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// Clipper minimol test & demo
/* (C) 2003 Kevin Cowtan */
// This is more of a demo application than a serious version
#include <clipper/clipper.h>
#include <clipper/clipper-minimol.h>
using namespace clipper;
class thing : std::string
{
public:
thing() { std::cout << "[CtorNull:\n"; }
thing( const std::string& s ) : std::string(s) { std::cout << "[CtorInit:" << *this << "\n"; }
thing( const thing& t ) : std::string(t) { std::cout << "[CtorCopy:" << *this << "\n"; }
~thing() { std::cout << "]Dtor:" << *this << "\n"; }
};
int main(int argc, char** argv)
{
// first test the property manager
PropertyManager p;
{
std::cout << "--make thing\n";
thing it( std::string("goodbye") );
std::cout << "--make prop\n";
Property<thing> prop( it );
std::cout << "--insert prop\n";
p.set_property( "b", prop );
std::cout << "--inserted prop\n";
p.set_property( "a", Property<String>( "hello" ) );
std::cout << p.exists_property( "a" ) << "\n";
std::cout << dynamic_cast<const Property<String>& >(p.get_property( "a" )).value() << "\n";
{
std::cout << "--copy mgr1\n";
PropertyManager p2;
std::cout << "--copy mgr2\n";
PropertyManager p1(p);
std::cout << "--copy mgr3\n";
p2 = p1;
std::cout << "--copy mgr4\n";
p2 = p;
std::cout << "--copy mgr5\n";
}
std::cout << "-- vector check\n";
std::vector<PropertyManager> v(3,p);
std::cout << "-- done vector check\n";
std::cout << "--delete prop\n";
p.delete_property( "b" );
std::cout << "--deleted prop\n";
}
std::cout << "--all gone!\n----------------------------------------\n\n";
// Now test sequence align
std::string s1 = "THEQUICKBOWNFOXJUMPSOVETHELAZY";
std::string s2 = "QUICKBRWNFXJUMPSVERTH3LAZYDOG";
std::string s3 = "ABCDEFTHELAZYDOGHIJKLMNOPQRSTUVWXYZ";
clipper::MSequenceAlign align, lalign(clipper::MSequenceAlign::LOCAL);
std::pair<std::vector<int>,std::vector<int> > result;
result = align( s1, s2 );
std::cout << s1 << std::endl;
for ( int i = 0; i < s1.size(); i++ )
std::cout << s1[i] << " " << (result.first[i]>=0 ? s2[result.first[i]] : ' ') << " " << i << " " << result.first[i] << std::endl;
std::cout << s2 << std::endl;
for ( int i = 0; i < s2.size(); i++ )
std::cout << s2[i] << " " << (result.second[i]>=0 ? s1[result.second[i]] : ' ') << " " << i << " " << result.second[i] << std::endl;
s1 = s2; s2 = s3;
result = align( s1, s2 );
std::cout << s1 << std::endl;
for ( int i = 0; i < s1.size(); i++ )
std::cout << s1[i] << " " << (result.first[i]>=0 ? s2[result.first[i]] : ' ') << " " << i << " " << result.first[i] << std::endl;
std::cout << s2 << std::endl;
for ( int i = 0; i < s2.size(); i++ )
std::cout << s2[i] << " " << (result.second[i]>=0 ? s1[result.second[i]] : ' ') << " " << i << " " << result.second[i] << std::endl;
result = lalign( s1, s2 );
std::cout << s1 << std::endl;
for ( int i = 0; i < s1.size(); i++ )
std::cout << s1[i] << " " << (result.first[i]>=0 ? s2[result.first[i]] : ' ') << " " << i << " " << result.first[i] << std::endl;
std::cout << s2 << std::endl;
for ( int i = 0; i < s2.size(); i++ )
std::cout << s2[i] << " " << (result.second[i]>=0 ? s1[result.second[i]] : ' ') << " " << i << " " << result.second[i] << std::endl;
exit(1);
// Now test minimol
MiniMol tempmol;
MMDBfile file;
file.read_file( argv[1] );
file.import_minimol( tempmol );
std::cout << tempmol.spacegroup().symbol_hall() << "\n";
std::cout << tempmol.cell().format() << "\n";
MiniMol mol;
mol.model() = tempmol.model();
for ( int p = 0; p < mol.size(); p++ )
for ( int m = 0; m < mol[p].size(); m++ )
for ( int a = 0; a < mol[p][m].size(); a++ ) {
std::cout << mol[p].id() << "\t" << mol[p][m].id() << "\t" << mol[p][m].type() << "\t<" << mol[p][m][a].id() << ">";
std::cout << "\t" << dynamic_cast<const Property<String>&>(mol[p][m][a].get_property("CID")).value();
if ( mol[p][m][a].exists_property("AltConf") ) std::cout << "\t" << dynamic_cast<const Property<String>&>(mol[p][m][a].get_property("AltConf")).value();
std::cout << " ANISO:" << mol[p][m][a].u_aniso_orth().is_null();
std::cout << "\n";
mol[p][m][a].set_coord_orth( Coord_orth(1.0,2.0,3.0) );
}
file.export_minimol( mol );
file.write_file( "mod.pdb" );
MMDBfile file2;
file2.export_minimol( mol );
file2.write_file( "cpy.pdb" );
// test non-bonding algorithm
MAtomNonBond nb( tempmol, 5.0 );
nb.debug();
for ( double x = -30.0; x < 50.0; x += 10.0 )
for ( double y = 320.0; y < 370.0; y += 10.0 )
for ( double z = 30.0; z < 80.0; z += 10.0 ) {
Coord_orth c(x,y,z);
std::cout << c.format() << std::endl;
std::vector<MAtomIndexSymmetry> atoms = nb(c,5.0);
for ( int i = 0; i < atoms.size(); i++ ) {
Coord_orth d = tempmol[atoms[i].polymer()][atoms[i].monomer()][atoms[i].atom()].coord_orth();
Coord_frac f1 = c.coord_frac( tempmol.cell() );
Coord_frac f2 = d.coord_frac( tempmol.cell() );
double l1 = ( f2.symmetry_copy_near( tempmol.spacegroup(), tempmol.cell(), f1 ) - f1 ).lengthsq( tempmol.cell() );
f2 = tempmol.spacegroup().symop(atoms[i].symmetry()) * f2;
double l2 = ( f2.lattice_copy_near( f1 ) - f1 ).lengthsq( tempmol.cell() );
std::cout << i << " " << l1 << " " << l2 << " " << std::endl;
}
}
// // Test selections and logical ops
// std::cout << "-----------------------------------------------------\n";
// MModel mol1 = mol.select( "*/13,14,15,16,17/N,CA,C" );
// for ( int p = 0; p < mol1.size(); p++ )
// for ( int m = 0; m < mol1[p].size(); m++ )
// for ( int a = 0; a < mol1[p][m].size(); a++ )
// std::cout << mol1[p].id() << "\t" << mol1[p][m].id() << "\t" << mol1[p][m].type() << "\t" << mol1[p][m][a].id() << "\n";
// std::cout << "-----------------------------------------------------\n";
// MModel mol2 = mol.select( "*/15,16/*" );
// for ( int p = 0; p < mol2.size(); p++ )
// for ( int m = 0; m < mol2[p].size(); m++ )
// for ( int a = 0; a < mol2[p][m].size(); a++ )
// std::cout << mol2[p].id() << "\t" << mol2[p][m].id() << "\t" << mol2[p][m].type() << "\t" << mol2[p][m][a].id() << "\n";
// std::cout << "-----------------------------------------------------\n";
// MModel mol3 = mol1 & mol2;
// for ( int p = 0; p < mol3.size(); p++ )
// for ( int m = 0; m < mol3[p].size(); m++ )
// for ( int a = 0; a < mol3[p][m].size(); a++ )
// std::cout << mol3[p].id() << "\t" << mol3[p][m].id() << "\t" << mol3[p][m].type() << "\t" << mol3[p][m][a].id() << "\n";
// std::cout << "-----------------------------------------------------\n";
// MModel mol4 = mol1 | mol2;
// for ( int p = 0; p < mol4.size(); p++ )
// for ( int m = 0; m < mol4[p].size(); m++ )
// for ( int a = 0; a < mol4[p][m].size(); a++ )
// std::cout << mol4[p].id() << "\t" << mol4[p][m].id() << "\t" << mol4[p][m].type() << "\t" << mol4[p][m][a].id() << "\n";
}
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