PDB.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
/*                                                                            */
/*                           ----  SPARTA   ----                              */
/*     Shifts Prediction from Analogue of Residue type and Torsion Angle      */
/*                           Yang Shen and Ad Bax                             */
/*                    J. Biomol. NMR, 38, 289-302 (2007)                      */
/*                 NIH, NIDDK, Laboratory of Chemical Physics                 */
/*                     version, 1.01 (build 2009.0928.17)                     */
/*                                                                            */
/*                      for any problem, please contact                       */
/*                          shenyang@niddk.nih.gov                            */
/*                                                                            */
/******************************************************************************/

#ifndef PDB_H
#define PDB_H

// AUTO-REMOVED #include <string>
#include <vector>
#include <map>
#include <algorithm>
#include <boost/unordered_map.hpp>

#include <utility/vector0.hh>

#include <core/pose/Pose.fwd.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace sparta {

typedef float Vec3[3];
typedef float Mat3[3][3];
typedef boost::unordered_map<int, boost::unordered_map<int, double> > DoubleD2;
typedef boost::unordered_map<int, double>  DoubleD1;

typedef struct CORdata {
  int atomNum, resNum;
  std::string atomName, resName, chainName;
  float X, Y, Z, B_Factor;
  Vec3 Coord;
} PDB_Entry;


typedef struct {
  int resID, atomNo;
  std::string resName;
  PDB_Entry atoms[6];

  Vec3 coordA[6];
  Vec3 center, norm;
  Mat3 transM;
  float rad;

  float ringFact;
} RingData;

typedef boost::unordered_map<int, PDB_Entry> Mol; //atom list indexed by atom number
typedef boost::unordered_map<int, Mol> Mols;


class PDB
{
  long sgn(float x);
  float arccos_(float x);
  void Vec3Zero(Vec3 v);
  void Vec3Copy(Vec3 v1, Vec3 v2);
  float Vec3Abs(Vec3 v);
  float Vec3DiffAbs(Vec3 v1, Vec3 v2);
  void Vec3Norm(Vec3 v);
  void Vec3Scale(Vec3 v, float s);
  void Vec3Add(Vec3 v1, Vec3 v2);
  void Vec3Sub(Vec3 v1, Vec3 v2);
  float Vec3Scalar(Vec3 v1, Vec3 v2);
  void Vec3Cross(Vec3 v1, Vec3 v2);
  void Mat3VecMult(Vec3 v, Mat3 m);
  void Vec3ScaleAdd(Vec3 v1, float s, Vec3 v2);

public:

  std::string PDBfileName;

  RingData Rings[2000]; //Aromatic ring list
  int RingNo;

  PDB_Entry EMPTY;

  //molecules
  Mols Conformers;
  //atom list indexed by conformer ID + atom number
  boost::unordered_map<int, boost::unordered_map<int, boost::unordered_map< std::string, PDB_Entry> > > ATOMS;
  //atom list indexed by conformer ID + residue number + atom name

  std::map<int, std::string> residList, residListOne; //resdiue lists with three-letter-aa and one-letter-aa name
  int r1, rN;

  boost::unordered_map<int, int> acceptorList; // Acceptor List for H-bond indexed by atom index
  boost::unordered_map<int, int> donorList; // Donor List for H-bond indexed by atom indeice of itself and its connected heavy atom
  boost::unordered_map<int, boost::unordered_map< std::string, float> > HBDistList; // HBond distance indexed by residue number and atom name
  boost::unordered_map<int, boost::unordered_map< std::string, float> > HBEnergyList; // HBond energy list indexed by residue number and atom name
  boost::unordered_map<int, boost::unordered_map< std::string, float> > HB_DHO_AngleList; // HBond angle (Donator-H-O) indexed by residue number and atom name
  boost::unordered_map<int, boost::unordered_map< std::string, float> > HB_HOA_AngleList; // HBond angle (H-O-Acceptor_base) indexed by residue number and atom name


  int SpherePointNo;
  Vec3 *SpherePoints;
  int SurfPrec ;
  boost::unordered_map< int, utility::vector0<int> > NeighborList;
  // Neighboring atom list, indexed by atom number of target atom, and utility::vector0 list of neighbor atoms
  boost::unordered_map< int,float> ResSurfaceFullList, ResSurfacePartList;
  // Residue Surface list, indexed by residue number, and surface area for this residue

  boost::unordered_map<int, boost::unordered_map< std::string,float> > AtomSurfaceFullList, AtomSurfacePartList;
  // Atom Surface list, indexed by residue number, atom name, and surface area for this residue
  boost::unordered_map< std::string, float > VDW_RAD; //VDW radius for different type of atoms

  boost::unordered_map<int, float> HN_S2;
  boost::unordered_map<int, boost::unordered_map< std::string, float> > ElectricField; // indexed by resID and atomName

  PDB();
  PDB(const std::string& fileName);

  //amino acid name convertion
  std::string getThreeAAName(char a);
  std::string getOneAAName(const std::string& a);

  //load pdb coordinates
  void loadPDB(const std::string &fileName);
  void loadPDB(std::istream &file);

  void loadPDB( core::pose::Pose const& pose );

  void loadPDB_Entry(const std::string &str, PDB_Entry &entry);
  std::string getField(const std::string &str, int index);

  //get atom
  PDB_Entry getEntry(int conformerID, int rNum, const std::string &aName); //get atom by residue number and atom name
  PDB_Entry getEntry(int conformerID, int aNum); //get atom by atom number

  //get angles and distances
  float getBondAngle(Vec3 A, Vec3 B, Vec3 C);
  float getBondAngle(PDB_Entry a, PDB_Entry b, PDB_Entry c);
  float getDihedralAngle(PDB_Entry a, PDB_Entry b, PDB_Entry c, PDB_Entry d);
  float getPhi(int conformerID, int resNum);
  float getPsi(int conformerID, int resNum);
  float getOmega(int conformerID, int resNum);
  float getChi1(int conformerID, int resNum);
  float getChi2(int conformerID, int resNum);
  float getDist(Vec3 A, Vec3 B);
  float getDist(PDB_Entry A, PDB_Entry B);

  bool isSSBonded(int conformerID, int resNum);

  //get ring current shifts
  void initOrbitalShift();
  float getOrbitalShift(int conformerID, int resNum, const std::string &aName);
  void calcPlane(RingData *ringP);

  //get H-bond information
  void initHBond(float DIST=3.5, float ANGLE=35);
  float getHBondDist(PDB_Entry D);
  float getHBondDist(int resNum, std::string atomName);
  PDB_Entry isAcceptor(PDB_Entry A); //check if an atom is an Acceptor for a H-Hond
  PDB_Entry isDonor(PDB_Entry D); //check if an aotm is a Donor for a H-hond, and return the connected heavy atom

  // void SphereCalcPoints(int divNo, Vec3 **pointAP, int *pointNoP);
  void calcTriangles( double x0, double y0, double z0,
    double x1, double y1, double z1,
    double x2, double y2, double z2,
    int rowStartA[], int rowNo, int quad,
    int row0, int ind0, int ind1,
    int row2, int ind2,
    Vec3 *pointA);
  void findNeighors(float rad_sol);
  //  void initSurface(float rad_sol );
  void calcSurface( float rad_sol );

  void calc_HN_S2( );
  void calc_ElectricField( );

  void collect_HN_S2_and_EF( );
};

}
}

#endif