| Previous changeset 4:df7ba4536f77 (2020-04-25) Next changeset 6:744a777e9f90 (2020-05-21) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c" |
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added:
select_points_SDF.py test-data/input.sdf test-data/input_v3000.sdf test-data/select_points_output.sdf test-data/select_points_output_v3000.sdf |
| b |
| diff -r df7ba4536f77 -r 82193638d0c5 select_points_SDF.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/select_points_SDF.py Mon May 04 07:41:40 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$$$$\n") + + +def main(): + parser = argparse.ArgumentParser(description='RDKit screen') + parser.add_argument('-i', '--input', + help="Input file") + parser.add_argument('-o', '--output', + help="Base name for output file (no extension).") + args = parser.parse_args() + + mol_coordinates = [] + all_coordinates = [] + with open(args.input) as file: + for line in file: + if line.strip() == '$$$$': + temp = get_coordinates(mol_coordinates) + all_coordinates.append(temp) + mol_coordinates.clear() + else: + mol_coordinates.append(line) + centers = select_points(all_coordinates) + with open(args.output, 'w+') as writer: + sdfout(centers, writer) + +if __name__ == "__main__": + main() |
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| diff -r df7ba4536f77 -r 82193638d0c5 test-data/input.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.sdf Mon May 04 07:41:40 2020 -0400 |
| b |
| b'@@ -0,0 +1,602 @@\n+\n+ RDKit 3D\n+\n+ 13 13 0 0 0 0 0 0 0 0999 V2000\n+ 9.8790 -5.4960 26.1730 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.4790 -4.3410 26.0680 S 0 0 1 0 0 0 0 0 0 0 0 0\n+ 7.1910 -5.0190 26.2290 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.4340 -3.4430 27.2120 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.4960 -3.4980 24.5920 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.7540 -3.0340 24.0580 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.5680 -1.8260 23.1510 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.8760 -1.0500 23.1440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.9060 -1.4610 22.3160 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.1060 -0.7790 22.3180 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.2770 0.3180 23.1500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.2420 0.7320 23.9810 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.0390 0.0410 23.9830 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 1\n+ 2 3 2 0\n+ 2 4 2 0\n+ 2 5 1 0\n+ 5 6 1 0\n+ 6 7 1 0\n+ 7 8 1 0\n+ 8 9 2 0\n+ 8 13 1 0\n+ 9 10 1 0\n+ 13 12 2 0\n+ 10 11 2 0\n+ 11 12 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 16 17 0 0 0 0 0 0 0 0999 V2000\n+ 9.5220 5.3850 22.9640 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.6910 5.7360 23.8810 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.4660 6.3160 24.8740 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.0740 5.3880 23.6220 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.4920 4.6500 22.4510 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.1760 3.3750 22.9180 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.2100 2.3170 23.4570 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.1390 2.4870 24.3210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.5720 1.3010 24.5250 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.2360 0.3380 23.8210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.0300 -1.0620 23.6930 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.8800 -1.8120 22.8830 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.9290 -1.1860 22.1980 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.1280 0.1820 22.3230 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.2670 0.9460 23.1470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.7690 -1.8980 21.4040 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 2 4 1 0\n+ 4 5 1 0\n+ 5 6 1 0\n+ 6 7 1 0\n+ 7 8 2 0\n+ 7 15 1 0\n+ 8 9 1 0\n+ 15 10 2 0\n+ 15 14 1 0\n+ 9 10 1 0\n+ 10 11 1 0\n+ 11 12 2 0\n+ 12 13 1 0\n+ 13 14 2 0\n+ 13 16 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 11 11 0 0 0 0 0 0 0 0999 V2000\n+ 10.1640 -0.7840 22.5400 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.2630 -0.1570 21.4780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.5870 0.8590 20.9670 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.0140 -0.7980 21.1040 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.1560 -0.2070 20.0890 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.5230 -0.2650 18.7510 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.7670 0.2590 17.8050 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.6370 0.8610 18.1030 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1890 0.9760 19.4120 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.9640 0.4250 20.4340 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.5280 0.5220 21.8940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 2 4 1 0\n+ 4 5 1 0\n+ 5 6 2 0\n+ 5 10 1 0\n+ 6 7 1 0\n+ 10 9 2 0\n+ 10 11 1 0\n+ 7 8 2 0\n+ 8 9 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 14 14 0 0 0 0 0 0 0 0999 V2000\n+ 11.6590 -1.5020 21.8060 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.3210 -1.6370 23.0350 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.0730 -0.5250 23.4440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 14.2180 -0.6570 23.6840 O '..b'020 23.1470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.9550 -5.4170 24.6470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.9660 -5.9220 23.5900 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.5010 -5.7070 24.0110 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.3510 -4.8000 26.2520 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.7670 -4.2080 26.4740 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 3 0\n+ 2 4 1 0\n+ 4 5 2 0\n+ 4 6 1 0\n+ 3 13 1 0\n+ 3 14 1 0\n+ 13 12 1 0\n+ 14 15 1 0\n+ 5 10 1 0\n+ 6 8 2 0\n+ 10 9 2 0\n+ 8 9 1 0\n+ 7 9 1 0\n+ 7 11 1 0\n+ 7 15 1 0\n+ 11 12 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 19 21 0 0 0 0 0 0 0 0999 V2000\n+ 13.9130 -1.2590 23.2230 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.5110 -0.9700 23.5310 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.1000 1.2550 21.1530 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.6150 -1.9330 22.8770 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.9240 -0.2280 22.6330 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.1650 -1.5840 23.1190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.7830 0.2880 17.8390 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.7420 0.7360 23.3590 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.7860 1.4690 18.5050 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.1970 0.4050 23.1350 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.1590 0.1020 21.5780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.3780 -1.0090 20.8940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.5260 -0.4030 19.8320 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.7680 -0.4040 18.4910 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.8860 0.7470 18.7550 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.0720 1.8050 19.5870 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.4050 1.4630 20.8980 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.5480 0.7300 21.1350 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3230 0.3480 20.0330 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 4 1 0\n+ 2 10 1 0\n+ 4 6 1 0\n+ 10 8 1 0\n+ 3 11 2 0\n+ 11 5 1 0\n+ 11 12 1 0\n+ 6 5 1 0\n+ 5 8 1 0\n+ 7 14 1 0\n+ 7 15 1 0\n+ 14 13 2 0\n+ 15 9 2 0\n+ 15 19 1 0\n+ 9 16 1 0\n+ 16 17 2 0\n+ 12 13 1 0\n+ 13 19 1 0\n+ 19 18 2 0\n+ 17 18 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 18 19 0 0 0 0 0 0 0 0999 V2000\n+ 8.5420 0.5850 24.9250 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.7940 1.3450 24.0240 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.2640 2.3450 23.4580 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.9260 0.9180 25.2490 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 14.0600 -1.8530 20.5550 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.5640 0.9570 23.6730 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.8450 0.2990 24.2350 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.4250 0.8450 23.8150 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.0070 0.9620 23.8500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.8550 0.3860 22.9070 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.5210 -0.8490 22.3430 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.3580 -1.4190 21.3580 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.3630 -1.5210 22.7290 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.5270 -0.9460 23.6770 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.5720 0.7280 25.0430 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.1400 0.2280 24.7420 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.3070 0.9270 22.4720 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7020 1.5370 22.7150 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 1 4 1 0\n+ 2 3 2 0\n+ 2 8 1 0\n+ 4 7 1 0\n+ 8 15 1 0\n+ 8 18 1 0\n+ 7 9 2 0\n+ 7 14 1 0\n+ 5 12 3 0\n+ 12 11 1 0\n+ 6 16 1 0\n+ 6 17 1 0\n+ 16 15 1 0\n+ 17 18 1 0\n+ 9 10 1 0\n+ 14 13 2 0\n+ 10 11 2 0\n+ 11 13 1 0\n+M END\n+$$$$\n' |
| b |
| diff -r df7ba4536f77 -r 82193638d0c5 test-data/input_v3000.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_v3000.sdf Mon May 04 07:41:40 2020 -0400 |
| b |
| b'@@ -0,0 +1,721 @@\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 13 13 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 C 9.879 -5.496 26.173 0\n+M V30 2 S 8.479 -4.341 26.068 0\n+M V30 3 O 7.191 -5.019 26.229 0\n+M V30 4 O 8.434 -3.443 27.212 0\n+M V30 5 N 8.496 -3.498 24.592 0\n+M V30 6 C 9.754 -3.034 24.058 0\n+M V30 7 C 9.568 -1.826 23.151 0\n+M V30 8 C 10.876 -1.05 23.144 0\n+M V30 9 C 11.906 -1.461 22.316 0\n+M V30 10 C 13.106 -0.779 22.318 0\n+M V30 11 C 13.277 0.318 23.15 0\n+M V30 12 C 12.242 0.732 23.981 0\n+M V30 13 C 11.039 0.041 23.983 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 1 2 1 CFG=1\n+M V30 2 2 2 3\n+M V30 3 2 2 4\n+M V30 4 1 2 5\n+M V30 5 1 5 6\n+M V30 6 1 6 7\n+M V30 7 1 7 8\n+M V30 8 2 8 9\n+M V30 9 1 8 13\n+M V30 10 1 9 10\n+M V30 11 2 10 11\n+M V30 12 1 11 12\n+M V30 13 2 13 12\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 16 17 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 C 9.522 5.385 22.964 0\n+M V30 2 C 10.691 5.736 23.881 0\n+M V30 3 O 10.466 6.316 24.874 0\n+M V30 4 N 12.074 5.388 23.622 0\n+M V30 5 C 12.492 4.65 22.451 0\n+M V30 6 C 13.176 3.375 22.918 0\n+M V30 7 C 12.21 2.317 23.457 0\n+M V30 8 C 11.139 2.487 24.321 0\n+M V30 9 N 10.572 1.301 24.525 0\n+M V30 10 C 11.236 0.338 23.821 0\n+M V30 11 C 11.03 -1.062 23.693 0\n+M V30 12 C 11.88 -1.812 22.883 0\n+M V30 13 C 12.929 -1.186 22.198 0\n+M V30 14 C 13.128 0.182 22.323 0\n+M V30 15 C 12.267 0.946 23.147 0\n+M V30 16 F 13.769 -1.898 21.404 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 1 1 2\n+M V30 2 2 2 3\n+M V30 3 1 2 4\n+M V30 4 1 4 5\n+M V30 5 1 5 6\n+M V30 6 1 6 7\n+M V30 7 2 7 8\n+M V30 8 1 7 15\n+M V30 9 1 8 9\n+M V30 10 1 9 10\n+M V30 11 2 15 10\n+M V30 12 1 10 11\n+M V30 13 2 11 12\n+M V30 14 1 12 13\n+M V30 15 2 13 14\n+M V30 16 1 13 16\n+M V30 17 1 15 14\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 11 11 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 C 10.164 -0.784 22.54 0\n+M V30 2 C 9.263 -0.157 21.478 0\n+M V30 3 O 9.587 0.859 20.967 0\n+M V30 4 N 8.014 -0.798 21.104 0\n+M V30 5 C 7.156 -0.207 20.089 0\n+M V30 6 C 7.523 -0.265 18.751 0\n+M V30 7 N 6.767 0.259 17.805 0\n+M V30 8 C 5.637 0.861 18.103 0\n+M V30 9 C 5.189 0.976 19.412 0\n+M V30 10 C 5.964 0.425 20.434 0\n+M V30 11 C 5.528 0.522 21.894 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 1 1 2\n+M V30 2 2 2 3\n+M V30 3 1 2 4\n+M V30 4 1 4 5\n+M V30 5 2 5 6\n+M V30 6 1 5 10\n+M V30 7 1 6 7\n+M V30 8 2 7 8\n+M V30 9 1 8 9\n+M V30 10 2 10 9\n+M V30 11 1 10 11\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 14 14 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 C 11.659 -1.502 21.806 0\n+M V30 2 O 12.321 -1.637 23.035 0\n+M V30 3 C 13.073 -0.525 23.444 0\n+M V30 4 O 14.218 -0.657 23.684 0\n+M V30 5 C 12.42 0.849 23.571 0\n+M V30 6 C 11.17 0.983 24.168 0\n+M V30 7 C 10.588 2.24 24.264 0\n+M V30 8 C 11.27 3.343 23.759 0\n+M V30 9 C 12.512 3.207 23.159 0\n+M V30 10 C 13.085 1.956 23.065 0\n+M V30 11 S 10.543 4.988 23.864 0\n+M V30 12 O 11.527 6.005 23.481 0\n+M V30 13 O 10.243 5.326 25.257 0\n+M V30 14 N 9.156 5.076 22.863 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 1 1 2\n+M V30 2 1 2 3\n+M V30 3 2 3 4\n+M V30 4 1 3 5\n+M V30 5 2 5 6\n+M V30 6 1 5 10\n+M V30 7 1 6 7\n+M V30 8 2 7 8\n+M V30 9 1 8 9\n+M V30 10 1 8 11\n+M V30 11 2 10 9\n+M V30 12 2 11 12\n+M V30 13 2 11 13\n+M V30 14 1 11 14 CFG=6\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 15 16 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 C 9.935 -0.519 25.099 0\n+M V30 2 N 11.151 -0.499 24.314 0\n+M V30 3 C 11.474 -1.689 23.578 0\n+M V30 4 C 12.697 -1.643 22.689 0\n+M V30 5 C 13.671 -0.515 22.98 0\n+M V30'..b'BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 7 7 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 N 3.785 2.023 19.567 0\n+M V30 2 C 4.751 1.187 19.156 0\n+M V30 3 C 5.193 0.102 19.956 0\n+M V30 4 N 6.118 -0.771 19.531 0\n+M V30 5 C 6.631 -0.544 18.275 0\n+M V30 6 N 6.296 0.461 17.443 0\n+M V30 7 C 5.36 1.316 17.878 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 1 1 2\n+M V30 2 2 2 3\n+M V30 3 1 2 7\n+M V30 4 1 3 4\n+M V30 5 2 4 5\n+M V30 6 1 5 6\n+M V30 7 2 7 6\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 15 16 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 N 9.956 1.422 21.355 0\n+M V30 2 C 9.817 0.455 21.963 0\n+M V30 3 O 7.362 -5.927 25.41 0\n+M V30 4 C 9.649 -0.698 22.751 0\n+M V30 5 N 10.264 -1.84 22.326 0\n+M V30 6 C 8.945 -0.599 23.939 0\n+M V30 7 N 9.593 -4.099 25.24 0\n+M V30 8 C 8.874 -1.71 24.773 0\n+M V30 9 C 9.513 -2.915 24.415 0\n+M V30 10 C 10.185 -2.902 23.147 0\n+M V30 11 C 9.955 -5.417 24.647 0\n+M V30 12 C 8.966 -5.922 23.59 0\n+M V30 13 C 7.501 -5.707 24.011 0\n+M V30 14 C 7.351 -4.8 26.252 0\n+M V30 15 C 8.767 -4.208 26.474 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 3 1 2\n+M V30 2 1 2 4\n+M V30 3 1 3 13\n+M V30 4 1 3 14\n+M V30 5 2 4 5\n+M V30 6 1 4 6\n+M V30 7 1 5 10\n+M V30 8 2 6 8\n+M V30 9 1 7 9\n+M V30 10 1 7 11\n+M V30 11 1 7 15\n+M V30 12 1 8 9\n+M V30 13 2 10 9\n+M V30 14 1 11 12\n+M V30 15 1 13 12\n+M V30 16 1 14 15\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 19 21 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 C 13.913 -1.259 23.223 0\n+M V30 2 N 12.511 -0.97 23.531 0\n+M V30 3 O 9.1 1.255 21.153 0\n+M V30 4 C 11.615 -1.933 22.877 0\n+M V30 5 N 9.924 -0.228 22.633 0\n+M V30 6 C 10.165 -1.584 23.119 0\n+M V30 7 N 6.783 0.288 17.839 0\n+M V30 8 C 10.742 0.736 23.359 0\n+M V30 9 N 4.786 1.469 18.505 0\n+M V30 10 C 12.197 0.405 23.135 0\n+M V30 11 C 9.159 0.102 21.578 0\n+M V30 12 C 8.378 -1.009 20.894 0\n+M V30 13 C 7.526 -0.403 19.832 0\n+M V30 14 C 7.768 -0.404 18.491 0\n+M V30 15 C 5.886 0.747 18.755 0\n+M V30 16 C 4.072 1.805 19.587 0\n+M V30 17 C 4.405 1.463 20.898 0\n+M V30 18 C 5.548 0.73 21.135 0\n+M V30 19 C 6.323 0.348 20.033 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 1 1 2\n+M V30 2 1 2 4\n+M V30 3 1 2 10\n+M V30 4 2 3 11\n+M V30 5 1 4 6\n+M V30 6 1 11 5\n+M V30 7 1 6 5\n+M V30 8 1 5 8\n+M V30 9 1 7 14\n+M V30 10 1 7 15\n+M V30 11 1 10 8\n+M V30 12 2 15 9\n+M V30 13 1 9 16\n+M V30 14 1 11 12\n+M V30 15 1 12 13\n+M V30 16 2 14 13\n+M V30 17 1 13 19\n+M V30 18 1 15 19\n+M V30 19 2 16 17\n+M V30 20 1 17 18\n+M V30 21 2 19 18\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 18 19 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 N 8.542 0.585 24.925 0\n+M V30 2 C 7.794 1.345 24.024 0\n+M V30 3 O 8.264 2.345 23.458 0\n+M V30 4 C 9.926 0.918 25.249 0\n+M V30 5 N 14.06 -1.853 20.555 0\n+M V30 6 O 3.564 0.957 23.673 0\n+M V30 7 C 10.845 0.299 24.235 0\n+M V30 8 N 6.425 0.845 23.815 0\n+M V30 9 C 12.007 0.962 23.85 0\n+M V30 10 C 12.855 0.386 22.907 0\n+M V30 11 C 12.521 -0.849 22.343 0\n+M V30 12 C 13.358 -1.419 21.358 0\n+M V30 13 C 11.363 -1.521 22.729 0\n+M V30 14 C 10.527 -0.946 23.677 0\n+M V30 15 C 5.572 0.728 25.043 0\n+M V30 16 C 4.14 0.228 24.742 0\n+M V30 17 C 4.307 0.927 22.472 0\n+M V30 18 C 5.702 1.537 22.715 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 1 1 2\n+M V30 2 1 1 4\n+M V30 3 2 2 3\n+M V30 4 1 2 8\n+M V30 5 1 4 7\n+M V30 6 3 5 12\n+M V30 7 1 6 16\n+M V30 8 1 6 17\n+M V30 9 2 7 9\n+M V30 10 1 7 14\n+M V30 11 1 8 15\n+M V30 12 1 8 18\n+M V30 13 1 9 10\n+M V30 14 2 10 11\n+M V30 15 1 12 11\n+M V30 16 1 11 13\n+M V30 17 2 14 13\n+M V30 18 1 16 15\n+M V30 19 1 17 18\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n' |
| b |
| diff -r df7ba4536f77 -r 82193638d0c5 test-data/select_points_output.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/select_points_output.sdf Mon May 04 07:41:40 2020 -0400 |
| b |
| @@ -0,0 +1,49 @@ +Frankenstein_ligand +Galaxy select_points_sdf tool + + 43 0 0 0 0 0 0 0 0 0999 V2000 + 9.8790 -5.4960 26.1730 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1910 -5.0190 26.2290 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.4340 -3.4430 27.2120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.4960 -3.4980 24.5920 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.5680 -1.8260 23.1510 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.9060 -1.4610 22.3160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.2770 0.3180 23.1500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.0390 0.0410 23.9830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.5220 5.3850 22.9640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.4660 6.3160 24.8740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.0740 5.3880 23.6220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.1760 3.3750 22.9180 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.1390 2.4870 24.3210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.7690 -1.8980 21.4040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.2630 -0.1570 21.4780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1560 -0.2070 20.0890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7670 0.2590 17.8050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.1890 0.9760 19.4120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5280 0.5220 21.8940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.1620 4.6860 25.3040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.9400 -0.0330 27.7960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.1320 0.2510 25.7380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.8590 3.5410 30.9720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.2750 -1.8280 28.1560 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5170 1.3480 30.0440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9910 0.4280 28.2890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.8910 -1.7080 26.0080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5080 2.5200 29.5440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.5820 -2.7550 24.6800 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.0170 1.3310 24.2360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.1930 2.3160 22.5030 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9740 3.1250 23.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6450 4.8530 25.2350 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7660 3.1150 23.7900 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.3930 -0.3170 23.0940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.4350 -1.7070 23.6420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.3170 3.0110 22.2490 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.8240 1.0110 23.7650 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4350 -0.4970 23.3480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9560 1.4220 21.3550 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9550 -5.4170 24.6470 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5010 -5.7070 24.0110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5720 0.7280 25.0430 C 0 0 0 0 0 0 0 0 0 0 0 0 +M END +$$$$ |
| b |
| diff -r df7ba4536f77 -r 82193638d0c5 test-data/select_points_output_v3000.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/select_points_output_v3000.sdf Mon May 04 07:41:40 2020 -0400 |
| b |
| @@ -0,0 +1,49 @@ +Frankenstein_ligand +Galaxy select_points_sdf tool + + 43 0 0 0 0 0 0 0 0 0999 V2000 + 9.8790 -5.4960 26.1730 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1910 -5.0190 26.2290 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.4340 -3.4430 27.2120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.4960 -3.4980 24.5920 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.5680 -1.8260 23.1510 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.9060 -1.4610 22.3160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.2770 0.3180 23.1500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.0390 0.0410 23.9830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.5220 5.3850 22.9640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.4660 6.3160 24.8740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.0740 5.3880 23.6220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.1760 3.3750 22.9180 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.1390 2.4870 24.3210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.7690 -1.8980 21.4040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.2630 -0.1570 21.4780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1560 -0.2070 20.0890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7670 0.2590 17.8050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.1890 0.9760 19.4120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5280 0.5220 21.8940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.1620 4.6860 25.3040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.9400 -0.0330 27.7960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.1320 0.2510 25.7380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.8590 3.5410 30.9720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.2750 -1.8280 28.1560 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5170 1.3480 30.0440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9910 0.4280 28.2890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.8910 -1.7080 26.0080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5080 2.5200 29.5440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.5820 -2.7550 24.6800 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.0170 1.3310 24.2360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.1930 2.3160 22.5030 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9740 3.1250 23.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6450 4.8530 25.2350 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7660 3.1150 23.7900 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.3930 -0.3170 23.0940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.4350 -1.7070 23.6420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.3170 3.0110 22.2490 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.8240 1.0110 23.7650 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4350 -0.4970 23.3480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9560 1.4220 21.3550 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9550 -5.4170 24.6470 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5010 -5.7070 24.0110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5720 0.7280 25.0430 C 0 0 0 0 0 0 0 0 0 0 0 0 +M END +$$$$ |