diff --git a/modules/mol/alg/pymod/export_entity_to_density.cc b/modules/mol/alg/pymod/export_entity_to_density.cc index 858740eeb9500d82ddcaa57d45bcbd0296ce0c80..24328ac747d3f477340e5d113bc9e4c590fdf03b 100644 --- a/modules/mol/alg/pymod/export_entity_to_density.cc +++ b/modules/mol/alg/pymod/export_entity_to_density.cc @@ -30,6 +30,7 @@ using namespace ost::mol::alg; #if OST_IMG_ENABLED + #include <ost/mol/alg/entity_to_density.hh> //"thin wrappers" for default parameters diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc index 14785ddf753a30194aa995ea0b195d56f08b9dcf..ce0be429c6afb0afd5b6b55b2252cc79d446dbbd 100644 --- a/modules/mol/alg/pymod/wrap_mol_alg.cc +++ b/modules/mol/alg/pymod/wrap_mol_alg.cc @@ -21,10 +21,14 @@ * Author Juergen Haas */ #include <boost/python.hpp> +#include <ost/config.hh> using namespace boost::python; void export_svdSuperPose(); + +#if OST_IMG_ENABLED void export_entity_to_density(); +#endif BOOST_PYTHON_MODULE(_mol_alg) { diff --git a/modules/mol/alg/src/CMakeLists.txt b/modules/mol/alg/src/CMakeLists.txt index adb666c1bf47005b5654c94aa4f01ed7b0ec6def..242eea3d8f3a4c80f29909b3ecad313df10753f7 100644 --- a/modules/mol/alg/src/CMakeLists.txt +++ b/modules/mol/alg/src/CMakeLists.txt @@ -30,3 +30,6 @@ module(NAME mol_alg SOURCES ${OST_MOL_ALG_SOURCES} HEADER_OUTPUT_DIR ost/mol/alg DEPENDS_ON ${MOL_ALG_DEPS}) +copy_if_different("." "${STAGE_DIR}/share/openstructure" + "atom_scattering_properties.txt" "ATOM_SCATTERING_PROPS" + "ost_mol_alg") diff --git a/modules/mol/alg/src/atom_scattering_properties.txt b/modules/mol/alg/src/atom_scattering_properties.txt new file mode 100644 index 0000000000000000000000000000000000000000..107a71bdfe10092cc10075d82318c5b34ca6a0c0 --- /dev/null +++ b/modules/mol/alg/src/atom_scattering_properties.txt @@ -0,0 +1,59 @@ +// SCATTERING PROPERTIES OF ATOMS +// (used by the entity_to_density_function of OST/OPENSTRUCTURE) +// Columns from left to right: 1) Element Symbol 2) Atomic Weight 3) c parameter used to compute scattering factors 4-7) a1-a4 parameters 8-11) b1-b4 parameters. +// Sources: parameters for scattering factors: it.iucr.org/ International tables for crystallography. First online edition (2006), Vol.C,Ch 6.1, pp. 554-595 +// Atomic Weights: www.chem.qmul.ac.uk/iupac/AtWt/ based on 2005 table published in Pure Appl. Chem., 78, 2051-2066 (2006) with 2007 changes +Al 26.982 1.115100 6.420200 1.900200 1.593600 1.964600 3.038700 0.742600 31.547199 85.088600 +As 74.922 2.531000 16.672300 6.070100 3.431300 4.277900 2.634500 0.264700 12.947900 47.797199 +At 210.000 13.710800 35.316299 19.021099 9.498870 7.425180 0.685870 3.974580 11.382400 45.471500 +Au 196.967 12.065800 16.881901 18.591299 25.558201 5.860000 0.461100 8.621600 1.482600 36.395599 +B 10.812 -0.193200 2.054500 1.332600 1.097900 0.706800 23.218500 1.021000 60.349800 0.140300 +Be 9.012 0.038500 1.591900 1.127800 0.539100 0.702900 43.642700 1.862300 103.483002 0.542000 +Br 79.904 2.955700 17.178900 5.235800 5.637700 3.985100 2.172300 16.579599 0.260900 41.432800 +C 12.011 0.215600 2.310000 1.020000 1.588600 0.865000 20.843899 10.207500 0.568700 51.651199 +Ca 40.078 1.375100 8.626600 7.387300 1.589900 1.021100 10.442100 0.659900 85.748398 178.436996 +Cd 112.412 5.069400 19.221399 17.644400 4.461000 1.602900 0.594600 6.908900 24.700800 87.482498 +Cl 35.453 -9.557400 11.460400 7.196400 6.255600 1.645500 0.010400 1.166200 18.519400 47.778400 +Co 58.933 1.011800 12.284100 7.340900 4.003400 2.348800 4.279100 0.278400 13.535900 71.169197 +Cr 51.996 1.183200 10.640600 7.353700 3.324000 1.492200 6.103800 0.392000 20.262600 98.739899 +Cu 63.546 1.191000 13.337999 7.167600 5.615800 1.673500 3.582800 0.247000 11.396600 64.812599 +F 18.998 0.277600 3.539200 2.641200 1.517000 1.024300 10.282499 4.294400 0.261500 26.147600 +Fe 55.845 1.036900 11.769500 7.357300 3.522200 2.304500 4.761100 0.307200 15.353500 76.880501 +Ga 69.723 1.718900 15.235400 6.700600 4.359100 2.962300 3.066900 0.241200 10.780500 61.413498 +Gd 157.253 2.419600 25.070900 19.079800 13.851800 3.545450 2.253410 0.181951 12.933100 101.397995 +Ge 72.641 2.131300 16.081600 6.374700 3.706800 3.683000 2.850900 0.251600 11.446800 54.762501 +Hf 178.492 8.581540 29.143999 15.172600 14.758600 4.300130 1.832620 9.599899 0.275116 72.028999 +Hg 200.592 12.608900 20.680901 19.041700 21.657499 5.967600 0.545000 8.448400 1.572900 38.324600 +I 126.904 4.071200 20.147200 18.994900 7.513800 2.273500 4.347000 0.381400 27.765999 66.877602 +Ir 192.217 11.472200 27.304899 16.729599 15.611500 5.833770 1.592790 8.865530 0.417916 45.001099 +K 39.098 1.422800 8.218599 7.439800 1.051900 0.865900 12.794900 0.774800 213.186996 41.684097 +Li 6.941 0.037700 1.128200 0.750800 0.617500 0.465300 3.954600 1.052400 85.390503 168.261002 +Mg 24.305 0.858400 5.420400 2.173500 1.226900 2.307300 2.827500 79.261101 0.380800 7.193700 +Mn 54.938 1.089600 11.281900 7.357300 3.019300 2.244100 5.340900 0.343200 17.867399 83.754303 +Mo 95.962 4.387500 3.702500 17.235600 12.887600 3.742900 0.277200 1.095800 11.004000 61.658401 +N 14.007 11.528999 12.212600 3.132200 2.012500 1.166300 0.005700 9.893300 28.997499 0.582600 +Na 22.990 0.676000 4.762600 3.173600 1.267400 1.112800 3.285000 8.842199 0.313600 129.423996 +Ni 58.693 1.034100 12.837600 7.292000 4.443800 2.380000 3.878500 0.256500 12.176300 66.342102 +O 15.999 0.250800 3.048500 2.286800 1.546300 0.867000 13.277100 5.701100 0.323900 32.908897 +Os 190.233 11.000500 28.189400 16.154999 14.930500 5.675890 1.629030 8.979480 0.382661 48.164700 +P 30.974 1.114900 6.434500 4.179100 1.780000 1.490800 1.906700 27.157000 0.526000 68.164497 +Pb 207.210 13.411800 31.061699 13.063700 18.441999 5.969600 0.690200 2.357600 8.618000 47.257900 +Pd 106.421 5.265930 19.331900 15.501699 5.295370 0.605844 0.698655 7.989290 25.205200 76.898598 +Pt 195.085 11.688300 27.005899 17.763901 15.713100 5.783700 1.512930 8.811740 0.424593 38.610298 +Re 186.207 10.472000 28.762100 15.718900 14.556400 5.441740 1.671910 9.092270 0.350500 52.086098 +Rh 102.905 5.328000 19.295700 14.350100 4.734250 1.289180 0.751536 8.217580 25.874901 98.606201 +Ru 101.072 5.378740 19.267399 12.918200 4.863370 1.567560 0.808520 8.434669 24.799700 94.292801 +S 32.066 0.866900 6.905300 5.203400 1.437900 1.586300 1.467900 22.215099 0.253600 56.172001 +Sb 121.760 4.590900 19.641800 19.045500 5.037100 2.682700 5.303400 0.460700 27.907400 75.282501 +Se 78.963 2.840900 17.000599 5.819600 3.973100 4.354300 2.409800 0.272600 15.237200 43.816299 +Si 28.086 1.140700 6.291500 3.035300 1.989100 1.541000 2.438600 32.333698 0.678500 81.693695 +Sn 118.711 4.782100 19.188900 19.100500 4.458500 2.466300 5.830300 0.503100 26.890900 83.957100 +Ta 180.948 9.243540 29.202400 15.229300 14.513500 4.764920 1.773330 9.370460 0.295977 63.364399 +Te 127.603 4.352000 19.964399 19.013800 6.144870 2.523900 4.817420 0.420885 28.528400 70.840302 +U 238.029 13.396600 36.022800 23.412800 14.949100 4.188000 0.529300 3.325300 16.092699 100.612999 +V 50.942 1.219900 10.297100 7.351100 2.070300 2.057100 6.865700 0.438500 26.893799 102.477997 +W 183.841 9.887500 29.081800 15.430000 14.432700 5.119820 1.720290 9.225900 0.321703 57.056000 +Y 88.906 1.912130 17.775999 10.294600 5.726290 3.265880 1.402900 12.800600 0.125599 104.353996 +Zn 65.382 1.304100 14.074300 7.031800 5.162500 2.410000 3.265500 0.233300 10.316299 58.709702 +Zr 91.2240 2.069290 17.876499 10.948000 5.417320 3.657210 1.276180 11.916000 0.117622 87.662697 +