/*=========================================================================

Program:   Visualization Toolkit
Module:    vtkMoleculeReaderBase.cxx
Language:  C++
Date:      $Date$
Version:   $Revision$


Copyright (c) 1993-2001 Ken Martin, Will Schroeder, Bill Lorensen 
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice,
 this list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright notice,
 this list of conditions and the following disclaimer in the documentation
 and/or other materials provided with the distribution.

* Neither name of Ken Martin, Will Schroeder, or Bill Lorensen nor the names
 of any contributors may be used to endorse or promote products derived
 from this software without specific prior written permission.

* Modified source versions must be plainly marked as such, and must not be
 misrepresented as being the original software.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

=========================================================================*/
#include "vtkMoleculeReaderBase.h"

#include "vtkCellArray.h"
#include "vtkCellType.h"
#include "vtkDataArray.h"
#include "vtkFloatArray.h"
#include "vtkObjectFactory.h"
#include "vtkPointData.h"
#include "vtkPolyData.h"
#include "vtkUnsignedCharArray.h"

#include <ctype.h>

vtkCxxRevisionMacro(vtkMoleculeReaderBase, "1.14");

static double vtkMoleculeReaderBaseCovRadius[103] = {
0.32 , 1.6 , 0.68 , 0.352 , 0.832 , 0.72 ,
0.68 , 0.68 , 0.64 , 1.12 , 0.972 , 1.1 , 1.352 , 1.2 , 1.036 ,
1.02 , 1 , 1.568 , 1.328 , 0.992 , 1.44 , 1.472 , 1.328 , 1.352 ,
1.352 , 1.34 , 1.328 , 1.62 , 1.52 , 1.448 , 1.22 , 1.168 , 1.208 ,
1.22 , 1.208 , 1.6 , 1.472 , 1.12 , 1.78 , 1.56 , 1.48 , 1.472 ,
1.352 , 1.4 , 1.448 , 1.5 , 1.592 , 1.688 , 1.632 , 1.46 , 1.46 ,
1.472 , 1.4 , 1.7 , 1.672 , 1.34 , 1.872 , 1.832 , 1.82 , 1.808 ,
1.8 , 1.8 , 1.992 , 1.792 , 1.76 , 1.752 , 1.74 , 1.728 , 1.72 ,
1.94 , 1.72 , 1.568 , 1.432 , 1.368 , 1.352 , 1.368 , 1.32 , 1.5 ,
1.5 , 1.7 , 1.552 , 1.54 , 1.54 , 1.68 , 1.208 , 1.9 , 1.8 ,
1.432 , 1.18 , 1.02 , 0.888 , 0.968 , 0.952 , 0.928 , 0.92 , 0.912 ,
0.9 , 0.888 , 0.88 , 0.872 , 0.86 , 0.848 , 0.84 };

static double vtkMoleculeReaderBaseAtomColors[][3] = {
  {255, 255, 255}, {127, 0, 127}, {255, 0, 255},
  {127, 127, 127}, {127, 0, 127}, {0, 255, 0},
  {0, 0, 255}, {255, 0, 0}, {0, 255, 255},
  {127, 127, 127}, {127, 127, 127}, {178, 153, 102},
  {127, 127, 127}, {51, 127, 229}, {0, 255, 255},
  {255, 255, 0}, {255, 127, 127}, {255, 255, 127},
  {127, 127, 127}, {51, 204, 204}, {127, 127, 127},
  {0, 178, 178}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {204, 0, 255}, {255, 0, 255},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {229, 102, 51}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 255, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {102, 51, 204}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {51, 127, 51}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}, {127, 127, 127},
  {127, 127, 127}, {127, 127, 127}
};

static double vtkMoleculeReaderBaseRadius[] = {
  1.2, 1.22, 1.75,  /* "H " "He" "Li" */
  1.50, 1.90, 1.80, /* "Be" "B " "C " */
  1.70, 1.60, 1.35, /* "N " "O " "F " */
  1.60, 2.31, 1.70, 
  2.05, 2.00, 2.70,
  1.85, 1.81, 1.91,
  2.31, 1.74, 1.80,
  1.60, 1.50, 1.40,  /* Ti-Cu and Ge are guestimates. */
  1.40, 1.40, 1.40,
  1.60, 1.40, 1.40,
  1.90, 1.80, 2.00,
  2.00, 1.95, 1.98,
  2.44, 2.40, 2.10,  /* Sr-Rh and Ba and La are guestimates. */
  2.00, 1.80, 1.80,
  1.80, 1.80, 1.80,
  1.60, 1.70, 1.60,
  1.90, 2.20, 2.20,
  2.20, 2.15, 2.20,
  2.62, 2.30, 2.30,
  2.30, 2.30, 2.30,  /* All of these are guestimates. */
  2.30, 2.30, 2.40,
  2.30, 2.30, 2.30,
  2.30, 2.30, 2.30,
  2.40, 2.50, 2.30,
  2.30, 2.30, 2.30,  /* All but Pt and Bi are guestimates. */
  2.30, 2.30, 2.40,
  2.30, 2.40, 2.50,
  2.50, 2.40, 2.40,
  2.40, 2.40, 2.90,
  2.60, 2.30, 2.30,   /* These are all guestimates. */
  2.30, 2.30, 2.30,
  2.30, 2.30, 2.30,
  2.30, 2.30, 2.30,
  2.30, 2.30, 2.30,
  2.30, 1.50 } ;

vtkMoleculeReaderBase::vtkMoleculeReaderBase()
{
  this->FileName = NULL;
  this->BScale = 1.0;
  this->HBScale = 1.0;
  this->AtomType = NULL;
  this->Points = NULL;
  this->RGB = NULL;
  this->Radii = NULL;
  this->NumberOfAtoms = 0;
}

vtkMoleculeReaderBase::~vtkMoleculeReaderBase()
{
  if (this->FileName)
    {
    delete [] this->FileName;
    }
  if(this->AtomType)
    {
    this->AtomType->Delete();
    }
  if(this->Points)
    {
    this->Points->Delete();
    }
  if(this->RGB)
    {
    this->RGB->Delete();
    }
  if(this->Radii)
    {
    this->Radii->Delete();
    }
}

void vtkMoleculeReaderBase::Execute()
{
  FILE *fp;

  if (!this->FileName) 
    {
    return;
    }

  if ((fp = fopen(this->FileName, "r")) == NULL) 
    {
    vtkErrorMacro(<< "File " << this->FileName << " not found");
    return;
    }
  vtkDebugMacro(<< "opening base file " << this->FileName);
  this->ReadMolecule(fp);
  fclose(fp);

  this->GetOutput()->Squeeze();
}

int vtkMoleculeReaderBase::ReadMolecule(FILE *fp)
{
  int i;
  vtkCellArray *newBonds;

  vtkDebugMacro(<< "Scanning the Molecule file");
  vtkPolyData *output = this->GetOutput();

  if ( !this->AtomType )
    {
    this->AtomType = vtkIdTypeArray::New();
    }
  else
    {
    this->AtomType->Reset();
    }

  if ( !this->Points )
    {
    this->Points = vtkPoints::New();
    }
  else
    {
    this->Points->Reset();
    }

  this->ReadSpecificMolecule(fp);

  vtkDebugMacro(<< "End of scanning");
  output->SetPoints(this->Points);

  newBonds = vtkCellArray::New();
  newBonds->Allocate(500);

  this->MakeBonds(this->Points, this->AtomType, newBonds);

  output->SetLines(newBonds);
  newBonds->Delete();

  vtkDebugMacro(<< "read " << this->NumberOfAtoms << " atoms and found " 
                << newBonds->GetNumberOfCells() << " bonds" << endl);

  if ( this->RGB )
    {
    this->RGB->Reset();
    }
  else
    {
    this->RGB = vtkUnsignedCharArray::New();
    }
  this->RGB->SetNumberOfComponents(3);
//  this->RGB->SetNumberOfTuples(this->NumberOfAtoms);
  this->RGB->Allocate(3*this->NumberOfAtoms);
  this->RGB->SetName("rgb_colors");

  for(i=0; i < this->NumberOfAtoms; i++)
    {
    this->RGB->InsertNextTuple(
      &vtkMoleculeReaderBaseAtomColors[AtomType->GetValue(i)][0]);
    }

  output->GetPointData()->SetScalars(this->RGB);

  if ( this->Radii )
    {
    this->Radii->Reset();
    }
  else
    {
    this->Radii = vtkFloatArray::New();
    }
  this->Radii->SetNumberOfComponents(3);
  //  this->Radii->SetNumberOfTuples(this->NumberOfAtoms);
  this->Radii->Allocate(3 * this->NumberOfAtoms);
  this->Radii->SetName("radius");

  // We're obliged here to insert the scalars "radius" 3 times to make it a
  // vector in order to use Glyph3D to color AND scale at the same time.

  for(i=0; i < this->NumberOfAtoms; i++)
    {
    this->Radii->InsertNextTuple3(
      vtkMoleculeReaderBaseRadius[AtomType->GetValue(i)],
      vtkMoleculeReaderBaseRadius[AtomType->GetValue(i)],
      vtkMoleculeReaderBaseRadius[AtomType->GetValue(i)]);
    }

  output->GetPointData()->SetVectors(this->Radii);

  return 0;
}

int vtkMoleculeReaderBase::MakeBonds(vtkPoints *newPts,
                                     vtkIdTypeArray *atype,
                                     vtkCellArray *newBonds)
{
  register int i, j;
  register int nbonds;
  register int nbonds_this_atom;     // this is not used for the moment
  register double dx, dy, dz;
  double max, dist;
  double X[3], Y[3];
  vtkIdType bond[2];

  nbonds = 0;
  for(i = this->NumberOfAtoms - 1; i > 0; i--) 
    {
    nbonds_this_atom = 0;
    bond[0] = i;
    newPts->GetPoint(i, X);
    for(j = i - 1; j >= 0 ; j--) 
      {
      /*
       * The outer loop index 'i' is AFTER the inner loop 'j': 'i'
       * leads 'j' in the list: since hydrogens traditionally follow
       * the heavy atom they're bonded to, this makes it easy to quit
       * bonding to hydrogens after one bond is made by breaking out of
       * the 'j' loop when 'i' is a hydrogen and we make a bond to it.
       * Working backwards like this makes it easy to find the heavy
       * atom that came 'just before' the Hydrogen. mp
       * Base distance criteria on vdw...lb                                 
       */

      /* never bond hydrogens to each other... */
      if (atype->GetValue(i) == 0 && atype->GetValue(j) == 0) 
        {
        continue;
        }

      dist = vtkMoleculeReaderBaseCovRadius[atype->GetValue(i)] +
        vtkMoleculeReaderBaseCovRadius[atype->GetValue(j)] + 0.56;
      max = dist*dist;

      if(atype->GetValue(i) == 0 || atype->GetValue(j) == 0)
        {
        max *= HBScale;
        }
      else
        {
        max *= BScale;
        }

      newPts->GetPoint(j, Y);
      dx = X[0] - Y[0];
      dist = dx * dx;

      if(dist > max ) 
        {
        continue;
        }

      dy = X[1] - Y[1];
      dist += dy * dy;
      if(dist > max ) 
        {
        continue;
        }

      dz = X[2] - Y[2];
      dist += dz * dz;
      if(dist > max ) 
        {
        continue;
        }

      bond[1] = j;
      newBonds->InsertNextCell(2, bond);

      nbonds++;
      nbonds_this_atom++;
      }
    }
  newBonds-> Squeeze();
  return nbonds;
}

int vtkMoleculeReaderBase::MakeAtomType(const char *atype)
{
  char      a, b;
  int       anum=0;

  a = atype[0];
  if (islower(a)) 
    {
    a = toupper(a);
    }
  b = atype[1];
  if (islower(b)) 
    {
    b = toupper(b);
    }
  switch (a) 
    {
  case 'A':
    if(b == 'C') anum = 89;
    else if(b == 'G') anum = 47;
    else if(b == 'L') anum = 13;
    else if(b == 'M') anum = 95;
    else if(b == 'R') anum = 18;
    else if(b == 'S') anum = 33;
    else if(b == 'T') anum = 85;
    else if(b == 'U') anum = 79;
    break;
  case 'B':
    if(b == 'A') anum = 56;
    else if(b == 'E') anum = 4;
    else if(b == 'I') anum = 83;
    else if(b == 'K') anum = 97;
    else if(b == 'R') anum = 35;
    else anum = 5;
    break;
  case 'C':
    if(b == 'L') anum = 17;
    else if(b == 'O') anum = 27;
    else if(b == 'R') anum = 24;
    else if(b == 'S') anum = 55;
    else if(b == 'U') anum = 29;
    else if(b == '0') anum = 6;
    else anum = 6;
    break;
  case 'D':
    anum = 66;
    break;
  case 'E':
    if(b == 'R') anum = 68;
    else if(b == 'S') anum = 99;
    else if(b == 'U') anum = 63;
    break;
  case 'F':
    if(b == 'E') anum = 26;
    else if(b == 'M') anum = 100;
    else if(b == 'R') anum = 87;
    else anum = 9;
    break;
  case 'G':
    if(b == 'A') anum = 31;
    else if(b == 'D') anum = 64;
    else if(b == 'E') anum = 32;
    break;
  case 'H':
    anum = 1;
    break;
  case 'I':
    if(b == 'N') anum = 49;
    else if(b == 'R') anum = 77;
    else anum = 53;
    break;
  case 'K':
    if(b == 'R') anum = 36;
    else anum = 19;
    break;
  case 'L':
    if(b == 'A') anum = 57;
    else if(b == 'I') anum = 3;
    else if(b == 'R') anum = 103;
    else if(b == 'U') anum = 71;
    break;
  case 'M':
    if(b == 'D') anum = 101;
    else if(b == 'G') anum = 12;
    else if(b == 'N') anum = 25;
    else if(b == 'O') anum = 42;
    break;
  case 'N':
    if(b == 'I') anum = 28;
    else anum = 7;
    break;
  case 'O':
    anum = 8;
    break;
  case 'P':
    if(b == 'A') anum = 91;
    else if(b == 'B') anum = 82;
    else if(b == 'D') anum = 46;
    else if(b == 'M') anum = 61;
    else if(b == 'O') anum = 84;
    else if(b == 'R') anum = 59;
    else if(b == 'T') anum = 78;
    else if(b == 'U') anum = 94;
    else anum = 15;
    break;
  case 'R':
    if(b == 'A') anum = 88;
    else if(b == 'B') anum = 37;
    else if(b == 'E') anum = 75;
    else if(b == 'H') anum = 45;
    else if(b == 'N') anum = 86;
    else if(b == 'U') anum = 44;
    break;
  case 'S':
    if(b == 'I') anum = 14;
    else if(b == 'R') anum = 38;
    else anum = 16;
    break;
  case 'T':
    if(b == 'A') anum = 73;
    else if(b == 'B') anum = 65;
    else if(b == 'C') anum = 43;
    else if(b == 'E') anum = 52;
    else if(b == 'H') anum = 90;
    else if(b == 'I') anum = 22;
    else if(b == 'L') anum = 81;
    else if(b == 'M') anum = 69;
    break;
  case 'U':
    anum = 92;
    break;
  case 'V':
    anum = 23;
    break;
  case 'W':
    anum = 74;
    break;
  case 'X':
    anum = 54;
    break;
  case 'Y':
    if(b == 'B') anum = 70;
    else anum = 39;
    break;
  case 'Z':
    if(b == 'N') anum = 30;
    else anum = 40;
    break;
  case ' ':
    anum = 104;
    break;
  default:
    anum = 6;
    break;
    }
  return (anum-1);
}

void vtkMoleculeReaderBase::PrintSelf(ostream& os, vtkIndent indent)
{
  this->Superclass::PrintSelf(os,indent);

  os << indent << "File Name: " 
    << (this->FileName ? this->FileName : "(none)") << endl;
  os << indent << "NumberOfAtoms: " << this->NumberOfAtoms  << endl;
  os << indent << "HBScale: " << this->HBScale << endl;
  os << indent << "BScale: " << this->BScale << endl;
}


