def align_sequences(self):
aout, bout = self.align()
list1 = []
list2 = []
for ind in range(len(aout)):
if aout[ind] != '-' and bout[ind] != '-':
aout[ind].vtk_arg_list['trace']['color'] = [1.0, 1.0, 1.0]
bout[ind].vtk_arg_list['trace']['color'] = [1.0, 1.0, 1.0]
list1.append(aout[ind].central_atom)
list2.append(bout[ind].central_atom)
ps = [self.target.atoms, self.template.atoms]
tm, rm = Superimpose._fit_pair_atoms([list1, list2])
Superimpose._transform(tm, rm, self.template.atoms)
self.template.parent.save_pdb('target.pdb')
self.target.parent.save_pdb('template.pdb')
rms = Superimpose._get_atoms_rms([list1, list2])
print 'initial rms = %s over %s atoms' % (rms, len(list1))
target_central_atoms = copy.deepcopy(list1)
template_central_atoms = copy.deepcopy(list2)
new_target_atoms = []
new_template_atoms = []
for i in range(len(target_central_atoms)):
#print '%s %s %s'%(target_central_atoms[i].dist(template_central_atoms[i]), target_central_atoms[i].res_type, template_central_atoms[i].res_type)
if target_central_atoms[i].dist(template_central_atoms[i]) < 8.0:
for atom in [list1[i], list2[i]]:
atom.parent.vtk_arg_list['trace']['color'] = [
1.0, 1.0, 0.0
]
atom.vtk_arg_list['atoms']['color'] = [1.0, 1.0, 0.0]
new_target_atoms.append(target_central_atoms[i])
new_template_atoms.append(template_central_atoms[i])
if len(new_target_atoms) > 5:
tm, rm = Superimpose._fit_pair_atoms(
[new_target_atoms, new_template_atoms])
Superimpose._transform(tm, rm, self.template.atoms)
self.template.parent.save_pdb('target.pdb')
self.target.parent.save_pdb('template.pdb')
rms = Superimpose._fit_atoms_rms(
[new_target_atoms, new_template_atoms])
print 'new rms = %s over %s atoms' % (rms, len(new_target_atoms))
else:
print 'fewer than 5 atoms fit good in second fit'
identical_pairs = 0
total_pairs = 0
for ind in range(len(aout)):
if aout[ind] != '-' and bout[ind] != '-':
if aout[ind].res_type1 == bout[ind].res_type1:
identical_pairs += 1
total_pairs += 1
return (identical_pairs + 0.0) / total_pairs
def align_sequences(self):
aout, bout = self.align()
list1 = []
list2 = []
for ind in range(len(aout)):
if aout[ind] != '-' and bout[ind] != '-':
aout[ind].vtk_arg_list['trace']['color'] = [1.0,1.0,1.0]
bout[ind].vtk_arg_list['trace']['color'] = [1.0,1.0,1.0]
list1.append(aout[ind].central_atom)
list2.append(bout[ind].central_atom)
ps = [self.target.atoms, self.template.atoms]
tm, rm = Superimpose._fit_pair_atoms([list1,list2])
Superimpose._transform(tm, rm, self.template.atoms)
self.template.parent.save_pdb('target.pdb')
self.target.parent.save_pdb('template.pdb')
rms = Superimpose._get_atoms_rms([list1, list2])
print 'initial rms = %s over %s atoms'%(rms, len(list1))
target_central_atoms = copy.deepcopy(list1)
template_central_atoms = copy.deepcopy(list2)
new_target_atoms = []
new_template_atoms = []
for i in range(len(target_central_atoms)):
#print '%s %s %s'%(target_central_atoms[i].dist(template_central_atoms[i]), target_central_atoms[i].res_type, template_central_atoms[i].res_type)
if target_central_atoms[i].dist(template_central_atoms[i]) < 8.0:
for atom in [list1[i], list2[i]]:
atom.parent.vtk_arg_list['trace']['color'] = [1.0,1.0,0.0]
atom.vtk_arg_list['atoms']['color'] = [1.0,1.0,0.0]
new_target_atoms.append(target_central_atoms[i])
new_template_atoms.append(template_central_atoms[i])
if len(new_target_atoms) > 5:
tm, rm = Superimpose._fit_pair_atoms([new_target_atoms,new_template_atoms])
Superimpose._transform(tm, rm, self.template.atoms)
self.template.parent.save_pdb('target.pdb')
self.target.parent.save_pdb('template.pdb')
rms = Superimpose._fit_atoms_rms([new_target_atoms, new_template_atoms])
print 'new rms = %s over %s atoms'%(rms, len(new_target_atoms))
else:
print 'fewer than 5 atoms fit good in second fit'
identical_pairs = 0
total_pairs = 0
for ind in range(len(aout)):
if aout[ind] != '-' and bout[ind] != '-':
if aout[ind].res_type1 == bout[ind].res_type1:
identical_pairs += 1
total_pairs += 1
return (identical_pairs + 0.0)/total_pairs
def align_structures(self):
aout, bout = self.align()
list1 = []
list2 = []
for ind in range(len(aout)):
if aout[ind] != '-' and bout[ind] != '-':
aout[ind].vtk_arg_list['trace']['color'] = [1.0, 1.0, 1.0]
bout[ind].vtk_arg_list['trace']['color'] = [1.0, 1.0, 1.0]
list1.append(aout[ind].central_atom)
list2.append(bout[ind].central_atom)
ps = [self.target.atoms, self.template.atoms]
tm, rm = Superimpose._fit_pair_atoms([list1, list2])
scores = 0.0
cntr = 0
for i in range(len(aout)):
if aout[i] != '-' and bout[i] != '-':
scores += self.score_by_key(aout[i].res_number,
bout[i].res_number,
[0.0, 0.11, 0.91, 0.0])
cntr += 1
print 'avg score %s' % (scores / cntr)
Superimpose._transform(tm, rm, self.template.atoms)
rms = Superimpose._get_atoms_rms([list1, list2])
print 'initial rms = %s over %s atoms' % (rms, len(list1))
for max_dist_for_pairing in [5.0, 4.0, 3.0]:
target_central_atoms = copy.deepcopy(list1)
template_central_atoms = copy.deepcopy(list2)
new_target_atoms = []
new_template_atoms = []
for i in range(len(target_central_atoms)):
#print '%s %s %s'%(target_central_atoms[i].dist(template_central_atoms[i]), target_central_atoms[i].res_type, template_central_atoms[i].res_type)
if target_central_atoms[i].dist(
template_central_atoms[i]) < max_dist_for_pairing:
new_target_atoms.append(target_central_atoms[i])
new_template_atoms.append(template_central_atoms[i])
if len(new_target_atoms) > 5:
tm, rm = Superimpose._fit_pair_atoms(
[new_target_atoms, new_template_atoms])
Superimpose._transform(tm, rm, self.template.atoms)
rms = Superimpose._fit_atoms_rms(
[new_target_atoms, new_template_atoms])
print 'new rms = %s over %s atom pairs < %s distance' % (
rms, len(new_target_atoms), max_dist_for_pairing)
else:
print 'fewer than 5 atoms fit good in fit'
for res in self.target.residues:
res.central_atom.vtk_arg_list['atoms']['color'] = [0.0, 0.0, 1.0]
for res in self.template.residues:
res.central_atom.vtk_arg_list['atoms']['color'] = [0.0, 0.0, 1.0]
target_central_atoms = copy.deepcopy(list1)
template_central_atoms = copy.deepcopy(list2)
max_dist_for_pairing = 2.0
for i in range(len(list1)):
for atom in [list1[i], list2[i]]:
atom.parent.vtk_arg_list['trace']['color'] = [1.0, 1.0, 1.0]
atom.vtk_arg_list['atoms']['color'] = [1.0, 1.0, 1.0]
if list1[i].dist(list2[i]) < max_dist_for_pairing:
new_target_atoms.append(target_central_atoms[i])
new_template_atoms.append(template_central_atoms[i])
for atom in [list1[i], list2[i]]:
atom.parent.vtk_arg_list['trace']['color'] = [
1.0, 1.0, 0.0
]
atom.vtk_arg_list['atoms']['color'] = [1.0, 1.0, 0.0]
if len(new_target_atoms) > 5:
# now transform the original list of equivalent (non-gap) alpha carbon
# atoms to get the overall rms
tm, rm = Superimpose._fit_pair_atoms(
[new_target_atoms, new_template_atoms])
Superimpose._transform(tm, rm, self.template.atoms)
rms = Superimpose._get_atoms_rms(
[new_target_atoms, new_template_atoms])
print 'final rms = %s over %s atom pairs < %s distance' % (
rms, len(new_target_atoms), max_dist_for_pairing)
else:
print 'fewer than 5 atoms fit good in final fit'
return rms, len(new_target_atoms)
def align_structures(self):
aout, bout = self.align()
list1 = []
list2 = []
for ind in range(len(aout)):
if aout[ind] != '-' and bout[ind] != '-':
aout[ind].vtk_arg_list['trace']['color'] = [1.0,1.0,1.0]
bout[ind].vtk_arg_list['trace']['color'] = [1.0,1.0,1.0]
list1.append(aout[ind].central_atom)
list2.append(bout[ind].central_atom)
ps = [self.target.atoms, self.template.atoms]
tm, rm = Superimpose._fit_pair_atoms([list1,list2])
scores = 0.0
cntr = 0
for i in range(len(aout)):
if aout[i] != '-' and bout[i] != '-':
scores += self.score_by_key(aout[i].res_number, bout[i].res_number, [0.0,0.11,0.91,0.0])
cntr += 1
print 'avg score %s'%(scores/cntr)
Superimpose._transform(tm, rm, self.template.atoms)
rms = Superimpose._get_atoms_rms([list1, list2])
print 'initial rms = %s over %s atoms'%(rms, len(list1))
for max_dist_for_pairing in [5.0,4.0,3.0]:
target_central_atoms = copy.deepcopy(list1)
template_central_atoms = copy.deepcopy(list2)
new_target_atoms = []
new_template_atoms = []
for i in range(len(target_central_atoms)):
#print '%s %s %s'%(target_central_atoms[i].dist(template_central_atoms[i]), target_central_atoms[i].res_type, template_central_atoms[i].res_type)
if target_central_atoms[i].dist(template_central_atoms[i]) < max_dist_for_pairing:
new_target_atoms.append(target_central_atoms[i])
new_template_atoms.append(template_central_atoms[i])
if len(new_target_atoms) > 5:
tm, rm = Superimpose._fit_pair_atoms([new_target_atoms,new_template_atoms])
Superimpose._transform(tm, rm, self.template.atoms)
rms = Superimpose._fit_atoms_rms([new_target_atoms, new_template_atoms])
print 'new rms = %s over %s atom pairs < %s distance'%(rms, len(new_target_atoms), max_dist_for_pairing)
else:
print 'fewer than 5 atoms fit good in fit'
for res in self.target.residues:
res.central_atom.vtk_arg_list['atoms']['color'] = [0.0,0.0,1.0]
for res in self.template.residues:
res.central_atom.vtk_arg_list['atoms']['color'] = [0.0,0.0,1.0]
target_central_atoms = copy.deepcopy(list1)
template_central_atoms = copy.deepcopy(list2)
max_dist_for_pairing = 2.0
for i in range(len(list1)):
for atom in [list1[i], list2[i]]:
atom.parent.vtk_arg_list['trace']['color'] = [1.0,1.0,1.0]
atom.vtk_arg_list['atoms']['color'] = [1.0,1.0,1.0]
if list1[i].dist(list2[i]) < max_dist_for_pairing:
new_target_atoms.append(target_central_atoms[i])
new_template_atoms.append(template_central_atoms[i])
for atom in [list1[i], list2[i]]:
atom.parent.vtk_arg_list['trace']['color'] = [1.0,1.0,0.0]
atom.vtk_arg_list['atoms']['color'] = [1.0,1.0,0.0]
if len(new_target_atoms) > 5:
# now transform the original list of equivalent (non-gap) alpha carbon
# atoms to get the overall rms
tm, rm = Superimpose._fit_pair_atoms([new_target_atoms,new_template_atoms])
Superimpose._transform(tm, rm, self.template.atoms)
rms = Superimpose._get_atoms_rms([new_target_atoms, new_template_atoms])
print 'final rms = %s over %s atom pairs < %s distance'%(rms, len(new_target_atoms), max_dist_for_pairing)
else:
print 'fewer than 5 atoms fit good in final fit'
return rms, len(new_target_atoms)