Mercurial > repos > bgruening > rdock_sort_filter
view select_points_SDF.py @ 6:d1ca4b45f615 draft default tip
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author | bgruening |
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date | Tue, 28 Jul 2020 08:45:01 -0400 |
parents | cc3fc71ef636 |
children |
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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\n00000000000000000000 3D\nCreated in Galaxy\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()