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libcifpp
Commit 3a968808 by maarten
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electron scattering support 

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@230 a1961a4f-ab94-4bcc-80e8-33b5a54de466
parent eb4f2f77
Showing with 267 additions and 27 deletions
include/cif++/AtomShape.h
......@@ -13,9 +13,10 @@ namespace libcif
class AtomShape
{
public:
AtomShape(const Atom& atom, float resHigh, float resLow);
AtomShape(const Atom& atom, float resHigh, float resLow,
float bFactor);
bool electronScattering);
AtomShape(const Atom& atom, float resHigh, float resLow,
bool electronScattering, float bFactor);
~AtomShape();
......
include/cif++/AtomType.h
......@@ -199,7 +199,8 @@ class AtomTypeTraits
// data type encapsulating the Waasmaier & Kirfel scattering factors
// in a simplified form (only a and b).
struct WKSF
// Added the electrion scattering factors as well
struct SFData
{
double a[6], b[6];
};
......@@ -207,7 +208,8 @@ class AtomTypeTraits
// to get the Cval and Siva values, use this constant as charge:
enum { kWKSFVal = -99 };
const WKSF& wksf(int charge = 0) const;
const SFData& wksf(int charge = 0) const;
const SFData& elsf() const;
private:
const struct AtomTypeInfo* mInfo;
......
src/AtomShape.cpp
......@@ -328,10 +328,11 @@ double DensityIntegration::integrateRadius(float perc, float occupancy, double y
struct AtomShapeImpl
{
AtomShapeImpl(AtomType symbol, int charge, float uIso, float occupancy, float resHigh, float resLow)
AtomShapeImpl(AtomType symbol, int charge, float uIso, float occupancy, float resHigh, float resLow, bool electronScattering)
: mSymbol(symbol), mCharge(charge), mUIso(uIso), mOccupancy(occupancy)
, mResHigh(resHigh), mResLow(resLow)
, mIntegrator(DensityIntegration::instance(resLow, resHigh))
, mElectronScattering(electronScattering)
{
auto st = mIntegrator.st();
auto sts = mIntegrator.sts();
......@@ -340,7 +341,8 @@ struct AtomShapeImpl
mYi = 0;
mFst = vector<double>(st.size(), 0);
auto& D = AtomTypeTraits(symbol).wksf(charge);
auto& D =
mElectronScattering ? AtomTypeTraits(symbol).elsf() : AtomTypeTraits(symbol).wksf(charge);
auto bIso = clipper::Util::u2b(uIso);
float as = mIntegrator.a() * mIntegrator.a();
......@@ -375,6 +377,7 @@ struct AtomShapeImpl
int mCharge;
float mUIso, mOccupancy;
float mResHigh, mResLow;
bool mElectronScattering;
const DensityIntegration& mIntegrator;
double mYi;
......@@ -400,15 +403,15 @@ struct AtomShapeImpl
// --------------------------------------------------------------------
AtomShape::AtomShape(const Atom& atom, float resHigh, float resLow)
AtomShape::AtomShape(const Atom& atom, float resHigh, float resLow, bool electronScattering)
: mImpl(new AtomShapeImpl(atom.type(), atom.charge(), atom.uIso(),
atom.occupancy(), resHigh, resLow))
atom.occupancy(), resHigh, resLow, electronScattering))
{
}
AtomShape::AtomShape(const Atom& atom, float resHigh, float resLow, float bFactor)
AtomShape::AtomShape(const Atom& atom, float resHigh, float resLow, bool electronScattering, float bFactor)
: mImpl(new AtomShapeImpl(atom.type(), atom.charge(), clipper::Util::b2u(bFactor),
1.0, resHigh, resLow))
1.0, resHigh, resLow, electronScattering))
{
}
......
src/AtomType.cpp
......@@ -141,14 +141,14 @@ uint32 kKnownAtomsCount = sizeof(kKnownAtoms) / sizeof(AtomTypeInfo);
// --------------------------------------------------------------------
// The coefficients from Waasmaier & Kirfel (1995), Acta Cryst. A51, 416-431.
struct WKSFData
struct SFDataArrayElement
{
AtomType symbol;
int8 charge;
AtomTypeTraits::WKSF sf;
AtomTypeTraits::SFData sf;
};
WKSFData kWKSFData[] = {
SFDataArrayElement kWKSFData[] = {
//{ H, 0, {{ 0.493002, 0.322912, 0.140191, 0.040810, 0.003038 },
// { 10.510900, 26.125700, 3.142360, 57.799698, 0.000000 }}},
......@@ -1005,8 +1005,206 @@ WKSFData kWKSFData[] = {
{ 0.061815, 0.606541, 3.245363, 13.616438, 3.245364, 0.000000}}}
};
} // namespace data
SFDataArrayElement kELSFData[] = {
{H, 0, {{ 0.034900, 0.120100, 0.197000, 0.057300, 0.119500 },
{ 0.534700, 3.586700, 12.347100, 18.952499, 38.626900 }}},
{He, 0, {{ 0.031700, 0.083800, 0.152600, 0.133400, 0.016400 },
{ 0.250700, 1.475100, 4.493800, 12.664600, 31.165300 }}},
{Li, 0, {{ 0.075000, 0.224900, 0.554800, 1.495400, 0.935400 },
{ 0.386400, 2.938300, 15.382900, 53.554501, 138.733704 }}},
{Be, 0, {{ 0.078000, 0.221000, 0.674000, 1.386700, 0.692500 },
{ 0.313100, 2.238100, 10.151700, 30.906099, 78.327301 }}},
{B, 0, {{ 0.090900, 0.255100, 0.773800, 1.213600, 0.460600 },
{ 0.299500, 2.115500, 8.381600, 24.129200, 63.131401 }}},
{C, 0, {{ 0.089300, 0.256300, 0.757000, 1.048700, 0.357500 },
{ 0.246500, 1.710000, 6.409400, 18.611300, 50.252300 }}},
{N, 0, {{ 0.102200, 0.321900, 0.798200, 0.819700, 0.171500 },
{ 0.245100, 1.748100, 6.192500, 17.389400, 48.143101 }}},
{O, 0, {{ 0.097400, 0.292100, 0.691000, 0.699000, 0.203900 },
{ 0.206700, 1.381500, 4.694300, 12.710500, 32.472599 }}},
{F, 0, {{ 0.108300, 0.317500, 0.648700, 0.584600, 0.142100 },
{ 0.205700, 1.343900, 4.278800, 11.393200, 28.788099 }}},
{Ne, 0, {{ 0.126900, 0.353500, 0.558200, 0.467400, 0.146000 },
{ 0.220000, 1.377900, 4.020300, 9.493400, 23.127800 }}},
{Na, 0, {{ 0.214200, 0.685300, 0.769200, 1.658900, 1.448200 },
{ 0.333400, 2.344600, 10.083000, 48.303699, 138.270004 }}},
{Mg, 0, {{ 0.231400, 0.686600, 0.967700, 2.188200, 1.133900 },
{ 0.327800, 2.272000, 10.924100, 39.289799, 101.974800 }}},
{Al, 0, {{ 0.239000, 0.657300, 1.201100, 2.558600, 1.231200 },
{ 0.313800, 2.106300, 10.416300, 34.455200, 98.534401 }}},
{Si, 0, {{ 0.251900, 0.637200, 1.379500, 2.508200, 1.050000 },
{ 0.307500, 2.017400, 9.674600, 29.374399, 80.473198 }}},
{P, 0, {{ 0.254800, 0.610600, 1.454100, 2.320400, 0.847700 },
{ 0.290800, 1.874000, 8.517600, 24.343399, 63.299599 }}},
{S, 0, {{ 0.249700, 0.562800, 1.389900, 2.186500, 0.771500 },
{ 0.268100, 1.671100, 7.026700, 19.537701, 50.388802 }}},
{Cl, 0, {{ 0.244300, 0.539700, 1.391900, 2.019700, 0.662100 },
{ 0.246800, 1.524200, 6.153700, 16.668699, 42.308601 }}},
{Ar, 0, {{ 0.238500, 0.501700, 1.342800, 1.889900, 0.607900 },
{ 0.228900, 1.369400, 5.256100, 14.092800, 35.536098 }}},
{K, 0, {{ 0.411500, 1.403100, 2.278400, 2.674200, 2.216200 },
{ 0.370300, 3.387400, 13.102900, 68.959198, 194.432907 }}},
{Ca, 0, {{ 0.405400, 1.388000, 2.160200, 3.753200, 2.206300 },
{ 0.349900, 3.099100, 11.960800, 53.935299, 142.389206 }}},
{Sc, 0, {{ 0.378700, 1.218100, 2.059400, 3.261800, 2.387000 },
{ 0.313300, 2.585600, 9.581300, 41.768799, 116.728203 }}},
{Ti, 0, {{ 0.382500, 1.259800, 2.000800, 3.061700, 2.069400 },
{ 0.304000, 2.486300, 9.278300, 39.075100, 109.458298 }}},
{V, 0, {{ 0.387600, 1.275000, 1.910900, 2.831400, 1.897900 },
{ 0.296700, 2.378000, 8.798100, 35.952801, 101.720100 }}},
{Cr, 0, {{ 0.404600, 1.369600, 1.894100, 2.080000, 1.219600 },
{ 0.298600, 2.395800, 9.140600, 37.470100, 113.712097 }}},
{Mn, 0, {{ 0.379600, 1.209400, 1.781500, 2.542000, 1.593700 },
{ 0.269900, 2.045500, 7.472600, 31.060400, 91.562202 }}},
{Fe, 0, {{ 0.394600, 1.272500, 1.703100, 2.314000, 1.479500 },
{ 0.271700, 2.044300, 7.600700, 29.971399, 86.226501 }}},
{Co, 0, {{ 0.411800, 1.316100, 1.649300, 2.193000, 1.283000 },
{ 0.274200, 2.037200, 7.720500, 29.968000, 84.938301 }}},
{Ni, 0, {{ 0.386000, 1.176500, 1.545100, 2.073000, 1.381400 },
{ 0.247800, 1.766000, 6.310700, 25.220400, 74.314598 }}},
{Cu, 0, {{ 0.431400, 1.320800, 1.523600, 1.467100, 0.856200 },
{ 0.269400, 1.922300, 7.347400, 28.989201, 90.624603 }}},
{Zn, 0, {{ 0.428800, 1.264600, 1.447200, 1.829400, 1.093400 },
{ 0.259300, 1.799800, 6.750000, 25.586000, 73.528397 }}},
{Ga, 0, {{ 0.481800, 1.403200, 1.656100, 2.460500, 1.105400 },
{ 0.282500, 1.978500, 8.754600, 32.523800, 98.552299 }}},
{Ge, 0, {{ 0.465500, 1.301400, 1.608800, 2.699800, 1.300300 },
{ 0.264700, 1.792600, 7.607100, 26.554100, 77.523804 }}},
{As, 0, {{ 0.451700, 1.222900, 1.585200, 2.795800, 1.263800 },
{ 0.249300, 1.643600, 6.815400, 22.368099, 62.039001 }}},
{Se, 0, {{ 0.447700, 1.167800, 1.584300, 2.808700, 1.195600 },
{ 0.240500, 1.544200, 6.323100, 19.461000, 52.023300 }}},
{Br, 0, {{ 0.479800, 1.194800, 1.869500, 2.695300, 0.820300 },
{ 0.250400, 1.596300, 6.965300, 19.849199, 50.323299 }}},
{Kr, 0, {{ 0.454600, 1.099300, 1.769600, 2.706800, 0.867200 },
{ 0.230900, 1.427900, 5.944900, 16.675200, 42.224300 }}},
{Rb, 0, {{ 1.016000, 2.852800, 3.546600, -7.780400, 12.114800 },
{ 0.485300, 5.092500, 25.785101, 130.451508, 138.677505 }}},
{Sr, 0, {{ 0.670300, 1.492600, 3.336800, 4.460000, 3.150100 },
{ 0.319000, 2.228700, 10.350400, 52.329102, 151.221603 }}},
{Y, 0, {{ 0.689400, 1.547400, 3.245000, 4.212600, 2.976400 },
{ 0.318900, 2.290400, 10.006200, 44.077099, 125.012001 }}},
{Zr, 0, {{ 0.671900, 1.468400, 3.166800, 3.955700, 2.892000 },
{ 0.303600, 2.124900, 8.923600, 36.845798, 108.204903 }}},
{Nb, 0, {{ 0.612300, 1.267700, 3.034800, 3.384100, 2.368300 },
{ 0.270900, 1.768300, 7.248900, 27.946501, 98.562401 }}},
{Mo, 0, {{ 0.677300, 1.479800, 3.178800, 3.082400, 1.838400 },
{ 0.292000, 2.060600, 8.112900, 30.533600, 100.065804 }}},
{Tc, 0, {{ 0.708200, 1.639200, 3.199300, 3.432700, 1.871100 },
{ 0.297600, 2.210600, 8.524600, 33.145599, 96.637703 }}},
{Ru, 0, {{ 0.673500, 1.493400, 3.096600, 2.725400, 1.559700 },
{ 0.277300, 1.971600, 7.324900, 26.689100, 90.558098 }}},
{Rh, 0, {{ 0.641300, 1.369000, 2.985400, 2.695200, 1.543300 },
{ 0.258000, 1.772100, 6.385400, 23.254900, 85.151703 }}},
{Pd, 0, {{ 0.590400, 1.177500, 2.651900, 2.287500, 0.868900 },
{ 0.232400, 1.501900, 5.159100, 15.542800, 46.821301 }}},
{Ag, 0, {{ 0.637700, 1.379000, 2.829400, 2.363100, 1.455300 },
{ 0.246600, 1.697400, 5.765600, 20.094299, 76.737198 }}},
{Cd, 0, {{ 0.636400, 1.424700, 2.780200, 2.597300, 1.788600 },
{ 0.240700, 1.682300, 5.658800, 20.721901, 69.110901 }}},
{In, 0, {{ 0.676800, 1.658900, 2.774000, 3.183500, 2.132600 },
{ 0.252200, 1.854500, 6.293600, 25.145700, 84.544800 }}},
{Sn, 0, {{ 0.722400, 1.961000, 2.716100, 3.560300, 1.897200 },
{ 0.265100, 2.060400, 7.301100, 27.549299, 81.334900 }}},
{Sb, 0, {{ 0.710600, 1.924700, 2.614900, 3.832200, 1.889900 },
{ 0.256200, 1.964600, 6.885200, 24.764799, 68.916801 }}},
{Te, 0, {{ 0.694700, 1.869000, 2.535600, 4.001300, 1.895500 },
{ 0.245900, 1.854200, 6.441100, 22.173000, 59.220600 }}},
{I, 0, {{ 0.704700, 1.948400, 2.594000, 4.152600, 1.505700 },
{ 0.245500, 1.863800, 6.763900, 21.800699, 56.439499 }}},
{Xe, 0, {{ 0.673700, 1.790800, 2.412900, 4.210000, 1.705800 },
{ 0.230500, 1.689000, 5.821800, 18.392799, 47.249599 }}},
{Cs, 0, {{ 1.270400, 3.801800, 5.661800, 0.920500, 4.810500 },
{ 0.435600, 4.205800, 23.434200, 136.778305, 171.756104 }}},
{Ba, 0, {{ 0.904900, 2.607600, 4.849800, 5.160300, 4.738800 },
{ 0.306600, 2.436300, 12.182100, 54.613499, 161.997803 }}},
{La, 0, {{ 0.840500, 2.386300, 4.613900, 5.151400, 4.794900 },
{ 0.279100, 2.141000, 10.340000, 41.914799, 132.020401 }}},
{Ce, 0, {{ 0.855100, 2.391500, 4.577200, 5.027800, 4.511800 },
{ 0.280500, 2.120000, 10.180800, 42.063301, 130.989304 }}},
{Pr, 0, {{ 0.909600, 2.531300, 4.526600, 4.637600, 4.369000 },
{ 0.293900, 2.247100, 10.826600, 48.884201, 147.602005 }}},
{Nd, 0, {{ 0.880700, 2.418300, 4.444800, 4.685800, 4.172500 },
{ 0.280200, 2.083600, 10.035700, 47.450600, 146.997604 }}},
{Pm, 0, {{ 0.947100, 2.546300, 4.352300, 4.478900, 3.908000 },
{ 0.297700, 2.227600, 10.576200, 49.361900, 145.358002 }}},
{Sm, 0, {{ 0.969900, 2.583700, 4.277800, 4.457500, 3.598500 },
{ 0.300300, 2.244700, 10.648700, 50.799400, 146.417892 }}},
{Eu, 0, {{ 0.869400, 2.241300, 3.919600, 3.969400, 4.549800 },
{ 0.265300, 1.859000, 8.399800, 36.739700, 125.708900 }}},
{Gd, 0, {{ 0.967300, 2.470200, 4.114800, 4.497200, 3.209900 },
{ 0.290900, 2.101400, 9.706700, 43.426998, 125.947403 }}},
{Tb, 0, {{ 0.932500, 2.367300, 3.879100, 3.967400, 3.799600 },
{ 0.276100, 1.951100, 8.929600, 41.593700, 131.012207 }}},
{Dy, 0, {{ 0.950500, 2.370500, 3.821800, 4.047100, 3.445100 },
{ 0.277300, 1.946900, 8.886200, 43.093800, 133.139603 }}},
{Ho, 0, {{ 0.924800, 2.242800, 3.618200, 3.791000, 3.791200 },
{ 0.266000, 1.818300, 7.965500, 33.112900, 101.813904 }}},
{Er, 0, {{ 1.037300, 2.482400, 3.655800, 3.892500, 3.005600 },
{ 0.294400, 2.079700, 9.415600, 45.805599, 132.772003 }}},
{Tm, 0, {{ 1.007500, 2.378700, 3.544000, 3.693200, 3.175900 },
{ 0.281600, 1.948600, 8.716200, 41.841999, 125.031998 }}},
{Yb, 0, {{ 1.034700, 2.391100, 3.461900, 3.655600, 3.005200 },
{ 0.285500, 1.967900, 8.761900, 42.330399, 125.649902 }}},
{Lu, 0, {{ 0.992700, 2.243600, 3.355400, 3.781300, 3.099400 },
{ 0.270100, 1.807300, 7.811200, 34.484901, 103.352600 }}},
{Hf, 0, {{ 1.029500, 2.291100, 3.411000, 3.949700, 2.492500 },
{ 0.276100, 1.862500, 8.096100, 34.271198, 98.529503 }}},
{Ta, 0, {{ 1.019000, 2.229100, 3.409700, 3.925200, 2.267900 },
{ 0.269400, 1.796200, 7.694400, 31.094200, 91.108902 }}},
{W, 0, {{ 0.985300, 2.116700, 3.357000, 3.798100, 2.279800 },
{ 0.256900, 1.674500, 7.009800, 26.923401, 81.390999 }}},
{Re, 0, {{ 0.991400, 2.085800, 3.453100, 3.881200, 1.852600 },
{ 0.254800, 1.651800, 6.884500, 26.723400, 81.721497 }}},
{Os, 0, {{ 0.981300, 2.032200, 3.366500, 3.623500, 1.974100 },
{ 0.248700, 1.597300, 6.473700, 23.281700, 70.925400 }}},
{Ir, 0, {{ 1.019400, 2.064500, 3.442500, 3.491400, 1.697600 },
{ 0.255400, 1.647500, 6.596600, 23.226900, 70.027199 }}},
{Pt, 0, {{ 0.914800, 1.809600, 3.213400, 3.295300, 1.575400 },
{ 0.226300, 1.381300, 5.324300, 17.598700, 60.017101 }}},
{Au, 0, {{ 0.967400, 1.891600, 3.399300, 3.052400, 1.260700 },
{ 0.235800, 1.471200, 5.675800, 18.711901, 61.528599 }}},
{Hg, 0, {{ 1.003300, 1.946900, 3.439600, 3.154800, 1.418000 },
{ 0.241300, 1.529800, 5.800900, 19.452000, 60.575298 }}},
{Tl, 0, {{ 1.068900, 2.103800, 3.603900, 3.492700, 1.828300 },
{ 0.254000, 1.671500, 6.350900, 23.153099, 78.709900 }}},
{Pb, 0, {{ 1.089100, 2.186700, 3.616000, 3.803100, 1.899400 },
{ 0.255200, 1.717400, 6.513100, 23.917000, 74.703903 }}},
{Bi, 0, {{ 1.100700, 2.230600, 3.568900, 4.154900, 2.038200 },
{ 0.254600, 1.735100, 6.494800, 23.646400, 70.377998 }}},
{Po, 0, {{ 1.156800, 2.435300, 3.645900, 4.406400, 1.717900 },
{ 0.264800, 1.878600, 7.174900, 25.176600, 69.282097 }}},
{At, 0, {{ 1.090900, 2.197600, 3.383100, 4.670000, 2.127700 },
{ 0.246600, 1.670700, 6.019700, 20.765699, 57.266300 }}},
{Rn, 0, {{ 1.075600, 2.163000, 3.317800, 4.885200, 2.048900 },
{ 0.240200, 1.616900, 5.764400, 19.456800, 52.500900 }}},
{Fr, 0, {{ 1.428200, 3.508100, 5.676700, 4.196400, 3.894600 },
{ 0.318300, 2.688900, 13.481600, 54.386600, 200.832108 }}},
{Ra, 0, {{ 1.312700, 3.124300, 5.298800, 5.389100, 5.413300 },
{ 0.288700, 2.289700, 10.827600, 43.538898, 145.610901 }}},
{Ac, 0, {{ 1.312800, 3.102100, 5.338500, 5.961100, 4.756200 },
{ 0.286100, 2.250900, 10.528700, 41.779598, 128.297302 }}},
{Th, 0, {{ 1.255300, 2.917800, 5.086200, 6.120600, 4.712200 },
{ 0.270100, 2.063600, 9.305100, 34.597698, 107.919998 }}},
{Pa, 0, {{ 1.321800, 3.144400, 5.437100, 5.644400, 4.010700 },
{ 0.282700, 2.225000, 10.245400, 41.116199, 124.444901 }}},
{U, 0, {{ 1.338200, 3.204300, 5.455800, 5.483900, 3.634200 },
{ 0.283800, 2.245200, 10.251900, 41.725101, 124.902298 }}},
{Np, 0, {{ 1.519300, 4.005300, 6.532700, -0.140200, 6.748900 },
{ 0.321300, 2.820600, 14.887800, 68.910301, 81.725700 }}},
{Pu, 0, {{ 1.351700, 3.293700, 5.321300, 4.646600, 3.571400 },
{ 0.281300, 2.241800, 9.995200, 42.793900, 132.173904 }}},
{Am, 0, {{ 1.213500, 2.796200, 4.754500, 4.573100, 4.478600 },
{ 0.248300, 1.843700, 7.542100, 29.384100, 112.457901 }}},
{Cm, 0, {{ 1.293700, 3.110000, 5.039300, 4.754600, 3.503100 },
{ 0.263800, 2.034100, 8.710100, 35.299198, 109.497200 }}},
{Bk, 0, {{ 1.291500, 3.102300, 4.930900, 4.600900, 3.466100 },
{ 0.261100, 2.002300, 8.437700, 34.155899, 105.891098 }}},
{Cf, 0, {{ 1.208900, 2.739100, 4.348200, 4.004700, 4.649700 },
{ 0.242100, 1.748700, 6.726200, 23.215300, 80.310799 }}}
};
} // namespace data
// --------------------------------------------------------------------
// AtomTypeTraits
......@@ -1066,7 +1264,7 @@ bool AtomTypeTraits::isMetal(const string& symbol)
return result;
}
auto AtomTypeTraits::wksf(int charge) const -> const WKSF&
auto AtomTypeTraits::wksf(int charge) const -> const SFData&
{
for (auto& sf: data::kWKSFData)
{
......@@ -1077,4 +1275,15 @@ auto AtomTypeTraits::wksf(int charge) const -> const WKSF&
throw runtime_error("No scattering factor found for " + name() + to_string(charge));
}
auto AtomTypeTraits::elsf() const -> const SFData&
{
for (auto& sf: data::kELSFData)
{
if (sf.symbol == mInfo->type)
return sf.sf;
}
throw runtime_error("No scattering factor found for " + name());
}
}
src/Compound.cpp
......@@ -114,7 +114,8 @@ class IsomerDB
IsomerDB::IsomerDB()
{
mrsrc::rsrc isomers("isomers.xml");
// mrsrc::rsrc isomers("isomers.xml");
mrsrc::rsrc isomers("isomers-with-sugar.xml");
if (not isomers)
throw runtime_error("Missing isomers.xml resource");
......
src/MapMaker.cpp
......@@ -194,20 +194,44 @@ void MapMaker<FTYPE>::recalculateFromMTZ(const fs::path& mtzFile,
atoms.push_back(a.toClipper());
HKL_data<F_phi> fc(hklInfo, mCell);
if (noBulk)
auto& exptl = structure.getFile().data()["exptl"];
if (not exptl.empty() and exptl.front()["method"] == "ELECTRON CRYSTALLOGRAPHY")
{
clipper::SFcalc_aniso_fft<float> sfc;
sfc(fc, atoms);
if (VERBOSE)
cerr << "Using electron scattering factors" << endl;
if (noBulk)
{
clipper::SFcalc_aniso_fft<float,clipper::sftElectron> sfc;
sfc(fc, atoms);
}
else
{
clipper::SFcalc_obs_bulk<float,clipper::sftElectron> sfcb;
sfcb(fc, fo, atoms);
if (VERBOSE)
cerr << "Bulk correction volume: " << sfcb.bulk_frac() << endl
<< "Bulk correction factor: " << sfcb.bulk_scale() << endl;
}
}
else
{
clipper::SFcalc_obs_bulk<float> sfcb;
sfcb(fc, fo, atoms);
if (VERBOSE)
cerr << "Bulk correction volume: " << sfcb.bulk_frac() << endl
<< "Bulk correction factor: " << sfcb.bulk_scale() << endl;
if (noBulk)
{
clipper::SFcalc_aniso_fft<float,clipper::sftWaasmaierKirfel> sfc;
sfc(fc, atoms);
}
else
{
clipper::SFcalc_obs_bulk<float,clipper::sftWaasmaierKirfel> sfcb;
sfcb(fc, fo, atoms);
if (VERBOSE)
cerr << "Bulk correction volume: " << sfcb.bulk_frac() << endl
<< "Bulk correction factor: " << sfcb.bulk_scale() << endl;
}
}
if (anisoScaling != as_None)
......
src/Structure.cpp
......@@ -470,7 +470,7 @@ clipper::Atom Atom::toClipper() const
void Atom::calculateRadius(float resHigh, float resLow, float perc)
{
AtomShape shape(*this, resHigh, resLow);
AtomShape shape(*this, resHigh, resLow, false);
mImpl->mRadius = shape.radius();
// verbose
......
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