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EnvSmoothEnergy.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 //
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 core/scoring/methods/EnvSmoothEnergy.cc
11 /// @brief Statistically derived rotamer pair potential class implementation
12 /// @author Phil Bradley
13 /// @author Andrew Leaver-Fay
14 
15 
16 // Unit headers
17 #include <core/scoring/methods/EnvSmoothEnergy.hh>
18 #include <core/scoring/methods/EnvSmoothEnergyCreator.hh>
19 
20 // Package headers
21 #include <core/chemical/AA.hh>
22 #include <core/chemical/VariantType.hh>
23 #include <core/conformation/Atom.hh>
24 // AUTO-REMOVED #include <core/scoring/EnvPairPotential.hh>
25 //#include <core/scoring/CachedData.hh>
26 //#include <core/scoring/ScoringManager.hh>
27 #include <core/scoring/Energies.hh>
28 // AUTO-REMOVED #include <core/scoring/EnergyGraph.hh>
29 #include <core/scoring/TwelveANeighborGraph.hh>
30 #include <core/scoring/ContextGraphTypes.hh>
31 
32 
33 // Project headers
34 #include <core/pose/Pose.hh>
35 #include <core/conformation/Residue.hh>
36 
37 #include <core/id/AtomID.hh>
38 #include <utility/vector1.hh>
39 
40 
41 
42 // Utility headers
43 
44 
45 
46 // C++
47 
48 
49 namespace core {
50 namespace scoring {
51 namespace methods {
52 
53 
54 /// @details This must return a fresh instance of the EnvSmoothEnergy class,
55 /// never an instance already in use
56 methods::EnergyMethodOP
57 EnvSmoothEnergyCreator::create_energy_method(
58  methods::EnergyMethodOptions const &
59 ) const {
60  return new EnvSmoothEnergy;
61 }
62 
63 ScoreTypes
64 EnvSmoothEnergyCreator::score_types_for_method() const {
65  ScoreTypes sts;
66  sts.push_back( envsmooth );
67  return sts;
68 }
69 
70 
71 //const core::Real start_sig = 9.9999;
72 //const core::Real end_sig = 10.001;
73 
74 Distance const start_sig = 9.8;
75 Distance const end_sig = 10.2;
76 
77 DistanceSquared const start_sig2 = start_sig*start_sig;
78 DistanceSquared const end_sig2 = end_sig*end_sig;
79 
80 
81 // This is temporary - this data will soon be read from a file in minirosetta_database
82 ///
83 ///core::Real envdata[20][40] = { { 0.215, 0.211, 0.199, 0.184, 0.168, 0.155, 0.152, 0.152, 0.156, 0.154, 0.161, 0.187, 0.222, 0.264, 0.290, 0.306, 0.290, 0.254, 0.191, 0.117, 0.037, -0.032, -0.098, -0.162, -0.241, -0.318, -0.393, -0.467, -0.547, -0.634, -0.721, -0.807, -0.894, -0.989, -1.089, -1.179, -1.241, -1.273, -1.282, -1.284 },
84 ///{1.947, 1.943, 1.936, 1.933, 1.932, 1.937, 1.934, 1.916, 1.842, 1.699, 1.509, 1.313, 1.124, 0.940, 0.740, 0.561, 0.369, 0.196, 0.008, -0.147, -0.277, -0.371, -0.448, -0.510, -0.567, -0.606, -0.644, -0.669, -0.700, -0.721, -0.734, -0.744, -0.758, -0.810, -0.867, -0.933, -0.976, -1.027, -1.064, -1.088 },
85 ///{-0.935, -0.923, -0.892, -0.847, -0.798, -0.752, -0.713, -0.668, -0.620, -0.564, -0.514, -0.466, -0.416, -0.351, -0.272, -0.172, -0.068, 0.043, 0.147, 0.264, 0.391, 0.526, 0.643, 0.741, 0.816, 0.863, 0.884, 0.886, 0.888, 0.900, 0.925, 0.951, 0.972, 0.983, 0.991, 0.997, 1.006, 1.013, 1.016, 1.016 },
86 ///{-0.286, -0.309, -0.346, -0.398, -0.442, -0.506, -0.562, -0.624, -0.652, -0.651, -0.620, -0.582, -0.534, -0.469, -0.377, -0.262, -0.129, 0.021, 0.190, 0.372, 0.561, 0.736, 0.907, 1.060, 1.204, 1.310, 1.389, 1.440, 1.473, 1.492, 1.509, 1.540, 1.573, 1.602, 1.615, 1.621, 1.619, 1.618, 1.616, 1.617 },
87 ///{ 0.760, 0.762, 0.772, 0.798, 0.863, 0.966, 1.085, 1.168, 1.192, 1.167, 1.104, 1.016, 0.896, 0.744, 0.566, 0.361, 0.166, -0.008, -0.149, -0.271, -0.371, -0.441, -0.476, -0.484, -0.470, -0.442, -0.400, -0.349, -0.277, -0.158, 0.009, 0.199, 0.353, 0.450, 0.497, 0.519, 0.533, 0.541, 0.548, 0.551 },
88 ///{-0.041, -0.050, -0.056, -0.055, -0.037, -0.028, -0.029, -0.051, -0.076, -0.096, -0.104, -0.106, -0.098, -0.078, -0.040, 0.007, 0.049, 0.080, 0.099, 0.120, 0.134, 0.150, 0.153, 0.150, 0.126, 0.072, -0.006, -0.104, -0.214, -0.341, -0.464, -0.579, -0.678, -0.788, -0.888, -1.000, -1.133, -1.311, -1.489, -1.579 },
89 ///{ 0.020, 0.018, 0.016, 0.013, 0.018, 0.044, 0.088, 0.140, 0.172, 0.181, 0.166, 0.137, 0.092, 0.033, -0.036, -0.104, -0.151, -0.179, -0.177, -0.159, -0.116, -0.062, -0.007, 0.040, 0.087, 0.128, 0.172, 0.209, 0.242, 0.263, 0.272, 0.277, 0.279, 0.282, 0.280, 0.275, 0.270, 0.271, 0.278, 0.284 },
90 ///{ 1.167, 1.170, 1.178, 1.193, 1.230, 1.270, 1.315, 1.326, 1.309, 1.247, 1.151, 1.038, 0.899, 0.746, 0.577, 0.407, 0.244, 0.091, -0.041, -0.159, -0.262, -0.362, -0.449, -0.517, -0.551, -0.557, -0.543, -0.514, -0.468, -0.401, -0.331, -0.268, -0.190, -0.082, 0.046, 0.144, 0.200, 0.224, 0.238, 0.244 },
91 ///{-0.026, -0.049, -0.092, -0.150, -0.214, -0.289, -0.359, -0.416, -0.456, -0.488, -0.510, -0.519, -0.508, -0.481, -0.438, -0.377, -0.282, -0.154, 0.018, 0.226, 0.454, 0.683, 0.908, 1.122, 1.328, 1.497, 1.638, 1.730, 1.800, 1.870, 1.969, 2.081, 2.168, 2.219, 2.244, 2.260, 2.266, 2.262, 2.254, 2.249 },
92 ///{ 1.128, 1.132, 1.141, 1.156, 1.178, 1.212, 1.251, 1.270, 1.244, 1.167, 1.060, 0.936, 0.791, 0.624, 0.449, 0.281, 0.131, -0.007, -0.130, -0.242, -0.333, -0.406, -0.452, -0.476, -0.471, -0.444, -0.396, -0.323, -0.229, -0.120, -0.010, 0.108, 0.222, 0.374, 0.552, 0.783, 0.986, 1.139, 1.208, 1.232 },
93 ///{ 0.756, 0.758, 0.766, 0.784, 0.807, 0.841, 0.874, 0.914, 0.910, 0.867, 0.766, 0.668, 0.557, 0.452, 0.333, 0.230, 0.133, 0.053, -0.028, -0.097, -0.169, -0.238, -0.317, -0.381, -0.423, -0.438, -0.443, -0.434, -0.423, -0.388, -0.387, -0.381, -0.412, -0.418, -0.438, -0.445, -0.454, -0.461, -0.466, -0.471 },
94 ///{-0.510, -0.515, -0.528, -0.545, -0.569, -0.579, -0.568, -0.513, -0.457, -0.397, -0.361, -0.322, -0.290, -0.250, -0.206, -0.152, -0.083, -0.006, 0.081, 0.162, 0.246, 0.327, 0.404, 0.462, 0.502, 0.529, 0.548, 0.561, 0.567, 0.576, 0.582, 0.594, 0.606, 0.621, 0.634, 0.645, 0.653, 0.662, 0.670, 0.675 },
95 ///{-1.240, -1.229, -1.194, -1.123, -1.022, -0.910, -0.810, -0.720, -0.620, -0.510, -0.394, -0.296, -0.204, -0.126, -0.054, -0.002, 0.042, 0.083, 0.137, 0.191, 0.247, 0.302, 0.359, 0.408, 0.430, 0.431, 0.409, 0.383, 0.354, 0.342, 0.336, 0.335, 0.338, 0.348, 0.360, 0.365, 0.370, 0.375, 0.380, 0.383 },
96 ///{-0.072, -0.067, -0.061, -0.055, -0.050, -0.066, -0.103, -0.174, -0.242, -0.309, -0.354, -0.386, -0.390, -0.372, -0.337, -0.284, -0.220, -0.130, -0.028, 0.099, 0.227, 0.361, 0.488, 0.602, 0.704, 0.786, 0.852, 0.898, 0.947, 1.006, 1.083, 1.158, 1.240, 1.335, 1.446, 1.548, 1.633, 1.702, 1.766, 1.796 },
97 ///{ 0.190, 0.188, 0.183, 0.177, 0.177, 0.173, 0.154, 0.111, 0.047, -0.032, -0.119, -0.200, -0.271, -0.324, -0.358, -0.363, -0.346, -0.297, -0.213, -0.097, 0.039, 0.189, 0.352, 0.519, 0.681, 0.831, 0.982, 1.116, 1.252, 1.380, 1.509, 1.606, 1.668, 1.699, 1.713, 1.719, 1.720, 1.720, 1.720, 1.720 },
98 ///{-0.321, -0.323, -0.327, -0.338, -0.351, -0.365, -0.371, -0.367, -0.350, -0.321, -0.283, -0.237, -0.186, -0.129, -0.072, -0.019, 0.030, 0.076, 0.121, 0.163, 0.202, 0.233, 0.252, 0.258, 0.249, 0.224, 0.179, 0.118, 0.056, 0.000, -0.057, -0.112, -0.159, -0.184, -0.196, -0.203, -0.211, -0.216, -0.220, -0.221 },
99 ///{ 0.073, 0.073, 0.073, 0.073, 0.073, 0.073, 0.066, 0.039, -0.004, -0.058, -0.102, -0.136, -0.149, -0.149, -0.139, -0.121, -0.087, -0.039, 0.020, 0.073, 0.124, 0.164, 0.197, 0.209, 0.199, 0.163, 0.118, 0.066, 0.015, -0.038, -0.083, -0.120, -0.147, -0.167, -0.182, -0.190, -0.197, -0.202, -0.206, -0.208 },
100 ///{ 1.137, 1.138, 1.138, 1.142, 1.143, 1.148, 1.145, 1.133, 1.094, 1.027, 0.942, 0.838, 0.729, 0.608, 0.489, 0.367, 0.253, 0.143, 0.036, -0.078, -0.183, -0.277, -0.353, -0.422, -0.482, -0.532, -0.569, -0.589, -0.592, -0.588, -0.577, -0.573, -0.567, -0.577, -0.585, -0.599, -0.602, -0.606, -0.605, -0.605 },
101 ///{ 1.430, 1.430, 1.430, 1.413, 1.374, 1.311, 1.240, 1.182, 1.134, 1.088, 1.022, 0.916, 0.773, 0.597, 0.407, 0.228, 0.051, -0.097, -0.239, -0.340, -0.410, -0.431, -0.428, -0.408, -0.381, -0.336, -0.263, -0.153, -0.014, 0.128, 0.247, 0.357, 0.474, 0.607, 0.729, 0.823, 0.877, 0.902, 0.912, 0.917 },
102 ///{ 1.037, 1.040, 1.046, 1.051, 1.051, 1.051, 1.050, 1.047, 1.021, 0.973, 0.896, 0.804, 0.684, 0.534, 0.362, 0.182, 0.018, -0.133, -0.254, -0.343, -0.397, -0.422, -0.424, -0.396, -0.343, -0.263, -0.178, -0.068, 0.049, 0.200, 0.367, 0.550, 0.725, 0.874, 0.991, 1.067, 1.115, 1.142, 1.158, 1.165 } };
103 
104 
105 core::Real const envdata_coarse[20][40] = {
106 { 0.86, 3.30, 3.30, 2.79, 1.75, 0.99, 0.91, 0.60, 0.46, 0.33, 0.19, 0.25, 0.20, 0.22, 0.18, 0.18, 0.12, 0.08,-0.03,-0.07,-0.18,-0.23,-0.26,-0.25,-0.29,-0.29,-0.28,-0.28,-0.29,-0.32,-0.35,-0.45,-0.59,-0.59,-0.74,-1.05,-0.71,-0.79,-0.71,-1.00},
107 {-0.28, 2.17, 2.17, 2.42, 2.20, 2.35, 1.99, 2.21, 2.12, 1.68, 1.48, 1.39, 1.26, 0.96, 0.84, 0.60, 0.40, 0.17,-0.00,-0.22,-0.37,-0.46,-0.53,-0.57,-0.61,-0.69,-0.69,-0.73,-0.72,-0.84,-0.68,-0.74,-0.67,-0.88,-0.93,-0.41,-1.15,-1.28,-1.28,-1.28},
108 {-0.50, 2.55, 2.55, 1.09,-0.12,-0.35,-0.42,-0.54,-0.48,-0.54,-0.52,-0.51,-0.42,-0.41,-0.31,-0.22,-0.11,-0.03, 0.12, 0.28, 0.39, 0.59, 0.65, 0.75, 0.93, 1.08, 1.20, 1.15, 1.18, 1.16, 1.07, 1.23, 1.26, 1.41, 1.85, 1.88, 1.02, 1.02, 1.02, 1.02},
109 {-0.17,-0.03,-0.03,-0.79,-0.83,-0.72,-0.87,-0.82,-0.81,-0.69,-0.65,-0.54,-0.45,-0.35,-0.25,-0.12, 0.07, 0.25, 0.40, 0.54, 0.77, 0.90, 1.10, 1.17, 1.35, 1.43, 1.50, 1.66, 1.72, 1.71, 1.68, 1.80, 1.86, 1.79, 1.53, 2.29, 2.06, 2.06, 1.01, 0.39},
110 { 0.83, 0.33, 0.01, 0.05, 0.34, 0.49, 0.77, 0.88, 1.07, 1.10, 1.07, 0.99, 0.89, 0.76, 0.58, 0.45, 0.28, 0.19, 0.10,-0.03,-0.16,-0.27,-0.32,-0.44,-0.53,-0.58,-0.65,-0.74,-0.80,-0.78,-0.74,-0.68,-0.58,-0.32,-0.41,-0.25,-0.39, 0.73, 0.51, 0.51},
111 { 0.36, 2.30, 2.30, 3.06, 2.20, 1.23, 0.75, 0.41, 0.19, 0.09, 0.00,-0.11,-0.11,-0.15,-0.16,-0.12,-0.11,-0.11,-0.12,-0.05,-0.07,-0.01, 0.02, 0.04, 0.12, 0.11, 0.09, 0.05, 0.03,-0.09,-0.13,-0.26,-0.33,-0.55,-0.62,-0.80,-0.83,-1.30,-0.94,-1.68},
112 {-0.42,-0.22,-0.38,-0.72,-0.47,-0.38,-0.18,-0.17,-0.07,-0.03,-0.04,-0.06,-0.15,-0.10,-0.15,-0.19,-0.20,-0.12,-0.01,-0.09, 0.02, 0.07, 0.20, 0.27, 0.34, 0.33, 0.37, 0.36, 0.31, 0.34, 0.23, 0.38, 0.38, 0.37, 0.17, 0.03, 0.60, 0.18, 0.18, 0.18},
113 {-0.63, 2.00, 2.00, 1.03, 0.94, 1.32, 1.35, 1.50, 1.30, 1.27, 1.06, 1.05, 1.02, 0.87, 0.74, 0.60, 0.48, 0.39, 0.18, 0.09,-0.09,-0.19,-0.28,-0.42,-0.55,-0.65,-0.78,-0.86,-0.97,-1.01,-1.07,-1.05,-1.03,-0.97,-1.02,-0.90,-0.84,-0.72,-0.76,-0.47},
114 { 0.09,-0.92,-1.60,-1.63,-1.51,-1.35,-1.24,-1.07,-0.87,-0.70,-0.59,-0.50,-0.41,-0.29,-0.17, 0.01, 0.21, 0.44, 0.63, 0.87, 1.18, 1.31, 1.51, 1.75, 1.89, 2.04, 2.20, 2.14, 2.20, 2.22, 2.24, 1.96, 2.04, 2.29, 2.42, 2.14, 2.61, 2.61, 2.61, 2.61},
115 { 0.38, 3.38, 3.38, 2.13, 1.48, 1.56, 1.44, 1.52, 1.28, 1.13, 1.10, 1.05, 0.85, 0.69, 0.50, 0.30, 0.15,-0.04,-0.12,-0.26,-0.30,-0.40,-0.51,-0.57,-0.61,-0.62,-0.60,-0.54,-0.43,-0.38,-0.26,-0.18,-0.09, 0.06, 0.41, 0.60, 0.01, 0.84, 0.62, 0.62},
116 { 0.04, 0.24, 0.69, 0.58, 0.65, 0.52, 0.75, 0.75, 0.73, 0.80, 0.84, 0.80, 0.88, 0.61, 0.52, 0.40, 0.30, 0.18, 0.12, 0.03,-0.11,-0.14,-0.22,-0.34,-0.42,-0.52,-0.62,-0.68,-0.80,-0.85,-0.96,-0.90,-0.91,-0.89,-0.70,-0.79,-0.33,-0.46,-0.28,-0.28},
117 { 0.48, 1.95, 1.95, 1.05,-0.21,-0.34,-0.35,-0.33,-0.33,-0.40,-0.34,-0.30,-0.31,-0.27,-0.21,-0.17,-0.14,-0.12, 0.00, 0.08, 0.16, 0.25, 0.38, 0.53, 0.60, 0.61, 0.75, 0.79, 0.78, 0.71, 0.71, 0.72, 0.85, 0.96, 1.09, 0.65, 0.93, 0.93, 0.57, 0.57},
118 { 0.96, 2.02, 2.02, 1.58, 0.24,-0.18,-0.37,-0.46,-0.36,-0.33,-0.26,-0.20,-0.18,-0.13,-0.10,-0.11,-0.07,-0.04,-0.00,-0.00, 0.08, 0.14, 0.23, 0.27, 0.42, 0.45, 0.43, 0.48, 0.55, 0.63, 0.62, 0.55, 0.56, 0.73, 0.44, 0.54, 0.78, 0.87, 0.64, 0.64},
119 {-0.19, 0.46, 0.46,-0.20,-0.30,-0.25,-0.49,-0.45,-0.51,-0.50,-0.41,-0.36,-0.36,-0.33,-0.27,-0.21,-0.18,-0.09, 0.04, 0.16, 0.32, 0.51, 0.58, 0.73, 0.89, 0.86, 0.98, 1.06, 0.97, 1.06, 1.02, 0.86, 0.80, 0.65, 0.93, 1.40, 2.15, 0.63, 0.41, 0.41},
120 {-0.67,-2.65,-2.20,-1.66,-1.17,-0.94,-0.63,-0.49,-0.44,-0.42,-0.34,-0.37,-0.41,-0.39,-0.31,-0.25,-0.19,-0.01, 0.07, 0.25, 0.40, 0.59, 0.76, 0.90, 1.16, 1.34, 1.54, 1.70, 1.84, 1.75, 1.82, 2.14, 2.21, 2.24, 2.09, 2.41, 1.77, 1.77, 1.77, 1.77},
121 {-0.06, 1.39, 2.54, 2.80, 1.26, 0.45, 0.39, 0.11,-0.08,-0.12,-0.19,-0.22,-0.21,-0.17,-0.17,-0.15,-0.14,-0.12,-0.11,-0.03, 0.02, 0.04, 0.11, 0.21, 0.17, 0.26, 0.31, 0.30, 0.29, 0.33, 0.21, 0.28, 0.18, 0.06,-0.07, 0.31,-0.02,-0.40,-0.92, 0.25},
122 {-0.47, 2.89, 2.89, 2.86, 1.39, 0.90, 0.82, 0.57, 0.28, 0.11, 0.01,-0.14,-0.19,-0.19,-0.24,-0.27,-0.28,-0.25,-0.18,-0.13,-0.08,-0.03, 0.09, 0.10, 0.17, 0.22, 0.20, 0.21, 0.29, 0.24, 0.25, 0.23, 0.18, 0.10, 0.43, 0.36,-0.07,-0.05,-0.28, 0.20},
123 {-0.09, 3.86, 3.86, 4.12, 2.10, 1.67, 1.69, 1.62, 1.44, 1.20, 1.05, 0.85, 0.73, 0.54, 0.40, 0.22, 0.05,-0.06,-0.17,-0.32,-0.38,-0.47,-0.52,-0.52,-0.54,-0.50,-0.47,-0.42,-0.36,-0.28,-0.25,-0.26,-0.17,-0.33,-0.18, 0.11, 0.01,-0.06,-0.00,-0.62},
124 {-0.00,-0.00, 1.55, 0.42, 0.76, 0.85, 0.96, 0.97, 1.05, 1.05, 0.95, 0.87, 0.65, 0.47, 0.19, 0.05,-0.09,-0.19,-0.32,-0.41,-0.47,-0.41,-0.41,-0.46,-0.34,-0.36,-0.29,-0.22,-0.25,-0.10, 0.10, 0.28, 0.39, 0.66, 0.34, 1.86, 1.86, 1.86, 1.86, 1.86},
125 { 1.40,-0.20, 0.01,-0.29, 0.24, 0.38, 0.55, 0.63, 0.70, 0.65, 0.58, 0.44, 0.30, 0.12,-0.01,-0.15,-0.18,-0.31,-0.33,-0.31,-0.28,-0.28,-0.26,-0.16,-0.14,-0.11,-0.05, 0.02,-0.02, 0.11, 0.16, 0.12, 0.17, 0.38, 0.45, 0.12, 0.74, 0.74, 0.38, 0.38} };
126 
127 
128 core::Real const envdata[20][40] = {
129 { 3.46, 3.33, 3.05, 2.54, 1.89, 1.30, 0.90, 0.65, 0.48, 0.35, 0.27, 0.23, 0.21, 0.21, 0.18, 0.16, 0.11, 0.06,-0.01,-0.09,-0.16,-0.21,-0.25,-0.26,-0.28,-0.28,-0.28,-0.29,-0.30,-0.33,-0.39,-0.46,-0.55,-0.63,-0.70,-0.74,-0.76,-0.81,-0.89,-1.00 },
130 { 2.60, 2.54, 2.47, 2.39, 2.29, 2.22, 2.18, 2.11, 1.97, 1.76, 1.55, 1.37, 1.20, 1.01, 0.81, 0.60, 0.40, 0.19,-0.01,-0.19,-0.33,-0.44,-0.51,-0.57,-0.62,-0.66,-0.69,-0.73,-0.74,-0.75,-0.73,-0.74,-0.76,-0.84,-0.93,-1.04,-1.14,-1.22,-1.27,-1.28 },
131 {-0.50,-0.47,-0.45,-0.43,-0.43,-0.43,-0.45,-0.48,-0.50,-0.52,-0.51,-0.48,-0.44,-0.38,-0.30,-0.22,-0.11, 0.00, 0.13, 0.27, 0.41, 0.54, 0.66, 0.79, 0.91, 1.02, 1.09, 1.13, 1.16, 1.18, 1.20, 1.24, 1.29, 1.35, 1.41, 1.46, 1.49, 1.50, 1.47, 1.43 },
132 {-0.81,-0.82,-0.82,-0.80,-0.80,-0.80,-0.81,-0.80,-0.77,-0.71,-0.63,-0.54,-0.45,-0.35,-0.23,-0.09, 0.07, 0.23, 0.40, 0.57, 0.74, 0.91, 1.06, 1.19, 1.32, 1.42, 1.53, 1.62, 1.68, 1.71, 1.74, 1.78, 1.82, 1.85, 1.88, 1.89, 1.88, 1.87, 1.86, 1.88 },
133 { 0.37, 0.36, 0.36, 0.38, 0.45, 0.56, 0.72, 0.88, 1.00, 1.05, 1.04, 0.97, 0.87, 0.74, 0.59, 0.45, 0.31, 0.19, 0.08,-0.03,-0.14,-0.25,-0.34,-0.43,-0.51,-0.59,-0.66,-0.72,-0.76,-0.76,-0.72,-0.64,-0.54,-0.43,-0.37,-0.32,-0.30,-0.26,-0.25,-0.24 },
134 { 2.37, 2.32, 2.26, 2.10, 1.78, 1.32, 0.86, 0.49, 0.26, 0.11, 0.00,-0.07,-0.11,-0.14,-0.14,-0.13,-0.12,-0.11,-0.10,-0.07,-0.05,-0.02, 0.02, 0.06, 0.09, 0.09, 0.08, 0.05, 0.00,-0.08,-0.15,-0.26,-0.37,-0.51,-0.64,-0.76,-0.84,-0.92,-0.99,-1.06 },
135 {-0.42,-0.35,-0.32,-0.32,-0.31,-0.28,-0.21,-0.15,-0.09,-0.06,-0.06,-0.08,-0.11,-0.13,-0.15,-0.17,-0.16,-0.14,-0.10,-0.05, 0.01, 0.09, 0.18, 0.25, 0.31, 0.34, 0.35, 0.35, 0.34, 0.34, 0.35, 0.36, 0.37, 0.36, 0.34, 0.33, 0.30, 0.26, 0.22, 0.18 },
136 { 1.39, 1.37, 1.35, 1.33, 1.32, 1.32, 1.32, 1.31, 1.28, 1.23, 1.15, 1.07, 0.97, 0.86, 0.74, 0.61, 0.48, 0.35, 0.21, 0.07,-0.06,-0.18,-0.30,-0.42,-0.54,-0.65,-0.76,-0.86,-0.94,-1.00,-1.04,-1.04,-1.03,-1.00,-0.95,-0.90,-0.85,-0.79,-0.73,-0.64 },
137 {-1.55,-1.60,-1.61,-1.57,-1.49,-1.36,-1.22,-1.05,-0.89,-0.73,-0.61,-0.50,-0.40,-0.28,-0.14, 0.03, 0.22, 0.43, 0.66, 0.89, 1.12, 1.33, 1.52, 1.71, 1.87, 2.00, 2.08, 2.14, 2.18, 2.21, 2.22, 2.23, 2.27, 2.32, 2.41, 2.49, 2.56, 2.60, 2.61, 2.61 },
138 { 2.77, 2.62, 2.40, 2.11, 1.83, 1.62, 1.48, 1.38, 1.29, 1.19, 1.10, 0.99, 0.85, 0.68, 0.50, 0.32, 0.15, 0.00,-0.12,-0.23,-0.32,-0.41,-0.49,-0.55,-0.59,-0.60,-0.57,-0.52,-0.44,-0.36,-0.27,-0.17,-0.05, 0.08, 0.23, 0.36, 0.47, 0.55, 0.60, 0.62 },
139 { 0.99, 0.98, 0.96, 0.95, 0.94, 0.92, 0.91, 0.89, 0.87, 0.85, 0.82, 0.77, 0.70, 0.61, 0.51, 0.40, 0.30, 0.20, 0.11, 0.02,-0.07,-0.15,-0.24,-0.33,-0.42,-0.52,-0.61,-0.69,-0.78,-0.85,-0.90,-0.91,-0.90,-0.87,-0.81,-0.72,-0.60,-0.49,-0.40,-0.33 },
140 {-0.17,-0.21,-0.22,-0.24,-0.26,-0.30,-0.33,-0.34,-0.35,-0.35,-0.34,-0.32,-0.29,-0.26,-0.22,-0.18,-0.13,-0.08,-0.01, 0.08, 0.17, 0.27, 0.38, 0.49, 0.58, 0.65, 0.71, 0.75, 0.76, 0.74, 0.74, 0.75, 0.79, 0.81, 0.84, 0.86, 0.89, 0.89, 0.86, 0.83 },
141 { 0.06, 0.04, 0.02,-0.02,-0.09,-0.20,-0.31,-0.37,-0.37,-0.32,-0.26,-0.22,-0.17,-0.14,-0.11,-0.09,-0.07,-0.04,-0.01, 0.03, 0.08, 0.15, 0.22, 0.30, 0.37, 0.42, 0.46, 0.50, 0.55, 0.59, 0.61, 0.61, 0.61, 0.61, 0.62, 0.63, 0.63, 0.64, 0.64, 0.64 },
142 {-0.19,-0.14,-0.15,-0.19,-0.27,-0.33,-0.41,-0.46,-0.48,-0.46,-0.42,-0.38,-0.35,-0.31,-0.27,-0.22,-0.15,-0.07, 0.04, 0.18, 0.32, 0.47, 0.60, 0.72, 0.82, 0.90, 0.96, 1.00, 1.02, 1.01, 0.96, 0.88, 0.79, 0.71, 0.66, 0.63, 0.60, 0.55, 0.48, 0.41 },
143 {-2.73,-2.48,-2.12,-1.70,-1.28,-0.95,-0.71,-0.55,-0.46,-0.41,-0.38,-0.38,-0.38,-0.36,-0.31,-0.24,-0.15,-0.03, 0.10, 0.25, 0.41, 0.58, 0.76, 0.94, 1.14, 1.34, 1.52, 1.66, 1.75, 1.82, 1.92, 2.05, 2.14, 2.21, 2.17, 2.11, 1.95, 1.84, 1.77, 1.77 },
144 { 1.44, 1.28, 1.08, 0.86, 0.66, 0.48, 0.32, 0.14,-0.01,-0.11,-0.17,-0.19,-0.20,-0.18,-0.17,-0.15,-0.14,-0.12,-0.08,-0.04, 0.01, 0.06, 0.11, 0.17, 0.21, 0.25, 0.28, 0.30, 0.29, 0.29, 0.26, 0.22, 0.16, 0.09, 0.03,-0.01,-0.03,-0.05,-0.04,-0.02 },
145 { 1.36, 1.32, 1.26, 1.18, 1.06, 0.92, 0.75, 0.55, 0.34, 0.15, 0.01,-0.10,-0.16,-0.20,-0.23,-0.25,-0.26,-0.23,-0.18,-0.13,-0.07,-0.01, 0.06, 0.11, 0.16, 0.19, 0.21, 0.23, 0.25, 0.25, 0.24, 0.21, 0.17, 0.13, 0.08, 0.03,-0.03,-0.07,-0.11,-0.14 },
146 { 2.92, 2.80, 2.64, 2.39, 2.11, 1.85, 1.69, 1.55, 1.41, 1.23, 1.05, 0.87, 0.71, 0.55, 0.39, 0.23, 0.08,-0.06,-0.18,-0.29,-0.38,-0.45,-0.50,-0.52,-0.52,-0.50,-0.46,-0.41,-0.36,-0.30,-0.26,-0.25,-0.24,-0.22,-0.16,-0.10,-0.04,-0.03,-0.03,-0.05 },
147 { 0.67, 0.69, 0.71, 0.73, 0.78, 0.85, 0.93, 0.98, 1.01, 1.00, 0.93, 0.81, 0.64, 0.45, 0.24, 0.07,-0.08,-0.19,-0.30,-0.38,-0.42,-0.43,-0.42,-0.41,-0.37,-0.34,-0.29,-0.24,-0.18,-0.06, 0.08, 0.22, 0.30, 0.34, 0.36, 0.37, 0.39, 0.41, 0.42, 0.43 },
148 { 0.01, 0.01, 0.04, 0.11, 0.23, 0.38, 0.51, 0.60, 0.64, 0.62, 0.55, 0.43, 0.29, 0.14, 0.00,-0.11,-0.20,-0.27,-0.30,-0.30,-0.29,-0.27,-0.23,-0.19,-0.14,-0.09,-0.05,-0.01, 0.03, 0.08, 0.12, 0.17, 0.24, 0.32, 0.39, 0.42, 0.41, 0.40, 0.39, 0.38 } };
149 
150 ////////////////////////////////////////////////////////////////////////////
151 
152 
153 /// c-tor
154 EnvSmoothEnergy::EnvSmoothEnergy() :
155  parent( new EnvSmoothEnergyCreator )
156 {}
157 
158 
159 /// clone
160 EnergyMethodOP
161 EnvSmoothEnergy::clone() const
162 {
163  return new EnvSmoothEnergy();
164 }
165 
166 
167 /////////////////////////////////////////////////////////////////////////////
168 // scoring
169 /////////////////////////////////////////////////////////////////////////////
170 
171 inline Real sqr ( Real x ) {
172  return x*x;
173 }
174 
175 
176 /// @details stores dScore/dNumNeighbors so that when neighbor atoms on adjacent
177 /// residues move, their influence on the score of the surrounding residues is
178 /// rapidly computed.
179 void
180 EnvSmoothEnergy::setup_for_derivatives(
181  pose::Pose & pose,
182  ScoreFunction const &
183 ) const
184 {
185  pose.update_residue_neighbors();
186  Size const nres( pose.total_residue() );
187 
188  residue_N_.clear();
189  residue_E_.clear();
190  residue_dEdN_.clear();
191 
192 
193  // iterate over all the residues in the protein and count their neighbours
194  // and save values of E, N, and dEdN
195  for ( Size i = 1; i <= nres; ++i ) {
196 
197  // get the appropriate residue from the pose.
198  conformation::Residue const & rsd( pose.residue(i) );
199  // currently this is only for protein residues
200  if( !rsd.is_protein() || rsd.aa() == chemical::aa_unk ) {
201  residue_dEdN_.push_back(0);
202  continue; //return;
203  }
204 
205  Size const atomindex_i = rsd.atom_index( representative_atom_name( rsd.aa() ));
206 
207  core::conformation::Atom const & atom_i = rsd.atom(atomindex_i);
208 
209  const Energies & energies( pose.energies() );
210  const TwelveANeighborGraph & graph ( energies.twelveA_neighbor_graph() );
211 
212  Real countN = 0.0;
213 
214  // iterate across neighbors within 12 angstroms
215  for ( graph::Graph::EdgeListConstIter
216  ir = graph.get_node(i)->const_edge_list_begin(),
217  ire = graph.get_node(i)->const_edge_list_end();
218  ir != ire; ++ir ) {
219  Size const j( (*ir)->get_other_ind( i ) );
220  conformation::Residue const & rsd_j( pose.residue(j) );
221  Size atomindex_j( rsd_j.type().nbr_atom() );
222 
223  core::conformation::Atom const & atom_j = rsd_j.atom(atomindex_j);
224 
225  Real sqdist = atom_i.xyz().distance_squared(atom_j.xyz());
226  countN += sigmoidish_neighbor( sqdist );
227  }
228 
229  Real score = 0;
230  Real dscoredN = 0;
231 
232  calc_energy( countN, rsd.aa(), score, dscoredN );
233 
234  residue_N_.push_back( countN );
235  residue_E_.push_back( score );
236  residue_dEdN_.push_back( dscoredN );
237 
238  //std::cout << "ENV: " << i << " " << score << std::endl;
239  }
240 
241 }
242 
243 void
244 EnvSmoothEnergy::setup_for_scoring(
245  pose::Pose & pose,
246  ScoreFunction const &
247 ) const
248 {
249  pose.update_residue_neighbors();
250 }
251 
252 /// @details counts the number of nbr atoms within a given radius of the for the input
253 /// residue. Because the representative atom on the input residue may be in a different
254 /// location than the representative atom on the same residue when scoring_begin() is called,
255 /// these neighbor counts cannot be reused; therefore, scoring_begin does not keep
256 /// neighbor counts.
257 void
258 EnvSmoothEnergy::residue_energy(
259  conformation::Residue const & rsd,
260  pose::Pose const & pose,
261  EnergyMap & emap
262 ) const
263 {
264  // ignore scoring residues which have been marked as "REPLONLY" residues (only the repulsive energy will be calculated)
265  if ( rsd.has_variant_type( core::chemical::REPLONLY ) ){
266  return;
267  }
268 
269  // currently this is only for protein residues
270  if ( ! rsd.is_protein() ) return;
271  if( rsd.aa() == chemical::aa_unk ) return;
272 
273  TwelveANeighborGraph const & graph ( pose.energies().twelveA_neighbor_graph() );
274  Size const atomindex_i = rsd.atom_index( representative_atom_name( rsd.aa() ));
275 
276  core::conformation::Atom const & atom_i = rsd.atom(atomindex_i);
277 
278  Real countN = 0.0;
279  // iterate across neighbors within 12 angstroms
280  for ( graph::Graph::EdgeListConstIter
281  ir = graph.get_node( rsd.seqpos() )->const_edge_list_begin(),
282  ire = graph.get_node( rsd.seqpos() )->const_edge_list_end();
283  ir != ire; ++ir ) {
284  Size const j( (*ir)->get_other_ind( rsd.seqpos() ) );
285  conformation::Residue const & rsd_j( pose.residue(j) );
286 
287  // if virtual residue, don't score
288  if (rsd_j.aa() == core::chemical::aa_vrt) continue;
289 
290  Size atomindex_j( rsd_j.nbr_atom() );
291 
292  core::conformation::Atom const & atom_j = rsd_j.atom(atomindex_j);
293 
294  Real sqdist = atom_i.xyz().distance_squared( atom_j.xyz() );
295  countN += sigmoidish_neighbor( sqdist );
296  }
297 
298  Real score = 0;
299  Real dscoredN = 0;
300 
301  calc_energy( countN, rsd.aa(), score, dscoredN );
302 
303  emap[ envsmooth ] += score;
304 }
305 
306 
307 /// @details Special cases handled for when an atom is both the representative
308 /// atom for an amino acid, and its nbr_atom.
309 void
310 EnvSmoothEnergy::eval_atom_derivative(
311  id::AtomID const & atom_id,
312  pose::Pose const & pose,
313  kinematics::DomainMap const & ,
314  ScoreFunction const &,
315  EnergyMap const & weights,
316  Vector & F1,
317  Vector & F2
318 ) const
319 {
320  // ignore scoring residues which have been marked as "REPLONLY" residues (only the repulsive energy will be calculated)
321  if ( pose.residue( atom_id.rsd() ).has_variant_type( core::chemical::REPLONLY )){
322  return;
323  }
324 
325  conformation::Residue const & rsd = pose.residue( atom_id.rsd() );
326 
327  if (! rsd.is_protein() ) return;
328  if ( rsd.aa() == chemical::aa_unk ) return;
329 
330  Size const i = rsd.seqpos();
331  Size const i_nbr_atom = rsd.type().nbr_atom();
332  Size const i_rep_atom = rsd.atom_index( representative_atom_name( rsd.aa() ));
333 
334  // forces act only on the nbr atom (CB or CA) or the representative atom
335  if( i_nbr_atom != (Size) atom_id.atomno() && i_rep_atom != (Size) atom_id.atomno() ) return;
336 
337  core::conformation::Atom const & atom_i = rsd.atom( atom_id.atomno() );
338 
339  TwelveANeighborGraph const & graph ( pose.energies().twelveA_neighbor_graph() );
340 
341  // its possible both of these are true
342  bool const input_atom_is_nbr( i_nbr_atom == Size (atom_id.atomno()) );
343  bool const input_atom_is_rep( i_rep_atom == Size ( atom_id.atomno() ));
344 
345  Vector f1(0.0), f2(0.0);
346 
347  for ( graph::Graph::EdgeListConstIter
348  ir = graph.get_node(i)->const_edge_list_begin(),
349  ire = graph.get_node(i)->const_edge_list_end();
350  ir != ire; ++ir ) {
351  Size const j( (*ir)->get_other_ind( i ) );
352  conformation::Residue const & rsd_j( pose.residue(j) );
353 
354  // if virtual residue, don't score
355  if (rsd_j.aa() == core::chemical::aa_vrt ) continue;
356 
357  if ( input_atom_is_nbr && input_atom_is_rep && (rsd_j.is_protein() && rsd_j.aa()<=core::chemical::num_canonical_aas) ) {
358  Size const resj_rep_atom = rsd_j.atom_index( representative_atom_name( rsd_j.aa() ));
359  Size const resj_nbr_atom = rsd_j.nbr_atom();
360  if ( resj_rep_atom == resj_nbr_atom ) {
361  /// two birds, one stone
362  increment_f1_f2_for_atom_pair(
363  atom_i, rsd_j.atom( resj_rep_atom ),
364  weights[ envsmooth ] * ( residue_dEdN_[ j ] + residue_dEdN_[ i ] ),
365  F1, F2 );
366  } else {
367  increment_f1_f2_for_atom_pair(
368  atom_i, rsd_j.atom( resj_rep_atom ),
369  weights[ envsmooth ] * ( residue_dEdN_[ j ] ),
370  F1, F2 );
371 
372  increment_f1_f2_for_atom_pair(
373  atom_i, rsd_j.atom( resj_nbr_atom ),
374  weights[ envsmooth ] * ( residue_dEdN_[ i ] ),
375  F1, F2 );
376  }
377  } else if ( input_atom_is_nbr && (rsd_j.is_protein() && rsd_j.aa()<=core::chemical::num_canonical_aas) ) {
378  Size const resj_rep_atom = rsd_j.atom_index( representative_atom_name( rsd_j.aa() ));
379 
380  increment_f1_f2_for_atom_pair(
381  atom_i, rsd_j.atom( resj_rep_atom ),
382  weights[ envsmooth ] * ( residue_dEdN_[ j ] ),
383  F1, F2 );
384 
385  } else {
386  Size const resj_nbr_atom = rsd_j.nbr_atom();
387  increment_f1_f2_for_atom_pair(
388  atom_i, rsd_j.atom( resj_nbr_atom ),
389  weights[ envsmooth ] * ( residue_dEdN_[ i ] ),
390  F1, F2 );
391 
392  }
393 
394  }
395 
396 }
397 
398 /// @details returns const & to static data members to avoid expense
399 /// of string allocation and destruction. Do not call this function
400 /// on non-canonical aas
401 std::string const &
402 EnvSmoothEnergy::representative_atom_name( chemical::AA const aa ) const
403 {
404  // assert( aa >= 1 && aa <= chemical::num_canonical_aas );
405 
406  static std::string const cbeta_string( "CB" );
407  static std::string const sgamma_string( "SG" );
408  static std::string const cgamma_string( "CG" );
409  static std::string const cdelta_string( "CD" );
410  static std::string const czeta_string( "CZ" );
411  static std::string const calpha_string( "CA" );
412  static std::string const ceps_1_string( "CE1" );
413  static std::string const cdel_1_string( "CD1" );
414  static std::string const ceps_2_string( "CE2" );
415  static std::string const sdelta_string( "SD" );
416 
417  switch ( aa ) {
418  case ( chemical::aa_ala ) : return cbeta_string; break;
419  case ( chemical::aa_cys ) : return sgamma_string; break;
420  case ( chemical::aa_asp ) : return cgamma_string; break;
421  case ( chemical::aa_glu ) : return cdelta_string; break;
422  case ( chemical::aa_phe ) : return czeta_string; break;
423  case ( chemical::aa_gly ) : return calpha_string; break;
424  case ( chemical::aa_his ) : return ceps_1_string; break;
425  case ( chemical::aa_ile ) : return cdel_1_string; break;
426  case ( chemical::aa_lys ) : return cdelta_string; break;
427  case ( chemical::aa_leu ) : return cgamma_string; break;
428  case ( chemical::aa_met ) : return sdelta_string; break;
429  case ( chemical::aa_asn ) : return cgamma_string; break;
430  case ( chemical::aa_pro ) : return cgamma_string; break;
431  case ( chemical::aa_gln ) : return cdelta_string; break;
432  case ( chemical::aa_arg ) : return czeta_string; break;
433  case ( chemical::aa_ser ) : return cbeta_string; break;
434  case ( chemical::aa_thr ) : return cbeta_string; break;
435  case ( chemical::aa_val ) : return cbeta_string; break;
436  case ( chemical::aa_trp ) : return ceps_2_string; break;
437  case ( chemical::aa_tyr ) : return czeta_string; break;
438  default :
439  utility_exit_with_message( "ERROR: Failed to find amino acid " + chemical::name_from_aa( aa ) + " in EnvSmooth::representative_atom_name" );
440  break;
441  }
442 
443  // unreachable
444  return calpha_string;
445 }
446 
447 /// @brief EnvSmoothEnergy distance cutoff
448 Distance
449 EnvSmoothEnergy::atomic_interaction_cutoff() const
450 {
451  return 0.0;
452 }
453 
454 /// @brief EnvSmoothEnergy
455 void
456 EnvSmoothEnergy::indicate_required_context_graphs( utility::vector1< bool > & context_graphs_required ) const
457 {
458  context_graphs_required[ twelve_A_neighbor_graph ] = true;
459 }
460 
461 void
462 EnvSmoothEnergy::calc_energy(
463  Real const neighbor_count,
464  chemical::AA const aa,
465  Real & score,
466  Real & dscore_dneighbor_count
467 ) const
468 {
469  Size low_bin = static_cast< Size > ( floor(neighbor_count));
470  Size high_bin = static_cast< Size > ( ceil(neighbor_count));
471  Real inter = neighbor_count - low_bin;
472 
473  int const aa_as_int = static_cast< int > (aa);
474 
475  if (high_bin < 40 ){
476  score = envdata[ aa_as_int - 1 ][ low_bin ] * (1.0-inter) +
477  envdata[ aa_as_int - 1 ][ high_bin ] * (inter);
478  dscore_dneighbor_count = envdata[ aa_as_int - 1 ][ high_bin ] -
479  envdata[ aa_as_int - 1 ][ low_bin ];
480  }else{
481  score = envdata[ aa_as_int - 1 ][ 39 ];
482  dscore_dneighbor_count = 0;
483  }
484  score *= 2.019; // this factor is from rosetta++ and fuck knows where it came from originally :-)
485  dscore_dneighbor_count *= 2.019;
486 }
487 
488 Real
489 EnvSmoothEnergy::sigmoidish_neighbor( DistanceSquared const sqdist ) const
490 {
491  if( sqdist > end_sig2 ) {
492  return 0.0;
493  } else if( sqdist < start_sig2 ) {
494  return 1.0;
495  } else {
496  Real dist = sqrt( sqdist );
497  return sqr(1.0 - sqr( (dist - start_sig) / (end_sig - start_sig) ) );
498  }
499 }
500 
501 
502 void
503 EnvSmoothEnergy::increment_f1_f2_for_atom_pair(
504  conformation::Atom const & atom1,
505  conformation::Atom const & atom2,
506  Real weighted_dScore_dN,
507  Vector & F1,
508  Vector & F2
509 ) const
510 {
511  DistanceSquared dist2 = atom1.xyz().distance_squared(atom2.xyz());
512  Distance dist( 0.0 ); // only used if start_sig2 <= dist2 <= end_sig2
513 
514  Real dNdd = 0;
515  if ( dist2 > end_sig2 ) {
516  dNdd = 0;
517  } else if ( dist2 < start_sig2 ) {
518  dNdd = 0.0;
519  } else {
520  dist = sqrt( dist2 );
521  Real x = (dist - start_sig)/ (end_sig - start_sig);
522  dNdd = 4*x*(-1 + x*x) / (end_sig - start_sig);
523  }
524 
525  Real dscoredd = ( weighted_dScore_dN ) * dNdd;
526  if ( dscoredd != 0 ) {
527 
528  Vector const f1( cross( atom1.xyz(), atom2.xyz() ));
529  Vector const f2( atom1.xyz() - atom2.xyz() );
530 
531  dscoredd /= dist;
532  F1 += dscoredd * f1;
533  F2 += dscoredd * f2;
534  }
535 
536 
537 }
538 
539 core::Size
540 EnvSmoothEnergy::version() const
541 {
542  return 1; // Initial versioning
543 }
544 }
545 }
546 }
547 
548 
549 
550 
551  /*
552  /////////// TEST LINEAR DERIVATIVE Correctness //////////////
553  {
554  core::Real dNdd_numerical=0;
555  core::Real dx = 0.001;
556 
557  core::Real dist1 = dist;
558  core::Real weight1;
559  if( dist1 > end_sig ) weight1 = 0;
560  else if( dist1 < start_sig ) weight1 = 1.0;
561  else weight1 = sqr(1.0 - sqr( (dist1 - start_sig) / (end_sig - start_sig) ) );
562 
563  core::Real dist2 = dist+dx;
564  core::Real weight2;
565  if( dist2 > end_sig ) weight2 = 0;
566  else if( dist2 < start_sig ) weight2 = 1.0;
567  else weight2 = sqr(1.0 - sqr( (dist2 - start_sig) / (end_sig - start_sig) ) );
568 
569  std::cout << "I: " << dNdd << " " << (weight2-weight1)/dx << std::endl;
570  }
571  *//*
572 
573  Real const q1 = 1.0;
574  Real const q2 = 1.0;
575  Real const max_dis( 5.5 );
576  Real const max_dis2( max_dis * max_dis );
577  Real const min_dis( 1.5 );
578  Real const min_dis2( min_dis * min_dis );
579  Real const C0( 322.0637 );
580  Real const die( 10.0 ); // 10r dielectric
581  Real const dEfac( -2.0 * C0 / die );
582 
583  Real dis2 = dist;
584 
585 
586  core::Real dscoredd = 0.0;
587  if ( dis2 > max_dis2 ) dscoredd = 0;
588  else if ( dis2 < min_dis2 ) dscoredd = 0.0; // flat in this region
589  else dscoredd = dEfac * q1 * q2 / ( dis2 * dis2 );
590 
591 
592  */
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