def generate_rigid_groups(axislist, matrix):
"""
Generates rigid groups from the list of rotation axis and checks
every group's suitability for an attached rigid group
"""
rigid_groups = []
for axis in axislist:
rigid_groups.append(cg.framework_crawler(axis[0], axis[1]))
vals = []
printer('\nChecking potential groups\' rigidity.')
for group in rigid_groups:
printer()
vals.append(check_rigidity(group, matrix))
accepted_groups = []
printer('\n')
for _ in range(len(vals)):
bestgroup = min(vals)
if bestgroup > RIGIDITY_THRESHOLD:
if len(accepted_groups) == 0:
printer('No suitable rigid groups detected.')
break
i = vals.index(bestgroup)
potential_group = rigid_groups[i]
print
if too_close(potential_group, accepted_groups):
printer('\nKill too similar group:', [k.name for k in potential_group])
vals[i] = 999
continue
accepted_groups.append(potential_group)
printer('Accepted rigid group:', [k.name for k in potential_group])
vals[i] = 999
return accepted_groups
def segment(srb):
"""
Function to segment a molecule in rigid groups that are allowed to
rotate against each other arround a defined axis.
"""
# atom1,atom2,axis=get_user_input()
tls_definitions = get_user_input(srb)
rigid_groups, rigid_namess, axiss = [], [], []
for tls_definition in tls_definitions:
rigid_groups.append(cg.framework_crawler(tls_definition[1], tls_definition[2]))
axiss.append(tls_definition[0])
rigid_names = []
for atom in rigid_groups[-1]:
rigid_names.append(atom.name)
#raw_matrix=raw_rotation_matrix(data,axis,rigid_group)
rigid_namess.append(rigid_names)
if len(rigid_namess) > 100:
namesets = []
for group in rigid_namess:
evalstring = '{'
for string in group:
evalstring += '\'' + string
evalstring += '\','
evalstring += '}'
nameset = eval(evalstring)
namesets.append(nameset)
hierachy = []
for i in range(len(namesets)):
hierachy.append([0, i])
group1 = namesets[i]
for j in range(len(namesets)):
group2 = namesets[j]
if not group1 == group2:
if group1.issubset(group2):
hierachy[j][0] += 1
hierachy = sorted(hierachy, key=lambda hierachy: hierachy[0], reverse=True)
sorted_rigid_groups = []
sorted_rigid_names = []
sorted_axiss = []
for hierach in hierachy:
sorted_rigid_groups.append(rigid_groups[hierach[1]])
sorted_rigid_names.append(rigid_names[hierach[1]])
sorted_axiss.append(axiss[hierach[1]])
#sys.exit()
print([i for i in sorted_rigid_names])
else:
sorted_rigid_groups = rigid_groups
sorted_rigid_names = rigid_names
sorted_axiss = axiss
return sorted_rigid_groups, sorted_rigid_names, sorted_axiss
