diff --git a/agl_v3/AGL for v.3.c b/agl_v3/AGL for v.3.c
deleted file mode 100755
index 8b3c4a5..0000000
--- a/agl_v3/AGL for v.3.c	
+++ /dev/null
@@ -1,433 +0,0 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <conio.h>
-#include <ctype.h> 
-#include <math.h>
-#include <string.h>
-
-
-double cell[3], a[10000][3], c[250][30][3];
-int num_atom_agl, atom_agl[250], mol[10000], atoms, num_atom[250];
-char type_at[10000][4], type[250][30][4];
-
-
-
-char conv(int fnumb, int dig_pos)
-{
-	int s, d, e;
-	char digit[10];
-
-
-	digit[0] = '0';
-	digit[1] = '1';
-	digit[2] = '2';
-	digit[3] = '3';
-	digit[4] = '4';
-	digit[5] = '5';
-	digit[6] = '6';
-	digit[7] = '7';
-	digit[8] = '8';
-	digit[9] = '9';
-
-	if (fnumb >= 100) 
-		s = (fnumb - fmod(fnumb, 100)) / 100;
-	else 
-		s = 0;
-	if (fnumb - s*100 >= 10) 
-		d = (fnumb - s*100 - fmod(fnumb - s*100, 10))/10;
-	else 
-		d = 0;
-	e = fnumb - s*100 - d*10;
-
-	if (dig_pos == 1) return digit[e];
-	if (dig_pos == 2) return digit[d];
-	if (dig_pos == 3) return digit[s];
-	else return digit[0];
-}
-
-
-
-void search()
-{
-	int i, j;
-
-
-	for (i=0; i<250; i++)
-		num_atom[i] = 0;
-
-	for (i=0; i<atoms; i++)
-		for (j=0; j<num_atom_agl; j++)
-			if (mol[i] == atom_agl[j])
-			{
-				c[j][num_atom[j]][0] = a[i][0];
-				c[j][num_atom[j]][1] = a[i][1];
-				c[j][num_atom[j]][2] = a[i][2];
-				type[j][num_atom[j]][0] = type_at[i][0];
-				type[j][num_atom[j]][1] = type_at[i][1];
-				type[j][num_atom[j]][2] = type_at[i][2];
-				type[j][num_atom[j]][3] = type_at[i][3];
-				num_atom[j]++;
-			}
-}
-
-
-
-void trans()
-{
-	int i, j, k, imin;
-	double x[3], tr[27][30][3], min, leng;
-
-
-	for (i=1; i<num_atom_agl; i++)
-	{
-		for (j=0; j<3; j++)
-			x[j] = 0;
-
-		for (j=0; j<i; j++)
-			for (k=0; k<3; k++)
-				x[k] += c[j][0][k];
-
-		for (j=0; j<3; j++)
-			x[j] = x[j] / i;
-
-		
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[0][k][0] = c[i][k][0];
-			tr[0][k][1] = c[i][k][1];
-			tr[0][k][2] = c[i][k][2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[1][k][0] = c[i][k][0] + cell[0];
-			tr[1][k][1] = c[i][k][1];
-			tr[1][k][2] = c[i][k][2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[2][k][0] = c[i][k][0];
-			tr[2][k][1] = c[i][k][1] + cell[1];
-			tr[2][k][2] = c[i][k][2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[3][k][0] = c[i][k][0];
-			tr[3][k][1] = c[i][k][1];
-			tr[3][k][2] = c[i][k][2] + cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[4][k][0] = c[i][k][0] - cell[0];
-			tr[4][k][1] = c[i][k][1];
-			tr[4][k][2] = c[i][k][2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[5][k][0] = c[i][k][0];
-			tr[5][k][1] = c[i][k][1] - cell[1];
-			tr[5][k][2] = c[i][k][2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[6][k][0] = c[i][k][0];
-			tr[6][k][1] = c[i][k][1];
-			tr[6][k][2] = c[i][k][2] - cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[7][k][0] = c[i][k][0] + cell[0];
-			tr[7][k][1] = c[i][k][1] + cell[1];
-			tr[7][k][2] = c[i][k][2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[8][k][0] = c[i][k][0] + cell[0];
-			tr[8][k][1] = c[i][k][1];
-			tr[8][k][2] = c[i][k][2] + cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[9][k][0] = c[i][k][0];
-			tr[9][k][1] = c[i][k][1] + cell[1];
-			tr[9][k][2] = c[i][k][2] + cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[10][k][0] = c[i][k][0] - cell[0];
-			tr[10][k][1] = c[i][k][1] - cell[1];
-			tr[10][k][2] = c[i][k][2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[11][k][0] = c[i][k][0] - cell[0];
-			tr[11][k][1] = c[i][k][1];
-			tr[11][k][2] = c[i][k][2] - cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[12][k][0] = c[i][k][0];
-			tr[12][k][1] = c[i][k][1] - cell[1];
-			tr[12][k][2] = c[i][k][2] - cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[13][k][0] = c[i][k][0] + cell[0];
-			tr[13][k][1] = c[i][k][1] - cell[1];
-			tr[13][k][2] = c[i][k][2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[14][k][0] = c[i][k][0] + cell[0];
-			tr[14][k][1] = c[i][k][1];
-			tr[14][k][2] = c[i][k][2] - cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[15][k][0] = c[i][k][0] - cell[0];
-			tr[15][k][1] = c[i][k][1] + cell[1];
-			tr[15][k][2] = c[i][k][2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[16][k][0] = c[i][k][0];
-			tr[16][k][1] = c[i][k][1] + cell[1];
-			tr[16][k][2] = c[i][k][2] - cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[17][k][0] = c[i][k][0] - cell[0];
-			tr[17][k][1] = c[i][k][1];
-			tr[17][k][2] = c[i][k][2] + cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[18][k][0] = c[i][k][0];
-			tr[18][k][1] = c[i][k][1] - cell[1];
-			tr[18][k][2] = c[i][k][2] + cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[19][k][0] = c[i][k][0] + cell[0];
-			tr[19][k][1] = c[i][k][1] + cell[1];
-			tr[19][k][2] = c[i][k][2] + cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[20][k][0] = c[i][k][0] - cell[0];
-			tr[20][k][1] = c[i][k][1] + cell[1];
-			tr[20][k][2] = c[i][k][2] + cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[21][k][0] = c[i][k][0] + cell[0];
-			tr[21][k][1] = c[i][k][1] - cell[1];
-			tr[21][k][2] = c[i][k][2] + cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[22][k][0] = c[i][k][0] + cell[0];
-			tr[22][k][1] = c[i][k][1] + cell[1];
-			tr[22][k][2] = c[i][k][2] - cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[23][k][0] = c[i][k][0] - cell[0];
-			tr[23][k][1] = c[i][k][1] - cell[1];
-			tr[23][k][2] = c[i][k][2] + cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[24][k][0] = c[i][k][0] - cell[0];
-			tr[24][k][1] = c[i][k][1] + cell[1];
-			tr[24][k][2] = c[i][k][2] - cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[25][k][0] = c[i][k][0] + cell[0];
-			tr[25][k][1] = c[i][k][1] - cell[1];
-			tr[25][k][2] = c[i][k][2] - cell[2];
-		}	
-
-		for (k=0; k<num_atom[i]; k++)
-		{
-			tr[26][k][0] = c[i][k][0] - cell[0];
-			tr[26][k][1] = c[i][k][1] - cell[1];
-			tr[26][k][2] = c[i][k][2] - cell[2];
-		}
-
-
-		imin = 0;
-		min = sqrt ((tr[0][0][0] - x[0])*(tr[0][0][0] - x[0]) + (tr[0][0][1] - x[1])*(tr[0][0][1] - x[1]) + (tr[0][0][2] - x[2])*(tr[0][0][2] - x[2]));
-		for (j=1; j<27; j++)
-		{
-			leng = sqrt ((tr[j][0][0] - x[0])*(tr[j][0][0] - x[0]) + (tr[j][0][1] - x[1])*(tr[j][0][1] - x[1]) + (tr[j][0][2] - x[2])*(tr[j][0][2] - x[2]));
-
-			if (leng < min)
-			{
-				min = leng;
-				imin = j;
-			}
-		}
-
-		
-		for (k=0; k<num_atom[i]; k++)
-		{
-			for (j=0; j<3; j++)
-			{
-				c[i][k][j] = tr[imin][k][j];
-			}
-		}
-	}
-}
-
-
-
-void coord_data(FILE *fs)
-{
-	int i, j, atom_num, atom_type;
-	double x, y, z;
-	char q[256];
-	
-
-	fscanf (fs, "%i", &atoms);
-	for (i=0; i<atoms; i++)
-	{
-		fscanf (fs, "%i", &atom_num);
-		for (j=0; j<4; j++) 
-			fscanf (fs, "%c", &type_at[i][j]);
-		fscanf (fs, "%lf", &x);
-		fscanf (fs, "%lf", &y);
-		fscanf (fs, "%lf", &z);
-		fscanf (fs, "%i", &atom_type);
-		fscanf (fs, "%i", &mol[i]);
-
-		fgets (q, 256, fs);
-
-		a[i][0] = x;
-		a[i][1] = y;
-		a[i][2] = z;
-	}
-
-	search();
-}
-
-
-
-void aglom(FILE *fin)
-{
-	int i;
-	char q[256];
-
-
-	fscanf (fin, "%i", &num_atom_agl); 
-	fgets (q, 256, fin);
-	for (i=0; i<num_atom_agl; i++)
-	{
-		fscanf (fin, "%i", &atom_agl[i]); 
-		fgets (q, 256, fin);
-	}
-}
-
-
-
-void output (FILE *fout)
-{
-	int i, k, inp;
-
-
-	inp = 1;
-	for (i=0; i<num_atom_agl; i++)
-		for (k=0; k<num_atom[i]; k++)
-		{
-			fprintf (fout, "ATOM  %5i  %c%c  MOL %5i    %8.3f%8.3f%8.3f\n", inp, type[i][k][2], type[i][k][3], i+1, c[i][k][0], c[i][k][1], c[i][k][2]);
-
-			inp++;
-		}
-}
-
-
-
-void main(void)
-{
-	char name[128], coord_name[128], out_name[128], q[128];
-	int i, k, agl;
-	FILE *f;
-	FILE *inp;
-	FILE *coord;
-	FILE *out;
-
-	
-	f=fopen ("input_agl.dat", "r");
-	for (i=0; i<10; i++)
-		fscanf (f, "%c", &q[i]);
-	fscanf (f, "%s", &name);
-	for (i=0; i<24; i++)
-		fscanf (f, "%c", &q[i]);
-	fscanf (f, "%i", &agl);
-	for (i=0; i<15; i++)
-		fscanf (f, "%c", &q[i]);
-	for (i=0; i<3; i++)
-		fscanf (f, "%lf", &cell[i]);
-	fgets (q, 128, f);
-	for (i=0; i<7; i++)
-		fscanf (f, "%c", &q[i]);
-	fscanf (f, "%s", &out_name);	
-	fclose (f);
-	
-
-	k = strlen (out_name);
-	out_name[k] = out_name[k-4];
-	out_name[k+1] = out_name[k-3];
-	out_name[k+2] = out_name[k-2];
-	out_name[k+3] = out_name[k-1];
-	out_name[k+4] = '\0';
-	inp=fopen (name, "r");
-	for (i=0; i<agl; i++)
-	{
-		fscanf (inp, "%s", &coord_name);
-		aglom (inp);
-
-
-		coord=fopen (coord_name, "r");
-		coord_data (coord);
-		fclose (coord);
-
-
-		trans();
-
-
-		out_name[k-4] = '_';
-		out_name[k-3] = conv (i+1, 3);
-		out_name[k-2] = conv (i+1, 2);
-		out_name[k-1] = conv (i+1, 1);
-		out=fopen (out_name, "w+");
-		output (out);
-		fclose (out);
-	}
-	fclose (inp);
-}
\ No newline at end of file
diff --git a/agl_v3/input_agl.dat b/agl_v3/input_agl.dat
deleted file mode 100755
index 8d24b53..0000000
--- a/agl_v3/input_agl.dat
+++ /dev/null
@@ -1,4 +0,0 @@
-File name:	meth.txt
-Number of aglomerates:	2
-Cell dimention:	24.42	24.40	24.49
-Output:	out.pdb
\ No newline at end of file
diff --git a/agl_v3/meth.txt b/agl_v3/meth.txt
deleted file mode 100755
index 80ea604..0000000
--- a/agl_v3/meth.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-meth.001
-  3
-4       -   56   ( 2.87)
-56      -   4    ( 2.87)   153  ( 2.89)
-153     -   56   ( 2.89)
-meth.002
-    4
-3       -   13   ( 3.02)   192  ( 3.01)
-13      -   3    ( 3.02)
-192     -   3    ( 3.01)   24   ( 3.09)
-24      -   192  ( 3.09)
\ No newline at end of file