diff --git a/pyext/src/restraint.py b/pyext/src/restraint.py index 8e466157e400b05ce17b5d8ced41dde1e0eb8caa..d44b46e8d061c4fac40d17334cc7be1673f6b12a 100755 --- a/pyext/src/restraint.py +++ b/pyext/src/restraint.py @@ -183,6 +183,9 @@ class GaussianEMRestraintWrapper(object): self.set_weight(weight) def center_target_density_on_model(self): + ''' + aligns the center of mass of the target GMM on the center of mass of the model + ''' target_com = IMP.algebra.Vector3D(0, 0, 0) target_mass = 0.0 for p in self.target_ps: @@ -228,6 +231,9 @@ class GaussianEMRestraintWrapper(object): return com def center_target_density_on_origin(self): + ''' + aligns the center of mass of the target GMM on the origin + ''' target_com = self.get_center_of_mass() print('target com', target_com) model_com = IMP.algebra.Vector3D(0, 0, 0) @@ -240,6 +246,10 @@ class GaussianEMRestraintWrapper(object): # IMP.pmi.tools.translate_hierarchies(self.densities,v) def center_model_on_target_density(self, input_object): + ''' + aligns the model on the target density + @param input_objects IMP.pmi.representation.Representation or IMP.pmi.topology.State + ''' if type(input_object) is IMP.pmi.representation.Representation: hier = input_object.prot elif type(input_object) is IMP.pmi.topology.State: @@ -271,6 +281,9 @@ class GaussianEMRestraintWrapper(object): IMP.core.transform(IMP.core.XYZ(p), transformation) def center_on_target_density(self): + ''' + align the model on target GMM + ''' target_com = self.get_center_of_mass() print('target com', target_com) model_com = self.get_center_of_mass(target=False) @@ -297,6 +310,10 @@ class GaussianEMRestraintWrapper(object): def set_weight(self,weight): + ''' + set the weight of the restraint + @param weight + ''' self.weight = weight self.rs.set_weight(weight) @@ -324,6 +341,9 @@ class GaussianEMRestraintWrapper(object): return self.rb def get_density_as_hierarchy(self): + ''' + returns a hierarchy whose leaves are the gaussian particles of the target GMM + ''' if self.em_root_hier is None: self.em_root_hier = IMP.atom.Copy.setup_particle(IMP.Particle(self.m),0) self.em_root_hier.set_name("GaussianEMRestraint_density_"+self.label)