Fix typos

data/npctransport.proto

@@ -345,7 +345,7 @@ message Statistics {
     //    optional double site_interactions_per_floater=1 [default=0]; // number of site interactions per floater
     //  optional double interacting_fraction=2 [default=0];   // fraction of floaters in interaction
     // optional double chains_per_interacting_floater=3 [default=0]; // number of FG chain per interacting floater
-    // optional double beads_per_interacting_floater=4 [default=0]; // number of FG beads per intercating floater
+    // optional double beads_per_interacting_floater=4 [default=0]; // number of FG beads per interacting floater
     optional double diffusion_coefficient=5 [default=0];
     optional double correlation_time=6 [default=0];
     optional double avg_n_transports=7 [default=0]; // avg number of times a particle of this type has crossed the channel

include/Scoring.h

@@ -186,7 +186,7 @@ class IMPNPCTRANSPORTEXPORT Scoring: public Object
         @param non_optimizable_beads particles container on which to apply bounding volume
                          and pair constraints only if they also involve optimizable beads
         @param optimizable_beads particles container on which to apply bounding volume
-                         and pair contstraints, either with other optimizable beads or with
+                         and pair constraints, either with other optimizable beads or with
                          non-optimizable ones.
         @param is_attr_interactions_on if false, only repulsive interactions will be
                                        computed between pairs of particles

src/BrownianDynamicsTAMDWithSlabSupport.cpp

@@ -27,7 +27,7 @@ ::do_advance_chunk
 
   // Relax all FG springs by going over all FGs and then updating all their springs by random diffusion + gradient just as BD of XYZ particles
   // Note that this is inefficient if there are no harmonic springs (backward support), but we only care about performance of new version
-  // where they are persent
+  // where they are present
   double dtfs_ikt(dtfs*ikt);
   for(unsigned int i=0; i<ps.size(); i++){
     if(!RelaxingSpring::get_is_setup(get_model(),

src/Scoring.cpp

@@ -599,7 +599,7 @@ Scoring::remove_particle_type
   // III. TODO: Clean interaction_pair_scors - actually not essential
   // IV. TODO: remove also for z-bias partricles map
   // V. TODO: remove also restrained anchor beads (complicated!)
-  // VI. force referesh of scoring function
+  // VI. force refresh of scoring function
   get_scoring_function(true);
 }
 

src/SimulationData.cpp

@@ -1250,7 +1250,7 @@ SimulationData::set_bounding_volume(double volume_A3){
 
 algebra::Cylinder3D SimulationData::get_cylinder() const {
   IMP_USAGE_CHECK(get_is_slab_with_cylindrical_pore(),
-                  "no slab with cylidrical pore defined");
+                  "no slab with cylindrical pore defined");
   algebra::Vector3D pt(0, 0, get_slab_thickness() / 2.0);
   algebra::Segment3D seg(pt, -pt);
   return algebra::Cylinder3D(seg, get_pore_radius());

test/test_sites_pairs_score.py

@@ -261,7 +261,7 @@ def _test_three(self, site_range, site_k, nonspec_range, nonspec_k,
         sos= IMP.rmf.SaveOptimizerState(m, f)
         sos.set_period(1000)
         bd.add_optimizer_state(sos)
-        print("optimizin")
+        print("optimizing")
         IMP.set_log_level(IMP.SILENT)
         bd.optimize(3000)
         print("done")