--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/select_points_SDF.py	Mon May 04 07:41:13 2020 -0400
@@ -0,0 +1,90 @@
+import argparse
+
+def get_coordinates(lines):
+    version = lines[3][34:39]
+    molecule = []
+    if version == 'V2000':
+        natom = int(lines[3][:3].strip())
+        for i in range(1, natom + 1):
+            temp = []
+            j = 3 + i
+            x = float(lines[j][:10].strip())
+            y = float(lines[j][11:20].strip())
+            z = float(lines[j][21:30].strip())
+            temp.extend([x, y, z])
+            molecule.append(temp)
+    else:
+        read = 0
+        for line in lines:
+            if "END ATOM" in line:
+                read = 0
+                break
+            if read:
+                temp = []
+                a = line.split(" ")
+                x, y, z = float(a[5]), float(a[6]), float(a[7])
+                temp.extend([x, y, z])
+                molecule.append(temp)
+            if "BEGIN ATOM" in line:
+                read = 1
+    return molecule
+
+
+def select_points(all_coordinates):
+    tol = 1.5
+    select = []
+
+    for molecule in all_coordinates:
+        for coordinates in molecule:
+            tv = 0
+            temp = []
+            x, y, z = coordinates
+            for record in select:
+                xr, yr, zr = record
+                if xr-tol < x and x < xr+tol and \
+                   yr-tol < y and y < yr+tol and \
+                   zr-tol < z and z < zr+tol:
+                    tv = 1
+                    break
+            if tv == 1:
+                continue
+            temp.extend([x, y, z])
+            select.append(temp)
+    return select
+
+
+def sdfout(centers, writer):
+    n = len(centers)
+    writer.write("Frankenstein_ligand\nGalaxy select_points_sdf tool\n\n")
+    writer.write("%3d  0  0  0  0  0  0  0  0  0999 V2000\n" % n)
+    for record in centers:
+        x, y, z = record
+        writer.write("%10.4f%10.4f%10.4f C   0  0  0  0  0  0  0  0  0  0  0  0\n" % (x, y, z))
+
+    writer.write("M  END\n$$$$\n")
+
+
+def main():
+    parser = argparse.ArgumentParser(description='RDKit screen')
+    parser.add_argument('-i', '--input',
+                        help="Input file")
+    parser.add_argument('-o', '--output',
+                        help="Base name for output file (no extension).")
+    args = parser.parse_args()
+
+    mol_coordinates = []
+    all_coordinates = []
+    with open(args.input) as file:
+        for line in file:
+            if line.strip() == '$$$$':
+                temp = get_coordinates(mol_coordinates)
+                all_coordinates.append(temp)
+                mol_coordinates.clear()
+            else:
+                mol_coordinates.append(line)
+    centers = select_points(all_coordinates)
+    with open(args.output, 'w+') as writer:
+        sdfout(centers, writer)
+
+if __name__ == "__main__":
+    main()