bool Chain::is_continuous() const
{
// go through and find elements where there is a chain break
const double dmin = 2.0;
std::vector<bool> cterm( dbmonomers.size(), false );
for ( int i = 0; i < int(dbmonomers.size()-1); i++ ) {
int j = i + 1;
const clipper::Coord_orth co1 = dbmonomers[i].coord_o3();
const clipper::Coord_orth co2 = dbmonomers[j].coord_p();
if ( co1.is_null() || co2.is_null() ) return false;
const double d2 = ( co1 - co2 ).lengthsq();
if ( d2 > dmin*dmin ) return false;
}
return true;
}
clipper::Coord_orth NucleicAcidTools::coord_adjust( const clipper::Coord_orth& co, const clipper::Coord_orth& cc3, const clipper::Coord_orth& cf3, const clipper::Coord_orth& cc4, const clipper::Coord_orth& cf4, double rad )
{
if ( co.is_null() ) return co;
clipper::Coord_orth result = co;
double w3 = 1.0 - sqrt( ( co - cf3 ).lengthsq() ) / rad;
double w4 = 1.0 - sqrt( ( co - cf4 ).lengthsq() ) / rad;
if ( w3 > 0.0 ) result += w3 * ( cc3 - cf3 );
if ( w4 > 0.0 ) result += w4 * ( cc4 - cf4 );
return result;
}
void SSfind::prep_search( const clipper::Xmap<float>& xmap, const double rhocut, const double radcut, const clipper::Coord_orth centre )
{
// make list of results
typedef clipper::Xmap<float>::Map_reference_index MRI;
srctrn.clear();
double r2cut = ( radcut > 0.0 ) ? radcut*radcut : 1.0e20;
clipper::Coord_frac cf = centre.coord_frac( xmap.cell() );
for ( MRI ix = xmap.first(); !ix.last(); ix.next() )
if ( xmap[ix] > rhocut ) {
clipper::Coord_frac df = ix.coord().coord_frac( xmap.grid_sampling() );
df = df.symmetry_copy_near( xmap.spacegroup(), xmap.cell(), cf ) - cf;
double r2 = df.lengthsq( xmap.cell() );
if ( r2 < r2cut )
srctrn.push_back( grid.index( ix.coord() ) );
}
}
clipper::RTop_orth NucleicAcidTools::symmetry_rtop( const std::vector<clipper::Coord_orth>& cowrk, clipper::Coord_orth& coref, const clipper::Spacegroup& spgr, const clipper::Cell& cell )
{
std::vector<clipper::Coord_frac> cwrk( cowrk.size() );
for ( int a = 0; a < cowrk.size(); a++ )
cwrk[a] = cowrk[a].coord_frac(cell);
clipper::Coord_frac cref = coref.coord_frac(cell);
clipper::Coord_frac c1, c2;
double d2, d2min(1.0e12);
int smin(0);
clipper::Coord_frac dmin(0.0,0.0,0.0);
for ( int s = 0; s < spgr.num_symops(); s++ )
for ( int a = 0; a < cwrk.size(); a++ ) {
c1 = ( spgr.symop(s) * cwrk[a] );
c2 = c1.lattice_copy_near( cref );
d2 = ( c2 - cref ).lengthsq( cell );
if ( d2 < d2min ) {
d2min = d2;
smin = s;
dmin = c2 - c1;
}
}
clipper::RTop_frac rf( spgr.symop(smin).rot(), spgr.symop(smin).trn()+dmin );
return rf.rtop_orth( cell );
}
NucleicAcid::NucleicAcid( const clipper::Coord_orth& cp, const clipper::Coord_orth& co5, const clipper::Coord_orth& cc5, const clipper::Coord_orth& cc4, const clipper::Coord_orth& co4, const clipper::Coord_orth& cc3, const clipper::Coord_orth& co3, const clipper::Coord_orth& cc2, const clipper::Coord_orth& cc1, const clipper::Coord_orth& cn, const clipper::String& type )
{
clipper::String t = type + "?";
typ = t.trim()[0];
clipper::Util::set_null( p_x );
clipper::Util::set_null( o5x );
clipper::Util::set_null( c5x );
clipper::Util::set_null( c4x );
clipper::Util::set_null( o4x );
clipper::Util::set_null( c3x );
clipper::Util::set_null( o3x );
clipper::Util::set_null( c2x );
clipper::Util::set_null( c1x );
clipper::Util::set_null( n_x );
if ( !cp.is_null() ) { p_x = cp.x(); p_y = cp.y(); p_z = cp.z(); }
if ( !co5.is_null() ) { o5x = co5.x(); o5y = co5.y(); o5z = co5.z(); }
if ( !cc5.is_null() ) { c5x = cc5.x(); c5y = cc5.y(); c5z = cc5.z(); }
if ( !cc4.is_null() ) { c4x = cc4.x(); c4y = cc4.y(); c4z = cc4.z(); }
if ( !co4.is_null() ) { o4x = co4.x(); o4y = co4.y(); o4z = co4.z(); }
if ( !cc3.is_null() ) { c3x = cc3.x(); c3y = cc3.y(); c3z = cc3.z(); }
if ( !co3.is_null() ) { o3x = co3.x(); o3y = co3.y(); o3z = co3.z(); }
if ( !cc2.is_null() ) { c2x = cc2.x(); c2y = cc2.y(); c2z = cc2.z(); }
if ( !cc1.is_null() ) { c1x = cc1.x(); c1y = cc1.y(); c1z = cc1.z(); }
if ( !cn.is_null() ) { n_x = cn.x(); n_y = cn.y(); n_z = cn.z(); }
set_flag();
}