## 'serial': 1}
cid1 = atom_obj[u-1]["chainID"]
cid2 = atom_obj[u]["chainID"]
res_name1 = atom_obj[u-1]["resName"].strip()
res_name2 = atom_obj[u]["resName"].strip()
res_num1 = atom_obj[u-1]["resSeq"]
res_num2 = atom_obj[u]["resSeq"]
atm_name1 = atom_obj[u-1]["name"].strip()
atm_name2 = atom_obj[u]["name"].strip()
x1 = atom_obj[u-1]["x"]
y1 = atom_obj[u-1]["y"]
z1 = atom_obj[u-1]["z"]
x2 = atom_obj[u]["x"]
y2 = atom_obj[u]["y"]
z2 = atom_obj[u]["z"]
Upos = tlsvld.array([x1,y1,z1])
Vpos = tlsvld.array([x2,y2,z2])
tls_group = 0
## Calculate the distance between two atoms
d = math.sqrt( (x1-x2)**2 + (y1-y2)**2 + (x1-x2)**2 )
#d = AtomMath.calc_distance(atom_obj[u-1], atom_obj[u])
if ( (d > 2.0) and (cid1 == cid2) ):
print "# BOND BREAK!"
continue
## Add newlines for new chain_id
if cid1 != cid2:
chain_type = get_chain_type(res_name2)
print "\n"
continue
#!/usr/bin/python import tlsvld import scipy import numpy import math U = tlsvld.array([[0.37471362,-0.07411912,-0.0379023],[-0.07411912,0.39010298,-0.03240841],[-0.0379023,-0.03240841,0.33057791]]) V = tlsvld.array([[0.38484156,-0.06933809,-0.04994903],[-0.06933809,0.41376374,-0.03275701],[-0.04994903,-0.03275701,0.33967632]]) #print U #print V #print "="*80 #U = scipy.array([[0.37471362,-0.07411912,-0.0379023],[-0.07411912,0.39010298,-0.03240841],[-0.0379023,-0.03240841,0.33057791]]) #V = scipy.array([[0.38484156,-0.06933809,-0.04994903],[-0.06933809,0.41376374,-0.03275701],[-0.04994903,-0.03275701,0.33967632]]) #V = scipy.array([[100.38484156,-0.06933809,-0.04994903],[-0.06933809,0.41376374,-0.03275701],[-0.04994903,-0.03275701,0.33967632]]) #print U #print V #print "="*80 #U = tlsvld.array([[7,7,7],[7,7,7],[7,7,7]]) #V = tlsvld.array([[4,4,4],[4,4,4],[4,4,4]]) W = tlsvld.array([[1.0,1.0,1.0],[1.0,1.0,1.0],[1.0,1.0,1.0]]) X = tlsvld.array([[4.0,4.0,4.0],[4.0,4.0,4.0],[4.0,4.0,4.0]]) print "SQD = ",tlsvld.sum_square_diff(W,X) #print "trace(U) = ", tlsvld.trace3x3(X) print "dtUV = ",tlsvld.diff_trace_uv(W,X) print tlsvld.mul3x3(U,V) print tlsvld.add3x3(U,V) print "SUM(W) = ",tlsvld.sum3x3(X) print tlsvld.subtract3x3(U,V)
cid2 = atom_obj[u]["chainID"]
res_name1 = atom_obj[u-1]["resName"].strip()
res_name2 = atom_obj[u]["resName"].strip()
res_num1 = atom_obj[u-1]["resSeq"]
res_num2 = atom_obj[u]["resSeq"]
atm_name1 = atom_obj[u-1]["name"].strip()
atm_name2 = atom_obj[u]["name"].strip()
#pos1 = atom_obj[u-1].position
#pos2 = atom_obj[u].position
x1 = atom_obj[u-1]["x"]
y1 = atom_obj[u-1]["y"]
z1 = atom_obj[u-1]["z"]
x2 = atom_obj[u]["x"]
y2 = atom_obj[u]["y"]
z2 = atom_obj[u]["z"]
Upos = tlsvld.array([x1,y1,z1])
Vpos = tlsvld.array([x2,y2,z2])
#tls_group = atom_obj[u-1].tls_group
tls_group = 0
d = math.sqrt( (x1-x2)**2 + (y1-y2)**2 + (x1-x2)**2 )
#d = AtomMath.calc_distance(atom_obj[u-1], atom_obj[u])
if ( (d > 2.0) and (cid1 == cid2) ):
print "# BOND BREAK!"
continue
## Add newlines for new chain_id
if cid1 != cid2:
chain_type = get_chain_type(res_name2)
print "\n"
continue