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init.cc
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7 // (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
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9 // (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.
10 
11 /// @file core/init.cc
12 /// @brief options system initialization routines
13 /// @author Sergey Lyskov
14 ///
15 
16 #ifdef USEMPI
17 #include <mpi.h> // Must go first
18 #include <basic/TracerToFile.hh>
19 #endif
20 
21 // Unit headers
22 #include <time.h>
23 #include <core/init.hh>
24 
25 // Project Headers
26 #include <core/svn_version.hh>
27 #include <core/types.hh>
28 #include <basic/options/option.hh>
29 #include <utility/basic_sys_util.hh>
30 #include <utility/excn/Exceptions.hh>
31 #include <utility/io/izstream.hh>
32 #include <basic/Tracer.hh>
33 #include <basic/prof.hh>
34 // Classes in core that must register with factorys
35 #include <core/scoring/constraints/ConstraintsEnergyCreator.hh>
36 #include <core/scoring/disulfides/CentroidDisulfideEnergyCreator.hh>
37 #include <core/scoring/disulfides/DisulfideMatchingEnergyCreator.hh>
38 #include <core/scoring/disulfides/FullatomDisulfideEnergyCreator.hh>
39 #include <core/scoring/etable/EtableEnergyCreator.hh>
40 
41 #include <core/scoring/hbonds/HBondEnergyCreator.hh>
42 #include <core/scoring/methods/EnergyMethodRegistrator.hh>
43 #include <core/scoring/methods/CenPairEnergyCreator.hh>
44 #include <core/scoring/methods/ChainbreakEnergyCreator.hh>
45 #include <core/scoring/methods/ContactOrderEnergyCreator.hh>
46 #include <core/scoring/methods/EnvEnergyCreator.hh>
47 #include <core/scoring/methods/EnvSmoothEnergyCreator.hh>
48 #include <core/scoring/methods/NMerRefEnergyCreator.hh>
49 #include <core/scoring/methods/NMerPSSMEnergyCreator.hh>
50 #include <core/scoring/methods/OmegaTetherEnergyCreator.hh>
51 #include <core/scoring/methods/P_AA_EnergyCreator.hh>
52 #include <core/scoring/methods/P_AA_pp_EnergyCreator.hh>
53 #include <core/scoring/methods/PackStatEnergyCreator.hh>
54 #include <core/scoring/methods/PairEnergyCreator.hh>
55 #include <core/scoring/methods/PeptideBondEnergyCreator.hh>
56 #include <core/scoring/methods/ProClosureEnergyCreator.hh>
57 #include <core/scoring/methods/BurialEnergyCreator.hh>
58 #include <core/scoring/methods/RG_Energy_FastCreator.hh>
59 #include <core/scoring/methods/SA_EnergyCreator.hh>
60 #include <core/scoring/methods/RMS_EnergyCreator.hh>
61 #include <core/scoring/methods/RamachandranEnergy2BCreator.hh>
62 #include <core/scoring/methods/RamachandranEnergyCreator.hh>
63 #include <core/scoring/methods/ReferenceEnergyCreator.hh>
64 #include <core/scoring/methods/ReferenceEnergyNoncanonicalCreator.hh>
65 #include <core/scoring/methods/SecondaryStructureEnergyCreator.hh>
66 #include <core/scoring/methods/VDW_EnergyCreator.hh>
67 #include <core/scoring/methods/dfire/DFIRE_EnergyCreator.hh>
68 
69 #include <core/pack/dunbrack/DunbrackEnergyCreator.hh>
70 
71 // define this for compiling a slimmed down version of mini libraries lacking about 3/4s of the code
72 // this is required for compiling a less memory hungry version of mini for Bluegene etc..
73 //#define MINI_SLIM
74 #ifndef MINI_SLIM
75 #include <core/scoring/carbon_hbonds/CarbonHBondEnergyCreator.hh>
76 #include <core/scoring/custom_pair_distance/FullatomCustomPairDistanceEnergyCreator.hh>
77 #include <core/scoring/methods/CustomAtomPairEnergyCreator.hh>
78 #include <core/scoring/electron_density/FastDensEnergyCreator.hh>
79 #include <core/scoring/electron_density/ElecDensCenEnergyCreator.hh>
80 #include <core/scoring/electron_density/ElecDensAllAtomCenEnergyCreator.hh>
81 #include <core/scoring/electron_density/ElecDensEnergyCreator.hh>
82 #include <core/scoring/electron_density/PattersonCorrEnergyCreator.hh>
83 #include <core/scoring/electron_density_atomwise/ElecDensAtomwiseEnergyCreator.hh>
84 //XRW_B_T1
85 //#include <core/scoring/etable/CoarseEtableEnergyCreator.hh>
86 //XRW_E_T1
87 #include <core/scoring/geometric_solvation/ExactOccludedHbondSolEnergyCreator.hh>
88 #include <core/scoring/geometric_solvation/GeometricSolEnergyCreator.hh>
89 #include <core/scoring/geometric_solvation/ContextIndependentGeometricSolEnergyCreator.hh>
90 #include <core/scoring/geometric_solvation/OccludedHbondSolEnergyCreator.hh>
91 #include <core/scoring/geometric_solvation/OccludedHbondSolEnergy_onebodyCreator.hh>
92 #include <core/scoring/hackelec/HackElecEnergyCreator.hh>
93 #include <core/scoring/hackelec/HackElecEnergyAroAroCreator.hh>
94 #include <core/scoring/hackelec/HackElecEnergyAroAllCreator.hh>
95 #include <core/scoring/hackelec/RNAHackElecEnergyCreator.hh>
96 #include <core/scoring/hackaro/HackAroEnergyCreator.hh>
97 #include <core/scoring/dna/DNAChiEnergyCreator.hh>
98 #include <core/scoring/dna/DNATorsionEnergyCreator.hh>
99 #include <core/scoring/methods/DNA_BaseEnergyCreator.hh>
100 #include <core/scoring/methods/DirectReadoutEnergyCreator.hh>
101 #include <core/scoring/methods/DistanceChainbreakEnergyCreator.hh>
102 #include <core/scoring/methods/Fa_MbenvEnergyCreator.hh>
103 #include <core/scoring/methods/Fa_MbsolvEnergyCreator.hh>
104 #include <core/scoring/methods/GenBornEnergyCreator.hh>
105 #include <core/scoring/methods/HybridVDW_EnergyCreator.hh>
106 #include <core/scoring/methods/LK_CosThetaEnergyCreator.hh>
107 #include <core/scoring/methods/LK_hackCreator.hh>
108 #include <core/scoring/methods/LK_BallEnergyCreator.hh>
109 #include <core/scoring/methods/LinearChainbreakEnergyCreator.hh>
110 #include <core/scoring/methods/MMBondAngleEnergyCreator.hh>
111 #include <core/scoring/methods/MMBondLengthEnergyCreator.hh>
112 #include <core/scoring/methods/CartesianBondedEnergyCreator.hh>
113 #include <core/scoring/methods/MMTorsionEnergyCreator.hh>
114 #include <core/scoring/methods/MMLJEnergyIntraCreator.hh>
115 #include <core/scoring/methods/MMLJEnergyInterCreator.hh>
116 #include <core/scoring/methods/MembraneCbetaEnergyCreator.hh>
117 #include <core/scoring/methods/MembraneCenPairEnergyCreator.hh>
118 #include <core/scoring/methods/MembraneEnvEnergyCreator.hh>
119 #include <core/scoring/methods/MembraneEnvPenaltiesCreator.hh>
120 #include <core/scoring/methods/MembraneLipoCreator.hh>
121 #include <core/scoring/methods/MembraneEnvSmoothEnergyCreator.hh>
122 #include <core/scoring/methods/pHEnergyCreator.hh>
123 #include <core/scoring/methods/PoissonBoltzmannEnergyCreator.hh>
124 #include <core/scoring/methods/ChemicalShiftAnisotropyEnergyCreator.hh>
125 #include <core/scoring/methods/DipolarCouplingEnergyCreator.hh>
126 #include <core/scoring/methods/ResidualDipolarCouplingEnergyCreator.hh>
127 #include <core/scoring/methods/ResidualDipolarCouplingEnergy_RohlCreator.hh>
128 #include <core/scoring/methods/SmoothCenPairEnergyCreator.hh>
129 #include <core/scoring/methods/SmoothEnvEnergyCreator.hh>
130 #include <core/scoring/methods/CenHBEnergyCreator.hh>
131 #include <core/scoring/methods/SuckerEnergyCreator.hh>
132 #include <core/scoring/methods/GaussianOverlapEnergyCreator.hh>
133 #include <core/scoring/methods/YHHPlanarityEnergyCreator.hh>
134 #include <core/pack/interaction_graph/SurfaceEnergyCreator.hh>
135 #include <core/pack/interaction_graph/HPatchEnergyCreator.hh>
136 #include <core/scoring/methods/SymmetricLigandEnergyCreator.hh>
137 #include <core/scoring/methods/UnfoldedStateEnergyCreator.hh>
138 #include <core/scoring/methods/WaterAdductHBondEnergyCreator.hh>
139 #include <core/scoring/methods/WaterAdductIntraEnergyCreator.hh>
140 #include <core/scoring/nv/NVscoreCreator.hh>
141 #include <core/scoring/orbitals/OrbitalsScoreCreator.hh>
142 #include <core/scoring/interface/DDPscoreCreator.hh>
143 #include <core/scoring/packing/HolesEnergyCreator.hh>
144 #include <core/scoring/packing/SurfVolEnergyCreator.hh>
145 #include <core/scoring/packing/SurfEnergyCreator.hh>
146 #include <core/scoring/rna/RG_Energy_RNACreator.hh>
147 #include <core/scoring/rna/RNA_BulgeEnergyCreator.hh>
148 #include <core/scoring/rna/RNA_DataBackboneEnergyCreator.hh>
149 #include <core/scoring/rna/RNA_FullAtomStackingEnergyCreator.hh>
150 #include <core/scoring/rna/RNA_LJ_BaseEnergyCreator.hh>
151 #include <core/scoring/rna/RNA_PairwiseLowResolutionEnergyCreator.hh>
152 #include <core/scoring/rna/RNA_SugarCloseEnergyCreator.hh>
153 #include <core/scoring/rna/RNA_TorsionEnergyCreator.hh>
154 #include <core/scoring/rna/RNA_VDW_EnergyCreator.hh>
155 #include <core/scoring/rna/RNA_Mg_EnergyCreator.hh>
156 #include <core/scoring/rna/RNA_FullAtomVDW_BasePhosphateCreator.hh>
157 #include <core/scoring/rna/chemical_shift/RNA_ChemicalShiftEnergyCreator.hh>
158 #include <core/scoring/sym_e/symECreator.hh>
159 #include <core/scoring/saxs/FastSAXSEnergyCreator.hh>
160 #include <core/scoring/saxs/SAXSEnergyCreator.hh>
161 #include <core/scoring/saxs/SAXSEnergyCreatorFA.hh>
162 #include <core/scoring/saxs/SAXSEnergyCreatorCEN.hh>
163 
164 
165 // Constraint registration
166 #include <core/scoring/constraints/ConstraintFactory.hh>
167 #include <core/scoring/constraints/BasicConstraintCreators.hh>
168 
169 #include <core/pack/dunbrack/DunbrackConstraintCreator.hh>
170 #include <core/scoring/constraints/SequenceProfileConstraintCreator.hh>
171 
172 // SilentStruct registration
173 #include <core/io/silent/SilentStructFactory.hh>
174 #include <core/io/silent/BasicSilentStructCreators.hh>
175 #include <core/import_pose/PDBSilentStructCreator.hh>
176 
177 // Sequence registration
178 #include <core/sequence/SequenceFactory.hh>
179 #include <core/sequence/BasicSequenceCreators.hh>
180 
181 // for registering TaskOperations, ResLvlTaskOperations, and ResFilters
182 #include <core/pack/task/operation/TaskOperationRegistrator.hh>
183 #include <core/pack/task/operation/TaskOperationCreators.hh>
184 #include <core/pack/task/operation/OperateOnCertainResiduesCreator.hh>
185 #include <core/pack/task/operation/NoRepackDisulfidesCreator.hh>
186 #include <core/pack/task/operation/OptCysHGCreator.hh>
187 #include <core/pack/task/operation/OptHCreator.hh>
188 #include <core/pack/task/operation/ResLvlTaskOperationRegistrator.hh>
189 #include <core/pack/task/operation/ResLvlTaskOperationCreators.hh>
190 #include <core/pack/task/operation/ResFilterRegistrator.hh>
191 #include <core/pack/task/operation/ResFilterCreators.hh>
192 #include <core/pack/task/operation/ReplicateTaskCreator.hh>
193 // (end for registering TaskOperations, ResLvlTaskOperations, and ResFilters)
194 
195 #endif
196 
197 #ifndef WIN_PYROSETTA
198  #include <platform/types.hh>
199 #endif
200 
201 #ifdef MAC
202 #include <mach-o/dyld.h> // for _NSGetExecutablePath
203 #endif
204 
205 
206 #include <basic/options/keys/in.OptionKeys.gen.hh>
207 #include <cstring>
208 
209 using basic::T;
210 using basic::Error;
211 using basic::Warning;
212 
213 // Windows headers
214 #if (defined WIN32) && (!defined WIN_PYROSETTA)
215 #include <windows.h>
216 #include <wincrypt.h>
217 #endif
218 
219 // STL headers
220 #include <fstream>
221 #include <sstream>
222 #include <string>
223 
224 // option key includes
225 
226 #include <basic/options/keys/out.OptionKeys.gen.hh>
227 #include <basic/options/keys/run.OptionKeys.gen.hh>
228 #include <basic/options/keys/corrections.OptionKeys.gen.hh>
229 #include <basic/options/keys/score.OptionKeys.gen.hh>
230 #include <basic/options/keys/OptionKeys.hh>
231 
232 // ResourceManager includes
233 #include <basic/resource_manager/ResourceLoaderRegistrator.hh>
234 #include <core/conformation/symmetry/SymmDataLoaderCreator.hh>
235 #include <core/conformation/symmetry/SymmDataOptionsCreator.hh>
236 #include <core/io/silent/SilentFileLoaderCreator.hh>
237 #include <core/io/silent/SilentFileOptionsCreator.hh>
238 #include <core/import_pose/PoseFromPDBLoaderCreator.hh>
239 #include <core/import_pose/import_pose_options_creator.hh>
240 #include <basic/resource_manager/ResourceOptionsRegistrator.hh>
241 #include <core/scoring/electron_density/ElectronDensityLoaderCreator.hh>
242 #include <core/scoring/electron_density/ElectronDensityOptionsCreator.hh>
243 #include <core/chemical/ResidueLoaderCreator.hh>
244 #include <core/chemical/ResidueLoaderOptionsCreator.hh>
245 
246 
247 
248 
249 //option key includes for deprecated pdbs
250 #include <basic/options/keys/LoopModel.OptionKeys.gen.hh>
251 
252 #include <core/pack/task/operation/ResFilterFactory.hh>
253 #include <core/pack/task/operation/ResLvlTaskOperationFactory.hh>
254 #include <core/pack/task/operation/TaskOperationFactory.hh>
255 #include <core/scoring/ScoringManager.hh>
256 #include <utility/vector0.hh>
257 #include <utility/vector1.hh>
258 
259 
260 #ifdef UNICODE
261 typedef std::wostringstream ostringstream_t;
262 #else
263 typedef std::ostringstream ostringstream_t;
264 #endif
265 
266 namespace core {
267 
268 /// The following global varialbles force the linker to always include
269 /// the EnergyMethodCreator files to be included in staticly linked
270 /// executables. These variables will be initialized before main()
271 /// begins during the "dynamic initialization" phase of loading.
272 /// During this time, the Registrotor classes will register their templated
273 /// EnergyMethods with the ScoringManager before main() begins.
274 
275 using namespace scoring::methods;
276 
277 static EnergyMethodRegistrator< scoring::constraints::ConstraintsEnergyCreator > ConstraintsEnergyCreator_registrator;
278 static EnergyMethodRegistrator< scoring::disulfides::CentroidDisulfideEnergyCreator > CentroidDisulfideEnergyCreator_registrator;
279 static EnergyMethodRegistrator< scoring::disulfides::DisulfideMatchingEnergyCreator > DisulfideMatchingEnergyCreator_registrator;
280 static EnergyMethodRegistrator< scoring::disulfides::FullatomDisulfideEnergyCreator > FullatomDisulfideEnergyCreator_registrator;
281 static EnergyMethodRegistrator< scoring::etable::EtableEnergyCreator > EtableEnergyCreator_registrator;
282 static EnergyMethodRegistrator< scoring::hbonds::HBondEnergyCreator > HBondEnergyCreator_registrator;
283 static EnergyMethodRegistrator< scoring::methods::ChainbreakEnergyCreator > ChainbreakEnergyCreator_registrator;
284 static EnergyMethodRegistrator< scoring::methods::CenPairEnergyCreator > CenPairEnergyCreator_registrator;
285 static EnergyMethodRegistrator< scoring::methods::ContactOrderEnergyCreator > ContactOrderEnergyCreator_registrator;
286 static EnergyMethodRegistrator< scoring::methods::EnvEnergyCreator > EnvEnergyCreator_registrator;
287 static EnergyMethodRegistrator< scoring::methods::EnvSmoothEnergyCreator > EnvSmoothEnergyCreator_registrator;
288 static EnergyMethodRegistrator< scoring::methods::OmegaTetherEnergyCreator > OmegaTetherEnergyCreator_registrator;
289 static EnergyMethodRegistrator< scoring::methods::NMerRefEnergyCreator > NMerRefEnergyCreator_registrator;
290 static EnergyMethodRegistrator< scoring::methods::NMerPSSMEnergyCreator > NMerPSSMEnergyCreator_registrator;
291 static EnergyMethodRegistrator< scoring::methods::P_AA_EnergyCreator > P_AA_EnergyCreator_registrator;
292 static EnergyMethodRegistrator< scoring::methods::P_AA_pp_EnergyCreator > P_AA_pp_EnergyCreator_registrator;
293 static EnergyMethodRegistrator< scoring::methods::PackStatEnergyCreator > PackStatEnergyCreator_registrator;
294 static EnergyMethodRegistrator< scoring::methods::PairEnergyCreator > PairEnergyCreator_registrator;
295 static EnergyMethodRegistrator< scoring::methods::PeptideBondEnergyCreator > PeptideBondEnergyCreator_registrator;
296 static EnergyMethodRegistrator< scoring::methods::ProClosureEnergyCreator > ProClosureEnergyCreator_registrator;
297 static EnergyMethodRegistrator< scoring::methods::BurialEnergyCreator > BurialCreator_registrator;
298 static EnergyMethodRegistrator< scoring::methods::RG_Energy_FastCreator > RG_Energy_FastCreator_registrator;
299 static EnergyMethodRegistrator< scoring::methods::SA_EnergyCreator > SA_EnergyCreator_registrator;
300 static EnergyMethodRegistrator< scoring::methods::RMS_EnergyCreator > RMS_EnergyCreator_registrator;
301 static EnergyMethodRegistrator< scoring::methods::RamachandranEnergy2BCreator > RamachandranEnergy2BCreator_registrator;
302 static EnergyMethodRegistrator< scoring::methods::RamachandranEnergyCreator > RamachandranEnergyCreator_registrator;
303 static EnergyMethodRegistrator< scoring::methods::ReferenceEnergyCreator > ReferenceEnergyCreator_registrator;
304 static EnergyMethodRegistrator< scoring::methods::ReferenceEnergyNoncanonicalCreator > ReferenceEnergyNoncanonicalCreator_registrator;
305 static EnergyMethodRegistrator< scoring::methods::SecondaryStructureEnergyCreator > SecondaryStructureEnergyCreator_registrator;
306 static EnergyMethodRegistrator< scoring::methods::VDW_EnergyCreator > VDW_EnergyCreator_registrator;
307 static EnergyMethodRegistrator< scoring::methods::dfire::DFIRE_EnergyCreator > DFIRE_EnergyCreator_registrator;
308 
309 static EnergyMethodRegistrator< pack::dunbrack::DunbrackEnergyCreator > DunbrackEnergyCreator_registrator;
310 
311 // define this for compiling a slimmed down version of mini libraries lacking about 3/4s of the code
312 // this is required for compiling a less memory hungry version of mini for Bluegene etc..
313 #ifndef MINI_SLIM
314 static EnergyMethodRegistrator< scoring::nv::NVscoreCreator > NVscoreCreator_registrator;
315 static EnergyMethodRegistrator< scoring::orbitals::OrbitalsScoreCreator > OrbitalsScoreCreator_registrator;
316 static EnergyMethodRegistrator< scoring::interface::DDPscoreCreator > DDPscoreCreator_registrator;
317 static EnergyMethodRegistrator< scoring::carbon_hbonds::CarbonHBondEnergyCreator > CarbonHBondEnergyCreator_registrator;
318 static EnergyMethodRegistrator< scoring::custom_pair_distance::FullatomCustomPairDistanceEnergyCreator > FullatomCustomPairDistanceEnergyCreator_registrator;
319 static EnergyMethodRegistrator< scoring::methods::CustomAtomPairEnergyCreator > CustomAtomPairEnergy_registrator;
320 static EnergyMethodRegistrator< scoring::electron_density::FastDensEnergyCreator > FastDensEnergyCreator_registrator;
321 static EnergyMethodRegistrator< scoring::electron_density::ElecDensCenEnergyCreator > ElecDensCenEnergyCreator_registrator;
322 static EnergyMethodRegistrator< scoring::electron_density::ElecDensAllAtomCenEnergyCreator > ElecDensAllAtomCenEnergyCreator_registrator;
323 static EnergyMethodRegistrator< scoring::electron_density::ElecDensEnergyCreator > ElecDensEnergyCreator_registrator;
324 static EnergyMethodRegistrator< scoring::electron_density::PattersonCorrEnergyCreator > PattersonCorrEnergyCreator_registrator;
325 static EnergyMethodRegistrator< scoring::electron_density_atomwise::ElecDensAtomwiseEnergyCreator > ElecDensAtomwiseEnergyCreator_registrator;
326 //XRW_B_T1
327 //static EnergyMethodRegistrator< scoring::etable::CoarseEtableEnergyCreator > CoarseEtableEnergyCreator_registrator;
328 //XRW_E_T1
329 static EnergyMethodRegistrator< scoring::geometric_solvation::ExactOccludedHbondSolEnergyCreator > ExactOccludedHbondSolEnergyCreator_registrator;
330 static EnergyMethodRegistrator< scoring::geometric_solvation::GeometricSolEnergyCreator > GeometricSolEnergyCreator_registrator;
331 static EnergyMethodRegistrator< scoring::geometric_solvation::ContextIndependentGeometricSolEnergyCreator > ContextIndependentGeometricSolEnergyCreator_registrator;
332 static EnergyMethodRegistrator< scoring::geometric_solvation::OccludedHbondSolEnergyCreator > OccludedHbondSolEnergyCreator_registrator;
333 static EnergyMethodRegistrator< scoring::geometric_solvation::OccludedHbondSolEnergy_onebodyCreator > OccludedHbondSolEnergy_onebodyCreator_registrator;
334 static EnergyMethodRegistrator< scoring::hackelec::HackElecEnergyCreator > HackElecEnergyCreator_registrator;
335 static EnergyMethodRegistrator< scoring::hackelec::RNAHackElecEnergyCreator > RNAHackElecEnergyCreator_registrator;
336 static EnergyMethodRegistrator< scoring::hackelec::HackElecEnergyAroAroCreator > HackElecEnergyAroAroCreator_registrator;
337 static EnergyMethodRegistrator< scoring::hackelec::HackElecEnergyAroAllCreator > HackElecEnergyAroAllCreator_registrator;
338 static EnergyMethodRegistrator< scoring::hackaro::HackAroEnergyCreator > HackAroEnergyCreator_registrator;
339 static EnergyMethodRegistrator< scoring::dna::DNAChiEnergyCreator > DNAChiEnergyCreator_registrator;
340 static EnergyMethodRegistrator< scoring::dna::DNATorsionEnergyCreator > DNATorsionEnergyCreator_registrator;
341 static EnergyMethodRegistrator< scoring::methods::DNA_BaseEnergyCreator > DNA_BaseEnergyCreator_registrator;
342 static EnergyMethodRegistrator< scoring::methods::DirectReadoutEnergyCreator > DirectReadoutEnergyCreator_registrator;
343 static EnergyMethodRegistrator< scoring::methods::DistanceChainbreakEnergyCreator > DistanceChainbreakEnergyCreator_registrator;
344 static EnergyMethodRegistrator< scoring::methods::Fa_MbenvEnergyCreator > Fa_MbenvEnergyCreator_registrator;
345 static EnergyMethodRegistrator< scoring::methods::Fa_MbsolvEnergyCreator > Fa_MbsolvEnergyCreator_registrator;
346 static EnergyMethodRegistrator< scoring::methods::GenBornEnergyCreator > GenBornEnergyCreator_registrator;
347 static EnergyMethodRegistrator< scoring::methods::HybridVDW_EnergyCreator > HybridVDW_EnergyCreator_registrator;
348 static EnergyMethodRegistrator< scoring::methods::LK_CosThetaEnergyCreator > LK_CosThetaEnergyCreator_registrator;
349 static EnergyMethodRegistrator< scoring::methods::LK_hackCreator > LK_hackCreator_registrator;
350 static EnergyMethodRegistrator< scoring::methods::LK_BallEnergyCreator > LK_BallEnergyCreator_registrator;
351 static EnergyMethodRegistrator< scoring::methods::LinearChainbreakEnergyCreator > LinearChainbreakEnergyCreator_registrator;
352 static EnergyMethodRegistrator< scoring::methods::MMBondAngleEnergyCreator > MMBondAngleEnergyCreator_registrator;
353 static EnergyMethodRegistrator< scoring::methods::CartesianBondedEnergyCreator > CartesianBondedEnergyCreator_registrator;
354 static EnergyMethodRegistrator< scoring::methods::MMBondLengthEnergyCreator > MMBondLengthEnergyCreator_registrator;
355 static EnergyMethodRegistrator< scoring::methods::MMTorsionEnergyCreator > MMTorsionEnergyCreator_registrator;
356 static EnergyMethodRegistrator< scoring::methods::MMLJEnergyInterCreator > MMLJEnergyInterCreator_registrator;
357 static EnergyMethodRegistrator< scoring::methods::MMLJEnergyIntraCreator > MMLJEnergyIntraCreator_registrator;
358 static EnergyMethodRegistrator< scoring::methods::MembraneCbetaEnergyCreator > MembraneCbetaEnergyCreator_registrator;
359 static EnergyMethodRegistrator< scoring::methods::MembraneCenPairEnergyCreator > MembraneCenPairEnergyCreator_registrator;
360 static EnergyMethodRegistrator< scoring::methods::MembraneEnvEnergyCreator > MembraneEnvEnergyCreator_registrator;
361 static EnergyMethodRegistrator< scoring::methods::MembraneEnvPenaltiesCreator > MembraneEnvPenaltiesCreator_registrator;
362 static EnergyMethodRegistrator< scoring::methods::SmoothCenPairEnergyCreator > SmoothCenPairEnergyCreator_registrator;
363 static EnergyMethodRegistrator< scoring::methods::SmoothEnvEnergyCreator > SmoothEnvEnergyCreator_registrator;
364 static EnergyMethodRegistrator< scoring::methods::CenHBEnergyCreator > CenHBEnergyCreator_registrator;
365 static EnergyMethodRegistrator< scoring::methods::MembraneLipoCreator > MembraneLipoCreator_registrator;
366 static EnergyMethodRegistrator< scoring::methods::MembraneEnvSmoothEnergyCreator > MembraneEnvSmoothEnergyCreator_registrator;
367 static EnergyMethodRegistrator< scoring::methods::pHEnergyCreator > pHEnergyCreator_registrator;
368 static EnergyMethodRegistrator< scoring::methods::ChemicalShiftAnisotropyEnergyCreator > ChemicalShiftAnisotropyEnergyCreator_registrator;
369 static EnergyMethodRegistrator< scoring::methods::DipolarCouplingEnergyCreator > DipolarCouplingEnergyCreator_registrator;
370 static EnergyMethodRegistrator< scoring::methods::ResidualDipolarCouplingEnergyCreator > ResidualDipolarCouplingEnergyCreator_registrator;
371 static EnergyMethodRegistrator< scoring::methods::ResidualDipolarCouplingEnergy_RohlCreator > ResidualDipolarCouplingEnergy_RohlCreator_registrator;
372 static EnergyMethodRegistrator< scoring::methods::SuckerEnergyCreator > SuckerEnergyCreator_registrator;
373 static EnergyMethodRegistrator< scoring::methods::GaussianOverlapEnergyCreator > GaussianOverlapEnergyCreator_registrator;
374 static EnergyMethodRegistrator< scoring::methods::YHHPlanarityEnergyCreator > YYHPlanarityEnergyCreator_registrator;
375 static EnergyMethodRegistrator< pack::interaction_graph::SurfaceEnergyCreator > SurfaceEnergyCreator_registrator;
376 static EnergyMethodRegistrator< pack::interaction_graph::HPatchEnergyCreator > HPatchEnergyCreator_registrator;
377 static EnergyMethodRegistrator< scoring::methods::SymmetricLigandEnergyCreator > SymmetricLigandEnergyCreator_registrator;
378 static EnergyMethodRegistrator< scoring::methods::UnfoldedStateEnergyCreator > UnfoldedStateEnergyCreator_registrator;
379 static EnergyMethodRegistrator< scoring::methods::WaterAdductHBondEnergyCreator > WaterAdductHBondEnergyCreator_registrator;
380 static EnergyMethodRegistrator< scoring::methods::WaterAdductIntraEnergyCreator > WaterAdductIntraEnergyCreator_registrator;
381 static EnergyMethodRegistrator< scoring::packing::HolesEnergyCreator > HolesEnergyCreator_registrator;
382 static EnergyMethodRegistrator< scoring::packing::SurfVolEnergyCreator > SurfVolEnergyCreator_registrator;
383 static EnergyMethodRegistrator< scoring::packing::SurfEnergyCreator > SurfEnergyCreator_registrator;
384 static EnergyMethodRegistrator< scoring::rna::RG_Energy_RNACreator > RG_Energy_RNACreator_registrator;
385 static EnergyMethodRegistrator< scoring::rna::RNA_BulgeEnergyCreator > RNA_BulgeEnergyCreator_registrator;
386 static EnergyMethodRegistrator< scoring::rna::RNA_DataBackboneEnergyCreator > RNA_DataBackboneEnergyCreator_registrator;
387 static EnergyMethodRegistrator< scoring::rna::RNA_FullAtomStackingEnergyCreator > RNA_FullAtomStackingEnergyCreator_registrator;
388 static EnergyMethodRegistrator< scoring::rna::RNA_LJ_BaseEnergyCreator > RNA_LJ_BaseEnergyCreator_registrator;
389 static EnergyMethodRegistrator< scoring::rna::RNA_PairwiseLowResolutionEnergyCreator > RNA_PairwiseLowResolutionEnergyCreator_registrator;
390 static EnergyMethodRegistrator< scoring::rna::RNA_SugarCloseEnergyCreator > RNA_SugarCloseEnergyCreator_registrator;
391 static EnergyMethodRegistrator< scoring::rna::RNA_TorsionEnergyCreator > RNA_TorsionEnergyCreator_registrator;
392 static EnergyMethodRegistrator< scoring::rna::RNA_VDW_EnergyCreator > RNA_VDW_EnergyCreator_registrator;
393 static EnergyMethodRegistrator< scoring::rna::RNA_Mg_EnergyCreator > RNA_Mg_EnergyCreator_registrator;
394 static EnergyMethodRegistrator< scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator > RNA_FullAtomVDW_BasePhosphateCreator_registrator;
395 static EnergyMethodRegistrator< scoring::rna::chemical_shift::RNA_ChemicalShiftEnergyCreator > NA_ChemicalShiftEnergyCreator_registrator;
396 static EnergyMethodRegistrator< scoring::sym_e::symECreator > symECreator_registrator;
397 static EnergyMethodRegistrator< scoring::methods::PoissonBoltzmannEnergyCreator > PoissonBoltzmannEnergyCreator_registrator;
398 
399 static EnergyMethodRegistrator< scoring::saxs::FastSAXSEnergyCreator > FastSAXSEnergyCreator_registrator;
400 static EnergyMethodRegistrator< scoring::saxs::SAXSEnergyCreatorCEN > SAXSEnergyCreatorCEN_registrator;
401 static EnergyMethodRegistrator< scoring::saxs::SAXSEnergyCreatorFA > SAXSEnergyCreatorFA_registrator;
402 static EnergyMethodRegistrator< scoring::saxs::SAXSEnergyCreator > SAXSEnergyCreator_registrator;
403 
404 /// Constraint Registrators
405 using namespace scoring::constraints;
406 static ConstraintRegistrator< core::scoring::constraints::AmbiguousConstraintCreator > AmbiguousConstraintCreator_registrator;
407 static ConstraintRegistrator< core::scoring::constraints::AmbiguousNMRConstraintCreator > AmbiguousNMRConstraintCreator_registrator;
408 static ConstraintRegistrator< core::scoring::constraints::AmbiguousNMRDistanceConstraintCreator > AmbiguousNMRDistanceConstraintCreator_registrator;
409 static ConstraintRegistrator< core::scoring::constraints::AngleConstraintCreator > AngleConstraintCreator_registrator;
410 static ConstraintRegistrator< core::scoring::constraints::AtomPairConstraintCreator > AtomPairConstraintCreator_registrator;
411 static ConstraintRegistrator< core::scoring::constraints::BigBinConstraintCreator > BigBinConstraintCreator_registrator;
412 static ConstraintRegistrator< core::scoring::constraints::CoordinateConstraintCreator > CoordinateConstraintCreator_registrator;
413 static ConstraintRegistrator< core::scoring::constraints::DihedralConstraintCreator > DihedralConstraintCreator_registrator;
414 static ConstraintRegistrator< core::scoring::constraints::DihedralPairConstraintCreator > DihedralPairConstraintCreator_registrator;
415 static ConstraintRegistrator< core::scoring::constraints::KofNConstraintCreator > KofNConstraintCreator_registrator;
416 static ConstraintRegistrator< core::scoring::constraints::LocalCoordinateConstraintCreator > LocalCoordinateConstraintCreator_registrator;
417 static ConstraintRegistrator< core::scoring::constraints::MultiConstraintCreator > MultiConstraintCreator_registrator;
418 static ConstraintRegistrator< core::scoring::constraints::FabConstraintCreator > FabConstraintCreator_registrator;
419 
420 static ConstraintRegistrator< core::pack::dunbrack::DunbrackConstraintCreator > DunbrackConstraintCreator_registrator;
421 static ConstraintRegistrator< core::scoring::constraints::SiteConstraintCreator > SiteConstraintCreator_registrator;
422 static ConstraintRegistrator< core::scoring::constraints::SiteConstraintResiduesCreator > SiteConstraintResiduesCreator_registrator;
423 static ConstraintRegistrator< core::scoring::constraints::SequenceProfileConstraintCreator > SequenceProfileConstraintCreator_registrator;
424 
425 // SilentStruct registrators
426 using namespace core::io::silent;
427 static SilentStructRegistrator< core::io::silent::ProteinSilentStructCreator > ProteinSilentStructCreator_registrator;
428 static SilentStructRegistrator< core::io::silent::ProteinSilentStruct_SinglePrecCreator > ProteinSilentStruct_SinglePrecCreator_registrator;
429 static SilentStructRegistrator< core::io::silent::RNA_SilentStructCreator > RNA_SilentStructCreator_registrator;
430 static SilentStructRegistrator< core::import_pose::PDBSilentStructCreator > PDBSilentStructCreator_registrator;
431 static SilentStructRegistrator< core::io::silent::BinaryProteinSilentStructCreator > BinaryProteinSilentStructCreator_registrator;
432 static SilentStructRegistrator< core::io::silent::ScoreFileSilentStructCreator > ScoreFileSilentStructCreator_registrator;
433 static SilentStructRegistrator< core::io::silent::BinaryRNASilentStructCreator > BinaryRNASilentStructCreator_registrator;
434 
435 // Sequence registrators
436 using namespace core::sequence;
437 static SequenceRegistrator< core::sequence::SimpleSequenceCreator > SimpleSequenceCreator_registrator;
438 static SequenceRegistrator< core::sequence::SequenceProfileCreator > SequenceProfileCreator_registrator;
439 static SequenceRegistrator< core::sequence::SequenceCouplingCreator > SequenceCouplingCreator_registrator;
440 static SequenceRegistrator< core::sequence::CompositeSequenceCreator > CompositeSequenceCreator_registrator;
441 
442 // perhaps these long registration lists live in their own separate file?
443 using namespace pack::task::operation;
444 // register TaskOperationCreators
445 static TaskOperationRegistrator< RestrictYSDesignCreator > RestrictYSDesignCreator_registrator;
446 static TaskOperationRegistrator< PreventRepackingCreator > PreventRepackingCreator_registrator;
447 static TaskOperationRegistrator< PreserveCBetaCreator > PreserveCBetaCreator_registrator;
448 static TaskOperationRegistrator< AppendRotamerSetCreator > AppendRotamerSetCreator_registrator;
449 static TaskOperationRegistrator< AppendRotamerCreator > AppendRotamerCreator_registrator;
450 static TaskOperationRegistrator< ExtraRotamersCreator > ExtraRotamersCreator_registrator;
451 static TaskOperationRegistrator< ExtraChiCutoffCreator > ExtraChiCutoffCreator_registrator;
452 static TaskOperationRegistrator< SetRotamerCouplingsCreator > SetRotamerCouplingsCreator_registrator;
453 static TaskOperationRegistrator< SetRotamerLinksCreator > SetRotamerLinksCreator_registrator;
454 static TaskOperationRegistrator< ReadResfileCreator > ReadResfileCreator_registrator;
455 static TaskOperationRegistrator< ReadResfileAndObeyLengthEventsCreator > ReadResfileAndObeyLengthEventsCreator_registrator;
456 static TaskOperationRegistrator< IncludeCurrentCreator > IncludeCurrentCreator_registrator;
457 static TaskOperationRegistrator< InitializeExtraRotsFromCommandlineCreator > InitializeExtraRotsFromCommandlineCreator_registrator;
458 static TaskOperationRegistrator< InitializeFromCommandlineCreator > InitializeFromCommandlineCreator_registrator;
459 static TaskOperationRegistrator< ExtraRotamersGenericCreator > ExtraRotamersGenericCreator_registrator;
460 static TaskOperationRegistrator< RotamerExplosionCreator > RotamerExplosionCreator_registrator;
461 static TaskOperationRegistrator< RestrictAbsentCanonicalAASCreator > RestrictAbsentCanonicalAASCreator_registrator;
462 static TaskOperationRegistrator< DisallowIfNonnativeCreator > DisallowIfNonnativeCreator_registrator;
463 static TaskOperationRegistrator< RestrictResidueToRepackingCreator > RestrictResidueToRepackingCreator_registrator;
464 static TaskOperationRegistrator< RestrictToRepackingCreator > RestrictToRepackingCreator_registrator;
465 static TaskOperationRegistrator< OperateOnCertainResiduesCreator > OperateOnCertainResiduesCreator_registrator;
466 static TaskOperationRegistrator< NoRepackDisulfidesCreator > NoRepackDisulfidesCreator_registrator;
467 static TaskOperationRegistrator< ReplicateTaskCreator > ReplicateTaskCreator_registrator;
468 static TaskOperationRegistrator< OptCysHGCreator > OptCysHGCreator_registrator;
469 static TaskOperationRegistrator< OptHCreator > OptHCreator_registrator;
470 // register ResLvlTaskOperationCreators
471 static ResLvlTaskOperationRegistrator< RestrictToRepackingRLTCreator > RestrictToRepackingRLTCreator_registrator;
472 static ResLvlTaskOperationRegistrator< RestrictAbsentCanonicalAASRLTCreator > RestrictAbsentCanonicalAASRLTCreator_registrator;
473 static ResLvlTaskOperationRegistrator< DisallowIfNonnativeRLTCreator > DisallowIfNonnativeRLTCreator_registrator;
474 static ResLvlTaskOperationRegistrator< PreventRepackingRLTCreator > PreventRepackingRLTCreator_registrator;
475 static ResLvlTaskOperationRegistrator< AddBehaviorRLTCreator > AddBehaviorRLTCreator_registrator;
476 // register ResFilterCreators
477 static ResFilterRegistrator< ResidueHasPropertyCreator > ResidueHasPropertyCreator_registrator;
478 static ResFilterRegistrator< ResidueLacksPropertyCreator > ResidueLacksPropertyCreator_registrator;
479 static ResFilterRegistrator< ResidueName3IsCreator > ResidueName3IsCreator_registrator;
480 static ResFilterRegistrator< ResidueName3IsntCreator > ResidueName3IsntCreator_registrator;
481 static ResFilterRegistrator< ResidueIndexIsCreator > ResidueIndexIsCreator_registrator;
482 static ResFilterRegistrator< ResidueIndexIsntCreator > ResidueIndexIsntCreator_registrator;
483 static ResFilterRegistrator< ResiduePDBIndexIsCreator > ResiduePDBIndexIsCreator_registrator;
484 static ResFilterRegistrator< ResiduePDBIndexIsntCreator > ResiduePDBIndexIsntCreator_registrator;
485 static ResFilterRegistrator< ChainIsCreator > ChainIsCreator_registrator;
486 static ResFilterRegistrator< ChainIsntCreator > ChainIsntCreator_registrator;
487 static ResFilterRegistrator< AnyResFilterCreator > AnyResFilterCreator_registrator;
488 static ResFilterRegistrator< AllResFilterCreator > AllResFilterCreator_registrator;
489 static ResFilterRegistrator< NoResFilterCreator > NoResFilterCreator_registrator;
490 static ResFilterRegistrator< ResidueTypeFilterCreator > ResidueTypeResFilterCreator_registrator;
491 
492 using basic::resource_manager::ResourceLoaderRegistrator;
493 static ResourceLoaderRegistrator< core::conformation::symmetry::SymmDataLoaderCreator > SymmDataLoaderCreator_registrator;
494 static ResourceLoaderRegistrator< core::io::silent::SilentFileLoaderCreator > SilentFileLoaderCreator_registrator;
495 static ResourceLoaderRegistrator< core::import_pose::PoseFromPDBLoaderCreator > PoseFromPDBLoaderCreator_registrator;
496 static ResourceLoaderRegistrator< core::scoring::electron_density::ElectronDensityLoaderCreator > ElectronDensityLoaderCreator_registrator;
497 static ResourceLoaderRegistrator< core::chemical::ResidueLoaderCreator > ResidueLoaderCreator_registrator;
498 
499 using basic::resource_manager::ResourceOptionsRegistrator;
500 static ResourceOptionsRegistrator< core::conformation::symmetry::SymmDataOptionsCreator > SymmDataOptionsCreator_registrator;
501 static ResourceOptionsRegistrator< core::import_pose::ImportPoseOptionsCreator > ImportPoseOptionsCreator_registrator;
502 static ResourceOptionsRegistrator< core::io::silent::SilentFileOptionsCreator > SilentFileOptionsCreator_registrator;
503 static ResourceOptionsRegistrator< core::scoring::electron_density::ElectronDensityOptionsCreator > ElectronDensityOptionsCreator_registrator;
504 static ResourceOptionsRegistrator< core::chemical::ResidueLoaderOptionsCreator > ResiudeLoaderOptionsCreator_registrator;
505 
506 #endif
507 
508 static basic::Tracer TR("core.init");
509 
510 using namespace numeric::random;
511 using namespace basic::options;
512 using namespace basic::options::OptionKeys;
513 
514 #ifdef USEMPI
515 void
516 init_mpi(int argc, char * argv []) {
517  int already_initialized( 0 );
518  MPI_Initialized( & already_initialized );
519  if ( already_initialized == 0 ) MPI_Init(&argc, &argv);
520 }
521 #else
522 void
523 init_mpi(int, char **) {}
524 #endif
525 
526 
527 void
528 init_options(int argc, char * argv []) {
529 #ifdef BOINC
530  std::cerr << "Initializing options.... ok " << std::endl;std::cerr.flush();
531 #endif
532 
533  // initialize options
534  initialize().load( argc, argv, false /* no "free" cmd line args (just discarded anyway) */ );
535 #ifdef BOINC
536  std::cerr << "Loaded options.... ok " << std::endl;std::cerr.flush();
537 #endif
538  process();
539 #ifdef BOINC
540  std::cerr << "Processed options.... ok " << std::endl; std::cerr.flush();
541 #endif
542 
543  // Set option system global
544  OptionCollection::set_show_accessed_options_flag( option[ out::show_accessed_options ].value() );
545 }
546 
547 void
548 init_tracers(){
549  // set Tracer options
550  basic::TracerOptions & TO( basic::Tracer::tracer_options() );
551 
552  if( option[ out::mute ].active() ) TO.muted = option[ out::mute ]();
553 
554  if( option[ out::unmute ].active() ) TO.unmuted = option[ out::unmute ]();
555  if( option[ out::level ].active() ) TO.level = option[ out::level ]();
556  if( option[ out::levels ].active() ) TO.levels = option[ out::levels ]();
557  if( option[ out::chname ].active() ) TO.print_channel_name = option[ out::chname ]();
558  if( option[ out::chtimestamp ].active() ) TO.timestamp = option[ out::chtimestamp ]();
559 
560  // Adding Tracer::flush_all_tracers to list of exit-callbacks so all tracer output got flush out when utility_exit is used.
561  utility::add_exit_callback(basic::Tracer::flush_all_tracers);
562 }
563 
564 void
565 init_score_function_corrections(){
566 
567  // set default corrections
568  if( option[corrections::correct]) {
569  // Pair energy
570  if ( ! option[ corrections::score::no_his_his_pairE ].user() ) {
571  option[corrections::score::no_his_his_pairE].value( true );
572  }
573 
574  // p_aa_pp
575  if ( ! option[ corrections::score::p_aa_pp ].user() ) {
576  option[corrections::score::p_aa_pp].value( "scoring/score_functions/P_AA_pp/P_AA_pp_08.2009" );
577  }
578  if ( ! option[ corrections::score::p_aa_pp_nogridshift ].user() ) {
579  option[corrections::score::p_aa_pp_nogridshift].value( true );
580  }
581 
582  //Ramachandran
583  if ( ! option[ corrections::score::rama_not_squared ].user() ) {
584  option[corrections::score::rama_not_squared].value( true );
585  }
586  if ( ! option[ corrections::score::rama_map ].user() ) {
587  option[ corrections::score::rama_map ].value("scoring/score_functions/rama/Rama09_noEH_kernel25_it08.dat");
588  }
589  //rotamer library
590  if ( ! option[ corrections::score::dun02_file ].user() ) {
591  option[corrections::score::dun02_file].value( "rotamer/bbdep02.May.sortlib-correct.12.2010" );
592  }
593 
594  //icoor
595  if ( ! option[ corrections::chemical::icoor_05_2009 ].user() ) {
596  option[corrections::chemical::icoor_05_2009].value( true );
597  }
598  if ( ! option[ score::hbond_params ].user() ) {
599  option[score::hbond_params].value( "correct_params" );
600  }
601 
602  if ( ! option[ corrections::score::ch_o_bond_potential ].user() ) {
603  option[ corrections::score::ch_o_bond_potential ].value("scoring/score_functions/carbon_hbond/ch_o_bond_potential_near_min_yf.dat");
604  }
605  }
606 }
607 
608 void
609 init_source_revision(){
610  if( option[ run::version ]() ) {
611  TR << "Mini-Rosetta version " << core::minirosetta_svn_version() << " from " << core::minirosetta_svn_url() << std::endl;
612  }
613 }
614 
615 void
616 init_paths(){
617  if( option[ in::path::path ].user() ){
618  utility::io::izstream::set_alternative_search_paths(
619  option[ in::path::path ]());
620  }
621 }
622 
623 /// @detail If you deprecate a long standing flag, add a line to this function to describe what the deprecated flag has been replaced with.
624 /// If the user specifies one of these flags, Rosetta will utility exit with a helpful message directing the user towards the new functionality
625 void check_deprecated_flags(){
626 
627  utility::vector1<std::string> error_messages;
628 
629  //Add deprecated flags and corresponding helpful error messages here. This is the only thing you need to do to deprecate a flag
630  if(option[LoopModel::input_pdb].user())
631  error_messages.push_back("-LoopModel:input_pdb is no longer used. Please use -s to input pdb files.");
632 
633 
634  if(error_messages.size() > 0)
635  {
636  utility::vector1<std::string>::const_iterator error_it;
637  for(error_it = error_messages.begin();error_it != error_messages.end();++error_it)
638  {
639  TR.Fatal << "ERROR: You have specified one or more deprecated flags:" <<std::endl;
640  TR.Fatal << *error_it <<std::endl;
641  }
642  std::exit(1);
643 
644  }
645 
646 }
647 
648 void
649 report_application_command(int argc, char * argv []){
650  TR << "command:";
651  for ( int i=0; i< argc; ++i ) {
652  TR << ' ' << argv[i];
653  }
654  TR << std::endl;
655 }
656 
657 void
658 init_random_number_generators(){
659  using namespace numeric::random;
660 
661  int seed = 1111111;
662  int seed_offset = 0;
663  bool const_seed = false;
664  bool use_time_as_seed = false;
665  if( option[ run::constant_seed ].active() ) const_seed = option[ run::constant_seed ]();
666  if( option[ run::jran ].active() ) seed = option[ run::jran ]();
667  if( option[ run::seed_offset ].active() ) seed_offset = option[ run::seed_offset ]();
668  if( option[ run::use_time_as_seed ].active() ) use_time_as_seed = option[ run::use_time_as_seed ]();
669 
670 #ifdef USEMPI
671  if( option[ out::mpi_tracer_to_file ].user() ){
672  int mpi_rank( 0 );
673  MPI_Comm_rank( MPI_COMM_WORLD, &mpi_rank );
674 
675  std::stringstream outfilename;
676  outfilename << option[ out::mpi_tracer_to_file ]() << "_" << mpi_rank;
677  basic::otstreamOP redirect_tracer = new basic::TracerToFile( outfilename.str() );
678  basic::Tracer::set_ios_hook( redirect_tracer, basic::Tracer::AllChannels, false );
679  basic::Tracer::super_mute( true );
680  }
681 
682 #endif
683 
684 
685  std::string random_device_name( option[ run::rng_seed_device ]() ); // typically /dev/urandom or /dev/random
686 
687  int real_seed;
688 
689  if( const_seed ) {
690  real_seed = seed + seed_offset;
691 #ifdef USEMPI
692  { // scope
693  /// Give a different RNG seed to each processor
694  int mpi_rank( 0 );
695  MPI_Comm_rank( MPI_COMM_WORLD, &mpi_rank );
696  real_seed += mpi_rank;
697  }
698 #endif
699  T("core.init") << "Constant seed mode, seed=" << seed << " seed_offset=" << seed_offset
700  << " real_seed=" << real_seed << std::endl;
701  }
702  else {
703 #if (defined WIN32) && (!defined WIN_PYROSETTA)
704  bool const on_windows_platform = true;
705 #else
706  bool const on_windows_platform = false;
707 #endif
708  // attempt to open rng device, if failure then fallback to time
709  std::ifstream random_device( random_device_name.c_str(), std::ios::in | std::ios::binary );
710  if ( ( random_device.fail() && !on_windows_platform ) || use_time_as_seed ) {
711  if ( !use_time_as_seed ) {
712  // notify user that opening rng device has failed
713  T("core.init") << "NOTICE: rng device failure, using time as seed" << std::endl;
714  }
715  random_device.close();
716 
717  //iwd When using time-based seed on a cluster, seed_offset is usually from 0 to num_processes.
718  //iwd If jobs start a few seconds apart, a simple sum of seed and seed_offset can lead to collisions.
719  //iwd Thus we multiply the time by some number larger than the largest expected value of seed_offset.
720  //iwd If anyone's using this on more than 1000 machines at a time, we need to increase this value.
721  //iwd (Rosetta++ used a multiplier of 20, which helps some, but is nonetheless too small.)
722  seed = time(0);
723  //seed = seed%10000; // PB-- USE THIS ON OUR CLUSTER TO GET UNIQUE RUNS
724  //real_seed = seed + seed_offset;
725  real_seed = 1000*seed + seed_offset;
726 
727 #ifdef USEMPI
728  // When we use MPI and time-based seeds on a cluster, adjust the RNG seed so that it is the seed of the head node
729  // (the node with an mpi rank of zero) plus the rank of the processer. This or is garentees that each node will
730  // have a unique seed.
731 
732  /// get the processor rank
733  int mpi_rank( 0 );
734  MPI_Comm_rank( MPI_COMM_WORLD, &mpi_rank );
735  // set the real_seed of each processor to the real seed of the head node
736  MPI_Bcast( &real_seed, 1, MPI_INT, 0, MPI_COMM_WORLD );
737  // adjust the real seed based on the rank
738  real_seed += mpi_rank;
739 #endif
740 
741  T("core.init") << "'Time' seed mode, seed=" << seed << " seed_offset=" << seed_offset
742  << " real_seed=" << real_seed << std::endl;
743  } else {
744  // grab seeds from device
745  uint32_t unsigned_32bit_seed;
746 
747 #if (defined WIN32) && (!defined WIN_PYROSETTA)
748  // windows random device name
749  random_device_name = "CryptGenRandom";
750 
751  // unique name for key container
752  ostringstream_t key_container_name;
753  key_container_name << "arzetta-" << GetCurrentProcessId() << "-" << GetCurrentThreadId();
754 
755  // init cryptographic provider, creates key container
756  HCRYPTPROV hCryptProv = 0;
757 
758  if ( !CryptAcquireContext( &hCryptProv, key_container_name.str().c_str(), NULL, PROV_RSA_AES, CRYPT_NEWKEYSET ) ) {
759  TR.Fatal << "FATAL: CryptAcquireContext unable to acquire cryptographic provider!" << std::endl;
760  TR.Fatal << std::hex << GetLastError() << std::endl;
761  std::exit( 1 );
762  }
763 
764  // grab the random number seed from CryptGenRandom
765  BYTE pbData[ 4 ];
766  if ( !CryptGenRandom( hCryptProv, 4, pbData ) ) {
767  TR.Fatal << "FATAL: Unable to obtain random number seed using CryptGenRandom!" << std::endl;
768  TR.Fatal << std::hex << GetLastError() << std::endl;
769  std::exit( 1 );
770  }
771 
772  // store seed in 'unsigned_32bit_seed'
773  unsigned_32bit_seed = pbData[ 0 ] + ( pbData[ 1 ] << 8 ) + ( pbData[ 2 ] << 16 ) + ( pbData[ 3 ] << 24 );
774 
775  // release cryptographic provider handle
776  if ( !CryptReleaseContext( hCryptProv, 0 ) ) {
777  TR.Fatal << "FATAL: CryptReleaseContext failed to release cryptographic provider!" << std::endl;
778  TR.Fatal << std::hex << GetLastError() << std::endl;
779  std::exit( 1 );
780  }
781 
782  // delete key container
783  if ( !CryptAcquireContext( &hCryptProv, key_container_name.str().c_str(), NULL, PROV_RSA_AES, CRYPT_DELETEKEYSET ) ) {
784  TR.Fatal << "FATAL: CryptAcquireContext failed to delete key container!" << std::endl;
785  TR.Fatal << std::hex << GetLastError() << std::endl;
786  std::exit( 1 );
787  }
788 
789 #else
790  random_device.read( reinterpret_cast< char * >( &unsigned_32bit_seed ), sizeof( uint32_t ));
791 #endif
792  random_device.close();
793 
794  // calculate actual seeds
795  seed = static_cast< int >( unsigned_32bit_seed );
796  real_seed = seed + seed_offset;
797 
798 #ifdef USEMPI
799  // Although not as critical with device-based seeding as with time-based clusters, when we use MPI and
800  // device-based seeds on a cluster, adjust the RNG seed so that it is the seed of the head node (the node with an
801  // mpi rank of zero) plus the rank of the processer. This or is garentees that each node will have a unique
802  // seed. Different OSs impliment their RNG differently and as we use increassingly large numbers of processors
803  // this may become an issue (but probaly not).
804 
805  /// get the processor rank
806  int mpi_rank( 0 );
807  MPI_Comm_rank( MPI_COMM_WORLD, &mpi_rank );
808  // set the real_seed of each processor to the real seed of the head node
809  MPI_Bcast( &real_seed, 1, MPI_INT, 0, MPI_COMM_WORLD );
810  // adjust the real seed based on the rank
811  real_seed += mpi_rank;
812 #endif
813 
814  // log seeds
815  T("core.init") << "'RNG device' seed mode, using '" << random_device_name << "', seed=" << seed << " seed_offset=" << seed_offset
816  << " real_seed=" << real_seed << std::endl;
817  }
818 
819  }
820 
821  /*numeric::random::RandomGenerator::initializeRandomGenerators(
822  real_seed, numeric::random::_RND_ConstantSeed_,
823  option[ run::rng ] );
824  */
825 #ifdef BOINC
826  std::cerr << "Initializing random generators... ok " << std::endl;std::cerr.flush();
827 #endif
828  init_random_generators(real_seed, _RND_NormalRun_, option[ run::rng ]);
829 
830  srand( time(NULL) ); // seed default random generator, this will expose all code that use non approved random methods
831 }
832 
833 /// @brief Initialize random generator systems (and send debug io to tracer with seed/mode info).
834 void init_random_generators(int const start_seed, RND_RunType run_type, std::string const & RGtype)
835 {
836  if( run_type == _RND_TestRun_ ) {
837  T("core.init.random") << "RandomGenerator:init: _RND_TestRun_ mode, seed=" << start_seed <<
838  " RG_type=" << RGtype << std::endl;
839  }
840  else {
841  T("core.init.random") << "RandomGenerator:init: Normal mode, seed=" << start_seed <<
842  " RG_type=" << RGtype << std::endl;
843  }
844 
845  RandomGenerator::initializeRandomGenerators(start_seed, run_type, RGtype);
846 }
847 
848 
849 void
850 random_delay(){
851  // no silly waiting in DEBUG or BOINC builds
852 #ifdef NDEBUG
853 #ifndef BOINC
854  if( !option[ run::nodelay ]() ){
855  if( option[ run::delay ]() > 0 ) {
856  int waittime = option[ run::delay ]();
857  TR << "Delaying start of mini for " << waittime << " seconds due to -delay option" << std::endl;
858  utility::sys_sleep( waittime );
859  } else
860  if( option[ run::random_delay ]() > 0 ) {
861  int waittime = (int) ( (Real)option[ run::random_delay ]() * numeric::random::uniform() );
862  TR << "Delaying of mini for " << waittime << " seconds (maximum = "
863  << option[ run::random_delay ]()
864  << " )" << std::endl
865  << "This prevents extreme IO levels when multiple jobs start simultaneously on" << std::endl
866  << "large computer clusters and is default now. To prevent this add the option -nodelay" << std::endl
867  << "To change the random wait time use -run::random_delay <int> " << std::endl;
868  utility::sys_sleep( waittime );
869  }
870  }
871 #endif
872 #endif
873 }
874 
875 void
876 locate_rosetta_database(){
877  if ( !option[ in::path::database ].user() ) {
878  std::string database_path;
879  char * descr = getenv("ROSETTA3_DB");
880  if ( descr ) {
881  TR << "found database environment variable ROSETTA3_DB: "<< descr << std::endl;
882  database_path = std::string( descr );
883  } else {
884 
885  char path[1024];
886  uint32_t path_size = sizeof( path );
887 
888 #ifdef MAC
889  _NSGetExecutablePath(path, &path_size );
890 #endif
891 #ifdef LINUX
892  readlink( "/proc/self/exe", path, path_size ); // This works on plain Linux, but not FreeBSD or Solaris.
893 #endif
894 #ifdef WIN32
895  TR << "There is some way to automatically figure out the path to rosetta_database with GetModuleFileName in Windows. This is already set up for linux and mac, its probably just one line to change in core/init.cc" << std::endl;
896  // I think its this -- can someone comment out and compile on Windows?
897  // GetModuleFileName( NULL, path, path_size );
898 #endif
899 
900  std::string path_string( path );
901  Size found = path_string.find("rosetta_source/"); //This better be in the path -- now part of the standard rosetta3 directory structure!
902  if ( found != std::string::npos && path_size > 0){
903  std::string rosetta_exe_dir = path_string.substr(0,found);
904  database_path = rosetta_exe_dir + "rosetta_database/";
905  TR << "Looking for database based on location of executable: " << database_path << std::endl;
906  } else {
907  TR << "Could not determine location of executable." << std::endl;
908  }
909 
910  }
911 
912  if ( database_path.size() > 0 ){
913  option[ in::path::database ].value( database_path );
914  } else {
915  TR << "Could not find database. Either specify -database or set environment variable ROSETTA3_DB." << std::endl;
916  }
917 
918  }
919 }
920 
921 void
922 init_profiling(){
923  basic::prof_reset(); //reads option run::profile -- starts clock TOTAL
924 }
925 
926 /// @brief Init basic core systems: options system, random system.
927 void init(int argc, char * argv [])
928 {
929  try{
930  //Initialize MPI
931  init_mpi(argc, argv);
932 
933  //The options system manages command line options
934  init_options(argc, argv);
935 
936  //Tracers control output to std::cout and std::cerr
937  init_tracers();
938 
939  //Initialize the latest and greatest score function parameters
940  init_score_function_corrections();
941 
942  //Choose to output source version control information?
943  init_source_revision();
944 
945  //Setup basic search paths
946  init_paths();
947 
948  //Check for deprecated flags specified by the user and output error messages if necessary
949  check_deprecated_flags();
950 
951  //Describe the application execution command
952  report_application_command(argc, argv);
953 
954  //Initalize random number generators
955  init_random_number_generators();
956 
957  //Choose to randomly delay execution to desyncronize parallel execution
958  random_delay();
959 
960  //Locate rosetta_database
961  locate_rosetta_database();
962 
963 #ifdef BOINC
964  std::cerr << "Initialization complete. " << std::endl;
965 #endif
966 
967  //Profiling measures execution performance
968  init_profiling();
969 
970  // help out user...
971  if ( argc == 1 ) TR << std::endl << "USEFUL TIP: Type -help to get the options for this Rosetta executable." << std::endl << std::endl;
972 
973  }
974  // Catch any Rosetta exceptions
975  catch( utility::excn::EXCN_Msg_Exception &e){
976  // print the error message to standard error
977  e.show( std::cerr );
978  // and rethrow to make sure we quit (or give caller opportunity to clean up or catch)
979  throw;
980  }
981 }
982 
983 
984 /// @brief wrapper for core system Init
985 void init( utility::vector1<std::string> const & args )
986 {
987  // create arguments in argc/argv format
988  int argc = args.size();
989  char **argv = new char*[ argc ];
990  for( int ii = 0; ii < argc; ++ii ) {
991  argv[ ii ] = new char[ args[ii+1].size()+1 ];
992  strncpy( argv[ii], args[ii+1].c_str(), args[ii+1].size() );
993  argv[ ii ][ args[ii+1].size() ] = 0; // ensure null termination
994  }
995 
996  // call init
997  init( argc, argv );
998 
999  // delete freestore
1000  for ( int ii = 0; ii < argc; ++ii ) {
1001  delete[] argv[ ii ];
1002  }
1003  delete[] argv;
1004 }
1005 
1006 } // namespace core
1007 
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