diff distance_finder.py @ 10:612c134546a2 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 6c84abdd07f292048bf2194073e2e938e94158c4"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/distance_finder.py	Wed Mar 25 16:51:33 2020 -0400
@@ -0,0 +1,109 @@
+# Reports distances of ligands to reference points. An example input for the points is:
+#
+# 5.655   1.497  18.223
+# 1.494  -8.367  18.574
+# 13.034   6.306  25.232
+#
+# Data can be space or tab separated but must contain 3 and only 3 numbers for the x, y and z coordinates
+#
+# That would encode 3 points.
+# Each record in the SDF input is read and the closest heavy atom to each of the reference points is recorded as
+# a property named distance1 where the numeric part is the index (starting from 1) of the points (in that example
+# there would be properties for distance1, distance2 and distance3.
+
+import argparse, os, sys, math
+from openbabel import pybel
+
+
+
+def log(*args, **kwargs):
+    """Log output to STDERR
+    """
+    print(*args, file=sys.stderr, ** kwargs)
+
+
+def execute(ligands_sdf, points_file, outfile):
+    """
+    :param ligands_sdf: A SDF with the 3D molecules to test
+    :param points_file: A file with the points to consider.
+    :param outfile: The name of the file for the SDF output
+    :return:
+    """
+
+
+    points = []
+
+    # read the points
+    with open(points_file, 'r') as f:
+        for line in f.readlines():
+            line.strip()
+            if line:
+                p = line.split()
+                if len(p) == 3:
+                    points.append((float(p[0]), float(p[1]), float(p[2])))
+                    log("Read points",p)
+                    continue
+            log("Failed to read line:", line)
+    log('Found', len(points), 'atom points')
+
+    sdf_writer = pybel.Outputfile("sdf", outfile, overwrite=True)
+
+    count = 0
+    for mol in pybel.readfile("sdf", ligands_sdf):
+        count += 1
+        if count % 50000 == 0:
+            log('Processed', count)
+
+        try:
+            # print("Processing mol", mol.title)
+
+            clone = pybel.Molecule(mol)
+            clone.removeh()
+
+            coords = []
+            for atom in clone.atoms:
+                coords.append(atom.coords)
+
+            p = 0
+            for point in points:
+                p += 1
+                distances = []
+                for i in coords:
+                    # calculates distance based on cartesian coordinates
+                    distance = math.sqrt((point[0] - i[0])**2 + (point[1] - i[1])**2 + (point[2] - i[2])**2)
+                    distances.append(distance)
+                    # log("distance:", distance)
+                min_distance = min(distances)
+                # log('Min:', min_distance)
+                # log(count, p, min_distance)
+
+                mol.data['distance' + str(p)] = min_distance
+
+            sdf_writer.write(mol)
+
+        except Exception as e:
+            log('Failed to handle molecule: '+ str(e))
+            continue
+
+    sdf_writer.close()
+    log('Wrote', count, 'molecules')
+
+
+def main():
+    global work_dir
+
+    parser = argparse.ArgumentParser(description='XChem distances - measure distances to particular points')
+
+    parser.add_argument('-i', '--input', help="SDF containing the 3D molecules to score)")
+    parser.add_argument('-p', '--points', help="PDB format file with atoms")
+    parser.add_argument('-o', '--outfile', default='output.sdf', help="File name for results")
+
+
+    args = parser.parse_args()
+    log("XChem distances args: ", args)
+
+    execute(args.input, args.points, args.outfile)
+
+
+if __name__ == "__main__":
+    main()