def show_constraints(self, mardi_path, pdb_path):
midas.process(self.session).unshow_objects('constraints')
if not mardi_path or not pdb_path:
return
show_satisfied = self.satisfied.get()
show_violated = self.violated.get()
if not (show_satisfied or show_violated):
return
lines = midas.midas_object_file('constraints')
model = pdb.model(self.session, pdb_path)
mardi = mardigras.bounds(self.session, mardi_path)
for (num_atom_1, num_atom_2), (rmin, rmax) in mardi.bounds_table.items():
num_atom_1 = translate_atom_name(num_atom_1, mardi, model)
num_atom_2 = translate_atom_name(num_atom_2, mardi, model)
pdb_atom_1 = model.num_atom_to_pdb_atom(num_atom_1)
pdb_atom_2 = model.num_atom_to_pdb_atom(num_atom_2)
if pdb_atom_1 and pdb_atom_2:
d = pyutil.distance(pdb_atom_1.xyz, pdb_atom_2.xyz)
if ((show_satisfied and d >= rmin and d <= rmax) or
(show_violated and (d < rmin or d > rmax))):
if d < .8 * rmin: color = 'blue'
elif d < rmin: color = 'cyan'
elif d <= rmax: color = 'green'
elif d < 1.2 * rmax: color = 'magenta'
else: color = 'red'
pdb_atom_1 = model.num_atom_to_pdb_atom(num_atom_1)
pdb_atom_2 = model.num_atom_to_pdb_atom(num_atom_2)
lines.add_line(pdb_atom_1.xyz, pdb_atom_2.xyz, color)
lines.show_objects(self.session)
def chimera_open_model(self, pdb_path):
if pdb_path == self.pdb_path:
return
if self.model:
chimera = self.chimera()
chimera.openModels.close([self.model])
self.model = None
# I suspect closing the model also eliminates all constraint pseudobonds
self.num_atom_pair_to_pseudobond = {}
self.pdb_path = pdb_path
chimera = self.chimera()
models = chimera.openModels.open(pdb_path, type='PDB')
self.model = models[0] # assume just one molecule in the PDB file
self.model.color = chimera.Color_lookup('gray')
trans = pdb.model(self.session, pdb_path).atom_translations
self.make_atom_tables(self.model.atoms, trans)
if self.pseudobond_group == None:
m = chimera.PseudoBondMgr_mgr()
self.pseudobond_group = m.newPseudoBondGroup('NOESY constraints')
del m
chimera.openModels.add([self.pseudobond_group], sameAs=self.model)
def show_constraint_lines(self, mardi_path, pdb_path, range_colors):
# unshow previous constraints
if not mardi_path or not pdb_path:
return
show_satisfied = self.show_satisfied.get()
show_violated = self.show_violated.get()
if not (show_satisfied or show_violated):
return
pdb_model = pdb.model(self.session, pdb_path)
mardi = mardigras.bounds(self.session, mardi_path)
for (num_atom_1, num_atom_2), (rmin,
rmax) in mardi.bounds_table.items():
num_atom_1 = translate_atom_name(num_atom_1, mardi, pdb_model)
num_atom_2 = translate_atom_name(num_atom_2, mardi, pdb_model)
pdb_atom_1 = pdb_model.num_atom_to_pdb_atom(num_atom_1)
pdb_atom_2 = pdb_model.num_atom_to_pdb_atom(num_atom_2)
if pdb_atom_1 and pdb_atom_2:
d = pyutil.distance(pdb_atom_1.xyz, pdb_atom_2.xyz)
if ((show_satisfied and d >= rmin and d <= rmax)
or (show_violated and (d < rmin or d > rmax))):
if d < .8 * rmin: color = range_colors[0]
elif d < rmin: color = range_colors[1]
elif d <= rmax: color = range_colors[2]
elif d < 1.2 * rmax: color = range_colors[3]
else: color = range_colors[4]
self.show_constraint(num_atom_1, num_atom_2, color)
def show_constraint_lines(self, mardi_path, pdb_path, range_colors):
# unshow previous constraints
if not mardi_path or not pdb_path:
return
show_satisfied = self.show_satisfied.get()
show_violated = self.show_violated.get()
if not (show_satisfied or show_violated):
return
pdb_model = pdb.model(self.session, pdb_path)
mardi = mardigras.bounds(self.session, mardi_path)
for (num_atom_1, num_atom_2), (rmin, rmax) in mardi.bounds_table.items():
num_atom_1 = translate_atom_name(num_atom_1, mardi, pdb_model)
num_atom_2 = translate_atom_name(num_atom_2, mardi, pdb_model)
pdb_atom_1 = pdb_model.num_atom_to_pdb_atom(num_atom_1)
pdb_atom_2 = pdb_model.num_atom_to_pdb_atom(num_atom_2)
if pdb_atom_1 and pdb_atom_2:
d = pyutil.distance(pdb_atom_1.xyz, pdb_atom_2.xyz)
if ((show_satisfied and d >= rmin and d <= rmax) or
(show_violated and (d < rmin or d > rmax))):
if d < .8 * rmin: color = range_colors[0]
elif d < rmin: color = range_colors[1]
elif d <= rmax: color = range_colors[2]
elif d < 1.2 * rmax: color = range_colors[3]
else: color = range_colors[4]
self.show_constraint(num_atom_1, num_atom_2, color)
def chimera_open_model(self, pdb_path):
if pdb_path == self.pdb_path:
return
if self.model:
chimera = self.chimera()
chimera.openModels.close([self.model])
self.model = None
# I suspect closing the model also eliminates all constraint pseudobonds
self.num_atom_pair_to_pseudobond = {}
self.pdb_path = pdb_path
chimera = self.chimera()
models = chimera.openModels.open(pdb_path, type='PDB')
self.model = models[0] # assume just one molecule in the PDB file
self.model.color = chimera.Color_lookup('gray')
trans = pdb.model(self.session, pdb_path).atom_translations
self.make_atom_tables(self.model.atoms, trans)
if self.pseudobond_group == None:
m = chimera.PseudoBondMgr_mgr()
self.pseudobond_group = m.newPseudoBondGroup('NOESY constraints')
del m
chimera.openModels.add([self.pseudobond_group], sameAs = self.model)
def assigned_pdb_atoms(session, pdb_path, condition):
assigned = []
model = pdb.model(session, pdb_path)
for a in model.pdb_atoms:
if model.find_resonance(a, condition):
assigned.append(a)
return assigned
def assigned_pdb_atoms(session, pdb_path, condition):
assigned = []
model = pdb.model(session, pdb_path)
for a in model.pdb_atoms:
if model.find_resonance(a, condition):
assigned.append(a)
return assigned
def get_models(self, pdb_paths):
models = []
bad_paths = ''
for pdb_path in pdb_paths:
model = pdb.model(self.session, pdb_path)
if model == None:
bad_paths = bad_paths + pdb_path + '\n'
else:
models.append(model)
if bad_paths:
self.progress_report("Couldn't open\n" + bad_paths)
return models
def get_models(self, pdb_paths):
models = []
bad_paths = ''
for pdb_path in pdb_paths:
model = pdb.model(self.session, pdb_path)
if model == None:
bad_paths = bad_paths + pdb_path + '\n'
else:
models.append(model)
if bad_paths:
self.progress_report("Couldn't open\n" + bad_paths)
return models
def midas_pick_to_pdb_atom(self, midas_atom_spec):
match = re.match('(#)(\d+)(:)(\d+)(@)(.+)', midas_atom_spec)
if match:
g = match.groups()
model_number = string.atoi(g[1])
path = self.model_path(model_number)
if path:
residue_number = string.atoi(g[3])
atom_name = g[5]
model = pdb.model(self.session, path)
num_atom = (residue_number, atom_name)
pdb_atom = model.num_atom_to_pdb_atom(num_atom)
return model, pdb_atom
return None, None
def midas_pick_to_pdb_atom(self, midas_atom_spec):
match = re.match('(#)(\d+)(:)(\d+)(@)(.+)', midas_atom_spec)
if match:
g = match.groups()
model_number = string.atoi(g[1])
path = self.model_path(model_number)
if path:
residue_number = string.atoi(g[3])
atom_name = g[5]
model = pdb.model(self.session, path)
num_atom = (residue_number, atom_name)
pdb_atom = model.num_atom_to_pdb_atom(num_atom)
return model, pdb_atom
return None, None
def initialize(self, session, peaks, stoppable):
self.models = []
for pdb_path in self.pdb_path_list:
m = pdb.model(session, pdb_path, stoppable) # read pdb files
self.models.append(m)
def initialize(self, session, peaks, stoppable):
self.models = []
for pdb_path in self.pdb_path_list:
m = pdb.model(session, pdb_path, stoppable) # read pdb files
self.models.append(m)