PDB.h

/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   Copyright (c) 2011-2016 The plumed team
   (see the PEOPLE file at the root of the distribution for a list of names)

   See http://www.plumed.org for more information.

   This file is part of plumed, version 2.

   plumed 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 of the License, or
   (at your option) any later version.

   plumed 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 plumed.  If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#ifndef __PLUMED_tools_PDB_h
#define __PLUMED_tools_PDB_h

#include "AtomNumber.h"
#include "Vector.h"
#include <vector>
#include <string>
#include "Log.h"
#include <map>


namespace PLMD{

/// Minimalistic pdb parser.
/// Contain positions, atomic indexes, occupancy and beta.
/// We should also add other info (e.g. residue name etc).
class PDB{
  std::vector<unsigned> block_ends;
  std::vector<std::string> atomsymb, chain;
  std::vector<unsigned> residue;
  std::vector<Vector> positions;
  std::vector<double> occupancy;
  std::vector<double> beta;
  std::vector<std::string> remark;
  std::vector<AtomNumber> numbers;
  std::map<AtomNumber,unsigned> number2index;
  std::vector<std::string> residuenames;
public:
/// Read the pdb from a file, scaling positions by a factor scale
  bool read(const std::string&file,bool naturalUnits,double scale);
/// Read from a file pointer
  bool readFromFilepointer(FILE *fp,bool naturalUnits,double scale);
/// Access to the position array
  const std::vector<Vector>     & getPositions()const;
/// Access to the occupancy array
  const std::vector<double>     & getOccupancy()const;
/// Access to the beta array
  const std::vector<double>     & getBeta()const;
/// This is used to set the keyword ARG - this is so we
/// we can use a1.* in the input for reference configurations 
  void setArgKeyword( const std::string& new_args );
/// Add information to the remark
  void addRemark( const std::vector<std::string>& v1 );
/// Access to the lines of REMARK 
  const std::vector<std::string>     & getRemark()const;
/// Access to the indexes
  const std::vector<AtomNumber> & getAtomNumbers()const;
/// Returns the number of atoms
  unsigned                        size()const;
/// Get the names of all the chains in the pdb file
  void getChainNames( std::vector<std::string>& chains ) const;
/// Get the residues in each of the chains
  void getResidueRange( const std::string& chainname, unsigned& res_start, unsigned& res_end, std::string& errmsg ) const;
/// Get the atoms in each of the chains 
  void getAtomRange( const std::string& chainname, AtomNumber& a_start, AtomNumber& a_end, std::string& errmsg ) const;
/// Get the chain ID that a particular residue is a part of
  std::string getChainID(const unsigned& resnumber) const;
///use the log to dump information  
  friend Log& operator<<(Log& ostr, const PDB& pdb);
/// return the name of a specific atom
  std::string getAtomName(AtomNumber a) const;
/// return the residue number for a specific atom
  unsigned getResidueNumber(AtomNumber a) const;
/// return the residue name for a specific atom
  std::string getResidueName(AtomNumber a) const;
/// get the name of the resnum'th residue
  std::string getResidueName(const unsigned& resnum ) const;
/// get the name of the resnum'th residue of chain
/// Chain=="*" matches any chain and makes it equivalent to getResidueName
  std::string getResidueName(const unsigned& resnum,const std::string& chain ) const;
/// Check if any of the residues are named name
  bool checkForResidue( const std::string& name ) const ;
/// Check if any of the atoms are named atom
  bool checkForAtom( const std::string& name ) const ;
/// Return the atom named aname from residue number resnum
  AtomNumber getNamedAtomFromResidue( const std::string& aname, const unsigned& resnum ) const;
/// Return the atom named aname from residue number resnum and chain.
/// Chain=="*" matches any chain and makes it equivalent to getNamedAtomFromResidue.
  AtomNumber getNamedAtomFromResidueAndChain( const std::string& aname, const unsigned& resnum, const std::string& chain ) const;
/// Access to the atoms of a residue 
  std::vector<AtomNumber> getAtomsInResidue(const unsigned& resnum,const std::string& chainid)const;
/// Access to the atoms of a chain 
  std::vector<AtomNumber> getAtomsInChain(const std::string& chainid)const;
/// Get the extents of the blocks containing the atoms
  const std::vector<unsigned> & getAtomBlockEnds() const ;
/// Get the number of blocks of atoms in the pdb
  unsigned getNumberOfAtomBlocks() const ;
/// Set the position array
  void setPositions(const std::vector<Vector> &v);
};

}
#endif