backup

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@193 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/AtomShape.h

+// AtomShape, analogue to the similarly named code in clipper
+
+#pragma once
+
+#include "cif++/Structure.h"
+
+namespace libcif
+{
+
+// --------------------------------------------------------------------
+// Class used in calculating radii
+
+class AtomShape
+{
+  public:
+	AtomShape(const Atom& atom, float resHigh, float resLow);
+
+	float radius() const;
+
+  private:
+	AtomType	mSymbol;
+	int			mCharge;
+	float		mUIso, mOccupancy;
+	float		mResHigh, mResLow;
+};
+	
+}

include/cif++/AtomType.h

@@ -197,6 +197,18 @@ class AtomTypeTraits
 		return mInfo->radii[type] / 100.f;
 		return mInfo->radii[type] / 100.f;
 	}
 	}
 	
 	
+	// data type encapsulating the Waasmaier & Kirfel scattering factors
+	// in a simplified form (only a and b).
+	struct WKSF
+	{
+		double a[6], b[6];
+	};
+	
+	// to get the Cval and Siva values, use this constant as charge:
+	enum { kWKSFVal = -99 };
+	
+	const WKSF& wksf(int charge = 0) const;
+
   private:
   private:
 	const struct AtomTypeInfo*	mInfo;
 	const struct AtomTypeInfo*	mInfo;
 };
 };

include/cif++/ResolutionCalculator.h

+// Lib for working with structures as contained in mmCIF and PDB files
+
+#pragma once
+
+#include "cif++/ResolutionCalculator.h"
+
+namespace libcif
+{
+
+// --------------------------------------------------------------------
+
+class ResolutionCalculator
+{
+  public:
+	ResolutionCalculator(double a, double b, double c,
+		double alpha, double beta, double gamma);
+	
+	double operator()(int h, int k, int l) const
+	{
+		double tmpres = h * h * mCoefs[0] + h * k * mCoefs[1] +
+					    h * l * mCoefs[2] + k * k * mCoefs[3] +
+					    k * l * mCoefs[4] + l * l * mCoefs[5];
+		
+		return 1.0 / std::sqrt(tmpres);
+	}
+	
+  private:
+	double	mCoefs[6];
+};
+
+}

include/cif++/Structure.h

@@ -125,6 +125,10 @@ class Atom
 	// get clipper format Atom
 	// get clipper format Atom
 	clipper::Atom toClipper() const;
 	clipper::Atom toClipper() const;
 
 
+	// Radius calculation based on integrating the density until perc of electrons is found
+	void calculateRadius(float resHigh, float resLow, float perc);
+	float radius() const;
+
   private:
   private:
  	struct AtomImpl*			mImpl;
  	struct AtomImpl*			mImpl;
 };
 };

src/AtomShape.cpp

+// Lib for working with structures as contained in file and PDB files
+
+#include "cif++/Structure.h"
+#include "cif++/AtomShape.h"
+#include "cif++/Point.h"
+
+#include <newuoa.h>
+
+using namespace std;
+
+namespace libcif
+{
+
+
+namespace {
+
+// --------------------------------------------------------------------
+
+template <class F>
+NewuoaClosure make_closure(F &function) {
+    struct Wrap {
+        static double call(void *data, long n, const double *values) {
+            return reinterpret_cast<F *>(data)->operator()(n, values);
+        }
+    };
+    return NewuoaClosure {&function, &Wrap::call};
+}
+
+// --------------------------------------------------------------------
+
+// sine integration function based on the description in
+//	GalSim: The modular galaxy image simulation toolkit
+//	B.T.P. Rowe et. al.
+//	DOI: 10.1016/j.ascom.2015.02.002
+
+double SineIntegration(double x)
+{
+	struct P { double n, d; };
+	double result = 0;
+	
+	if (x <= 4)
+	{
+		const P kP[] =
+		{
+			{	1,							1,						},
+			{	-4.54393409816329991e-2,	1.01162145739225565e-2	},
+			{	1.15457225751016682e-3,		4.99175116169755106e-5	},
+			{	-1.41018536821330254e-5,	1.55654986308745614e-7	},
+			{	9.43280809438713025e-8,		3.28067571055789734e-10	},
+			{	-3.53201978997168357e-10,	4.5049097575386581e-13	},
+			{	7.08240282274875911e-13,	3.21107051193712168e-16	},
+			{	-6.05338212010422477e-16,	0						}
+		};
+		
+		double xs = x * x;
+		double xi = 1;
+		double sn = 0, sd = 0;
+		
+		for (auto p: kP)
+		{
+			sn += xi * p.n;
+			sd += xi * p.d;
+			xi *= xs;
+		}
+
+		result = x * (sn / sd);
+	}	
+	else
+	{
+		const P
+			kF[] = 
+			{
+				{ 1,                          1,                           },
+				{ 7.44437068161936700618e2,   7.46437068161927678031e2,    },
+				{ 1.96396372895146869801e5,   1.97865247031583951450e5,    },
+				{ 2.37750310125431834034e7,   2.41535670165126845144e7,    },
+				{ 1.43073403821274636888e9,   1.47478952192985464958e9,    },
+				{ 4.33736238870432522765e10,  4.58595115847765779830e10,   },
+				{ 6.40533830574022022911e11,  7.08501308149515401563e11,   },
+				{ 4.20968180571076940208e12,  5.06084464593475076774e12,   },
+				{ 1.00795182980368574617e13,  1.43468549171581016479e13,   },
+				{ 4.94816688199951963482e12,  1.11535493509914254097e13,   },
+				{ -4.94701168645415959931e11, 0                            }
+			},
+			kG[] = {
+				{ 1,                         1,                              },
+				{ 8.1359520115168615e2,      8.19595201151451564e2,          },
+				{ 2.35239181626478200e5,     2.40036752835578777e5,          },
+				{ 3.12557570795778731e7,     3.26026661647090822e7,          },
+				{ 2.06297595146763354e9,     2.23355543278099360e9,          },
+				{ 6.83052205423625007e10,    7.87465017341829930e10,         },
+				{ 1.09049528450362786e12,    1.39866710696414565e12,         },
+				{ 7.57664583257834349e12,    1.17164723371736605e13,         },
+				{ 1.81004487464664575e13,    4.01839087307656620e13,         },
+				{ 6.43291613143049485e12,    3.99653257887490811e13,         },
+				{ -1.36517137670871689e12,   0                               }
+			};
+		
+		double xs = pow(x, -2);
+		double xi = 1;
+		
+		double sn = 0, sd = 0;
+		for (auto p: kF)
+		{
+			sn += xi * p.n;
+			sd += xi * p.d;
+			xi *= xs;
+		}
+		
+		double fx = (sn / sd) / x;
+		
+		sn = 0;
+		sd = 0;
+		xi = 1;
+		for (auto p : kG)
+		{
+			sn += xi * p.n;
+			sd += xi * p.d;
+			xi *= xs;
+		}
+		
+		double gx = (sn / sd) / (x * x);
+		
+		result = libcif::kPI / 2 - fx * cos(x) - gx * sin(x);
+	}
+	
+	return result;
+}
+
+// --------------------------------------------------------------------
+// Internal class to cache some common data
+
+class DensityIntegration
+{
+  public:
+	DensityIntegration(float resolutionLow, float resolutionHigh);
+
+	double IntegrateRadius(float perc, AtomType symbol, int charge,
+		float uIso, float occupancy) const;
+	double IntegrateDensity(double r, int ks, const vector<double>& fst) const;
+	
+	tuple<double,vector<double>> InitData(AtomType symbol, int charge,
+		float uIso, float occupancy) const;
+
+  private:
+	float	mA, mB;
+	int		mM;
+
+	// Gauss-Legendre quadrature weights and abscissae
+	vector<double>	mWA, mST, mSTS;
+};
+
+DensityIntegration::DensityIntegration(float resolutionLow, float resolutionHigh)
+{
+	mA = 0.5f / resolutionLow;
+	mB = 0.5f / resolutionHigh;
+	
+	mM = static_cast<int>(12.0 * sqrt(1.2 * mB) + 1);
+	if (mM < 3)
+		mM = 3;
+	
+	int N = 2 * mM;
+//	int J = N;
+	double xr = mB - mA;
+	double xh = .5 * xr;
+	double xm = 0.5 * (mB + mA);
+
+	mWA = vector<double>(N, 0);
+	mST = vector<double>(N, 0);
+	mSTS = vector<double>(N, 0);
+	
+	for (int i = 1, j = N; i <= mM; ++i, --j)
+	{
+		double z, zo, dp;
+		
+		z = cos(libcif::kPI * (i - 0.25) / (N + 0.5));
+
+		do
+		{
+			double p1 = 1;
+			double p2 = 0;
+
+			for (int k = 1; k <= N; ++k)
+			{
+				double p3 = p2;
+				p2 = p1;
+				p1 = ((2 * k - 1) * z * p2 - (k - 1) * p3) / k;
+			}
+			
+			dp = N * (z * p1 - p2) / (z * z - 1);
+			zo = z;
+			z = z - p1 / dp;
+		}
+		while (abs(z - zo) > 3e-14);
+			
+		mWA[i - 1] = xr / ((1 - z * z) * dp * dp);
+		mWA[j - 1] = mWA[i - 1];
+		mST[i - 1] = xm - xh * z;
+		mST[j - 1] = xm + xh * z;
+	}
+
+	transform(mST.begin(), mST.end(), mSTS.begin(), [](double s) { return s * s; });
+}
+
+// --------------------------------------------------------------------
+
+tuple<double,vector<double>> DensityIntegration::InitData(AtomType symbol, int charge,
+		float uIso, float occupancy) const
+{
+	double yi = 0;
+	vector<double> fst(mST.size(), 0);
+
+	auto& D = AtomTypeTraits(symbol).wksf(charge);
+	auto bIso = clipper::Util::u2b(uIso);
+	
+	for (int i = 0; i < 6; ++i)
+	{
+		double bi = D.b[i] + bIso;
+		yi += D.a[i] * (exp(-bi * mA * mA) - exp(-bi * mB * mB)) / bi;
+	}
+	
+	for (size_t i = 0; i < mST.size(); ++i)
+	{
+		double t = 0;
+		for (int j = 0; j < 6; ++j)
+		{
+			double bj = D.b[j] + bIso;
+			t += D.a[j] * exp(-bj * mSTS[i]);
+		}
+
+		fst[i] = occupancy * mWA[i] * t * mST[i];
+	}
+
+	return make_tuple(yi, fst);
+}
+
+// --------------------------------------------------------------------
+// Calculate Radius integral over r of calculated density
+// code inspired by radint.f in edstats
+
+double DensityIntegration::IntegrateDensity(double r, int ks, const vector<double>& fst) const
+{
+	double y = 0;
+	
+	double rt = r;
+	if (rt < 0)
+		rt = 0;
+	
+	if (rt > 1e-10)
+	{
+		double t = 4 * libcif::kPI * rt;
+		y = 0;
+		
+		for (int i = 0; i < mST.size(); ++i)
+			y += fst[i] * SineIntegration(t * mST[i]);
+		
+		if (r < 0)
+			y = y - ks * r;
+	}
+	
+	return ks * y;
+}
+
+double DensityIntegration::IntegrateRadius(float perc, AtomType symbol, int charge,
+	float uIso, float occupancy) const
+{
+	// Initilialise parameters
+	
+	double yi;
+	vector<double> fst;
+	
+	tie(yi, fst) = InitData(symbol, charge, uIso, occupancy);
+	
+	double yt = perc * 0.25 * libcif::kPI * occupancy * yi;
+	double initialValue = 0.25;
+	
+
+	// code from newuoa-example
+    const long variables_count = 1;
+    const long number_of_interpolation_conditions = (variables_count + 1)*(variables_count + 2)/2;
+    double variables_values[] = { initialValue };
+    const double initial_trust_region_radius = 1e-3;
+    const double final_trust_region_radius = 1e3;
+    const long max_function_calls_count = 100;
+    const size_t working_space_size = NEWUOA_WORKING_SPACE_SIZE(variables_count,
+                                                                number_of_interpolation_conditions);
+    double working_space[working_space_size];
+
+    auto function = [&] (long n, const double *x)
+    {
+		assert(n == 1);
+		return this->IntegrateDensity(x[0], -1, fst);
+    };
+    auto closure = make_closure(function);
+
+    double result = newuoa_closure(
+            &closure,
+            variables_count,
+            number_of_interpolation_conditions,
+            variables_values,
+            initial_trust_region_radius,
+            final_trust_region_radius,
+            max_function_calls_count,
+            working_space);
+
+    // 
+    
+    const double kRE = 5e-5;
+    
+    double y1 = 0;
+    double y2 = -result;
+    double x1 = 0;
+    double x2 = variables_values[0];
+    
+    if (y2 > yt)
+    {
+	    for (int it = 0; it < 100; ++it)
+	    {
+	    	double x = 0.5 * (x1 + x2);
+	    	double y = IntegrateDensity(x, 1, fst);
+	    	
+	    	if (abs(y - yt) < kRE * abs(yt))
+	    	{
+	    		result = x;
+	    		break;
+	    	}
+	    	
+	    	if ((y1 < yt and y < yt) or (y1 > yt and y > yt))
+	    	{
+	    		x1 = x;
+	    		y1 = y;
+	    	}
+	    	else
+	    	{
+	    		x2 = x;
+	    		y2 = y;
+	    	}
+	    }
+    }
+    else
+    	result = x2;
+
+	return result;
+}
+
+
+
+} // namespace
+	
+AtomShape::AtomShape(const Atom& atom, float resHigh, float resLow)
+	: mSymbol(atom.type())
+	, mCharge(atom.charge())
+	, mUIso(atom.uIso())
+	, mOccupancy(atom.occupancy())
+	, mResHigh(resHigh)
+	, mResLow(resLow)
+{
+}
+
+float AtomShape::radius() const
+{
+	DensityIntegration di(mResLow, mResHigh);
+	
+	return di.IntegrateRadius(0.95, mSymbol, mCharge, mUIso, mOccupancy);
+}
+
+
+}

src/AtomType.cpp

@@ -8,6 +8,9 @@ using namespace std;
 namespace libcif
 namespace libcif
 {
 {
 
 
+namespace data
+{
+
 const float kNA = nan("1");
 const float kNA = nan("1");
 
 
 const AtomTypeInfo kKnownAtoms[] =
 const AtomTypeInfo kKnownAtoms[] =
@@ -136,12 +139,454 @@ const AtomTypeInfo kKnownAtoms[] =
 uint32 kKnownAtomsCount = sizeof(kKnownAtoms) / sizeof(AtomTypeInfo);
 uint32 kKnownAtomsCount = sizeof(kKnownAtoms) / sizeof(AtomTypeInfo);
 
 
 // --------------------------------------------------------------------
 // --------------------------------------------------------------------
+// The coefficients from Waasmaier & Kirfel (1995), Acta Cryst. A51, 416-431.
+
+struct WKSFData
+{
+	AtomType				symbol;
+	int8					charge;
+	AtomTypeTraits::WKSF	sf;
+};
+
+WKSFData kWKSFData[] = {
+{ H,	0,	{{  0.413048,  0.294953,  0.187491,  0.080701,  0.023736,  0.000049},
+			 { 15.569946, 32.398468,  5.711404, 61.889874,  1.334118,  0.000000}}},
+{ He,	0,	{{  0.732354,  0.753896,  0.283819,  0.190003,  0.039139,  0.000487},
+			 { 11.553918,  4.595831,  1.546299, 26.463964,  0.377523,  0.000000}}},
+{ Li,	0,	{{  0.974637,  0.158472,  0.811855,  0.262416,  0.790108,  0.002542},
+			 {  4.334946,  0.342451, 97.102966,201.363831,  1.409234,  0.000000}}},
+{ Be,	0,	{{  1.533712,  0.638283,  0.601052,  0.106139,  1.118414,  0.002511},
+			 { 42.662079,  0.595420, 99.106499,  0.151340,  1.843093,  0.000000}}},
+{ B,	0,	{{  2.085185,  1.064580,  1.062788,  0.140515,  0.641784,  0.003823},
+			 { 23.494068,  1.137894, 61.238976,  0.114886,  0.399036,  0.000000}}},
+{ C,	0,	{{  2.657506,  1.078079,  1.490909, -4.241070,  0.713791,  4.297983},
+			 { 14.780758,  0.776775, 42.086842, -0.000294,  0.239535,  0.000000}}},
+{ N,	0,	{{ 11.893780,  3.277479,  1.858092,  0.858927,  0.912985,-11.804902},
+			 {  0.000158, 10.232723, 30.344690,  0.656065,  0.217287,  0.000000}}},
+{ O,	0,	{{  2.960427,  2.508818,  0.637853,  0.722838,  1.142756,  0.027014},
+			 { 14.182259,  5.936858,  0.112726, 34.958481,  0.390240,  0.000000}}},
+{ F,	0,	{{  3.511943,  2.772244,  0.678385,  0.915159,  1.089261,  0.032557},
+			 { 10.687859,  4.380466,  0.093982, 27.255203,  0.313066,  0.000000}}},
+{ Ne,	0,	{{  4.183749,  2.905726,  0.520513,  1.135641,  1.228065,  0.025576},
+			 {  8.175457,  3.252536,  0.063295, 21.813910,  0.224952,  0.000000}}},
+{ Na,	0,	{{  4.910127,  3.081783,  1.262067,  1.098938,  0.560991,  0.079712},
+			 {  3.281434,  9.119178,  0.102763,132.013947,  0.405878,  0.000000}}},
+{ Mg,	0,	{{  4.708971,  1.194814,  1.558157,  1.170413,  3.239403,  0.126842},
+			 {  4.875207,108.506081,  0.111516, 48.292408,  1.928171,  0.000000}}},
+{ Al,	0,	{{  4.730796,  2.313951,  1.541980,  1.117564,  3.154754,  0.139509},
+			 {  3.628931, 43.051167,  0.095960,108.932388,  1.555918,  0.000000}}},
+{ Si,	0,	{{  5.275329,  3.191038,  1.511514,  1.356849,  2.519114,  0.145073},
+			 {  2.631338, 33.730728,  0.081119, 86.288643,  1.170087,  0.000000}}},
+{ P,	0,	{{  1.950541,  4.146930,  1.494560,  1.522042,  5.729711,  0.155233},
+			 {  0.908139, 27.044952,  0.071280, 67.520187,  1.981173,  0.000000}}},
+{ S,	0,	{{  6.372157,  5.154568,  1.473732,  1.635073,  1.209372,  0.154722},
+			 {  1.514347, 22.092527,  0.061373, 55.445175,  0.646925,  0.000000}}},
+{ Cl,	0,	{{  1.446071,  6.870609,  6.151801,  1.750347,  0.634168,  0.146773},
+			 {  0.052357,  1.193165, 18.343416, 46.398396,  0.401005,  0.000000}}},
+{ Ar,	0,	{{  7.188004,  6.638454,  0.454180,  1.929593,  1.523654,  0.265954},
+			 {  0.956221, 15.339877, 15.339862, 39.043823,  0.062409,  0.000000}}},
+{ K,	0,	{{  8.163991,  7.146945,  1.070140,  0.877316,  1.486434,  0.253614},
+			 { 12.816323,  0.808945,210.327011, 39.597652,  0.052821,  0.000000}}},
+{ Ca,	0,	{{  8.593655,  1.477324,  1.436254,  1.182839,  7.113258,  0.196255},
+			 { 10.460644,  0.041891, 81.390381,169.847839,  0.688098,  0.000000}}},
+{ Sc,	0,	{{  1.476566,  1.487278,  1.600187,  9.177463,  7.099750,  0.157765},
+			 { 53.131023,  0.035325,137.319489,  9.098031,  0.602102,  0.000000}}},
+{ Ti,	0,	{{  9.818524,  1.522646,  1.703101,  1.768774,  7.082555,  0.102473},
+			 {  8.001879,  0.029763, 39.885422,120.157997,  0.532405,  0.000000}}},
+{ V,	0,	{{ 10.473575,  1.547881,  1.986381,  1.865616,  7.056250,  0.067744},
+			 {  7.081940,  0.026040, 31.909672,108.022842,  0.474882,  0.000000}}},
+{ Cr,	0,	{{ 11.007069,  1.555477,  2.985293,  1.347855,  7.034779,  0.065510},
+			 {  6.366281,  0.023987, 23.244839,105.774498,  0.429369,  0.000000}}},
+{ Mn,	0,	{{ 11.709542,  1.733414,  2.673141,  2.023368,  7.003180, -0.147293},
+			 {  5.597120,  0.017800, 21.788420, 89.517914,  0.383054,  0.000000}}},
+{ Fe,	0,	{{ 12.311098,  1.876623,  3.066177,  2.070451,  6.975185, -0.304931},
+			 {  5.009415,  0.014461, 18.743040, 82.767876,  0.346506,  0.000000}}},
+{ Co,	0,	{{ 12.914510,  2.481908,  3.466894,  2.106351,  6.960892, -0.936572},
+			 {  4.507138,  0.009126, 16.438129, 76.987320,  0.314418,  0.000000}}},
+{ Ni,	0,	{{ 13.521865,  6.947285,  3.866028,  2.135900,  4.284731, -2.762697},
+			 {  4.077277,  0.286763, 14.622634, 71.966080,  0.004437,  0.000000}}},
+{ Cu,	0,	{{ 14.014192,  4.784577,  5.056806,  1.457971,  6.932996, -3.254477},
+			 {  3.738280,  0.003744, 13.034982, 72.554794,  0.265666,  0.000000}}},
+{ Zn,	0,	{{ 14.741002,  6.907748,  4.642337,  2.191766, 38.424042,-36.915829},
+			 {  3.388232,  0.243315, 11.903689, 63.312130,  0.000397,  0.000000}}},
+{ Ga,	0,	{{ 15.758946,  6.841123,  4.121016,  2.714681,  2.395246, -0.847395},
+			 {  3.121754,  0.226057, 12.482196, 66.203621,  0.007238,  0.000000}}},
+{ Ge,	0,	{{ 16.540613,  1.567900,  3.727829,  3.345098,  6.785079,  0.018726},
+			 {  2.866618,  0.012198, 13.432163, 58.866047,  0.210974,  0.000000}}},
+{ As,	0,	{{ 17.025642,  4.503441,  3.715904,  3.937200,  6.790175, -2.984117},
+			 {  2.597739,  0.003012, 14.272119, 50.437996,  0.193015,  0.000000}}},
+{ Se,	0,	{{ 17.354071,  4.653248,  4.259489,  4.136455,  6.749163, -3.160982},
+			 {  2.349787,  0.002550, 15.579460, 45.181202,  0.177432,  0.000000}}},
+{ Br,	0,	{{ 17.550570,  5.411882,  3.937180,  3.880645,  6.707793, -2.492088},
+			 {  2.119226, 16.557184,  0.002481, 42.164009,  0.162121,  0.000000}}},
+{ Kr,	0,	{{ 17.655279,  6.848105,  4.171004,  3.446760,  6.685200, -2.810592},
+			 {  1.908231, 16.606236,  0.001598, 39.917473,  0.146896,  0.000000}}},
+{ Rb,	0,	{{  8.123134,  2.138042,  6.761702,  1.156051, 17.679546,  1.139548},
+			 { 15.142385, 33.542667,  0.129372,224.132507,  1.713368,  0.000000}}},
+{ Sr,	0,	{{ 17.730219,  9.795867,  6.099763,  2.620025,  0.600053,  1.140251},
+			 {  1.563060, 14.310868,  0.120574,135.771317,  0.120574,  0.000000}}},
+{ Y,	0,	{{ 17.792040, 10.253252,  5.714949,  3.170516,  0.918251,  1.131787},
+			 {  1.429691, 13.132816,  0.112173,108.197029,  0.112173,  0.000000}}},
+{ Zr,	0,	{{ 17.859772, 10.911038,  5.821115,  3.512513,  0.746965,  1.124859},
+			 {  1.310692, 12.319285,  0.104353, 91.777542,  0.104353,  0.000000}}},
+{ Nb,	0,	{{ 17.958399, 12.063054,  5.007015,  3.287667,  1.531019,  1.123452},
+			 {  1.211590, 12.246687,  0.098615, 75.011948,  0.098615,  0.000000}}},
+{ Mo,	0,	{{  6.236218, 17.987711, 12.973127,  3.451426,  0.210899,  1.108770},
+			 {  0.090780,  1.108310, 11.468720, 66.684151,  0.090780,  0.000000}}},
+{ Tc,	0,	{{ 17.840963,  3.428236,  1.373012, 12.947364,  6.335469,  1.074784},
+			 {  1.005729, 41.901382,119.320541,  9.781542,  0.083391,  0.000000}}},
+{ Ru,	0,	{{  6.271624, 17.906738, 14.123269,  3.746008,  0.908235,  1.043992},
+			 {  0.077040,  0.928222,  9.555345, 35.860680,123.552246,  0.000000}}},
+{ Rh,	0,	{{  6.216648, 17.919739,  3.854252,  0.840326, 15.173498,  0.995452},
+			 {  0.070789,  0.856121, 33.889484,121.686691,  9.029517,  0.000000}}},
+{ Pd,	0,	{{  6.121511,  4.784063, 16.631683,  4.318258, 13.246773,  0.883099},
+			 {  0.062549,  0.784031,  8.751391, 34.489983,  0.784031,  0.000000}}},
+{ Ag,	0,	{{  6.073874, 17.155437,  4.173344,  0.852238, 17.988686,  0.756603},
+			 {  0.055333,  7.896512, 28.443739,110.376106,  0.716809,  0.000000}}},
+{ Cd,	0,	{{  6.080986, 18.019468,  4.018197,  1.303510, 17.974669,  0.603504},
+			 {  0.048990,  7.273646, 29.119284, 95.831207,  0.661231,  0.000000}}},
+{ In,	0,	{{  6.196477, 18.816183,  4.050479,  1.638929, 17.962912,  0.333097},
+			 {  0.042072,  6.695665, 31.009790,103.284348,  0.610714,  0.000000}}},
+{ Sn,	0,	{{ 19.325171,  6.281571,  4.498866,  1.856934, 17.917318,  0.119024},
+			 {  6.118104,  0.036915, 32.529045, 95.037186,  0.565651,  0.000000}}},
+{ Sb,	0,	{{  5.394956,  6.549570, 19.650681,  1.827820, 17.867832, -0.290506},
+			 { 33.326523,  0.030974,  5.564929, 87.130966,  0.523992,  0.000000}}},
+{ Te,	0,	{{  6.660302,  6.940756, 19.847015,  1.557175, 17.802427, -0.806668},
+			 { 33.031654,  0.025750,  5.065547, 84.101616,  0.487660,  0.000000}}},
+{ I,	0,	{{ 19.884502,  6.736593,  8.110516,  1.170953, 17.548716, -0.448811},
+			 {  4.628591,  0.027754, 31.849096, 84.406387,  0.463550,  0.000000}}},
+{ Xe,	0,	{{ 19.978920, 11.774945,  9.332182,  1.244749, 17.737501, -6.065902},
+			 {  4.143356,  0.010142, 28.796200, 75.280685,  0.413616,  0.000000}}},
+{ Cs,	0,	{{ 17.418674,  8.314444, 10.323193,  1.383834, 19.876251, -2.322802},
+			 {  0.399828,  0.016872, 25.605827,233.339676,  3.826915,  0.000000}}},
+{ Ba,	0,	{{ 19.747343, 17.368477, 10.465718,  2.592602, 11.003653, -5.183497},
+			 {  3.481823,  0.371224, 21.226641,173.834274,  0.010719,  0.000000}}},
+{ La,	0,	{{ 19.966019, 27.329655, 11.018425,  3.086696, 17.335455,-21.745489},
+			 {  3.197408,  0.003446, 19.955492,141.381973,  0.341817,  0.000000}}},
+{ Ce,	0,	{{ 17.355122, 43.988499, 20.546650,  3.130670, 11.353665,-38.386017},
+			 {  0.328369,  0.002047,  3.088196,134.907654, 18.832960,  0.000000}}},
+{ Pr,	0,	{{ 21.551311, 17.161730, 11.903859,  2.679103,  9.564197, -3.871068},
+			 {  2.995675,  0.312491, 17.716705,152.192825,  0.010468,  0.000000}}},
+{ Nd,	0,	{{ 17.331244, 62.783924, 12.160097,  2.663483, 22.239950,-57.189842},
+			 {  0.300269,  0.001320, 17.026001,148.748993,  2.910268,  0.000000}}},
+{ Pm,	0,	{{ 17.286388, 51.560162, 12.478557,  2.675515, 22.960947,-45.973682},
+			 {  0.286620,  0.001550, 16.223755,143.984512,  2.796480,  0.000000}}},
+{ Sm,	0,	{{ 23.700363, 23.072214, 12.777782,  2.684217, 17.204367,-17.452166},
+			 {  2.689539,  0.003491, 15.495437,139.862473,  0.274536,  0.000000}}},
+{ Eu,	0,	{{ 17.186195, 37.156837, 13.103387,  2.707246, 24.419271,-31.586687},
+			 {  0.261678,  0.001995, 14.787360,134.816299,  2.581883,  0.000000}}},
+{ Gd,	0,	{{ 24.898117, 17.104952, 13.222581,  3.266152, 48.995213,-43.505684},
+			 {  2.435028,  0.246961, 13.996325,110.863091,  0.001383,  0.000000}}},
+{ Tb,	0,	{{ 25.910013, 32.344139, 13.765117,  2.751404, 17.064405,-26.851971},
+			 {  2.373912,  0.002034, 13.481969,125.836510,  0.236916,  0.000000}}},
+{ Dy,	0,	{{ 26.671785, 88.687576, 14.065445,  2.768497, 17.067781,-83.279831},
+			 {  2.282593,  0.000665, 12.920230,121.937187,  0.225531,  0.000000}}},
+{ Ho,	0,	{{ 27.150190, 16.999819, 14.059334,  3.386979, 46.546471,-41.165253},
+			 {  2.169660,  0.215414, 12.213148,100.506783,  0.001211,  0.000000}}},
+{ Er,	0,	{{ 28.174887, 82.493271, 14.624002,  2.802756, 17.018515,-77.135223},
+			 {  2.120995,  0.000640, 11.915256,114.529938,  0.207519,  0.000000}}},
+{ Tm,	0,	{{ 28.925894, 76.173798, 14.904704,  2.814812, 16.998117,-70.839813},
+			 {  2.046203,  0.000656, 11.465375,111.411980,  0.199376,  0.000000}}},
+{ Yb,	0,	{{ 29.676760, 65.624069, 15.160854,  2.830288, 16.997850,-60.313812},
+			 {  1.977630,  0.000720, 11.044622,108.139153,  0.192110,  0.000000}}},
+{ Lu,	0,	{{ 30.122866, 15.099346, 56.314899,  3.540980, 16.943729,-51.049416},
+			 {  1.883090, 10.342764,  0.000780, 89.559250,  0.183849,  0.000000}}},
+{ Hf,	0,	{{ 30.617033, 15.145351, 54.933548,  4.096253, 16.896156,-49.719837},
+			 {  1.795613,  9.934469,  0.000739, 76.189705,  0.175914,  0.000000}}},
+{ Ta,	0,	{{ 31.066359, 15.341823, 49.278297,  4.577665, 16.828321,-44.119026},
+			 {  1.708732,  9.618455,  0.000760, 66.346199,  0.168002,  0.000000}}},
+{ W,	0,	{{ 31.507900, 15.682498, 37.960129,  4.885509, 16.792112,-32.864574},
+			 {  1.629485,  9.446448,  0.000898, 59.980675,  0.160798,  0.000000}}},
+{ Re,	0,	{{ 31.888456, 16.117104, 42.390297,  5.211669, 16.767591,-37.412682},
+			 {  1.549238,  9.233474,  0.000689, 54.516373,  0.152815,  0.000000}}},
+{ Os,	0,	{{ 32.210297, 16.678440, 48.559906,  5.455839, 16.735533,-43.677956},
+			 {  1.473531,  9.049695,  0.000519, 50.210201,  0.145771,  0.000000}}},
+{ Ir,	0,	{{ 32.004436,  1.975454, 17.070105, 15.939454,  5.990003,  4.018893},
+			 {  1.353767, 81.014175,  0.128093,  7.661196, 26.659403,  0.000000}}},
+{ Pt,	0,	{{ 31.273891, 18.445440, 17.063745,  5.555933,  1.575270,  4.050394},
+			 {  1.316992,  8.797154,  0.124741, 40.177994,  1.316997,  0.000000}}},
+{ Au,	0,	{{ 16.777390, 19.317156, 32.979683,  5.595453, 10.576854, -6.279078},
+			 {  0.122737,  8.621570,  1.256902, 38.008820,  0.000601,  0.000000}}},
+{ Hg,	0,	{{ 16.839890, 20.023823, 28.428564,  5.881564,  4.714706,  4.076478},
+			 {  0.115905,  8.256927,  1.195250, 39.247227,  1.195250,  0.000000}}},
+{ Tl,	0,	{{ 16.630795, 19.386616, 32.808571,  1.747191,  6.356862,  4.066939},
+			 {  0.110704,  7.181401,  1.119730, 90.660263, 26.014978,  0.000000}}},
+{ Pb,	0,	{{ 16.419567, 32.738590,  6.530247,  2.342742, 19.916475,  4.049824},
+			 {  0.105499,  1.055049, 25.025890, 80.906593,  6.664449,  0.000000}}},
+{ Bi,	0,	{{ 16.282274, 32.725136,  6.678302,  2.694750, 20.576559,  4.040914},
+			 {  0.101180,  1.002287, 25.714146, 77.057549,  6.291882,  0.000000}}},
+{ Po,	0,	{{ 16.289164, 32.807171, 21.095163,  2.505901,  7.254589,  4.046556},
+			 {  0.098121,  0.966265,  6.046622, 76.598068, 28.096128,  0.000000}}},
+{ At,	0,	{{ 16.011461, 32.615547,  8.113899,  2.884082, 21.377867,  3.995684},
+			 {  0.092639,  0.904416, 26.543257, 68.372963,  5.499512,  0.000000}}},
+{ Rn,	0,	{{ 16.070229, 32.641106, 21.489658,  2.299218,  9.480184,  4.020977},
+			 {  0.090437,  0.876409,  5.239687, 69.188477, 27.632641,  0.000000}}},
+{ Fr,	0,	{{ 16.007385, 32.663830, 21.594351,  1.598497, 11.121192,  4.003472},
+			 {  0.087031,  0.840187,  4.954467,199.805801, 26.905106,  0.000000}}},
+{ Ra,	0,	{{ 32.563690, 21.396671, 11.298093,  2.834688, 15.914965,  3.981773},
+			 {  0.801980,  4.590666, 22.758972,160.404388,  0.083544,  0.000000}}},
+{ Ac,	0,	{{ 15.914053, 32.535042, 21.553976, 11.433394,  3.612409,  3.939212},
+			 {  0.080511,  0.770669,  4.352206, 21.381622,130.500748,  0.000000}}},
+{ Th,	0,	{{ 15.784024, 32.454899, 21.849222,  4.239077, 11.736191,  3.922533},
+			 {  0.077067,  0.735137,  4.097976,109.464111, 20.512138,  0.000000}}},
+{ Pa,	0,	{{ 32.740208, 21.973675, 12.957398,  3.683832, 15.744058,  3.886066},
+			 {  0.709545,  4.050881, 19.231543,117.255005,  0.074040,  0.000000}}},
+{ U,	0,	{{ 15.679275, 32.824306, 13.660459,  3.687261, 22.279434,  3.854444},
+			 {  0.071206,  0.681177, 18.236156,112.500038,  3.930325,  0.000000}}},
+{ Np,	0,	{{ 32.999901, 22.638077, 14.219973,  3.672950, 15.683245,  3.769391},
+			 {  0.657086,  3.854918, 17.435474,109.464485,  0.068033,  0.000000}}},
+{ Pu,	0,	{{ 33.281178, 23.148544, 15.153755,  3.031492, 15.704215,  3.664200},
+			 {  0.634999,  3.856168, 16.849735,121.292038,  0.064857,  0.000000}}},
+{ Am,	0,	{{ 33.435162, 23.657259, 15.576339,  3.027023, 15.746100,  3.541160},
+			 {  0.612785,  3.792942, 16.195778,117.757004,  0.061755,  0.000000}}},
+{ Cm,	0,	{{ 15.804837, 33.480801, 24.150198,  3.655563, 15.499866,  3.390840},
+			 {  0.058619,  0.590160,  3.674720,100.736191, 15.408296,  0.000000}}},
+{ Bk,	0,	{{ 15.889072, 33.625286, 24.710381,  3.707139, 15.839268,  3.213169},
+			 {  0.055503,  0.569571,  3.615472, 97.694786, 14.754303,  0.000000}}},
+{ Cf,	0,	{{ 33.794075, 25.467693, 16.048487,  3.657525, 16.008982,  3.005326},
+			 {  0.550447,  3.581973, 14.357388, 96.064972,  0.052450,  0.000000}}},
+{ H,	-1,	{{  0.702260,  0.763666,  0.248678,  0.261323,  0.023017,  0.000425},
+			 { 23.945604, 74.897919,  6.773289,233.583450,  1.337531,  0.000000}}},
+{ Li,	+1,	{{  0.432724,  0.549257,  0.376575, -0.336481,  0.976060,  0.001764},
+			 {  0.260367,  1.042836,  7.885294,  0.260368,  3.042539,  0.000000}}},
+{ Be,	+2,	{{  3.055430, -2.372617,  1.044914,  0.544233,  0.381737, -0.653773},
+			 {  0.001226,  0.001227,  1.542106,  0.456279,  4.047479,  0.000000}}},
+{ C, AtomTypeTraits::kWKSFVal,
+			{{  1.258489,  0.728215,  1.119856,  2.168133,  0.705239,  0.019722},
+			 { 10.683769,  0.208177,  0.836097, 24.603704, 58.954273,  0.000000}}},
+{ O,	-1,	{{  3.106934,  3.235142,  1.148886,  0.783981,  0.676953,  0.046136},
+			 { 19.868080,  6.960252,  0.170043, 65.693512,  0.630757,  0.000000}}},
+{ O,	-2,	{{  3.990247,  2.300563,  0.607200,  1.907882,  1.167080,  0.025429},
+			 { 16.639956,  5.636819,  0.108493, 47.299709,  0.379984,  0.000000}}},
+{ F,	-1,	{{  0.457649,  3.841561,  1.432771,  0.801876,  3.395041,  0.069525},
+			 {  0.917243,  5.507803,  0.164955, 51.076206, 15.821679,  0.000000}}},
+{ Na,	+1,	{{  3.148690,  4.073989,  0.767888,  0.995612,  0.968249,  0.045300},
+			 {  2.594987,  6.046925,  0.070139, 14.122657,  0.217037,  0.000000}}},
+{ Mg,	+2,	{{  3.062918,  4.135106,  0.853742,  1.036792,  0.852520,  0.058851},
+			 {  2.015803,  4.417941,  0.065307,  9.669710,  0.187818,  0.000000}}},
+{ Al,	+3,	{{  4.132015,  0.912049,  1.102425,  0.614876,  3.219136,  0.019397},
+			 {  3.528641,  7.378344,  0.133708,  0.039065,  1.644728,  0.000000}}},
+{ Si, AtomTypeTraits::kWKSFVal,
+			{{  2.879033,  3.072960,  1.515981,  1.390030,  4.995051,  0.146030},
+			 {  1.239713, 38.706276,  0.081481, 93.616333,  2.770293,  0.000000}}},
+{ Si,	+4,	{{  3.676722,  3.828496,  1.258033,  0.419024,  0.720421,  0.097266},
+			 {  1.446851,  3.013144,  0.064397,  0.206254,  5.970222,  0.000000}}},
+{ Cl,	-1,	{{  1.061802,  7.139886,  6.524271,  2.355626, 35.829403,-34.916603},
+			 {  0.144727,  1.171795, 19.467655, 60.320301,  0.000436,  0.000000}}},
+{ K,	+1,	{{-17.609339,  1.494873,  7.150305, 10.899569, 15.808228,  0.257164},
+			 { 18.840979,  0.053453,  0.812940, 22.264105, 14.351593,  0.000000}}},
+{ Ca,	+2,	{{  8.501441, 12.880483,  9.765095,  7.156669,  0.711160,-21.013187},
+			 { 10.525848, -0.004033,  0.010692,  0.684443, 27.231771,  0.000000}}},
+{ Sc,	+3,	{{  7.104348,  1.511488,-53.669773, 38.404816, 24.532240,  0.118642},
+			 {  0.601957,  0.033386, 12.572138, 10.859736, 14.125230,  0.000000}}},
+{ Ti,	+2,	{{  7.040119,  1.496285,  9.657304,  0.006534,  1.649561,  0.150362},
+			 {  0.537072,  0.031914,  8.009958,201.800293, 24.039482,  0.000000}}},
+{ Ti,	+3,	{{ 36.587933,  7.230255, -9.086077,  2.084594, 17.294008,-35.111282},
+			 {  0.000681,  0.522262,  5.262317, 15.881716,  6.149805,  0.000000}}},
+{ Ti,	+4,	{{ 45.355537,  7.092900,  7.483858,-43.498817,  1.678915, -0.110628},
+			 {  9.252186,  0.523046, 13.082852, 10.193876,  0.023064,  0.000000}}},
+{ V,	+2,	{{  7.754356,  2.064100,  2.576998,  2.011404,  7.126177, -0.533379},
+			 {  7.066315,  0.014993,  7.066308, 22.055786,  0.467568,  0.000000}}},
+{ V,	+3,	{{  9.958480,  1.596350,  1.483442,-10.846044, 17.332867,  0.474921},
+			 {  6.763041,  0.056895, 17.750029,  0.328826,  0.388013,  0.000000}}},
+{ V,	+5,	{{ 15.575018,  8.448095,  1.612040, -9.721855,  1.534029,  0.552676},
+			 {  0.682708,  5.566640, 10.527077,  0.907961,  0.066667,  0.000000}}},
+{ Cr,	+2,	{{ 10.598877,  1.565858,  2.728280,  0.098064,  6.959321,  0.049870},
+			 {  6.151846,  0.023519, 17.432816, 54.002388,  0.426301,  0.000000}}},
+{ Cr,	+3,	{{  7.989310,  1.765079,  2.627125,  1.829380,  6.980908, -0.192123},
+			 {  6.068867,  0.018342,  6.068887, 16.309284,  0.420864,  0.000000}}},
+{ Mn,	+2,	{{ 11.287712, 26.042414,  3.058096,  0.090258,  7.088306,-24.566132},
+			 {  5.506225,  0.000774, 16.158575, 54.766354,  0.375580,  0.000000}}},
+{ Mn,	+3,	{{  6.926972,  2.081342, 11.128379,  2.375107, -0.419287, -0.093713},
+			 {  0.378315,  0.015054,  5.379957, 14.429586,  0.004939,  0.000000}}},
+{ Mn,	+4,	{{ 12.409131,  7.466993,  1.809947,-12.138477, 10.780248,  0.672146},
+			 {  0.300400,  0.112814, 12.520756,  0.168653,  5.173237,  0.000000}}},
+{ Fe,	+2,	{{ 11.776765, 11.165097,  3.533495,  0.165345,  7.036932, -9.676919},
+			 {  4.912232,  0.001748, 14.166556, 42.381958,  0.341324,  0.000000}}},
+{ Fe,	+3,	{{  9.721638, 63.403847,  2.141347,  2.629274,  7.033846,-61.930725},
+			 {  4.869297,  0.000293,  4.867602, 13.539076,  0.338520,  0.000000}}},
+{ Co,	+2,	{{  6.993840, 26.285812, 12.254289,  0.246114,  4.017407,-24.796852},
+			 {  0.310779,  0.000684,  4.400528, 35.741447, 12.536393,  0.000000}}},
+{ Co,	+3,	{{  6.861739,  2.678570, 12.281889,  3.501741, -0.179384, -1.147345},
+			 {  0.309794,  0.008142,  4.331703, 11.914167, 11.914167,  0.000000}}},
+{ Ni,	+2,	{{ 12.519017, 37.832058,  4.387257,  0.661552,  6.949072,-36.344471},
+			 {  3.933053,  0.000442, 10.449184, 23.860998,  0.283723,  0.000000}}},
+{ Ni,	+3,	{{ 13.579366,  1.902844, 12.859268,  3.811005, -6.838595, -0.317618},
+			 {  0.313140,  0.012621,  3.906407, 10.894311,  0.344379,  0.000000}}},
+{ Cu,	+1,	{{ 12.960763, 16.342150,  1.110102,  5.520682,  6.915452,-14.849320},
+			 {  3.576010,  0.000975, 29.523218, 10.114283,  0.261326,  0.000000}}},
+{ Cu,	+2,	{{ 11.895569, 16.344978,  5.799817,  1.048804,  6.789088,-14.878383},
+			 {  3.378519,  0.000924,  8.133653, 20.526524,  0.254741,  0.000000}}},
+{ Zn,	+2,	{{ 13.340772, 10.428857,  5.544489,  0.762295,  6.869172, -8.945248},
+			 {  3.215913,  0.001413,  8.542680, 21.891756,  0.239215,  0.000000}}},
+{ Ga,	+3,	{{ 13.123875, 35.288189,  6.126979,  0.611551,  6.724807,-33.875122},
+			 {  2.809960,  0.000323,  6.831534, 16.784311,  0.212002,  0.000000}}},
+{ Ge,	+4,	{{  6.876636,  6.779091,  9.969591,  3.135857,  0.152389,  1.086542},
+			 {  2.025174,  0.176650,  3.573822,  7.685848, 16.677574,  0.000000}}},
+{ Br,	-1,	{{ 17.714310,  6.466926,  6.947385,  4.402674, -0.697279,  1.152674},
+			 {  2.122554, 19.050768,  0.152708, 58.690361, 58.690372,  0.000000}}},
+{ Rb,	+1,	{{ 17.684320,  7.761588,  6.680874,  2.668883,  0.070974,  1.133263},
+			 {  1.710209, 14.919863,  0.128542, 31.654478,  0.128543,  0.000000}}},
+{ Sr,	+2,	{{ 17.694973,  1.275762,  6.154252,  9.234786,  0.515995,  1.125309},
+			 {  1.550888, 30.133041,  0.118774, 13.821799,  0.118774,  0.000000}}},
+{ Y,	+3,	{{ 46.660366, 10.369686,  4.623042,-62.170834, 17.471146, 19.023842},
+			 { -0.019971, 13.180257,  0.176398, -0.016727,  1.467348,  0.000000}}},
+{ Zr,	+4,	{{  6.802956, 17.699253, 10.650647, -0.248108,  0.250338,  0.827902},
+			 {  0.096228,  1.296127, 11.240715, -0.219259, -0.219021,  0.000000}}},
+{ Nb,	+3,	{{ 17.714323,  1.675213,  7.483963,  8.322464, 11.143573, -8.339573},
+			 {  1.172419, 30.102791,  0.080255, -0.002983, 10.456687,  0.000000}}},
+{ Nb,	+5,	{{ 17.580206,  7.633277, 10.793497,  0.180884, 67.837921,-68.024780},
+			 {  1.165852,  0.078558,  9.507652, 31.621656, -0.000438,  0.000000}}},
+{ Mo,	+3,	{{  7.447050, 17.778122, 11.886068,  1.997905,  1.789626, -1.898764},
+			 {  0.072000,  1.073145,  9.834720, 28.221746, -0.011674,  0.000000}}},
+{ Mo,	+5,	{{  7.929879, 17.667669, 11.515987,  0.500402, 77.444084,-78.056595},
+			 {  0.068856,  1.068064,  9.046229, 26.558945, -0.000473,  0.000000}}},
+{ Mo,	+6,	{{ 34.757683,  9.653037,  6.584769,-18.628115,  2.490594,  1.141916},
+			 {  1.301770,  7.123843,  0.094097,  1.617443, 12.335434,  0.000000}}},
+{ Ru,	+3,	{{ 17.894758, 13.579529, 10.729251,  2.474095, 48.227997,-51.905243},
+			 {  0.902827,  8.740579,  0.045125, 24.764954, -0.001699,  0.000000}}},
+{ Ru,	+4,	{{ 17.845776, 13.455084, 10.229087,  1.653524, 14.059795,-17.241762},
+			 {  0.901070,  8.482392,  0.045972, 23.015272, -0.004889,  0.000000}}},
+{ Rh,	+3,	{{ 17.758621, 14.569813,  5.298320,  2.533579,  0.879753,  0.960843},
+			 {  0.841779,  8.319533,  0.069050, 23.709131,  0.069050,  0.000000}}},
+{ Rh,	+4,	{{ 17.716188, 14.446654,  5.185801,  1.703448,  0.989992,  0.959941},
+			 {  0.840572,  8.100647,  0.068995, 22.357307,  0.068995,  0.000000}}},
+{ Pd,	+2,	{{  6.122282, 15.651012,  3.513508,  9.060790,  8.771199,  0.879336},
+			 {  0.062424,  8.018296, 24.784275,  0.776457,  0.776457,  0.000000}}},
+{ Pd,	+4,	{{  6.152421,-96.069023, 31.622141, 81.578255, 17.801403,  0.915874},
+			 {  0.063951, 11.090354, 13.466152,  9.758302,  0.783014,  0.000000}}},
+{ Ag,	+1,	{{  6.091192,  4.019526, 16.948174,  4.258638, 13.889437,  0.785127},
+			 {  0.056305,  0.719340,  7.758938, 27.368349,  0.719340,  0.000000}}},
+{ Ag,	+2,	{{  6.401808, 48.699802,  4.799859,-32.332523, 16.356710,  1.068247},
+			 {  0.068167,  0.942270, 20.639496,  1.100365,  6.883131,  0.000000}}},
+{ Cd,	+2,	{{  6.093711, 43.909691, 17.041306,-39.675117, 17.958918,  0.664795},
+			 {  0.050624,  8.654143, 15.621396, 11.082067,  0.667591,  0.000000}}},
+{ In,	+3,	{{  6.206277, 18.497746,  3.078131, 10.524613,  7.401234,  0.293677},
+			 {  0.041357,  6.605563, 18.792250,  0.608082,  0.608082,  0.000000}}},
+{ Sn,	+2,	{{  6.353672,  4.770377, 14.672025,  4.235959, 18.002131, -0.042519},
+			 {  0.034720,  6.167891,  6.167879, 29.006456,  0.561774,  0.000000}}},
+{ Sn,	+4,	{{ 15.445732,  6.420892,  4.562980,  1.713385, 18.033537, -0.172219},
+			 {  6.280898,  0.033144,  6.280899, 17.983601,  0.557980,  0.000000}}},
+{ Sb,	+3,	{{ 10.189171, 57.461918, 19.356573,  4.862206,-45.394096,  1.516108},
+			 {  0.089485,  0.375256,  5.357987, 22.153736,  0.297768,  0.000000}}},
+{ Sb,	+5,	{{ 17.920622,  6.647932, 12.724075,  1.555545,  7.600591, -0.445371},
+			 {  0.522315,  0.029487,  5.718210, 16.433775,  5.718204,  0.000000}}},
+{ I,	-1,	{{ 20.010330, 17.835524,  8.104130,  2.231118,  9.158548, -3.341004},
+			 {  4.565931,  0.444266, 32.430672, 95.149040,  0.014906,  0.000000}}},
+{ Cs,	+1,	{{ 19.939056, 24.967621, 10.375884,  0.454243, 17.660248,-19.394306},
+			 {  3.770511,  0.004040, 25.311275, 76.537766,  0.384730,  0.000000}}},
+{ Ba,	+2,	{{ 19.750200, 17.513683, 10.884892,  0.321585, 65.149834,-59.618172},
+			 {  3.430748,  0.361590, 21.358307, 70.309402,  0.001418,  0.000000}}},
+{ La,	+3,	{{ 19.688887, 17.345703, 11.356296,  0.099418, 82.358124,-76.846909},
+			 {  3.146211,  0.339586, 18.753832, 90.345459,  0.001072,  0.000000}}},
+{ Ce,	+3,	{{ 26.593231, 85.866432, -6.677695, 12.111847, 17.401903,-80.313423},
+			 {  3.280381,  0.001012,  4.313575, 17.868504,  0.326962,  0.000000}}},
+{ Ce,	+4,	{{ 17.457533, 25.659941, 11.691037, 19.695251,-16.994749, -3.515096},
+			 {  0.311812, -0.003793, 16.568687,  2.886395, -0.008931,  0.000000}}},
+{ Pr,	+3,	{{ 20.879841, 36.035797, 12.135341,  0.283103, 17.167803,-30.500784},
+			 {  2.870897,  0.002364, 16.615236, 53.909359,  0.306993,  0.000000}}},
+{ Pr,	+4,	{{ 17.496082, 21.538509, 20.403114, 12.062211, -7.492043, -9.016722},
+			 {  0.294457, -0.002742,  2.772886, 15.804613, -0.013556,  0.000000}}},
+{ Nd,	+3,	{{ 17.120077, 56.038139, 21.468307, 10.000671,  2.905866,-50.541992},
+			 {  0.291295,  0.001421,  2.743681, 14.581367, 22.485098,  0.000000}}},
+{ Pm,	+3,	{{ 22.221066, 17.068142, 12.805423,  0.435687, 52.238770,-46.767181},
+			 {  2.635767,  0.277039, 14.927315, 45.768017,  0.001455,  0.000000}}},
+{ Sm,	+3,	{{ 15.618565, 19.538092, 13.398946, -4.358811, 24.490461, -9.714854},
+			 {  0.006001,  0.306379, 14.979594,  0.748825,  2.454492,  0.000000}}},
+{ Eu,	+2,	{{ 23.899035, 31.657497, 12.955752,  1.700576, 16.992199,-26.204315},
+			 {  2.467332,  0.002230, 13.625002, 35.089481,  0.253136,  0.000000}}},
+{ Eu,	+3,	{{ 17.758327, 33.498665, 24.067188, 13.436883, -9.019134,-19.768026},
+			 {  0.244474, -0.003901,  2.487526, 14.568011, -0.015628,  0.000000}}},
+{ Gd,	+3,	{{ 24.344999, 16.945311, 13.866931,  0.481674, 93.506378,-88.147179},
+			 {  2.333971,  0.239215, 12.982995, 43.876347,  0.000673,  0.000000}}},
+{ Tb,	+3,	{{ 24.878252, 16.856016, 13.663937,  1.279671, 39.271294,-33.950317},
+			 {  2.223301,  0.227290, 11.812528, 29.910065,  0.001527,  0.000000}}},
+{ Dy,	+3,	{{ 16.864344, 90.383461, 13.675473,  1.687078, 25.540651,-85.150650},
+			 {  0.216275,  0.000593, 11.121207, 26.250975,  2.135930,  0.000000}}},
+{ Ho,	+3,	{{ 16.837524, 63.221336, 13.703766,  2.061602, 26.202621,-58.026505},
+			 {  0.206873,  0.000796, 10.500283, 24.031883,  2.055060,  0.000000}}},
+{ Er,	+3,	{{ 16.810127, 22.681061, 13.864114,  2.294506, 26.864477,-17.513460},
+			 {  0.198293,  0.002126,  9.973341, 22.836388,  1.979442,  0.000000}}},
+{ Tm,	+3,	{{ 16.787500, 15.350905, 14.182357,  2.299111, 27.573771,-10.192087},
+			 {  0.190852,  0.003036,  9.602934, 22.526880,  1.912862,  0.000000}}},
+{ Yb,	+2,	{{ 28.443794, 16.849527, 14.165081,  3.445311, 28.308853,-23.214935},
+			 {  1.863896,  0.183811,  9.225469, 23.691355,  0.001463,  0.000000}}},
+{ Yb,	+3,	{{ 28.191629, 16.828087, 14.167848,  2.744962, 23.171774,-18.103676},
+			 {  1.842889,  0.182788,  9.045957, 20.799847,  0.001759,  0.000000}}},
+{ Lu,	+3,	{{ 28.828693, 16.823227, 14.247617,  3.079559, 25.647667,-20.626528},
+			 {  1.776641,  0.175560,  8.575531, 19.693701,  0.001453,  0.000000}}},
+{ Hf,	+4,	{{ 29.267378, 16.792543, 14.785310,  2.184128, 23.791996,-18.820383},
+			 {  1.697911,  0.168313,  8.190025, 18.277578,  0.001431,  0.000000}}},
+{ Ta,	+5,	{{ 29.539469, 16.741854, 15.182070,  1.642916, 16.437447,-11.542459},
+			 {  1.612934,  0.160460,  7.654408, 17.070732,  0.001858,  0.000000}}},
+{ W,	+6,	{{ 29.729357, 17.247808, 15.184488,  1.154652,  0.739335,  3.945157},
+			 {  1.501648,  0.140803,  6.880573, 14.299601, 14.299618,  0.000000}}},
+{ Os,	+4,	{{ 17.113485, 15.792370, 23.342392,  4.090271,  7.671292,  3.988390},
+			 {  0.131850,  7.288542,  1.389307, 19.629425,  1.389307,  0.000000}}},
+{ Ir,	+3,	{{ 31.537575, 16.363338, 15.597141,  5.051404,  1.436935,  4.009459},
+			 {  1.334144,  7.451918,  0.127514, 21.705648,  0.127515,  0.000000}}},
+{ Ir,	+4,	{{ 30.391249, 16.146996, 17.019068,  4.458904,  0.975372,  4.006865},
+			 {  1.328519,  7.181766,  0.127337, 19.060146,  1.328519,  0.000000}}},
+{ Pt,	+2,	{{ 31.986849, 17.249048, 15.269374,  5.760234,  1.694079,  4.032512},
+			 {  1.281143,  7.625512,  0.123571, 24.190826,  0.123571,  0.000000}}},
+{ Pt,	+4,	{{ 41.932713, 16.339224, 17.653894,  6.012420,-12.036877,  4.094551},
+			 {  1.111409,  6.466086,  0.128917, 16.954155,  0.778721,  0.000000}}},
+{ Au,	+1,	{{ 32.124306, 16.716476, 16.814100,  7.311565,  0.993064,  4.040792},
+			 {  1.216073,  7.165378,  0.118715, 20.442486, 53.095985,  0.000000}}},
+{ Au,	+3,	{{ 31.704271, 17.545767, 16.819551,  5.522640,  0.361725,  4.042679},
+			 {  1.215561,  7.220506,  0.118812, 20.050970,  1.215562,  0.000000}}},
+{ Hg,	+1,	{{ 28.866837, 19.277540, 16.776051,  6.281459,  3.710289,  4.068430},
+			 {  1.173967,  7.583842,  0.115351, 29.055994,  1.173968,  0.000000}}},
+{ Hg,	+2,	{{ 32.411079, 18.690371, 16.711773,  9.974835, -3.847611,  4.052869},
+			 {  1.162980,  7.329806,  0.114518, 22.009489, 22.009493,  0.000000}}},
+{ Tl,	+1,	{{ 32.295044, 16.570049, 17.991013,  1.535355,  7.554591,  4.054030},
+			 {  1.101544,  0.110020,  6.528559, 52.495068, 20.338634,  0.000000}}},
+{ Tl,	+3,	{{ 32.525639, 19.139185, 17.100321,  5.891115, 12.599463, -9.256075},
+			 {  1.094966,  6.900992,  0.103667, 18.489614, -0.001401,  0.000000}}},
+{ Pb,	+2,	{{ 27.392647, 16.496822, 19.984501,  6.813923,  5.233910,  4.065623},
+			 {  1.058874,  0.106305,  6.708123, 24.395554,  1.058874,  0.000000}}},
+{ Pb,	+4,	{{ 32.505657, 20.014240, 14.645661,  5.029499,  1.760138,  4.044678},
+			 {  1.047035,  6.670321,  0.105279, 16.525040,  0.105279,  0.000000}}},
+{ Bi,	+3,	{{ 32.461437, 19.438683, 16.302486,  7.322662,  0.431704,  4.043703},
+			 {  0.997930,  6.038867,  0.101338, 18.371586, 46.361046,  0.000000}}},
+{ Bi,	+5,	{{ 16.734028, 20.580494,  9.452623, 61.155834,-34.041023,  4.113663},
+			 {  0.105076,  4.773282, 11.762162,  1.211775,  1.619408,  0.000000}}},
+{ Ra,	+2,	{{  4.986228, 32.474945, 21.947443, 11.800013, 10.807292,  3.956572},
+			 {  0.082597,  0.791468,  4.608034, 24.792431,  0.082597,  0.000000}}},
+{ Ac,	+3,	{{ 15.584983, 32.022125, 21.456327,  0.757593, 12.341252,  3.838984},
+			 {  0.077438,  0.739963,  4.040735, 47.525002, 19.406845,  0.000000}}},
+{ Th,	+4,	{{ 15.515445, 32.090691, 13.996399, 12.918157,  7.635514,  3.831122},
+			 {  0.074499,  0.711663,  3.871044, 18.596891,  3.871044,  0.000000}}},
+{ U,	+3,	{{ 15.360309, 32.395657, 21.961290,  1.325894, 14.251453,  3.706622},
+			 {  0.067815,  0.654643,  3.643409, 39.604965, 16.330570,  0.000000}}},
+{ U,	+4,	{{ 15.355091, 32.235306,  0.557745, 14.396367, 21.751173,  3.705863},
+			 {  0.067789,  0.652613, 42.354237, 15.908239,  3.553231,  0.000000}}},
+{ U,	+6,	{{ 15.333844, 31.770849, 21.274414, 13.872636,  0.048519,  3.700591},
+			 {  0.067644,  0.646384,  3.317894, 14.650250, 75.339699,  0.000000}}},
+{ Np,	+3,	{{ 15.378152, 32.572132, 22.206125,  1.413295, 14.828381,  3.603370},
+			 {  0.064613,  0.631420,  3.561936, 37.875511, 15.546129,  0.000000}}},
+{ Np,	+4,	{{ 15.373926, 32.423019, 21.969994,  0.662078, 14.969350,  3.603039},
+			 {  0.064597,  0.629658,  3.476389, 39.438942, 15.135764,  0.000000}}},
+{ Np,	+6,	{{ 15.359986, 31.992825, 21.412458,  0.066574, 14.568174,  3.600942},
+			 {  0.064528,  0.624505,  3.253441, 67.658318, 13.980832,  0.000000}}},
+{ Pu,	+3,	{{ 15.356004, 32.769127, 22.680210,  1.351055, 15.416232,  3.428895},
+			 {  0.060590,  0.604663,  3.491509, 37.260635, 14.981921,  0.000000}}},
+{ Pu,	+4,	{{ 15.416219, 32.610569, 22.256662,  0.719495, 15.518152,  3.480408},
+			 {  0.061456,  0.607938,  3.411848, 37.628792, 14.464360,  0.000000}}},
+{ Pu,	+6,	{{ 15.436506, 32.289719, 14.726737, 15.012391,  7.024677,  3.502325},
+			 {  0.061815,  0.606541,  3.245363, 13.616438,  3.245364,  0.000000}}}
+};
+
+} // namespace data
+
+
+// --------------------------------------------------------------------
 // AtomTypeTraits
 // AtomTypeTraits
 
 
 AtomTypeTraits::AtomTypeTraits(const string& symbol)
 AtomTypeTraits::AtomTypeTraits(const string& symbol)
 	: mInfo(nullptr)
 	: mInfo(nullptr)
 {
 {
-	for (auto& i: kKnownAtoms)
+	for (auto& i: data::kKnownAtoms)
 	{
 	{
 		if (cif::iequals(i.symbol, symbol))
 		if (cif::iequals(i.symbol, symbol))
 		{
 		{
@@ -158,14 +603,14 @@ AtomTypeTraits::AtomTypeTraits(AtomType t)
 {
 {
 	if (t < H or t > Lr)
 	if (t < H or t > Lr)
 		throw invalid_argument("atomType out of range");
 		throw invalid_argument("atomType out of range");
-	mInfo = &kKnownAtoms[t];
+	mInfo = &data::kKnownAtoms[t];
 }
 }
 
 
 bool AtomTypeTraits::isElement(const string& symbol)
 bool AtomTypeTraits::isElement(const string& symbol)
 {
 {
 	bool result = false;
 	bool result = false;
 	
 	
-	for (auto& i: kKnownAtoms)
+	for (auto& i: data::kKnownAtoms)
 	{
 	{
 		if (cif::iequals(i.symbol, symbol))
 		if (cif::iequals(i.symbol, symbol))
 		{
 		{
@@ -181,7 +626,7 @@ bool AtomTypeTraits::isMetal(const string& symbol)
 {
 {
 	bool result = false;
 	bool result = false;
 	
 	
-	for (auto& i: kKnownAtoms)
+	for (auto& i: data::kKnownAtoms)
 	{
 	{
 		if (cif::iequals(i.symbol, symbol))
 		if (cif::iequals(i.symbol, symbol))
 		{
 		{
@@ -193,4 +638,15 @@ bool AtomTypeTraits::isMetal(const string& symbol)
 	return result;
 	return result;
 }
 }
 
 
+auto AtomTypeTraits::wksf(int charge) const -> const WKSF&
+{
+	for (auto& sf: data::kWKSFData)
+	{
+		if (sf.symbol == mInfo->type and sf.charge == charge)
+			return sf.sf;
+	}
+
+	throw runtime_error("No scattering factor found for " + name() + to_string(charge));
+}
+	
 }
 }

src/ResolutionCalculator.cpp

+// --------------------------------------------------------------------
+
+#include "cif++/ResolutionCalculator.h"
+
+using namespace std;
+
+namespace libcif
+{
+
+ResolutionCalculator::ResolutionCalculator(double a, double b, double c,
+		double alpha, double beta, double gamma)
+{
+	double deg2rad = atan(1.0) / 45.0;
+	
+	double ca = cos(deg2rad * alpha);
+	double sa = sin(deg2rad * alpha);
+	double cb = cos(deg2rad * beta);
+	double sb = sin(deg2rad * beta);
+	double cg = cos(deg2rad * gamma);
+	double sg = sin(deg2rad * gamma);
+	
+	double cast = (cb * cg - ca) / (sb * sg);
+	double cbst = (cg * ca - cb) / (sg * sa);
+	double cgst = (ca * cb - cg) / (sa * sb);
+	
+	double sast = sqrt(1 - cast * cast);
+	double sbst = sqrt(1 - cbst * cbst);
+	double sgst = sqrt(1 - cgst * cgst);
+
+	double ast = 1 / (a * sb * sgst);
+	double bst = 1 / (b * sg * sast);
+	double cst = 1 / (c * sa * sbst);
+	
+	mCoefs[0] = ast * ast;
+	mCoefs[1] = 2 * ast * bst * cgst;
+	mCoefs[2] = 2 * ast * cst * cbst;
+	mCoefs[3] = bst * bst;
+	mCoefs[4] = 2 * bst * cst * cast;
+	mCoefs[5] = cst * cst;
+}
+
+}

src/Structure.cpp

@@ -11,6 +11,7 @@
 #include "cif++/PDB2Cif.h"
 #include "cif++/PDB2Cif.h"
 #include "cif++/CifParser.h"
 #include "cif++/CifParser.h"
 #include "cif++/Cif2PDB.h"
 #include "cif++/Cif2PDB.h"
+#include "cif++/AtomShape.h"
 
 
 using namespace std;
 using namespace std;
 
 
@@ -258,6 +259,11 @@ struct AtomImpl
 		return mCompound != nullptr and mCompound->isWater();
 		return mCompound != nullptr and mCompound->isWater();
 	}
 	}
 
 
+	float radius() const
+	{
+		return mRadius;
+	}
+
 	const File&			mFile;
 	const File&			mFile;
 	string				mId;
 	string				mId;
 	int					mRefcount;
 	int					mRefcount;
@@ -265,6 +271,7 @@ struct AtomImpl
 	const Compound*		mCompound;
 	const Compound*		mCompound;
 	Point				mLocation;
 	Point				mLocation;
 	AtomType			mType;
 	AtomType			mType;
+	float				mRadius = nan("4");
 	
 	
 //	const entity&		mEntity;
 //	const entity&		mEntity;
 //	std::string			mAsymId;
 //	std::string			mAsymId;
@@ -421,6 +428,21 @@ clipper::Atom Atom::toClipper() const
 	return mImpl->toClipper();
 	return mImpl->toClipper();
 }
 }
 
 
+void Atom::calculateRadius(float resHigh, float resLow, float perc)
+{
+	AtomShape shape(*this, resHigh, resLow);
+	mImpl->mRadius = shape.radius();
+
+	// verbose
+	if (VERBOSE > 1)
+		cout << "Calculated radius for " << AtomTypeTraits(mImpl->mType).name() << " with charge " << charge() << " is " << mImpl->mRadius << endl;
+}
+
+float Atom::radius() const
+{
+	return mImpl->mRadius;
+}
+
 // --------------------------------------------------------------------
 // --------------------------------------------------------------------
 // residue
 // residue