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IMP Reference Guide  2.16.0
The Integrative Modeling Platform
version 2.16.0
ProteinLocalizationRestraint.h
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1 /**
2  * \file IMP/npc/ProteinLocalizationRestraint.h
3  * \brief protein localization restraints
4  *
5  * Restrict max distance between at least one pair of particles of any
6  * two distinct types. It also handles multiple copies of the same particles.
7  *
8  * Copyright 2007-2021 IMP Inventors. All rights reserved.
9  *
10  */
11 
12 #ifndef IMPNPC_PROTEIN_LOCALIZATION_RESTRAINT_H
13 #define IMPNPC_PROTEIN_LOCALIZATION_RESTRAINT_H
14 
15 #include <IMP/Pointer.h>
16 #include <IMP/Restraint.h>
17 #include <IMP/npc/npc_config.h>
18 #include <IMP/SingletonContainer.h>
19 
20 IMPNPC_BEGIN_NAMESPACE
21 
22 //! Restrain particles by their z coordinate
23 /** Each particle's z coordinate is harmonically restrained to lie between
24  the given lower and upper bounds.
25  */
26 class IMPNPCEXPORT ZAxialPositionRestraint : public Restraint
27 {
28  IMP::PointerMember<IMP::SingletonContainer> sc_;
29  double lower_bound_;
30  double upper_bound_;
31  double sigma_;
32  bool consider_radius_;
33 public:
34  ZAxialPositionRestraint(Model *m, SingletonContainerAdaptor sc,
35  double lower_bound, double upper_bound, bool consider_radius, double sigma=1);
36  ZAxialPositionRestraint(Model *m,
37  double lower_bound, double upper_bound, bool consider_radius, double sigma=1);
38 
39 #ifndef IMP_DOXYGEN
40  void add_particle(Particle *p);
41  void add_particles(const ParticlesTemp &ps);
42  void set_particles(const ParticlesTemp &ps);
43 #endif
44 
45  double unprotected_evaluate(
46  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
47  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
48 
49  IMP_OBJECT_METHODS(ZAxialPositionRestraint);;
50 };
51 
52 //! Restrain particles by their z coordinate
53 /** Each particle's z coordinate is harmonically restrained to lie above
54  the given lower bound.
55  */
56 class IMPNPCEXPORT ZAxialPositionLowerRestraint : public Restraint
57 {
58  IMP::PointerMember<IMP::SingletonContainer> sc_;
59  double lower_bound_;
60  double sigma_;
61  bool consider_radius_;
62 public:
63  ZAxialPositionLowerRestraint(Model *m, SingletonContainerAdaptor sc,
64  double lower_bound, bool consider_radius, double sigma=1);
65  ZAxialPositionLowerRestraint(Model *m,
66  double lower_bound, bool consider_radius, double sigma=1);
67 
68 #ifndef IMP_DOXYGEN
69  void add_particle(Particle *p);
70  void add_particles(const ParticlesTemp &ps);
71  void set_particles(const ParticlesTemp &ps);
72 #endif
73 
74  double unprotected_evaluate(
75  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
76  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
77 
78  IMP_OBJECT_METHODS(ZAxialPositionLowerRestraint);;
79 };
80 
81 //! Restrain particles by their z coordinate
82 /** Each particle's z coordinate is harmonically restrained to lie below
83  the given upper bound.
84  */
85 class IMPNPCEXPORT ZAxialPositionUpperRestraint : public Restraint
86 {
87  IMP::PointerMember<IMP::SingletonContainer> sc_;
88  double upper_bound_;
89  double sigma_;
90  bool consider_radius_;
91 public:
92  ZAxialPositionUpperRestraint(Model *m, SingletonContainerAdaptor sc,
93  double upper_bound, bool consider_radius, double sigma=1);
94  ZAxialPositionUpperRestraint(Model *m,
95  double upper_bound, bool consider_radius, double sigma=1);
96 
97 #ifndef IMP_DOXYGEN
98  void add_particle(Particle *p);
99  void add_particles(const ParticlesTemp &ps);
100  void set_particles(const ParticlesTemp &ps);
101 #endif
102 
103  double unprotected_evaluate(
104  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
105  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
106 
107  IMP_OBJECT_METHODS(ZAxialPositionUpperRestraint);;
108 };
109 
110 
111 //! Restrain particles by their y coordinate
112 /** Each particle's y coordinate is harmonically restrained to lie between
113  the given lower and upper bounds.
114  */
115 class IMPNPCEXPORT YAxialPositionRestraint : public Restraint
116 {
117  IMP::PointerMember<IMP::SingletonContainer> sc_;
118  double lower_bound_;
119  double upper_bound_;
120  double sigma_;
121  bool consider_radius_;
122 public:
123  YAxialPositionRestraint(Model *m, SingletonContainerAdaptor sc,
124  double lower_bound, double upper_bound, bool consider_radius, double sigma=1);
125  YAxialPositionRestraint(Model *m,
126  double lower_bound, double upper_bound, bool consider_radius, double sigma=1);
127 
128 #ifndef IMP_DOXYGEN
129  void add_particle(Particle *p);
130  void add_particles(const ParticlesTemp &ps);
131  void set_particles(const ParticlesTemp &ps);
132 #endif
133 
134  double unprotected_evaluate(
135  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
136  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
137 
138  IMP_OBJECT_METHODS(YAxialPositionRestraint);;
139 };
140 
141 //! Restrain particles by their y coordinate
142 /** Each particle's y coordinate is harmonically restrained to lie above
143  the given lower bound.
144  */
145 class IMPNPCEXPORT YAxialPositionLowerRestraint : public Restraint
146 {
147  IMP::PointerMember<IMP::SingletonContainer> sc_;
148  double lower_bound_;
149  double sigma_;
150  bool consider_radius_;
151 public:
152  YAxialPositionLowerRestraint(Model *m, SingletonContainerAdaptor sc,
153  double lower_bound, bool consider_radius, double sigma=1);
154  YAxialPositionLowerRestraint(Model *m,
155  double lower_bound, bool consider_radius, double sigma=1);
156 
157 #ifndef IMP_DOXYGEN
158  void add_particle(Particle *p);
159  void add_particles(const ParticlesTemp &ps);
160  void set_particles(const ParticlesTemp &ps);
161 #endif
162 
163  double unprotected_evaluate(
164  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
165  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
166 
167  IMP_OBJECT_METHODS(YAxialPositionLowerRestraint);;
168 };
169 
170 //! Restrain particles by their y coordinate
171 /** Each particle's y coordinate is harmonically restrained to lie below
172  the given upper bound.
173  */
174 class IMPNPCEXPORT YAxialPositionUpperRestraint : public Restraint
175 {
176  IMP::PointerMember<IMP::SingletonContainer> sc_;
177  double upper_bound_;
178  double sigma_;
179  bool consider_radius_;
180 public:
181  YAxialPositionUpperRestraint(Model *m, SingletonContainerAdaptor sc,
182  double upper_bound, bool consider_radius, double sigma=1);
183  YAxialPositionUpperRestraint(Model *m,
184  double upper_bound, bool consider_radius, double sigma=1);
185 
186 #ifndef IMP_DOXYGEN
187  void add_particle(Particle *p);
188  void add_particles(const ParticlesTemp &ps);
189  void set_particles(const ParticlesTemp &ps);
190 #endif
191 
192  double unprotected_evaluate(
193  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
194  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
195 
196  IMP_OBJECT_METHODS(YAxialPositionUpperRestraint);;
197 };
198 
199 
200 //! Restrain particles by their distance from the z axis in the xy plane
201 /** Each particle's distance to the z axis is harmonically restrained to
202  lie between the given lower and upper bounds.
203  */
204 class IMPNPCEXPORT XYRadialPositionRestraint : public Restraint
205 {
206  IMP::PointerMember<IMP::SingletonContainer> sc_;
207  double lower_bound_;
208  double upper_bound_;
209  double sigma_;
210  bool consider_radius_;
211 public:
212  XYRadialPositionRestraint(Model *m, SingletonContainerAdaptor sc,
213  double lower_bound, double upper_bound, bool consider_radius, double sigma=1);
214  XYRadialPositionRestraint(Model *m,
215  double lower_bound, double upper_bound, bool consider_radius, double sigma=1);
216 
217 #ifndef IMP_DOXYGEN
218  void add_particle(Particle *p);
219  void add_particles(const ParticlesTemp &ps);
220  void set_particles(const ParticlesTemp &ps);
221 #endif
222 
223  double unprotected_evaluate(
224  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
225  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
226 
227  IMP_OBJECT_METHODS(XYRadialPositionRestraint);;
228 };
229 
230 //! Restrain particles by their distance from the z axis in the xy plane
231 /** Each particle's distance to the z axis is harmonically restrained to
232  lie above the given lower bound.
233  */
234 class IMPNPCEXPORT XYRadialPositionLowerRestraint : public Restraint
235 {
236  IMP::PointerMember<IMP::SingletonContainer> sc_;
237  double lower_bound_;
238  double sigma_;
239  bool consider_radius_;
240 public:
241  XYRadialPositionLowerRestraint(Model *m, SingletonContainerAdaptor sc,
242  double lower_bound, bool consider_radius, double sigma=1);
243  XYRadialPositionLowerRestraint(Model *m,
244  double lower_bound, bool consider_radius, double sigma=1);
245 
246 #ifndef IMP_DOXYGEN
247  void add_particle(Particle *p);
248  void add_particles(const ParticlesTemp &ps);
249  void set_particles(const ParticlesTemp &ps);
250 #endif
251 
252  double unprotected_evaluate(
253  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
254  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
255 
256  IMP_OBJECT_METHODS(XYRadialPositionLowerRestraint);;
257 };
258 
259 //! Restrain particles by their distance from the z axis in the xy plane
260 /** Each particle's distance to the z axis is harmonically restrained to
261  lie below the given upper bound.
262  */
263 class IMPNPCEXPORT XYRadialPositionUpperRestraint : public Restraint
264 {
265  IMP::PointerMember<IMP::SingletonContainer> sc_;
266  double upper_bound_;
267  double sigma_;
268  bool consider_radius_;
269 public:
270  XYRadialPositionUpperRestraint(Model *m, SingletonContainerAdaptor sc,
271  double upper_bound, bool consider_radius, double sigma=1);
272  XYRadialPositionUpperRestraint(Model *m,
273  double upper_bound, bool consider_radius, double sigma=1);
274 
275 #ifndef IMP_DOXYGEN
276  void add_particle(Particle *p);
277  void add_particles(const ParticlesTemp &ps);
278  void set_particles(const ParticlesTemp &ps);
279 #endif
280 
281  double unprotected_evaluate(
282  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
283  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
284 
285  IMP_OBJECT_METHODS(XYRadialPositionUpperRestraint);;
286 };
287 
288 
289 //! Try to keep all particle surfaces in contact
290 /** The particles (each of which should be a core::XYZR) are harmonically
291  restrained such that each particle's sphere surface is in contact
292  with every other surface.
293  */
294 class IMPNPCEXPORT ProteinContactRestraint : public Restraint
295 {
296  IMP::PointerMember<IMP::SingletonContainer> sc_;
297  double tolerance_factor_;
298  double sigma_;
299 public:
300  ProteinContactRestraint(Model *m, SingletonContainerAdaptor sc,
301  double tolerance_factor, double sigma=0.1);
302  ProteinContactRestraint(Model *m,
303  double tolerance_factor, double sigma=0.1);
304 
305 #ifndef IMP_DOXYGEN
306  void add_particle(Particle *p);
307  void add_particles(const ParticlesTemp &ps);
308  void set_particles(const ParticlesTemp &ps);
309 #endif
310 
311  double unprotected_evaluate(
312  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
313  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
314 
315  IMP_OBJECT_METHODS(ProteinContactRestraint);;
316 };
317 
318 
319 //! Try to keep particle surfaces in contact in a chain
320 /** The particles (each of which should be a core::XYZR) are harmonically
321  restrained such that each particle's sphere surface is in contact
322  with the surface of the previous particle.
323  */
324 class IMPNPCEXPORT ProteinChainRestraint : public Restraint
325 {
326  IMP::PointerMember<IMP::SingletonContainer> sc_;
327  double sigma_;
328 public:
329  ProteinChainRestraint(Model *m, SingletonContainerAdaptor sc,
330  double sigma=0.1);
331  ProteinChainRestraint(Model *m,
332  double sigma=0.1);
333 
334 #ifndef IMP_DOXYGEN
335  void add_particle(Particle *p);
336  void add_particles(const ParticlesTemp &ps);
337  void set_particles(const ParticlesTemp &ps);
338 #endif
339 
340  double unprotected_evaluate(
341  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
342  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
343 
344  IMP_OBJECT_METHODS(ProteinChainRestraint);;
345 };
346 
347 
348 //! Try to keep particles localized on a membrane surface
349 /** The membrane is defined in this case to be a half torus in the xy
350  plane with center at the origin.
351  */
352 class IMPNPCEXPORT MembraneSurfaceLocationRestraint : public Restraint
353 {
354  IMP::PointerMember<IMP::SingletonContainer> sc_;
355  double R_;
356  double r_;
357  double sigma_;
358  double thickness_;
359 public:
360  MembraneSurfaceLocationRestraint(Model *m, SingletonContainerAdaptor sc,
361  double R, double r, double thickness, double sigma=2);
362  MembraneSurfaceLocationRestraint(Model *m,
363  double R, double r, double thickness, double sigma=2);
364 
365 #ifndef IMP_DOXYGEN
366  void add_particle(Particle *p);
367  void add_particles(const ParticlesTemp &ps);
368  void set_particles(const ParticlesTemp &ps);
369 #endif
370 
371  double unprotected_evaluate(
372  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
373  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
374 
375  IMP_OBJECT_METHODS(MembraneSurfaceLocationRestraint);;
376 };
377 
378 
379 //! Try to keep one set of particles localized on a membrane surface
380 /** The membrane is defined in this case to be a half torus in the xy
381  plane with center at the origin. One of the two sets of particles
382  (whichever is closer) is restrained to the membrane surface.
383  */
384 class IMPNPCEXPORT MembraneSurfaceLocationConditionalRestraint : public Restraint
385 {
386  IMP::PointerMember<IMP::SingletonContainer> sc1_;
387  IMP::PointerMember<IMP::SingletonContainer> sc2_;
388  double R_;
389  double r_;
390  double sigma_;
391  double thickness_;
392 public:
393  MembraneSurfaceLocationConditionalRestraint(Model *m, SingletonContainerAdaptor sc1, SingletonContainerAdaptor sc2,
394  double R, double r, double thickness, double sigma=2);
395  MembraneSurfaceLocationConditionalRestraint(Model *m,
396  double R, double r, double thickness, double sigma=2);
397 
398 #ifndef IMP_DOXYGEN
399  void add_particle1(Particle *p);
400  void add_particle2(Particle *p);
401  void add_particles1(const ParticlesTemp &ps);
402  void add_particles2(const ParticlesTemp &ps);
403  void set_particles1(const ParticlesTemp &ps);
404  void set_particles2(const ParticlesTemp &ps);
405 #endif
406 
407  double unprotected_evaluate(
408  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
409  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
410 
411  IMP_OBJECT_METHODS(MembraneSurfaceLocationConditionalRestraint);;
412 };
413 
414 
415 //! Try to keep particles away from a membrane
416 /** The membrane is defined in this case to be a half torus in the xy
417  plane with center at the origin.
418  */
419 class IMPNPCEXPORT MembraneExclusionRestraint : public Restraint
420 {
421  IMP::PointerMember<IMP::SingletonContainer> sc_;
422  double R_;
423  double r_;
424  double sigma_;
425  double thickness_;
426 public:
427  MembraneExclusionRestraint(Model *m, SingletonContainerAdaptor sc,
428  double R, double r, double thickness, double sigma=2);
429  MembraneExclusionRestraint(Model *m,
430  double R, double r, double thickness, double sigma=2);
431 
432 #ifndef IMP_DOXYGEN
433  void add_particle(Particle *p);
434  void add_particles(const ParticlesTemp &ps);
435  void set_particles(const ParticlesTemp &ps);
436 #endif
437 
438  double unprotected_evaluate(
439  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
440  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
441 
442  IMP_OBJECT_METHODS(MembraneExclusionRestraint);;
443 };
444 
445 
446 //! Try to keep particles on the pore side of a membrane
447 /** The membrane is defined in this case to be a half torus in the xy
448  plane with center at the origin.
449  */
450 class IMPNPCEXPORT PoreSideVolumeLocationRestraint : public Restraint
451 {
452  IMP::PointerMember<IMP::SingletonContainer> sc_;
453  double R_;
454  double r_;
455  double sigma_;
456  double thickness_;
457  bool consider_radius_;
458 public:
459  PoreSideVolumeLocationRestraint(Model *m, SingletonContainerAdaptor sc,
460  double R, double r, double thickness, bool consider_radius, double sigma=2);
461  PoreSideVolumeLocationRestraint(Model *m,
462  double R, double r, double thickness, bool consider_radius, double sigma=2);
463 
464 #ifndef IMP_DOXYGEN
465  void add_particle(Particle *p);
466  void add_particles(const ParticlesTemp &ps);
467  void set_particles(const ParticlesTemp &ps);
468 #endif
469 
470  double unprotected_evaluate(
471  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
472  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
473 
474  IMP_OBJECT_METHODS(PoreSideVolumeLocationRestraint);;
475 };
476 
477 
478 //! Try to keep particles on the perinuclear side of a membrane
479 /** The membrane is defined in this case to be a half torus in the xy
480  plane with center at the origin.
481  */
482 class IMPNPCEXPORT PerinuclearVolumeLocationRestraint : public Restraint
483 {
484  IMP::PointerMember<IMP::SingletonContainer> sc_;
485  double R_;
486  double r_;
487  double sigma_;
488  double thickness_;
489  bool consider_radius_;
490 public:
491  PerinuclearVolumeLocationRestraint(Model *m, SingletonContainerAdaptor sc,
492  double R, double r, double thickness, bool consider_radius, double sigma=2);
493  PerinuclearVolumeLocationRestraint(Model *m,
494  double R, double r, double thickness, bool consider_radius, double sigma=2);
495 
496 #ifndef IMP_DOXYGEN
497  void add_particle(Particle *p);
498  void add_particles(const ParticlesTemp &ps);
499  void set_particles(const ParticlesTemp &ps);
500 #endif
501 
502  double unprotected_evaluate(
503  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
504  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
505 
506  IMP_OBJECT_METHODS(PerinuclearVolumeLocationRestraint);;
507 };
508 
509 
510 //! Restrain two interparticle distances to be the same
511 /** This restraint must be given 4 particles. They are restrained to
512  be symmetric, by enforcing a harmonic penalty on the difference
513  between the distance between the first 2 particles and the distance
514  between the last two.
515  */
516 class IMPNPCEXPORT AssemblySymmetryByDistanceRestraint : public Restraint
517 {
518  IMP::PointerMember<IMP::SingletonContainer> sc_;
519  double sigma_;
520 public:
521  AssemblySymmetryByDistanceRestraint(Model *m, SingletonContainerAdaptor sc,
522  double sigma=4);
523  AssemblySymmetryByDistanceRestraint(Model *m,
524  double sigma=4);
525 
526 #ifndef IMP_DOXYGEN
527  void add_particle(Particle *p);
528  void add_particles(const ParticlesTemp &ps);
529  void set_particles(const ParticlesTemp &ps);
530 #endif
531 
532  double unprotected_evaluate(
533  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
534  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
535 
536  IMP_OBJECT_METHODS(AssemblySymmetryByDistanceRestraint);;
537 };
538 
539 
540 //! Restrain two interparticle dihedrals to be the same
541 /** This restraint must be given 8 particles. They are restrained to
542  be symmetric, by enforcing a harmonic penalty on the difference
543  between the dihedral angle between the first 4 particles and the dihedral
544  between the last 4.
545  */
546 class IMPNPCEXPORT AssemblySymmetryByDihedralRestraint
547  : public Restraint
548 {
549  IMP::PointerMember<IMP::SingletonContainer> sc_;
550  double sigma_;
551 public:
552  AssemblySymmetryByDihedralRestraint(Model *m, SingletonContainerAdaptor sc,
553  double sigma=0.1);
554  AssemblySymmetryByDihedralRestraint(Model *m,
555  double sigma=0.1);
556 
557 #ifndef IMP_DOXYGEN
558  void add_particle(Particle *p);
559  void add_particles(const ParticlesTemp &ps);
560  void set_particles(const ParticlesTemp &ps);
561 #endif
562 
563  double unprotected_evaluate(
564  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
565  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
566 
567  IMP_OBJECT_METHODS(AssemblySymmetryByDihedralRestraint);;
568 };
569 
570 //! Restrain a set of particles to be proximate to each other
571 /** Each particle is harmonically restrained to be no more than
572  `max_dist` away from every other particle.
573  */
574 class IMPNPCEXPORT ProteinProximityRestraint
575  : public Restraint
576 {
577  IMP::PointerMember<IMP::SingletonContainer> sc_;
578  double sigma_;
579  double max_dist_;
580 public:
581  ProteinProximityRestraint(Model *m, SingletonContainerAdaptor sc,
582  double max_dist, double sigma=0.1);
583  ProteinProximityRestraint(Model *m,
584  double max_dist, double sigma=0.1);
585 
586 #ifndef IMP_DOXYGEN
587  void add_particle(Particle *p);
588  void add_particles(const ParticlesTemp &ps);
589  void set_particles(const ParticlesTemp &ps);
590 #endif
591 
592  double unprotected_evaluate(
593  IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE;
594  ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
595 
596  IMP_OBJECT_METHODS(ProteinProximityRestraint);;
597 };
598 
599 
600 
601 IMPNPC_END_NAMESPACE
602 
603 #endif /* IMPNPC_PROTEIN_LOCALIZATION_RESTRAINT_H */
IMP::npc::PerinuclearVolumeLocationRestraint
Try to keep particles on the perinuclear side of a membrane.
Definition: ProteinLocalizationRestraint.h:482
IMP::npc::ZAxialPositionUpperRestraint
Restrain particles by their z coordinate.
Definition: ProteinLocalizationRestraint.h:85
IMP::rmf::add_particles
void add_particles(RMF::FileHandle fh, const ParticlesTemp &hs)
SingletonContainer.h
A container for Singletons.
IMP::npc::AssemblySymmetryByDihedralRestraint
Restrain two interparticle dihedrals to be the same.
Definition: ProteinLocalizationRestraint.h:546
IMP_OBJECT_METHODS
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition: object_macros.h:25
IMP::npc::YAxialPositionUpperRestraint
Restrain particles by their y coordinate.
Definition: ProteinLocalizationRestraint.h:174
IMP::npc::XYRadialPositionRestraint
Restrain particles by their distance from the z axis in the xy plane.
Definition: ProteinLocalizationRestraint.h:204
IMP::rmf::add_particle
void add_particle(RMF::FileHandle fh, Particle *hs)
IMP::npc::PoreSideVolumeLocationRestraint
Try to keep particles on the pore side of a membrane.
Definition: ProteinLocalizationRestraint.h:450
IMP::npc::MembraneSurfaceLocationConditionalRestraint
Try to keep one set of particles localized on a membrane surface.
Definition: ProteinLocalizationRestraint.h:384
IMP::npc::ZAxialPositionRestraint
Restrain particles by their z coordinate.
Definition: ProteinLocalizationRestraint.h:26
IMP::npc::AssemblySymmetryByDistanceRestraint
Restrain two interparticle distances to be the same.
Definition: ProteinLocalizationRestraint.h:516
IMP::npc::ProteinContactRestraint
Try to keep all particle surfaces in contact.
Definition: ProteinLocalizationRestraint.h:294
IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:73
IMP::npc::MembraneExclusionRestraint
Try to keep particles away from a membrane.
Definition: ProteinLocalizationRestraint.h:419
IMP::npc::ProteinChainRestraint
Try to keep particle surfaces in contact in a chain.
Definition: ProteinLocalizationRestraint.h:324
IMP::npc::XYRadialPositionLowerRestraint
Restrain particles by their distance from the z axis in the xy plane.
Definition: ProteinLocalizationRestraint.h:234
IMP::npc::MembraneSurfaceLocationRestraint
Try to keep particles localized on a membrane surface.
Definition: ProteinLocalizationRestraint.h:352
Pointer.h
A nullptr-initialized pointer to an IMP Object.
IMP::npc::ProteinProximityRestraint
Restrain a set of particles to be proximate to each other.
Definition: ProteinLocalizationRestraint.h:574
IMP::Particle
Class to handle individual particles of a Model object.
Definition: Particle.h:41
Restraint.h
Abstract base class for all restraints.
IMP::npc::ZAxialPositionLowerRestraint
Restrain particles by their z coordinate.
Definition: ProteinLocalizationRestraint.h:56
IMP::npc::XYRadialPositionUpperRestraint
Restrain particles by their distance from the z axis in the xy plane.
Definition: ProteinLocalizationRestraint.h:263
IMP::npc::YAxialPositionLowerRestraint
Restrain particles by their y coordinate.
Definition: ProteinLocalizationRestraint.h:145
IMP::ModelObject::do_get_inputs
virtual ModelObjectsTemp do_get_inputs() const =0
IMP_OVERRIDE
#define IMP_OVERRIDE
Cause a compile error if this method does not override a parent method.
Definition: compiler_macros.h:78
IMP::DerivativeAccumulator
Class for adding derivatives from restraints to the model.
Definition: DerivativeAccumulator.h:24
IMP::npc::YAxialPositionRestraint
Restrain particles by their y coordinate.
Definition: ProteinLocalizationRestraint.h:115
IMP::Restraint
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:54