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by Morten Kjeldgaard
version 2.0.3 |
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// Clipper app to convert HL coeffs to phi/fom or back
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/* Copyright 2003-2004 Kevin Cowtan & University of York all rights reserved */
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#include <clipper/clipper.h> |
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#include <clipper/clipper-ccp4.h> |
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int main( int argc, char** argv ) |
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{
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CCP4Program prog( "chltofom", "0.1", "$Date: 2004/05/01" ); |
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// defaults
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clipper::String title; |
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clipper::String ipfile = "NONE"; |
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clipper::String ipcolf = "NONE"; |
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clipper::String ipcolh = "NONE"; |
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clipper::String ipcolp = "NONE"; |
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clipper::String opfile = "hltofom.mtz"; |
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clipper::String opcol = "hltofom"; |
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// command input
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CCP4CommandInput args( argc, argv, true ); |
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int arg = 0; |
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while ( ++arg < args.size() ) { |
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if ( args[arg] == "-title" ) { |
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if ( ++arg < args.size() ) title = args[arg]; |
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} else if ( args[arg] == "-mtzin" ) { |
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if ( ++arg < args.size() ) ipfile = args[arg]; |
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} else if ( args[arg] == "-mtzout" ) { |
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if ( ++arg < args.size() ) opfile = args[arg]; |
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} else if ( args[arg] == "-colin-hl" ) { |
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if ( ++arg < args.size() ) ipcolh = args[arg]; |
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} else if ( args[arg] == "-colin-phifom" ) { |
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if ( ++arg < args.size() ) ipcolp = args[arg]; |
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} else if ( args[arg] == "-colin-fo" ) { |
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if ( ++arg < args.size() ) ipcolf = args[arg]; |
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} else if ( args[arg] == "-colout" ) { |
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if ( ++arg < args.size() ) opcol = args[arg]; |
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} else { |
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std::cout << "Unrecognized:\t" << args[arg] << "\n"; |
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args.clear(); |
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}
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}
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if ( args.size() <= 1 ) { |
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std::cout << "Usage: chltofom\n\t-mtzin <filename>\n\t-mtzout <filename>\n\t-colin-fo <colpath>\n\t-colin-hl <colpath>\n\t-colin-phifom <colpath>\n\t-colout <colpath>\nIf -colin-hl is specified, conversion is ABCD->phi/fom.\nIf -colin-phifom is specified, conversion is phi/fom->ABCD.\nIf -colin-fo is specified, weighted map coefficients are calculated in addition.\nIf no FOM is present, it is set to 0.99.\n"; |
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exit(1); |
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}
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// make data objects
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clipper::CCP4MTZfile mtzin, mtzout; |
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clipper::HKL_info hkls; |
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// actual work
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mtzin.open_read( ipfile ); |
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mtzin.import_hkl_info( hkls ); |
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clipper::HKL_data<clipper::data32::Phi_fom> phiw( hkls ); |
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clipper::HKL_data<clipper::data32::ABCD> abcd( hkls ); |
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clipper::HKL_data<clipper::data32::F_sigF> fsig( hkls ); |
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clipper::HKL_data<clipper::data32::F_phi> fphi( hkls ); |
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if ( ipcolh != "NONE" ) mtzin.import_hkl_data( abcd, ipcolh ); |
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if ( ipcolp != "NONE" ) mtzin.import_hkl_data( phiw, ipcolp ); |
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if ( ipcolf != "NONE" ) mtzin.import_hkl_data( fsig, ipcolf ); |
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clipper::String opbase = mtzin.assigned_paths()[0]; |
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if ( opcol == "" ) opcol = opbase.substr( 0, opbase.find(".") ); |
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else if ( opcol[0] != '/' ) opcol = opbase.notail()+"/"+opcol; |
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mtzin.close_read(); |
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mtzout.open_append( ipfile, opfile ); |
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// compute phi+fom from abcd
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if ( ipcolh != "NONE" ) { |
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phiw.compute( abcd, clipper::data32::Compute_phifom_from_abcd() ); |
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mtzout.export_hkl_data( phiw, opcol ); |
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}
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// compute abcd from phi+fom
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if ( ipcolp != "NONE" ) { |
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// if weights absent, then set to 0.99
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clipper::HKL_data_base::HKL_reference_index ih; |
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for ( ih = phiw.first(); !ih.last(); ih.next() ) |
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if ( !clipper::Util::is_nan( phiw[ih].fom() ) ) break; |
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if ( ih.last() ) |
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for ( ih = phiw.first(); !ih.last(); ih.next() ) phiw[ih].fom() = 0.99; |
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abcd.compute( phiw, clipper::data32::Compute_abcd_from_phifom() ); |
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mtzout.export_hkl_data( abcd, opcol ); |
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}
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// compute weighted F from F + phi
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if ( ipcolf != "NONE" ) { |
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fphi.compute( fsig, phiw, clipper::data32::Compute_fphi_from_fsigf_phifom() ); |
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mtzout.export_hkl_data( fphi, opcol ); |
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}
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mtzout.close_append(); |
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}
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