OpenStructure: stage/include/ost/mol/builder.hh Source File

00001 
00002 //------------------------------------------------------------------------------
00003 // This file is part of the OpenStructure project <www.openstructure.org>
00004 //
00005 // Copyright (C) 2008-2011 by the OpenStructure authors
00006 //
00007 // This library is free software; you can redistribute it and/or modify it under
00008 // the terms of the GNU Lesser General Public License as published by the Free
00009 // Software Foundation; either version 3.0 of the License, or (at your option)
00010 // any later version.
00011 // This library is distributed in the hope that it will be useful, but WITHOUT
00012 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
00013 // FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
00014 // details.
00015 //
00016 // You should have received a copy of the GNU Lesser General Public License
00017 // along with this library; if not, write to the Free Software Foundation, Inc.,
00018 // 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
00019 //------------------------------------------------------------------------------
00020 #ifndef OST_MOL_BASE_BUILDER_HH
00021 #define OST_MOL_BASE_BUILDER_HH
00022 
00023 #include "module_config.hh"
00024 
00025 #include "atom_handle.hh"
00026 #include "residue_handle.hh"
00027 #include "chain_handle.hh"
00028 #include "entity_handle.hh"
00029 #include "bond_handle.hh"
00030 #include "xcs_editor.hh"
00031 
00032 
00033 namespace ost { namespace mol {
00034 
00035 // a helper class to easily create entities
00036 class DLLEXPORT Builder {
00037 public:
00038    Builder(): ent_(CreateEntity()), edi_(ent_.EditXCS(BUFFERED_EDIT)) {
00039    }
00040 
00041    // conversion to entity handle
00042    operator EntityHandle() { return ent_; }
00043 
00044    Builder& Chain(const String& name) {
00045      chain_ = edi_.InsertChain(name);
00046      res_ = ResidueHandle();
00047      atom_ = AtomHandle();
00048      return *this;
00049    }
00050 
00051    Builder& Residue(const String& name) {
00052      res_ = edi_.AppendResidue(chain_, name);
00053      atom_ = AtomHandle();
00054      return *this;
00055    }
00056 
00057    Builder& OneLetterCode(char olc) {
00058      res_.SetOneLetterCode(olc);
00059      return *this;
00060    }
00061 
00062    Builder& Atom(const String& name, const geom::Vec3& pos=geom::Vec3()) {
00063      edi_.InsertAtom(res_, name, pos);
00064      return *this;
00065    }
00066    Builder& Gly(bool connect=true) {
00067      this->Residue("GLY");
00068      this->Atom("N");
00069      this->Atom("CA");
00070      this->Atom("C");
00071      this->Atom("O");
00072      if (connect) {
00073        edi_.Connect(res_.FindAtom("N"), res_.FindAtom("CA"));
00074        edi_.Connect(res_.FindAtom("CA"), res_.FindAtom("C"));
00075        edi_.Connect(res_.FindAtom("C"), res_.FindAtom("O"));
00076      }
00077      return *this;
00078    }
00079    Builder& ConnectToPrev() {
00080      AtomHandle ah = res_.FindAtom("N");
00081      AtomHandle pa = res_.GetPrev().FindAtom("C");
00082      if (pa) {
00083        edi_.Connect(pa, ah);
00084      }
00085      return *this;
00086    }
00087 private:
00088    EntityHandle  ent_;
00089    ChainHandle   chain_;
00090    ResidueHandle res_;
00091    AtomHandle    atom_;
00092    XCSEditor     edi_;
00093 
00094 
00095 };
00096 
00097 }}
00098 #endif
00099