TRANS.append(random.uniform(-1,1)*tscale)
if verbose: print('translation=', TRANS)
#rot = [1,0,0,180]
#for the rotation axis, use xscale
rot = []
for ind in range(3):
rot.append(random.uniform(-1,1)*xscale)
#for the rotation angle
rot.append(random.uniform(-1,1)*ascale)
if verbose: print('axis=', rot[:3], ' and angle=', rot[-1])
#torsions:
dihe = []
for ind in range(ndihe):
dihe.append(dscale * random.uniform(-1,1))
if verbose: print('dihe=', dihe)
conf = Conformation(m, origin, TRANS, rot, dihe)
new_coords = conf.getCoords()
#verify that no new bonds would be formed for this conformation
m.allAtoms.updateCoords(new_coords, ind=coord_index)
#remove all original bonds and set hasBonds to 0 on all levels
del(m.allAtoms.bonds)
m.hasBonds=0
for c in m.chains: c.hasBonds=0
for r in m.chains.residues: r.hasBonds=0
for a in m.allAtoms:
a.bonds = BondSet([])
a.hasBonds = 0
m.buildBondsByDistance()
newLen = len(m.allAtoms.bonds[0])
if verbose: print("originally %d bonds form; after transformation %d bonds form" %(orig, newLen))
new_d = {}
eline = states[i + 1]
#build a states from each of the lines in statefile
#State:\t 4.847 -2.386 14.760 -0.413 0.552 -0.724 4.257 58.27 -33.47 -87.92 134.64 -36.46 114.79 -44.86 -74.96 -118.53 77.29 139.08 78.23 -52.09 -12.69 35.08 -118.21 -175.94\n'
fl = map(float, sline.split()[1:])
assert len(fl) == length_of_state
# 0 1 2 3 4 5 6 [7....
#[t1,t2,t3,q1,q2,q3,q4,tors1,tors2, tors3....
#
translation = fl[:3]
quaternion = [fl[6], fl[3:6]]
#energy = eline.split()[8]
energy = eline.split()[index_of_energy]
torsion_angles = []
if ntors > 0:
torsion_angles = fl[7:]
newConf = Conformation(lig, origin, translation, quaternion,
torsion_angles)
newCrds = newConf.getCoords()
if interim_state:
#here's where to add back the origin or ?
newCrds -= origin
#write some MODEL stuff then newCrds
ostr = "MODEL %d\n" % ctr
outptr.write(ostr)
ctr += 1
ostr = "REMARK AD4 RESULT: %s\n" % energy #put energy here...
outptr.write(ostr)
#lig.parser.write_with_new_coords(newCrds,outptr)
ct = 0
for l in ligLines:
if l.find("ATOM") == 0 or l.find("HETATM") == 0:
cc = newCrds[ct]
TRANS.append(random.uniform(-1,1)*tscale)
if verbose: print 'translation=', TRANS
#rot = [1,0,0,180]
#for the rotation axis, use xscale
rot = []
for ind in range(3):
rot.append(random.uniform(-1,1)*xscale)
#for the rotation angle
rot.append(random.uniform(-1,1)*ascale)
if verbose: print 'axis=', rot[:3], ' and angle=', rot[-1]
#torsions:
dihe = []
for ind in range(ndihe):
dihe.append(dscale * random.uniform(-1,1))
if verbose: print 'dihe=', dihe
conf = Conformation(m, origin, TRANS, rot, dihe)
new_coords = conf.getCoords()
#verify that no new bonds would be formed for this conformation
m.allAtoms.updateCoords(new_coords, ind=coord_index)
#remove all original bonds and set hasBonds to 0 on all levels
del(m.allAtoms.bonds)
m.hasBonds=0
for c in m.chains: c.hasBonds=0
for r in m.chains.residues: r.hasBonds=0
for a in m.allAtoms:
a.bonds = BondSet([])
a.hasBonds = 0
m.buildBondsByDistance()
newLen = len(m.allAtoms.bonds[0])
if verbose: print "originally %d bonds form; after transformation %d bonds form" %(orig, newLen)
new_d = {}
eline =states[i+1]
#build a states from each of the lines in statefile
#State:\t 4.847 -2.386 14.760 -0.413 0.552 -0.724 4.257 58.27 -33.47 -87.92 134.64 -36.46 114.79 -44.86 -74.96 -118.53 77.29 139.08 78.23 -52.09 -12.69 35.08 -118.21 -175.94\n'
fl = map(float, sline.split()[1:])
assert len(fl)==length_of_state
# 0 1 2 3 4 5 6 [7....
#[t1,t2,t3,q1,q2,q3,q4,tors1,tors2, tors3....
#
translation = fl[:3]
quaternion = [fl[6],fl[3:6]]
#energy = eline.split()[8]
energy = eline.split()[index_of_energy]
torsion_angles = []
if ntors>0:
torsion_angles = fl[7:]
newConf = Conformation(lig,origin,translation, quaternion, torsion_angles)
newCrds = newConf.getCoords()
if interim_state:
#here's where to add back the origin or ?
newCrds -= origin
#write some MODEL stuff then newCrds
ostr = "MODEL %d\n"%ctr
outptr.write(ostr)
ctr += 1
ostr = "REMARK AD4 RESULT: %s\n" %energy #put energy here...
outptr.write(ostr)
#lig.parser.write_with_new_coords(newCrds,outptr)
ct = 0
for l in ligLines:
if l.find("ATOM")==0 or l.find("HETATM")==0:
cc = newCrds[ct]
