/*
FILE:     xtal.C
*/
/*
VERSION:  1.600
*/
/*
DATE:     2/3/2005
*/
/*
  Comments and Questions to: sw-help@rcsb.rutgers.edu
*/
/*
COPYRIGHT 1999-2005 Rutgers - The State University of New Jersey

This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR
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*/
/*
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*/
#include <stdio.h>
#include <string.h>
#include "class.h"
#include "xtal.h"
#include "atom.h"
#include "symop.h"
#include "gridcell.h"
#include "list.h"

static char lowerchar (const char c)
{
       if ((c >= 'A') && (c <= 'Z')) return char(c+('z'-'Z'));
       else return c;
}

static void lower(const char* s1, char* s2)
{
       int i = 0, len;
       len = strlen(s1);
       while ((i <= len)) {
            s2[i] = lowerchar(s1[i]);
            i++;
       }
       s2[i] = '\0';
}

xtal::xtal()
{
       a = b = c = 0.0;
       alpha = beta = gamma = 90.0;
       cosalpha = cosbeta = cosgamma = 1.0; 
       atlist = 0;
       xtalgrid = 0;
}

xtal::~xtal()
{
       Clear();
}

void xtal::Clear()
{
       if (atlist) delete [] atlist;
       atlist = 0;
       if (xtalgrid) delete xtalgrid;
       xtalgrid = 0;
       atl.DeleteList();
       oplist.DeleteList();
}

int xtal::init(const NDBCELLCONST *cell, _MOLECULE *mol, const int remove_hydrogen)
{
       int i, j, k;
       symop newsym;
       float oper[3][4];
       atom newat;
       _ATOM *_atom = NULL;
       _RESIDUE *residue = NULL;
       _CHAIN *chain = NULL;

       a = cell->a; b = cell->b; c = cell->c;
       alpha = cell->alpha;
       beta = cell->beta;
       gamma = cell->gamma;
       strcpy(sg, cell->space_group);

       cosalpha = float(cos(double(degtorad * alpha)));
       cosbeta = float(cos(double(degtorad * beta)));
       cosgamma = float(cos(double(degtorad * gamma)));

       for (i = 0; i < 3; i++) {
            for (j = 0; j < 3; j++)
                 xform[i][j] = cell->o_to_f[i][j];
            xform[i][3] = cell->o_to_f_v[i];
       }

       numsym = cell->nop;
       for (i = 0; i < numsym; i++) {
            newsym.setopid(i);
            for (j = 0; j < 3; j++) {
                 for (k = 0; k < 3; k++) {
                      oper[j][k] = cell->symops[i].rot[j][k];
                 }
                 oper[j][3] = cell->symops[i].trans[j];
            }
            newsym.setop(oper);
            oplist.append(newsym);
       }

       numatoms = 0;
       chain = mol->GetFirstChain();
       while (chain) {
            if (chain->op() == 1) {
                 residue = chain->GetFirstResidue();
                 while (residue) {
                      _atom = residue->GetFirstAtom();
                      while (_atom) {
                           if (remove_hydrogen && _atom->is_hydrogen()) {
                                _atom = residue->GetNextAtom();
                                continue;
                           }
                           numatoms++;
                           if (chain->chain_type() > 0)
                                newat.settp(NdbToken[chain->chain_type()-1].TokenName);
                           else newat.settp(_atom->type());
                           newat.setnum(_atom->atnum());
                           // newat.setattp(_atom->atmtype());
                           newat.setattp(_atom->pdb_atmnam());
                           newat.setatomtype(_atom->atom_type());
                           newat.setrestp(_atom->restype());
                           newat.setchntp(_atom->chnid());
                           newat.setalt_loc(_atom->alt_loc()[0]);
                           newat.setresnum(_atom->resnum());
                           newat.setx(_atom->orig().x);
                           newat.sety(_atom->orig().y);
                           newat.setz(_atom->orig().z);
                           newat.setocc(_atom->occ());
                           newat.settemp(_atom->t_fct());
                           newat.setcrys(this);
                           atl.append(newat);
                           _atom = residue->GetNextAtom();
                      }
                      residue = chain->GetNextResidue();
                 }
            }
            chain = mol->GetNextChain();
       }
       numatomsAsym = numatoms;
       return (numatoms);
}

void xtal::init(const int num_a, COORD **coord_a, const int num_b, COORD **coord_b)
{
       int i;
       symop newsym;
       float oper[3][4];
       atom newat;

       a = b = c = 1000.0;
       alpha = beta = gamma = 90.0;
       strcpy(sg, "P 1");

       cosalpha = float(cos(double(degtorad * alpha)));
       cosbeta = float(cos(double(degtorad * beta)));
       cosgamma = float(cos(double(degtorad * gamma)));

       xform[0][0] = xform[1][1] = xform[2][2] = 1.0 / a;
       xform[0][1] = xform[0][2] = xform[0][3] =
       xform[1][0] = xform[1][2] = xform[1][3] =
       xform[2][0] = xform[2][1] = xform[2][3] = 0.0;

       numsym = 1;
       oper[0][0] = oper[1][1] = oper[2][2] = 1;
       oper[0][1] = oper[0][2] = oper[0][3] =
       oper[1][0] = oper[1][2] = oper[1][3] =
       oper[2][0] = oper[2][1] = oper[2][3] = 0;
       newsym.setopid(0);
       newsym.setop(oper);
       oplist.append(newsym);

       numatoms = 0;
       for (i = 0; i < num_a; i++) {
            numatoms++;
            newat.setnum(numatoms);
            newat.setchntp("a");
            newat.setx(coord_a[i]->x);
            newat.sety(coord_a[i]->y);
            newat.setz(coord_a[i]->z);
            newat.setcrys(this);
            atl.append(newat);
       }
       for (i = 0; i < num_b; i++) {
            numatoms++;
            newat.setnum(numatoms);
            newat.setchntp("b");
            newat.setx(coord_b[i]->x);
            newat.sety(coord_b[i]->y);
            newat.setz(coord_b[i]->z);
            newat.setcrys(this);
            atl.append(newat);
       }
       numatomsAsym = numatoms;
}

void xtal::setSymms(List<symop> s)
{
  oplist = s;
  numsym = s.length();
}

// Use the list of symmetry operations on the list of atoms in the asymmetric
// unit to generate the array of atoms in the entire unit cell.  If the
// atoms are known to be in cartesian, then first convert all of them to
// fractional.  Delete the initial list data structure, to save space.  
// Each copy of the asymmetric unit is contiguous.
void xtal::getSymmAtoms()
{
  int ats = 0; 
  int initnumatoms = numatoms; 
  ListObj<symop> *ptr = oplist.front()->rest(); 
  ListObj<atom> *atpt; 

  numatoms *= numsym;
  numatomsAsym *= numsym; 
  atlist = new atom[numatoms+1];
  atpt = atl.front();
  // Copy all of the asymmetric unit atoms into the array.  Assumes the
  // first symmetry operation is identity.
  for (int i=0; i < initnumatoms; i++) 
    {
      atlist[i]=atpt->firstval();
      if (orth=='c') atlist[i].fractionalize();
      atpt=atpt->rest();
    }
  ats=initnumatoms;  
  for (int j = 1; j < numsym; j++) //assumes first symmetry is identity
    { 
      for (int k=0; k<initnumatoms; k++)
          atlist[ats++] = atlist[k].symrel(ptr->firstval());
      ptr = ptr->rest();
    }
  atl.DeleteList();
}

//////////////////////////////////////////////////////////////////////
//		     Data Member Access Methods
//////////////////////////////////////////////////////////////////////

// Return the list of symmetry operations
List<symop> xtal::syms()
{
  return oplist;
}

char* xtal::Space()
{
  return sg;
}

char* xtal::xtalName()
{
  return crysnm;
}

// Return the list of atoms.  This is *only* the atoms in the asymmetric
// unit.  The entire cell is stored in an array, for fast random access.
List<atom> xtal::ats()
{
  return atl;
}

// Return a pointer to the beginning of the array of atoms
atom* xtal::crysAtoms()
{
  return atlist;
}

// Return a pointer to the grid partitioning the crystal
grid* xtal::crysGrid()
{
  return xtalgrid;
}

// Return the cell dimensions of the crystal
cellDim xtal::aval()
{
  return a;
}

cellDim xtal::bval()
{
  return b;
}

cellDim xtal::cval()
{
  return c;
}

cellDim xtal::alphaval()
{
  return alpha;
}

cellDim xtal::betaval()
{
  return beta;
}

cellDim xtal::gammaval()
{
  return gamma;
}

// Return the number of atoms in the crystal...beware...this changes
// between when the crystal is read in and when the symmetry related
// atoms are calculated
int xtal::numberAtoms()
{
  return numatoms;
}

int xtal::numSource()
{
  return numsrc;
}

int xtal::numTarget()
{
  return numtar;
}

//////////////////////////////////////////////////////////////////////
//		   Data member manipulation methods
//////////////////////////////////////////////////////////////////////

// Record whether coordinates are in fractional or cartesian
void xtal::setorth(const char ort)
{
  orth=ort;
}

void xtal::setnumAts(const int num)
{
  numatoms = num;
}

void xtal::setnumAtsAsym(const int num)
{
  numatomsAsym = num;
}

void xtal::setAtl (List<atom> l)
{
  atl = l;
}

// Set up grid data structure for crystal...call grid constructor.
void xtal::makeGrid()
{ int elts;
  elts = int(floor (1+exp((log(double(numatomsAsym)))/3)));
  xtalgrid = new grid(elts,this);
}

// Translate all atoms in the crystal into the center unit cell.  Note
// this should only be called after all of the symmetry related atoms
// have been generated.  Otherwise the program will crash (atom array
// not generated yet) and even if it didn't, would not work correctly,
// since after generating the symmetry related atoms, some of them might
// not be in the center unit cell.
void xtal::moveAllAtomsToCenter()
{
  for (int i = 0; i < numatoms; i++)
    atlist[i].moveToCenterCell();
}

// Hash each atom into the appropriate grid element.  Again, make sure
// this is done *after* the symmetry related atoms are generated.
void xtal::placeAtomsInGrid()
{
//  delete xtalgrid;

  this->makeGrid(); 
  for (int i=0; i < numatoms; i++) 
      atlist[i].placeAtomInGrid(xtalgrid); 
}

// Delete all the atoms in the crystal's atom array
void xtal::deleteAtoms()
{
  delete [] atlist;
}

// Delete a crystal's grid...call grid destructor  
void xtal::deleteGrid()
{
  delete xtalgrid;
}

void xtal::setsg(xtal* crys)
{
  strcpy(sg,crys->sg);
}

void xtal::setxform(xtal* crys)
{
  xform[0][0] = crys->xform[0][0];
  xform[0][1] = crys->xform[0][1];
  xform[0][2] = crys->xform[0][2];
  xform[0][3] = crys->xform[0][3];
  xform[1][0] = crys->xform[1][0];
  xform[1][1] = crys->xform[1][1];
  xform[1][2] = crys->xform[1][2];
  xform[1][3] = crys->xform[1][3];
  xform[2][0] = crys->xform[2][0];
  xform[2][1] = crys->xform[2][1];
  xform[2][2] = crys->xform[2][2];
  xform[2][3] = crys->xform[2][3];
}

///////////////////////////////////////////////////////////////////////
// Methods for selecting atoms with particular feature from entire list
///////////////////////////////////////////////////////////////////////

List<atom*>* xtal::selectAtoms(const char *selectType)
{
       char inpt[100];
       List<atom*>* fromatoms = NULL;
       int lastpos;

       while (!fromatoms || (fromatoms->length()==0)) {
            lower(selectType, inpt);
            fromatoms = parseall(inpt, 0, lastpos, this);
       }
       return fromatoms;
}

// Select atoms of some range number (a la BANG), but also their symmetry
// related versions.
List<atom*> xtal::selectSymAtoms(const int lo, int hi)
{
  List<atom*> al;
  int nsym= oplist.length();
  int losym=0;
  int offset = numatoms/nsym;

  if (hi>=offset) hi=offset;
  for (int i=lo-1; i<hi; i++)
    for (int j=losym; j < nsym; j++)
       al.append(atlist[i+offset*j].atptr());
  return al;
}

// Select all atoms (including symmetry related) with particular residue number
List<atom*> xtal::selectResAtoms(const int resid)
{
  List<atom*> al;
  int lowat=0;
  int numat=numatoms;

  for (int i=lowat; i<numat; i++)
     if(atlist[i].res()==resid) al.append(atlist[i].atptr());
  return al;
}  

// Select all atoms (including symmetry related) with particular chain id
List<atom*> xtal::selectChainAtoms(const char *chn)
{
  List<atom*> al;
  int lowat=0;
  int numat=numatoms;

  for (int i=lowat; i<numat; i++)
     if (!strcmp(atlist[i].chain(), chn)) al.append(atlist[i].atptr());
  return al;
}  

// Select all atoms (including symmetry related) with particular type
List<atom*> xtal::selectTypeAtoms(const char* ty)
{
  List<atom*> al;
  char at[7];
  int lowat = 0;
  int numat = numatoms;

  for (int i=lowat; i<numat; i++)
    {
     lower(atlist[i].typ(), at);	 
     if(strstr(at,ty)) al.append(atlist[i].atptr());
    }
  return al;
}  

// Select all atoms (including symmetry related) with particular atom type
// and base type
List<atom*> xtal::selectAtomTypeAtoms(const char* bty, const char* ty)
{
  List<atom*> al;
  char at[4];
  char bt[4];
  int lowat=0;
  int numat=numatoms;

  for (int i=lowat; i<numat; i++)
    {
     lower(atlist[i].resType(), bt);	 
     lower(atlist[i].attyp(), at);	 
     if((strcmp(at,ty)==0) && (strcmp(bt,bty)==0))
          al.append(atlist[i].atptr());
    }
  return al;
}  

// Select all atoms (including symmetry related) with particular type
List<atom*> xtal::selectAtomTypeAtoms(const char* ty)
{
  List<atom*> al;
  char at[4];
  int lowat=0;
  int numat=numatoms;

  for (int i=lowat; i<numat; i++)
    {
     lower(atlist[i].attyp(), at);	 
     if((strcmp(at,ty)==0))
          al.append(atlist[i].atptr());
    }
  return al;
}  

// Select all atoms (including symmetry related) that match particular type
List<atom*> xtal::selectAtomLikeAtoms(const char* ty)
{
  List<atom*> al;
  char at[4];
  int lowat=0;
  int numat=numatoms;

  for (int i=lowat; i<numat; i++)
    {
     lower(atlist[i].attyp(), at);	 
     if((strstr(at,ty)))
          al.append(atlist[i].atptr());
    }
  return al;
}  

// Select all atoms (including symmetry related) with particular residue type
List<atom*> xtal::selectResTypeAtoms(const char* ty)
{
  List<atom*> al;
  char at[4];
  int lowat=0;
  int numat=numatoms;

  for (int i=lowat; i<numat; i++)
    {
     lower(atlist[i].resType(), at);	 
     if(strcmp(at,ty)==0) al.append(atlist[i].atptr());
    }
  return al;
}