/**
 *  \file PDBParser.h
 *  \brief A class with static functions for parsing PDB files
 *
 *  Copyright 2007-2013 IMP Inventors. All rights reserved.
 *
 */

#include <IMP/atom/internal/pdb.h>

IMPATOM_BEGIN_INTERNAL_NAMESPACE

bool is_ATOM_rec(const String& pdb_line)
{
  return (pdb_line[0] == 'A' && pdb_line[1] == 'T' &&
          pdb_line[2] == 'O' && pdb_line[3] == 'M');
}

bool is_HETATM_rec(const String& pdb_line)
{
  return (pdb_line[0] == 'H' && pdb_line[1] == 'E' && pdb_line[2] == 'T' &&
          pdb_line[3] == 'A' && pdb_line[4] == 'T' && pdb_line[5] == 'M');
}

bool is_MODEL_rec(const String& pdb_line)
{
  return (pdb_line[0] == 'M' && pdb_line[1] == 'O' && pdb_line[2] == 'D' &&
          pdb_line[3] == 'E' && pdb_line[4] == 'L');
}

bool is_ENDMDL_rec(const String& pdb_line)
{
  return (pdb_line[0] == 'E' && pdb_line[1] == 'N' && pdb_line[2] == 'D' &&
          pdb_line[3] == 'M' && pdb_line[4] == 'D' && pdb_line[5] == 'L');
}

bool is_CONECT_rec(const String& pdb_line)
{
  return (pdb_line[0] == 'C' && pdb_line[1] == 'O' && pdb_line[2] == 'N' &&
          pdb_line[3] == 'E' && pdb_line[4] == 'C' && pdb_line[5] == 'T');
}

int model_index(const String& pdb_line)
{
  return atoi(pdb_line.substr(model_index_field_).c_str());
}

int atom_number(const String& pdb_line)
{
  return atoi(pdb_line.substr(atom_number_field_).c_str());
}

String atom_type(const String& pdb_line)
{
  String atom_type_string = pdb_line.substr(atom_type_field_, 4);
  return atom_type_string;
}

char atom_alt_loc_indicator(const String& pdb_line)
{
  return pdb_line[atom_alt_loc_field_];
}

String atom_residue_name(const String& pdb_line)
{
  String res_name = pdb_line.substr(atom_res_name_field_, 3);
  return res_name;
}

char atom_chain_id(const String& pdb_line)
{
  return pdb_line[atom_chain_id_field_];
}

short atom_residue_number(const String& pdb_line)
{
  return atoi(pdb_line.substr(atom_res_number_field_, 4).c_str());
}

char atom_residue_icode(const String& pdb_line)
{
  return pdb_line[atom_res_insertion_field_];
}

float atom_xcoord(const String& pdb_line)
{
  return atof(pdb_line.substr(atom_xcoord_field_, 8).c_str());
}

float atom_ycoord(const String& pdb_line)
{
  return atof(pdb_line.substr(atom_ycoord_field_, 8).c_str());
}

float atom_zcoord(const String& pdb_line)
{
  return atof(pdb_line.substr(atom_zcoord_field_, 8).c_str());
}

float atom_occupancy(const String& pdb_line)
{
  if(pdb_line.length() >= atom_occupancy_field_ + 6)
    return atof(pdb_line.substr(atom_occupancy_field_, 6).c_str());
  return 0.0;
}

float atom_temp_factor(const String& pdb_line)
{
  if(pdb_line.length() >= atom_temp_factor_field_ + 6)
    return atof(pdb_line.substr(atom_temp_factor_field_, 6).c_str());
  return 0.0;
}

String atom_element(const String& pdb_line)
{
  String element_name;
  if(pdb_line.length() >= atom_element_field_ + 2)
    element_name = pdb_line.substr(atom_element_field_, 2);
  return element_name;
}

base::Vector<unsigned short> connected_atoms(const String& pdb_line)
{
  base::Vector<unsigned short> conn_atoms;
  if (is_CONECT_rec(pdb_line)) {
    // (1-6) - "CONECT"
    // (7-11), (12-16), ...,(57-61) - serial numbers of connected atoms
    const unsigned short atom_index_len = 5;
    unsigned short atom_index_start = 6;
    unsigned short line_len = pdb_line.length();
    if (line_len > 61)
      line_len = 61;

    while ((atom_index_start + atom_index_len) <= line_len) {
      String atom_index_str =
          pdb_line.substr(atom_index_start, atom_index_len);
      short sh_atom_index = atoi(atom_index_str.c_str());
      if (sh_atom_index > 0)
        conn_atoms.push_back(sh_atom_index);
      atom_index_start += atom_index_len;
    }
  }
  return conn_atoms;
}

IMPATOM_END_INTERNAL_NAMESPACE