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FastSAXSEnergy.cc
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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 //
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9 
10 /// @file core/scoring/saxs/SAXSEnergy.cc
11 /// @brief FastSAX scoring of Stovgaard et al (BMC Bioinf. 2010)
12 /// @author Frank DiMaio
13 
14 
15 #include <core/scoring/saxs/FastSAXSEnergy.hh>
16 
17 // Unit headers
18 // AUTO-REMOVED #include <core/scoring/Energies.hh>
19 #include <core/scoring/EnergyMap.hh>
20 #include <core/scoring/ScoreType.hh>
21 #include <core/scoring/methods/WholeStructureEnergy.hh>
22 #include <core/scoring/methods/EnergyMethod.hh>
23 
24 // Project headers
25 #include <core/pose/Pose.hh>
26 #include <core/pose/util.hh>
27 #include <core/chemical/AtomType.hh>
28 #include <core/conformation/Residue.hh>
29 #include <core/chemical/AA.hh>
30 
31 #include <core/id/AtomID.hh>
32 // AUTO-REMOVED #include <core/id/NamedAtomID.hh>
33 // AUTO-REMOVED #include <core/io/pdb/pose_io.hh>
34 // AUTO-REMOVED #include <core/io/pdb/file_data.hh>
35 
36 // AUTO-REMOVED #include <numeric/interpolation/spline/Interpolator.hh>
37 // AUTO-REMOVED #include <numeric/interpolation/spline/SplineGenerator.hh>
38 
39 // Options
40 #include <basic/options/option.hh>
41 #include <basic/options/keys/OptionKeys.hh>
42 // AUTO-REMOVED #include <basic/options/keys/in.OptionKeys.gen.hh>
43 #include <basic/options/keys/score.OptionKeys.gen.hh>
44 
45 // AUTO-REMOVED #include <basic/datacache/BasicDataCache.hh>
46 // AUTO-REMOVED #include <core/pose/datacache/CacheableDataType.hh>
47 
48 // AUTO-REMOVED #include <core/chemical/ChemicalManager.hh>
49 
50 // ObjexxFCL headers
51 #include <ObjexxFCL/format.hh>
52 
53 
54 // Utility headers
55 // AUTO-REMOVED #include <basic/prof.hh>
56 // AUTO-REMOVED #include <basic/database/open.hh>
57 #include <basic/Tracer.hh>
58 #include <utility/io/izstream.hh>
59 #include <utility/io/ozstream.hh>
60 
61 // C++
62 #include <iomanip>
63 #include <string>
64 
65 #include <core/scoring/saxs/FastSAXSEnergyCreator.hh>
66 #include <utility/vector1.hh>
67 
68 //Auto Headers
69 //#include <core/import_pose/import_pose.hh>
70 namespace core {
71 namespace scoring {
72 namespace saxs {
73 
74 // tracer
75 static basic::Tracer TR("core.scoring.saxs.FastSAXSEnergy");
76 
77 // ref spectrum
78 core::Real ref_spectrum[][21] = {
79  { 5.792, 8.982, 17.724, 14.211, 14.357, 12.804, 13.373, 13.644, 10.085, 15.369, 0.403, 0.244, 5.651, 10.567, 3.123, 3.229, 8.363, 7.223, 9.634, 8.322, 1.213 },
80  { 5.791, 8.978, 17.724, 14.219, 14.359, 12.811, 13.373, 13.652, 10.087, 15.369, 0.406, 0.254, 5.660, 10.585, 3.131, 3.236, 8.372, 7.233, 9.647, 8.327, 1.215 },
81  { 5.818, 8.969, 17.702, 14.217, 14.345, 12.801, 13.358, 13.651, 10.096, 15.350, 0.389, 0.246, 5.657, 10.610, 3.126, 3.232, 8.366, 7.236, 9.648, 8.321, 1.202 },
82  { 5.892, 8.955, 17.634, 14.185, 14.291, 12.755, 13.297, 13.618, 10.110, 15.291, 0.334, 0.216, 5.620, 10.607, 3.083, 3.189, 8.323, 7.207, 9.617, 8.272, 1.145 },
83  { 6.016, 8.937, 17.519, 14.126, 14.200, 12.673, 13.207, 13.548, 10.120, 15.195, 0.240, 0.152, 5.552, 10.576, 2.999, 3.099, 8.243, 7.145, 9.549, 8.190, 1.051 },
84  { 6.125, 8.920, 17.420, 14.108, 14.131, 12.625, 13.151, 13.500, 10.128, 15.122, 0.189, 0.131, 5.518, 10.559, 2.924, 3.017, 8.182, 7.104, 9.511, 8.135, 0.979 },
85  { 6.265, 8.904, 17.292, 14.080, 14.041, 12.548, 13.084, 13.415, 10.129, 15.033, 0.132, 0.094, 5.486, 10.496, 2.817, 2.907, 8.097, 7.038, 9.439, 8.065, 0.887 },
86  { 6.406, 8.880, 17.171, 14.073, 13.955, 12.483, 13.038, 13.324, 10.131, 14.953, 0.120, 0.087, 5.487, 10.403, 2.701, 2.800, 8.019, 6.971, 9.358, 8.012, 0.800 },
87  { 6.554, 8.854, 17.063, 14.086, 13.895, 12.387, 13.037, 13.232, 10.135, 14.892, 0.106, 0.074, 5.529, 10.300, 2.548, 2.723, 7.958, 6.894, 9.235, 7.962, 0.704 },
88  { 6.729, 8.838, 16.926, 14.083, 13.806, 12.265, 13.066, 13.107, 10.142, 14.846, 0.078, 0.053, 5.571, 10.187, 2.337, 2.622, 7.915, 6.777, 9.040, 7.894, 0.594 },
89  { 6.930, 8.840, 16.690, 14.063, 13.598, 12.181, 13.158, 12.976, 10.132, 14.777, 0.071, 0.048, 5.573, 10.092, 2.060, 2.418, 7.878, 6.616, 8.813, 7.828, 0.504 },
90  { 7.162, 8.884, 16.432, 14.006, 13.304, 12.154, 13.266, 12.792, 10.070, 14.647, 0.078, 0.061, 5.496, 10.029, 1.689, 2.119, 7.718, 6.395, 8.694, 7.732, 0.441 },
91  { 7.368, 9.014, 16.582, 14.221, 13.239, 11.948, 13.055, 12.384, 10.033, 14.781, 0.047, 0.044, 5.647, 9.986, 1.403, 1.848, 7.442, 6.407, 8.621, 7.582, 0.350 },
92  { 7.521, 9.125, 17.042, 14.145, 12.997, 11.711, 12.436, 12.548, 10.198, 14.983, 0.052, 0.047, 5.703, 9.886, 1.464, 1.495, 7.541, 6.483, 8.700, 7.385, 0.331 },
93  { 7.675, 9.331, 17.065, 14.310, 12.708, 11.441, 12.176, 13.209, 10.364, 14.809, 0.053, 0.044, 5.718, 9.876, 1.577, 1.727, 7.575, 6.462, 8.588, 7.070, 0.222 },
94  { 7.867, 9.525, 16.703, 14.020, 12.900, 11.256, 12.302, 13.196, 10.522, 14.427, 0.050, 0.039, 5.842, 9.891, 1.795, 2.000, 7.500, 6.215, 8.193, 6.744, 0.143 },
95  { 8.031, 9.714, 16.793, 13.572, 12.835, 11.010, 12.513, 12.988, 10.798, 14.329, 0.040, 0.037, 5.747, 9.908, 1.962, 2.205, 7.900, 5.974, 7.711, 6.610, 0.128 },
96  { 8.232, 9.836, 16.536, 13.610, 12.656, 10.851, 12.999, 12.934, 11.101, 13.971, 0.036, 0.039, 5.603, 9.976, 1.850, 2.394, 7.607, 5.667, 7.668, 6.567, 0.103 },
97  { 8.458, 9.880, 16.213, 13.648, 12.582, 10.745, 13.317, 12.937, 11.405, 13.662, 0.051, 0.057, 5.566, 9.742, 1.553, 2.364, 7.104, 5.533, 7.825, 6.394, 0.099 },
98  { 8.734, 10.022, 15.934, 13.379, 12.391, 10.406, 13.383, 12.525, 11.473, 13.808, 0.043, 0.042, 5.584, 9.379, 1.177, 2.243, 6.811, 5.734, 8.353, 6.235, 0.066 },
99  { 9.066, 10.353, 15.636, 12.895, 12.286, 9.744, 13.116, 12.007, 11.465, 13.986, 0.047, 0.045, 5.262, 8.802, 0.990, 2.082, 6.546, 5.920, 8.058, 6.417, 0.068 },
100  { 9.416, 10.743, 15.348, 12.423, 12.120, 9.064, 12.806, 11.822, 11.492, 14.110, 0.054, 0.051, 4.776, 7.966, 1.081, 1.919, 6.260, 5.898, 7.043, 6.631, 0.095 },
101  { 9.740, 11.025, 15.208, 12.127, 11.893, 8.743, 12.620, 11.920, 11.494, 14.388, 0.056, 0.048, 4.518, 7.051, 1.319, 1.666, 6.008, 5.551, 6.200, 6.450, 0.133 },
102  { 10.019, 11.209, 15.235, 11.930, 11.832, 8.685, 12.571, 12.022, 11.462, 14.568, 0.077, 0.055, 4.506, 6.505, 1.700, 1.350, 5.848, 5.073, 6.101, 5.948, 0.200 },
103  { 10.265, 11.408, 15.404, 11.818, 11.861, 8.661, 12.431, 12.022, 11.400, 14.581, 0.072, 0.046, 4.554, 6.416, 2.073, 1.091, 5.742, 4.728, 6.662, 5.521, 0.190 },
104  { 10.485, 11.565, 15.722, 11.730, 11.910, 8.579, 12.132, 11.886, 11.337, 14.424, 0.096, 0.055, 4.604, 6.688, 2.171, 1.090, 5.672, 4.556, 7.372, 5.548, 0.210 },
105  { 10.717, 11.641, 16.156, 11.546, 11.930, 8.450, 11.726, 11.482, 11.297, 14.103, 0.086, 0.048, 4.731, 7.251, 2.032, 1.237, 5.565, 4.502, 7.849, 6.028, 0.180 },
106  { 10.965, 11.659, 16.681, 11.287, 11.925, 8.274, 11.276, 10.877, 11.285, 13.630, 0.124, 0.069, 5.025, 7.866, 1.871, 1.410, 5.407, 4.452, 7.529, 6.567, 0.235 },
107  { 11.211, 11.721, 17.097, 11.020, 11.896, 8.121, 10.780, 10.324, 11.297, 13.251, 0.114, 0.062, 5.326, 8.308, 1.835, 1.449, 5.186, 4.363, 6.676, 6.815, 0.208 },
108  { 11.442, 11.837, 17.230, 10.840, 11.780, 7.931, 10.174, 10.110, 11.402, 13.243, 0.139, 0.075, 5.369, 8.239, 1.869, 1.408, 4.887, 4.181, 5.881, 6.696, 0.233 },
109  { 11.658, 12.062, 17.045, 10.710, 11.493, 7.770, 9.567, 10.189, 11.532, 13.641, 0.111, 0.060, 5.097, 7.755, 1.870, 1.191, 4.563, 3.940, 5.409, 6.352, 0.187 },
110  { 11.861, 12.360, 16.612, 10.562, 11.068, 7.615, 9.010, 10.361, 11.626, 14.109, 0.111, 0.060, 4.733, 7.021, 1.779, 0.909, 4.289, 3.648, 5.222, 5.916, 0.183 },
111  { 12.051, 12.657, 15.996, 10.303, 10.627, 7.439, 8.529, 10.385, 11.699, 14.449, 0.149, 0.081, 4.470, 6.165, 1.638, 0.803, 4.074, 3.374, 5.261, 5.481, 0.244 },
112  { 12.219, 12.949, 15.265, 9.915, 10.239, 7.290, 8.077, 10.253, 11.756, 14.726, 0.176, 0.098, 4.380, 5.443, 1.523, 0.770, 4.006, 3.186, 5.465, 5.144, 0.304 },
113  { 12.354, 13.224, 14.564, 9.455, 9.898, 7.272, 7.694, 10.036, 11.861, 14.941, 0.116, 0.066, 4.346, 5.142, 1.346, 0.571, 4.160, 3.070, 5.725, 4.947, 0.233 },
114  { 12.476, 13.460, 13.725, 9.040, 9.465, 7.105, 7.313, 9.869, 12.028, 14.996, 0.156, 0.089, 4.237, 5.061, 1.320, 0.677, 4.377, 2.922, 5.787, 4.842, 0.339 },
115  { 12.582, 13.711, 12.865, 8.682, 8.934, 7.156, 7.221, 9.791, 12.219, 14.957, 0.134, 0.080, 3.981, 5.471, 1.272, 0.625, 4.659, 2.657, 5.842, 4.872, 0.363 },
116  { 12.681, 13.964, 12.054, 8.345, 8.394, 7.229, 7.345, 9.891, 12.445, 14.875, 0.131, 0.087, 3.613, 6.043, 1.314, 0.627, 4.792, 2.242, 6.013, 4.944, 0.457 },
117  { 12.786, 14.185, 11.294, 7.936, 7.908, 7.181, 7.534, 9.904, 12.685, 14.705, 0.217, 0.156, 3.302, 6.365, 1.534, 0.869, 4.650, 1.868, 6.394, 4.962, 0.681 },
118  { 12.878, 14.354, 10.869, 7.458, 7.686, 7.365, 8.019, 9.906, 12.952, 14.434, 0.175, 0.136, 2.956, 7.040, 1.550, 0.754, 4.384, 1.469, 6.953, 4.951, 0.566 },
119  { 12.962, 14.469, 10.517, 6.826, 7.602, 7.460, 8.613, 9.656, 13.214, 13.746, 0.211, 0.173, 2.580, 7.290, 1.709, 0.900, 4.069, 1.393, 7.417, 4.859, 0.529 },
120  { 13.032, 14.559, 10.238, 6.111, 7.583, 7.624, 9.400, 9.307, 13.408, 12.603, 0.239, 0.204, 2.096, 7.442, 1.801, 1.117, 3.838, 1.547, 7.585, 4.843, 0.487 },
121  { 13.087, 14.687, 9.800, 5.377, 7.537, 7.690, 10.363, 8.688, 13.464, 11.340, 0.319, 0.277, 1.582, 7.438, 1.911, 1.435, 3.774, 1.995, 7.613, 4.834, 0.533 },
122  { 13.130, 14.857, 9.316, 4.699, 7.438, 7.693, 11.288, 7.846, 13.452, 10.506, 0.404, 0.335, 1.158, 7.480, 1.995, 1.620, 3.819, 2.616, 7.731, 4.771, 0.615 },
123  { 13.169, 15.097, 8.983, 4.290, 7.216, 7.658, 11.924, 6.964, 13.396, 10.236, 0.488, 0.349, 0.921, 7.532, 2.091, 1.560, 3.855, 3.374, 8.062, 4.576, 0.671 },
124  { 13.228, 15.367, 9.028, 4.275, 6.741, 7.692, 12.075, 6.399, 13.335, 10.330, 0.531, 0.330, 0.847, 7.680, 2.255, 1.310, 3.851, 4.233, 8.504, 4.366, 0.682 },
125  { 13.310, 15.635, 9.941, 4.798, 5.988, 7.822, 11.833, 6.411, 13.317, 10.488, 0.508, 0.314, 0.951, 7.807, 2.506, 1.045, 3.812, 5.100, 8.882, 4.270, 0.639 },
126  { 13.407, 15.865, 11.468, 5.689, 5.080, 7.936, 11.072, 6.904, 13.424, 10.146, 0.700, 0.526, 1.604, 7.913, 2.848, 1.177, 3.652, 5.724, 8.933, 4.524, 0.828 },
127  { 13.409, 16.023, 14.272, 7.015, 4.739, 8.128, 10.843, 7.788, 13.674, 9.670, 0.475, 0.469, 1.307, 8.752, 2.839, 0.920, 3.701, 6.086, 9.007, 4.934, 0.649 },
128  { 13.428, 16.120, 15.414, 7.848, 4.726, 8.211, 10.317, 8.329, 13.874, 8.681, 0.663, 0.759, 1.538, 8.946, 2.836, 1.119, 3.592, 6.113, 9.573, 5.830, 0.853 },
129  { 13.429, 16.122, 16.070, 8.492, 5.115, 8.209, 9.842, 8.817, 14.105, 7.768, 0.832, 1.064, 2.204, 8.227, 2.715, 1.187, 3.629, 6.077, 10.749, 7.011, 0.983 }
130 };
131 
132 
133 ScoreTypes FastSAXSEnergyCreator::score_types_for_method() const {
134  ScoreTypes sts;
135  sts.push_back( fastsaxs );
136  return sts;
137 }
138 
139 methods::EnergyMethodOP FastSAXSEnergyCreator::create_energy_method( methods::EnergyMethodOptions const &) const {
140  return new FastSAXSEnergy();
141 }
142 
143 FastSAXSEnergy::FastSAXSEnergy() :
144  parent( new FastSAXSEnergyCreator ) {
145  chi2=0;
146  dchi2_dca.clear();
147  dchi2_dsc.clear();
148 }
149 
150 /// clone
151 methods::EnergyMethodOP FastSAXSEnergy::clone() const {
152  return new FastSAXSEnergy( *this );
153 }
154 
155 void FastSAXSEnergy::setup_for_scoring( pose::Pose & pose, ScoreFunction const & ) const {
156  using namespace core::chemical;
157 
158  // 1 compute backbone and sidechain mass centers
159  core::Size nres = pose.total_residue();
160  utility::vector1< numeric::xyzVector< core::Real> > bb_coms( nres, numeric::xyzVector< core::Real>(0,0,0) );
161  utility::vector1< numeric::xyzVector< core::Real> > sc_coms( nres, numeric::xyzVector< core::Real>(0,0,0) );
162  for (int i=1; i<=(int)nres; ++i) {
163  core::conformation::Residue const &rsd_i = pose.residue(i);
164  core::Size nbb=0, nsc=0;
165  for (int j=1; j<=(int)rsd_i.nheavyatoms(); ++j) {
166  if (rsd_i.aa() == aa_pro && j==(int)rsd_i.nheavyatoms()) // PRO NV (is_virtual() call doesn't seem to work here)
167  continue;
168  if (j<=(int)rsd_i.last_backbone_atom()+1) { // +1 includes CB in bb calcs
169  bb_coms[i] += rsd_i.atom(j).xyz(); nbb++;
170  } else {
171  sc_coms[i] += rsd_i.atom(j).xyz(); nsc++;
172  }
173  }
174  bb_coms[i] /= nbb;
175  if (nsc != 0)
176  sc_coms[i] /= nsc;
177  }
178 
179  // 1A load the input spectrum
180  core::Size NQ;
181  utility::vector1< core::Real >::iterator q, i_obs, i_sig;
182  load_fastsax_spectrum( NQ, q, i_obs, i_sig);
183 
184  // 1B load formfactors
185  utility::vector1< utility::vector1< core::Real > >::iterator formfactors;
186  load_form_factors( NQ, q, formfactors );
187 
188  // 2 loop over all pseudo-center pairs + compute debye formula
189  utility::vector1< core::Real > i_calc(NQ, 0.0);
190 
191  for (int i=1; i<=(int)nres; ++i) {
192  core::chemical::AA aa_i = pose.residue(i).aa();
193 
194  if (aa2idx(aa_i) == 0) continue; // no scattering defined
195 
196  int ff_i = 1; // generic backbone is in idx 1
197  if (aa_i == aa_gly) // gly-specialized
198  ff_i = aa2idx(aa_gly);
199  else if (aa_i == aa_ala) // ala-specialized
200  ff_i = aa2idx(aa_ala);
201 
202  for (int k=1; k<=(int)NQ; ++k)
203  i_calc[k] += formfactors[ ff_i-1 ][k] * formfactors[ ff_i-1 ][k];
204 
205  // bb->bb
206  for (int j=i+1; j<=(int)nres; ++j) {
207  core::chemical::AA aa_j = pose.residue(j).aa();
208 
209  int ff_j = 1; // generic backbone is in idx 1
210  if (aa_j == aa_gly) // gly-specialized
211  ff_j = aa2idx(aa_gly);
212  else if (aa_j == aa_ala) // ala-specialized
213  ff_j = aa2idx(aa_ala);
214  if (ff_j == 0) continue; // no scattering defined
215 
216  // dist i->j
217  core::Real r = (bb_coms[i]-bb_coms[j]).length();
218  for (int k=1; k<=(int)NQ; ++k) {
219  core::Real rq = r*q[k-1];
220  i_calc[k] += 2 * std::sin(rq) / rq * formfactors[ ff_i-1 ][k] * formfactors[ ff_j-1 ][k];
221  }
222  }
223 
224  // bb->sc
225  for (int j=1; j<=(int)nres; ++j) {
226  core::chemical::AA aa_j = pose.residue(j).aa();
227  if (aa_j == aa_gly || aa_j == aa_ala) continue; // no SC scatterers for these
228  int ff_j = aa2idx( aa_j );
229  if (ff_j == 0) continue; // no scattering defined
230 
231  core::Real r = (bb_coms[i]-sc_coms[j]).length();
232 
233  for (int k=1; k<=(int)NQ; ++k) {
234  core::Real rq = r*q[k-1];
235  i_calc[k] += 2 * std::sin(rq) / rq * formfactors[ ff_i-1 ][k] * formfactors[ ff_j-1 ][k];
236  }
237  }
238 
239  // sc->sc
240  if (aa_i == aa_gly || aa_i == aa_ala) continue;
241  ff_i = aa2idx( aa_i );
242 
243  for (int k=1; k<=(int)NQ; ++k)
244  i_calc[k] += formfactors[ ff_i-1 ][k] * formfactors[ ff_i-1 ][k];
245 
246  for (int j=i+1; j<=(int)nres; ++j) {
247  core::chemical::AA aa_j = pose.residue(j).aa();
248  if (aa_j == aa_gly || aa_j == aa_ala) continue; // no SC scatterers for these
249  int ff_j = aa2idx( aa_j );
250  if (ff_j == 0) continue; // no scattering defined
251 
252  core::Real r = (sc_coms[i]-sc_coms[j]).length();
253 
254  for (int k=1; k<=(int)NQ; ++k) {
255  core::Real rq = r*q[k-1];
256  i_calc[k] += 2 * std::sin(rq) / rq * formfactors[ ff_i-1 ][k] * formfactors[ ff_j-1 ][k];
257  }
258  }
259  }
260 
261  // 3 chi-squared
262  // fit c
263  core::Real c_num = 0, c_denom = 0;
264  for (int k=0; k<=(int)NQ-1; ++k) {
265  c_num += i_calc[k+1]*i_obs[k] / (i_sig[k]*i_sig[k]);
266  c_denom += i_calc[k+1]*i_calc[k+1]/ (i_sig[k]*i_sig[k]);
267  }
268  c = c_num / c_denom;
269 
270  // chi^2
271  chi2=0.0;
272  r_chi2.resize( NQ );
273  for (int k=0; k<=(int)NQ-1; ++k) {
274  core::Real temp = (i_obs[k]-c*i_calc[k+1]) / i_sig[k];
275  chi2 += temp*temp;
276 
277  // store chi residuals for derivative computations
278  r_chi2[k+1] = temp/i_sig[k];
279  }
280  chi2 /= (NQ-1);
281 
282  // shamelessly stolen from RDC code
283  if ( basic::options::option[ basic::options::OptionKeys::score::saxs::print_i_calc ].user() ) {
284  std::string filename( basic::options::option[ basic::options::OptionKeys::score::saxs::print_i_calc ]() );
285  utility::io::ozstream out;
286 
287  out.open_append( filename );
288  Size const width( 12 );
289  using namespace core::pose::datacache;
290  using namespace ObjexxFCL::fmt;
291 
292  std::string tag( core::pose::tag_from_pose(pose) );
293  out << A( 6, "TAG ") << tag << std::endl;
294  for (int k=0; k<=(int)NQ-1; ++k) {
295  out << F( width, 6, q[k]) << F( width, 6, c*i_calc[k+1]) << std::endl;
296  }
297  out << "//" <<std::endl;
298  out.close();
299  }
300  //for (int k=0; k<=NQ-1; ++k) {
301  // TR.Debug << c*i_calc[k+1] << std::endl;
302  //}
303  TR.Debug << " c=" << c << ", chi2=" << chi2 << std::endl;
304 }
305 
306 void FastSAXSEnergy::finalize_total_energy(pose::Pose & /*pose*/, ScoreFunction const &, EnergyMap & emap) const {
307  // all the work is done in setup for scoring
308  // just return results here
309  emap[ fastsaxs ] += chi2; // should we scale by #reses?
310 }
311 
312 void FastSAXSEnergy::setup_for_derivatives( pose::Pose & pose, ScoreFunction const & ) const {
313  using namespace core::chemical;
314 
315  // 1 compute backbone and sidechain mass centers'
316  // these (like chi2 residuals) could be saved from 'setup_for_scoring' ... is it worth the overhead?
317  core::Size nres = pose.total_residue();
318  utility::vector1< numeric::xyzVector< core::Real> > bb_coms( nres, numeric::xyzVector< core::Real>(0,0,0) );
319  utility::vector1< numeric::xyzVector< core::Real> > sc_coms( nres, numeric::xyzVector< core::Real>(0,0,0) );
320  for (int i=1; i<=(int)nres; ++i) {
321  core::conformation::Residue const &rsd_i = pose.residue(i);
322  core::Size nbb=0, nsc=0;
323  for (int j=1; j<=(int)rsd_i.nheavyatoms(); ++j) {
324  if (rsd_i.aa() == aa_pro && j==(int)rsd_i.nheavyatoms())
325  continue; // pro NV: check for 'atom_type().is_virtual()' doesn't work here?
326  if (j<=(int)rsd_i.last_backbone_atom()+1) { // +1 includes CB in bb calcs
327  bb_coms[i] += rsd_i.atom(j).xyz(); nbb++;
328  } else {
329  sc_coms[i] += rsd_i.atom(j).xyz(); nsc++;
330  }
331  }
332  bb_coms[i] /= nbb;
333  if (nsc != 0)
334  sc_coms[i] /= nsc;
335  }
336 
337  // 1A load the input spectrum
338  core::Size NQ;
339  utility::vector1< core::Real >::iterator q, i_obs, i_sig;
340  load_fastsax_spectrum( NQ, q, i_obs, i_sig);
341 
342  // 1B load formfactors
343  utility::vector1< utility::vector1< core::Real > >::iterator formfactors;
344  load_form_factors( NQ, q, formfactors );
345 
346  // 2 loop over all pseudo-center pairs + compute derivatives
347  // sum into dchi2_dca_s, dchi2_dsc_s
348  utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > dchi2_dca_s, dchi2_dsc_s;
349  dchi2_dca_s.resize( nres ); dchi2_dsc_s.resize( nres );
350  for (int i=1; i<=(int)nres; ++i) {
351  dchi2_dca_s[i].resize( NQ );
352  dchi2_dsc_s[i].resize( NQ );
353  for (int k=1; k<=(int)NQ; ++k) {
354  dchi2_dca_s[i][k] = numeric::xyzVector< core::Real >(0,0,0);
355  dchi2_dsc_s[i][k] = numeric::xyzVector< core::Real >(0,0,0);
356  }
357  }
358 
359  for (int i=1; i<=(int)nres; ++i) {
360  core::chemical::AA aa_i = pose.residue(i).aa();
361 
362  if (aa2idx(aa_i) == 0) continue; // no scattering defined
363 
364  int ff_i = 1; // generic backbone is in idx 1
365  if (aa_i == aa_gly) ff_i = aa2idx(aa_gly);
366  else if (aa_i == aa_ala) ff_i = aa2idx(aa_ala);
367 
368  // bb->bb
369  for (int j=i+1; j<=(int)nres; ++j) {
370  core::chemical::AA aa_j = pose.residue(j).aa();
371 
372  int ff_j = 1; // generic backbone is in idx 1
373  if (aa_j == aa_gly) ff_j = aa2idx(aa_gly);
374  else if (aa_j == aa_ala) ff_j = aa2idx(aa_ala);
375  if (ff_j == 0) continue; // no scattering defined
376 
377  // dist i->j
378  core::Real r = (bb_coms[i]-bb_coms[j]).length();
379  numeric::xyzVector< core::Real > rdir = (bb_coms[i]-bb_coms[j])/(r*r);
380  for (int k=1; k<=(int)NQ; ++k) {
381  core::Real rq = r*q[k-1];
382  core::Real dumm = (cos(rq) - sin(rq)/rq) * formfactors[ ff_i-1 ][k] * formfactors[ ff_j-1 ][k];
383  dchi2_dca_s[i][k] -= dumm*rdir;
384  dchi2_dca_s[j][k] += dumm*rdir;
385  }
386  }
387 
388  // bb->sc
389  for (int j=1; j<=(int)nres; ++j) {
390  core::chemical::AA aa_j = pose.residue(j).aa();
391  if (aa_j == aa_gly || aa_j == aa_ala) continue; // no SC scatterers for these
392  int ff_j = aa2idx( aa_j );
393  if (ff_j == 0) continue; // no scattering defined
394 
395  core::Real r = (bb_coms[i]-sc_coms[j]).length();
396  numeric::xyzVector< core::Real > rdir = (bb_coms[i]-sc_coms[j])/(r*r);
397  for (int k=1; k<=(int)NQ; ++k) {
398  core::Real rq = r*q[k-1];
399  core::Real dumm = (cos(rq) - sin(rq)/rq) * formfactors[ ff_i-1 ][k] * formfactors[ ff_j-1 ][k];
400  dchi2_dca_s[i][k] -= dumm*rdir;
401  dchi2_dsc_s[j][k] += dumm*rdir;
402  }
403  }
404 
405  // sc->sc
406  if (aa_i == aa_gly || aa_i == aa_ala) continue;
407  ff_i = aa2idx( aa_i );
408 
409  for (int j=i+1; j<=(int)nres; ++j) {
410  core::chemical::AA aa_j = pose.residue(j).aa();
411  if (aa_j == aa_gly || aa_j == aa_ala) continue; // no SC scatterers for these
412  int ff_j = aa2idx( aa_j );
413  if (ff_j == 0) continue; // no scattering defined
414 
415  core::Real r = (sc_coms[i]-sc_coms[j]).length();
416  numeric::xyzVector< core::Real > rdir = (sc_coms[i]-sc_coms[j])/(r*r);
417  for (int k=1; k<=(int)NQ; ++k) {
418  core::Real rq = r*q[k-1];
419  core::Real dumm = (cos(rq) - sin(rq)/rq) * formfactors[ ff_i-1 ][k] * formfactors[ ff_j-1 ][k];
420  dchi2_dsc_s[i][k] -= dumm*rdir;
421  dchi2_dsc_s[j][k] += dumm*rdir;
422  }
423  }
424  }
425 
426  // 3 sum
427  dchi2_dca.resize( nres );
428  dchi2_dsc.resize( nres );
429  for (int i=1; i<=(int)nres; ++i) {
430  dchi2_dca[i] = 0.0;
431  dchi2_dsc[i] = 0.0;
432  for (int k=1; k<=(int)NQ; ++k) {
433  dchi2_dca[i] += r_chi2[k]*dchi2_dca_s[i][k];
434  dchi2_dsc[i] += r_chi2[k]*dchi2_dsc_s[i][k];
435  }
436  dchi2_dca[i] *= 4*c/(NQ-1);
437  dchi2_dsc[i] *= 4*c/(NQ-1);
438  }
439 }
440 
441 void FastSAXSEnergy::eval_atom_derivative(
442  id::AtomID const & id,
443  pose::Pose const & pose,
444  kinematics::DomainMap const &, // domain_map,
445  ScoreFunction const & ,
446  EnergyMap const & weights,
447  Vector & F1,
448  Vector & F2
449 ) const {
450  int resid = id.rsd();
451  int atmid = id.atomno();
452  core::conformation::Residue const &rsd_i = pose.residue(resid);
453  numeric::xyzVector<core::Real> X = pose.xyz(id);
454 
455  // if (hydrogen) return
456  if ( rsd_i.aa() != core::chemical::aa_vrt && !rsd_i.atom_type(atmid).is_heavyatom() ) return;
457 
458  // if PRO NV return
459  if (rsd_i.aa() == core::chemical::aa_pro && atmid==(int)rsd_i.nheavyatoms())
460  return; // pro NV: check for 'atom_type().is_virtual()' doesn't work here?
461 
462  // look up derivative for this atom's glob, divide by # of atoms in the glob
463  numeric::xyzVector< core::Real > dCCdx;
464  core::Size natoms_glob;
465  if (atmid <= (int)rsd_i.last_backbone_atom() ) {
466  natoms_glob = rsd_i.last_backbone_atom();
467  dCCdx = dchi2_dca[resid] / natoms_glob;
468  } else {
469  if (rsd_i.aa() != core::chemical::aa_pro)
470  natoms_glob = rsd_i.nheavyatoms() - rsd_i.last_backbone_atom();
471  else
472  natoms_glob = rsd_i.nheavyatoms() - rsd_i.last_backbone_atom() - 1;
473  dCCdx = dchi2_dsc[resid] / natoms_glob;
474  }
475 
476  // ???? numeric
477 
478  numeric::xyzVector<core::Real> atom_x = X;
479  numeric::xyzVector<core::Real> const f2( dCCdx );
480  numeric::xyzVector<core::Real> atom_y = -f2 + atom_x;
481  Vector const f1( atom_x.cross( atom_y ) );
482 
483  F1 += weights[ fastsaxs ] * f1;
484  F2 += weights[ fastsaxs ] * f2;
485 }
486 
487 // remaps core::chem::AA enums to indices in the formfactor table
488 // returns 0 if mapping not found (nonstd AA, etc.)
489 core::Size aa2idx( core::chemical::AA aa ) {
490  using namespace core::chemical;
491 
492  static std::map< core::chemical::AA, int > ff_mapping;
493 
494  // key: BB ALA* ARG ASN ASP CYS GLN GLU GLY* HIS ILE LEU LYS MET PHE PRO SER THR TRP TYR VAL
495  if (ff_mapping.size() == 0) {
496  ff_mapping[ aa_ala ] = 2;
497  ff_mapping[ aa_arg ] = 3;
498  ff_mapping[ aa_asn ] = 4;
499  ff_mapping[ aa_asp ] = 5;
500  ff_mapping[ aa_cys ] = 6;
501  ff_mapping[ aa_gln ] = 7;
502  ff_mapping[ aa_glu ] = 8;
503  ff_mapping[ aa_gly ] = 9;
504  ff_mapping[ aa_his ] = 10;
505  ff_mapping[ aa_ile ] = 11;
506 
507  ff_mapping[ aa_leu ] = 12;
508  ff_mapping[ aa_lys ] = 13;
509  ff_mapping[ aa_met ] = 14;
510  ff_mapping[ aa_phe ] = 15;
511  ff_mapping[ aa_pro ] = 16;
512  ff_mapping[ aa_ser ] = 17;
513  ff_mapping[ aa_thr ] = 18;
514  ff_mapping[ aa_trp ] = 19;
515  ff_mapping[ aa_tyr ] = 20;
516  ff_mapping[ aa_val ] = 21;
517  }
518 
519  if (ff_mapping.find( aa ) != ff_mapping.end())
520  return ff_mapping[ aa ];
521  else
522  return 0;
523 }
524 
525 
526 // load saxs spectrum from file
527 // only hit disk the first time this is called
528 // file name given by -score:saxs:ref_spectrum <file>
529 void load_fastsax_spectrum(
530  core::Size &nq,
531  utility::vector1< core::Real >::iterator &q,
532  utility::vector1< core::Real >::iterator &i_obs,
533  utility::vector1< core::Real >::iterator &i_sig) {
534  static utility::vector1< core::Real > saved_q, saved_i_obs, saved_i_sig;
535 
536  if (saved_q.size() == 0) {
537  // load map from disk
538  TR << "Loading SAXS spectrum" << std::endl;
539  if (!basic::options::option[ basic::options::OptionKeys::score::saxs::ref_spectrum ].user()) {
540  TR.Warning << "[ ERROR ] No SAXS spectrum specified!" << std::endl;
541  exit(1);
542  } else {
543  std::string file_name = basic::options::option[ basic::options::OptionKeys::score::saxs::ref_spectrum ]();
544  utility::io::izstream input(file_name.c_str());
545  std::string line;
546 
547  while( getline( input, line ) ) {
548  if ( line.substr(0,1) == "#" ) continue;
549  if ( line.length() == 0 ) continue;
550  std::istringstream line_stream( line );
551  core::Real q_k,i_k,sig_k;
552  line_stream >> q_k >> i_k >> sig_k;
553  TR.Debug << " read " << q_k << ": (" << i_k << " , " << sig_k << ")" << std::endl;
554 
555  saved_q.push_back( q_k );
556  saved_i_obs.push_back( i_k );
557  saved_i_sig.push_back( sig_k );
558  }
559  }
560  }
561 
562  q = saved_q.begin();
563  i_obs = saved_i_obs.begin();
564  i_sig = saved_i_sig.begin();
565  nq = saved_q.size();
566 }
567 
568 // load per-resiude form factors (resampled onto the same grid as the input spectrum)
569 // cache resampled values so resampling only happens once for each q_in
570 // use linear resampling because I'm lazy (also matlab doesn't show a diffence between spline interp until the 4th sig digit)
571 void load_form_factors(
572  core::Size nq,
573  utility::vector1< core::Real >::iterator &q_in,
574  utility::vector1< utility::vector1< core::Real > >::iterator &spectrum) {
575  static utility::vector1< utility::vector1< core::Real > > saved_spectrum;
576 
577  if (saved_spectrum.size() == 0 || saved_spectrum[1].size() != nq) {
578  saved_spectrum.resize( 21 );
579  for ( int j=1; j<=21; ++j )
580  saved_spectrum[j].resize( nq );
581 
582  for (int i=1; i<=(int)nq; ++i) {
583 
584  int q_bucket = (int)std::floor(q_in[i-1]/0.015);
585  if (q_bucket >= 50) {
586  TR << "[ WARNING ] Input data extends to higher resolution than stored structure factors (1.33A)" << std::endl;
587  TR << " Results may be inaccurate!" << std::endl;
588 
589  for ( int j=1; j<=21; ++j ) {
590  saved_spectrum[j][i] = ref_spectrum[50][j-1];
591  }
592  } else {
593  core::Real wt = (q_in[i-1] - (q_bucket)*0.015)/0.015;
594 
595  for (int j=1; j<=21; ++j ) {
596  saved_spectrum[j][i] = (1-wt)*ref_spectrum[q_bucket][j-1] + wt*ref_spectrum[q_bucket+1][j-1];
597  }
598  }
599  }
600  }
601 
602  spectrum = saved_spectrum.begin();
603 }
604 core::Size
605 FastSAXSEnergy::version() const
606 {
607  return 1; // Initial versioning
608 }
609 
610 
611 } // saxs
612 } // scoring
613 } // core
614 
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