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KinematicPerturber.hh
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9 
10 /// @file protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.hh
11 /// @brief Header file for KinematicPerturbers used by the kineamtic mover
12 /// @author Florian Richter, floric@u.washington.edu, march 2009
13 /// @author Amelie Stein, amelie.stein@ucsf.edu, October 2012 -- refactoring vicinity sampling & new perturbers
14 
15 #ifndef INCLUDED_protocols_loops_loop_closure_kinematic_closure_KinematicPerturber_hh
16 #define INCLUDED_protocols_loops_loop_closure_kinematic_closure_KinematicPerturber_hh
17 
18 #include <protocols/loops/loop_closure/kinematic_closure/KinematicMover.fwd.hh>
19 #include <protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.fwd.hh>
20 
21 // Rosetta Headers
22 #include <core/types.hh>
23 #include <core/pose/Pose.fwd.hh>
24 #include <core/scoring/Ramachandran.fwd.hh>
25 #include <core/scoring/Ramachandran2B.fwd.hh>
26 #include <core/chemical/AA.hh>
27 
28 #include <core/kinematics/MoveMap.fwd.hh>
29 
30 // Utility Headers
31 #include <utility/LexicographicalIterator.hh> //not OPable; needs full header
32 #include <utility/vector1.hh>
33 #include <utility/pointer/ReferenceCount.hh>
34 
35 // C++ Headers
36 #include <string>
37 #include <map>
38 
39 namespace protocols {
40  namespace loops {
41  namespace loop_closure {
42  namespace kinematic_closure {
43 
44  /// @brief pure virtual base class for KinematicPerturber. KinematicPerturbers determine HOW loops should be perturbed. The base class contains a provision for determining WHERE they should be perturbed: MoveMap sensitivity.
45  class KinematicPerturber : public utility::pointer::ReferenceCount {
46 
47  public:
48 
49  KinematicPerturber();
50  virtual ~KinematicPerturber();
51 
52  virtual
53  std::string perturber_type() const = 0;
54 
55  void
56  set_kinmover( KinematicMoverCAP kinmover ){ kinmover_ = kinmover; }
57 
58  void
59  set_movemap( core::kinematics::MoveMapCOP mm );
60 
61  core::kinematics::MoveMapCOP
62  get_movemap() const ;
63 
64  /// @brief function that perturbs the chain, i.e. sets new values
65  /// @brief for the torsions, bond angles and bond lengths
66  /// @brief note: the torsions/angles/lengths that are input to this
67  /// @brief function will be identical to the ones in the pose,
68  /// @brief i.e. only the dof values that are explicitly set by
69  /// @brief this function plus the pivots will have changed after loop closure
70  virtual
71  void
72  perturb_chain(
73  core::pose::Pose const & pose,
74  utility::vector1< core::Real> & torsions,
75  utility::vector1< core::Real> & bond_ang,
76  utility::vector1< core::Real> & bond_len
77  ) = 0; // needs to be non-const for Taboo Sampling
78 
79 
80  /// @brief after the kinmover has closed the loop, the perturber needs
81  /// @brief to put the solutions into the pose
82  /// @brief note: the base class version of this function sets the torsions,
83  /// @brief so any KinematicPerturber that only changes the torsions will not have
84  /// @brief to implement this function
85  virtual
86  void
87  set_pose_after_closure(
88  core::pose::Pose & pose,
89  utility::vector1< core::Real> const & torsions,
90  utility::vector1< core::Real> const & , //bond_ang,
91  utility::vector1< core::Real> const & ,//bond_len,
92  bool //closure_successful
93  ) const;
94 
95  virtual
96  bool perturber_exhausted() const {
97  return false; }
98 
99  void
100  set_max_sample_iterations( core::Size sample_its ){
101  max_sample_iterations_ = sample_its; }
102 
103  core::Size
104  max_sample_iterations() const {
105  return max_sample_iterations_; }
106 
107  void clear_torsion_string_stack() { } // only actually used for TabooSampling
108 
109  protected:
110 
111  //for access to the kinematic mover that owns this perturber
112  KinematicMoverCAP kinmover_;
113 
114  core::Size max_sample_iterations_;
115 
116  private:
117  core::kinematics::MoveMapCOP movemap_;
118 
119  };
120 
121 
122 
123  /// @brief torsion sampling kinematic perturber
124  class TorsionSamplingKinematicPerturber : public KinematicPerturber {
125 
126  public:
127 
128  typedef KinematicPerturber parent;
129 
130  TorsionSamplingKinematicPerturber( KinematicMoverCAP kinmover_in );
131 
132  ~TorsionSamplingKinematicPerturber();
133 
134  std::string perturber_type() const {
135  return "TorsionSampleKinematicPerturber"; }
136 
137  ///@brief varies torsions always and bond angles sometimes. Currently torsion varying will respect a movemap if present; angles do NOT look for a movemap.
138  void
139  perturb_chain(
140  core::pose::Pose const & pose,
141  utility::vector1< core::Real> & torsions,
142  utility::vector1< core::Real> & bond_ang,
143  utility::vector1< core::Real> & //bond_len
144  ) ;
145 
146 
147  void
148  set_pose_after_closure(
149  core::pose::Pose & pose,
150  utility::vector1< core::Real> const & torsions,
151  utility::vector1< core::Real> const & bond_ang,
152  utility::vector1< core::Real> const & bond_len,
153  bool closure_successful
154  ) const;
155 
156  void
157  set_vary_ca_bond_angles( bool vary_ca_bond_angles ) {
158  vary_ca_bond_angles_ = vary_ca_bond_angles; }
159 
160  private:
161 
162  bool vary_ca_bond_angles_;
163  bool sample_omega_for_pre_prolines_;
164 
165  core::scoring::Ramachandran const & rama_;
166 
167  };
168 
169 
170  /// @brief vicinity sampling kinematic perturber
171  /// @author Amelie Stein (just the refactoring)
172  class VicinitySamplingKinematicPerturber : public KinematicPerturber {
173 
174  public:
175 
176  typedef KinematicPerturber parent;
177 
178  VicinitySamplingKinematicPerturber( KinematicMoverCAP kinmover_in );
179 
180  ~VicinitySamplingKinematicPerturber();
181 
182  std::string perturber_type() const {
183  return "VicinitySampleKinematicPerturber"; }
184 
185  ///@brief varies torsions always and bond angles sometimes. Currently torsion varying will respect a movemap if present; angles do NOT look for a movemap. -- note that the analytic closure and pivot selection currently do not respect movemaps though
186  void
187  perturb_chain(
188  core::pose::Pose const & pose,
189  utility::vector1< core::Real> & torsions,
190  utility::vector1< core::Real> & bond_ang,
191  utility::vector1< core::Real> & //bond_len
192  ) ;
193 
194 
195  void
196  set_pose_after_closure(
197  core::pose::Pose & pose,
198  utility::vector1< core::Real> const & torsions,
199  utility::vector1< core::Real> const & bond_ang,
200  utility::vector1< core::Real> const & bond_len,
201  bool closure_successful
202  ) const;
203 
204  void
205  set_vary_ca_bond_angles( bool vary_ca_bond_angles ) {
206  vary_ca_bond_angles_ = vary_ca_bond_angles; }
207 
208 
209  void
210  set_degree_vicinity( core::Real degree_vicinity ) {
211  degree_vicinity_ = degree_vicinity; }
212 
213  private:
214 
215  bool vary_ca_bond_angles_;
216  core::Real degree_vicinity_;
217  bool sample_omega_for_pre_prolines_;
218 
219  };
220 
221 
222 
223  /// @brief WARNING WARNING UNTESTED!!!! torsion sweeping kinematic perturber
224  /// @brief WARNING WARNING UNTESTED!!!! used to work in other implementation
225  /// @brief probably works now, but to make sure you shoud doublecheck
226  // @brief if you plan to use
227  ///@details Here's some commentary on why the TorsionSweepingKinematicPerturber is Fun and Awesome to use! Basically, you take the loop as given and search for solutions nearby. Its purpose is not to produce large changes, but instead to produce small perturbations to find the bottom of the current energy well. It's not meant to be used for the original KIC protocol, in which the pivots are changed regularly: you can't sweep through nonpivot torsion space if the pivots don't stay the same.
228  class TorsionSweepingKinematicPerturber : public KinematicPerturber {
229 
230  public:
231 
232  TorsionSweepingKinematicPerturber();
233  ~TorsionSweepingKinematicPerturber();
234 
235  std::string perturber_type() const {
236  return "TorsionSweepingKinematicPerturber"; }
237 
238  ///@brief movemap control NOT IMPLEMENTED in TorsionSweepingKP. It is also NOT NEEDED because you can use set_nonpivot_res_to_sweep instead.
239  void
240  perturb_chain(
241  core::pose::Pose const & pose,
242  utility::vector1< core::Real > & torsions,
243  utility::vector1< core::Real > & bond_ang,
244  utility::vector1< core::Real > & //bond_len
245  ) ;
246 
247  bool perturber_exhausted() const {
248  return sweep_iterator_.at_end(); }
249 
250  void set_nonpivot_res_to_sweep( utility::vector1< Size > const & resids );
251  void set_nonpivot_bb_torsion_id( utility::vector1< Size > const & bbtorids );
252  void set_sweep_start_angle( utility::vector1< core::Real > const & angles_in_degrees );
253  void set_sweep_step_size( utility::vector1< core::Real > const & angle_steps_in_degrees );
254  void set_sweep_nsteps( utility::vector1< Size > const & nsteps );
255 
256 
257  private:
258 
259  utility::vector1< core::Size > nonpivot_res_to_sweep_;
260  utility::vector1< core::Size > sweep_torsion_ids_;
261  utility::vector1< core::Real > sweep_nonpivot_torsion_starts_;
262  utility::vector1< core::Real > sweep_step_sizes_;
263  mutable utility::LexicographicalIterator sweep_iterator_;
264 
265  }; // TorsionSweepingKinematicPerturber
266 
267 
268 
269  /// @author Amelie Stein
270  /// @brief neighbor-dependent torsion sampling kinematic perturber -- uses rama2b for phi/psi lookup
271  class NeighborDependentTorsionSamplingKinematicPerturber : public KinematicPerturber {
272 
273  public:
274 
275  typedef KinematicPerturber parent;
276 
277  NeighborDependentTorsionSamplingKinematicPerturber( KinematicMoverCAP kinmover_in );
278 
279  ~NeighborDependentTorsionSamplingKinematicPerturber();
280 
281  std::string perturber_type() const {
282  return "NeighborDependentTorsionSamplingKinematicPerturber"; }
283 
284  void
285  perturb_chain(
286  core::pose::Pose const & pose,
287  utility::vector1< core::Real> & torsions,
288  utility::vector1< core::Real> & bond_ang,
289  utility::vector1< core::Real> & //bond_len
290  ) ;
291 
292 
293  void
294  set_pose_after_closure(
295  core::pose::Pose & pose,
296  utility::vector1< core::Real> const & torsions,
297  utility::vector1< core::Real> const & bond_ang,
298  utility::vector1< core::Real> const & bond_len,
299  bool closure_successful
300  ) const;
301 
302  void
303  set_vary_ca_bond_angles( bool vary_ca_bond_angles ) {
304  vary_ca_bond_angles_ = vary_ca_bond_angles; }
305 
306 
307  private:
308 
309  bool vary_ca_bond_angles_;
310  bool sample_omega_for_pre_prolines_;
311 
312  core::scoring::Ramachandran2B const & rama_;
313 
314  };
315 
316 
317 
318 
319 
320 
321  /// @brief torsion-restricted kinematic perturber (still samples randomly, but only within a given torsion bin)
322  /// @author Amelie Stein
323  class TorsionRestrictedKinematicPerturber : public KinematicPerturber {
324 
325  public:
326 
327  typedef KinematicPerturber parent;
328 
329  TorsionRestrictedKinematicPerturber( KinematicMoverCAP kinmover_in, std::string torsion_bins );
330 
331  ~TorsionRestrictedKinematicPerturber();
332 
333  std::string perturber_type() const {
334  return "TorsionRestrictedKinematicPerturber"; }
335 
336  void
337  perturb_chain(
338  core::pose::Pose const & pose,
339  utility::vector1< core::Real> & torsions,
340  utility::vector1< core::Real> & bond_ang,
341  utility::vector1< core::Real> & //bond_len
342  ) ;
343 
344 
345  void
346  set_pose_after_closure(
347  core::pose::Pose & pose,
348  utility::vector1< core::Real> const & torsions,
349  utility::vector1< core::Real> const & bond_ang,
350  utility::vector1< core::Real> const & bond_len,
351  bool closure_successful
352  ) const;
353 
354  void
355  set_vary_ca_bond_angles( bool vary_ca_bond_angles ) {
356  vary_ca_bond_angles_ = vary_ca_bond_angles; }
357 
358 
359  private:
360 
361  bool vary_ca_bond_angles_;
362  bool sample_omega_for_pre_prolines_;
363  std::string predefined_torsions_;
364 
365  core::scoring::Ramachandran const & rama_;
366 
367  };
368 
369 
370 
371 
372 
373  /// @brief Taboo-sampling kinematic perturber (still samples randomly, but only within a specific torsion bin, and the Taboo sampler ensures that this torsion bin is varied in each iteration)
374  /// @author Amelie Stein
375  class TabooSamplingKinematicPerturber : public KinematicPerturber {
376 
377  public:
378 
379  typedef KinematicPerturber parent;
380 
381  // check if both c'tors are used -- if not, remove the unused one
382  TabooSamplingKinematicPerturber( KinematicMoverCAP kinmover_in );
383 
384  ~TabooSamplingKinematicPerturber();
385 
386  std::string perturber_type() const {
387  return "TabooSamplingKinematicPerturber"; }
388 
389  void
390  perturb_chain(
391  core::pose::Pose const & pose,
392  utility::vector1< core::Real> & torsions,
393  utility::vector1< core::Real> & bond_ang,
394  utility::vector1< core::Real> & //bond_len
395  ) ;
396 
397 
398  void
399  set_pose_after_closure(
400  core::pose::Pose & pose,
401  utility::vector1< core::Real> const & torsions,
402  utility::vector1< core::Real> const & bond_ang,
403  utility::vector1< core::Real> const & bond_len,
404  bool closure_successful
405  ) const;
406 
407  void
408  set_vary_ca_bond_angles( bool vary_ca_bond_angles ) {
409  vary_ca_bond_angles_ = vary_ca_bond_angles; }
410 
411 
412  void clear_torsion_string_stack() {
413  random_torsion_strings_.clear();
414  }
415 
416  protected:
417 
418  void
419  refill_torsion_string_vector();
420 
421  std::string
422  next_torsion_string();
423 
424  private:
425 
426  bool vary_ca_bond_angles_;
427  bool sample_omega_for_pre_prolines_;
428 
429  // for Taboo Sampling
430  core::Size num_strings_;
431  utility::vector1< std::string > random_torsion_strings_; // holds a list of random torsion bin strings to be sampled, to ensure diversity -- accessed (and filled, if necessary) by next_torsion_string( pose )
432 
433  core::scoring::Ramachandran const & rama_;
434 
435 
436 
437  };
438 
439 
440 
441  /// @brief Neighbor-dependent Taboo-sampling kinematic perturber (still samples randomly, but only within a given torsion bin; the Taboo sampler ensures that this torsion bin is varied in each iteration) that uses neighbor-dependent Ramachandran distributions (rama2b)
442  /// @author Amelie Stein
443  /// @date Mon May 21 11:39:26 PDT 2012
444  class NeighborDependentTabooSamplingKinematicPerturber : public KinematicPerturber {
445 
446  public:
447 
448  typedef KinematicPerturber parent;
449 
450  NeighborDependentTabooSamplingKinematicPerturber( KinematicMoverCAP kinmover_in );
451 
452  ~NeighborDependentTabooSamplingKinematicPerturber();
453 
454  std::string perturber_type() const {
455  return "NeighborDependentTabooSamplingKinematicPerturber"; }
456 
457  void
458  perturb_chain(
459  core::pose::Pose const & pose,
460  utility::vector1< core::Real> & torsions,
461  utility::vector1< core::Real> & bond_ang,
462  utility::vector1< core::Real> & //bond_len
463  ) ;
464 
465 
466  void
467  set_pose_after_closure(
468  core::pose::Pose & pose,
469  utility::vector1< core::Real> const & torsions,
470  utility::vector1< core::Real> const & bond_ang,
471  utility::vector1< core::Real> const & bond_len,
472  bool closure_successful
473  ) const;
474 
475  void
476  set_vary_ca_bond_angles( bool vary_ca_bond_angles ) {
477  vary_ca_bond_angles_ = vary_ca_bond_angles; }
478 
479 
480  void clear_torsion_string_stack() {
481  random_torsion_strings_.clear();
482  }
483 
484  protected:
485 
486  void
487  refill_torsion_string_vector();
488 
489  std::string
490  next_torsion_string();
491 
492  private:
493 
494  bool vary_ca_bond_angles_;
495  bool sample_omega_for_pre_prolines_;
496 
497 
498  core::Size num_strings_;
499  utility::vector1< std::string > random_torsion_strings_; // holds a list of random torsion bin strings to be sampled, to ensure diversity -- accessed (and filled, if necessary) by next_torsion_string( pose )
500 
501  core::scoring::Ramachandran2B const & rama_;
502 
503 
504 
505  }; // NeighborDependentTabooSamplingKinematicPerturber
506 
507 
508 
509 
510 
511 
512 
513  } // namespace kinematic_closure
514  } // namespace loop_closure
515  } // namespace moves
516 } // namespace protocols
517 
518 #endif //INCLUDED_protocols_loops_loop_closure_kinematic_closure_KinematicPerturber_hh
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