main()
{
int i = 0, j = 0, k = 0, l = 0, n = 0, c = 0, h = 0,
a = 0, b = 0, d = 0, e = 0, f = 0, p = 0, q = 0,
r = 0, s = 0, t = 0, // Counters
flag = 0, // Flag for corresponding atom types
write_warn = 0,
count_amid = 0,
count_gua = 0,
point_cam [1000],
point_nam [1000],
point_oam [1000],
point_cgua [1000],
point_ngua [1000][3],
point_nplan [1000],
point_n2 [1000], // Keep number of N atoms with type N.2
line_length = 1000, // Length of the line
atoms_number, // Number of atoms
bonds_number; // Number of bonds
char buffer [line_length], // Buffer with line_length number of chars - max width of one row
// Define string sufficiently large to store a line of input
*rule_0 [max_numb_atoms], // For the first rules
*rule_1 [max_numb_atoms], // For the second rules
*rule_2 [max_numb_atoms], // For the third rules
*rule_3 [max_numb_atoms], // For the first rules
*rule_4 [max_numb_atoms], // For the second rules
*rule_5 [max_numb_atoms], // For the second rules
*rule_6 [max_numb_atoms], // For N.pl3 type
*rule_7 [max_numb_atoms]; // For N.2 type
ATOM atom;
BOND bond;
// Initialization of pointers for atoms names and types and for bonds types
for (i = 0; i < max_numb_atoms; i++)
{
atom.name [i] = (char *) malloc (max_name_len);
atom.type [i] = (char *) malloc (max_name_len);
rule_0 [i] = (char *) malloc (line_length);
rule_1 [i] = (char *) malloc (line_length);
rule_2 [i] = (char *) malloc (line_length);
rule_3 [i] = (char *) malloc (line_length);
rule_4 [i] = (char *) malloc (line_length);
rule_5 [i] = (char *) malloc (line_length);
rule_6 [i] = (char *) malloc (line_length);
rule_7 [i] = (char *) malloc (line_length);
}
for (j = 0; j < max_numb_bonds; j++)
{
bond.type [j] = (char *) malloc (max_name_len);
}
FILE *mol2, *mol, *pdb, *warn, *fopen();
// Open working files for reading and writting
mol2 = fopen ("input.mol2", "r");
mol = fopen ("mol", "w" );
pdb = fopen ("input_ligand.pdb", "w" );
warn = fopen ("warning", "w" );
// Reading from *.mol2 file
fgets (buffer, line_length, mol2);
while (strncmp (buffer, "@<TRIPOS>MOLECULE", 17) != 0 ) fgets (buffer, line_length, mol2);
// Reading the name of the molecule
fgets (buffer, line_length, mol2);
fprintf (warn, "%s", buffer);
// Reading atoms and bonds numbers
fgets (buffer, line_length, mol2);
sscanf (buffer, "%i %i", &atoms_number, &bonds_number);
// Reading data for atoms
fgets (buffer, line_length, mol2);
while (strncmp (buffer, "@<TRIPOS>ATOM", 13) != 0 ) fgets (buffer, line_length, mol2);
fprintf (mol, "%i\n", atoms_number);
for (i = 0; i < atoms_number; i++)
{
fgets (buffer, line_length, mol2);
sscanf (buffer, "%i %s %f %f %f %s %s %s %f", &atom.number [i], atom.name [i],
&atom.coordx [i], &atom.coordy [i], &atom.coordz [i],
atom.type [i], atom.type2, atom.type3, &atom.charge [i]);
// Corresponding atoms types
// Check for unknown atom type
if (strcmp (atom.type [i], "H") != 0 && strcmp (atom.type [i], "C.3") != 0 &&
strcmp (atom.type [i], "C.2") != 0 && strcmp (atom.type [i], "C.1") != 0 &&
strcmp (atom.type [i], "C.ar") != 0 && strcmp (atom.type [i], "C.cat") != 0 &&
strcmp (atom.type [i], "N.4") != 0 && strcmp (atom.type [i], "N.3") != 0 &&
strcmp (atom.type [i], "N.am") != 0 && strcmp (atom.type [i], "N.2") != 0 &&
strcmp (atom.type [i], "N.pl3") != 0 && strcmp (atom.type [i], "N.ar") != 0 &&
strcmp (atom.type [i], "N.1") != 0 && strcmp (atom.type [i], "O.3") != 0 &&
strcmp (atom.type [i], "O.2") != 0 && strcmp (atom.type [i], "O.co2") != 0 &&
strcmp (atom.type [i], "O.am") != 0 && strcmp (atom.type [i], "P.3") != 0 &&
strcmp (atom.type [i], "S.3") != 0 && strcmp (atom.type [i], "S.2") != 0 &&
strcmp (atom.type [i], "S.o2") != 0 && strcmp (atom.type [i], "S.o") != 0 &&
strcmp (atom.type [i], "F") != 0 && strcmp (atom.type [i], "Br") != 0 &&
strcmp (atom.type [i], "Cl") != 0 && strcmp (atom.type [i], "I") != 0 &&
strcmp (atom.type [i], "K") != 0 && strcmp (atom.type [i], "Na") != 0 &&
strcmp (atom.type [i], "Mg") != 0 && strcmp (atom.type [i], "Ca") != 0 &&
strcmp (atom.type [i], "Zn") != 0 && strcmp (atom.type [i], "Fe") != 0)
{
fprintf (warn, "%s %s\n", "Warning: Unknown atom type", atom.type [i]);
write_warn = 1;
strcpy (atom.type [i], "dummy");
}
if (strcmp (atom.type [i], "H") == 0) strcpy (atom.type [i], "h");
if (strcmp (atom.type [i], "C.3") == 0) strcpy (atom.type [i], "c3");
if (strcmp (atom.type [i], "C.2") == 0) strcpy (atom.type [i], "c2");
if (strcmp (atom.type [i], "C.1") == 0) strcpy (atom.type [i], "c1");
if (strcmp (atom.type [i], "C.ar") == 0) strcpy (atom.type [i], "ca");
if (strcmp (atom.type [i], "C.cat") == 0) strcpy (atom.type [i], "c2");
if (strcmp (atom.type [i], "N.4") == 0) strcpy (atom.type [i], "n3");
if (strcmp (atom.type [i], "N.3") == 0) strcpy (atom.type [i], "n3");
if (strcmp (atom.type [i], "N.am") == 0) strcpy (atom.type [i], "nm");
if (strcmp (atom.type [i], "N.2") == 0) {strcpy (atom.type [i], "n2");
point_n2 [f] = atom.number [i]; f++;}
if (strcmp (atom.type [i], "N.pl3") == 0) {strcpy (atom.type [i], "np");
point_nplan [e] = atom.number [i]; e++;}
if (strcmp (atom.type [i], "N.ar") == 0) strcpy (atom.type [i], "nr");
if (strcmp (atom.type [i], "N.1") == 0) strcpy (atom.type [i], "n1");
if (strcmp (atom.type [i], "O.3") == 0) strcpy (atom.type [i], "o3");
if (strcmp (atom.type [i], "O.2") == 0) strcpy (atom.type [i], "o2");
if (strcmp (atom.type [i], "O.co2") == 0) strcpy (atom.type [i], "o2");
if (strcmp (atom.type [i], "O.am") == 0) strcpy (atom.type [i], "o2am");
if (strcmp (atom.type [i], "P.3") == 0) strcpy (atom.type [i], "p33");
if (strcmp (atom.type [i], "S.3") == 0) strcpy (atom.type [i], "s32");
if (strcmp (atom.type [i], "S.2") == 0) strcpy (atom.type [i], "s2");
if (strcmp (atom.type [i], "S.o2") == 0) strcpy (atom.type [i], "s34");
if (strcmp (atom.type [i], "S.o") == 0) strcpy (atom.type [i], "s34");
if (strcmp (atom.type [i], "F") == 0) strcpy (atom.type [i], "f");
if (strcmp (atom.type [i], "Br") == 0) strcpy (atom.type [i], "br");
if (strcmp (atom.type [i], "Cl") == 0) strcpy (atom.type [i], "cl");
if (strcmp (atom.type [i], "I") == 0) strcpy (atom.type [i], "i");
if (strcmp (atom.type [i], "K") == 0) strcpy (atom.type [i], "k");
if (strcmp (atom.type [i], "Na") == 0) strcpy (atom.type [i], "na");
if (strcmp (atom.type [i], "Mg") == 0) strcpy (atom.type [i], "mg");
if (strcmp (atom.type [i], "Ca") == 0) strcpy (atom.type [i], "calcium");
if (strcmp (atom.type [i], "Zn") == 0) strcpy (atom.type [i], "zn");
if (strcmp (atom.type [i], "Fe") == 0) strcpy (atom.type [i], "fe2");
// Writing information about atoms in *.pdb file
fprintf (pdb, "%s%7i%5s%4s%6s%12.3f%8.3f%8.3f%6s%6s\n", "ATOM", i+1,
atom.name [i], "mol", "0", atom.coordx [i], atom.coordy [i], atom.coordz [i], "1.00", "10.00");
lower (atom.name [i], 10); // Will be used in bonds
lower (atom.type [i], 10);
rmchr (atom.type [i], '.'); // Remove point from string type1
// Writing information about atoms in *.pdb file
fprintf (mol, "%s %s%s %s %s %s %5.3f\n", "name", "mol.", atom.name [i],
"type", atom.type [i], "charge", atom.charge [i]);
}
fprintf (pdb, "%s", "END");
// Reading data for bonds
fgets (buffer, line_length, mol2); // One row should be jumped - it contains @<TRIPOS>BOND
fprintf (mol, "%i\n", bonds_number);
for (j = 0; j < bonds_number; j++)
{
fgets (buffer, line_length, mol2);
sscanf (buffer, "%i %i %i %s", &l, &bond.origin [j], &bond.target[j], bond.type [j]);
// Equvalent numbers to bonds types
if (strcmp (bond.type [j], "ar") == 0) strcpy (bond.type [j], "1.5"); // Aromatic bond is equal to 1.5
if (strcmp (bond.type [j], "am") == 0)
{
strcpy (bond.type [j], "1.25");
if (strchr (atom.name [bond.origin [j] - 1], 'n' ) && strchr (atom.name [bond.target [j] - 1], 'c' ))
{
point_nam [count_amid] = bond.origin [j];
point_cam [count_amid] = bond.target [j];
count_amid ++;
}
if (strchr (atom.name [bond.target [j] - 1], 'n' ) && strchr (atom.name [bond.origin [j] - 1], 'c' ))
{
point_nam [count_amid] = bond.target [j];
point_cam [count_amid] = bond.origin [j];
count_amid ++;
}
else continue;
}
}
for (j = 0; j < bonds_number; j++)
{
for (l = 0; l < count_amid; l++)
// Check for C and O atoms
if (bond.origin [j] == point_cam [l] & strcmp (atom.type [bond.target [j] - 1], "o2") == 0)
{
strcpy (bond.type [j], "1.75");
point_oam [l] = bond.target [j];
}
else if (bond.target [j] == point_cam [l] & strcmp (atom.type [bond.origin [j] - 1], "o2") == 0)
{
strcpy (bond.type [j], "1.75");
point_oam [l] = bond.origin [j];
}
}
// Accumulation of all information in the ATOM structure
for (i = 0; i < atoms_number; i++)
{
for (j = 0; i < 10; i++)
atom.bonds [i][j] = 0; // Initialization of the array with 0
atom.bondtypes [i][j] = 0; // Initialization of the array with 0
}
for (i = 0; i < atoms_number; i++)
{
n = 0; // Initialization of bonds counter
atom.number [i] = i + 1; // Counter for numbers of atoms
for (j = 0; j < bonds_number; j++)
{
if (bond.origin [j] == atom.number [i])
{
atom.bonds [i][n] = bond.target [j]; // Array for atoms connected with the current atom
atom.bondtypes [i][n] = atof (bond.type [j]); // Types of bonds connected with the current atom
n++;
}
if (bond.target [j] == atom.number [i])
{
atom.bonds [i][n] = bond.origin [j]; // Array for atoms connected with the current atom
atom.bondtypes [i][n] = atof (bond.type [j]); // Types of bonds connected with the current atom
n++;
}
}
atom.countbonds [i] = n; // Counter for numbers of bonds
}
// Creation of first hybrid-type rule
for (l = 0; l < count_amid; l++)
{
for (n = 0; n < 3; n++)
if (strcmp (atom.type [atom.bonds [point_nam [l] - 1][n] - 1], "h") != 0 ) continue;
else
{
if (point_cam [l] == 0 || atom.bonds [point_cam [l] - 1][0] == 0 || atom.bonds [point_cam [l] - 1][1] == 0
|| atom.bonds [point_cam [l] - 1][2] == 0) continue;
else
{
strcat (rule_0 [l], "mol.");
strcat (rule_0 [l], atom.name [point_cam [l] - 1]);
strcat (rule_0 [l], " mol.");
strcat (rule_0 [l], atom.name [atom.bonds [point_cam [l]-1][0] - 1]);
strcat (rule_0 [l], " mol.");
strcat (rule_0 [l], atom.name [atom.bonds [point_cam [l]-1][1] - 1]);
strcat (rule_0 [l], " mol.");
strcat (rule_0 [l], atom.name [atom.bonds [point_cam [l]-1][2] - 1]);
strcat (rule_0 [l], " 150 0\n");
t ++;
}
if (point_cam [l] == 0 || point_oam [l] == 0 || point_nam [l] == 0 || atom.bonds [point_nam [l] - 1][n] == 0) continue;
else
{
strcat (rule_1 [l], "mol.");
strcat (rule_1 [l], atom.name [point_cam [l] - 1]);
strcat (rule_1 [l], " mol.");
strcat (rule_1 [l], atom.name [point_oam [l] - 1]);
strcat (rule_1 [l], " mol.");
strcat (rule_1 [l], atom.name [point_nam [l] - 1]);
strcat (rule_1 [l], " mol.");
strcat (rule_1 [l], atom.name [atom.bonds [point_nam [l] - 1][n] - 1]);
strcat (rule_1 [l], " 150 0\n");
r ++;
break;
}
}
}
// Creation of second hybrid-type rule
for (l = 0; l < count_amid; l++)
if (point_nam [l] == 0 || atom.bonds [point_nam [l] - 1][0] == 0 || atom.bonds [point_nam [l] - 1][1] == 0
|| atom.bonds [point_nam [l] - 1][2] == 0) continue;
else
{
strcat (rule_2 [l], "mol.");
strcat (rule_2 [l], atom.name [point_nam [l] - 1]);
strcat (rule_2 [l], " mol.");
strcat (rule_2 [l], atom.name [atom.bonds [point_nam [l]-1][0] - 1]);
strcat (rule_2 [l], " mol.");
strcat (rule_2 [l], atom.name [atom.bonds [point_nam [l]-1][1] - 1]);
strcat (rule_2 [l], " mol.");
strcat (rule_2 [l], atom.name [atom.bonds [point_nam [l]-1][2] - 1]);
strcat (rule_2 [l], " 150 0\n");
s ++;
}
// atoms in guanid-type bond
for (i = 0; i < atoms_number; i++)
{
if (strcmp (atom.type [i], "c2") == 0 &
atom.countbonds [i] == 3 &
strcmp (atom.type [atom.bonds [i][0] - 1], "np") == 0 &
strcmp (atom.type [atom.bonds [i][1] - 1], "np") == 0 &
strcmp (atom.type [atom.bonds [i][2] - 1], "np") == 0 )
{
point_ngua [count_gua][0] = atom.bonds [i][0];
point_ngua [count_gua][1] = atom.bonds [i][1];
point_ngua [count_gua][2] = atom.bonds [i][2];
point_cgua [count_gua] = atom.number [i];
count_gua++;
}
}
// Formation of the third, fourth and fifth rules
for (l = 0; l < count_gua; l++)
{
a = 0; b = 0; d = 0; // Initialization of counters
if (point_ngua [l][0] == 0 || point_cgua [l] == 0 || point_ngua [l][1] == 0 ||
atom.bonds [point_ngua [l][1] - 1][0] == 0 ||
atom.bonds [point_ngua [l][1] - 1][1] == 0 ||
atom.bonds [point_ngua [l][1] - 1][2] == 0) continue;
if (a == 0)
{
strcat (rule_3 [l], "mol.");
strcat (rule_3 [l], atom.name [point_ngua [l][0] - 1]);
strcat (rule_3 [l], " mol.");
strcat (rule_3 [l], atom.name [point_cgua [l] - 1]);
strcat (rule_3 [l], " mol.");
strcat (rule_3 [l], atom.name [point_ngua [l][1] - 1]);
strcat (rule_3 [l], " mol.");
for (n = 0; n < 3; n++)
{
if (atom.bonds [point_ngua [l][1] - 1][n] != point_cgua [l] && atom.bonds [point_ngua [l][1] - 1][n] != 0)
{
strcat (rule_3 [l], atom.name [atom.bonds [point_ngua [l][1] - 1][n] - 1]);
break;
}
else continue;
}
strcat (rule_3 [l], " 150 0\n");
a ++;
}
if (point_ngua [l][0] == 0 || point_cgua [l] == 0 || point_ngua [l][2] == 0 ||
atom.bonds [point_ngua [l][2] - 1][0] == 0 ||
atom.bonds [point_ngua [l][2] - 1][1] == 0 ||
atom.bonds [point_ngua [l][2] - 1][2] == 0) continue;
if (b == 0)
{
strcat (rule_4 [l], "mol.");
strcat (rule_4 [l], atom.name [point_ngua [l][0] - 1]);
strcat (rule_4 [l], " mol.");
strcat (rule_4 [l], atom.name [point_cgua [l] - 1]);
strcat (rule_4 [l], " mol.");
strcat (rule_4 [l], atom.name [point_ngua [l][2] - 1]);
strcat (rule_4 [l], " mol.");
for (n = 0; n < 3; n++)
{
if (atom.bonds [point_ngua [l][2] - 1][n] != point_cgua [l] && atom.bonds [point_ngua [l][2] - 1][n] != 0)
{
strcat (rule_4 [l], atom.name [atom.bonds [point_ngua [l][2] - 1][n] - 1]);
break;
}
else continue;
}
strcat (rule_4 [l], " 150 0\n");
b ++;
}
if (point_ngua [l][2] == 0 || point_cgua [l] == 0 || point_ngua [l][0] == 0 ||
atom.bonds [point_ngua [l][0] - 1][0] == 0 ||
atom.bonds [point_ngua [l][0] - 1][1] == 0 ||
atom.bonds [point_ngua [l][0] - 1][2] == 0) continue;
if (d == 0)
{
strcat (rule_5 [l], "mol.");
strcat (rule_5 [l], atom.name [point_ngua [l][2] - 1]);
strcat (rule_5 [l], " mol.");
strcat (rule_5 [l], atom.name [point_cgua [l] - 1]);
strcat (rule_5 [l], " mol.");
strcat (rule_5 [l], atom.name [point_ngua [l][0] - 1]);
strcat (rule_5 [l], " mol.");
for (n = 0; n < 3; n++)
{
if (atom.bonds [point_ngua [l][0] - 1][n] != point_cgua [l] && atom.bonds [point_ngua [l][0] - 1][n] != 0)
{
strcat (rule_5 [l], atom.name [atom.bonds [point_ngua [l][0] - 1][n] - 1]);
break;
}
else continue;
}
strcat (rule_5 [l], " 150 0\n");
d ++;
}
}
// Formation of the sixth rule
for (j = 0; j < e; j++)
{
if (i = point_nplan [j])
{
if (atom.bondtypes[point_nplan [j] - 1][0] == 2 || atom.bondtypes[point_nplan [j] - 1][1] == 2) continue;
if (atom.bondtypes[point_nplan [j] - 1][0] == 0 || atom.bondtypes[point_nplan [j] - 1][1] == 0 ||
atom.bondtypes[point_nplan [j] - 1][2] == 0)
{
fprintf (warn, "%s\n", "Warning: N.pl3 atom with 2 single bonds");
write_warn = 1;
continue;
}
else
{
if (point_nplan [j] == 0 || atom.bonds [point_nplan [j] - 1] [0] == 0
|| atom.bonds [point_nplan [j] - 1] [1] == 0 || atom.bonds [point_nplan [j] - 1] [2] == 0) continue;
else
{
q ++;
strcat (rule_6 [q], "mol.");
strcat (rule_6 [q], atom.name [point_nplan [j] - 1]);
strcat (rule_6 [q], " mol.");
strcat (rule_6 [q], atom.name [atom.bonds [point_nplan [j] - 1] [0] - 1]);
strcat (rule_6 [q], " mol.");
strcat (rule_6 [q], atom.name [atom.bonds [point_nplan [j] - 1] [1] - 1]);
strcat (rule_6 [q], " mol.");
strcat (rule_6 [q], atom.name [atom.bonds [point_nplan [j] - 1] [2] - 1]);
strcat (rule_6 [q], " 150 0\n");
}
}
}
}
// Formation of the seventh rule
for (j = 0; j < f; j++)
{
if (i = point_n2 [j])
{
if (atom.bondtypes[point_n2 [j] - 1][0] == 2 || atom.bondtypes[point_n2 [j] - 1][1] == 2) continue;
else
{
if (point_n2 [j] == 0 || atom.bonds [point_n2 [j] - 1] [0] == 0
|| atom.bonds [point_n2 [j] - 1] [1] == 0 || atom.bonds [point_n2 [j] - 1] [2] == 0) continue;
else
{
p ++;
strcat (rule_7 [p], "mol.");
strcat (rule_7 [p], atom.name [point_n2 [j] - 1]);
strcat (rule_7 [p], " mol.");
strcat (rule_7 [p], atom.name [atom.bonds [point_n2 [j] - 1] [0] - 1]);
strcat (rule_7 [p], " mol.");
strcat (rule_7 [p], atom.name [atom.bonds [point_n2 [j] - 1] [1] - 1]);
strcat (rule_7 [p], " mol.");
strcat (rule_7 [p], atom.name [atom.bonds [point_n2 [j] - 1] [2] - 1]);
strcat (rule_7 [p], " 150 0\n");
}
}
}
}
// Writing information about bonds in mol file
for (j = 0; j < bonds_number; j++)
fprintf (mol, "%s%s %s%s %s\n", "mol.", atom.name [bond.origin [j] - 1],
"mol.", atom.name [bond.target [j] - 1], bond.type [j]);
// End of mol file
if (count_gua == 0 && r == 0 && s == 0 && q == 0 && p == 0)
fprintf (mol, "%s\n%s\n%s\n", "0", "0", "0"); // mol file have to end with three zeros
else
{
fprintf (mol, "%s\n", "0");
fprintf (mol, "%i %s\n", (t + r + s + 3*count_gua + q + p), "hybrid");
for (l = 0; l < count_amid; l++)
{
if (strcmp (rule_0 [l], "") == 0) continue;
else fprintf (mol, "%s", rule_0 [l]);
}
for (l = 0; l < count_amid; l++)
{
if (strcmp (rule_1 [l], "") == 0) continue;
else fprintf (mol, "%s", rule_1 [l]);
}
for (l = 0; l < s; l++)
{
if (strcmp (rule_2 [l], "") == 0) continue;
else fprintf (mol, "%s", rule_2 [l]);
}
for (l = 0; l < count_gua; l++)
{
fprintf (mol, "%s", rule_3 [l]);
fprintf (mol, "%s", rule_4 [l]);
fprintf (mol, "%s", rule_5 [l]);
}
for (l = 1; l < q + 1; l++)
{
if (strcmp (rule_6 [l], "") == 0) continue;
else fprintf (mol, "%s", rule_6 [l]);
}
for (l = 1; l < p + 1; l++)
{
if (strcmp (rule_7 [l], "") == 0) continue;
else fprintf (mol, "%s", rule_7 [l]);
}
fprintf (mol, "%s\n", "0");
}
// Clean of warning file if there is no warnings
if (write_warn == 0)
{
remove ("warning"); // Remove file with written molecule name
warn = fopen ("warning", "w" ); // Create a new empty file
}
// Before termination, free up space and close files
// Free located for atom_name and type1 memory
for (i = 0; i < max_numb_atoms; ++i)
{
free (atom.name [i]);
free (atom.type [i]);
free (rule_0 [i]);
free (rule_1 [i]);
free (rule_2 [i]);
free (rule_3 [i]);
free (rule_4 [i]);
free (rule_5 [i]);
free (rule_6 [i]);
free (rule_7 [i]);
}
for (j = 0; j < max_numb_bonds; ++j)
{
free (bond.type [j]);
}
// Close working files
fclose (mol2); // Close *.mol2 file
fclose (mol); // Close template file
fclose (pdb); // Close *.pdb file
fclose (warn); // Close warning file
}
std::vector<bed> getpeaksChr(const std::string &chrname) const {
if (peak_argv != "") return peaks.at(rmchr(chrname));
else return std::vector<bed>();
}
