//------------------------------------------------------------------------------ // This file is part of the OpenStructure project <www.openstructure.org> // // Copyright (C) 2008-2011 by the OpenStructure authors // // This library is free software; you can redistribute it and/or modify it under // the terms of the GNU Lesser General Public License as published by the Free // Software Foundation; either version 3.0 of the License, or (at your option) // any later version. // This library is distributed in the hope that it will be useful, but WITHOUT // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS // FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more // details. // // You should have received a copy of the GNU Lesser General Public License // along with this library; if not, write to the Free Software Foundation, Inc., // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA //------------------------------------------------------------------------------ /* * Author Niklaus Johner */ #include <ost/base.hh> #include <ost/mol/mol.hh> #include "structure_analysis.hh" namespace ost { namespace mol { namespace alg { geom::Vec3List GetPosListFromView(const EntityView& view){ CheckHandleValidity(view); geom::Vec3List vl; AtomViewList atoms=view.GetAtomList(); vl.reserve(atoms.size()); for (AtomViewList::const_iterator i=atoms.begin(), e=atoms.end(); i!=e; ++i) { vl.push_back(i->GetPos()); } return vl; } Real CalculateAverageAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle& density_map){ Real sum,v; sum=0; CheckHandleValidity(density_map); for (geom::Vec3List::const_iterator v1=vl.begin(),e=vl.end(); v1!=e; ++v1) { img::Point p(density_map.CoordToIndex(*v1)); v=density_map.GetReal(p); sum=sum+v; } return sum/float(vl.size()); } void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 basis_vec){ mol::XCSEditor edi=eh.EditXCS(mol::BUFFERED_EDIT); geom::Vec3 cm,wrapped_cm,shift; edi=eh.EditXCS(); ResidueHandleList residues=eh.GetResidueList(); unsigned int n_residues=eh.GetResidueCount(); for (unsigned int i=0; i<n_residues; ++i) { ResidueHandle r=residues[i]; cm=r.GetCenterOfMass(); wrapped_cm=geom::WrapVec3(cm,cell_center,basis_vec); if (wrapped_cm==cm) continue; AtomHandleList atoms=r.GetAtomList(); unsigned int n_atoms=r.GetAtomCount(); shift=wrapped_cm-cm; for (unsigned int j=0; j<n_atoms; ++j) { edi.SetAtomPos(atoms[j],atoms[j].GetPos()+shift); } } } }}} //ns