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// Clipper app to perform structure factor calculation
/* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */
#include <clipper/clipper.h>
#include <clipper/clipper-contrib.h>
#include <clipper/clipper-ccp4.h>
#include <clipper/clipper-mmdb.h>
#include "ccp4-extras.h"
int main( int argc, char** argv )
{
CCP4program prog( "csfcalc", "0.1", "$Date: 2004/06/01" );
// defaults
clipper::String ippdb = "NONE";
clipper::String ipfile = "NONE";
clipper::String ipcolfo = "NONE";
clipper::String ipcolfree = "NONE";
clipper::String opfile = "sfcalc.mtz";
clipper::String opcol = "sfcalc";
bool bulk = true;
int freeflag = 0;
int n_refln = 1000;
int n_param = 20;
int verbose = 0;
// command input
CommandInput args( argc, argv, true );
int arg = 0;
while ( ++arg < args.size() ) {
if ( args[arg] == "-pdbin" ) {
if ( ++arg < args.size() ) ippdb = args[arg];
} else if ( args[arg] == "-mtzin" ) {
if ( ++arg < args.size() ) ipfile = args[arg];
} else if ( args[arg] == "-colin-fo" ) {
if ( ++arg < args.size() ) ipcolfo = args[arg];
} else if ( args[arg] == "-colin-free" ) {
if ( ++arg < args.size() ) ipcolfree = args[arg];
} else if ( args[arg] == "-mtzout" ) {
if ( ++arg < args.size() ) opfile = args[arg];
} else if ( args[arg] == "-colout" ) {
if ( ++arg < args.size() ) opcol = args[arg];
} else if ( args[arg] == "-free-flag" ) {
if ( ++arg < args.size() ) freeflag = clipper::String(args[arg]).i();
} else if ( args[arg] == "-num-reflns" ) {
if ( ++arg < args.size() ) n_refln = clipper::String(args[arg]).i();
} else if ( args[arg] == "-num-params" ) {
if ( ++arg < args.size() ) n_param = clipper::String(args[arg]).i();
} else if ( args[arg] == "-no-bulk" ) {
bulk = false;
} else if ( args[arg] == "-verbose" ) {
if ( ++arg < args.size() ) verbose = clipper::String(args[arg]).i();
} else {
std::cout << "Unrecognized:\t" << args[arg] << "\n";
args.clear();
}
}
if ( args.size() <= 1 ) {
std::cout << "Usage: csfcalc\n\t-pdbin <filename>\n\t-mtzin <filename>\n\t-colin-fo <colpath>\n\t-colin-free <colpath>\n\t-mtzout <filename>\n\t-colout <colpath>\n\t-free-flag <free set>\n\t-num-reflns <reflns per spline param>\n\t-num-params <spline params>\n\t-no-bulk\nStructure factor calculation with bulk solvent correction.\n";
exit(1);
}
// make data objects
clipper::CCP4MTZfile mtzin, mtzout;
clipper::MTZcrystal cxtl;
clipper::HKL_info hkls;
double bulkfrc, bulkscl;
typedef clipper::HKL_data_base::HKL_reference_index HRI;
// open file
mtzin.open_read( ipfile );
mtzin.import_hkl_info( hkls );
mtzin.import_crystal( cxtl, ipcolfo );
clipper::HKL_data<clipper::data32::F_sigF> fo( hkls, cxtl );
clipper::HKL_data<clipper::data32::Flag> free( hkls, cxtl );
mtzin.import_hkl_data( fo, ipcolfo );
if ( ipcolfree != "NONE" ) mtzin.import_hkl_data( free, ipcolfree );
if ( opcol[0] != '/' ) opcol = mtzin.assigned_paths()[0].notail()+"/"+opcol;
mtzin.close_read();
// atomic model
clipper::MMDBManager mmdb;
mmdb.SetFlag( MMDBF_AutoSerials | MMDBF_IgnoreDuplSeqNum );
mmdb.ReadPDBASCII( (char*)ippdb.c_str() );
// get a list of all the atoms
clipper::mmdb::PPCAtom psel;
int hndl, nsel;
hndl = mmdb.NewSelection();
mmdb.SelectAtoms( hndl, 0, 0, SKEY_NEW );
mmdb.GetSelIndex( hndl, psel, nsel );
clipper::MMDBAtom_list atoms( psel, nsel );
mmdb.DeleteSelection( hndl );
// calculate structure factors
clipper::HKL_data<clipper::data32::F_phi> fc( hkls, cxtl );
if ( bulk ) {
clipper::SFcalc_obs_bulk<float> sfcb;
sfcb( fc, fo, atoms );
bulkfrc = sfcb.bulk_frac();
bulkscl = sfcb.bulk_scale();
} else {
clipper::SFcalc_aniso_fft<float> sfc;
sfc( fc, atoms );
bulkfrc = bulkscl = 0.0;
}
// now do sigmaa calc
clipper::HKL_data<clipper::data32::F_phi> fb( hkls, cxtl ), fd( hkls, cxtl );
clipper::HKL_data<clipper::data32::Phi_fom> phiw( hkls, cxtl );
clipper::HKL_data<clipper::data32::Flag> flag( hkls, cxtl );
for ( HRI ih = flag.first(); !ih.last(); ih.next() )
if ( !fo[ih].missing() && (free[ih].missing()||free[ih].flag()==freeflag) )
flag[ih].flag() = clipper::SFweight_spline<float>::BOTH;
else
flag[ih].flag() = clipper::SFweight_spline<float>::NONE;
// do sigmaa calc
clipper::SFweight_spline<float> sfw( n_refln, n_param );
bool fl = sfw( fb, fd, phiw, fo, fc, flag );
// expand to p1 and calc map coeffs
clipper::HKL_info hkls1( clipper::Spacegroup::p1(),
hkls.cell(), hkls.resolution(), true );
clipper::HKL_data<clipper::data32::F_phi> fd1( hkls1, cxtl );
clipper::HKL_data<clipper::data32::F_phi> fdu( hkls1, cxtl );
clipper::HKL_data<clipper::data32::F_phi> fdv( hkls1, cxtl );
clipper::HKL_data<clipper::data32::F_phi> fdw( hkls1, cxtl );
clipper::HKL_data<clipper::data32::F_phi> fduu( hkls1, cxtl );
clipper::HKL_data<clipper::data32::F_phi> fdvv( hkls1, cxtl );
clipper::HKL_data<clipper::data32::F_phi> fdww( hkls1, cxtl );
clipper::HKL_data<clipper::data32::F_phi> fduv( hkls1, cxtl );
clipper::HKL_data<clipper::data32::F_phi> fdvw( hkls1, cxtl );
clipper::HKL_data<clipper::data32::F_phi> fdwu( hkls1, cxtl );
for ( HRI ih = fd1.first(); !ih.last(); ih.next() ) {
clipper::HKL hkl = ih.hkl();
std::complex<float> c = std::complex<float>( fd[hkl] );
float h = clipper::Util::twopi() * hkl.h();
float k = clipper::Util::twopi() * hkl.k();
float l = clipper::Util::twopi() * hkl.l();
fd1[ih] = clipper::data32::F_phi( c );
fdu[ih] = clipper::data32::F_phi( c * std::complex<float>( 0.0, h ) );
fdv[ih] = clipper::data32::F_phi( c * std::complex<float>( 0.0, k ) );
fdw[ih] = clipper::data32::F_phi( c * std::complex<float>( 0.0, l ) );
fduu[ih] = clipper::data32::F_phi( c * float( h * h ) );
fdvv[ih] = clipper::data32::F_phi( c * float( k * k ) );
fdww[ih] = clipper::data32::F_phi( c * float( l * l ) );
fduv[ih] = clipper::data32::F_phi( c * float( h * k ) );
fdvw[ih] = clipper::data32::F_phi( c * float( k * l ) );
fdwu[ih] = clipper::data32::F_phi( c * float( l * h ) );
}
// calc maps
clipper::Grid_sampling grid( hkls1.spacegroup(), cxtl, hkls1.resolution(), 2.5 );
clipper::Xmap<float> xmap1( hkls1.spacegroup(), cxtl, grid );
clipper::Xmap<float> xmapu( hkls1.spacegroup(), cxtl, grid );
clipper::Xmap<float> xmapv( hkls1.spacegroup(), cxtl, grid );
clipper::Xmap<float> xmapw( hkls1.spacegroup(), cxtl, grid );
clipper::Xmap<float> xmapuu( hkls1.spacegroup(), cxtl, grid );
clipper::Xmap<float> xmapvv( hkls1.spacegroup(), cxtl, grid );
clipper::Xmap<float> xmapww( hkls1.spacegroup(), cxtl, grid );
clipper::Xmap<float> xmapuv( hkls1.spacegroup(), cxtl, grid );
clipper::Xmap<float> xmapvw( hkls1.spacegroup(), cxtl, grid );
clipper::Xmap<float> xmapwu( hkls1.spacegroup(), cxtl, grid );
xmap1.fft_from( fd1 );
xmapu.fft_from( fdu );
xmapv.fft_from( fdv );
xmapw.fft_from( fdw );
xmapuu.fft_from( fduu );
xmapvv.fft_from( fdvv );
xmapww.fft_from( fdww );
xmapuv.fft_from( fduv );
xmapvw.fft_from( fdvw );
xmapwu.fft_from( fdwu );
// write difference map
clipper::CCP4MAPfile mapout;
mapout.open_write( "reftest.map" );
mapout.export_xmap( xmap1 );
mapout.close_write();
// now loop over atoms and calculate parameter gradients and curvatures
const double radius = 4.5;
clipper::Grid_range gd( xmap1.cell(), xmap1.grid_sampling(), radius );
clipper::Coord_grid g0, g1;
std::vector<clipper::AtomShapeFn::TYPE> params;
params.push_back( clipper::AtomShapeFn::X );
params.push_back( clipper::AtomShapeFn::Y );
params.push_back( clipper::AtomShapeFn::Z );
params.push_back( clipper::AtomShapeFn::Occ );
params.push_back( clipper::AtomShapeFn::Uiso );
std::vector<double> func( atoms.size() );
std::vector<std::vector<double> > grad( atoms.size() );
std::vector<clipper::Matrix<double> > curv( atoms.size() );
std::vector<std::vector<double> > grad1( atoms.size() );
std::vector<clipper::Matrix<double> > curv1( atoms.size() );
double f, rho;
std::vector<double> g(5);
clipper::Matrix<double> c(5,5);
clipper::Xmap<float>::Map_reference_coord i0, iu, iv, iw;
for ( int a = 0; a < atoms.size(); a++ ) {
func[a] = 0.0;
grad[a].resize( 5, 0.0 );
curv[a].resize( 5, 5, 0.0 );
grad1[a].resize( 5, 0.0 );
curv1[a].resize( 5, 5, 0.0 );
clipper::Grad_frac<double> gf( 0.0, 0.0, 0.0 );
clipper::Grad_orth<double> go( 0.0, 0.0, 0.0 );
clipper::Curv_frac<double> cf( clipper::Mat33<double>( 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 ) );
clipper::Curv_orth<double> co( clipper::Mat33<double>( 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 ) );
clipper::AtomShapeFn sf( atoms[a].coord_orth(), atoms[a].element(),
atoms[a].u_iso(), atoms[a].occupancy() );
sf.agarwal_params() = params;
g0 = xmap1.coord_map( atoms[a].coord_orth() ).coord_grid() + gd.min();
g1 = xmap1.coord_map( atoms[a].coord_orth() ).coord_grid() + gd.max();
i0 = clipper::Xmap<float>::Map_reference_coord( xmap1, g0 );
for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() )
for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() )
for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() )
if ( (iw.coord_orth()-atoms[a].coord_orth()).lengthsq() <
radius*radius ) {
rho = xmap1[iw];
sf.rho_curv( iw.coord_orth(), f, g, c );
func[a] += f * rho;
for ( int i = 0; i < 5; i++ )
grad[a][i] += g[i] * rho;
for ( int i = 0; i < 5; i++ )
for ( int j = 0; j < 5; j++ )
curv[a](i,j) += c(i,j) * rho;
gf[0] += f * xmapu[iw];
gf[1] += f * xmapv[iw];
gf[2] += f * xmapw[iw];
cf(0,0) += f * xmapuu[iw];
cf(1,1) += f * xmapvv[iw];
cf(2,2) += f * xmapww[iw];
cf(0,1) += f * xmapuv[iw];
cf(1,2) += f * xmapvw[iw];
cf(2,0) += f * xmapwu[iw];
}
cf(1,0) = cf(0,1);
cf(2,1) = cf(1,2);
cf(0,2) = cf(2,0);
go = gf.grad_orth( cxtl );
co = cf.curv_orth( cxtl );
for ( int i = 0; i < 3; i++ )
grad1[a][i] = -go[i];
for ( int i = 0; i < 3; i++ )
for ( int j = 0; j < 3; j++ )
curv1[a](i,j) = -co(i,j);
}
for ( int a = 0; a < atoms.size(); a++ ) {
std::vector<double> gxyz(3), gxyz1(3);
clipper::Matrix<double> cxyz(3,3), cxyz1(3,3);
for ( int i = 0; i < 3; i++ )
gxyz[i] = grad[a][i];
for ( int i = 0; i < 3; i++ )
gxyz1[i] = grad1[a][i];
for ( int i = 0; i < 3; i++ )
for ( int j = 0; j < 3; j++ )
cxyz(i,j) = curv[a](i,j);
for ( int i = 0; i < 3; i++ )
for ( int j = 0; j < 3; j++ )
cxyz1(i,j) = curv1[a](i,j);
std::cout << "grad " << a << " [" << atoms[a].element() << "]\t" << gxyz[0] << " \t" << gxyz[1] << " \t" << gxyz[2] << "\n";
std::cout << "grad " << a << " [" << atoms[a].element() << "]\t" << gxyz1[0] << " \t" << gxyz1[1] << " \t" << gxyz1[2] << "\n";
std::cout << "curv " << a << " [" << atoms[a].element() << "]\t" << cxyz(0,0) << " \t" << cxyz(1,1) << " \t" << cxyz(2,2) << "\n";
std::cout << "curv " << a << " [" << atoms[a].element() << "]\t" << cxyz1(0,0) << " \t" << cxyz1(1,1) << " \t" << cxyz1(2,2) << "\n";
std::cout << "curv " << a << " [" << atoms[a].element() << "]\t" << cxyz(0,1) << " \t" << cxyz(1,2) << " \t" << cxyz(2,0) << "\n";
std::cout << "curv " << a << " [" << atoms[a].element() << "]\t" << cxyz1(0,1) << " \t" << cxyz1(1,2) << " \t" << cxyz1(2,0) << "\n";
}
/*
// now calculate shifts to parameters
for ( int a = 0; a < atoms.size(); a++ ) {
// not all cross terms available, so calc xyz and U shifts independently
std::vector<double> gxyz(3), sxyz(3);
clipper::Matrix<double> cxyz(3,3);
for ( int i = 0; i < 3; i++ )
gxyz[i] = grad[a][i];
for ( int i = 0; i < 3; i++ )
for ( int j = 0; j < 3; j++ )
cxyz(i,j) = curv[a](i,j);
sxyz = cxyz.solve(gxyz);
double gu = grad[a][4];
double cu = curv[a](4,4);
double su = gu/cu;
std::cout << "grad " << a << " [" << atoms[a].element() << "]\t" << gxyz[0] << " \t" << gxyz[1] << " \t" << gxyz[2] << " \t" << gu << "\n";
std::cout << "Atom " << a << " [" << atoms[a].element() << "]\t" << sxyz[0] << " \t" << sxyz[1] << " \t" << sxyz[2] << " \t" << su << "\n";
}
*/
}
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