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2 // -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
3 // vi: set ts=2 noet:
4 //
5 // (c) Copyright Rosetta Commons Member Institutions.
6 // (c) This file is part of the Rosetta software suite and is made available under license.
7 // (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
8 // (c) For more information, see http://www.rosettacommons.org. Questions about this can be
9 // (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.
10 
11 /// @file Mike Tyka
12 /// @brief
13 ///
14 
15 /// Note: This is an extremely crude and slow implementation of cartesian MD in rosetta.
16 /// I make no promises as to this codes correctness. use at own risk.
17 /// Nor is this code efficient. Nor is it intended for production simulations.
18 
19 
20 // Unit headers
21 #include <protocols/cartesian/md.hh>
22 // AUTO-REMOVED #include <core/optimization/AtomTreeMinimizer.hh>
23 
24 // Package headers
25 #include <core/id/AtomID.hh>
26 #include <core/optimization/types.hh>
27 // AUTO-REMOVED #include <core/optimization/Multifunc.hh>
28 #include <core/chemical/ResidueType.hh>
29 #include <core/conformation/Conformation.hh>
30 #include <core/conformation/Residue.hh>
31 #include <core/conformation/Atom.hh>
32 // AUTO-REMOVED #include <core/kinematics/AtomTree.hh>
33 // AUTO-REMOVED #include <core/kinematics/DomainMap.hh>
34 
35 // Project headers
36 #include <core/pose/Pose.hh>
37 #include <core/scoring/Energies.hh>
38 #include <core/scoring/EnergyMap.hh>
39 #include <core/scoring/ScoreType.hh>
40 #include <core/scoring/ScoreFunction.hh>
41 // AUTO-REMOVED #include <core/scoring/NeighborList.hh>
42 // AUTO-REMOVED #include <core/scoring/hbonds/hbonds.hh>
43 // AUTO-REMOVED #include <core/scoring/hbonds/HBondSet.hh>
44 // AUTO-REMOVED #include <core/io/pdb/file_data.hh>
45 
46 // // ObjexxFCL headers
47 // AUTO-REMOVED #include <ObjexxFCL/FArray2D.hh>
48 #include <ObjexxFCL/string.functions.hh>
49 #include <ObjexxFCL/format.hh>
50 
51 // // Numeric headers
52 // AUTO-REMOVED #include <numeric/conversions.hh>
53 // AUTO-REMOVED #include <numeric/random/random.hh>
54 
55 #include <iostream>
56 #include <fstream>
57 // AUTO-REMOVED #include <core/optimization/MinimizerOptions.hh>
58 
59 #include <basic/Tracer.hh>
60 
61 #include <utility/vector1.hh>
62 #include <numeric/NumericTraits.hh>
63 #include <numeric/random/random.fwd.hh>
64 
65 
66 using namespace ObjexxFCL;
67 using namespace ObjexxFCL::fmt;
68 
69 namespace protocols {
70 namespace cartesian {
71 
72 static basic::Tracer TR("core.optimization.md");
73 
74 float sqr(float t){ return t*t; }
75 
76 
77 MolecularDynamics::MolecularDynamics(
78  core::pose::PoseOP & inputpose,
79  core::scoring::ScoreFunction const & scorefxn
80 ):
81 pose( inputpose )
82 {
83 
84  scorefxn( *pose );
85  mm.set_bb ( true );
86  mm.set_chi( true );
87  min_map.setup( *pose, mm );
88  core::kinematics::DomainMap const & dmap = min_map.domain_map();
89 
90  pose->energies().set_use_nblist( *pose, dmap, true );
91  scorefxn.setup_for_minimizing( *pose, min_map );
92 
93  createCartesianArray( );
94  createBondList( );
95  createAngleList( );
96  createDihedralList( );
97  setDihedralDerivatives();
98 
99 }
100 
101 
102 
103 
104 
105 
106 
107 
108 
109 
110 
111 
112 
113 
114 
115 
116 
117 
118 
119 
120 
121 void MolecularDynamics::createCartesianArray( )
122 {
123  using namespace core;
124 
125  Size const nres( pose->total_residue() );
126  cartom.clear();
127  for ( Size ir = 1; ir <= nres; ++ir ) {
128  conformation::Residue const & rsd( pose->residue( ir ) );
129  for (Size i = 1; i <= rsd.natoms(); i++ ){
130  id::AtomID atom_id( i, ir );
131  CartesianAtom atom;
132  atom.index = i;
133  atom.res = ir;
134  atom.atom_id = atom_id;
135 
136  atom.force = core::Vector(0,0,0);
137  atom.velocity = core::Vector(0,0,0);
138  atom.position = pose->xyz( atom_id );
139 
140  atom.old_force = core::Vector(0,0,0);
141  atom.old_velocity = core::Vector(0,0,0);
142  atom.old_position = core::Vector(0,0,0);
143 
144  atom.mass = 12.001; // assume carbon for now, we can be more accurate later.
145  cartom.push_back(atom);
146  }
147  }
148 
149 }
150 
151 void MolecularDynamics::setCartesianPositionsFromPose( )
152 {
153  using namespace core;
154 
155  for ( Size i = 1; i <= cartom.size(); i ++ ){
156  cartom[i].position = pose->xyz( cartom[i].atom_id );
157  }
158 }
159 
160 
161 
162 void MolecularDynamics::setPosePositionsFromCartesian( )
163 {
164  using namespace core;
165 
166  for ( Size i = 1; i <= cartom.size(); i ++ ){
167  pose->set_xyz( cartom[i].atom_id, cartom[i].position );
168  }
169 }
170 
171 
172 void MolecularDynamics::zeroForces( )
173 {
174  using namespace core;
175 
176  for ( Size i = 1; i <= cartom.size(); i ++ ){
177  cartom[i].force = core::Vector( 0,0,0 );
178  }
179 }
180 
181 int MolecularDynamics::findCartomAtom(
182  const core::id::AtomID &id1
183 )
184 {
185  using namespace core;
186 
187  int number=-1; int i;
188  for ( i = 1; i <= (int)cartom.size(); i ++ ){
189  if( (cartom[i].atom_id.rsd() == id1.rsd() ) &&
190  (cartom[i].atom_id.atomno() == id1.atomno() )
191  ) { number = i; break; }
192  }
193  if( i > (int)cartom.size()) number = -1;
194  return number;
195 }
196 
197 void MolecularDynamics::getCartesianDerivatives(
198  core::scoring::ScoreFunction const & scorefxn
199 )
200 {
201  using namespace core;
202 
203  using namespace core::optimization;
204  Size const nres( pose->total_residue() );
205  scorefxn.setup_for_derivatives( *pose);
206  int count = 1;
207  for ( Size ir = 1; ir <= nres; ++ir ) {
208  conformation::Residue const & rsd( pose->residue( ir ) );
209  for (Size i = 1; i <= rsd.natoms(); i++ ){
210  id::AtomID atom_id( i, ir );
211  core::Vector F1(0,0,0),F2(0,0,0);
212  scorefxn.eval_npd_atom_derivative( atom_id, *pose, min_map.domain_map(), F1, F2 );
213  cartom[count].force = F2;
214  count += 1;
215  }
216  }
217 
218  //std::cout << "Get cartesian derivates \n";
219  // Now handle torsonal derivatives aka dEdphi
220 
221 
222  // now loop over the torsions in the map (the map MUST be a map of everything!)
223 
224  int imap( 1 ); // for indexing into de_dvars( imap )
225  for ( MinimizerMap::iterator it=min_map.begin(), ite=min_map.end();
226  it != ite; ++it, ++imap ) {
227  using namespace id;
228 
229  DOF_Node const & dof_node( **it );
230 
231  // NOTE: deriv is in the units of the degree of freedom as
232  // represented internally, without any scale factors applied
233  // ie the units returned by pose->get_atom_tree_torsion(...)
234  //
235  //
236  // type -- units
237  // -------------------
238  // PHI -- radians
239  // THETA -- radians
240  // D -- angstroms
241  // RB1-3 -- angstroms
242  // RB4-6 -- degrees (!)
243 
244  Real deriv = 0.0;
245 
246  /*kinematics::tree::Atom const & atom
247  ( pose->atom_tree().atom( dof_node.atom_id() ) );*/
248 
249  // eg rama,Paa,dunbrack,and torsional constraints
250  deriv = scorefxn.eval_dof_derivative
251  ( dof_node.dof_id(), dof_node.torsion_id(), *pose );
252  // deriv /= min_map.torsion_scale_factor( dof_node );
253 
254 
255  if( deriv == 0 ) continue;
256  // work out which atoms are involved !
257  AtomID id1;
258  AtomID id2;
259  AtomID id3;
260  AtomID id4;
261 
262  pose->conformation().get_torsion_angle_atom_ids(
263  dof_node.torsion_id(),
264  id1,id2,id3,id4 );
265 
266  // std::cout << " " << id1.atomno() << " " << id2.atomno() << " " << id3.atomno() << " " << id4.atomno() << " -- ";
267 
268  // work out the inices in the cartom array !
269  //Size i;
270  int no1= findCartomAtom( id1 ); if( no1 < 0 ) std::cerr << "ERROR ERROR ERROR id1 \n";
271  int no2= findCartomAtom( id2 ); if( no2 < 0 ) std::cerr << "ERROR ERROR ERROR id2 \n";
272  int no3= findCartomAtom( id3 ); if( no3 < 0 ) std::cerr << "ERROR ERROR ERROR id3 \n";
273  int no4= findCartomAtom( id4 ); if( no4 < 0 ) std::cerr << "ERROR ERROR ERROR id4 \n";
274 // int no2=-1; for ( i = 1; i <= cartom.size(); i ++ ) if( cartom[i].atom_id == id2 ) { no2 = i; break; } if( i > cartom.size()) std::cerr << "ERROR ERROR ERROR no2 \n";
275 // int no3=-1; for ( i = 1; i <= cartom.size(); i ++ ) if( cartom[i].atom_id == id3 ) { no3 = i; break; } if( i > cartom.size()) std::cerr << "ERROR ERROR ERROR no3 \n";
276 // int no4=-1; for ( i = 1; i <= cartom.size(); i ++ ) if( cartom[i].atom_id == id4 ) { no4 = i; break; } if( i > cartom.size()) std::cerr << "ERROR ERROR ERROR no4 \n";
277 
278 
279  //std::cout << " " << cartom[no1].atom_id.rsd() << " " << cartom[no2].atom_id.rsd()
280  // << " " << cartom[no3].atom_id.rsd() << " " << cartom[no4].atom_id.rsd();
281  //std::cout << " " << deriv << " ";
282 
283 
284  // convert to cartesian derivatives on those atoms using the usual MD code - lift from PD
285 
286 
287  //float epot_dihedral_this=0;
288  float /*phi,*/ sin_phi, cos_phi;
289  core::Vector vti_vta, vta_vtb, vtb_vtj;
290  core::Vector nrml1, nrml2, nrml3;
291  float inv_nrml1_mag, inv_nrml2_mag, inv_nrml3_mag;
292 
293  core::Vector dcosdnrml1;
294  core::Vector dcosdnrml2;
295  core::Vector dsindnrml3;
296  core::Vector dsindnrml2;
297  core::Vector f, fi, fab, fj;
298 
299 
300  vti_vta.x() = cartom[no1].position.x() - cartom[no2].position.x();
301  vti_vta.y() = cartom[no1].position.y() - cartom[no2].position.y();
302  vti_vta.z() = cartom[no1].position.z() - cartom[no2].position.z();
303 
304  vta_vtb.x() = cartom[no2].position.x() - cartom[no3].position.x();
305  vta_vtb.y() = cartom[no2].position.y() - cartom[no3].position.y();
306  vta_vtb.z() = cartom[no2].position.z() - cartom[no3].position.z();
307 
308  vtb_vtj.x() = cartom[no3].position.x() - cartom[no4].position.x();
309  vtb_vtj.y() = cartom[no3].position.y() - cartom[no4].position.y();
310  vtb_vtj.z() = cartom[no3].position.z() - cartom[no4].position.z();
311 
312  fi.x() = 0;
313  fi.y() = 0;
314  fi.z() = 0;
315  fab.x() = 0;
316  fab.y() = 0;
317  fab.z() = 0;
318  fj.x() = 0;
319  fj.y() = 0;
320  fj.z() = 0;
321 
322  nrml1.x() = (vti_vta.y() * vta_vtb.z() - vti_vta.z() * vta_vtb.y());
323  nrml1.y() = (vti_vta.z() * vta_vtb.x() - vti_vta.x() * vta_vtb.z());
324  nrml1.z() = (vti_vta.x() * vta_vtb.y() - vti_vta.y() * vta_vtb.x());
325 
326  nrml2.x() = (vta_vtb.y() * vtb_vtj.z() - vta_vtb.z() * vtb_vtj.y());
327  nrml2.y() = (vta_vtb.z() * vtb_vtj.x() - vta_vtb.x() * vtb_vtj.z());
328  nrml2.z() = (vta_vtb.x() * vtb_vtj.y() - vta_vtb.y() * vtb_vtj.x());
329 
330  nrml3.x() = (vta_vtb.y() * nrml1.z() - vta_vtb.z() * nrml1.y());
331  nrml3.y() = (vta_vtb.z() * nrml1.x() - vta_vtb.x() * nrml1.z());
332  nrml3.z() = (vta_vtb.x() * nrml1.y() - vta_vtb.y() * nrml1.x());
333 
334  inv_nrml1_mag = 1.0 / sqrt(sqr(nrml1.x()) + sqr(nrml1.y()) + sqr(nrml1.z()));
335  inv_nrml2_mag = 1.0 / sqrt(sqr(nrml2.x()) + sqr(nrml2.y()) + sqr(nrml2.z()));
336  inv_nrml3_mag = 1.0 / sqrt(sqr(nrml3.x()) + sqr(nrml3.y()) + sqr(nrml3.z()));
337 
338  cos_phi = (nrml1.x() * nrml2.x() + nrml1.y() * nrml2.y() + nrml1.z() * nrml2.z()) * inv_nrml1_mag * inv_nrml2_mag;
339  sin_phi = (nrml3.x() * nrml2.x() + nrml3.y() * nrml2.y() + nrml3.z() * nrml2.z()) * inv_nrml3_mag * inv_nrml2_mag;
340 
341  nrml2.x() *= inv_nrml2_mag;
342  nrml2.y() *= inv_nrml2_mag;
343  nrml2.z() *= inv_nrml2_mag;
344 
345  //phi = -atan2(sin_phi, cos_phi); // set but never used ~Labonte
346 
347  if(fabs(sin_phi) > 0.1) {
348  nrml1.x() *= inv_nrml1_mag;
349  nrml1.y() *= inv_nrml1_mag;
350  nrml1.z() *= inv_nrml1_mag;
351 
352  dcosdnrml1.x() = inv_nrml1_mag * (nrml1.x() * cos_phi - nrml2.x());
353  dcosdnrml1.y() = inv_nrml1_mag * (nrml1.y() * cos_phi - nrml2.y());
354  dcosdnrml1.z() = inv_nrml1_mag * (nrml1.z() * cos_phi - nrml2.z());
355 
356  dcosdnrml2.x() = inv_nrml2_mag * (nrml2.x() * cos_phi - nrml1.x());
357  dcosdnrml2.y() = inv_nrml2_mag * (nrml2.y() * cos_phi - nrml1.y());
358  dcosdnrml2.z() = inv_nrml2_mag * (nrml2.z() * cos_phi - nrml1.z());
359 
360  } else {
361  nrml3.x() *= inv_nrml3_mag;
362  nrml3.y() *= inv_nrml3_mag;
363  nrml3.z() *= inv_nrml3_mag;
364 
365  dsindnrml3.x() = inv_nrml3_mag * (nrml3.x() * sin_phi - nrml2.x());
366  dsindnrml3.y() = inv_nrml3_mag * (nrml3.y() * sin_phi - nrml2.y());
367  dsindnrml3.z() = inv_nrml3_mag * (nrml3.z() * sin_phi - nrml2.z());
368 
369  dsindnrml2.x() = inv_nrml2_mag * (nrml2.x() * sin_phi - nrml3.x());
370  dsindnrml2.y() = inv_nrml2_mag * (nrml2.y() * sin_phi - nrml3.y());
371  dsindnrml2.z() = inv_nrml2_mag * (nrml2.z() * sin_phi - nrml3.z());
372  }
373 
374  //dihedral.phi = phi;
375 
376  deriv *= -1;
377 
378  // forces
379  if(fabs(sin_phi) > 0.1) {
380  deriv /= sin_phi;
381  fi.x() += deriv * (vta_vtb.y() * dcosdnrml1.z() - vta_vtb.z() * dcosdnrml1.y());
382  fi.y() += deriv * (vta_vtb.z() * dcosdnrml1.x() - vta_vtb.x() * dcosdnrml1.z());
383  fi.z() += deriv * (vta_vtb.x() * dcosdnrml1.y() - vta_vtb.y() * dcosdnrml1.x());
384 
385  fj.x() += deriv * (vta_vtb.z() * dcosdnrml2.y() - vta_vtb.y() * dcosdnrml2.z());
386  fj.y() += deriv * (vta_vtb.x() * dcosdnrml2.z() - vta_vtb.z() * dcosdnrml2.x());
387  fj.z() += deriv * (vta_vtb.y() * dcosdnrml2.x() - vta_vtb.x() * dcosdnrml2.y());
388 
389  fab.x() += deriv * (vti_vta.z() * dcosdnrml1.y() - vti_vta.y() * dcosdnrml1.z() + vtb_vtj.y() * dcosdnrml2.z() - vtb_vtj.z() * dcosdnrml2.y());
390  fab.y() += deriv * (vti_vta.x() * dcosdnrml1.z() - vti_vta.z() * dcosdnrml1.x() + vtb_vtj.z() * dcosdnrml2.x() - vtb_vtj.x() * dcosdnrml2.z());
391  fab.z() += deriv * (vti_vta.y() * dcosdnrml1.x() - vti_vta.x() * dcosdnrml1.y() + vtb_vtj.x() * dcosdnrml2.y() - vtb_vtj.y() * dcosdnrml2.x());
392 
393  } else {
394  deriv /= -cos_phi;
395 
396  fi.x() += deriv * ((vta_vtb.y() * vta_vtb.y() + vta_vtb.z() * vta_vtb.z()) * dsindnrml3.x() - vta_vtb.x() * vta_vtb.y() * dsindnrml3.y() - vta_vtb.x() * vta_vtb.z() * dsindnrml3.z());
397  fi.y() += deriv * ((vta_vtb.z() * vta_vtb.z() + vta_vtb.x() * vta_vtb.x()) * dsindnrml3.y() - vta_vtb.y() * vta_vtb.z() * dsindnrml3.z() - vta_vtb.y() * vta_vtb.x() * dsindnrml3.x());
398  fi.z() += deriv * ((vta_vtb.x() * vta_vtb.x() + vta_vtb.y() * vta_vtb.y()) * dsindnrml3.z() - vta_vtb.z() * vta_vtb.x() * dsindnrml3.x() - vta_vtb.z() * vta_vtb.y() * dsindnrml3.y());
399 
400  fj.x() += deriv * (dsindnrml2.y() * vta_vtb.z() - dsindnrml2.z() * vta_vtb.y());
401  fj.y() += deriv * (dsindnrml2.z() * vta_vtb.x() - dsindnrml2.x() * vta_vtb.z());
402  fj.z() += deriv * (dsindnrml2.x() * vta_vtb.y() - dsindnrml2.y() * vta_vtb.x());
403 
404  fab.x() += deriv * (-(vta_vtb.y() * vti_vta.y() + vta_vtb.z() * vti_vta.z()) * dsindnrml3.x()
405  + (2.0 * vta_vtb.x() * vti_vta.y() - vti_vta.x() * vta_vtb.y()) * dsindnrml3.y()
406  + (2.0 * vta_vtb.x() * vti_vta.z() - vti_vta.x() * vta_vtb.z()) * dsindnrml3.z() + dsindnrml2.z() * vtb_vtj.y() - dsindnrml2.y() * vtb_vtj.z());
407  fab.y() += deriv * (-(vta_vtb.z() * vti_vta.z() + vta_vtb.x() * vti_vta.x()) * dsindnrml3.y()
408  + (2.0 * vta_vtb.y() * vti_vta.z() - vti_vta.y() * vta_vtb.z()) * dsindnrml3.z()
409  + (2.0 * vta_vtb.y() * vti_vta.x() - vti_vta.y() * vta_vtb.x()) * dsindnrml3.x() + dsindnrml2.x() * vtb_vtj.z() - dsindnrml2.z() * vtb_vtj.x());
410  fab.z() += deriv * (-(vta_vtb.x() * vti_vta.x() + vta_vtb.y() * vti_vta.y()) * dsindnrml3.z()
411  + (2.0 * vta_vtb.z() * vti_vta.x() - vti_vta.z() * vta_vtb.x()) * dsindnrml3.x()
412  + (2.0 * vta_vtb.z() * vti_vta.y() - vti_vta.z() * vta_vtb.y()) * dsindnrml3.y() + dsindnrml2.y() * vtb_vtj.x() - dsindnrml2.x() * vtb_vtj.y());
413  }
414 
415 // fi.mul(PhysicsConst::invAngstrom);
416 // fab.mul(PhysicsConst::invAngstrom);
417 // fj.mul(PhysicsConst::invAngstrom);
418 
419  // add to cartesian derivatives
420 
421  // std::cout << fi.x() << " " ;
422  // std::cout << fi.y() << " " ;
423  // std::cout << fi.z() << " " ;
424  // std::cout << " | ";
425  // std::cout << fab.x() - fi.x() << " " ;
426  // std::cout << fab.y() - fi.y() << " " ;
427  // std::cout << fab.z() - fi.z() << " " ;
428  // std::cout << " | ";
429  // std::cout << fj.x() - fab.x() << " " ;
430  // std::cout << fj.y() - fab.y() << " " ;
431  // std::cout << fj.z() - fab.z() << " " ;
432  // std::cout << " | ";
433  // std::cout << fj.x() << " " ;
434  // std::cout << fj.y() << " " ;
435  // std::cout << fj.z() << " " ;
436  // std::cout << std::endl;
437 
438 
439  cartom[no1].force.x() += fi.x();
440  cartom[no1].force.y() += fi.y();
441  cartom[no1].force.z() += fi.z();
442 
443  cartom[no2].force.x() += fab.x() - fi.x();
444  cartom[no2].force.y() += fab.y() - fi.y();
445  cartom[no2].force.z() += fab.z() - fi.z();
446 
447  cartom[no3].force.x() += fj.x() - fab.x();
448  cartom[no3].force.y() += fj.y() - fab.y();
449  cartom[no3].force.z() += fj.z() - fab.z();
450 
451  cartom[no4].force.x() -= fj.x();
452  cartom[no4].force.y() -= fj.y();
453  cartom[no4].force.z() -= fj.z();
454 
455  //epot_dihedral += epot_dihedral_this;
456 
457  // DONE
458 
459  } // loop over map
460 
461 
462 
463 }
464 
465 
466 
467 
468 
469 void MolecularDynamics::createBondList( )
470 {
471  using namespace core;
472 
473  Size const nres( pose->total_residue() );
474  bondlist.clear();
475 
476  for ( Size i = 1; i <= cartom.size(); i ++ ){
477  // for each atom get neighbours within the residue;
478  conformation::Residue const & rsd( pose->residue( cartom[i].atom_id.rsd() ) );
479  core::chemical::AtomIndices indices = rsd.bonded_neighbor( cartom[i].atom_id.atomno() );
480  for ( Size j = 1; j <= indices.size(); j++ ){
481  if( int(indices[j]) < int(cartom[i].atom_id.atomno()) ) continue;
482  //std::cout << indices[j] << " ";
483  MD_Bond newbond;
484  newbond.atom_id_1 = cartom[i].atom_id;
485  newbond.atom_id_2 = id::AtomID( indices[j], cartom[i].atom_id.rsd() );
486  newbond.index1 = -1;
487  newbond.index2 = -1;
488 
489  bondlist.push_back( newbond );
490  }
491  }
492 
493  // add residue bonds!
494  for ( Size ir = 1; ir < nres; ++ir ) {
495  conformation::Residue const & rsd1( pose->residue( ir ) );
496  conformation::Residue const & rsd2( pose->residue( ir+1 ) );
497 
498  if( !rsd1.is_bonded( rsd2 ) ) continue;
499 
500  //`nstd::cout << "RES " << ir << std::endl;
501 
502  int atom1 = rsd1.connect_atom( rsd2 );
503  int atom2 = rsd2.connect_atom( rsd1 );
504 
505  MD_Bond newbond;
506  newbond.atom_id_1 = id::AtomID( atom1, ir );
507  newbond.atom_id_2 = id::AtomID( atom2, ir+1 );
508  newbond.index1 = atom1;
509  newbond.index2 = atom2;
510 
511  bondlist.push_back( newbond );
512  }
513 
514  // post process the list
515  // find all the indices
516  for ( Size i = 1; i <= bondlist.size(); i ++ ){
517  bondlist[i].index1 = -1;
518  bondlist[i].index2 = -1;
519  for ( Size j = 1; j <= cartom.size(); j ++ ){
520  if( bondlist[i].atom_id_1 == cartom[j].atom_id ) bondlist[i].index1 = j;
521  if( bondlist[i].atom_id_2 == cartom[j].atom_id ) bondlist[i].index2 = j;
522  }
523  if( bondlist[i].index1 <= 0) std::cout << "CODE ERROR!\n";
524  if( bondlist[i].index2 <= 0) std::cout << "CODE ERROR!\n";
525 
526  // measure length
527 
528  bondlist[i].length = pose->xyz( bondlist[i].atom_id_1 ).distance( pose->xyz( bondlist[i].atom_id_2 ) );
529 /*
530  std::cout <<
531  bondlist[i].atom_id_1.rsd() << " " <<
532  bondlist[i].atom_id_1.atomno() << " " <<
533  bondlist[i].index1 << " " <<
534  bondlist[i].atom_id_2.rsd() << " " <<
535  bondlist[i].atom_id_2.atomno() << " " <<
536  bondlist[i].index2 << " " <<
537  bondlist[i].length << " " <<
538  std::endl;
539 */
540 
541  }
542 
543 
544 
545 }
546 
547 
548 void MolecularDynamics::createAngleList( )
549 {
550  using namespace core;
551 
552  //Size const nres( pose->total_residue() );
553  anglelist.clear();
554 
555  for ( Size i = 1; i <= bondlist.size(); i ++ ){
556  for ( Size j = 1; j <= bondlist.size(); j ++ ){
557  if(i == j) continue;
558 
559  MD_Angle newangle;
560  if( bondlist[i].index1 == bondlist[j].index1 ){
561  newangle.index1 = bondlist[i].index2;
562  newangle.index2 = bondlist[i].index1;
563  newangle.index3 = bondlist[j].index2;
564  } else
565  if( bondlist[i].index1 == bondlist[j].index2 ){
566  newangle.index1 = bondlist[i].index2;
567  newangle.index2 = bondlist[i].index1;
568  newangle.index3 = bondlist[j].index1;
569  } else
570  if( bondlist[i].index2 == bondlist[j].index1 ){
571  newangle.index1 = bondlist[i].index1;
572  newangle.index2 = bondlist[i].index2;
573  newangle.index3 = bondlist[j].index2;
574  } else
575  if( bondlist[i].index2 == bondlist[j].index2 ){
576  newangle.index1 = bondlist[i].index1;
577  newangle.index2 = bondlist[i].index2;
578  newangle.index3 = bondlist[j].index1;
579  } else
580  continue;
581 
582  if( newangle.index1 > newangle.index3 ) continue;
583 
584  newangle.atom_id_1 = cartom[ newangle.index1 ].atom_id;
585  newangle.atom_id_2 = cartom[ newangle.index2 ].atom_id;
586  newangle.atom_id_3 = cartom[ newangle.index3 ].atom_id;
587  newangle.length = pose->xyz( newangle.atom_id_1 ).distance( pose->xyz( newangle.atom_id_3 ) );
588  /*
589  std::cout <<
590  newangle.atom_id_1.rsd() << " " <<
591  newangle.atom_id_1.atomno() << " " <<
592  newangle.index1 << " " <<
593  newangle.atom_id_2.rsd() << " " <<
594  newangle.atom_id_2.atomno() << " " <<
595  newangle.index2 << " " <<
596  newangle.atom_id_3.rsd() << " " <<
597  newangle.atom_id_3.atomno() << " " <<
598  newangle.index3 << " " <<
599  newangle.length << " " <<
600  std::endl;
601 */
602  anglelist.push_back( newangle );
603  }
604  }
605 
606 
607 
608 }
609 
610 MD_HarmonicDihedral MolecularDynamics::createDihedral(
611  const core::conformation::Residue &rsd1,
612  const core::conformation::Residue &rsd2,
613  const core::conformation::Residue &rsd3,
614  const core::conformation::Residue &rsd4,
615  std::string name1,
616  std::string name2,
617  std::string name3,
618  std::string name4
619 ){
620  using namespace core;
621 
622 
623  MD_HarmonicDihedral newdihed;
624  newdihed.atom_id_1 = id::AtomID( rsd1.atom_index( name1 ) ,rsd1.seqpos() );
625  newdihed.atom_id_2 = id::AtomID( rsd2.atom_index( name2 ) ,rsd2.seqpos() );
626  newdihed.atom_id_3 = id::AtomID( rsd3.atom_index( name3 ) ,rsd3.seqpos() );
627  newdihed.atom_id_4 = id::AtomID( rsd4.atom_index( name4 ) ,rsd4.seqpos() );
628  newdihed.index1 = findCartomAtom( newdihed.atom_id_1 );
629  newdihed.index2 = findCartomAtom( newdihed.atom_id_2 );
630  newdihed.index3 = findCartomAtom( newdihed.atom_id_3 );
631  newdihed.index4 = findCartomAtom( newdihed.atom_id_4 );
632 
633  if( (newdihed.index1 < 0) ) std::cout << "Can't find" << name1 << std::endl;
634  if( (newdihed.index2 < 0) ) std::cout << "Can't find" << name2 << std::endl;
635  if( (newdihed.index3 < 0) ) std::cout << "Can't find" << name3 << std::endl;
636  if( (newdihed.index4 < 0) ) std::cout << "Can't find" << name4 << std::endl;
637  if(
638  (newdihed.index1 < 0) ||
639  (newdihed.index2 < 0) ||
640  (newdihed.index3 < 0) ||
641  (newdihed.index4 < 0)
642  ){
643  std::cout
644  << name1 << " "
645  << name2 << " "
646  << name3 << " "
647  << name4 << " "
648  << newdihed.atom_id_1.rsd() << " "
649  << newdihed.atom_id_2.rsd() << " "
650  << newdihed.atom_id_3.rsd() << " "
651  << newdihed.atom_id_4.rsd() << " "
652  << newdihed.atom_id_1.atomno() << " "
653  << newdihed.atom_id_2.atomno() << " "
654  << newdihed.atom_id_3.atomno() << " "
655  << newdihed.atom_id_4.atomno() << " "
656  << std::endl;
657  exit(0);
658  }
659 
660  newdihed.angle = 0;
661  return newdihed;
662 }
663 
664 
665 
666 MD_HarmonicDihedral MolecularDynamics::createDihedral(
667  const core::conformation::Residue &rsd,
668  std::string name1,
669  std::string name2,
670  std::string name3,
671  std::string name4
672 ){
673  using namespace core;
674 
675  MD_HarmonicDihedral newdihed;
676  newdihed.atom_id_1 = id::AtomID( rsd.atom_index( name1 ) ,rsd.seqpos() );
677  newdihed.atom_id_2 = id::AtomID( rsd.atom_index( name2 ) ,rsd.seqpos() );
678  newdihed.atom_id_3 = id::AtomID( rsd.atom_index( name3 ) ,rsd.seqpos() );
679  newdihed.atom_id_4 = id::AtomID( rsd.atom_index( name4 ) ,rsd.seqpos() );
680  newdihed.index1 = findCartomAtom( newdihed.atom_id_1 );
681  newdihed.index2 = findCartomAtom( newdihed.atom_id_2 );
682  newdihed.index3 = findCartomAtom( newdihed.atom_id_3 );
683  newdihed.index4 = findCartomAtom( newdihed.atom_id_4 );
684 
685  if( (newdihed.index1 < 0) ) std::cout << "Can't find" << name1 << std::endl;
686  if( (newdihed.index2 < 0) ) std::cout << "Can't find" << name2 << std::endl;
687  if( (newdihed.index3 < 0) ) std::cout << "Can't find" << name3 << std::endl;
688  if( (newdihed.index4 < 0) ) std::cout << "Can't find" << name4 << std::endl;
689  if(
690  (newdihed.index1 < 0) ||
691  (newdihed.index2 < 0) ||
692  (newdihed.index3 < 0) ||
693  (newdihed.index4 < 0)
694  ){
695  std::cout
696  << name1 << " "
697  << name2 << " "
698  << name3 << " "
699  << name4 << " "
700  << newdihed.atom_id_1.rsd() << " "
701  << newdihed.atom_id_2.rsd() << " "
702  << newdihed.atom_id_3.rsd() << " "
703  << newdihed.atom_id_4.rsd() << " "
704  << newdihed.atom_id_1.atomno() << " "
705  << newdihed.atom_id_2.atomno() << " "
706  << newdihed.atom_id_3.atomno() << " "
707  << newdihed.atom_id_4.atomno() << " "
708  << std::endl;
709  exit(0);
710  }
711 
712  newdihed.angle = 0;
713  return newdihed;
714 }
715 
716 /// Yes i know this is hard coded stuff. Read warning at the top of this file.
717 void MolecularDynamics::createDihedralList( )
718 {
719  using namespace core;
720  int ir;
721  for( ir = 1; ir < (int)pose->total_residue(); ir ++ ){
722  const conformation::Residue &rsd = pose->residue( ir );
723 
724 
725  if( ( !(rsd.aa() == chemical::aa_pro) ) &&
726  ( ir != 1 ) &&
727  ( ir < ( (int)pose->total_residue() - 1 ) )
728  ){
729 
730  dihedrallist.push_back( createDihedral(
731  pose->residue( ir - 1 ),
732  pose->residue( ir ),
733  pose->residue( ir ),
734  pose->residue( ir ),
735  "C", "CA", "N", "H" ) );
736 
737  dihedrallist.push_back( createDihedral(
738  pose->residue( ir ),
739  pose->residue( ir + 1 ),
740  pose->residue( ir ),
741  pose->residue( ir ),
742  "CA", "N", "C", "O" ) );
743 
744  }
745 
746  //if( rsd.aa() == chemical::aa_ala )
747  //if( rsd.aa() == chemical::aa_cys )
748  if( rsd.aa() == chemical::aa_asp ){
749  //std::cout << "Preparring ASP\n";
750  dihedrallist.push_back( createDihedral( rsd, "CB", "OD1", "CG", "OD2" ) );
751  }
752  if( rsd.aa() == chemical::aa_glu ){
753  //std::cout << "Preparring ASP\n";
754  dihedrallist.push_back( createDihedral( rsd, "CG", "OE1", "CD", "OE2" ) );
755  }
756  if( rsd.aa() == chemical::aa_phe ){
757  //std::cout << "Preparring PHE\n";
758 
759  // Ring Dihedrals
760  dihedrallist.push_back( createDihedral( rsd, "CB", "CG", "CD2", "HD2" ) );
761 
762  dihedrallist.push_back( createDihedral( rsd, "HE2", "CE2", "CZ", "HZ" ) );
763  dihedrallist.push_back( createDihedral( rsd, "HZ", "CZ", "CE1","HE1" ) );
764  dihedrallist.push_back( createDihedral( rsd, "HE1", "CE1","CD1", "HD1" ) );
765  dihedrallist.push_back( createDihedral( rsd, "HD1", "CD1", "CG", "CB" ) );
766 
767  dihedrallist.push_back( createDihedral( rsd, "CD1", "CG", "CD2", "HD2" ) );
768  dihedrallist.push_back( createDihedral( rsd, "CG", "CD2","CE2", "HE2" ) );
769  dihedrallist.push_back( createDihedral( rsd, "CD2", "CE2", "CZ", "HZ" ) );
770  dihedrallist.push_back( createDihedral( rsd, "CE2", "CZ", "CE1","HE1" ) );
771  dihedrallist.push_back( createDihedral( rsd, "CZ", "CE1","CD1", "HD1" ) );
772  dihedrallist.push_back( createDihedral( rsd, "CE1", "CD1", "CG", "CB" ) );
773 
774  dihedrallist.push_back( createDihedral( rsd, "CB", "CG", "CD2", "CE2" ) );
775  dihedrallist.push_back( createDihedral( rsd, "HD2", "CD2","CE2", "CZ" ) );
776  dihedrallist.push_back( createDihedral( rsd, "HE2", "CE2", "CZ", "CE1" ) );
777  dihedrallist.push_back( createDihedral( rsd, "HZ", "CZ", "CE1","CD1" ) );
778  dihedrallist.push_back( createDihedral( rsd, "HE1", "CE1","CD1", "CG" ) );
779  dihedrallist.push_back( createDihedral( rsd, "HD1", "CD1", "CG", "CD2" ) );
780 
781  // Impropers
782  dihedrallist.push_back( createDihedral( rsd, "CG", "CE2", "CD2", "HD2" ) );
783  dihedrallist.push_back( createDihedral( rsd, "CD2", "CZ", "CE2", "HE2" ) );
784  dihedrallist.push_back( createDihedral( rsd, "CZ", "CD2", "CE2", "HE2" ) );
785  dihedrallist.push_back( createDihedral( rsd, "CE1", "CE2", "CZ", "HZ" ) );
786  dihedrallist.push_back( createDihedral( rsd, "CD1", "CZ", "CE1", "HE1" ) );
787  dihedrallist.push_back( createDihedral( rsd, "CG", "CE1", "CD1", "HD1" ) );
788  dihedrallist.push_back( createDihedral( rsd, "CD1", "CD2", "CG", "CB" ) );
789  }
790 
791  //if( rsd.aa() == chemical::aa_gly )
792  if( rsd.aa() == chemical::aa_his ){
793 
794  if( rsd.has( "HE2" ) ){
795  dihedrallist.push_back( createDihedral( rsd, "CE1", "CD2", "NE2","HE2" ) );
796  dihedrallist.push_back( createDihedral( rsd, "CG", "NE2","CD2", "HD2" ) );
797  dihedrallist.push_back( createDihedral( rsd, "ND1", "NE2", "CE1", "HE1" ) );
798  dihedrallist.push_back( createDihedral( rsd, "ND1", "CD2", "CG", "CB" ) );
799 
800  dihedrallist.push_back( createDihedral( rsd, "CB", "CG", "CD2","HD2" ) );
801  dihedrallist.push_back( createDihedral( rsd, "HD2","CD2", "NE2","HE2" ) );
802  dihedrallist.push_back( createDihedral( rsd, "HE2", "NE2", "CE1", "HE1" ) );
803  dihedrallist.push_back( createDihedral( rsd, "HE1", "CE1", "ND1","CG" ) );
804 
805  dihedrallist.push_back( createDihedral( rsd, "CB", "CG", "CD2","NE2" ) );
806  dihedrallist.push_back( createDihedral( rsd, "HD2","CD2", "NE2","CE1" ) );
807  dihedrallist.push_back( createDihedral( rsd, "HE2", "NE2", "CE1", "ND1" ) );
808  }else{
809  // HD1 torsions misssing - fix this - mike
810  dihedrallist.push_back( createDihedral( rsd, "CG", "NE2","CD2", "HD2" ) );
811  dihedrallist.push_back( createDihedral( rsd, "ND1", "NE2", "CE1", "HE1" ) );
812  dihedrallist.push_back( createDihedral( rsd, "ND1", "CD2", "CG", "CB" ) );
813 
814  dihedrallist.push_back( createDihedral( rsd, "CB", "CG", "CD2","HD2" ) );
815  dihedrallist.push_back( createDihedral( rsd, "HE1", "CE1", "ND1","CG" ) );
816 
817  dihedrallist.push_back( createDihedral( rsd, "CB", "CG", "CD2","NE2" ) );
818  dihedrallist.push_back( createDihedral( rsd, "HD2","CD2", "NE2","CE1" ) );
819 
820 
821 
822  }
823  }
824  //if( rsd.aa() == chemical::aa_ile )
825  //if( rsd.aa() == chemical::aa_lys )
826  //if( rsd.aa() == chemical::aa_leu )
827  //if( rsd.aa() == chemical::aa_met )
828  if( rsd.aa() == chemical::aa_asn ){
829  //std::cout << "Preparring ASN\n";
830  dihedrallist.push_back( createDihedral( rsd, "CB", "ND2", "CG", "OD1" ) );
831  dihedrallist.push_back( createDihedral( rsd, "CG", "1HD2", "ND2", "2HD2" ) );
832 
833  dihedrallist.push_back( createDihedral( rsd, "OD1", "CG", "ND2", "1HD2" ) );
834  dihedrallist.push_back( createDihedral( rsd, "OD1", "CG", "ND2", "2HD2" ) );
835  dihedrallist.push_back( createDihedral( rsd, "CB", "CG", "ND2", "1HD2" ) );
836  dihedrallist.push_back( createDihedral( rsd, "CB", "CG", "ND2", "2HD2" ) );
837 
838  }
839  //if( rsd.aa() == chemical::aa_pro )
840  if( rsd.aa() == chemical::aa_gln ){
841  //std::cout << "Preparring GLN\n";
842  dihedrallist.push_back( createDihedral( rsd, "CG", "NE2", "CD", "OE1" ) );
843  dihedrallist.push_back( createDihedral( rsd, "CD", "1HE2", "NE2", "2HE2" ) );
844 
845  dihedrallist.push_back( createDihedral( rsd, "OE1", "CG", "NE2", "1HE2" ) );
846  dihedrallist.push_back( createDihedral( rsd, "OE1", "CG", "NE2", "2HE2" ) );
847  dihedrallist.push_back( createDihedral( rsd, "CG", "CD", "NE2", "1HE2" ) );
848  dihedrallist.push_back( createDihedral( rsd, "CG", "CD", "NE2", "2HE2" ) );
849  }
850  if( rsd.aa() == chemical::aa_arg ){
851  //std::cout << "Preparring ARG\n";
852  dihedrallist.push_back( createDihedral( rsd, "NE", "NH1", "CZ", "NH2" ) );
853  dihedrallist.push_back( createDihedral( rsd, "CD", "CZ", "NE", "HE" ) );
854  dihedrallist.push_back( createDihedral( rsd, "CZ", "1HH1", "NH1", "2HH1" ) );
855  dihedrallist.push_back( createDihedral( rsd, "CZ", "1HH2", "NH2", "2HH2" ) );
856 
857  dihedrallist.push_back( createDihedral( rsd, "NH1", "CZ", "NH2", "1HH2" ) );
858  dihedrallist.push_back( createDihedral( rsd, "NH1", "CZ", "NH2", "2HH2" ) );
859  dihedrallist.push_back( createDihedral( rsd, "NE", "CZ", "NH2", "1HH2" ) );
860  dihedrallist.push_back( createDihedral( rsd, "NE", "CZ", "NH2", "2HH2" ) );
861 
862  dihedrallist.push_back( createDihedral( rsd, "NH2", "CZ", "NH1", "1HH1" ) );
863  dihedrallist.push_back( createDihedral( rsd, "NH2", "CZ", "NH1", "2HH1" ) );
864  dihedrallist.push_back( createDihedral( rsd, "NE", "CZ", "NH1", "1HH1" ) );
865  dihedrallist.push_back( createDihedral( rsd, "NE", "CZ", "NH1", "2HH1" ) );
866 
867  dihedrallist.push_back( createDihedral( rsd, "NH2", "CZ", "NE", "CD" ) );
868  dihedrallist.push_back( createDihedral( rsd, "NH2", "CZ", "NE", "HE" ) );
869  dihedrallist.push_back( createDihedral( rsd, "NH1", "CZ", "NE", "CD" ) );
870  dihedrallist.push_back( createDihedral( rsd, "NH2", "CZ", "NE", "HE" ) );
871 
872 
873 
874  };
875  //if( rsd.aa() == chemical::aa_ser )
876  //if( rsd.aa() == chemical::aa_thr
877  //if( rsd.aa() == chemical::aa_val )
878  if( rsd.aa() == chemical::aa_trp ){
879 
880  //std::cout << "Preparring TRP\n";
881 
882  dihedrallist.push_back( createDihedral( rsd, "CD1", "CE2", "NE1", "HE1" ) );
883  dihedrallist.push_back( createDihedral( rsd, "CE2", "CH2", "CZ2", "HZ2" ) );
884  dihedrallist.push_back( createDihedral( rsd, "CZ2", "CZ3", "CH2", "HH2" ) );
885  dihedrallist.push_back( createDihedral( rsd, "CH2", "CE3", "CZ3", "HZ3" ) );
886  dihedrallist.push_back( createDihedral( rsd, "CZ3", "CD2", "CE3", "HE3" ) );
887  dihedrallist.push_back( createDihedral( rsd, "CG", "NE1", "CD1", "HD1" ) );
888  dihedrallist.push_back( createDihedral( rsd, "CD1", "CD2", "CG", "CB" ) );
889 
890  dihedrallist.push_back( createDihedral( rsd, "CB", "CG", "CD1", "HD1" ) );
891  dihedrallist.push_back( createDihedral( rsd, "HD1", "CD1", "NE1", "HE1" ) );
892  dihedrallist.push_back( createDihedral( rsd, "HE1", "NE1", "CE2", "CZ2" ) );
893  dihedrallist.push_back( createDihedral( rsd, "NE1", "CE2", "CZ2", "HZ2" ) );
894  dihedrallist.push_back( createDihedral( rsd, "CE2", "CZ2", "CH2", "HH2" ) );
895  dihedrallist.push_back( createDihedral( rsd, "HH2", "CH2", "CZ3", "HZ3" ) );
896  dihedrallist.push_back( createDihedral( rsd, "HZ3", "CZ3", "CE3", "HE3" ) );
897  dihedrallist.push_back( createDihedral( rsd, "HE3", "CE3", "CD2", "CG" ) );
898  dihedrallist.push_back( createDihedral( rsd, "CE3", "CD2", "CG", "CB" ) );
899 
900  dihedrallist.push_back( createDihedral( rsd, "CB", "CG", "CD1", "NE1" ) );
901  dihedrallist.push_back( createDihedral( rsd, "HD1", "CD1", "NE1", "CE2" ) );
902  dihedrallist.push_back( createDihedral( rsd, "HE1", "NE1", "CE2", "CD2" ) );
903  dihedrallist.push_back( createDihedral( rsd, "NE1", "CE2", "CZ2", "CH2" ) );
904  dihedrallist.push_back( createDihedral( rsd, "CE2", "CZ2", "CH2", "CZ3" ) );
905  dihedrallist.push_back( createDihedral( rsd, "HH2", "CH2", "CZ3", "CE3" ) );
906  dihedrallist.push_back( createDihedral( rsd, "HZ3", "CZ3", "CE3", "CD2" ) );
907  dihedrallist.push_back( createDihedral( rsd, "HE3", "CE3", "CD2", "CE2" ) );
908  dihedrallist.push_back( createDihedral( rsd, "CE3", "CD2", "CG", "CD1" ) );
909 
910 
911  dihedrallist.push_back( createDihedral( rsd, "CD2", "CE2", "CZ2", "CH2" ) );
912  dihedrallist.push_back( createDihedral( rsd, "CE2", "CZ2", "CH2", "CZ3" ) );
913  dihedrallist.push_back( createDihedral( rsd, "CZ2", "CH2", "CZ3", "CE3" ) );
914  dihedrallist.push_back( createDihedral( rsd, "CH2", "CZ3", "CE3", "CD2" ) );
915  dihedrallist.push_back( createDihedral( rsd, "CZ3", "CE3", "CD2", "CE2" ) );
916  dihedrallist.push_back( createDihedral( rsd, "CE3", "CD2", "CE2", "CZ2" ) );
917 
918 
919  }
920 
921  if( rsd.aa() == chemical::aa_tyr ){
922  //std::cout << "Preparring TYR\n";
923 
924  // Ring Dihedrals
925  dihedrallist.push_back( createDihedral( rsd, "CB", "CG", "CD2", "HD2" ) );
926  dihedrallist.push_back( createDihedral( rsd, "HD2", "CD2","CE2", "HE2" ) );
927  dihedrallist.push_back( createDihedral( rsd, "HE2", "CE2", "CZ", "OH" ) );
928  dihedrallist.push_back( createDihedral( rsd, "OH", "CZ", "CE1","HE1" ) );
929  dihedrallist.push_back( createDihedral( rsd, "HE1", "CE1","CD1", "HD1" ) );
930  dihedrallist.push_back( createDihedral( rsd, "HD1", "CD1", "CG", "CB" ) );
931 
932  dihedrallist.push_back( createDihedral( rsd, "CD1", "CG", "CD2", "HD2" ) );
933  dihedrallist.push_back( createDihedral( rsd, "CG", "CD2","CE2", "HE2" ) );
934  dihedrallist.push_back( createDihedral( rsd, "CD2", "CE2", "CZ", "OH" ) );
935  dihedrallist.push_back( createDihedral( rsd, "CE2", "CZ", "CE1","HE1" ) );
936  dihedrallist.push_back( createDihedral( rsd, "CZ", "CE1","CD1", "HD1" ) );
937  dihedrallist.push_back( createDihedral( rsd, "CE1", "CD1", "CG", "CB" ) );
938 
939  dihedrallist.push_back( createDihedral( rsd, "CB", "CG", "CD2", "CE2" ) );
940  dihedrallist.push_back( createDihedral( rsd, "HD2", "CD2","CE2", "CZ" ) );
941  dihedrallist.push_back( createDihedral( rsd, "HE2", "CE2", "CZ", "CE1" ) );
942  dihedrallist.push_back( createDihedral( rsd, "OH", "CZ", "CE1","CD1" ) );
943  dihedrallist.push_back( createDihedral( rsd, "HE1", "CE1","CD1", "CG" ) );
944  dihedrallist.push_back( createDihedral( rsd, "HD1", "CD1", "CG", "CD2" ) );
945 
946  // Impropers
947  dihedrallist.push_back( createDihedral( rsd, "CG", "CE2", "CD2", "HD2" ) );
948  dihedrallist.push_back( createDihedral( rsd, "CD2", "CZ", "CE2", "HE2" ) );
949  dihedrallist.push_back( createDihedral( rsd, "CZ", "CD2", "CE2", "HE2" ) );
950  dihedrallist.push_back( createDihedral( rsd, "CE1", "CE2", "CZ", "OH" ) );
951  dihedrallist.push_back( createDihedral( rsd, "CD1", "CZ", "CE1", "HE1" ) );
952  dihedrallist.push_back( createDihedral( rsd, "CG", "CE1", "CD1", "HD1" ) );
953  dihedrallist.push_back( createDihedral( rsd, "CD1", "CD2", "CG", "CB" ) );
954 
955 
956  }
957 
958 
959 
960  }
961 
962 }
963 
964 
965 
966 void MolecularDynamics::setDihedralDerivatives( ){
967  using namespace core;
968  for ( Size i = 1; i <= dihedrallist.size(); i ++ ){
969 
970  // work out which atoms are involved !
971  int no1 = dihedrallist[i].index1;
972  int no2 = dihedrallist[i].index2;
973  int no3 = dihedrallist[i].index3;
974  int no4 = dihedrallist[i].index4;
975 
976  //std::cout << no1 << " " << no2 << " " << no3 << " " << no4 << " "
977  // << std::endl;
978 
979  //float epot_dihedral_this=0;
980  float phi, sin_phi, cos_phi;
981  core::Vector vti_vta, vta_vtb, vtb_vtj;
982  core::Vector nrml1, nrml2, nrml3;
983  float inv_nrml1_mag, inv_nrml2_mag, inv_nrml3_mag;
984 
985  core::Vector dcosdnrml1;
986  core::Vector dcosdnrml2;
987  core::Vector dsindnrml3;
988  core::Vector dsindnrml2;
989 
990  vti_vta.x() = cartom[no1].position.x() - cartom[no2].position.x();
991  vti_vta.y() = cartom[no1].position.y() - cartom[no2].position.y();
992  vti_vta.z() = cartom[no1].position.z() - cartom[no2].position.z();
993 
994  vta_vtb.x() = cartom[no2].position.x() - cartom[no3].position.x();
995  vta_vtb.y() = cartom[no2].position.y() - cartom[no3].position.y();
996  vta_vtb.z() = cartom[no2].position.z() - cartom[no3].position.z();
997 
998  vtb_vtj.x() = cartom[no3].position.x() - cartom[no4].position.x();
999  vtb_vtj.y() = cartom[no3].position.y() - cartom[no4].position.y();
1000  vtb_vtj.z() = cartom[no3].position.z() - cartom[no4].position.z();
1001 
1002  nrml1.x() = (vti_vta.y() * vta_vtb.z() - vti_vta.z() * vta_vtb.y());
1003  nrml1.y() = (vti_vta.z() * vta_vtb.x() - vti_vta.x() * vta_vtb.z());
1004  nrml1.z() = (vti_vta.x() * vta_vtb.y() - vti_vta.y() * vta_vtb.x());
1005 
1006  nrml2.x() = (vta_vtb.y() * vtb_vtj.z() - vta_vtb.z() * vtb_vtj.y());
1007  nrml2.y() = (vta_vtb.z() * vtb_vtj.x() - vta_vtb.x() * vtb_vtj.z());
1008  nrml2.z() = (vta_vtb.x() * vtb_vtj.y() - vta_vtb.y() * vtb_vtj.x());
1009 
1010  nrml3.x() = (vta_vtb.y() * nrml1.z() - vta_vtb.z() * nrml1.y());
1011  nrml3.y() = (vta_vtb.z() * nrml1.x() - vta_vtb.x() * nrml1.z());
1012  nrml3.z() = (vta_vtb.x() * nrml1.y() - vta_vtb.y() * nrml1.x());
1013 
1014  inv_nrml1_mag = 1.0 / sqrt(sqr(nrml1.x()) + sqr(nrml1.y()) + sqr(nrml1.z()));
1015  inv_nrml2_mag = 1.0 / sqrt(sqr(nrml2.x()) + sqr(nrml2.y()) + sqr(nrml2.z()));
1016  inv_nrml3_mag = 1.0 / sqrt(sqr(nrml3.x()) + sqr(nrml3.y()) + sqr(nrml3.z()));
1017 
1018  cos_phi = (nrml1.x() * nrml2.x() + nrml1.y() * nrml2.y() + nrml1.z() * nrml2.z()) * inv_nrml1_mag * inv_nrml2_mag;
1019  sin_phi = (nrml3.x() * nrml2.x() + nrml3.y() * nrml2.y() + nrml3.z() * nrml2.z()) * inv_nrml3_mag * inv_nrml2_mag;
1020 
1021  nrml2.x() *= inv_nrml2_mag;
1022  nrml2.y() *= inv_nrml2_mag;
1023  nrml2.z() *= inv_nrml2_mag;
1024 
1025  phi = -atan2(sin_phi, cos_phi);
1026  dihedrallist[i].angle = phi;
1027  }
1028 
1029 }
1030 
1031 
1032 
1033 
1034 
1035 void MolecularDynamics::doBondDerivatives( float &totalepot )
1036 {
1037  using namespace core;
1038 
1039  float k = 600;
1040  for ( Size i = 1; i <= bondlist.size(); i ++ ){
1041 
1042  core::Vector f2 = pose->xyz( bondlist[i].atom_id_1 ) - pose->xyz( bondlist[i].atom_id_2 );
1043  float length = pose->xyz( bondlist[i].atom_id_1 ).distance( pose->xyz( bondlist[i].atom_id_2 ) );
1044 
1045  totalepot += 0.5 * k * sqr(length - bondlist[i].length);
1046 
1047  float deriv = k * (length - bondlist[i].length);
1048 
1049  f2 *= deriv / length;
1050 
1051  cartom[ bondlist[i].index1].force += f2;
1052  cartom[ bondlist[i].index2].force -= f2;
1053  }
1054 
1055 
1056 }
1057 
1058 
1059 void MolecularDynamics::doAngleDerivatives( float &totalepot )
1060 {
1061  using namespace core;
1062 
1063  float k = 600;
1064  for ( Size i = 1; i <= anglelist.size(); i ++ ){
1065 
1066  core::Vector f2 = pose->xyz( anglelist[i].atom_id_1 ) - pose->xyz( anglelist[i].atom_id_3 );
1067  float length = pose->xyz( anglelist[i].atom_id_1 ).distance( pose->xyz( anglelist[i].atom_id_3 ) );
1068 
1069  totalepot += 0.5 * k * sqr(length - anglelist[i].length);
1070 
1071  float deriv = k * (length - anglelist[i].length);
1072 
1073  f2 *= deriv / length;
1074 
1075  cartom[ anglelist[i].index1 ].force += f2;
1076  cartom[ anglelist[i].index3 ].force -= f2;
1077  }
1078 
1079 }
1080 
1081 
1082 
1083 void MolecularDynamics::doDihedralDerivatives(
1084  float &totalepot
1085 )
1086 {
1087  using namespace core;
1088 
1089  // float totene_b4 = totalepot;
1090 
1091  float k = 200;
1092  for ( Size i = 1; i <= dihedrallist.size(); i ++ ){
1093 
1094 
1095  // work out which atoms are involved !
1096 
1097  int no1 = dihedrallist[i].index1;
1098  int no2 = dihedrallist[i].index2;
1099  int no3 = dihedrallist[i].index3;
1100  int no4 = dihedrallist[i].index4;
1101 
1102 
1103  //float epot_dihedral_this=0;
1104  float phi, sin_phi, cos_phi;
1105  core::Vector vti_vta, vta_vtb, vtb_vtj;
1106  core::Vector nrml1, nrml2, nrml3;
1107  float inv_nrml1_mag, inv_nrml2_mag, inv_nrml3_mag;
1108 
1109  core::Vector dcosdnrml1(0,0,0);
1110  core::Vector dcosdnrml2(0,0,0);
1111  core::Vector dsindnrml3(0,0,0);
1112  core::Vector dsindnrml2(0,0,0);
1113  core::Vector f, fi, fab, fj;
1114 
1115 
1116  vti_vta.x() = cartom[no1].position.x() - cartom[no2].position.x();
1117  vti_vta.y() = cartom[no1].position.y() - cartom[no2].position.y();
1118  vti_vta.z() = cartom[no1].position.z() - cartom[no2].position.z();
1119 
1120  vta_vtb.x() = cartom[no2].position.x() - cartom[no3].position.x();
1121  vta_vtb.y() = cartom[no2].position.y() - cartom[no3].position.y();
1122  vta_vtb.z() = cartom[no2].position.z() - cartom[no3].position.z();
1123 
1124  vtb_vtj.x() = cartom[no3].position.x() - cartom[no4].position.x();
1125  vtb_vtj.y() = cartom[no3].position.y() - cartom[no4].position.y();
1126  vtb_vtj.z() = cartom[no3].position.z() - cartom[no4].position.z();
1127 
1128  fi.x() = 0;
1129  fi.y() = 0;
1130  fi.z() = 0;
1131  fab.x() = 0;
1132  fab.y() = 0;
1133  fab.z() = 0;
1134  fj.x() = 0;
1135  fj.y() = 0;
1136  fj.z() = 0;
1137 
1138  nrml1.x() = (vti_vta.y() * vta_vtb.z() - vti_vta.z() * vta_vtb.y());
1139  nrml1.y() = (vti_vta.z() * vta_vtb.x() - vti_vta.x() * vta_vtb.z());
1140  nrml1.z() = (vti_vta.x() * vta_vtb.y() - vti_vta.y() * vta_vtb.x());
1141 
1142  nrml2.x() = (vta_vtb.y() * vtb_vtj.z() - vta_vtb.z() * vtb_vtj.y());
1143  nrml2.y() = (vta_vtb.z() * vtb_vtj.x() - vta_vtb.x() * vtb_vtj.z());
1144  nrml2.z() = (vta_vtb.x() * vtb_vtj.y() - vta_vtb.y() * vtb_vtj.x());
1145 
1146  nrml3.x() = (vta_vtb.y() * nrml1.z() - vta_vtb.z() * nrml1.y());
1147  nrml3.y() = (vta_vtb.z() * nrml1.x() - vta_vtb.x() * nrml1.z());
1148  nrml3.z() = (vta_vtb.x() * nrml1.y() - vta_vtb.y() * nrml1.x());
1149 
1150  inv_nrml1_mag = 1.0 / sqrt(sqr(nrml1.x()) + sqr(nrml1.y()) + sqr(nrml1.z()));
1151  inv_nrml2_mag = 1.0 / sqrt(sqr(nrml2.x()) + sqr(nrml2.y()) + sqr(nrml2.z()));
1152  inv_nrml3_mag = 1.0 / sqrt(sqr(nrml3.x()) + sqr(nrml3.y()) + sqr(nrml3.z()));
1153 
1154  cos_phi = (nrml1.x() * nrml2.x() + nrml1.y() * nrml2.y() + nrml1.z() * nrml2.z()) * inv_nrml1_mag * inv_nrml2_mag;
1155  sin_phi = (nrml3.x() * nrml2.x() + nrml3.y() * nrml2.y() + nrml3.z() * nrml2.z()) * inv_nrml3_mag * inv_nrml2_mag;
1156 
1157  nrml2.x() *= inv_nrml2_mag;
1158  nrml2.y() *= inv_nrml2_mag;
1159  nrml2.z() *= inv_nrml2_mag;
1160 
1161  phi = -atan2(sin_phi, cos_phi);
1162 
1163  if(fabs(sin_phi) > 0.1) {
1164  nrml1.x() *= inv_nrml1_mag;
1165  nrml1.y() *= inv_nrml1_mag;
1166  nrml1.z() *= inv_nrml1_mag;
1167 
1168  dcosdnrml1.x() = inv_nrml1_mag * (nrml1.x() * cos_phi - nrml2.x());
1169  dcosdnrml1.y() = inv_nrml1_mag * (nrml1.y() * cos_phi - nrml2.y());
1170  dcosdnrml1.z() = inv_nrml1_mag * (nrml1.z() * cos_phi - nrml2.z());
1171 
1172  dcosdnrml2.x() = inv_nrml2_mag * (nrml2.x() * cos_phi - nrml1.x());
1173  dcosdnrml2.y() = inv_nrml2_mag * (nrml2.y() * cos_phi - nrml1.y());
1174  dcosdnrml2.z() = inv_nrml2_mag * (nrml2.z() * cos_phi - nrml1.z());
1175 
1176  } else {
1177  nrml3.x() *= inv_nrml3_mag;
1178  nrml3.y() *= inv_nrml3_mag;
1179  nrml3.z() *= inv_nrml3_mag;
1180 
1181  dsindnrml3.x() = inv_nrml3_mag * (nrml3.x() * sin_phi - nrml2.x());
1182  dsindnrml3.y() = inv_nrml3_mag * (nrml3.y() * sin_phi - nrml2.y());
1183  dsindnrml3.z() = inv_nrml3_mag * (nrml3.z() * sin_phi - nrml2.z());
1184 
1185  dsindnrml2.x() = inv_nrml2_mag * (nrml2.x() * sin_phi - nrml3.x());
1186  dsindnrml2.y() = inv_nrml2_mag * (nrml2.y() * sin_phi - nrml3.y());
1187  dsindnrml2.z() = inv_nrml2_mag * (nrml2.z() * sin_phi - nrml3.z());
1188  }
1189 
1190  double diff = phi - dihedrallist[i].angle;
1191  if(diff < -numeric::NumericTraits< double >::pi() ) diff += 2*numeric::NumericTraits< double >::pi();
1192  if(diff < -numeric::NumericTraits< double >::pi() ) diff += 2*numeric::NumericTraits< double >::pi();
1193  if(diff > numeric::NumericTraits< double >::pi() ) diff -= 2*numeric::NumericTraits< double >::pi();
1194  if(diff > numeric::NumericTraits< double >::pi() ) diff -= 2*numeric::NumericTraits< double >::pi();
1195  totalepot += k * sqr(diff);
1196  double deriv = -2.0 * k * diff;
1197  //std::cout << "BAH! " << phi << " " << dihedrallist[i].angle << " " << diff << " " << deriv << " " << numeric::NumericTraits< double >::pi() << std::endl;
1198  // forces
1199  if(fabs(sin_phi) > 0.1) {
1200  deriv /= sin_phi;
1201  fi.x() += deriv * (vta_vtb.y() * dcosdnrml1.z() - vta_vtb.z() * dcosdnrml1.y());
1202  fi.y() += deriv * (vta_vtb.z() * dcosdnrml1.x() - vta_vtb.x() * dcosdnrml1.z());
1203  fi.z() += deriv * (vta_vtb.x() * dcosdnrml1.y() - vta_vtb.y() * dcosdnrml1.x());
1204 
1205  fj.x() += deriv * (vta_vtb.z() * dcosdnrml2.y() - vta_vtb.y() * dcosdnrml2.z());
1206  fj.y() += deriv * (vta_vtb.x() * dcosdnrml2.z() - vta_vtb.z() * dcosdnrml2.x());
1207  fj.z() += deriv * (vta_vtb.y() * dcosdnrml2.x() - vta_vtb.x() * dcosdnrml2.y());
1208 
1209  fab.x() += deriv * (vti_vta.z() * dcosdnrml1.y() - vti_vta.y() * dcosdnrml1.z() + vtb_vtj.y() * dcosdnrml2.z() - vtb_vtj.z() * dcosdnrml2.y());
1210  fab.y() += deriv * (vti_vta.x() * dcosdnrml1.z() - vti_vta.z() * dcosdnrml1.x() + vtb_vtj.z() * dcosdnrml2.x() - vtb_vtj.x() * dcosdnrml2.z());
1211  fab.z() += deriv * (vti_vta.y() * dcosdnrml1.x() - vti_vta.x() * dcosdnrml1.y() + vtb_vtj.x() * dcosdnrml2.y() - vtb_vtj.y() * dcosdnrml2.x());
1212 
1213  } else {
1214  deriv /= -cos_phi;
1215 
1216  fi.x() += deriv * ((vta_vtb.y() * vta_vtb.y() + vta_vtb.z() * vta_vtb.z()) * dsindnrml3.x() - vta_vtb.x() * vta_vtb.y() * dsindnrml3.y() - vta_vtb.x() * vta_vtb.z() * dsindnrml3.z());
1217  fi.y() += deriv * ((vta_vtb.z() * vta_vtb.z() + vta_vtb.x() * vta_vtb.x()) * dsindnrml3.y() - vta_vtb.y() * vta_vtb.z() * dsindnrml3.z() - vta_vtb.y() * vta_vtb.x() * dsindnrml3.x());
1218  fi.z() += deriv * ((vta_vtb.x() * vta_vtb.x() + vta_vtb.y() * vta_vtb.y()) * dsindnrml3.z() - vta_vtb.z() * vta_vtb.x() * dsindnrml3.x() - vta_vtb.z() * vta_vtb.y() * dsindnrml3.y());
1219 
1220  fj.x() += deriv * (dsindnrml2.y() * vta_vtb.z() - dsindnrml2.z() * vta_vtb.y());
1221  fj.y() += deriv * (dsindnrml2.z() * vta_vtb.x() - dsindnrml2.x() * vta_vtb.z());
1222  fj.z() += deriv * (dsindnrml2.x() * vta_vtb.y() - dsindnrml2.y() * vta_vtb.x());
1223 
1224  fab.x() += deriv * (-(vta_vtb.y() * vti_vta.y() + vta_vtb.z() * vti_vta.z()) * dsindnrml3.x()
1225  + (2.0 * vta_vtb.x() * vti_vta.y() - vti_vta.x() * vta_vtb.y()) * dsindnrml3.y()
1226  + (2.0 * vta_vtb.x() * vti_vta.z() - vti_vta.x() * vta_vtb.z()) * dsindnrml3.z() + dsindnrml2.z() * vtb_vtj.y() - dsindnrml2.y() * vtb_vtj.z());
1227  fab.y() += deriv * (-(vta_vtb.z() * vti_vta.z() + vta_vtb.x() * vti_vta.x()) * dsindnrml3.y()
1228  + (2.0 * vta_vtb.y() * vti_vta.z() - vti_vta.y() * vta_vtb.z()) * dsindnrml3.z()
1229  + (2.0 * vta_vtb.y() * vti_vta.x() - vti_vta.y() * vta_vtb.x()) * dsindnrml3.x() + dsindnrml2.x() * vtb_vtj.z() - dsindnrml2.z() * vtb_vtj.x());
1230  fab.z() += deriv * (-(vta_vtb.x() * vti_vta.x() + vta_vtb.y() * vti_vta.y()) * dsindnrml3.z()
1231  + (2.0 * vta_vtb.z() * vti_vta.x() - vti_vta.z() * vta_vtb.x()) * dsindnrml3.x()
1232  + (2.0 * vta_vtb.z() * vti_vta.y() - vti_vta.z() * vta_vtb.y()) * dsindnrml3.y() + dsindnrml2.y() * vtb_vtj.x() - dsindnrml2.x() * vtb_vtj.y());
1233  }
1234 
1235 // fi.mul(PhysicsConst::invAngstrom);
1236 // fab.mul(PhysicsConst::invAngstrom);
1237 // fj.mul(PhysicsConst::invAngstrom);
1238 
1239  // add to cartesian derivatives
1240 
1241  cartom[no1].force.x() += fi.x();
1242  cartom[no1].force.y() += fi.y();
1243  cartom[no1].force.z() += fi.z();
1244 
1245  cartom[no2].force.x() += fab.x() - fi.x();
1246  cartom[no2].force.y() += fab.y() - fi.y();
1247  cartom[no2].force.z() += fab.z() - fi.z();
1248 
1249  cartom[no3].force.x() += fj.x() - fab.x();
1250  cartom[no3].force.y() += fj.y() - fab.y();
1251  cartom[no3].force.z() += fj.z() - fab.z();
1252 
1253  cartom[no4].force.x() -= fj.x();
1254  cartom[no4].force.y() -= fj.y();
1255  cartom[no4].force.z() -= fj.z();
1256 
1257  }
1258 
1259 }
1260 
1261 void MolecularDynamics::createCartesianDerivatives( core::scoring::ScoreFunction const & scorefxn )
1262 {
1263  using namespace core;
1264  //std::cout << "setup_for_scoring" << std::endl;
1265  Size const nres( pose->total_residue() );
1266 
1267  scorefxn.setup_for_derivatives( *pose);
1268  cartom.clear();
1269  for ( Size ir = 1; ir <= nres; ++ir ) {
1270  // get the appropriate residue from the pose->
1271  conformation::Residue const & rsd( pose->residue( ir ) );
1272 
1273  //std::cout << "Res: " << ir << " " << rsd.natoms() << std::endl;
1274 
1275  // iterate across neighbors within 12 angstroms
1276  for (Size i = 1; i <= rsd.natoms(); i++ ){
1277  id::AtomID atom_id( i, ir );
1278 
1279  CartesianAtom atom;
1280  core::Vector F1(0,0,0),F2(0,0,0);
1281  scorefxn.eval_npd_atom_derivative( atom_id, *pose, min_map.domain_map(), F1, F2 );
1282  atom.index = i;
1283  atom.res = ir;
1284  atom.atom_id = atom_id;
1285  atom.force = F2;
1286  atom.old_force = core::Vector(0,0,0);
1287  atom.old_velocity = core::Vector(0,0,0);
1288  atom.old_position = core::Vector(0,0,0);
1289  cartom.push_back(atom);
1290 
1291  }
1292 
1293  }
1294 
1295 
1296 
1297 }
1298 
1299 
1300 
1301 void MolecularDynamics::setInitialSpeeds(double tgtTemp )
1302 {
1303  using namespace core;
1304  double sigma;
1305  //int natom = cartom.size();
1306 
1307  for ( Size i = 1; i <= cartom.size(); i ++ )
1308  {
1309  sigma = sqrt( 1.38065E-23 * tgtTemp / (cartom[i].mass * 1.66053878E-27) );
1310  cartom[i].velocity.x() = numeric::random::gaussian() * sigma;
1311  cartom[i].velocity.y() = numeric::random::gaussian() * sigma;
1312  cartom[i].velocity.z() = numeric::random::gaussian() * sigma;
1313  }
1314 }
1315 
1316 
1317 void MolecularDynamics::calcKineticEnergy(
1318  float &ekin,
1319  float &Temp
1320 )
1321 {
1322  using namespace core;
1323  ekin = 0;
1324 
1325  for ( Size i = 1; i <= cartom.size(); i ++ )
1326  {
1327  ekin += (0.5 * cartom[i].mass * 1.66053878E-27 * inner_product(cartom[i].velocity,cartom[i].velocity));
1328  }
1329 
1330  // Calculate Temperature from K = 2NkBT/2
1331  Temp = 2.0 * ekin / (3 * cartom.size() * 8.31 / 6.022E23 ); //
1332 
1333 }
1334 
1335 
1336 void MolecularDynamics::applyForces_BeeMan(
1337  float &kin,
1338  float &temp
1339 )
1340 {
1341  using namespace core;
1342 
1343  //int i;
1344  double t;
1345  //double t2;
1346  double tinvmass;
1347  core::Vector dr, dv;
1348  core::Vector t2a;
1349 
1350  t = 1E-15;
1351  //t2 = sqr(t); // set but never used ~Labonte
1352 
1353  float forcemul = -( 1E10 / 6.0221418E23 * 4184.0);
1354 
1355  for ( Size i = 1; i <= cartom.size(); i ++ )
1356  {
1357  tinvmass = t / (6.0 * (cartom[i].mass * 1.66053878E-27 ) ); // t div 6m
1358 
1359  // finish change in velocity using a(n+1)
1360  dv.x() = ((2.0) * cartom[i].force.x() * forcemul ) * tinvmass;
1361  dv.y() = ((2.0) * cartom[i].force.y() * forcemul ) * tinvmass;
1362  dv.z() = ((2.0) * cartom[i].force.z() * forcemul ) * tinvmass;
1363  cartom[i].velocity += dv;
1364  }
1365 
1366  calcKineticEnergy( kin, temp ); //calculate instanteneous temperature & pressure
1367 
1368  kin *= 6.0221418E23 / 4184.0;
1369 
1370  //applyThermostat(); //adjust velocities according to Thermostat
1371 
1372  // predict new positions
1373  for ( Size i = 1; i <= cartom.size(); i ++ )
1374  {
1375  tinvmass = t / (6.0 * cartom[i].mass * 1.66053878E-27 ); // t div 6m
1376 
1377  // change in position
1378  dr.x() = t * (cartom[i].velocity.x() + (4.0 * cartom[i].force.x() - cartom[i].old_force.x()) * forcemul* tinvmass);
1379  dr.y() = t * (cartom[i].velocity.y() + (4.0 * cartom[i].force.y() - cartom[i].old_force.y()) * forcemul* tinvmass);
1380  dr.z() = t * (cartom[i].velocity.z() + (4.0 * cartom[i].force.z() - cartom[i].old_force.z()) * forcemul* tinvmass);
1381 
1382  dr /= 1E-10;
1383 
1384  dv.x() = (5.0 * cartom[i].force.x() - cartom[i].old_force.x()) * forcemul* tinvmass;
1385  dv.y() = (5.0 * cartom[i].force.y() - cartom[i].old_force.y()) * forcemul* tinvmass;
1386  dv.z() = (5.0 * cartom[i].force.z() - cartom[i].old_force.z()) * forcemul* tinvmass;
1387 
1388  //update positions and speeds.
1389  //std::cout << dr.x() << " " << dr.z() << " "<< dr.z() << " " << std::endl;
1390  cartom[i].position += dr;
1391  cartom[i].velocity += dv;
1392 
1393  // save current force as next Step's old force
1394  cartom[i].old_force = cartom[i].force;
1395  }
1396 
1397 
1398 }
1399 
1400 
1401 void MolecularDynamics::applyForces_LangevinIntegration(
1402  double T,
1403  float &kin,
1404  float &temp
1405 )
1406 {
1407  using namespace core;
1408  //int i;
1409  core::Vector dr, dv;
1410  double t = 1E-15;
1411  double tinvmass;
1412  float forcemul = -( 1E10 / 6.0221418E23 * 4184.0);
1413 
1414  double gamma = 10E12;
1415  double gammat = gamma * t;
1416  double gt = gammat; // these are the consecutive powers for the series expnsions
1417  double gt2 = gt * gt;
1418  double gt3 = gt * gt2;
1419  double gt4 = gt2 * gt2;
1420  double gt5 = gt2 * gt3;
1421  double gt6 = gt3 * gt3;
1422  double gt7 = gt3 * gt4;
1423  double gt8 = gt4 * gt4;
1424  double gt9 = gt4 * gt5;
1425 
1426  double c0; // langevin coefficients
1427  double c1;
1428  double c2;
1429 
1430  double egammat;
1431  double varv;
1432  double varr;
1433  double crv;
1434 
1435  double kTdivm;
1436  double sigmav;
1437  double sigmar;
1438  double n1x, n2x;
1439  double n1y, n2y;
1440  double n1z, n2z;
1441  core::Vector deltav;
1442  core::Vector deltar;
1443 
1444  if(gammat > 0.05) {
1445  // when the friction coeffcient is relatively large, run langevin dynamics
1446  // the parameters must be calculated using exponential functions
1447  c0 = exp(-gammat); // langevin coefficients
1448  c1 = (1 - c0) / gammat;
1449  c2 = (1 - c1) / gammat;
1450 
1451  egammat = exp(-gammat);
1452  varv = (1.0 - sqr(egammat));
1453  varr = (2.0 * gammat - 3.0 + (4.0 - egammat) * egammat);
1454  crv = sqr(1.0 - egammat) / (sqrt(varv * varr));
1455  } else {
1456  // when the friction coeffcient is in the midrange we can approximate the paramters
1457  // by taylor expansion which is a little faster
1458  c0 =
1459  1 - gt + 0.5 * gt2 - gt3 / 6.0 + gt4 / 24.0 - gt5 / 120.0 + gt6 / 720.0 - gt7 / 5040.0 + gt8 / 40320.0 -
1460  gt9 / 362880.0;
1461  c1 =
1462  1 - (0.5 * gt - gt2 / 6.0 + gt3 / 24.0 - gt4 / 120.0 + gt5 / 720.0 - gt6 / 5040.0 + gt7 / 40320.0 -
1463  gt8 / 362880.0);
1464  c2 =
1465  0.5 - gt / 6.0 + gt2 / 24.0 - gt3 / 120.0 + gt4 / 720.0 - gt5 / 5040.0 + gt6 / 40320.0 - gt7 / 362880.0;
1466 
1467  varr = 2.0 * gt3 / 3.0 - gt4 / 2.0 + 7.0 * gt5 / 30.0 - gt6 / 12.0
1468  + 31.0 * gt7 / 1260.0 - gt8 / 160.0 + 127.0 * gt9 / 90720.0;
1469  varv = 2.0 * gt - 2.0 * gt2 + 4.0 * gt3 / 3.0 - 2.0 * gt4 / 3.0 + 4.0 * gt5 / 15.0
1470  - 4.0 * gt6 / 45.0 + 8.0 * gt7 / 315.0 - 2.0 * gt8 / 315.0 + 4.0 * gt9 / 2835.0;
1471  crv = sqrt(3.0) * (0.5 - 3.0 * gt / 16.0 - 17.0 * gt2 / 1280.0 + 17.0 * gt3 / 6144.0
1472  + 40967.0 * gt4 / 34406400.0 - 57203.0 * gt5 / 275251200.0 -
1473  1429487.0 * gt6 / 13212057600.0);
1474  }
1475 
1476  //if(Step > 0) {
1477  for ( Size i = 1; i <= cartom.size(); i ++ )
1478  {
1479  tinvmass = t / (cartom[i].mass * 1.66053878E-27); // t div m
1480 
1481  // finish change in velocity using a(n+1)
1482  dv.x() = (1.0 - c0 / c1) * cartom[i].force.x() * forcemul * tinvmass / gammat;
1483  dv.y() = (1.0 - c0 / c1) * cartom[i].force.y() * forcemul * tinvmass / gammat;
1484  dv.z() = (1.0 - c0 / c1) * cartom[i].force.z() * forcemul * tinvmass / gammat;
1485  cartom[i].velocity += dv;
1486  }
1487  //}
1488 
1489  // The velocities are now "real", i.e. finished and thus now is the time
1490  // to calculate the kinetic energy and apply any barostat
1491  // note no other thermostats are called here because
1492  // langevin dynamics regultes the temperature itself - thermostat
1493  // is built-in so to speak
1494  calcKineticEnergy( kin, temp);
1495  kin *= 6.0221418E23 / 4184.0;
1496 
1497  //if(Step < (Steps - 1)) {
1498  for ( Size i = 1; i <= cartom.size(); i ++ )
1499  {
1500  tinvmass = t / (cartom[i].mass * 1.66053878E-27); // t div m
1501 
1502  kTdivm = 1.38065E-23 * T / (cartom[i].mass * 1.66053878E-27);
1503  sigmav = sqrt(kTdivm * varv);
1504  sigmar = sqrt(kTdivm * varr) / gamma;
1505 
1506  n1x = numeric::random::gaussian();
1507  n2y = numeric::random::gaussian();
1508  n2x = numeric::random::gaussian();
1509  n1z = numeric::random::gaussian();
1510  n1y = numeric::random::gaussian();
1511  n2z = numeric::random::gaussian();
1512 
1513  deltav = core::Vector(sigmav * (crv * n1x + sqrt(1.0 - sqr(crv)) * n2x),
1514  sigmav * (crv * n1y + sqrt(1.0 - sqr(crv)) * n2y),
1515  sigmav * (crv * n1z + sqrt(1.0 - sqr(crv)) * n2z));
1516  deltar = core::Vector(sigmar * n1x, sigmar * n1y, sigmar * n1z);
1517 
1518  // change in position
1519  dr.x() = t * (c1 * cartom[i].velocity.x() + c2 * cartom[i].force.x() * forcemul * tinvmass) + deltar.x();
1520  dr.y() = t * (c1 * cartom[i].velocity.y() + c2 * cartom[i].force.y() * forcemul * tinvmass) + deltar.y();
1521  dr.z() = t * (c1 * cartom[i].velocity.z() + c2 * cartom[i].force.z() * forcemul * tinvmass) + deltar.z();
1522  dr *= 1E10;
1523 
1524  // finish change in velocity using a(n+1)
1525  dv.x() = (c0 * c2) * cartom[i].force.x() * forcemul * tinvmass / c1 + deltav.x();
1526  dv.y() = (c0 * c2) * cartom[i].force.y() * forcemul * tinvmass / c1 + deltav.y();
1527  dv.z() = (c0 * c2) * cartom[i].force.z() * forcemul * tinvmass / c1 + deltav.z();
1528 
1529  cartom[i].position += dr;
1530  cartom[i].velocity *= c0;
1531  cartom[i].velocity += dv;
1532  }
1533  //}
1534 
1535 
1536 }
1537 
1538 
1539 
1540 void MolecularDynamics::applyForces_ConjugateGradient(
1541  int Step,
1542  float &current_energy,
1543  float &m_OldEnergy
1544  )
1545 {
1546  using namespace core;
1547 
1548  core::Vector f;
1549  static double m_StepMultiplier = 1.0;
1550  float StepSize = 0.000001;
1551  float forcemul = 1; // ( 1E10 / 6.0221418E23 * 4184.0);
1552  //static bool backstep = false;
1553 
1554  //std::cout << "-----> " << m_StepMultiplier << std::endl;
1555  if(Step != 0) {
1556  if((current_energy < m_OldEnergy)) { // energy did go down on last Step
1557 
1558  //if( !backstep ){
1559  double fmagold, fmagnew, gamma;
1560  m_StepMultiplier *= 1.2;
1561  //std::cout << "ENERGY_IMPROVEMENT\n";
1562  fmagold = 0;
1563  fmagnew = 0;
1564  for ( Size i = 1; i <= cartom.size(); i ++ ) { // calculate the inner dots of the current force
1565  fmagold += cartom[i].old_force.dot( cartom[i].old_force );
1566  core::Vector ftemp = cartom[i].old_force - cartom[i].force;
1567  fmagnew += ftemp.dot( cartom[i].force );
1568  }
1569 
1570  //b = ( (gnew - gprev)*(new) / prev^2
1571 
1572  if(fmagold != 0)
1573  gamma = fmagnew / fmagold;
1574  else
1575  gamma = 0;
1576 
1577  if (gamma < 0 ) gamma = 0;
1578  std::cout << "gamma: " << gamma << std::endl;
1579 
1580  //gamma = 0;
1581  for ( Size i = 1; i <= cartom.size(); i ++ ) { // save positions & forces
1582  cartom[i].velocity = cartom[i].old_velocity; // set to old direction
1583  cartom[i].velocity *= gamma; // multiply the old direction with gamma
1584  cartom[i].velocity -= cartom[i].force * forcemul; // and add current force to make current direction
1585  cartom[i].velocity *= 1;
1586  cartom[i].old_position = cartom[i].position; // save position
1587  cartom[i].old_force = cartom[i].force * forcemul; // save old forces
1588  cartom[i].old_velocity = cartom[i].velocity;; // save old directions
1589  }
1590  m_OldEnergy = current_energy;
1591  //backstep = false; // set but never used ~Labonte
1592  //} else {
1593  // std::cout << "BACKSTEP\n";
1594 
1595  //}
1596  } else { // we went up the other side
1597  //std::cout << "ENERGY_UP\n" << current_energy << " " << m_OldEnergy << " ";
1598 
1599  m_StepMultiplier *= 0.5 / 1.2;
1600  for ( Size i = 1; i <= cartom.size(); i ++ ) {
1601  cartom[i].position = cartom[i].old_position; // restore old position
1602  //cartom[i].force = cartom[i].old_force / forcemul; // restore old forces
1603  }
1604  //m_OldEnergy += 1; // no idea what this is !?
1605 
1606  //backstep = true; // set but never used ~Labonte
1607  //return;
1608 
1609  }
1610  } else { // this block is for Step == 0 - its just a standard SD Step
1611  for ( Size i = 1; i < cartom.size(); i++ ) {
1612  cartom[i].old_position = cartom[i].position; // save position (old position = current position)
1613  cartom[i].old_force = cartom[i].force * forcemul; // save old forces
1614  cartom[i].old_velocity = -cartom[i].force * forcemul; // save old directions, equal to old force
1615  cartom[i].velocity = -cartom[i].force * forcemul; // save old directions, equal to old force
1616  }
1617  m_OldEnergy = current_energy;
1618  }
1619 
1620  for ( Size i = 1; i <= cartom.size(); i ++ ) {
1621  f = cartom[i].velocity;
1622  f *= StepSize * m_StepMultiplier;
1623  //if( sqr(f.x()) + sqr(f.y()) + sqr (f.z()) > 0.2 )
1624  // std::cout << "DISP: " << i << f.x() << " " << f.y() << " " << f.z() << std::endl;
1625  cartom[i].position += f;
1626  }
1627 
1628 }
1629 
1630 
1631 
1632 
1633 void MolecularDynamics::doMinimising(
1634  core::scoring::ScoreFunction const & scorefxn
1635 )
1636 {
1637  using namespace core;
1638 
1639  const int Steps = 400;
1640  int Step = 0;
1641  float kin = 0;
1642  //float temp = 0;
1643  float pot = 0;
1644  int mcount = 1;
1645 
1646  std::ofstream pdbfile;
1647  std::string filename ( "min.pdb" );
1648  pdbfile.open( filename.c_str() , std::ios::out );
1649 
1650  float cov_epot=0;
1651  //float startTemp = 100;
1652  //float TargetTemp=startTemp;
1653 
1654  float current_energy;
1655  float m_OldEnergy;
1656 
1657  for( Step = 0; Step < Steps; Step ++ ){
1658  pose::Pose pose2( *pose);
1659  current_energy = scorefxn( pose2 );
1660  pot = current_energy;
1661  cov_epot = 0;
1662 
1663  zeroForces( );
1664  getCartesianDerivatives( scorefxn );
1665  doBondDerivatives( cov_epot );
1666  doAngleDerivatives( cov_epot );
1667  doDihedralDerivatives( cov_epot );
1668  current_energy += cov_epot;
1669 
1670  std::cout << Step << " " << pot << " " << cov_epot << " " << kin << " " << pot+kin << std::endl;
1671 
1672  if(Step == 0 ) m_OldEnergy = current_energy;
1673  applyForces_ConjugateGradient( Step, current_energy, m_OldEnergy );
1674 
1675  setPosePositionsFromCartesian( );
1676 
1677  //if( ( Step % 50 ) == 0 ){
1678  pdbfile << "MODEL " << I(5, mcount ) << std::endl;
1679  pose->dump_pdb( pdbfile );
1680  pdbfile << "ENDMDL" << std::endl;
1681  mcount++;
1682  //}
1683  pdbfile.flush();
1684  }
1685 
1686  pdbfile.close();
1687 
1688 
1689 }
1690 
1691 
1692 
1693 
1694 
1695 void MolecularDynamics::doMD( core::scoring::ScoreFunction const & scorefxn,
1696  int Steps,
1697  float startTemp,
1698  float endTemp
1699 ){
1700  using namespace core;
1701  setInitialSpeeds(startTemp);
1702 
1703  int Step = 0;
1704  float kin = 0;
1705  float temp = 0;
1706  float pot = 0;
1707  int mcount = 1;
1708 
1709  std::ofstream pdbfile;
1710  std::string filename ( "md." + right_string_of(startTemp,4,'0') + ".pdb" );
1711  pdbfile.open( filename.c_str() , std::ios::out );
1712 
1713  float cov_epot=0;
1714  float TargetTemp=startTemp;
1715  for( Step = 0; Step < Steps; Step ++ ){
1716  pose::Pose pose2(*pose);
1717  pot += scorefxn( pose2 );
1718  if( ( Step % 20 ) == 0 ){
1719  std::cout << Step << " " << pot << " " << cov_epot << " " << kin << " " << pot+kin+cov_epot << " " << temp << "(" << TargetTemp << ")" << std::endl;
1720  }
1721  //zeroForces( cartom );
1722  getCartesianDerivatives( scorefxn );
1723  pot = 0;
1724  cov_epot = 0;
1725  doBondDerivatives(cov_epot );
1726  doAngleDerivatives( cov_epot);
1727  doDihedralDerivatives( cov_epot );
1728 
1729  float ratio = (float)Step/(float)Steps;
1730  TargetTemp = std::max(0.01, ratio*endTemp + (1.0-ratio)*startTemp );
1731  applyForces_LangevinIntegration( TargetTemp , kin, temp );
1732  //applyForces_BeeMan( cartom, kin, temp );
1733 
1734  setPosePositionsFromCartesian( );
1735 
1736  if( ( Step % 100 ) == 0 ){
1737  pdbfile << "MODEL " << I(5, mcount ) << std::endl;
1738  pose->dump_pdb( pdbfile );
1739  pdbfile << "ENDMDL" << std::endl;
1740  mcount++;
1741  }
1742  pdbfile.flush();
1743  }
1744 
1745  pdbfile.close();
1746 
1747 
1748 }
1749 
1750 
1751 
1752 
1753 
1754 
1755 
1756 
1757 
1758 
1759 
1760 
1761 
1762 
1763 
1764 
1765 
1766 
1767 
1768 
1769 
1770 
1771 
1772 
1773 
1774 
1775 
1776 
1777 
1778 void MolecularDynamics::testCartesianDerivatives( core::scoring::ScoreFunction const & scorefxn )
1779 {
1780  using namespace core;
1781 
1782  // score it !
1783  Real start_score = scorefxn( *pose );
1784  scorefxn.show(std::cout, *pose);
1785  std::cout << "STARTSCORE: " << start_score << std::endl;
1786 /*
1787  Residue rsd_mod = pose->residue(4);
1788 
1789  std::cout << rsd_mod.xyz(4).z() << std::endl;
1790  // move an atom
1791  Vector test = rsd_mod.xyz(4).xyz();
1792  Vector dd(0,0,0.1); yy
1793  Vector newvec;
1794 
1795  newvec = rsd_mod.xyz(4) + dd;
1796  pose->residue(4).atom(3).set_xyz(4, newvec);
1797 
1798  pose->set_residue
1799  pose->set_xyz( id, pose->xyz( id ) + dx );
1800 
1801  scorefxn( *pose );
1802  scorefxn.show(std::cout, *pose);
1803  std::cout << pose->residue(4).atom(3).xyz().z() << std::endl;
1804 */
1805  const float dd = 0.00001;
1806  Vector dx(dd,0,0);
1807  Vector dy(0,dd,0);
1808  Vector dz(0,0,dd);
1809 
1810  utility::vector1< CartesianAtom > cartom;
1811  utility::vector1< Vector > numeriv;
1812 
1813 
1814  std::cout << "Calculating derivatives \n";
1815 
1816  createCartesianArray( );
1817  getCartesianDerivatives( scorefxn );
1818 
1819 
1820  //int cend = clock();
1821  pose->energies().reset_nblist();
1822  std::cout << "STARTSCORE: --------- " << std::endl;
1823  start_score = scorefxn( *pose );
1824  scorefxn.show(std::cout, *pose);
1825 
1826 
1827 
1828  //std::cout << "setup_for_scoring" << std::endl;
1829  Size const nres( pose->total_residue() );
1830 
1831  for ( Size ir = 1; ir <= nres; ++ir ) {
1832  // get the appropriate residue from the pose->
1833  conformation::Residue const & rsd( pose->residue( ir ) );
1834  std::cout << "IR: " << ir << std::endl;
1835  // iterate across neighbors within 12 angstroms
1836  for (Size i = 1; i <= rsd.natoms(); i++ ){
1837  id::AtomID atom_id( i, ir );
1838 
1839  pose->energies().clear();
1840  start_score = scorefxn( *pose );
1841 
1842  Real new_score;
1843  Real deriv;
1844  Vector deriv_vector;
1845  Vector safepos = pose->xyz( atom_id );
1846  pose->set_xyz( atom_id, safepos + dx );
1847  pose->energies().clear();
1848  new_score = scorefxn( *pose );
1849  deriv = (new_score - start_score)/dd;
1850  deriv_vector.x(deriv);
1851 
1852  pose->set_xyz( atom_id, safepos + dy );
1853  pose->energies().clear();
1854  new_score = scorefxn( *pose );
1855  deriv = (new_score - start_score)/dd;
1856  deriv_vector.y(deriv);
1857 
1858 
1859  pose->set_xyz( atom_id, safepos + dz );
1860  pose->energies().clear();
1861  new_score = scorefxn( *pose );
1862  deriv = (new_score - start_score)/dd;
1863  deriv_vector.z(deriv);
1864  pose->set_xyz( atom_id, safepos );
1865 
1866  numeriv.push_back( deriv_vector );
1867  }
1868 
1869  }
1870 
1871 
1872  for( Size i = 1; i < cartom.size(); i++ ){
1873 
1874  if( ( fabs( cartom[i].force.x() - numeriv[i].x() ) > 0.1 ) ||
1875  ( fabs( cartom[i].force.y() - numeriv[i].y() ) > 0.1 ) ||
1876  ( fabs( cartom[i].force.z() - numeriv[i].z() ) > 0.1 ) ) {
1877  std::cout << "DRV: "
1878  << cartom[i].res << " "
1879  << cartom[i].index << " "
1880  << cartom[i].force.x() << " "
1881  << cartom[i].force.y() << " "
1882  << cartom[i].force.z() << " "
1883  << numeriv[i].x() << " "
1884  << numeriv[i].y() << " "
1885  << numeriv[i].z() << " "
1886  << std::endl;
1887 
1888 
1889  }else{
1890  std::cout << "DRVT: "
1891  << cartom[i].res << " "
1892  << cartom[i].index << " "
1893  << cartom[i].force.x() << " "
1894  << cartom[i].force.y() << " "
1895  << cartom[i].force.z() << " "
1896  << numeriv[i].x() << " "
1897  << numeriv[i].y() << " "
1898  << numeriv[i].z() << " "
1899  << std::endl;
1900 
1901 
1902  }
1903 
1904  }
1905 
1906 
1907 }
1908 
1909 
1910 
1911 
1912 
1913 
1914 
1915 
1916 
1917 
1918 } // namespace optimization
1919 } // namespace core
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