
qcprot.FreeDMatrix(xyz1)
qcprot.FreeDMatrix(xyz2)
qcprot.FreeDArray(rot)
return rmsd, transformed_coor
def refineRMSD(smotif_coors, pair, csmotif, rmsd_cutoff):
tsmotif_coors = copy.deepcopy(smotif_coors)
frag_a1 = tsmotif_coors[pair[0]]
frag_a2 = tsmotif_coors[pair[1]]
frag_a = combine_arrays(frag_a1, frag_a2)
frag_b1 = getcoo(csmotif[1])
frag_b2 = getcoo(csmotif[2])
frag_b = combine_arrays(frag_b1, frag_b2)
frag_a, a_cen = centerCoo(frag_a)
frag_b, b_cen = centerCoo(frag_b)
frag_aca = getCAcoo(frag_a)
frag_bca = getCAcoo(frag_b)
fraglen = len(frag_aca[0])
xyz1 = qcprot.MakeDMatrix(3, fraglen)
xyz2 = qcprot.MakeDMatrix(3, fraglen)
for i in range(0, fraglen):
qcprot.SetDArray(0, i, xyz1, frag_aca[0][i])
qcprot.SetDArray(1, i, xyz1, frag_aca[1][i])
qcprot.SetDArray(2, i, xyz1, frag_aca[2][i])
for i in range(0, fraglen):
qcprot.SetDArray(0, i, xyz2, frag_bca[0][i])
qcprot.SetDArray(1, i, xyz2, frag_bca[1][i])
qcprot.SetDArray(2, i, xyz2, frag_bca[2][i])
rot = qcprot.MakeDvector(9)
# *********
rmsd = qcprot.CalcRMSDRotationalMatrix(xyz1, xyz2, fraglen, rot)
# *********
if rmsd > rmsd_cutoff:
# exit without further computation
# free memory
qcprot.FreeDMatrix(xyz1)
qcprot.FreeDMatrix(xyz2)
qcprot.FreeDArray(rot)
return [], rmsd
else:
rotmat = [None] * 9
for i in range(0, 9):
rotmat[i] = qcprot.GetDvector(i, rot)
cm_frag_b1 = translateCM(frag_b1, b_cen)
cm_frag_b2 = translateCM(frag_b2, b_cen)
rot_frag_b1 = applyRot(cm_frag_b1, rotmat)
rot_frag_b2 = applyRot(cm_frag_b2, rotmat)
trans_frag_b1 = applyTranslation(rot_frag_b1, a_cen)
trans_frag_b2 = applyTranslation(rot_frag_b2, a_cen)
tsmotif_coors.pop(pair[0])
tsmotif_coors.insert(pair[0], trans_frag_b1)
tsmotif_coors.pop(pair[1])
tsmotif_coors.insert(pair[1], trans_frag_b2)
qcprot.FreeDMatrix(xyz1)
qcprot.FreeDMatrix(xyz2)
qcprot.FreeDArray(rot)
return tsmotif_coors, rmsd
def rmsdQCP4(pair, presse, alt_smotif_log, csmotif, direction, cutoff):
"""
TODO Delete this function
:param pair:
:param presse:
:param alt_smotif_log:
:param csmotif:
:param direction:
:param cutoff:
:return:
"""
from utility.alt_smotif_util import delete_last_sse
if direction == 'left':
frag_b = getcoo(csmotif[2])
native_fragb_2ndsse = (csmotif[1])[:]
frag_a = copy.deepcopy(presse[pair[1]])
presse = delete_last_sse(presse, alt_smotif_log)
else:
frag_a = copy.deepcopy(presse[pair[0]])
frag_b = getcoo(csmotif[1])
native_fragb_2ndsse = (csmotif[2])[:]
presse = delete_last_sse(presse, alt_smotif_log)
frag_a, a_cen = centerCoo(frag_a)
frag_b, b_cen = centerCoo(frag_b)
frag_aca = getCAcoo(frag_a)
frag_bca = getCAcoo(frag_b)
fraglen = len(frag_aca[0])
xyz1 = qcprot.MakeDMatrix(3, fraglen)
xyz2 = qcprot.MakeDMatrix(3, fraglen)
for i in range(0, fraglen):
qcprot.SetDArray(0, i, xyz1, frag_aca[0][i])
qcprot.SetDArray(1, i, xyz1, frag_aca[1][i])
qcprot.SetDArray(2, i, xyz1, frag_aca[2][i])
for i in range(0, fraglen):
qcprot.SetDArray(0, i, xyz2, frag_bca[0][i])
qcprot.SetDArray(1, i, xyz2, frag_bca[1][i])
qcprot.SetDArray(2, i, xyz2, frag_bca[2][i])
rot = qcprot.MakeDvector(9)
# *********
rmsd = qcprot.CalcRMSDRotationalMatrix(xyz1, xyz2, fraglen, rot)
# *********
if rmsd > cutoff:
# exit without further computation
# free memory
qcprot.FreeDMatrix(xyz1)
qcprot.FreeDMatrix(xyz2)
qcprot.FreeDArray(rot)
return rmsd, []
rotmat = [None] * 9
for i in range(0, 9):
rotmat[i] = qcprot.GetDvector(i, rot)
# translate the other SSE of the current smotif
sse_2nd_coos = getcoo(native_fragb_2ndsse)
cm_sse2nd = translateCM(sse_2nd_coos, b_cen)
rot_sse_2nd = applyRot(cm_sse2nd, rotmat)
trans_sse2nd = applyTranslation(rot_sse_2nd, a_cen)
# append the translated coordinates
temp_holder = presse[:]
if direction == 'left':
temp_holder.insert(0, trans_sse2nd)
else:
temp_holder.append(trans_sse2nd)
# free memory
qcprot.FreeDMatrix(xyz1)
qcprot.FreeDMatrix(xyz2)
qcprot.FreeDArray(rot)
return rmsd, temp_holder
def rmsdQCP3(previous_smotif, csmotif, direction, cutoff, previous_sse_index):
"""
:param previous_smotif:
:param csmotif:
:param direction:
:param cutoff:
:param previous_sse_index:
:return:
"""
psmotif = (previous_smotif[2][1])[:]
psmotif_index = previous_sse_index[-1]
if direction == 'left':
frag_b = getcoo(csmotif[2])
native_fragb_2ndsse = (csmotif[1])[:]
frag_a = copy.deepcopy(psmotif[psmotif_index])
else:
frag_a = copy.deepcopy(psmotif[psmotif_index])
frag_b = getcoo(csmotif[1])
native_fragb_2ndsse = (csmotif[2])[:]
frag_a, a_cen = centerCoo(frag_a)
frag_b, b_cen = centerCoo(frag_b)
frag_aca = getCAcoo(frag_a)
frag_bca = getCAcoo(frag_b)
fraglen = len(frag_aca[0])
xyz1 = qcprot.MakeDMatrix(3, fraglen)
xyz2 = qcprot.MakeDMatrix(3, fraglen)
for i in range(0, fraglen):
qcprot.SetDArray(0, i, xyz1, frag_aca[0][i])
qcprot.SetDArray(1, i, xyz1, frag_aca[1][i])
qcprot.SetDArray(2, i, xyz1, frag_aca[2][i])
for i in range(0, fraglen):
qcprot.SetDArray(0, i, xyz2, frag_bca[0][i])
qcprot.SetDArray(1, i, xyz2, frag_bca[1][i])
qcprot.SetDArray(2, i, xyz2, frag_bca[2][i])
rot = qcprot.MakeDvector(9)
# *********
rmsd = qcprot.CalcRMSDRotationalMatrix(xyz1, xyz2, fraglen, rot)
# *********
if rmsd > cutoff:
# exit without further computation
# free memory
qcprot.FreeDMatrix(xyz1)
qcprot.FreeDMatrix(xyz2)
qcprot.FreeDArray(rot)
return rmsd, []
rotmat = [None] * 9
for i in range(0, 9):
rotmat[i] = qcprot.GetDvector(i, rot)
# translate the other SSE of the current smotif
sse_2nd_coos = getcoo(native_fragb_2ndsse)
cm_sse2nd = translateCM(sse_2nd_coos, b_cen)
rot_sse_2nd = applyRot(cm_sse2nd, rotmat)
trans_sse2nd = applyTranslation(rot_sse_2nd, a_cen)
# append the translated coordinates
temp_holder = (psmotif)[:]
if direction == 'left':
temp_holder.insert(0, trans_sse2nd)
else:
temp_holder.append(trans_sse2nd)
# free memory
qcprot.FreeDMatrix(xyz1)
qcprot.FreeDMatrix(xyz2)
qcprot.FreeDArray(rot)
return rmsd, temp_holder
def rmsdQCP(psmotif, csmotif, direction, cutoff, previous_sse_index):
"""
use rmsdQCP
:param psmotif:
:param csmotif:
:param direction:
:param cutoff:
:param previous_sse_index:
:return:
"""
psmotif = (psmotif[1])[:]
psmotif_index = previous_sse_index[-1]
if psmotif_index == 0:
indexa = 1
indexb = 2
elif psmotif_index == 1:
indexa = 2
indexb = 1
else:
print "Error"
# Extra careful about this if-else loop, the trick is finding the the correct arrays
if direction == 'left':
native_fraga = getcoo(psmotif[indexa])
frag_a = getcoo(psmotif[indexa])
frag_b = getcoo(csmotif[2])
native_fragb_2ndsse = (csmotif[1])[:]
native_fraga_2ndsse = getcoo(psmotif[indexb])
else:
native_fraga = getcoo(psmotif[indexa])
frag_a = getcoo(psmotif[indexa])
frag_b = getcoo(csmotif[1])
native_fragb_2ndsse = (csmotif[2])[:]
native_fraga_2ndsse = getcoo(psmotif[indexb])
frag_a, a_cen = centerCoo(frag_a)
frag_b, b_cen = centerCoo(frag_b)
frag_aca = getCAcoo(frag_a)
frag_bca = getCAcoo(frag_b)
fraglen = len(frag_aca[0])
xyz1 = qcprot.MakeDMatrix(3, fraglen)
xyz2 = qcprot.MakeDMatrix(3, fraglen)
for i in range(0, fraglen):
qcprot.SetDArray(0, i, xyz1, frag_aca[0][i])
qcprot.SetDArray(1, i, xyz1, frag_aca[1][i])
qcprot.SetDArray(2, i, xyz1, frag_aca[2][i])
for i in range(0, fraglen):
qcprot.SetDArray(0, i, xyz2, frag_bca[0][i])
qcprot.SetDArray(1, i, xyz2, frag_bca[1][i])
qcprot.SetDArray(2, i, xyz2, frag_bca[2][i])
rot = qcprot.MakeDvector(9)
# *********
rmsd = qcprot.CalcRMSDRotationalMatrix(xyz1, xyz2, fraglen, rot)
# *********
if rmsd > cutoff:
# exit without further computation
# free memory
qcprot.FreeDMatrix(xyz1)
qcprot.FreeDMatrix(xyz2)
qcprot.FreeDArray(rot)
return rmsd, []
rotmat = [None] * 9
for i in range(0, 9):
rotmat[i] = qcprot.GetDvector(i, rot)
# translate the other SSE of the current smotif
sse_2nd_coos = getcoo(native_fragb_2ndsse)
cm_sse2nd = translateCM(sse_2nd_coos, b_cen)
rot_sse_2nd = applyRot(cm_sse2nd, rotmat)
trans_sse2nd = applyTranslation(rot_sse_2nd, a_cen)
# return 3 arrays of coordinates
# The order problem ?
if direction == 'left':
if psmotif_index == 0:
transformed_coor = [
trans_sse2nd, native_fraga, native_fraga_2ndsse
]
else:
transformed_coor = [
trans_sse2nd, native_fraga_2ndsse, native_fraga
]
else:
if psmotif_index == 1: # double check this
transformed_coor = [
native_fraga_2ndsse, native_fraga, trans_sse2nd
]
else:
transformed_coor = [
native_fraga, native_fraga_2ndsse, trans_sse2nd
]
# free memory
qcprot.FreeDMatrix(xyz1)
qcprot.FreeDMatrix(xyz2)
qcprot.FreeDArray(rot)
return rmsd, transformed_coor