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/*! \file minimol_seq.h
Header file for atomic sequence types */
//C Copyright (C) 2000-2006 Kevin Cowtan and University of York
//L
//L This library is free software and is distributed under the terms
//L and conditions of version 2.1 of the GNU Lesser General Public
//L Licence (LGPL) with the following additional clause:
//L
//L `You may also combine or link a "work that uses the Library" to
//L produce a work containing portions of the Library, and distribute
//L that work under terms of your choice, provided that you give
//L prominent notice with each copy of the work that the specified
//L version of the Library is used in it, and that you include or
//L provide public access to the complete corresponding
//L machine-readable source code for the Library including whatever
//L changes were used in the work. (i.e. If you make changes to the
//L Library you must distribute those, but you do not need to
//L distribute source or object code to those portions of the work
//L not covered by this licence.)'
//L
//L Note that this clause grants an additional right and does not impose
//L any additional restriction, and so does not affect compatibility
//L with the GNU General Public Licence (GPL). If you wish to negotiate
//L other terms, please contact the maintainer.
//L
//L You can redistribute it and/or modify the library under the terms of
//L the GNU Lesser General Public License as published by the Free Software
//L Foundation; either version 2.1 of the License, or (at your option) any
//L later version.
//L
//L This library is distributed in the hope that it will be useful, but
//L WITHOUT ANY WARRANTY; without even the implied warranty of
//L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
//L Lesser General Public License for more details.
//L
//L You should have received a copy of the CCP4 licence and/or GNU
//L Lesser General Public License along with this library; if not, write
//L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK.
//L The GNU Lesser General Public can also be obtained by writing to the
//L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
//L MA 02111-1307 USA
#ifndef CLIPPER_MINIMOL_SEQ
#define CLIPPER_MINIMOL_SEQ
#include "minimol.h"
namespace clipper {
//! Polymer sequence object
/*! The polymer sequence object represents the named sequence of a
single chain. */
class MPolymerSequence
{
public:
MPolymerSequence() {} //!< null constructor
const String& id() const { return id_; } //!< get sequence ID
void set_id( const String& s ); //!< set sequence ID
const String& sequence() const { return seq_; } //!< get sequence ID
void set_sequence( const String& s ); //!< set sequence ID
static String id_tidy( const String& id ) { return id; } //!< convert ID to std format
static bool id_match( const String& id1, const String& id2, const MM::MODE& mode ) { return id1 == id2; } //!< compare two ids
private:
String id_;
String seq_;
};
//! Molecule sequence obeject
/*! The molecule sequence object is a list of polymer sequence
objects representing the named sequences of all the chains in a
molecule. */
class MMoleculeSequence
{
public:
//! number of polymer sequences in model
int size() const { return children.size(); }
//! get polymer sequence
const MPolymerSequence& operator[] ( const int& i ) const { return children[i]; }
//! set polymer sequence
MPolymerSequence& operator[] ( const int& i ) { return children[i]; }
//! get polymer sequence by id
const MPolymerSequence& find( const String& n, const MM::MODE mode=MM::UNIQUE ) const;
//! set polymer sequence by id
MPolymerSequence& find( const String& n, const MM::MODE mode=MM::UNIQUE );
//! lookup polymer sequence by id
int lookup( const String& str, const MM::MODE& mode ) const;
void insert( const MPolymerSequence& add, int pos=-1 ); //!< add polymer sequence
bool is_null() const { return (size()==0); } //!< test for null model
private:
typedef MPolymerSequence CHILDTYPE;
std::vector<CHILDTYPE> children;
};
} // namespace clipper
#endif
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