| Next changeset 1:8e214e52e461 (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:
rbdock.py rdock_macros.xml select_points_SDF.py select_points_SDF.xml test-data/broken_ligand.sdf test-data/input.sdf test-data/input_v3000.sdf test-data/ligand.mol test-data/ligand.sdf test-data/ligands_names.sdf test-data/ligands_nonames.sdf test-data/poses-ascending.sdf test-data/poses-desc-noglobal.sdf test-data/poses-descending.sdf test-data/poses-filt-0.2.sdf test-data/poses-filt-only.sdf test-data/poses.sdf test-data/receptor.as test-data/receptor.mol2 test-data/receptor.prm test-data/select_points_output.sdf test-data/select_points_output_v3000.sdf test-data/wrong_receptor.prm |
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| diff -r 000000000000 -r 7a4306d69801 rbdock.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rbdock.py Mon May 04 07:41:13 2020 -0400 |
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| @@ -0,0 +1,28 @@ +import subprocess +import argparse + +def main(): + parser = argparse.ArgumentParser(description='Simple wrapper for rbdock') + parser.add_argument('-n', '--num', type=int, help='Number of docking poses to generate') + parser.add_argument('-s', '--seed', type=int, help='Random seed') + args = parser.parse_args() + + cmd = ['rbdock', '-i', 'ligands.sdf', '-r', 'receptor.prm', '-p', 'dock.prm', '-n', str(args.num), '-o', 'rdock_output'] + if args.seed != None: + cmd += ['-s', str(args.seed)] + + ps = subprocess.Popen(cmd, stdout=subprocess.PIPE) + + error_counter = 0 + for stdout_line in iter(ps.stdout.readline, ''): + if 'RBT_DOCKING_ERROR' in str(stdout_line): + error_counter += 1 + if error_counter == 10: + print(ps.stdout) + exit(23) + if ps.poll() != None: + print(ps.stdout) + exit(int(ps.poll())) + +if __name__ == "__main__": + main() |
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| diff -r 000000000000 -r 7a4306d69801 rdock_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdock_macros.xml Mon May 04 07:41:13 2020 -0400 |
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| @@ -0,0 +1,12 @@ +<macros> + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1003571</citation> + </citations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2013.1-0">rdock</requirement> + </requirements> + </xml> +</macros> |
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| diff -r 000000000000 -r 7a4306d69801 select_points_SDF.py --- /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() |
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| diff -r 000000000000 -r 7a4306d69801 select_points_SDF.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/select_points_SDF.xml Mon May 04 07:41:13 2020 -0400 |
| [ |
| @@ -0,0 +1,62 @@ +<tool id="ctb_frankenstein_ligand" name="Create Frankenstein ligand" version="0.1.0"> + <description>for docking active site definition</description> + <requirements> + <requirement type="package" version="3.7">python</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/select_points_SDF.py' + -i '$infile' + -o '$outfile' + ]]></command> + <inputs> + <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/> + </inputs> + <outputs> + <data name="outfile" format="sdf"/> + </outputs> + <tests> + <test> + <param name="infile" value="input.sdf" ftype="sdf"/> + <output name="outfile" ftype='sdf' file="select_points_output.sdf"/> + </test> + <test> + <param name="infile" value="input_v3000.sdf" ftype="sdf"/> + <output name="outfile" ftype='sdf' file="select_points_output_v3000.sdf"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +Converts an SD file containing multiple molecules into a 'Frankenstein ligand' with a 3D shape combining all ligands, which can be used for definition of an active site with rDock. + +This tool is based on a Perl script originally written by Peter Schmidtke. + +_____ + +.. class:: infomark + +**Input** + + - SD file containing multiple molecules. + +_____ + +.. class:: infomark + +**Output** + + - SD file containing the 'Frankenstein ligand'. + ]]></help> + <citations> + <citation type="doi">10.1371/journal.pcbi.1003571</citation> + <citation type="bibtex"> + @article{rdock, + author = {Peter Schmidtke}, + title = {'Select points' script for generation of a Frankenstein ligand}, + url = {https://github.com/InformaticsMatters/docking-validation/blob/master/scripts/select_points_SDF.pl} + }</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 7a4306d69801 test-data/broken_ligand.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/broken_ligand.sdf Mon May 04 07:41:13 2020 -0400 |
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| @@ -0,0 +1,159 @@ +Cc1ccsc1C1(O)CCOC1 + OpenBabel03262013053D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 2.6244 -0.3204 0.0030 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1487 -0.0653 -0.0019 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.5577 1.2199 0.0010 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7851 1.2166 -0.0030 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4005 -0.3714 0.0020 S 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1829 -0.9540 -0.0102 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7593 -3.2703 1.1063 C 0 0 3 0 0 0 0 0 0 0 0 0 + 0.3797 -2.5572 0.0072 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7298 -2.3113 -0.2964 C 0 0 0 0 0 2 0 0 0 0 0 0 + 0.3797 -2.5572 0.0072 C 0 0 0 0 0 2 0 0 0 0 0 0 + 0.3797 -2.5572 0.0072 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3797 -2.5572 0.0072 C 0 0 0 0 0 2 0 0 0 0 0 0 + 3.1460 0.6144 0.0045 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8955 -0.8785 -0.8702 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8896 -0.8781 0.8782 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1148 2.0915 0.0058 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3714 2.0694 -0.0084 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6424 -1.9351 0.5862 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 13 1 0 0 0 0 + 1 14 1 0 0 0 0 + 1 15 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 6 2 0 0 0 0 + 3 4 2 0 0 0 0 + 3 16 1 0 0 0 0 + 4 5 1 0 0 0 0 + 4 17 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 12 1 0 0 0 0 + 8 18 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 1 0 0 0 0 +M END +$$$$ +1S3V + OpenBabel07031809403D + + 54 56 0 0 1 0 0 0 0 0999 V2000 + -0.0237 32.0851 0.4630 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0257 32.5701 2.5090 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5816 31.2781 2.5290 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2645 30.7721 3.8370 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.1514 29.5300 3.5680 C 0 0 1 0 0 0 0 0 0 0 0 0 + -2.3824 28.4990 2.7070 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7845 29.0260 1.3530 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3126 30.4241 1.4480 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6244 28.9840 4.9610 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2442 26.5599 4.7800 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.1391 25.6479 4.2580 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.8561 24.2849 4.1780 C 0 0 0 0 0 0 0 0 0 0 0 0 + -7.0120 23.8848 3.0290 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6611 23.8468 4.6560 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5581 22.0928 3.4830 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7132 24.7349 5.1800 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4583 25.1339 6.0060 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0123 26.0899 5.2580 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4676 30.8241 0.4170 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8412 32.3751 -0.5420 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2388 32.9722 1.4960 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2847 33.4632 3.4970 N 0 0 0 0 0 0 0 0 0 0 0 0 + -4.6273 27.9210 4.8320 N 0 0 0 0 0 0 0 0 0 0 0 0 + -5.8230 23.4168 3.6560 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.1441 22.5778 4.6930 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5192 24.2169 5.6340 O 0 0 0 0 0 0 0 0 0 0 0 0 + -6.0522 28.2910 4.7350 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8817 31.5647 4.2416 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4982 30.5088 4.5555 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0329 29.7742 2.9881 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0645 27.6908 2.4734 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5623 28.1183 3.3032 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5506 28.9693 0.5897 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9492 28.3958 1.0737 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0540 29.8010 5.5275 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7656 28.5900 5.4903 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.0962 26.0040 3.8974 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.7524 24.4932 2.1715 H 0 0 0 0 0 0 0 0 0 0 0 0 + -7.6062 23.0393 2.7052 H 0 0 0 0 0 0 0 0 0 0 0 0 + -7.5820 24.4781 3.7333 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7376 22.7384 3.1952 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1884 21.0868 3.6389 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3042 22.0856 2.6981 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8011 25.7764 6.8076 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4051 24.5711 6.3386 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1871 25.7386 5.1495 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2964 26.7805 5.6864 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2433 33.2980 -0.6110 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0822 31.6679 -1.2201 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8759 34.3850 3.4637 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.8862 33.2055 4.2651 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.2045 28.9156 3.8635 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.6528 27.3942 4.6458 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.3454 28.8348 5.6245 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 19 1 0 0 0 0 + 1 20 1 0 0 0 0 + 2 22 1 0 0 0 0 + 3 2 2 0 0 0 0 + 3 8 1 0 0 0 0 + 4 3 1 0 0 0 0 + 4 28 1 0 0 0 0 + 4 29 1 0 0 0 0 + 5 4 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 9 1 0 0 0 0 + 5 30 1 6 0 0 0 + 6 7 1 0 0 0 0 + 6 31 1 0 0 0 0 + 6 32 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 33 1 0 0 0 0 + 7 34 1 0 0 0 0 + 8 19 2 0 0 0 0 + 9 35 1 0 0 0 0 + 9 36 1 0 0 0 0 + 11 10 2 0 0 0 0 + 11 37 1 0 0 0 0 + 12 11 1 0 0 0 0 + 13 38 1 0 0 0 0 + 13 39 1 0 0 0 0 + 13 40 1 0 0 0 0 + 14 12 2 0 0 0 0 + 15 25 1 0 0 0 0 + 15 41 1 0 0 0 0 + 15 42 1 0 0 0 0 + 15 43 1 0 0 0 0 + 16 14 1 0 0 0 0 + 16 26 1 0 0 0 0 + 17 26 1 0 0 0 0 + 17 44 1 0 0 0 0 + 17 45 1 0 0 0 0 + 17 46 1 0 0 0 0 + 18 10 1 0 0 0 0 + 18 16 2 0 0 0 0 + 18 47 1 0 0 0 0 + 20 48 1 0 0 0 0 + 20 49 1 0 0 0 0 + 21 1 2 0 0 0 0 + 21 2 1 0 0 0 0 + 22 50 1 0 0 0 0 + 22 51 1 0 0 0 0 + 23 9 1 0 0 0 0 + 23 10 1 0 0 0 0 + 23 27 1 0 0 0 0 + 24 12 1 0 0 0 0 + 24 13 1 0 0 0 0 + 25 14 1 0 0 0 0 + 27 52 1 0 0 0 0 + 27 53 1 0 0 0 0 + 27 54 1 0 0 0 0 +M END +$$$$ |
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| diff -r 000000000000 -r 7a4306d69801 test-data/input.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.sdf Mon May 04 07:41:13 2020 -0400 |
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| b'@@ -0,0 +1,602 @@\n+\n+ RDKit 3D\n+\n+ 13 13 0 0 0 0 0 0 0 0999 V2000\n+ 9.8790 -5.4960 26.1730 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.4790 -4.3410 26.0680 S 0 0 1 0 0 0 0 0 0 0 0 0\n+ 7.1910 -5.0190 26.2290 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.4340 -3.4430 27.2120 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.4960 -3.4980 24.5920 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.7540 -3.0340 24.0580 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.5680 -1.8260 23.1510 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.8760 -1.0500 23.1440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.9060 -1.4610 22.3160 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.1060 -0.7790 22.3180 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.2770 0.3180 23.1500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.2420 0.7320 23.9810 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.0390 0.0410 23.9830 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 1\n+ 2 3 2 0\n+ 2 4 2 0\n+ 2 5 1 0\n+ 5 6 1 0\n+ 6 7 1 0\n+ 7 8 1 0\n+ 8 9 2 0\n+ 8 13 1 0\n+ 9 10 1 0\n+ 13 12 2 0\n+ 10 11 2 0\n+ 11 12 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 16 17 0 0 0 0 0 0 0 0999 V2000\n+ 9.5220 5.3850 22.9640 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.6910 5.7360 23.8810 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.4660 6.3160 24.8740 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.0740 5.3880 23.6220 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.4920 4.6500 22.4510 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.1760 3.3750 22.9180 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.2100 2.3170 23.4570 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.1390 2.4870 24.3210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.5720 1.3010 24.5250 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.2360 0.3380 23.8210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.0300 -1.0620 23.6930 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.8800 -1.8120 22.8830 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.9290 -1.1860 22.1980 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.1280 0.1820 22.3230 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.2670 0.9460 23.1470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.7690 -1.8980 21.4040 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 2 4 1 0\n+ 4 5 1 0\n+ 5 6 1 0\n+ 6 7 1 0\n+ 7 8 2 0\n+ 7 15 1 0\n+ 8 9 1 0\n+ 15 10 2 0\n+ 15 14 1 0\n+ 9 10 1 0\n+ 10 11 1 0\n+ 11 12 2 0\n+ 12 13 1 0\n+ 13 14 2 0\n+ 13 16 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 11 11 0 0 0 0 0 0 0 0999 V2000\n+ 10.1640 -0.7840 22.5400 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.2630 -0.1570 21.4780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.5870 0.8590 20.9670 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.0140 -0.7980 21.1040 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.1560 -0.2070 20.0890 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.5230 -0.2650 18.7510 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.7670 0.2590 17.8050 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.6370 0.8610 18.1030 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1890 0.9760 19.4120 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.9640 0.4250 20.4340 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.5280 0.5220 21.8940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 2 4 1 0\n+ 4 5 1 0\n+ 5 6 2 0\n+ 5 10 1 0\n+ 6 7 1 0\n+ 10 9 2 0\n+ 10 11 1 0\n+ 7 8 2 0\n+ 8 9 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 14 14 0 0 0 0 0 0 0 0999 V2000\n+ 11.6590 -1.5020 21.8060 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.3210 -1.6370 23.0350 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.0730 -0.5250 23.4440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 14.2180 -0.6570 23.6840 O '..b'020 23.1470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.9550 -5.4170 24.6470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.9660 -5.9220 23.5900 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.5010 -5.7070 24.0110 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.3510 -4.8000 26.2520 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.7670 -4.2080 26.4740 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 3 0\n+ 2 4 1 0\n+ 4 5 2 0\n+ 4 6 1 0\n+ 3 13 1 0\n+ 3 14 1 0\n+ 13 12 1 0\n+ 14 15 1 0\n+ 5 10 1 0\n+ 6 8 2 0\n+ 10 9 2 0\n+ 8 9 1 0\n+ 7 9 1 0\n+ 7 11 1 0\n+ 7 15 1 0\n+ 11 12 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 19 21 0 0 0 0 0 0 0 0999 V2000\n+ 13.9130 -1.2590 23.2230 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.5110 -0.9700 23.5310 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.1000 1.2550 21.1530 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.6150 -1.9330 22.8770 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.9240 -0.2280 22.6330 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.1650 -1.5840 23.1190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.7830 0.2880 17.8390 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.7420 0.7360 23.3590 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.7860 1.4690 18.5050 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.1970 0.4050 23.1350 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.1590 0.1020 21.5780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.3780 -1.0090 20.8940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.5260 -0.4030 19.8320 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.7680 -0.4040 18.4910 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.8860 0.7470 18.7550 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.0720 1.8050 19.5870 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.4050 1.4630 20.8980 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.5480 0.7300 21.1350 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3230 0.3480 20.0330 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 4 1 0\n+ 2 10 1 0\n+ 4 6 1 0\n+ 10 8 1 0\n+ 3 11 2 0\n+ 11 5 1 0\n+ 11 12 1 0\n+ 6 5 1 0\n+ 5 8 1 0\n+ 7 14 1 0\n+ 7 15 1 0\n+ 14 13 2 0\n+ 15 9 2 0\n+ 15 19 1 0\n+ 9 16 1 0\n+ 16 17 2 0\n+ 12 13 1 0\n+ 13 19 1 0\n+ 19 18 2 0\n+ 17 18 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 18 19 0 0 0 0 0 0 0 0999 V2000\n+ 8.5420 0.5850 24.9250 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.7940 1.3450 24.0240 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.2640 2.3450 23.4580 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.9260 0.9180 25.2490 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 14.0600 -1.8530 20.5550 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.5640 0.9570 23.6730 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.8450 0.2990 24.2350 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.4250 0.8450 23.8150 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.0070 0.9620 23.8500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.8550 0.3860 22.9070 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.5210 -0.8490 22.3430 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.3580 -1.4190 21.3580 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.3630 -1.5210 22.7290 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.5270 -0.9460 23.6770 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.5720 0.7280 25.0430 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.1400 0.2280 24.7420 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.3070 0.9270 22.4720 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7020 1.5370 22.7150 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 1 4 1 0\n+ 2 3 2 0\n+ 2 8 1 0\n+ 4 7 1 0\n+ 8 15 1 0\n+ 8 18 1 0\n+ 7 9 2 0\n+ 7 14 1 0\n+ 5 12 3 0\n+ 12 11 1 0\n+ 6 16 1 0\n+ 6 17 1 0\n+ 16 15 1 0\n+ 17 18 1 0\n+ 9 10 1 0\n+ 14 13 2 0\n+ 10 11 2 0\n+ 11 13 1 0\n+M END\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 7a4306d69801 test-data/input_v3000.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_v3000.sdf Mon May 04 07:41:13 2020 -0400 |
| b |
| b'@@ -0,0 +1,721 @@\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 13 13 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 C 9.879 -5.496 26.173 0\n+M V30 2 S 8.479 -4.341 26.068 0\n+M V30 3 O 7.191 -5.019 26.229 0\n+M V30 4 O 8.434 -3.443 27.212 0\n+M V30 5 N 8.496 -3.498 24.592 0\n+M V30 6 C 9.754 -3.034 24.058 0\n+M V30 7 C 9.568 -1.826 23.151 0\n+M V30 8 C 10.876 -1.05 23.144 0\n+M V30 9 C 11.906 -1.461 22.316 0\n+M V30 10 C 13.106 -0.779 22.318 0\n+M V30 11 C 13.277 0.318 23.15 0\n+M V30 12 C 12.242 0.732 23.981 0\n+M V30 13 C 11.039 0.041 23.983 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 1 2 1 CFG=1\n+M V30 2 2 2 3\n+M V30 3 2 2 4\n+M V30 4 1 2 5\n+M V30 5 1 5 6\n+M V30 6 1 6 7\n+M V30 7 1 7 8\n+M V30 8 2 8 9\n+M V30 9 1 8 13\n+M V30 10 1 9 10\n+M V30 11 2 10 11\n+M V30 12 1 11 12\n+M V30 13 2 13 12\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 16 17 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 C 9.522 5.385 22.964 0\n+M V30 2 C 10.691 5.736 23.881 0\n+M V30 3 O 10.466 6.316 24.874 0\n+M V30 4 N 12.074 5.388 23.622 0\n+M V30 5 C 12.492 4.65 22.451 0\n+M V30 6 C 13.176 3.375 22.918 0\n+M V30 7 C 12.21 2.317 23.457 0\n+M V30 8 C 11.139 2.487 24.321 0\n+M V30 9 N 10.572 1.301 24.525 0\n+M V30 10 C 11.236 0.338 23.821 0\n+M V30 11 C 11.03 -1.062 23.693 0\n+M V30 12 C 11.88 -1.812 22.883 0\n+M V30 13 C 12.929 -1.186 22.198 0\n+M V30 14 C 13.128 0.182 22.323 0\n+M V30 15 C 12.267 0.946 23.147 0\n+M V30 16 F 13.769 -1.898 21.404 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 1 1 2\n+M V30 2 2 2 3\n+M V30 3 1 2 4\n+M V30 4 1 4 5\n+M V30 5 1 5 6\n+M V30 6 1 6 7\n+M V30 7 2 7 8\n+M V30 8 1 7 15\n+M V30 9 1 8 9\n+M V30 10 1 9 10\n+M V30 11 2 15 10\n+M V30 12 1 10 11\n+M V30 13 2 11 12\n+M V30 14 1 12 13\n+M V30 15 2 13 14\n+M V30 16 1 13 16\n+M V30 17 1 15 14\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 11 11 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 C 10.164 -0.784 22.54 0\n+M V30 2 C 9.263 -0.157 21.478 0\n+M V30 3 O 9.587 0.859 20.967 0\n+M V30 4 N 8.014 -0.798 21.104 0\n+M V30 5 C 7.156 -0.207 20.089 0\n+M V30 6 C 7.523 -0.265 18.751 0\n+M V30 7 N 6.767 0.259 17.805 0\n+M V30 8 C 5.637 0.861 18.103 0\n+M V30 9 C 5.189 0.976 19.412 0\n+M V30 10 C 5.964 0.425 20.434 0\n+M V30 11 C 5.528 0.522 21.894 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 1 1 2\n+M V30 2 2 2 3\n+M V30 3 1 2 4\n+M V30 4 1 4 5\n+M V30 5 2 5 6\n+M V30 6 1 5 10\n+M V30 7 1 6 7\n+M V30 8 2 7 8\n+M V30 9 1 8 9\n+M V30 10 2 10 9\n+M V30 11 1 10 11\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 14 14 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 C 11.659 -1.502 21.806 0\n+M V30 2 O 12.321 -1.637 23.035 0\n+M V30 3 C 13.073 -0.525 23.444 0\n+M V30 4 O 14.218 -0.657 23.684 0\n+M V30 5 C 12.42 0.849 23.571 0\n+M V30 6 C 11.17 0.983 24.168 0\n+M V30 7 C 10.588 2.24 24.264 0\n+M V30 8 C 11.27 3.343 23.759 0\n+M V30 9 C 12.512 3.207 23.159 0\n+M V30 10 C 13.085 1.956 23.065 0\n+M V30 11 S 10.543 4.988 23.864 0\n+M V30 12 O 11.527 6.005 23.481 0\n+M V30 13 O 10.243 5.326 25.257 0\n+M V30 14 N 9.156 5.076 22.863 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 1 1 2\n+M V30 2 1 2 3\n+M V30 3 2 3 4\n+M V30 4 1 3 5\n+M V30 5 2 5 6\n+M V30 6 1 5 10\n+M V30 7 1 6 7\n+M V30 8 2 7 8\n+M V30 9 1 8 9\n+M V30 10 1 8 11\n+M V30 11 2 10 9\n+M V30 12 2 11 12\n+M V30 13 2 11 13\n+M V30 14 1 11 14 CFG=6\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 15 16 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 C 9.935 -0.519 25.099 0\n+M V30 2 N 11.151 -0.499 24.314 0\n+M V30 3 C 11.474 -1.689 23.578 0\n+M V30 4 C 12.697 -1.643 22.689 0\n+M V30 5 C 13.671 -0.515 22.98 0\n+M V30'..b'BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 7 7 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 N 3.785 2.023 19.567 0\n+M V30 2 C 4.751 1.187 19.156 0\n+M V30 3 C 5.193 0.102 19.956 0\n+M V30 4 N 6.118 -0.771 19.531 0\n+M V30 5 C 6.631 -0.544 18.275 0\n+M V30 6 N 6.296 0.461 17.443 0\n+M V30 7 C 5.36 1.316 17.878 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 1 1 2\n+M V30 2 2 2 3\n+M V30 3 1 2 7\n+M V30 4 1 3 4\n+M V30 5 2 4 5\n+M V30 6 1 5 6\n+M V30 7 2 7 6\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 15 16 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 N 9.956 1.422 21.355 0\n+M V30 2 C 9.817 0.455 21.963 0\n+M V30 3 O 7.362 -5.927 25.41 0\n+M V30 4 C 9.649 -0.698 22.751 0\n+M V30 5 N 10.264 -1.84 22.326 0\n+M V30 6 C 8.945 -0.599 23.939 0\n+M V30 7 N 9.593 -4.099 25.24 0\n+M V30 8 C 8.874 -1.71 24.773 0\n+M V30 9 C 9.513 -2.915 24.415 0\n+M V30 10 C 10.185 -2.902 23.147 0\n+M V30 11 C 9.955 -5.417 24.647 0\n+M V30 12 C 8.966 -5.922 23.59 0\n+M V30 13 C 7.501 -5.707 24.011 0\n+M V30 14 C 7.351 -4.8 26.252 0\n+M V30 15 C 8.767 -4.208 26.474 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 3 1 2\n+M V30 2 1 2 4\n+M V30 3 1 3 13\n+M V30 4 1 3 14\n+M V30 5 2 4 5\n+M V30 6 1 4 6\n+M V30 7 1 5 10\n+M V30 8 2 6 8\n+M V30 9 1 7 9\n+M V30 10 1 7 11\n+M V30 11 1 7 15\n+M V30 12 1 8 9\n+M V30 13 2 10 9\n+M V30 14 1 11 12\n+M V30 15 1 13 12\n+M V30 16 1 14 15\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 19 21 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 C 13.913 -1.259 23.223 0\n+M V30 2 N 12.511 -0.97 23.531 0\n+M V30 3 O 9.1 1.255 21.153 0\n+M V30 4 C 11.615 -1.933 22.877 0\n+M V30 5 N 9.924 -0.228 22.633 0\n+M V30 6 C 10.165 -1.584 23.119 0\n+M V30 7 N 6.783 0.288 17.839 0\n+M V30 8 C 10.742 0.736 23.359 0\n+M V30 9 N 4.786 1.469 18.505 0\n+M V30 10 C 12.197 0.405 23.135 0\n+M V30 11 C 9.159 0.102 21.578 0\n+M V30 12 C 8.378 -1.009 20.894 0\n+M V30 13 C 7.526 -0.403 19.832 0\n+M V30 14 C 7.768 -0.404 18.491 0\n+M V30 15 C 5.886 0.747 18.755 0\n+M V30 16 C 4.072 1.805 19.587 0\n+M V30 17 C 4.405 1.463 20.898 0\n+M V30 18 C 5.548 0.73 21.135 0\n+M V30 19 C 6.323 0.348 20.033 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 1 1 2\n+M V30 2 1 2 4\n+M V30 3 1 2 10\n+M V30 4 2 3 11\n+M V30 5 1 4 6\n+M V30 6 1 11 5\n+M V30 7 1 6 5\n+M V30 8 1 5 8\n+M V30 9 1 7 14\n+M V30 10 1 7 15\n+M V30 11 1 10 8\n+M V30 12 2 15 9\n+M V30 13 1 9 16\n+M V30 14 1 11 12\n+M V30 15 1 12 13\n+M V30 16 2 14 13\n+M V30 17 1 13 19\n+M V30 18 1 15 19\n+M V30 19 2 16 17\n+M V30 20 1 17 18\n+M V30 21 2 19 18\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n+\n+ OpenBabel04062010473D\n+\n+ 0 0 0 0 0 999 V3000\n+M V30 BEGIN CTAB\n+M V30 COUNTS 18 19 0 0 0\n+M V30 BEGIN ATOM\n+M V30 1 N 8.542 0.585 24.925 0\n+M V30 2 C 7.794 1.345 24.024 0\n+M V30 3 O 8.264 2.345 23.458 0\n+M V30 4 C 9.926 0.918 25.249 0\n+M V30 5 N 14.06 -1.853 20.555 0\n+M V30 6 O 3.564 0.957 23.673 0\n+M V30 7 C 10.845 0.299 24.235 0\n+M V30 8 N 6.425 0.845 23.815 0\n+M V30 9 C 12.007 0.962 23.85 0\n+M V30 10 C 12.855 0.386 22.907 0\n+M V30 11 C 12.521 -0.849 22.343 0\n+M V30 12 C 13.358 -1.419 21.358 0\n+M V30 13 C 11.363 -1.521 22.729 0\n+M V30 14 C 10.527 -0.946 23.677 0\n+M V30 15 C 5.572 0.728 25.043 0\n+M V30 16 C 4.14 0.228 24.742 0\n+M V30 17 C 4.307 0.927 22.472 0\n+M V30 18 C 5.702 1.537 22.715 0\n+M V30 END ATOM\n+M V30 BEGIN BOND\n+M V30 1 1 1 2\n+M V30 2 1 1 4\n+M V30 3 2 2 3\n+M V30 4 1 2 8\n+M V30 5 1 4 7\n+M V30 6 3 5 12\n+M V30 7 1 6 16\n+M V30 8 1 6 17\n+M V30 9 2 7 9\n+M V30 10 1 7 14\n+M V30 11 1 8 15\n+M V30 12 1 8 18\n+M V30 13 1 9 10\n+M V30 14 2 10 11\n+M V30 15 1 12 11\n+M V30 16 1 11 13\n+M V30 17 2 14 13\n+M V30 18 1 16 15\n+M V30 19 1 17 18\n+M V30 END BOND\n+M V30 END CTAB\n+M END\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 7a4306d69801 test-data/ligand.mol --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.mol Mon May 04 07:41:13 2020 -0400 |
| b |
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| diff -r 000000000000 -r 7a4306d69801 test-data/ligand.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.sdf Mon May 04 07:41:13 2020 -0400 |
| b |
| @@ -0,0 +1,116 @@ +1S3V + OpenBabel07031809403D + + 54 56 0 0 1 0 0 0 0 0999 V2000 + -0.0237 32.0851 0.4630 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0257 32.5701 2.5090 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5816 31.2781 2.5290 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2645 30.7721 3.8370 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.1514 29.5300 3.5680 C 0 0 1 0 0 0 0 0 0 0 0 0 + -2.3824 28.4990 2.7070 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7845 29.0260 1.3530 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3126 30.4241 1.4480 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6244 28.9840 4.9610 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2442 26.5599 4.7800 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.1391 25.6479 4.2580 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.8561 24.2849 4.1780 C 0 0 0 0 0 0 0 0 0 0 0 0 + -7.0120 23.8848 3.0290 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6611 23.8468 4.6560 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5581 22.0928 3.4830 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7132 24.7349 5.1800 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4583 25.1339 6.0060 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0123 26.0899 5.2580 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4676 30.8241 0.4170 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8412 32.3751 -0.5420 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2388 32.9722 1.4960 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2847 33.4632 3.4970 N 0 0 0 0 0 0 0 0 0 0 0 0 + -4.6273 27.9210 4.8320 N 0 0 0 0 0 0 0 0 0 0 0 0 + -5.8230 23.4168 3.6560 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.1441 22.5778 4.6930 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5192 24.2169 5.6340 O 0 0 0 0 0 0 0 0 0 0 0 0 + -6.0522 28.2910 4.7350 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8817 31.5647 4.2416 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4982 30.5088 4.5555 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0329 29.7742 2.9881 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0645 27.6908 2.4734 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5623 28.1183 3.3032 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5506 28.9693 0.5897 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9492 28.3958 1.0737 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0540 29.8010 5.5275 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7656 28.5900 5.4903 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.0962 26.0040 3.8974 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.7524 24.4932 2.1715 H 0 0 0 0 0 0 0 0 0 0 0 0 + -7.6062 23.0393 2.7052 H 0 0 0 0 0 0 0 0 0 0 0 0 + -7.5820 24.4781 3.7333 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7376 22.7384 3.1952 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1884 21.0868 3.6389 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3042 22.0856 2.6981 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8011 25.7764 6.8076 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4051 24.5711 6.3386 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1871 25.7386 5.1495 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2964 26.7805 5.6864 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2433 33.2980 -0.6110 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0822 31.6679 -1.2201 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8759 34.3850 3.4637 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.8862 33.2055 4.2651 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.2045 28.9156 3.8635 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.6528 27.3942 4.6458 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.3454 28.8348 5.6245 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 19 1 0 0 0 0 + 1 20 1 0 0 0 0 + 2 22 1 0 0 0 0 + 3 2 2 0 0 0 0 + 3 8 1 0 0 0 0 + 4 3 1 0 0 0 0 + 4 28 1 0 0 0 0 + 4 29 1 0 0 0 0 + 5 4 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 9 1 0 0 0 0 + 5 30 1 6 0 0 0 + 6 7 1 0 0 0 0 + 6 31 1 0 0 0 0 + 6 32 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 33 1 0 0 0 0 + 7 34 1 0 0 0 0 + 8 19 2 0 0 0 0 + 9 35 1 0 0 0 0 + 9 36 1 0 0 0 0 + 11 10 2 0 0 0 0 + 11 37 1 0 0 0 0 + 12 11 1 0 0 0 0 + 13 38 1 0 0 0 0 + 13 39 1 0 0 0 0 + 13 40 1 0 0 0 0 + 14 12 2 0 0 0 0 + 15 25 1 0 0 0 0 + 15 41 1 0 0 0 0 + 15 42 1 0 0 0 0 + 15 43 1 0 0 0 0 + 16 14 1 0 0 0 0 + 16 26 1 0 0 0 0 + 17 26 1 0 0 0 0 + 17 44 1 0 0 0 0 + 17 45 1 0 0 0 0 + 17 46 1 0 0 0 0 + 18 10 1 0 0 0 0 + 18 16 2 0 0 0 0 + 18 47 1 0 0 0 0 + 20 48 1 0 0 0 0 + 20 49 1 0 0 0 0 + 21 1 2 0 0 0 0 + 21 2 1 0 0 0 0 + 22 50 1 0 0 0 0 + 22 51 1 0 0 0 0 + 23 9 1 0 0 0 0 + 23 10 1 0 0 0 0 + 23 27 1 0 0 0 0 + 24 12 1 0 0 0 0 + 24 13 1 0 0 0 0 + 25 14 1 0 0 0 0 + 27 52 1 0 0 0 0 + 27 53 1 0 0 0 0 + 27 54 1 0 0 0 0 +M END +$$$$ |
| b |
| diff -r 000000000000 -r 7a4306d69801 test-data/ligands_names.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligands_names.sdf Mon May 04 07:41:13 2020 -0400 |
| b |
| @@ -0,0 +1,170 @@ +1-pyrimethamine + Cerius2 12180216023D 1 1.00000 + Structure written by MMmdl. + 30 31 0 0 0 0 0 0 0 0999 V2000 + -2.8357 0.2028 0.4209 N 0 0 0 0 0 0 + -2.8255 -1.1104 0.1969 C 0 0 0 0 0 0 + -1.7271 -1.8218 -0.0537 N 0 0 0 0 0 0 + -0.5417 -1.1654 -0.0884 C 0 0 0 0 0 0 + -0.4439 0.2086 0.1358 C 0 0 0 0 0 0 + -1.6550 0.8467 0.4052 C 0 0 0 0 0 0 + 0.8362 0.9302 0.0951 C 0 0 0 0 0 0 + 1.6327 1.0444 1.2466 C 0 0 0 0 0 0 + 2.8536 1.7244 1.2069 C 0 0 0 0 0 0 + 3.2885 2.2979 0.0146 C 0 0 0 0 0 0 + 2.5126 2.1980 -1.1375 C 0 0 0 0 0 0 + 1.2918 1.5178 -1.0966 C 0 0 0 0 0 0 + -4.0141 -1.7715 0.2232 N 0 0 0 0 0 0 + -1.7348 2.2137 0.6034 N 0 0 0 0 0 0 + 4.7918 3.1344 -0.0351 Cl 0 0 0 0 0 0 + 0.4261 -3.4744 -0.6318 C 0 0 0 0 0 0 + 0.6932 -1.9936 -0.3864 C 0 0 0 0 0 0 + 1.3065 0.6014 2.1872 H 0 0 0 0 0 0 + 3.4548 1.8000 2.1100 H 0 0 0 0 0 0 + 2.8462 2.6451 -2.0710 H 0 0 0 0 0 0 + 0.6948 1.4500 -2.0056 H 0 0 0 0 0 0 + -4.0348 -2.7663 0.0556 H 0 0 0 0 0 0 + -4.8657 -1.2631 0.4089 H 0 0 0 0 0 0 + -0.9674 2.6820 1.0738 H 0 0 0 0 0 0 + -2.6605 2.5780 0.8038 H 0 0 0 0 0 0 + 1.3655 -3.9964 -0.8406 H 0 0 0 0 0 0 + -0.2391 -3.6219 -1.4893 H 0 0 0 0 0 0 + -0.0337 -3.9462 0.2432 H 0 0 0 0 0 0 + 1.3880 -1.9081 0.4572 H 0 0 0 0 0 0 + 1.1868 -1.5858 -1.2763 H 0 0 0 0 0 0 + 1 2 2 0 0 0 + 1 6 1 0 0 0 + 2 3 1 0 0 0 + 2 13 1 0 0 0 + 3 4 2 0 0 0 + 4 5 1 0 0 0 + 4 17 1 0 0 0 + 5 6 2 0 0 0 + 5 7 1 0 0 0 + 6 14 1 0 0 0 + 7 8 2 0 0 0 + 7 12 1 0 0 0 + 8 9 1 0 0 0 + 8 18 1 0 0 0 + 9 10 2 0 0 0 + 9 19 1 0 0 0 + 10 11 1 0 0 0 + 10 15 1 0 0 0 + 11 12 2 0 0 0 + 11 20 1 0 0 0 + 12 21 1 0 0 0 + 13 22 1 0 0 0 + 13 23 1 0 0 0 + 14 24 1 0 0 0 + 14 25 1 0 0 0 + 16 17 1 0 0 0 + 16 26 1 0 0 0 + 16 27 1 0 0 0 + 16 28 1 0 0 0 + 17 29 1 0 0 0 + 17 30 1 0 0 0 +M END +> <Name> +1-pyrimethamine + +> <Family> +A + +> <PC_uM> +3.7 + +> <TG_uM> +0.39 + +> <RL_uM> +2.3 + +> <set> +1 + +$$$$ +1-3062 + Cerius2 12180216023D 1 1.00000 + Structure written by MMmdl. + 30 31 0 0 0 0 0 0 0 0999 V2000 + -2.8168 0.2065 0.4735 N 0 0 0 0 0 0 + -2.8206 -1.1045 0.2371 C 0 0 0 0 0 0 + -1.7327 -1.8208 -0.0438 N 0 0 0 0 0 0 + -0.5439 -1.1720 -0.0988 C 0 0 0 0 0 0 + -0.4317 0.1989 0.1374 C 0 0 0 0 0 0 + -1.6324 0.8424 0.4390 C 0 0 0 0 0 0 + 0.8521 0.9130 0.0752 C 0 0 0 0 0 0 + 1.6858 0.9917 1.2029 C 0 0 0 0 0 0 + 2.9119 1.6650 1.1430 C 0 0 0 0 0 0 + 3.3184 2.2713 -0.0498 C 0 0 0 0 0 0 + 2.4965 2.2018 -1.1763 C 0 0 0 0 0 0 + 1.2730 1.5284 -1.1135 C 0 0 0 0 0 0 + -4.0128 -1.7579 0.2830 N 0 0 0 0 0 0 + -1.6980 2.2076 0.6534 N 0 0 0 0 0 0 + 4.8189 3.1175 -0.1945 Cl 0 0 0 0 0 0 + 0.3929 -3.4780 -0.7058 C 0 0 0 0 0 0 + 0.6782 -2.0057 -0.4320 C 0 0 0 0 0 0 + 3.8777 1.7088 2.5773 Cl 0 0 0 0 0 0 + 1.3763 0.5224 2.1357 H 0 0 0 0 0 0 + 2.7982 2.6697 -2.1110 H 0 0 0 0 0 0 + 0.6467 1.4886 -2.0046 H 0 0 0 0 0 0 + -4.0437 -2.7510 0.1067 H 0 0 0 0 0 0 + -4.8568 -1.2458 0.4914 H 0 0 0 0 0 0 + -0.9218 2.6660 1.1184 H 0 0 0 0 0 0 + -2.6181 2.5747 0.8742 H 0 0 0 0 0 0 + 1.3238 -4.0040 -0.9412 H 0 0 0 0 0 0 + -0.2872 -3.5999 -1.5556 H 0 0 0 0 0 0 + -0.0575 -3.9650 0.1657 H 0 0 0 0 0 0 + 1.3854 -1.9447 0.4035 H 0 0 0 0 0 0 + 1.1636 -1.5839 -1.3199 H 0 0 0 0 0 0 + 1 2 2 0 0 0 + 1 6 1 0 0 0 + 2 3 1 0 0 0 + 2 13 1 0 0 0 + 3 4 2 0 0 0 + 4 5 1 0 0 0 + 4 17 1 0 0 0 + 5 6 2 0 0 0 + 5 7 1 0 0 0 + 6 14 1 0 0 0 + 7 8 2 0 0 0 + 7 12 1 0 0 0 + 8 9 1 0 0 0 + 8 19 1 0 0 0 + 9 10 2 0 0 0 + 9 18 1 0 0 0 + 10 11 1 0 0 0 + 10 15 1 0 0 0 + 11 12 2 0 0 0 + 11 20 1 0 0 0 + 12 21 1 0 0 0 + 13 22 1 0 0 0 + 13 23 1 0 0 0 + 14 24 1 0 0 0 + 14 25 1 0 0 0 + 16 17 1 0 0 0 + 16 26 1 0 0 0 + 16 27 1 0 0 0 + 16 28 1 0 0 0 + 17 29 1 0 0 0 + 17 30 1 0 0 0 +M END +> <Name> +1-3062 + +> <Family> +A + +> <PC_uM> +1.08 + +> <TG_uM> +0.094 + +> <RL_uM> +0.19 + +> <set> +0 + +$$$$ |
| b |
| diff -r 000000000000 -r 7a4306d69801 test-data/ligands_nonames.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligands_nonames.sdf Mon May 04 07:41:13 2020 -0400 |
| b |
| @@ -0,0 +1,170 @@ + + Cerius2 12180216023D 1 1.00000 + Structure written by MMmdl. + 30 31 0 0 0 0 0 0 0 0999 V2000 + -2.8357 0.2028 0.4209 N 0 0 0 0 0 0 + -2.8255 -1.1104 0.1969 C 0 0 0 0 0 0 + -1.7271 -1.8218 -0.0537 N 0 0 0 0 0 0 + -0.5417 -1.1654 -0.0884 C 0 0 0 0 0 0 + -0.4439 0.2086 0.1358 C 0 0 0 0 0 0 + -1.6550 0.8467 0.4052 C 0 0 0 0 0 0 + 0.8362 0.9302 0.0951 C 0 0 0 0 0 0 + 1.6327 1.0444 1.2466 C 0 0 0 0 0 0 + 2.8536 1.7244 1.2069 C 0 0 0 0 0 0 + 3.2885 2.2979 0.0146 C 0 0 0 0 0 0 + 2.5126 2.1980 -1.1375 C 0 0 0 0 0 0 + 1.2918 1.5178 -1.0966 C 0 0 0 0 0 0 + -4.0141 -1.7715 0.2232 N 0 0 0 0 0 0 + -1.7348 2.2137 0.6034 N 0 0 0 0 0 0 + 4.7918 3.1344 -0.0351 Cl 0 0 0 0 0 0 + 0.4261 -3.4744 -0.6318 C 0 0 0 0 0 0 + 0.6932 -1.9936 -0.3864 C 0 0 0 0 0 0 + 1.3065 0.6014 2.1872 H 0 0 0 0 0 0 + 3.4548 1.8000 2.1100 H 0 0 0 0 0 0 + 2.8462 2.6451 -2.0710 H 0 0 0 0 0 0 + 0.6948 1.4500 -2.0056 H 0 0 0 0 0 0 + -4.0348 -2.7663 0.0556 H 0 0 0 0 0 0 + -4.8657 -1.2631 0.4089 H 0 0 0 0 0 0 + -0.9674 2.6820 1.0738 H 0 0 0 0 0 0 + -2.6605 2.5780 0.8038 H 0 0 0 0 0 0 + 1.3655 -3.9964 -0.8406 H 0 0 0 0 0 0 + -0.2391 -3.6219 -1.4893 H 0 0 0 0 0 0 + -0.0337 -3.9462 0.2432 H 0 0 0 0 0 0 + 1.3880 -1.9081 0.4572 H 0 0 0 0 0 0 + 1.1868 -1.5858 -1.2763 H 0 0 0 0 0 0 + 1 2 2 0 0 0 + 1 6 1 0 0 0 + 2 3 1 0 0 0 + 2 13 1 0 0 0 + 3 4 2 0 0 0 + 4 5 1 0 0 0 + 4 17 1 0 0 0 + 5 6 2 0 0 0 + 5 7 1 0 0 0 + 6 14 1 0 0 0 + 7 8 2 0 0 0 + 7 12 1 0 0 0 + 8 9 1 0 0 0 + 8 18 1 0 0 0 + 9 10 2 0 0 0 + 9 19 1 0 0 0 + 10 11 1 0 0 0 + 10 15 1 0 0 0 + 11 12 2 0 0 0 + 11 20 1 0 0 0 + 12 21 1 0 0 0 + 13 22 1 0 0 0 + 13 23 1 0 0 0 + 14 24 1 0 0 0 + 14 25 1 0 0 0 + 16 17 1 0 0 0 + 16 26 1 0 0 0 + 16 27 1 0 0 0 + 16 28 1 0 0 0 + 17 29 1 0 0 0 + 17 30 1 0 0 0 +M END +> <Name> +1-pyrimethamine + +> <Family> +A + +> <PC_uM> +3.7 + +> <TG_uM> +0.39 + +> <RL_uM> +2.3 + +> <set> +1 + +$$$$ + + Cerius2 12180216023D 1 1.00000 + Structure written by MMmdl. + 30 31 0 0 0 0 0 0 0 0999 V2000 + -2.8168 0.2065 0.4735 N 0 0 0 0 0 0 + -2.8206 -1.1045 0.2371 C 0 0 0 0 0 0 + -1.7327 -1.8208 -0.0438 N 0 0 0 0 0 0 + -0.5439 -1.1720 -0.0988 C 0 0 0 0 0 0 + -0.4317 0.1989 0.1374 C 0 0 0 0 0 0 + -1.6324 0.8424 0.4390 C 0 0 0 0 0 0 + 0.8521 0.9130 0.0752 C 0 0 0 0 0 0 + 1.6858 0.9917 1.2029 C 0 0 0 0 0 0 + 2.9119 1.6650 1.1430 C 0 0 0 0 0 0 + 3.3184 2.2713 -0.0498 C 0 0 0 0 0 0 + 2.4965 2.2018 -1.1763 C 0 0 0 0 0 0 + 1.2730 1.5284 -1.1135 C 0 0 0 0 0 0 + -4.0128 -1.7579 0.2830 N 0 0 0 0 0 0 + -1.6980 2.2076 0.6534 N 0 0 0 0 0 0 + 4.8189 3.1175 -0.1945 Cl 0 0 0 0 0 0 + 0.3929 -3.4780 -0.7058 C 0 0 0 0 0 0 + 0.6782 -2.0057 -0.4320 C 0 0 0 0 0 0 + 3.8777 1.7088 2.5773 Cl 0 0 0 0 0 0 + 1.3763 0.5224 2.1357 H 0 0 0 0 0 0 + 2.7982 2.6697 -2.1110 H 0 0 0 0 0 0 + 0.6467 1.4886 -2.0046 H 0 0 0 0 0 0 + -4.0437 -2.7510 0.1067 H 0 0 0 0 0 0 + -4.8568 -1.2458 0.4914 H 0 0 0 0 0 0 + -0.9218 2.6660 1.1184 H 0 0 0 0 0 0 + -2.6181 2.5747 0.8742 H 0 0 0 0 0 0 + 1.3238 -4.0040 -0.9412 H 0 0 0 0 0 0 + -0.2872 -3.5999 -1.5556 H 0 0 0 0 0 0 + -0.0575 -3.9650 0.1657 H 0 0 0 0 0 0 + 1.3854 -1.9447 0.4035 H 0 0 0 0 0 0 + 1.1636 -1.5839 -1.3199 H 0 0 0 0 0 0 + 1 2 2 0 0 0 + 1 6 1 0 0 0 + 2 3 1 0 0 0 + 2 13 1 0 0 0 + 3 4 2 0 0 0 + 4 5 1 0 0 0 + 4 17 1 0 0 0 + 5 6 2 0 0 0 + 5 7 1 0 0 0 + 6 14 1 0 0 0 + 7 8 2 0 0 0 + 7 12 1 0 0 0 + 8 9 1 0 0 0 + 8 19 1 0 0 0 + 9 10 2 0 0 0 + 9 18 1 0 0 0 + 10 11 1 0 0 0 + 10 15 1 0 0 0 + 11 12 2 0 0 0 + 11 20 1 0 0 0 + 12 21 1 0 0 0 + 13 22 1 0 0 0 + 13 23 1 0 0 0 + 14 24 1 0 0 0 + 14 25 1 0 0 0 + 16 17 1 0 0 0 + 16 26 1 0 0 0 + 16 27 1 0 0 0 + 16 28 1 0 0 0 + 17 29 1 0 0 0 + 17 30 1 0 0 0 +M END +> <Name> +1-3062 + +> <Family> +A + +> <PC_uM> +1.08 + +> <TG_uM> +0.094 + +> <RL_uM> +0.19 + +> <set> +0 + +$$$$ |
| b |
| diff -r 000000000000 -r 7a4306d69801 test-data/poses-ascending.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poses-ascending.sdf Mon May 04 07:41:13 2020 -0400 |
| b |
| @@ -0,0 +1,130 @@ +COCC(C)C(CCl)c1cccc(Br)c1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 15 15 0 0 0 0 0 0 0 0999 V2000 + 10.1119 -3.9277 5.3225 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.0310 -3.0413 5.0553 O 0 0 0 0 0 0 0 0 0 0 0 0 + 7.9945 -3.7187 4.3397 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8246 -2.7535 4.0816 C 0 0 1 0 0 0 0 0 0 0 0 0 + 5.7024 -3.4607 3.3058 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3075 -2.0336 5.3805 C 0 0 1 0 0 0 0 0 0 0 0 0 + 5.2468 -0.9323 5.0952 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.6163 -0.0866 6.5353 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9603 -2.9922 6.5383 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.7490 -3.7097 6.5798 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4577 -4.5984 7.6187 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.3584 -4.7793 8.6615 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.5372 -4.0453 8.6712 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.7688 -4.2708 10.0891 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8278 -3.1495 7.6389 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 6 0 0 0 + 6 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 10 1 0 0 0 0 + 9 15 2 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 1 0 0 0 0 +M END +> <Name> +COCC(C)C(CCl)c1cccc(Br)c1 + +> <TransFSScore> +0.000052 + +$$$$ +COCC(C)C(CO)c1ccc(Br)cc1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 16 16 0 0 0 0 0 0 0 0999 V2000 + 8.0891 -17.4910 5.6428 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.7776 -17.2166 6.8572 O 0 0 0 0 0 0 0 0 0 0 0 0 + 9.8614 -18.1239 7.0701 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.5740 -17.7750 8.3957 C 0 0 1 0 0 0 0 0 0 0 0 0 + 9.6152 -18.0787 9.5619 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.9364 -18.5267 8.5391 C 0 0 1 0 0 0 0 0 0 0 0 0 + 11.7889 -20.0488 8.2998 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.0437 -20.6799 9.3396 O 0 0 0 0 0 0 0 0 0 0 0 0 + 13.0327 -17.9696 7.6253 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.1839 -17.4039 8.2015 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.2110 -16.8983 7.4013 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.0973 -16.9557 6.0161 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.4814 -16.2619 4.9318 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 13.9696 -17.5220 5.4242 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.9423 -18.0292 6.2262 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.5383 -20.5488 10.1686 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 6 0 0 0 + 6 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 16 1 0 0 0 0 + 9 10 1 0 0 0 0 + 9 15 2 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 1 0 0 0 0 + 12 14 2 0 0 0 0 + 14 15 1 0 0 0 0 +M END +> <Name> +COCC(C)C(CO)c1ccc(Br)cc1 + +> <TransFSScore> +0.000113 + +$$$$ +COCC(C)OCCOc1ccc(Br)cc1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 16 16 0 0 0 0 0 0 0 0999 V2000 + -3.9406 -3.6524 26.0345 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0091 -3.2577 25.0376 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6782 -3.1793 25.5508 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7080 -2.7487 24.4377 C 0 0 1 0 0 0 0 0 0 0 0 0 + -1.0018 -1.3118 24.0009 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6316 -2.8817 24.9410 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0553 -4.2385 25.0759 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3836 -4.2980 25.8222 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7118 -5.6728 26.0281 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.8212 -5.9445 26.7790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9743 -5.1619 26.8458 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0387 -5.5484 27.6691 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9457 -6.7188 28.4197 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3792 -7.2299 29.5403 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8038 -7.5103 28.3520 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7442 -7.1209 27.5286 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 10 16 2 0 0 0 0 + 11 12 2 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 2 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <Name> +COCC(C)OCCOc1ccc(Br)cc1 + +> <TransFSScore> +0.029289 + +$$$$ |
| b |
| diff -r 000000000000 -r 7a4306d69801 test-data/poses-desc-noglobal.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poses-desc-noglobal.sdf Mon May 04 07:41:13 2020 -0400 |
| b |
| @@ -0,0 +1,130 @@ +COCC(C)C(CCl)c1cccc(Br)c1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 15 15 0 0 0 0 0 0 0 0999 V2000 + 10.5975 -1.6265 24.3456 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9876 -2.4972 23.3994 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.5655 -2.3484 23.4275 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.9288 -3.2311 22.3401 C 0 0 1 0 0 0 0 0 0 0 0 0 + 8.0397 -4.7166 22.7175 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4621 -2.8051 21.9660 C 0 0 1 0 0 0 0 0 0 0 0 0 + 5.4266 -3.1085 23.0863 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5671 -2.0982 24.5513 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3532 -1.4007 21.3371 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4668 -0.2249 22.1042 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3963 1.0427 21.5193 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1859 1.1744 20.1518 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0190 0.0317 19.3806 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7201 0.1935 17.5198 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0801 -1.2369 19.9634 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 1 0 0 0 + 6 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 10 1 0 0 0 0 + 9 15 2 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 1 0 0 0 0 +M END +> <Name> +COCC(C)C(CCl)c1cccc(Br)c1 + +> <TransFSScore> +0.258377 + +$$$$ +COCC(C)C(CO)c1ccc(Br)cc1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 16 16 0 0 0 0 0 0 0 0999 V2000 + 5.1209 -3.0737 26.6189 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2470 -2.2997 25.4319 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6087 -2.1896 25.0116 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6915 -1.2882 23.7597 C 0 0 1 0 0 0 0 0 0 0 0 0 + 8.1245 -0.7354 23.6481 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2475 -2.0456 22.4671 C 0 0 1 0 0 0 0 0 0 0 0 0 + 4.8752 -2.7399 22.6419 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9977 -4.0000 23.2991 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2126 -1.1502 21.2243 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1393 -1.7450 19.9523 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0915 -0.9617 18.7969 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1145 0.4251 18.9029 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0611 1.4863 17.3396 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1760 1.0355 20.1544 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2225 0.2504 21.3109 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0953 -4.3353 23.4490 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 6 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 1 0 0 0 + 6 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 16 1 0 0 0 0 + 9 10 1 0 0 0 0 + 9 15 2 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 1 0 0 0 0 + 12 14 2 0 0 0 0 + 14 15 1 0 0 0 0 +M END +> <Name> +COCC(C)C(CO)c1ccc(Br)cc1 + +> <TransFSScore> +0.173348 + +$$$$ +COCC(C)OCCOc1ccc(Br)cc1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 16 16 0 0 0 0 0 0 0 0999 V2000 + 5.6650 -5.5958 25.3680 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.1057 -4.4972 26.0732 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0785 -3.4881 26.3491 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4358 -2.3388 27.1440 C 0 0 1 0 0 0 0 0 0 0 0 0 + 4.9482 -2.8397 28.5054 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4151 -1.2967 27.2873 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6267 -0.5481 26.0900 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.3817 0.2676 25.7585 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.6866 1.1011 24.6394 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7821 0.4960 23.4174 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7162 -0.8770 23.1782 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.8146 -1.3676 21.8707 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9820 -0.4818 20.8080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1007 -1.1472 19.0431 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0584 0.8879 21.0380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9602 1.3731 22.3447 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 10 16 2 0 0 0 0 + 11 12 2 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 2 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <Name> +COCC(C)OCCOc1ccc(Br)cc1 + +> <TransFSScore> +0.900000 + +$$$$ |
| b |
| diff -r 000000000000 -r 7a4306d69801 test-data/poses-descending.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poses-descending.sdf Mon May 04 07:41:13 2020 -0400 |
| b |
| @@ -0,0 +1,130 @@ +COCC(C)OCCOc1ccc(Br)cc1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 16 16 0 0 0 0 0 0 0 0999 V2000 + 5.6650 -5.5958 25.3680 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.1057 -4.4972 26.0732 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0785 -3.4881 26.3491 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4358 -2.3388 27.1440 C 0 0 1 0 0 0 0 0 0 0 0 0 + 4.9482 -2.8397 28.5054 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4151 -1.2967 27.2873 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6267 -0.5481 26.0900 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.3817 0.2676 25.7585 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.6866 1.1011 24.6394 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7821 0.4960 23.4174 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7162 -0.8770 23.1782 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.8146 -1.3676 21.8707 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9820 -0.4818 20.8080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1007 -1.1472 19.0431 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0584 0.8879 21.0380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9602 1.3731 22.3447 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 10 16 2 0 0 0 0 + 11 12 2 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 2 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <Name> +COCC(C)OCCOc1ccc(Br)cc1 + +> <TransFSScore> +0.900000 + +$$$$ +COCC(C)C(CCl)c1cccc(Br)c1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 15 15 0 0 0 0 0 0 0 0999 V2000 + 10.5975 -1.6265 24.3456 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9876 -2.4972 23.3994 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.5655 -2.3484 23.4275 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.9288 -3.2311 22.3401 C 0 0 1 0 0 0 0 0 0 0 0 0 + 8.0397 -4.7166 22.7175 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4621 -2.8051 21.9660 C 0 0 1 0 0 0 0 0 0 0 0 0 + 5.4266 -3.1085 23.0863 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5671 -2.0982 24.5513 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3532 -1.4007 21.3371 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4668 -0.2249 22.1042 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3963 1.0427 21.5193 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1859 1.1744 20.1518 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0190 0.0317 19.3806 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7201 0.1935 17.5198 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0801 -1.2369 19.9634 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 1 0 0 0 + 6 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 10 1 0 0 0 0 + 9 15 2 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 1 0 0 0 0 +M END +> <Name> +COCC(C)C(CCl)c1cccc(Br)c1 + +> <TransFSScore> +0.258377 + +$$$$ +COCC(C)C(CO)c1ccc(Br)cc1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 16 16 0 0 0 0 0 0 0 0999 V2000 + 5.1209 -3.0737 26.6189 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2470 -2.2997 25.4319 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6087 -2.1896 25.0116 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6915 -1.2882 23.7597 C 0 0 1 0 0 0 0 0 0 0 0 0 + 8.1245 -0.7354 23.6481 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2475 -2.0456 22.4671 C 0 0 1 0 0 0 0 0 0 0 0 0 + 4.8752 -2.7399 22.6419 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9977 -4.0000 23.2991 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2126 -1.1502 21.2243 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1393 -1.7450 19.9523 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0915 -0.9617 18.7969 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1145 0.4251 18.9029 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0611 1.4863 17.3396 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1760 1.0355 20.1544 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2225 0.2504 21.3109 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0953 -4.3353 23.4490 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 6 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 1 0 0 0 + 6 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 16 1 0 0 0 0 + 9 10 1 0 0 0 0 + 9 15 2 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 1 0 0 0 0 + 12 14 2 0 0 0 0 + 14 15 1 0 0 0 0 +M END +> <Name> +COCC(C)C(CO)c1ccc(Br)cc1 + +> <TransFSScore> +0.173348 + +$$$$ |
| b |
| diff -r 000000000000 -r 7a4306d69801 test-data/poses-filt-0.2.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poses-filt-0.2.sdf Mon May 04 07:41:13 2020 -0400 |
| b |
| @@ -0,0 +1,86 @@ +COCC(C)OCCOc1ccc(Br)cc1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 16 16 0 0 0 0 0 0 0 0999 V2000 + 1.5854 -4.4167 26.8713 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.9171 -3.9650 27.0697 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.3204 -3.0325 26.0654 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0629 -3.7637 24.9341 C 0 0 1 0 0 0 0 0 0 0 0 0 + 3.0725 -4.5314 24.0556 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.7894 -2.7836 24.1743 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.8770 -3.3338 23.4307 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3647 -2.3248 22.3968 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2636 -1.9969 21.5481 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5320 -1.2441 20.4392 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2993 -1.6247 19.1173 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.6084 -0.7491 18.0695 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1526 0.5029 18.3492 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.5557 1.6873 16.9327 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3970 0.8871 19.6636 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0874 0.0098 20.7062 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 6 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 10 16 2 0 0 0 0 + 11 12 2 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 2 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <Name> +COCC(C)OCCOc1ccc(Br)cc1 + +> <TransFSScore> +0.239591 + +$$$$ +COCC(C)C(CCl)c1cccc(Br)c1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 15 15 0 0 0 0 0 0 0 0999 V2000 + 10.5975 -1.6265 24.3456 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9876 -2.4972 23.3994 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.5655 -2.3484 23.4275 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.9288 -3.2311 22.3401 C 0 0 1 0 0 0 0 0 0 0 0 0 + 8.0397 -4.7166 22.7175 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4621 -2.8051 21.9660 C 0 0 1 0 0 0 0 0 0 0 0 0 + 5.4266 -3.1085 23.0863 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5671 -2.0982 24.5513 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3532 -1.4007 21.3371 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4668 -0.2249 22.1042 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3963 1.0427 21.5193 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1859 1.1744 20.1518 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0190 0.0317 19.3806 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7201 0.1935 17.5198 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0801 -1.2369 19.9634 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 1 0 0 0 + 6 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 10 1 0 0 0 0 + 9 15 2 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 1 0 0 0 0 +M END +> <Name> +COCC(C)C(CCl)c1cccc(Br)c1 + +> <TransFSScore> +0.258377 + +$$$$ |
| b |
| diff -r 000000000000 -r 7a4306d69801 test-data/poses-filt-only.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poses-filt-only.sdf Mon May 04 07:41:13 2020 -0400 |
| b |
| @@ -0,0 +1,130 @@ +COCC(C)C(CCl)c1cccc(Br)c1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 15 15 0 0 0 0 0 0 0 0999 V2000 + 10.5975 -1.6265 24.3456 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9876 -2.4972 23.3994 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.5655 -2.3484 23.4275 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.9288 -3.2311 22.3401 C 0 0 1 0 0 0 0 0 0 0 0 0 + 8.0397 -4.7166 22.7175 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4621 -2.8051 21.9660 C 0 0 1 0 0 0 0 0 0 0 0 0 + 5.4266 -3.1085 23.0863 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5671 -2.0982 24.5513 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3532 -1.4007 21.3371 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4668 -0.2249 22.1042 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3963 1.0427 21.5193 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1859 1.1744 20.1518 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0190 0.0317 19.3806 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7201 0.1935 17.5198 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0801 -1.2369 19.9634 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 1 0 0 0 + 6 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 10 1 0 0 0 0 + 9 15 2 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 1 0 0 0 0 +M END +> <Name> +COCC(C)C(CCl)c1cccc(Br)c1 + +> <TransFSScore> +0.258377 + +$$$$ +COCC(C)OCCOc1ccc(Br)cc1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 16 16 0 0 0 0 0 0 0 0999 V2000 + 1.5854 -4.4167 26.8713 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.9171 -3.9650 27.0697 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.3204 -3.0325 26.0654 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0629 -3.7637 24.9341 C 0 0 1 0 0 0 0 0 0 0 0 0 + 3.0725 -4.5314 24.0556 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.7894 -2.7836 24.1743 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.8770 -3.3338 23.4307 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3647 -2.3248 22.3968 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2636 -1.9969 21.5481 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5320 -1.2441 20.4392 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2993 -1.6247 19.1173 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.6084 -0.7491 18.0695 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1526 0.5029 18.3492 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.5557 1.6873 16.9327 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3970 0.8871 19.6636 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0874 0.0098 20.7062 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 6 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 10 16 2 0 0 0 0 + 11 12 2 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 2 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <Name> +COCC(C)OCCOc1ccc(Br)cc1 + +> <TransFSScore> +0.239591 + +$$$$ +COCC(C)OCCOc1ccc(Br)cc1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 16 16 0 0 0 0 0 0 0 0999 V2000 + 5.6650 -5.5958 25.3680 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.1057 -4.4972 26.0732 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0785 -3.4881 26.3491 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4358 -2.3388 27.1440 C 0 0 1 0 0 0 0 0 0 0 0 0 + 4.9482 -2.8397 28.5054 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4151 -1.2967 27.2873 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6267 -0.5481 26.0900 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.3817 0.2676 25.7585 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.6866 1.1011 24.6394 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7821 0.4960 23.4174 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7162 -0.8770 23.1782 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.8146 -1.3676 21.8707 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9820 -0.4818 20.8080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1007 -1.1472 19.0431 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0584 0.8879 21.0380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9602 1.3731 22.3447 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 10 16 2 0 0 0 0 + 11 12 2 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 2 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <Name> +COCC(C)OCCOc1ccc(Br)cc1 + +> <TransFSScore> +0.900000 + +$$$$ |
| b |
| diff -r 000000000000 -r 7a4306d69801 test-data/poses.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poses.sdf Mon May 04 07:41:13 2020 -0400 |
| b |
| b'@@ -0,0 +1,2730 @@\n+COCC(C)C(CCl)c1cccc(Br)c1\n+ OpenBabel03162018053D\n+libRbt.so/2013.1/901 2013/11/27\n+ 15 15 0 0 0 0 0 0 0 0999 V2000\n+ 10.5975 -1.6265 24.3456 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.9876 -2.4972 23.3994 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.5655 -2.3484 23.4275 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.9288 -3.2311 22.3401 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 8.0397 -4.7166 22.7175 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.4621 -2.8051 21.9660 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 5.4266 -3.1085 23.0863 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.5671 -2.0982 24.5513 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3532 -1.4007 21.3371 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.4668 -0.2249 22.1042 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3963 1.0427 21.5193 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.1859 1.1744 20.1518 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0190 0.0317 19.3806 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7201 0.1935 17.5198 Br 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0801 -1.2369 19.9634 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 5 1 1 0 0 0\n+ 4 6 1 0 0 0 0\n+ 6 7 1 1 0 0 0\n+ 6 9 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 9 10 1 0 0 0 0\n+ 9 15 2 0 0 0 0\n+ 10 11 2 0 0 0 0\n+ 11 12 1 0 0 0 0\n+ 12 13 2 0 0 0 0\n+ 13 14 1 0 0 0 0\n+ 13 15 1 0 0 0 0\n+M END\n+> <Name>\n+COCC(C)C(CCl)c1cccc(Br)c1\n+\n+> <TransFSScore>\n+0.258377\n+\n+$$$$\n+COCC(C)C(CCl)c1cccc(Br)c1\n+ OpenBabel03162018053D\n+libRbt.so/2013.1/901 2013/11/27\n+ 15 15 0 0 0 0 0 0 0 0999 V2000\n+ 5.6183 -0.0012 26.1615 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.1674 -1.0474 25.3681 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1412 -1.6856 24.6032 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7556 -2.7964 23.7339 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 4.6702 -3.4858 22.8925 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.9796 -2.3138 22.8727 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 7.6828 -3.4659 22.0996 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.1636 -4.8702 23.0913 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.7068 -1.0412 22.0446 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.9589 0.2496 22.5488 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.7362 1.3947 21.7787 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.2313 1.2861 20.4884 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.9256 0.0281 19.9861 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.2267 -0.1367 18.2360 Br 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.1388 -1.1182 20.7563 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 5 1 6 0 0 0\n+ 4 6 1 0 0 0 0\n+ 6 7 1 6 0 0 0\n+ 6 9 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 9 10 1 0 0 0 0\n+ 9 15 2 0 0 0 0\n+ 10 11 2 0 0 0 0\n+ 11 12 1 0 0 0 0\n+ 12 13 2 0 0 0 0\n+ 13 14 1 0 0 0 0\n+ 13 15 1 0 0 0 0\n+M END\n+> <Name>\n+COCC(C)C(CCl)c1cccc(Br)c1\n+\n+> <TransFSScore>\n+0.047733\n+\n+$$$$\n+COCC(C)C(CCl)c1cccc(Br)c1\n+ OpenBabel03162018053D\n+libRbt.so/2013.1/901 2013/11/27\n+ 15 15 0 0 0 0 0 0 0 0999 V2000\n+ 7.9912 -4.2501 22.2375 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.3105 -3.3249 23.0780 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.2107 -2.3148 23.5412 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.4791 -1.3723 24.5125 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 8.4280 -0.2734 25.0159 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.1337 -0.7983 23.9352 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 5.3067 0.0046 24.9796 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.6297 -0.9578 26.3221 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.2752 -0.1245 22.5547 C 0 0 0 0 '..b'-1.1938 19.3289 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.9926 -1.8088 20.5659 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 5 1 6 0 0 0\n+ 4 6 1 0 0 0 0\n+ 6 7 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 8 9 1 0 0 0 0\n+ 9 10 1 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 10 16 2 0 0 0 0\n+ 11 12 2 0 0 0 0\n+ 12 13 1 0 0 0 0\n+ 13 14 1 0 0 0 0\n+ 13 15 2 0 0 0 0\n+ 15 16 1 0 0 0 0\n+M END\n+> <Name>\n+COCC(C)OCCOc1ccc(Br)cc1\n+\n+> <TransFSScore>\n+0.052545\n+\n+$$$$\n+COCC(C)OCCOc1ccc(Br)cc1\n+ OpenBabel03162018053D\n+libRbt.so/2013.1/901 2013/11/27\n+ 16 16 0 0 0 0 0 0 0 0999 V2000\n+ 1.5854 -4.4167 26.8713 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.9171 -3.9650 27.0697 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.3204 -3.0325 26.0654 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.0629 -3.7637 24.9341 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 3.0725 -4.5314 24.0556 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.7894 -2.7836 24.1743 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.8770 -3.3338 23.4307 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3647 -2.3248 22.3968 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.2636 -1.9969 21.5481 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.5320 -1.2441 20.4392 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.2993 -1.6247 19.1173 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.6084 -0.7491 18.0695 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.1526 0.5029 18.3492 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.5557 1.6873 16.9327 Br 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3970 0.8871 19.6636 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0874 0.0098 20.7062 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 5 1 6 0 0 0\n+ 4 6 1 0 0 0 0\n+ 6 7 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 8 9 1 0 0 0 0\n+ 9 10 1 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 10 16 2 0 0 0 0\n+ 11 12 2 0 0 0 0\n+ 12 13 1 0 0 0 0\n+ 13 14 1 0 0 0 0\n+ 13 15 2 0 0 0 0\n+ 15 16 1 0 0 0 0\n+M END\n+> <Name>\n+COCC(C)OCCOc1ccc(Br)cc1\n+\n+> <TransFSScore>\n+0.239591\n+\n+$$$$\n+COCC(C)OCCOc1ccc(Br)cc1\n+ OpenBabel03162018053D\n+libRbt.so/2013.1/901 2013/11/27\n+ 16 16 0 0 0 0 0 0 0 0999 V2000\n+ 5.6650 -5.5958 25.3680 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1057 -4.4972 26.0732 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0785 -3.4881 26.3491 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.4358 -2.3388 27.1440 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 4.9482 -2.8397 28.5054 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.4151 -1.2967 27.2873 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.6267 -0.5481 26.0900 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.3817 0.2676 25.7585 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.6866 1.1011 24.6394 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7821 0.4960 23.4174 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7162 -0.8770 23.1782 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.8146 -1.3676 21.8707 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.9820 -0.4818 20.8080 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.1007 -1.1472 19.0431 Br 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0584 0.8879 21.0380 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.9602 1.3731 22.3447 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 5 1 1 0 0 0\n+ 4 6 1 0 0 0 0\n+ 6 7 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 8 9 1 0 0 0 0\n+ 9 10 1 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 10 16 2 0 0 0 0\n+ 11 12 2 0 0 0 0\n+ 12 13 1 0 0 0 0\n+ 13 14 1 0 0 0 0\n+ 13 15 2 0 0 0 0\n+ 15 16 1 0 0 0 0\n+M END\n+> <Name>\n+COCC(C)OCCOc1ccc(Br)cc1\n+\n+> <TransFSScore>\n+0.900000\n+\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 7a4306d69801 test-data/receptor.as |
| b |
| Binary file test-data/receptor.as has changed |
| b |
| diff -r 000000000000 -r 7a4306d69801 test-data/receptor.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/receptor.mol2 Mon May 04 07:41:13 2020 -0400 |
| b |
| b'@@ -0,0 +1,6069 @@\n+@<TRIPOS>MOLECULE\n+receptor.pdb\n+ 3013 3048 0 0 0\n+SMALL\n+GASTEIGER\n+\n+@<TRIPOS>ATOM\n+ 1 N 16.0520 41.0190 15.4650 N.4 1 VAL1 0.2275\n+ 2 CA 15.2450 42.0270 14.7460 C.3 1 VAL1 0.0555\n+ 3 C 14.1180 41.2820 14.0050 C.2 1 VAL1 0.2618\n+ 4 O 13.2440 40.5890 14.5350 O.2 1 VAL1 -0.2696\n+ 5 CB 16.0900 42.8220 13.7240 C.3 1 VAL1 0.0050\n+ 6 CG1 15.3310 44.0210 13.1490 C.3 1 VAL1 -0.0571\n+ 7 CG2 17.4520 43.2500 14.2510 C.3 1 VAL1 -0.0571\n+ 8 H1 16.8010 41.4790 15.9620 H 1 VAL1 0.2002\n+ 9 H2 15.4660 40.5250 16.1230 H 1 VAL1 0.2002\n+ 10 H3 16.4410 40.3630 14.8020 H 1 VAL1 0.2002\n+ 11 HA 14.8280 42.7360 15.4610 H 1 VAL1 0.0951\n+ 12 HB 16.4690 42.1440 12.9590 H 1 VAL1 0.0355\n+ 13 HG11 15.9670 44.5470 12.4370 H 1 VAL1 0.0234\n+ 14 HG12 14.4300 43.6730 12.6430 H 1 VAL1 0.0234\n+ 15 HG13 15.0550 44.6980 13.9570 H 1 VAL1 0.0234\n+ 16 HG21 17.9850 43.8020 13.4770 H 1 VAL1 0.0234\n+ 17 HG22 17.3200 43.8870 15.1250 H 1 VAL1 0.0234\n+ 18 HG23 18.0280 42.3680 14.5290 H 1 VAL1 0.0234\n+ 19 N 14.2650 41.4590 12.7080 N.am 2 GLY2 -0.3021\n+ 20 CA 13.3910 40.8770 11.6990 C.3 2 GLY2 0.0883\n+ 21 C 12.8860 42.0140 10.8100 C.2 2 GLY2 0.2308\n+ 22 O 13.3350 43.1700 10.8420 O.2 2 GLY2 -0.2741\n+ 23 H 15.0220 42.0290 12.3590 H 2 GLY2 0.1494\n+ 24 HA2 13.9510 40.1530 11.1070 H 2 GLY2 0.0558\n+ 25 HA3 12.5540 40.3770 12.1870 H 2 GLY2 0.0558\n+ 26 N 11.9410 41.5950 10.0180 N.am 3 SER3 -0.3008\n+ 27 CA 11.2600 42.4710 9.0470 C.3 3 SER3 0.1226\n+ 28 C 9.7770 42.0580 9.1450 C.2 3 SER3 0.2362\n+ 29 O 9.5540 40.9440 9.6580 O.2 3 SER3 -0.2737\n+ 30 CB 11.8720 42.2070 7.6870 C.3 3 SER3 0.0711\n+ 31 OG 12.1980 40.8290 7.5230 O.3 3 SER3 -0.3927\n+ 32 H 11.6440 40.6300 10.0520 H 3 SER3 0.1496\n+ 33 HA 11.4250 43.5130 9.3190 H 3 SER3 0.0618\n+ 34 HB2 11.1640 42.4900 6.9080 H 3 SER3 0.0580\n+ 35 HB3 12.7840 42.7940 7.5780 H 3 SER3 0.0580\n+ 36 HG 12.5830 40.6920 6.6540 H 3 SER3 0.2095\n+ 37 N 8.9500 42.9530 8.6670 N.am 4 LEU4 -0.3024\n+ 38 CA 7.5000 42.7870 8.6020 C.3 4 LEU4 0.0997\n+ 39 C 7.0610 42.3920 7.1710 C.2 4 LEU4 0.2340\n+ 40 O 7.2180 43.2070 6.2410 O.2 4 LEU4 -0.2738\n+ 41 CB 6.8560 44.1050 8.9850 C.3 4 LEU4 -0.0236\n+ 42 CG 5.4220 44.0040 9.4470 C.3 4 LEU4 -0.0446\n+ 43 CD1 5.2730 42.9590 10.5730 C.3 4 LEU4 -0.0626\n+ 44 CD2 5.0360 45.3300 10.1100 C.3 4 LEU4 -0.0626\n+ 45 H 9.3050 43.8290 8.3110 H 4 LEU4 0.1495\n+ 46 HA 7.1920 42.0030 9.2940 H 4 LEU4 0.0594\n+ 47 HB2 7.4160 44.5590 9.8020 H 4 LEU4 0.0290\n+ 48 HB3 6.8600 44.7750 8.1260 H 4 LEU4 0.0290\n+ 49 HG 4.8070 43.6030 8.6410 H 4 LEU4 0.0296\n+ 50 HD11 4.2300 42.9080 10.8860 H 4 LEU4 0'..b' 2889 1693 1698 1\n+ 2890 1386 1387 2\n+ 2891 1675 1674 1\n+ 2892 1587 1597 1\n+ 2893 1587 1596 1\n+ 2894 1587 1585 1\n+ 2895 1356 1358 am\n+ 2896 1459 1461 2\n+ 2897 1459 1460 1\n+ 2898 1329 1323 1\n+ 2899 1461 1473 1\n+ 2900 1592 1585 1\n+ 2901 1406 1408 ar\n+ 2902 1700 1697 1\n+ 2903 1409 1411 ar\n+ 2904 1581 1589 1\n+ 2905 1472 1460 1\n+ 2906 1460 1471 1\n+ 2907 1723 1732 1\n+ 2908 1723 1724 1\n+ 2909 1614 1617 1\n+ 2910 1614 1615 1\n+ 2911 1575 1565 1\n+ 2912 1585 1586 1\n+ 2913 1697 1701 1\n+ 2914 1697 1702 1\n+ 2915 1358 1365 1\n+ 2916 1358 1366 1\n+ 2917 1331 1326 1\n+ 2918 1574 1564 1\n+ 2919 1324 1323 1\n+ 2920 1324 1325 2\n+ 2921 1565 1564 1\n+ 2922 1565 1576 1\n+ 2923 1437 1428 1\n+ 2924 1564 1573 1\n+ 2925 1617 1625 1\n+ 2926 1617 1624 1\n+ 2927 1428 1438 1\n+ 2928 1428 1439 1\n+ 2929 1268 1269 2\n+ 2930 1268 1285 am\n+ 2931 1323 1326 1\n+ 2932 1323 1322 1\n+ 2933 1707 1714 1\n+ 2934 1707 1713 1\n+ 2935 1707 1708 1\n+ 2936 1310 1309 2\n+ 2937 1330 1326 1\n+ 2938 1326 1327 1\n+ 2939 1709 1708 2\n+ 2940 1411 1420 1\n+ 2941 1411 1410 ar\n+ 2942 1408 1417 1\n+ 2943 1408 1410 ar\n+ 2944 1662 1661 2\n+ 2945 1674 1682 1\n+ 2946 1674 1661 am\n+ 2947 1738 1725 1\n+ 2948 1294 1285 1\n+ 2949 1734 1724 1\n+ 2950 1724 1725 1\n+ 2951 1724 1735 1\n+ 2952 1708 1710 am\n+ 2953 1285 1286 1\n+ 2954 1615 1616 2\n+ 2955 1615 1628 am\n+ 2956 1637 1628 1\n+ 2957 1586 1593 1\n+ 2958 1586 1594 1\n+ 2959 1586 1595 1\n+ 2960 1309 1322 am\n+ 2961 1309 1308 1\n+ 2962 1322 1328 1\n+ 2963 1661 1660 1\n+ 2964 1410 1419 1\n+ 2965 1316 1307 1\n+ 2966 1725 1737 1\n+ 2967 1725 1736 1\n+ 2968 1628 1629 1\n+ 2969 1672 1664 1\n+ 2970 1298 1290 1\n+ 2971 1320 1312 1\n+ 2972 1333 1327 1\n+ 2973 1327 1328 1\n+ 2974 1327 1332 1\n+ 2975 1631 1630 2\n+ 2976 1303 1292 1\n+ 2977 1307 1308 1\n+ 2978 1307 1287 am\n+ 2979 1710 1716 1\n+ 2980 1710 1715 1\n+ 2981 1328 1334 1\n+ 2982 1328 1335 1\n+ 2983 1286 1295 1\n+ 2984 1286 1287 1\n+ 2985 1286 1289 1\n+ 2986 1308 1317 1\n+ 2987 1308 1311 1\n+ 2988 1671 1663 1\n+ 2989 1302 1292 1\n+ 2990 1299 1290 1\n+ 2991 1290 1289 1\n+ 2992 1290 1291 1\n+ 2993 1639 1632 1\n+ 2994 1664 1663 1\n+ 2995 1664 1665 1\n+ 2996 1664 1673 1\n+ 2997 1660 1663 1\n+ 2998 1660 1669 1\n+ 2999 1660 1659 1\n+ 3000 1667 1665 ar\n+ 3001 1312 1321 1\n+ 3002 1312 1313 1\n+ 3003 1312 1311 1\n+ 3004 1287 1288 2\n+ 3005 1630 1629 1\n+ 3006 1630 1645 am\n+ 3007 1292 1291 1\n+ 3008 1292 1293 1\n+ 3009 1629 1632 1\n+ 3010 1629 1638 1\n+ 3011 1663 1670 1\n+ 3012 1665 1666 ar\n+ 3013 1296 1289 1\n+ 3014 1648 1647 2\n+ 3015 1289 1297 1\n+ 3016 1315 1313 ar\n+ 3017 1313 1314 ar\n+ 3018 1304 1293 1\n+ 3019 1659 1647 am\n+ 3020 1659 1668 1\n+ 3021 1311 1318 1\n+ 3022 1311 1319 1\n+ 3023 1642 1633 1\n+ 3024 1632 1640 1\n+ 3025 1632 1633 1\n+ 3026 1291 1300 1\n+ 3027 1291 1301 1\n+ 3028 1647 1646 1\n+ 3029 1293 1305 1\n+ 3030 1293 1306 1\n+ 3031 1645 1646 1\n+ 3032 1645 1651 1\n+ 3033 1652 1646 1\n+ 3034 1633 1641 1\n+ 3035 1633 1634 1\n+ 3036 1646 1649 1\n+ 3037 1658 1651 1\n+ 3038 1634 1635 2\n+ 3039 1634 1636 am\n+ 3040 1644 1636 1\n+ 3041 1651 1657 1\n+ 3042 1651 1650 1\n+ 3043 1636 1643 1\n+ 3044 1653 1649 1\n+ 3045 1649 1650 1\n+ 3046 1649 1654 1\n+ 3047 1650 1655 1\n+ 3048 1650 1656 1\n' |
| b |
| diff -r 000000000000 -r 7a4306d69801 test-data/receptor.prm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/receptor.prm Mon May 04 07:41:13 2020 -0400 |
| b |
| @@ -0,0 +1,3 @@ +RBT_PARAMETER_FILE_V1.00 +RECEPTOR_FILE receptor.mol2 +RECEPTOR_FLEX 3.0 |
| b |
| diff -r 000000000000 -r 7a4306d69801 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 07:41:13 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 000000000000 -r 7a4306d69801 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 07:41:13 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 000000000000 -r 7a4306d69801 test-data/wrong_receptor.prm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wrong_receptor.prm Mon May 04 07:41:13 2020 -0400 |
| b |
| @@ -0,0 +1,3 @@ +RBT_PARAMETER_FILE_V1.00 +RECEPTOR_FILE a_terrible_mistake.mol2 +RECEPTOR_FLEX 3.0 |