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StepWiseRNA_VirtualRiboseSampler.hh
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1 // -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
2 // vi: set ts=2 noet:
3 //
4 // (c) Copyright Rosetta Commons Member Institutions.
5 // (c) This file is part of the Rosetta software suite and is made available under license.
6 // (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
7 // (c) For more information, see http://www.rosettacommons.org. Questions about this can be
8 // (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.
9 
10 /// @file StepWiseRNA_Util.hh
11 /// @brief
12 /// @detailed
13 ///
14 /// @author Parin Sripakdeevong
15 
16 
17 #ifndef INCLUDED_protocols_swa_rna_StepWiseRNA_VirtualRiboseSampler_HH
18 #define INCLUDED_protocols_swa_rna_StepWiseRNA_VirtualRiboseSampler_HH
19 
20 #include <core/pose/Pose.fwd.hh>
21 #include <core/types.hh>
22 #include <utility/vector1.hh>
23 #include <numeric/xyzMatrix.hh>
24 #include <numeric/xyzVector.hh>
25 #include <string>
26 #include <map>
27 #include <core/chemical/AA.hh>
28 #include <core/io/silent/RNA_SilentStruct.hh>
29 #include <core/io/silent/SilentFileData.hh>
30 #include <numeric/angle.functions.hh> // Need this to prevent the compiling error: 'principal_angle_degrees' is not a member of 'numeric' Oct 14, 2009
31 #include <core/kinematics/MoveMap.hh>
32 #include <core/scoring/ScoreFunction.fwd.hh>
33 #include <core/conformation/Residue.hh>
34 #include <set>
35 #include <ObjexxFCL/string.functions.hh>
36 #include <core/kinematics/FoldTree.fwd.hh>
37 #include <core/kinematics/FoldTree.hh>
38 #include <core/scoring/constraints/ConstraintSet.fwd.hh>
39 #include <core/scoring/constraints/ConstraintSet.hh>
40 
41 #include <protocols/swa/rna/StepWiseRNA_Util.hh>
42 #include <protocols/swa/rna/StepWiseRNA_VDW_Bin_Screener.fwd.hh>
43 #include <protocols/swa/rna/StepWiseRNA_JobParameters.hh> //June 02, 2011
44 #include <core/pose/Pose.hh> //June 02, 2011
45 #include <core/scoring/rna/RNA_Util.hh> //June 02, 2011
46 
47 
48 namespace protocols {
49 namespace swa {
50 namespace rna {
51 
52 class FB_Pose_Data{
53 
54  public:
55 
56  FB_Pose_Data():
57  score( 0.0 ),
58  tag("tag_blah"),
59  base_tag("base_tag_blah"),
60  Is_chain_close(false),
61  base_rep_score(999999)
62 
63  {
64  }
65 
66  ~FB_Pose_Data(){};
67 
68  public:
69 
70  core::Real score;
71  core::pose::PoseOP pose_OP;
72  std::string tag;
73  std::string base_tag;
74  bool Is_chain_close;
75  core::Real base_rep_score;
76  core::kinematics::FoldTree starting_fold_tree;
77  core::scoring::constraints::ConstraintSetOP starting_cst_set_OP;
78 
79 };
80 
81 
82 
83 class FloatingBaseChainClosureJobParameter{
84 
85  public:
86 
87 
88  FloatingBaseChainClosureJobParameter(core::Size const input_moving_res, core::Size const input_reference_res):
89  sample_sugar(true),
90  moving_res ( input_moving_res ),
91  reference_res( input_reference_res ),
92  moving_res_pucker_state( ALL ),
93  bulge_res_pucker_state( ALL ),
94  moving_res_base_state( BOTH ),
95  bulge_res_base_state( BOTH )
96  {
97 
98  PDL.clear(); //pose_data_list
99  Is_prepend= (moving_res>reference_res) ? false: true;
100  bulge_res= (Is_prepend) ? reference_res-1: reference_res+1;
101  bulge_suite = (Is_prepend) ? bulge_res : bulge_res-1;
102  five_prime_chain_break= (Is_prepend) ? moving_res: moving_res-1;
103 
104  ////////////////////////Consistency check!////////////////////////////////////////
105  if(Is_prepend){
106  if(moving_res+2!=reference_res){
107  std::cout << "moving_res= " << moving_res << " reference_res= " << reference_res;
108  utility_exit_with_message("prepend, but moving_res+2!=reference_res!");
109  }
110  }else{
111  if(moving_res-2!=reference_res){
112  std::cout << "moving_res= " << moving_res << " reference_res= " << reference_res;
113  utility_exit_with_message("append, but moving_res-2!=reference_res!");
114  }
115  }
116 
117  }
118 
119  FloatingBaseChainClosureJobParameter():
120  sample_sugar( false)
121  {
122  PDL.clear(); //pose_data_list
123  };
124 
125  ~FloatingBaseChainClosureJobParameter(){};
126 
127 
128  void
129  check_compatibility(core::Size const nres) const{
130  using namespace ObjexxFCL;
131 
132  if(moving_res<1 || moving_res> nres) utility_exit_with_message( "moving_res<1 || moving_res> nres. moving_res= " + string_of(moving_res) );
133  if(bulge_res <1 || bulge_res> nres) utility_exit_with_message( "bulge_res <1 || bulge_res> nres. bulge_res= " + string_of(bulge_res) );
134  if(reference_res<1 || reference_res> nres) utility_exit_with_message( "reference_res<1 || reference_res> nres. reference_res= " + string_of(reference_res) );
135 
136  //Should check here that moving_res contain virtual ribose and bulge_res is a virtual_rna_residue?
137  }
138 
139  void
140  set_base_and_pucker_state(core::pose::Pose const & pose, StepWiseRNA_JobParametersCOP const & JP){
141 
142  ////////////////////////June 02, 2011 Add BaseState and PuckerState information///
143  moving_res_pucker_state=ALL;
144  if( Contain_seq_num(moving_res, JP->working_force_north_ribose_list() ) ) moving_res_pucker_state=NORTH;
145  if( Contain_seq_num(moving_res, JP->working_force_south_ribose_list() ) ) moving_res_pucker_state=SOUTH;
146 
147  moving_res_base_state = (core::scoring::rna::is_purine( pose.residue( moving_res ) ) ) ? BOTH: ANTI;
148  if( Contain_seq_num(moving_res, JP->working_force_syn_chi_res_list() ) ) moving_res_base_state=SYN;
149 
150  bulge_res_pucker_state=ALL;
151  if( Contain_seq_num(bulge_res, JP->working_force_north_ribose_list() ) ) bulge_res_pucker_state=NORTH;
152  if( Contain_seq_num(bulge_res, JP->working_force_south_ribose_list() ) ) bulge_res_pucker_state=SOUTH;
153 
154  bulge_res_base_state = (core::scoring::rna::is_purine( pose.residue( bulge_res ) ) ) ? BOTH: ANTI;
155  if( Contain_seq_num(bulge_res, JP->working_force_syn_chi_res_list() ) ) bulge_res_base_state=SYN;
156 
157  ////////////////////////Print data!////////////////////////////////////////
158  std::cout << "FloatingBaseChainClosureJobParameter: " << std::endl;
159  Output_boolean(" Is_prepend= " , Is_prepend);
160  std::cout << " reference_res=" << reference_res;
161 
162  std::cout <<" moving_res=" << moving_res;
163  print_base_state("|base_state=", moving_res_base_state );
164  print_ribose_pucker_state("|pucker_state=", moving_res_pucker_state);
165 
166  std::cout << " bulge_res= " << bulge_res;
167  print_base_state("|base_state=", bulge_res_base_state );
168  print_ribose_pucker_state("|pucker_state=", bulge_res_pucker_state);
169 
170  std::cout << " bulge_suite= " << bulge_suite << " five_prime_chain_break= " << five_prime_chain_break;
171 
172  }
173 
174  public:
175  bool sample_sugar;
176  core::Size moving_res;
177  core::Size reference_res;
178  bool Is_prepend;
179  core::Size bulge_res;
180  core::Size bulge_suite;
181  core::Size five_prime_chain_break;
182  PuckerState moving_res_pucker_state;
183  PuckerState bulge_res_pucker_state;
184  BaseState moving_res_base_state;
185  BaseState bulge_res_base_state;
186  utility::vector1< pose_data_struct2 > PDL; //pose_data_list of possible ribose conformations.
187 
188 };
189 
190 
191 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////
192 
193 bool
194 fast_full_atom_VDW_repulsion_screen(core::pose::Pose const & pose, core::Size const res_1, core::Size const res_2, bool const Is_prepend);
195 
196 
197 //Duplication of Chain_break_screening function from StepWiseRNA_ResidueSampler.cc. NEED TO MERGE THEM BACK TOGETHER AFTER TESTING! Apr 20,2010. Parin S.
198 bool
199 floating_base_full_atom_van_der_Waals_screening(core::pose::Pose & current_pose_screen,
200  core::Real const & base_rep_score,
201  core::scoring::ScoreFunctionOP const & atr_rep_screening_scorefxn,
202  SillyCountStruct & count_data,
203  bool const verbose);
204 
205 //Duplication of Chain_break_screening function from StepWiseRNA_ResidueSampler.cc. NEED TO MERGE THEM BACK TOGETHER AFTER TESTING! Apr 20,2010. Parin S.
206 bool
207 floating_base_chain_break_screening(core::pose::Pose & chain_break_screening_pose,
208  core::scoring::ScoreFunctionOP const & chainbreak_scorefxn,
209  SillyCountStruct & count_data,
210  core::Size const & five_prime_res,
211  std::string const & tag,
212  bool const verbose);
213 
214 
215 utility::vector1< FB_Pose_Data >
216 floating_base_chain_closure_setup(utility::vector1< pose_data_struct2 > const & input_pose_data_list,
217  FloatingBaseChainClosureJobParameter const & FB_job_params,
218  core::scoring::ScoreFunctionOP const & atr_rep_screening_scorefxn,
219  core::scoring::ScoreFunctionOP const & full_scorefxn,
220  core::pose::Pose & viewer_pose,
221  bool const do_minimize);
222 
223 void
224 floating_base_chain_closure_sampling(utility::vector1< FB_Pose_Data > & pose_data_list,
225  core::pose::Pose & viewer_pose,
226  FloatingBaseChainClosureJobParameter const & FB_job_params,
227  core::scoring::ScoreFunctionOP const & chainbreak_scorefxn,
228  core::scoring::ScoreFunctionOP const & atr_rep_screening_scorefxn,
229  StepWiseRNA_VDW_Bin_ScreenerOP const & VDW_bin_screener,
230  bool const CCD_grid_index_screen);
231 
232 
233 utility::vector1< pose_data_struct2 >
234 floating_base_chain_closure_post_process(utility::vector1< FB_Pose_Data > & pose_data_list,
235  core::pose::Pose & viewer_pose,
236  core::scoring::ScoreFunctionOP const & sampling_scorefxn,
237  FloatingBaseChainClosureJobParameter const & FB_job_params,
238  bool const rm_chain_break_jump_point=true);
239 
240 utility::vector1< pose_data_struct2 >
241 sample_virtual_ribose_and_bulge_and_close_chain(core::pose::Pose & viewer_pose,
242  FloatingBaseChainClosureJobParameter const & FB_job_params,
243  std::string const name,
244  core::scoring::ScoreFunctionOP const & scorefxn,
245  core::scoring::ScoreFunctionOP const & sampling_scorefxn,
246  core::scoring::ScoreFunctionOP const & atr_rep_screening_scorefxn,
247  core::scoring::ScoreFunctionOP const & chainbreak_scorefxn,
248  StepWiseRNA_JobParametersCOP & job_parameters,
249  bool const virtual_ribose_is_from_prior_step=true);
250 
251 
252 void
253 minimize_all_sampled_floating_bases(core::pose::Pose & viewer_pose,
254  utility::vector1<FloatingBaseChainClosureJobParameter> const & FB_JP_list,
255  utility::vector1< pose_data_struct2 > & pose_data_list,
256  core::scoring::ScoreFunctionOP const & sampling_scorefxn,
257  StepWiseRNA_JobParametersCOP const & job_parameters,
258  bool const virtual_ribose_is_from_prior_step=true);
259 
260 
261 bool
262 Is_ribose_virtual( core::pose::Pose const & pose, core::Size const previous_moving_res, core::Size const previous_bulge_res);
263 
264 void
265 copy_bulge_res_and_ribose_torsion(FloatingBaseChainClosureJobParameter const & FB_job_params, core::pose::Pose & pose, core::pose::Pose const & template_pose);
266 
267 void
268 enumerate_starting_pose_data_list(utility::vector1< pose_data_struct2 > & starting_pose_data_list,
269  utility::vector1< FloatingBaseChainClosureJobParameter > const & FB_CC_JP_list,
270  core::pose::Pose const & pose);
271 
272 
273 utility::vector1< FloatingBaseChainClosureJobParameter >
274 setup_FB_CC_JP_list(core::pose::Pose const & pose, utility::vector1< std::string > const & sample_virtual_ribose_string_list, StepWiseRNA_JobParametersCOP & job_parameters);
275 
276 void
277 sample_user_specified_virtual_riboses(core::pose::Pose & pose, utility::vector1< std::string > const & sample_virtual_ribose_string_list,
278  StepWiseRNA_JobParametersCOP & job_parameters, core::scoring::ScoreFunctionOP const & scorefxn,
279  std::string const silent_file_out, std::string const input_tag);
280 
281 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////
282 
283 
284 }
285 }
286 }
287 
288 #endif
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