score.c

最经典的分子对结软件

    (
      contact,
      label,
      molecule,
      &grid->receptor,
      atom,
      rec_atom,
      &score
    );

    inter->total += score;
  }
}


/* ///////////////////////////////////////////////////////////////

Routine to compute the intramolecular contact score
between two ligand atoms.

2/97 te

/////////////////////////////////////////////////////////////// */

void calc_intra_contact
(
  SCORE_CONTACT *contact,
  LABEL		*label,
  MOLECULE	*molecule,
  int		atomi,
  int		atomj,
  SCORE_PART	*intra
)
{
  float score;

  calc_pairwise_contact
  (
    contact,
    label,
    molecule,
    molecule,
    atomi,
    atomj,
    &score
  );

  intra->total += score;
}


/* ///////////////////////////////////////////////////////////////

Routine to compute the contact score between any two atoms.

2/97 te

/////////////////////////////////////////////////////////////// */

void calc_pairwise_contact
(
  SCORE_CONTACT	*contact,
  LABEL		*label,
  MOLECULE	*origin,
  MOLECULE	*target,
  int		origin_atom,
  int		target_atom,
  float		*score
)
{
  float reference;
  float sq_distance;

  if
  (
    origin->atom[origin_atom].heavy_flag &&
    target->atom[target_atom].heavy_flag &&
    ((sq_distance = square_distance
      (origin->coord[origin_atom], target->coord[target_atom]))
        < SQR (contact->distance))
  )
  {
    reference = contact->clash_overlap *
      (label->vdw.member[origin->atom[origin_atom].vdw_id].radius +
      label->vdw.member[target->atom[target_atom].vdw_id].radius);

    if (sq_distance < SQR (reference))
      *score = contact->clash_penalty;

    else
      *score = -1;
  }

  else
    *score = 0;
}


/* ///////////////////////////////////////////////////////////////

Routine to add contact score components.

2/97 te

/////////////////////////////////////////////////////////////// */

void sum_contact
(
  SCORE_PART	*sum,
  SCORE_PART	*increment
)
{
  sum->total += increment->total;
}


/* ///////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////

Routine to compute the intermolecular energy score between
a ligand atom and the receptor.

2/97 te

/////////////////////////////////////////////////////////////// */

void calc_inter_energy
(
  SCORE_GRID	*grid,
  SCORE_ENERGY	*energy,
  LABEL		*label,
  MOLECULE	*molecule,
  int		atom,
  SCORE_PART	*inter
)
{
  if (!energy->vdw_init_flag)
    initialize_vdw_energy (energy, &label->vdw);

  if (label->vdw.member[molecule->atom[atom].vdw_id].well_depth != 0.0)
  {
    if (grid->flag)
      calc_inter_energy_grid (grid, energy, label, molecule, atom, inter);

    else
      calc_inter_score_cont
      (
        grid,
        (void *) energy,
        energy->distance,
        (void (*)()) calc_inter_energy_cont,
        label,
        molecule,
        atom,
        inter
      );
  }
}


/* ///////////////////////////////////////////////////////////////

Routine to initialize vdw parameters.

2/97 te

/////////////////////////////////////////////////////////////// */

void initialize_vdw_energy
(
  SCORE_ENERGY	*energy,
  LABEL_VDW	*label_vdw
)
{
  int i;

  if (!label_vdw->init_flag)
    get_vdw_labels (label_vdw);

  ecalloc
  (
    (void **) &energy->vdwA,
    label_vdw->total,
    sizeof (float),
    "energy vdwA terms",
    global.outfile
  );

  ecalloc
  (
    (void **) &energy->vdwB,
    label_vdw->total,
    sizeof (float),
    "energy vdwB terms",
    global.outfile
  );

  for (i = 0; i < label_vdw->total; i++)
  {
    energy->vdwA[i] = sqrt (label_vdw->member[i].well_depth *
      (float) energy->attractive_exponent /
      (float) (energy->repulsive_exponent - energy->attractive_exponent) *
      pow (2 * label_vdw->member[i].radius, energy->repulsive_exponent));

    energy->vdwB[i] = sqrt (label_vdw->member[i].well_depth *
      (float) energy->repulsive_exponent /
      (float) (energy->repulsive_exponent - energy->attractive_exponent) *
      pow (2 * label_vdw->member[i].radius, energy->attractive_exponent));
  }

  energy->dielectric_factor = 332.0 / energy->dielectric_factor;
  energy->vdw_init_flag = TRUE;
}


/* /////////////////////////////////////////////////////////////// */

void free_vdw_energy (SCORE_ENERGY *energy)
{
  efree ((void **) &energy->vdwA);
  efree ((void **) &energy->vdwB);
}


/* ///////////////////////////////////////////////////////////////

Routine to compute the intermolecular energy score using a 
precomputed grid.

2/97 te

/////////////////////////////////////////////////////////////// */

void calc_inter_energy_grid
(
  SCORE_GRID	*grid,
  SCORE_ENERGY	*energy,
  LABEL		*label,
  MOLECULE	*molecule,
  int		atom,
  SCORE_PART	*inter
)
{
  int index[8];
  int out_flag;
  XYZ cube_coord;

  void get_index_ (XYZ, XYZ, float *, int *, int *, int *, float *);
  float get_value_ (float *, XYZ, int *);

  if (label->vdw.member[molecule->atom[atom].vdw_id].well_depth != 0.0)
  {
    get_index_
    (
      molecule->coord[atom],
      grid->origin,
      &grid->spacing,
      grid->span,
      &out_flag,
      index,
      cube_coord
    );

    if (out_flag == 0)
    {
      inter->vdw +=
        (
          energy->vdwA[molecule->atom[atom].vdw_id] *
            get_value_(energy->avdw, cube_coord, index) -
          energy->vdwB[molecule->atom[atom].vdw_id] *
            get_value_(energy->bvdw, cube_coord, index)
        ) * energy->scale_vdw;

      inter->electro +=
        molecule->atom[atom].charge *
        get_value_(energy->es, cube_coord, index) *
        energy->scale_electro;

      inter->total = inter->vdw + inter->electro;
    }
  }
}


/* ///////////////////////////////////////////////////////////////

Routine to compute the intermolecular energy score in a continuous
fashion given a ligand atom and a receptor atom.

2/97 te

/////////////////////////////////////////////////////////////// */

void calc_inter_energy_cont
(
  SCORE_GRID	*grid,
  SCORE_ENERGY	*energy,
  LABEL		*label,
  MOLECULE	*molecule,
  int		atom,
  int		rec_atom,
  SCORE_PART	*inter
)
{
  float vdwA, vdwB, electro;

  if (label->vdw.member[grid->receptor.atom[rec_atom].vdw_id].well_depth != 0.0)
  {
    calc_pairwise_energy
    (
      energy,
      label,
      molecule,
      &grid->receptor,
      atom,
      rec_atom,
      &vdwA,
      &vdwB,
      &electro
    );

    inter->vdw += (vdwA - vdwB) * energy->scale_vdw;
    inter->electro += electro * energy->scale_electro;
    inter->total = inter->vdw + inter->electro;
  }
}


/* ///////////////////////////////////////////////////////////////

Routine to compute the intramolecular energy score
between two ligand atoms.

2/97 te

/////////////////////////////////////////////////////////////// */

void calc_intra_energy
(
  SCORE_ENERGY	*energy,
  LABEL		*label,
  MOLECULE	*molecule,
  int		atomi,
  int		atomj,
  SCORE_PART	*intra
)
{
  float vdwA, vdwB, electro;

  calc_pairwise_energy
  (
    energy,
    label,
    molecule,
    molecule,
    atomi,
    atomj,
    &vdwA,
    &vdwB,
    &electro
  );

  intra->vdw += (vdwA - vdwB) * energy->scale_vdw;
  intra->electro += electro * energy->scale_electro;
  intra->total = intra->vdw + intra->electro;

/*
  fprintf (global.outfile, "%s %s %f\n",
    molecule->atom[atomi].name,
    molecule->atom[atomj].name,
    vdwA - vdwB + electro);
*/
}


/* ///////////////////////////////////////////////////////////////

Routine to compute the energy score between any two atoms.

2/97 te

/////////////////////////////////////////////////////////////// */

void calc_pairwise_energy
(
  SCORE_ENERGY	*energy,
  LABEL		*label,
  MOLECULE	*origin,
  MOLECULE	*target,
  int		origin_atom,
  int		target_atom,
  float		*vdwA,
  float		*vdwB,
  float		*electro
)
{
  int power_exponent;
  float power_distance;
  float distance;
  int square_flag = TRUE;

  if (!energy->vdw_init_flag)
    initialize_vdw_energy (energy, &label->vdw);

  if
  (
    (label->vdw.member[origin->atom[origin_atom].vdw_id].well_depth != 0.0) &&
    (label->vdw.member[target->atom[target_atom].vdw_id].well_depth != 0.0) &&
    ((distance = square_distance
      (origin->coord[origin_atom], target->coord[target_atom]))
      <= SQR (energy->distance))
  )
  {
    distance = 1.0 / MAX (distance, DISTANCE_MIN);

    if (energy->repulsive_exponent % 2)
    {
      power_exponent = energy->repulsive_exponent;
      distance = sqrt (distance);
      square_flag = FALSE;
    }

    else
      power_exponent = energy->repulsive_exponent / 2;

    POWER (distance, power_exponent, power_distance);

    *vdwA =
      energy->vdwA[origin->atom[origin_atom].vdw_id] *
      energy->vdwA[target->atom[target_atom].vdw_id] *
      power_distance;

    if (square_flag == TRUE)
    {
      if (energy->repulsive_exponent % 2)
      {
        power_exponent = energy->attractive_exponent;
        distance = sqrt (distance);
        square_flag = FALSE;
      }

      else
        power_exponent = energy->attractive_exponent / 2;
    }

    else
      power_exponent = energy->attractive_exponent;

    POWER (distance, power_exponent, power_distance);

    *vdwB =
      energy->vdwB[origin->atom[origin_atom].vdw_id] *
      energy->vdwB[target->atom[target_atom].vdw_id] *
      power_distance;

    *electro =
      energy->dielectric_factor *
      origin->atom[origin_atom].charge *
      target->atom[target_atom].charge *
      (energy->distance_dielectric == TRUE
          ? (square_flag == TRUE ? distance : SQR (distance))
          : (square_flag == TRUE ? sqrt (distance) : distance));
  }

  else
    *vdwA = *vdwB = *electro = 0;
}


/* ///////////////////////////////////////////////////////////////

Routine to add energy score components.

2/97 te

/////////////////////////////////////////////////////////////// */

void sum_energy
(
  SCORE_PART	*sum,
  SCORE_PART	*increment
)
{
  sum->vdw += increment->vdw;
  sum->electro += increment->electro;
  sum->total = sum->vdw + sum->electro;
}


/* ///////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////

Routine to compute the intermolecular chemical score between
a ligand atom and the receptor.

2/97 te