Squashed 'modules/pmi/' changes from a5c6a4c..b927010

b927010 Replace IMP.pmi examples for Travis builds.
02dcf5d Use items(), not iteritems(), to work with Python 3.
ca40763 Suppress more 'was not used' warnings.
86d029f Suppress more 'not used' warnings.
4c4b24f Make floating-point comparison more reliable.
0395b69 Use correct PDB atom names.
df1a78b Suppress more 'was not used' warnings.
8ad14f5 Suppress more 'was not used' warnings.
4be6e3b Use standard PDB atom naming.
4fdc78f Suppress 'linker_restraints was not used' warnings.
8622238 fixing test_dof.py
c120ea6 fixing test_io_crosslink.py
dbc2079 making mover disabling faster
d1614ea removing useless file
28c7d99 fix Segments test
258c44f adding an InternalCoordinatesConstraint
1f6e165 fix test for Segments
876c3cf fix Segments class
691a4aa adding a self adaptive scheme
401c486 fix draw_component_composition bug
223879e add self_adaptive monte carlo scheme
4d74785 returns copy and state indexes
ecd8778 get the number of links per residue
f845cf2 fixes when rmfs are in subdirectories
397496d 1 Fixed ReferenceFrame issue for RB clones, 2 added a new RigidBody symmetry constraint

git-subtree-dir: modules/pmi
git-subtree-split: b92701077ea8e84c55ac65109b5bef6b6dbeb5e2

modules/pmi/include/InternalCoordinatesConstraint.h

@@ -0,0 +1,48 @@
+/**
+ *  \file IMP/pmi/InternalCoordinatesConstraint.h
+ *  \brief A modifier that enforce identical internal coordinates for NonRigidMembers.
+ *
+ *  Copyright 2007-2016 IMP Inventors. All rights reserved.
+ */
+
+#ifndef IMPPMI_PMI_SINGLETON_MODIFIER_H
+#define IMPPMI_PMI_SINGLETON_MODIFIER_H
+
+#include <IMP/SingletonModifier.h>
+#include <IMP/singleton_macros.h>
+
+IMPPMI_BEGIN_NAMESPACE
+
+//! An example singleton modifier
+/** A simple singleton modifier which ensures the x,y,z coordinates
+    stay in a box by wrapping them.
+
+    Such a class could be coupled with an IMP::core::SingletonConstraint
+    or IMP::container::SingletonsConstraint to keep a set of particles
+    in a box.
+
+    \include range_restrictionExampleSingletonModifier.py
+
+    The source code is as follows:
+    \include InternalCoordinatesConstraint.h
+    \include InternalCoordinatesConstraint.cpp
+ */
+class IMPPMIEXPORT InternalCoordinatesConstraint : public SingletonModifier {
+
+ public:
+  InternalCoordinatesConstraint();
+
+  // note, Doxygen wants a semicolon at the end of macro lines
+  virtual void apply_index(Model *m, ParticleIndex p) const
+      IMP_OVERRIDE;
+  virtual ModelObjectsTemp do_get_inputs(
+      Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE;
+  virtual ModelObjectsTemp do_get_outputs(
+      Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE;
+  IMP_SINGLETON_MODIFIER_METHODS(InternalCoordinatesConstraint);
+  IMP_OBJECT_METHODS(InternalCoordinatesConstraint);
+};
+
+IMPPMI_END_NAMESPACE
+
+#endif /* IMPPMI_PMI_SINGLETON_MODIFIER_H */

modules/pmi/pyext/src/dof/__init__.py

@@ -78,6 +78,7 @@ def create_rigid_body(self,
 
         # First, is this already a rigid body?
         if type(rigid_parts) is IMP.core.RigidBody:
+            print("WARNING: Rigid Body Already Setup")
             rb = rigid_parts
             model=rb.get_model()
             if name is not None:
@@ -91,7 +92,17 @@ def create_rigid_body(self,
             if not hiers:
                 print("WARNING: No hierarchies were passed to create_rigid_body()")
                 return []
-            rb = IMP.atom.create_rigid_body(hiers)
+
+            #we need to use the following constructor because the IMP.core.create_rigid_body seems
+            #to construct an arbitrary reference frame, which will be different for all copies.
+            #therefore, symmetry won't work all the time
+            tr=IMP.algebra.Transformation3D(IMP.algebra.get_identity_rotation_3d(),IMP.core.XYZ(hiers[0].get_particle()).get_coordinates())
+            rf = IMP.algebra.ReferenceFrame3D(tr)
+            rbp=IMP.Particle(hiers[0].get_model())
+            rb=IMP.core.RigidBody.setup_particle(rbp,rf)
+            for h in hiers:
+                rb.add_member(h.get_particle())
+
         self.rigid_bodies.append(rb)
         rb.set_coordinates_are_optimized(True)
         rb_mover = IMP.core.RigidBodyMover(rb.get_model(), rb, max_trans,
@@ -102,6 +113,7 @@ def create_rigid_body(self,
         rb_movers.append(rb_mover)
         self.movers_particles_map[rb_mover]=[]
         self.movers_rb_map[rb_mover]=[rb]
+        rb_mover.set_was_used(True)
         for h in hiers:
             self.movers_particles_map[rb_mover]+=IMP.atom.get_leaves(h)
         ### setup nonrigid parts
@@ -128,6 +140,7 @@ def create_rigid_body(self,
                     self.fb_movers.append(fbmv)
                     self.movers_particles_map[fbmv]=IMP.atom.get_leaves(h)
                     self.movers_xyz_map[fbmv]=IMP.atom.get_leaves(h)
+                    fbmv.set_was_used(True)
                     rb_movers.append(fbmv)
 
         self.movers += rb_movers # probably need to store more info
@@ -202,11 +215,13 @@ def create_super_rigid_body(self,
         if chain_min_length is None and chain_max_length is None:
             mv = self._setup_srb(srb_groups,max_trans,max_rot,axis)
             if mv:
+                mv.set_was_used(True)
                 srb_movers.append(mv)
         elif chain_min_length is not None and chain_max_length is not None:
             for hs in IMP.pmi.tools.sublist_iterator(srb_groups, chain_min_length, chain_max_length):
                 mv = self._setup_srb(hs,max_trans,max_rot,axis)
                 if mv:
+                    mv.set_was_used(True)
                     srb_movers.append(mv)
         else:
             raise Exception("DegreesOfFreedom: SetupSuperRigidBody: if you want chain, specify min AND max")
@@ -268,6 +283,7 @@ def create_flexible_beads(self,
             self.flexible_beads.append(h)
             fbmv=IMP.core.BallMover(p.get_model(), p, max_trans)
             fb_movers.append(fbmv)
+            fbmv.set_was_used(True)
             self.fb_movers.append(fbmv)
             self.movers_particles_map[fbmv]=IMP.atom.get_leaves(h)
             self.movers_xyz_map[fbmv]=IMP.atom.get_leaves(h)
@@ -289,6 +305,7 @@ def create_nuisance_mover(self,
                                   step_size)
         if name is not None:
             mv.set_name(name)
+        mv.set_was_used(True)
         self.nuisances.append(nuisance_p)
         self.movers.append(mv)
         return [mv]
@@ -321,7 +338,8 @@ def constrain_symmetry(self,
                            references,
                            clones,
                            transform,
-                           resolution='all'):
+                           resolution='all',
+                           type="AXIAL"):
         """Create a symmetry constraint. Checks:
         same number of particles
         disable ANY movers involving symmetry copies
@@ -335,6 +353,7 @@ def constrain_symmetry(self,
         @param resolution Only used if you pass PMI objects.
                If you have a multires system, assuming each are rigid
                bodies you probably only need one resolution.
+        @param type of symmetry. Implemented = AXIAL, RIGID_BODY
         """
 
         # get all RBs and particles
@@ -353,24 +372,62 @@ def constrain_symmetry(self,
         #for ref,clone in zip(ref_rbs+ref_beads,clones_rbs+clones_beads):
         #    print(clone.get_particle().get_index(),ref.get_particle().get_index())
         #    IMP.core.Reference.setup_particle(clone.get_particle(),ref.get_particle())
-        for ref,clone in zip(href,hclones):
-            IMP.core.Reference.setup_particle(clone.get_particle(),ref.get_particle())
+        for ref,clone in zip(ref_rbs,clones_rbs):
+            IMP.core.Reference.setup_particle(clone,ref)
+
+        for ref,clone in zip(ref_beads,clones_beads):
+            IMP.core.Reference.setup_particle(clone,ref)
+
+        # removing movers involved in clones
+        self.disable_movers(hclones)
+
+        if type=="AXIAL":
+            sm = IMP.core.TransformationSymmetry(transform)
+
+
+        if type=="RIGID_BODY":
+            p=IMP.Particle(self.mdl)
+            p.set_name("RigidBody_Symmetry")
+            rb=IMP.core.RigidBody.setup_particle(p,IMP.algebra.ReferenceFrame3D(transform))
+            for cp in [(10,0,0),(0,10,0),(0,0,10)]:
+                p=IMP.Particle(self.mdl)
+                IMP.core.XYZ.setup_particle(p,cp)
+                rb.add_member(p)
+            sm = IMP.core.TransformationSymmetry(rb.get_particle_index())
+            self.rigid_bodies.append(rb)
+            rb.set_coordinates_are_optimized(True)
+            rb_mover_tr = IMP.core.RigidBodyMover(rb.get_model(), rb.get_particle_index(), 0.0, 1.0)
+            rb_mover_rt = IMP.core.RigidBodyMover(rb.get_model(), rb.get_particle_index(), 10.0, 0.0)
+
+            rb_mover_tr.set_name("RigidBody_Symmetry_Mover_Translate")
+            rb_mover_rt.set_name("RigidBody_Symmetry_Mover_Rotate")
+            print('Created rigid body symmetry restraint')
+            self.movers_particles_map[rb_mover_tr]=[]
+            self.movers_particles_map[rb_mover_rt]=[]
+            self.movers_rb_map[rb_mover_tr]=[rb]
+            self.movers_rb_map[rb_mover_rt]=[rb]
+            for h in hclones:
+                self.movers_particles_map[rb_mover_tr]+=IMP.atom.get_leaves(h)
+                self.movers_particles_map[rb_mover_rt]+=IMP.atom.get_leaves(h)
+            self.movers.append(rb_mover_tr) # probably need to store more info
+            self.movers.append(rb_mover_rt) # probably need to store more info
+            self._rb2mov[rb] = [rb_mover_tr,rb_mover_rt] #dictionary relating rb to movers
+            #self._rb2mov[rb] = [rb_mover_tr] #dictionary relating rb to movers
 
-        sm = IMP.core.TransformationSymmetry(transform.get_inverse())
         lsc = IMP.container.ListSingletonContainer(
-            self.mdl,[p.get_particle().get_index() for p in hclones])
+            self.mdl,[p.get_particle().get_index() for p in clones_rbs+clones_beads])
         c = IMP.container.SingletonsConstraint(sm, None, lsc)
         self.mdl.add_score_state(c)
         print('Created symmetry restraint for',len(ref_rbs),'rigid bodies and',
               len(ref_beads),'flexible beads')
 
-        # removing movers involved in clones
+
         #sym_movers = []
 
         #sym_movers = [m for cl in clones_rbs for m in self._rb2mov[cl]]
         #self.movers = [m for m in self.movers if m not in sym_movers]
         self.mdl.update()
-        self.disable_movers(hclones)
+
 
     def __repr__(self):
         # would like something fancy like this:
@@ -437,14 +494,21 @@ def disable_movers(self,objects,mover_types=None):
         fixed_xyz=set()
         if mover_types is None: mover_types=[]
 
-        for key in self.movers_particles_map:
-            for h in hierarchies:
-                if h in self.movers_particles_map[key] and (type(key) in mover_types or not mover_types):
-                    tmp_set.add(key)
-                    if key in self.movers_rb_map:
-                        fixed_rb|=set(self.movers_rb_map[key])
-                    if key in self.movers_xyz_map:
-                        fixed_xyz|=set(self.movers_xyz_map[key])
+        inv_map = {}
+        for mv, ps in self.movers_particles_map.items():
+            for p in ps:
+                if p in inv_map: inv_map[p].append(mv)
+                else: inv_map[p]=[mv]
+
+        for h in hierarchies:
+            if h in inv_map:
+                for mv in inv_map[h]:
+                    if (type(mv) in mover_types or not mover_types):
+                        tmp_set.add(mv)
+                        if mv in self.movers_rb_map:
+                            fixed_rb|=set(self.movers_rb_map[mv])
+                        if mv in self.movers_xyz_map:
+                            fixed_xyz|=set(self.movers_xyz_map[mv])
         print("Fixing %s movers" %(str(len(list(tmp_set)))))
         self.disabled_movers+=list(tmp_set)
         return list(fixed_xyz),list(fixed_rb)

modules/pmi/pyext/src/io/__init__.py

@@ -312,7 +312,7 @@ def get_best_models(stat_files,
         # append to the lists
         score_list += fields[score_key]
         for rmf in fields[rmf_file_key]:
-            rmf_file_list.append(os.path.join(root_directory_of_stat_file,rmf))
+            rmf_file_list.append(os.path.join(root_directory_of_stat_file,"/".join(rmf.split("/")[-4:])))
 
         rmf_file_frame_list += fields[rmf_file_frame_key]