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Changeset 8:7a871df65202 (2020-07-28)

Previous changeset 7:7b2f205b3f68 (2019-10-02) Next changeset 9:90ea16534012 (2021-12-21)

Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"

modified:
convert_pdbqt_to_sdf.py
docking.xml
test-data/box.txt
test-data/ligand1_docked.sdf
test-data/ligand2_docked.sdf

added:
test-data/ligand_docked.sdf

removed:
test-data/ligand3_docked.sdf
test-data/ligand4_docked.sdf
test-data/ligand5_docked.sdf

diff -r 7b2f205b3f68 -r 7a871df65202 convert_pdbqt_to_sdf.py
--- a/convert_pdbqt_to_sdf.py Wed Oct 02 12:49:30 2019 -0400
+++ b/convert_pdbqt_to_sdf.py Tue Jul 28 08:13:41 2020 -0400

@@ -1,6 +1,6 @@
-import pybel, openbabel
import sys

+from openbabel import pybel, openbabel

def main():
if len(sys.argv) == 3:

diff -r 7b2f205b3f68 -r 7a871df65202 docking.xml
--- a/docking.xml Wed Oct 02 12:49:30 2019 -0400
+++ b/docking.xml Tue Jul 28 08:13:41 2020 -0400

[

@@ -1,9 +1,13 @@
-<tool id="docking" name="VINA Docking" version="0.3.0">
+<tool id="docking" name="VINA Docking" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <macros>
+        <token name="@TOOL_VERSION@">1.1.2</token>
+        <token name="@GALAXY_VERSION@">0</token>
+    </macros>
     <description>tool to perform protein-ligand docking with Autodock Vina</description>
     <requirements>
-        <requirement type="package" version="1.1.2">autodock-vina</requirement>
-        <requirement type="package" version="2.4.1">openbabel</requirement>
-        <requirement type="package" version="20190722">parallel</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">autodock-vina</requirement>
+        <requirement type="package" version="3.1.1">openbabel</requirement>
+        <requirement type="package" version="20200722">parallel</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if $ligands.is_of_type("sdf")
@@ -97,7 +101,7 @@
             <param name="ligands" value="input_ligand.pdbqt"/>
             <param name="box" value="box.txt"/>
             <output_collection name="sdf_outputs" type="list" count="1">
-                <element name="ligand1_docked" file="ligand1_docked.sdf" lines_diff="20"/>
+                <element name="ligand1_docked" file="ligand_docked.sdf" lines_diff="1084"/>
             </output_collection>
         </test>

@@ -114,10 +118,10 @@
             <param name="size_y" value="10.205999999999996" />
             <param name="size_z" value="15.521999999999991" />
             <param name="seed" value="true" />
-            <param name="seed_value" value="1" />
+            <param name="seed_value" value="8" />
             <param name="exh" value="10" />
             <output_collection name="sdf_outputs" type="list" count="1">
-                <element name="ligand1_docked" file="ligand_params.sdf" lines_diff="20"/>
+                <element name="ligand1_docked" file="ligand_params.sdf" lines_diff="1084"/>
             </output_collection>
         </test>

diff -r 7b2f205b3f68 -r 7a871df65202 test-data/box.txt
--- a/test-data/box.txt Wed Oct 02 12:49:30 2019 -0400
+++ b/test-data/box.txt Tue Jul 28 08:13:41 2020 -0400

@@ -1,4 +1,4 @@
-
+seed = 8
size_x =  18.768
size_y =  10.205999999999996
size_z =  15.521999999999991

diff -r 7b2f205b3f68 -r 7a871df65202 test-data/ligand1_docked.sdf
--- a/test-data/ligand1_docked.sdf Wed Oct 02 12:49:30 2019 -0400
+++ b/test-data/ligand1_docked.sdf Tue Jul 28 08:13:41 2020 -0400

b'@@ -1,39 +1,39 @@\n =\n- OpenBabel09021916083D\n+ OpenBabel07272015563D\n \n 18 19 0 0 1 0 0 0 0 0999 V2000\n- 34.9000 -44.6750 75.3700 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.6880 -44.2080 75.8770 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.5200 -44.3960 75.1540 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.5270 -45.0480 73.9140 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.7620 -45.5050 73.4310 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.9390 -45.3290 74.1410 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.2740 -45.2520 73.1310 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.2120 -46.1670 72.0750 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.0360 -46.3510 71.3570 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 28.8990 -45.6380 71.6800 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 28.9370 -44.7260 72.7230 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.1110 -44.5390 73.4420 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.0530 -44.4790 76.0980 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.3930 -44.6860 76.3330 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 37.2720 -44.2530 75.4010 C 0 0 2 0 0 0 0 0 0 0 0 0\n- 37.3200 -42.7760 75.0190 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 37.7140 -42.4870 73.8720 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.9750 -41.9560 75.8920 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 2 1 0 0 0 0\n+ 34.9430 -44.6790 75.3760 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.9810 -45.3120 74.1360 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 33.8000 -45.4860 73.4300 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 32.5650 -45.0460 73.9280 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.5600 -44.4150 75.1790 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 33.7310 -44.2300 75.8970 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 31.3080 -45.2470 73.1490 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.1600 -44.5040 73.4380 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 28.9830 -44.6880 72.7230 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 28.9280 -45.6270 71.7060 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 30.0510 -46.3710 71.4040 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 31.2300 -46.1900 72.1180 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 36.0990 -44.4850 76.1000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.4420 -44.6700 76.3250 C 0 0 0 0 0 1 0 0 0 0 0 0\n+ 37.3130 -44.2430 75.3990 C 0 0 2 0 0 3 0 0 0 0 0 0\n+ 37.3440 -42.7630 75.0270 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.7170 -42.4800 73.8720 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.9800 -41.9400 75.8900 O 0 0 0 0 0 1 0 0 0 0 0 0\n+ 1 6 1 0 0 0 0\n 1 13 1 0 0 0 0\n- 3 2 2 0 0 0 0\n- 4 3 1 0 0 0 0\n- 5 4 2 0 0 0 0\n- 5 6 1 0 0 0 0\n- 6 1 2 0 0 0 0\n- 7 12 1 0 0 0 0\n+ 2 1 2 0 0 0 0\n+ 3 4 2 0 0 0 0\n+ 3 2 1 0 0 0 0\n+ 4 5 1 0 0 0 0\n+ 5 6 2 0 0 0 0\n+ 7 8 1 0 0 0 0\n 7 4 1 0 0 0 0\n- 8 7 2 0 0 0 0\n- 9 10 2 0 0 0 0\n- 9 8 1 0 0 0 0\n- 10 11 1 0 0 0 0\n- 11 12 2 0 0 0 0\n+ 9 8 2 0 0 0 0\n+ 10 9 1 0 0 0 0\n+ 11 10 2 0 0 0 0\n+ 11 12 1 0 0 0 0\n+ 12 7 2 0 0 0 0\n 15 13 1 0 0 0 0\n 15 14 1 1 0 0 0\n 16 15 1 0 0 0 0\n@@ -70,52 +70,52 @@\n \n $$$$\n =\n- OpenBabel09021916083D\n+ OpenBabel07272015563D\n \n 18 19 0 0 1 0 0 0 0 0999 V2000\n- 34.9890 -44.7290 75.3400 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.7740 -44.3230 75.8900 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.5980 -44.5060 75.1780 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.6020 -45.0920 73.9050 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.8400 -45.4880 73.3780 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.0250 -45.3160 74.0770 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.3410 -45.2900 73.1330 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.1700 -44.5940 73.4530 C 0 0 0 '..b"3 1 1 0 0 0 0\n 15 14 1 6 0 0 0\n 15 13 1 0 0 0 0\n 16 15 1 0 0 0 0\n@@ -541,7 +541,7 @@\n 8\n \n > <REMARK>\n- VINA RESULT: -5.1 4.107 6.896\n+ VINA RESULT: -5.1 4.047 6.722\n Name = \n 5 active torsions:\n status: ('A' for Active; 'I' for Inactive)\n@@ -560,59 +560,59 @@\n -5.1\n \n > <RMSD_LB>\n-4.107\n+4.047\n \n > <RMSD_UB>\n-6.896\n+6.722\n \n $$$$\n =\n- OpenBabel09021916083D\n+ OpenBabel07272015563D\n \n 18 19 0 0 1 0 0 0 0 0999 V2000\n- 35.8450 -42.2310 77.0780 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.0840 -42.9180 78.0230 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.5460 -42.2360 79.1040 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.7510 -40.8600 79.2720 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.5220 -40.1980 78.3060 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.0650 -40.8630 77.2170 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.1760 -40.1210 80.4330 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.8090 -40.1720 80.7280 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.2870 -39.4820 81.8170 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.1130 -38.7390 82.6370 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.4700 -38.6740 82.3630 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.9940 -39.3620 81.2750 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.3760 -42.9230 76.0120 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.2250 -44.3750 76.2200 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.7070 -44.2960 76.1830 C 0 0 2 0 0 0 0 0 0 0 0 0\n- 36.0740 -45.0710 75.0320 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.5290 -46.2040 74.7760 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.1520 -44.5080 74.4110 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 6 2 0 0 0 0\n+ 34.7830 -43.5140 77.4980 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.4850 -42.9340 78.5520 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 34.8800 -41.9340 79.2970 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 33.5800 -41.4840 79.0200 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.9010 -42.0860 77.9530 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 33.4900 -43.0900 77.1990 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 32.9520 -40.4040 79.8370 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.6620 -39.9490 79.5500 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 31.0700 -38.9400 80.3000 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 31.7620 -38.3580 81.3500 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 33.0380 -38.7940 81.6500 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 33.6320 -39.8030 80.9010 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 35.3540 -44.5150 76.7420 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.8330 -45.5620 74.6810 C 0 0 0 0 0 1 0 0 0 0 0 0\n+ 35.7350 -44.2270 75.4010 C 0 0 2 0 0 3 0 0 0 0 0 0\n+ 37.0480 -43.4510 75.4500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.0400 -42.2980 74.9780 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.0320 -44.0110 75.9720 O 0 0 0 0 0 1 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 2 3 2 0 0 0 0\n- 3 4 1 0 0 0 0\n+ 4 3 1 0 0 0 0\n 4 7 1 0 0 0 0\n 5 4 2 0 0 0 0\n+ 6 1 2 0 0 0 0\n 6 5 1 0 0 0 0\n- 7 8 2 0 0 0 0\n 7 12 1 0 0 0 0\n+ 8 7 2 0 0 0 0\n 8 9 1 0 0 0 0\n 9 10 2 0 0 0 0\n- 11 10 1 0 0 0 0\n+ 10 11 1 0 0 0 0\n 12 11 2 0 0 0 0\n- 13 15 1 0 0 0 0\n 13 1 1 0 0 0 0\n 15 14 1 6 0 0 0\n- 16 15 1 0 0 0 0\n- 17 16 1 0 0 0 0\n- 18 16 2 0 0 0 0\n+ 15 16 1 0 0 0 0\n+ 15 13 1 0 0 0 0\n+ 16 18 1 0 0 0 0\n+ 17 16 2 0 0 0 0\n M END\n > <MODEL>\n 9\n \n > <REMARK>\n- VINA RESULT: -5.1 4.937 7.596\n+ VINA RESULT: -5.0 4.531 6.799\n Name = \n 5 active torsions:\n status: ('A' for Active; 'I' for Inactive)\n@@ -628,12 +628,12 @@\n F 4\n \n > <SCORE>\n--5.1\n+-5.0\n \n > <RMSD_LB>\n-4.937\n+4.531\n \n > <RMSD_UB>\n-7.596\n+6.799\n \n $$$$\n"

diff -r 7b2f205b3f68 -r 7a871df65202 test-data/ligand2_docked.sdf
--- a/test-data/ligand2_docked.sdf Wed Oct 02 12:49:30 2019 -0400
+++ b/test-data/ligand2_docked.sdf Tue Jul 28 08:13:41 2020 -0400

b'@@ -1,39 +1,39 @@\n =\n- OpenBabel09021916093D\n+ OpenBabel07272015563D\n \n 16 16 0 0 0 0 0 0 0 0999 V2000\n- 30.7270 -43.7450 76.1540 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.2320 -43.8770 76.1820 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.9030 -44.5770 75.1900 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.2880 -44.7130 75.1870 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.9550 -45.4820 74.0800 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.0120 -44.1090 76.2270 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.3700 -43.3850 77.2450 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.1200 -42.7180 78.3740 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.9820 -43.2890 77.1920 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.4390 -44.2310 76.2340 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.8300 -44.9440 76.7890 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 37.2890 -43.4500 75.5420 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 37.0090 -42.3660 75.0480 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.6760 -43.9990 75.3480 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.7980 -44.7930 74.1950 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.6010 -46.1780 74.4680 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 2 1 0 0 0 0\n- 2 9 2 0 0 0 0\n- 3 2 1 0 0 0 0\n- 4 3 2 0 0 0 0\n- 4 6 1 0 0 0 0\n- 5 4 1 0 0 0 0\n- 6 10 1 0 0 0 0\n- 6 7 2 0 0 0 0\n- 7 8 1 0 0 0 0\n+ 30.6630 -43.6920 75.9580 C 0 0 0 0 0 1 0 0 0 0 0 0\n+ 34.9860 -42.7620 78.3530 C 0 0 0 0 0 1 0 0 0 0 0 0\n+ 32.1620 -43.8570 76.0460 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.8840 -43.2860 77.0850 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 34.2670 -43.4120 77.1940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.9330 -44.1500 76.2010 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.2380 -44.7360 75.1320 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.8570 -44.5700 75.0810 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 34.9310 -45.5200 74.0510 C 0 0 0 0 0 1 0 0 0 0 0 0\n+ 37.2490 -43.5480 75.6000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.3550 -44.3030 76.2650 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.0120 -42.4630 75.0840 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.7080 -45.0190 76.8410 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.6290 -44.1290 75.4640 C 0 0 0 0 0 2 0 0 0 0 0 0\n+ 38.5260 -46.2360 74.4260 C 0 0 0 0 0 1 0 0 0 0 0 0\n+ 38.8100 -44.8480 74.2700 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 3 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 5 2 0 0 0 0\n+ 5 2 1 0 0 0 0\n+ 6 11 1 0 0 0 0\n+ 6 5 1 0 0 0 0\n+ 7 6 2 0 0 0 0\n+ 8 7 1 0 0 0 0\n+ 8 3 2 0 0 0 0\n 9 7 1 0 0 0 0\n 10 11 1 0 0 0 0\n- 12 10 1 0 0 0 0\n- 13 12 2 0 0 0 0\n- 14 12 1 0 0 0 0\n- 15 16 1 0 0 0 0\n- 15 14 1 0 0 0 0\n+ 11 13 1 0 0 0 0\n+ 12 10 2 0 0 0 0\n+ 14 10 1 0 0 0 0\n+ 16 15 1 0 0 0 0\n+ 16 14 1 0 0 0 0\n M END\n > <MODEL>\n 1\n@@ -67,47 +67,47 @@\n \n $$$$\n =\n- OpenBabel09021916093D\n+ OpenBabel07272015563D\n \n 16 16 0 0 0 0 0 0 0 0999 V2000\n- 30.7330 -43.6060 76.3350 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.2340 -43.7750 76.2880 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.0410 -43.2270 77.2740 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.4260 -43.3690 77.2600 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.2450 -42.7520 78.3610 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.0040 -44.0990 76.2100 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.2200 -44.6770 75.1980 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.8090 -45.4740 74.0590 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.8400 -44.4960 75.2690 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.4270 -44.2630 76.1860 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.8070 -45.0000 76.7160 H 0 0 0 0 0 0 0 0 0 0 0 0'..b" 0 0 0\n+ 6 11 1 0 0 0 0\n 7 6 1 0 0 0 0\n- 7 8 1 0 0 0 0\n- 9 7 2 0 0 0 0\n- 10 12 1 0 0 0 0\n+ 7 9 1 0 0 0 0\n+ 8 7 2 0 0 0 0\n+ 10 14 1 0 0 0 0\n 11 10 1 0 0 0 0\n- 12 13 2 0 0 0 0\n- 12 14 1 0 0 0 0\n- 15 14 1 0 0 0 0\n- 15 16 1 0 0 0 0\n+ 11 13 1 0 0 0 0\n+ 12 10 2 0 0 0 0\n+ 16 14 1 0 0 0 0\n+ 16 15 1 0 0 0 0\n M END\n > <MODEL>\n 8\n \n > <REMARK>\n- VINA RESULT: -4.3 3.964 5.892\n+ VINA RESULT: -4.3 3.225 4.866\n Name = \n 7 active torsions:\n status: ('A' for Active; 'I' for Inactive)\n@@ -536,54 +536,54 @@\n -4.3\n \n > <RMSD_LB>\n-3.964\n+3.225\n \n > <RMSD_UB>\n-5.892\n+4.866\n \n $$$$\n =\n- OpenBabel09021916093D\n+ OpenBabel07272015563D\n \n 16 16 0 0 0 0 0 0 0 0999 V2000\n- 36.2810 -45.5880 74.7420 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.7970 -45.3090 74.6830 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.0060 -45.8780 73.6960 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.6360 -45.6430 73.6170 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.8340 -46.2940 72.5230 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.0540 -44.8050 74.5810 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.8200 -44.2170 75.6010 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.2240 -43.3170 76.6570 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.1850 -44.4900 75.6220 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.6450 -44.5600 74.5200 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.0630 -45.1230 75.0810 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.0510 -43.6230 73.7590 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.5710 -43.0480 72.8120 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 28.6490 -43.2470 74.1530 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 27.7000 -44.2290 73.8180 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 27.2950 -44.1460 72.4540 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 2 1 1 0 0 0 0\n- 2 9 2 0 0 0 0\n- 3 2 1 0 0 0 0\n+ 35.5480 -45.7130 74.5570 C 0 0 0 0 0 1 0 0 0 0 0 0\n+ 31.3000 -46.2290 71.9160 C 0 0 0 0 0 1 0 0 0 0 0 0\n+ 34.0930 -45.3600 74.3510 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.3660 -45.9050 73.3020 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 32.0260 -45.5970 73.0790 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.4110 -44.6960 73.9630 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.1140 -44.1190 75.0320 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.4520 -44.4680 75.1980 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 31.4790 -43.1430 75.9840 C 0 0 0 0 0 1 0 0 0 0 0 0\n+ 29.5910 -43.3600 72.9660 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.0360 -44.3410 73.7720 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.2420 -42.8290 72.0750 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.3620 -44.8570 74.2720 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.1920 -42.8760 73.2290 C 0 0 0 0 0 2 0 0 0 0 0 0\n+ 28.2990 -41.2320 74.9080 C 0 0 0 0 0 1 0 0 0 0 0 0\n+ 27.9580 -42.5780 74.5830 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 5 1 0 0 0 0\n+ 3 1 1 0 0 0 0\n+ 3 8 1 0 0 0 0\n 4 3 2 0 0 0 0\n- 4 6 1 0 0 0 0\n 5 4 1 0 0 0 0\n- 6 7 2 0 0 0 0\n+ 5 6 2 0 0 0 0\n+ 6 7 1 0 0 0 0\n+ 7 8 2 0 0 0 0\n 7 9 1 0 0 0 0\n- 7 8 1 0 0 0 0\n- 10 6 1 0 0 0 0\n+ 10 14 1 0 0 0 0\n 10 11 1 0 0 0 0\n- 12 14 1 0 0 0 0\n- 12 10 1 0 0 0 0\n- 13 12 2 0 0 0 0\n- 15 14 1 0 0 0 0\n+ 11 6 1 0 0 0 0\n+ 11 13 1 0 0 0 0\n+ 12 10 2 0 0 0 0\n+ 14 16 1 0 0 0 0\n 16 15 1 0 0 0 0\n M END\n > <MODEL>\n 9\n \n > <REMARK>\n- VINA RESULT: -4.3 3.971 6.363\n+ VINA RESULT: -4.3 4.096 6.992\n Name = \n 7 active torsions:\n status: ('A' for Active; 'I' for Inactive)\n@@ -604,9 +604,9 @@\n -4.3\n \n > <RMSD_LB>\n-3.971\n+4.096\n \n > <RMSD_UB>\n-6.363\n+6.992\n \n $$$$\n"

diff -r 7b2f205b3f68 -r 7a871df65202 test-data/ligand3_docked.sdf
--- a/test-data/ligand3_docked.sdf Wed Oct 02 12:49:30 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b"@@ -1,594 +0,0 @@\n-=\n- OpenBabel09021916093D\n-\n- 15 15 0 0 0 0 0 0 0 0999 V2000\n- 35.5160 -44.1770 76.5970 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.5400 -44.3480 75.6050 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.8770 -44.9300 74.3780 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.1800 -45.3120 74.1400 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 37.1490 -45.1400 75.1290 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.8160 -44.5650 76.3550 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.5720 -45.5740 74.8710 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 39.4810 -44.8440 75.2860 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.7610 -46.6440 74.2600 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.3170 -42.2230 77.9920 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.0570 -43.6050 77.7570 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.2440 -43.9490 75.8370 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.4200 -44.9350 76.4520 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.8380 -45.0140 73.4880 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.1260 -46.2430 73.3400 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 11 1 0 0 0 0\n- 2 12 1 0 0 0 0\n- 2 1 2 0 0 0 0\n- 3 2 1 0 0 0 0\n- 4 3 2 0 0 0 0\n- 4 5 1 0 0 0 0\n- 5 6 2 0 0 0 0\n- 6 1 1 0 0 0 0\n- 7 5 1 0 0 0 0\n- 7 8 1 0 0 0 0\n- 9 7 2 0 0 0 0\n- 11 10 1 0 0 0 0\n- 12 13 1 0 0 0 0\n- 14 3 1 0 0 0 0\n- 15 14 1 0 0 0 0\n-M END\n-> <MODEL>\n-1\n-\n-> <REMARK>\n- VINA RESULT: -4.7 0.000 0.000\n- Name = \n- 7 active torsions:\n- status: ('A' for Active; 'I' for Inactive)\n- 1 A between atoms: C_1 and O_11\n- 2 A between atoms: C_2 and C_5\n- 3 A between atoms: C_3 and O_11\n- 4 A between atoms: C_7 and O_13\n- 5 A between atoms: C_8 and O_12\n- 6 A between atoms: C_9 and O_12\n- 7 A between atoms: C_10 and O_13\n- x y z vdW Elec q Type\n- _______ _______ _______ _____ _____ ______ ____\n-\n-> <TORSDO>\n-F 4\n-\n-> <SCORE>\n--4.7\n-\n-> <RMSD_LB>\n-0.000\n-\n-> <RMSD_UB>\n-0.000\n-\n-$$$$\n-=\n- OpenBabel09021916093D\n-\n- 15 15 0 0 0 0 0 0 0 0999 V2000\n- 34.4290 -45.2520 74.5550 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.1990 -44.7310 75.8360 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.2630 -44.2340 76.5960 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.5440 -44.2810 76.0890 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.7700 -44.8010 74.8140 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.7120 -45.2930 74.0520 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.1730 -44.8380 74.2550 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.6020 -43.8130 73.7110 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.8260 -45.8920 74.3700 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.8550 -44.9990 72.7490 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.3040 -45.6970 73.9090 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.9220 -44.7010 76.3480 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.2040 -43.5000 76.0850 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.9060 -43.7790 77.8380 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.2090 -42.4370 78.2190 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 2 1 0 0 0 0\n- 2 12 1 0 0 0 0\n- 2 3 2 0 0 0 0\n- 3 14 1 0 0 0 0\n- 4 3 1 0 0 0 0\n- 5 4 2 0 0 0 0\n- 6 1 2 0 0 0 0\n- 6 5 1 0 0 0 0\n- 7 9 1 0 0 0 0\n- 7 5 1 0 0 0 0\n- 8 7 2 0 0 0 0\n- 10 11 1 0 0 0 0\n- 11 1 1 0 0 0 0\n- 13 12 1 0 0 0 0\n- 14 15 1 0 0 0 0\n-M END\n-> <MODEL>\n-2\n-\n-> <REMARK>\n- VINA RESULT: -4.5 0.957 3.283\n- Name = \n- 7 active torsions:\n- status: ('A' for Active; 'I' for Inactive)\n- 1 A between atoms: C_1 and O_11\n- 2 A between atoms: C_2 and C_5\n- 3 A between atoms: C_3 and O_11\n- 4 A bet"..b" 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.5520 -39.7420 79.5360 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.4610 -40.9870 77.5540 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.6930 -42.1710 77.2810 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.0820 -40.0230 77.0640 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.5580 -38.7910 82.5190 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.6150 -38.5740 81.4700 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.3180 -39.9000 81.2450 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.4360 -38.8530 80.8500 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.8920 -41.7040 79.3540 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.4610 -42.4730 78.2320 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 11 1 0 0 0 0\n- 2 1 1 0 0 0 0\n- 2 12 1 0 0 0 0\n- 3 14 1 0 0 0 0\n- 3 2 2 0 0 0 0\n- 4 5 2 0 0 0 0\n- 4 3 1 0 0 0 0\n- 5 6 1 0 0 0 0\n- 6 1 2 0 0 0 0\n- 7 5 1 0 0 0 0\n- 8 7 1 0 0 0 0\n- 9 7 2 0 0 0 0\n- 11 10 1 0 0 0 0\n- 13 12 1 0 0 0 0\n- 15 14 1 0 0 0 0\n-M END\n-> <MODEL>\n-8\n-\n-> <REMARK>\n- VINA RESULT: -3.7 4.675 6.625\n- Name = \n- 7 active torsions:\n- status: ('A' for Active; 'I' for Inactive)\n- 1 A between atoms: C_1 and O_11\n- 2 A between atoms: C_2 and C_5\n- 3 A between atoms: C_3 and O_11\n- 4 A between atoms: C_7 and O_13\n- 5 A between atoms: C_8 and O_12\n- 6 A between atoms: C_9 and O_12\n- 7 A between atoms: C_10 and O_13\n- x y z vdW Elec q Type\n- _______ _______ _______ _____ _____ ______ ____\n-\n-> <TORSDO>\n-F 4\n-\n-> <SCORE>\n--3.7\n-\n-> <RMSD_LB>\n-4.675\n-\n-> <RMSD_UB>\n-6.625\n-\n-$$$$\n-=\n- OpenBabel09021916093D\n-\n- 15 15 0 0 0 0 0 0 0 0999 V2000\n- 34.1480 -43.6220 77.0860 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.8810 -43.8000 76.5150 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.7470 -44.4510 75.2840 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.8720 -44.8960 74.6230 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.1320 -44.7170 75.1930 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.2690 -44.0730 76.4230 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.3620 -45.2200 74.4740 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.8640 -44.4890 73.6130 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.8100 -46.3410 74.7860 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.8100 -41.7230 78.4140 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.1440 -42.9800 78.2990 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.7600 -43.3380 77.1680 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.3800 -42.0080 76.8280 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.4580 -44.5350 74.8260 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.1740 -44.2830 73.4500 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 11 1 0 0 0 0\n- 2 1 1 0 0 0 0\n- 2 12 1 0 0 0 0\n- 3 2 2 0 0 0 0\n- 4 5 2 0 0 0 0\n- 4 3 1 0 0 0 0\n- 5 6 1 0 0 0 0\n- 6 1 2 0 0 0 0\n- 7 9 1 0 0 0 0\n- 7 5 1 0 0 0 0\n- 8 7 2 0 0 0 0\n- 11 10 1 0 0 0 0\n- 13 12 1 0 0 0 0\n- 14 3 1 0 0 0 0\n- 15 14 1 0 0 0 0\n-M END\n-> <MODEL>\n-9\n-\n-> <REMARK>\n- VINA RESULT: -3.7 1.807 2.240\n- Name = \n- 7 active torsions:\n- status: ('A' for Active; 'I' for Inactive)\n- 1 A between atoms: C_1 and O_11\n- 2 A between atoms: C_2 and C_5\n- 3 A between atoms: C_3 and O_11\n- 4 A between atoms: C_7 and O_13\n- 5 A between atoms: C_8 and O_12\n- 6 A between atoms: C_9 and O_12\n- 7 A between atoms: C_10 and O_13\n- x y z vdW Elec q Type\n- _______ _______ _______ _____ _____ ______ ____\n-\n-> <TORSDO>\n-F 4\n-\n-> <SCORE>\n--3.7\n-\n-> <RMSD_LB>\n-1.807\n-\n-> <RMSD_UB>\n-2.240\n-\n-$$$$\n"

diff -r 7b2f205b3f68 -r 7a871df65202 test-data/ligand4_docked.sdf
--- a/test-data/ligand4_docked.sdf Wed Oct 02 12:49:30 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b"@@ -1,621 +0,0 @@\n-=\n- OpenBabel09021916103D\n-\n- 17 17 0 0 1 0 0 0 0 0999 V2000\n- 33.6530 -43.4110 76.9560 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.5760 -44.3910 75.8160 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.3800 -45.0310 75.5040 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.9550 -44.6740 76.4480 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.2790 -45.9490 74.4680 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.3990 -46.2450 73.7200 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.6040 -45.6350 73.9920 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.6850 -44.7210 75.0350 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.2300 -43.9700 75.3420 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.3670 -43.9700 78.1430 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.0650 -44.6170 77.7760 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.6770 -44.4160 78.7460 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.1170 -42.9680 78.9600 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.2970 -40.4860 78.7440 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.3820 -41.6490 79.0800 C 0 0 2 0 0 0 0 0 0 0 0 0\n- 33.8390 -41.4730 80.3820 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.5070 -41.7050 81.0450 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 10 1 0 0 0 0\n- 2 1 1 0 0 0 0\n- 3 2 1 0 0 0 0\n- 3 4 1 0 0 0 0\n- 5 3 2 0 0 0 0\n- 6 7 2 0 0 0 0\n- 6 5 1 0 0 0 0\n- 7 8 1 0 0 0 0\n- 8 9 1 0 0 0 0\n- 8 2 2 0 0 0 0\n- 10 12 1 0 0 0 0\n- 10 13 1 0 0 0 0\n- 11 10 1 0 0 0 0\n- 13 15 1 0 0 0 0\n- 15 14 1 1 0 0 0\n- 15 16 1 0 0 0 0\n- 16 17 1 0 0 0 0\n-M END\n-> <MODEL>\n-1\n-\n-> <REMARK>\n- VINA RESULT: -4.7 0.000 0.000\n- Name = \n- 6 active torsions:\n- status: ('A' for Active; 'I' for Inactive)\n- 1 A between atoms: C_1 and C_3\n- 2 A between atoms: C_3 and C_4\n- 3 A between atoms: C_3 and O_12\n- 4 A between atoms: C_4 and N_11\n- 5 A between atoms: C_5 and C_6\n- 6 A between atoms: C_5 and N_11\n- x y z vdW Elec q Type\n- _______ _______ _______ _____ _____ ______ ____\n-\n-> <TORSDO>\n-F 5\n-\n-> <SCORE>\n--4.7\n-\n-> <RMSD_LB>\n-0.000\n-\n-> <RMSD_UB>\n-0.000\n-\n-$$$$\n-=\n- OpenBabel09021916103D\n-\n- 17 17 0 0 1 0 0 0 0 0999 V2000\n- 33.7330 -43.3710 76.9460 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.6010 -44.3820 75.8380 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.6940 -44.7140 75.0420 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.2330 -43.9510 75.3500 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.6020 -45.6330 74.0050 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.3890 -46.2380 73.7470 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.2810 -45.9390 74.5100 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.3930 -45.0150 75.5410 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.9660 -44.6710 76.4840 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.3590 -43.9470 78.1740 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.0640 -44.6080 77.8500 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.6220 -44.3800 78.7300 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.0770 -42.9630 79.0400 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.2850 -40.4890 78.7630 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.3570 -41.6340 79.1280 C 0 0 2 0 0 0 0 0 0 0 0 0\n- 33.8170 -41.4200 80.4250 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.9040 -41.7450 80.4530 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 10 1 0 0 0 0\n- 2 1 1 0 0 0 0\n- 3 4 1 0 0 0 0\n- 3 2 2 0 0 0 0\n- 5 3 1 0 0 0 0\n- 6 5 2 0 0 0 0\n- 6 7 1 0 0 0 0\n- 7 8 2 0 0 0 0\n- 8 2 1 0 0 0 0\n- 8 9 1 0 0 0 0\n- 10 12 1 0 0 0 0\n- 10 13 1 0 0 0 0\n- 11 10 1 0 0 0 0\n- 13 15 1 0 0 0 0\n- 15 14 1 1 0 0 0\n- 15 16 1 0 0 0 0\n-"..b"l 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.1420 -45.8880 71.7040 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 29.2370 -45.6460 72.1060 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.4900 -46.7980 72.0060 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 29.9400 -45.9370 70.2240 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 27.6540 -44.9350 70.1160 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 28.4930 -46.1700 69.8420 C 0 0 2 0 0 0 0 0 0 0 0 0\n- 27.9460 -47.2850 70.5340 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 28.6250 -47.9690 70.6330 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 2 1 0 0 0 0\n- 2 3 2 0 0 0 0\n- 2 8 1 0 0 0 0\n- 3 5 1 0 0 0 0\n- 4 3 1 0 0 0 0\n- 5 6 2 0 0 0 0\n- 7 6 1 0 0 0 0\n- 8 7 2 0 0 0 0\n- 9 8 1 0 0 0 0\n- 10 12 1 0 0 0 0\n- 10 11 1 0 0 0 0\n- 10 1 1 0 0 0 0\n- 13 10 1 0 0 0 0\n- 15 14 1 1 0 0 0\n- 15 13 1 0 0 0 0\n- 15 16 1 0 0 0 0\n- 16 17 1 0 0 0 0\n-M END\n-> <MODEL>\n-8\n-\n-> <REMARK>\n- VINA RESULT: -4.0 5.260 7.358\n- Name = \n- 6 active torsions:\n- status: ('A' for Active; 'I' for Inactive)\n- 1 A between atoms: C_1 and C_3\n- 2 A between atoms: C_3 and C_4\n- 3 A between atoms: C_3 and O_12\n- 4 A between atoms: C_4 and N_11\n- 5 A between atoms: C_5 and C_6\n- 6 A between atoms: C_5 and N_11\n- x y z vdW Elec q Type\n- _______ _______ _______ _____ _____ ______ ____\n-\n-> <TORSDO>\n-F 5\n-\n-> <SCORE>\n--4.0\n-\n-> <RMSD_LB>\n-5.260\n-\n-> <RMSD_UB>\n-7.358\n-\n-$$$$\n-=\n- OpenBabel09021916103D\n-\n- 17 17 0 0 1 0 0 0 0 0999 V2000\n- 34.5130 -42.2860 79.2430 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.8220 -40.9820 79.5390 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.5300 -39.9010 80.0590 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.2420 -40.0700 80.3530 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.9200 -38.6890 80.3540 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.5660 -38.5460 80.1320 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.8260 -39.5890 79.6190 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.4550 -40.7940 79.3320 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.4800 -42.0860 78.6800 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.7760 -42.4750 77.7840 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.0570 -41.5630 77.4250 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.9240 -42.8340 77.3540 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.8910 -43.4140 77.4580 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.4060 -45.3030 75.9060 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.8430 -43.8980 76.0240 C 0 0 2 0 0 0 0 0 0 0 0 0\n- 36.5490 -43.0220 75.1550 O 0 0 0 0 0 0 0 0 0 0 0 0\n- 35.9180 -42.5470 74.5930 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 2 1 0 0 0 0\n- 2 3 1 0 0 0 0\n- 3 4 1 0 0 0 0\n- 3 5 2 0 0 0 0\n- 6 5 1 0 0 0 0\n- 7 6 2 0 0 0 0\n- 8 2 2 0 0 0 0\n- 8 7 1 0 0 0 0\n- 9 8 1 0 0 0 0\n- 10 1 1 0 0 0 0\n- 11 10 1 0 0 0 0\n- 12 10 1 0 0 0 0\n- 13 10 1 0 0 0 0\n- 15 14 1 1 0 0 0\n- 15 13 1 0 0 0 0\n- 16 15 1 0 0 0 0\n- 17 16 1 0 0 0 0\n-M END\n-> <MODEL>\n-9\n-\n-> <REMARK>\n- VINA RESULT: -3.9 3.392 6.457\n- Name = \n- 6 active torsions:\n- status: ('A' for Active; 'I' for Inactive)\n- 1 A between atoms: C_1 and C_3\n- 2 A between atoms: C_3 and C_4\n- 3 A between atoms: C_3 and O_12\n- 4 A between atoms: C_4 and N_11\n- 5 A between atoms: C_5 and C_6\n- 6 A between atoms: C_5 and N_11\n- x y z vdW Elec q Type\n- _______ _______ _______ _____ _____ ______ ____\n-\n-> <TORSDO>\n-F 5\n-\n-> <SCORE>\n--3.9\n-\n-> <RMSD_LB>\n-3.392\n-\n-> <RMSD_UB>\n-6.457\n-\n-$$$$\n"

diff -r 7b2f205b3f68 -r 7a871df65202 test-data/ligand5_docked.sdf
--- a/test-data/ligand5_docked.sdf Wed Oct 02 12:49:30 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b"@@ -1,585 +0,0 @@\n-=\n- OpenBabel09021916103D\n-\n- 16 18 0 0 1 0 0 0 0 0999 V2000\n- 35.0590 -45.0990 74.7630 C 0 0 2 0 0 0 0 0 0 0 0 0\n- 34.0860 -44.5170 76.0710 S 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.6340 -44.9860 75.2690 C 0 0 2 0 0 0 0 0 0 0 0 0\n- 32.9250 -45.7580 74.1550 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.2710 -45.6170 73.7660 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.4120 -44.4980 75.8690 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.0250 -44.7450 77.1440 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.5510 -45.2630 77.7960 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 29.8160 -44.1840 77.4030 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 29.4430 -43.5860 76.2710 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.4050 -43.7650 75.2880 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.7470 -45.5580 74.8960 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.7940 -44.2900 75.3300 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 37.2940 -43.5240 75.1590 S 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.5060 -45.0170 74.8210 C 0 0 1 0 0 0 0 0 0 0 0 0\n- 37.4200 -46.0180 74.6370 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 5 1 1 0 0 0\n- 1 15 1 0 0 0 0\n- 1 2 1 0 0 0 0\n- 3 6 1 6 0 0 0\n- 3 2 1 0 0 0 0\n- 4 3 1 0 0 0 0\n- 5 4 1 0 0 0 0\n- 6 7 1 0 0 0 0\n- 7 9 1 0 0 0 0\n- 7 8 1 0 0 0 0\n- 10 9 2 0 0 0 0\n- 11 6 2 0 0 0 0\n- 11 10 1 0 0 0 0\n- 12 13 1 0 0 0 0\n- 14 13 1 0 0 0 0\n- 15 16 1 1 0 0 0\n- 15 14 1 0 0 0 0\n- 16 12 1 0 0 0 0\n-M END\n-> <MODEL>\n-1\n-\n-> <REMARK>\n- VINA RESULT: -5.2 0.000 0.000\n- Name = \n- 2 active torsions:\n- status: ('A' for Active; 'I' for Inactive)\n- 1 A between atoms: C_5 and C_7\n- 2 A between atoms: C_10 and C_11\n- x y z vdW Elec q Type\n- _______ _______ _______ _____ _____ ______ ____\n-\n-> <TORSDO>\n-F 2\n-\n-> <SCORE>\n--5.2\n-\n-> <RMSD_LB>\n-0.000\n-\n-> <RMSD_UB>\n-0.000\n-\n-$$$$\n-=\n- OpenBabel09021916103D\n-\n- 16 18 0 0 1 0 0 0 0 0999 V2000\n- 33.8500 -44.7820 74.9490 C 0 0 2 0 0 0 0 0 0 0 0 0\n- 35.4480 -44.9340 74.3020 S 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.1510 -44.3520 75.7640 C 0 0 2 0 0 0 0 0 0 0 0 0\n- 35.1930 -44.2700 76.7620 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 33.8900 -44.2950 76.2310 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 37.5630 -44.0470 75.6910 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.0840 -42.9300 75.1270 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 37.5490 -42.2030 74.7340 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 39.4400 -42.9460 75.1780 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 39.7680 -44.0930 75.7740 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.6290 -44.8130 76.1020 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.2980 -46.1930 72.6390 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 30.5800 -45.0930 72.9130 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 31.2460 -44.2290 74.2080 S 0 0 0 0 0 0 0 0 0 0 0 0\n- 32.6910 -45.1630 74.1630 C 0 0 1 0 0 0 0 0 0 0 0 0\n- 32.5530 -46.2320 73.3200 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 5 1 1 0 0 0\n- 2 1 1 0 0 0 0\n- 2 3 1 0 0 0 0\n- 3 6 1 6 0 0 0\n- 3 4 1 0 0 0 0\n- 5 4 1 0 0 0 0\n- 6 11 2 0 0 0 0\n- 7 9 1 0 0 0 0\n- 7 6 1 0 0 0 0\n- 8 7 1 0 0 0 0\n- 9 10 2 0 0 0 0\n- 10 11 1 0 0 0 0\n- 12 13 1 0 0 0 0\n- 12 16 1 0 0 0 0\n- 13 14 1 0 0 0 0\n- 15 16 1 6 0 0 0\n- 15 14 1 0 0 0 0\n- 15 1 1 0 0 0 0\n-M END\n-> <MODEL>\n-2\n-\n-> <REMARK>\n- VINA RESULT: -5.1 3.519 6.461\n- Name = \n- 2 active torsions:\n- status: ('A' for Active; 'I' for Inactive)\n- 1 A between atoms: C_5 and C_7\n- 2 A between atoms: C_10 and"..b"0.7220 C 0 0 2 0 0 0 0 0 0 0 0 0\n- 38.1600 -42.6100 70.5790 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 37.6960 -43.4000 71.6480 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 40.5350 -41.8360 69.8210 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 41.8320 -42.2250 69.8670 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 42.1950 -42.8820 70.5040 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 42.5650 -41.5890 68.9170 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 41.7130 -40.7870 68.2780 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 40.4400 -40.9040 68.8150 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.0960 -45.1840 75.9490 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 37.3050 -44.1650 76.3190 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 37.4170 -42.8720 75.2310 S 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.2710 -43.8340 74.0870 C 0 0 1 0 0 0 0 0 0 0 0 0\n- 38.6330 -45.0340 74.6340 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 5 1 1 0 0 0\n- 1 15 1 0 0 0 0\n- 2 1 1 0 0 0 0\n- 3 6 1 6 0 0 0\n- 3 2 1 0 0 0 0\n- 4 3 1 0 0 0 0\n- 4 5 1 0 0 0 0\n- 6 7 1 0 0 0 0\n- 7 8 1 0 0 0 0\n- 9 7 1 0 0 0 0\n- 10 11 1 0 0 0 0\n- 10 9 2 0 0 0 0\n- 11 6 2 0 0 0 0\n- 12 13 1 0 0 0 0\n- 14 13 1 0 0 0 0\n- 15 16 1 6 0 0 0\n- 15 14 1 0 0 0 0\n- 16 12 1 0 0 0 0\n-M END\n-> <MODEL>\n-8\n-\n-> <REMARK>\n- VINA RESULT: -4.6 6.586 8.750\n- Name = \n- 2 active torsions:\n- status: ('A' for Active; 'I' for Inactive)\n- 1 A between atoms: C_5 and C_7\n- 2 A between atoms: C_10 and C_11\n- x y z vdW Elec q Type\n- _______ _______ _______ _____ _____ ______ ____\n-\n-> <TORSDO>\n-F 2\n-\n-> <SCORE>\n--4.6\n-\n-> <RMSD_LB>\n-6.586\n-\n-> <RMSD_UB>\n-8.750\n-\n-$$$$\n-=\n- OpenBabel09021916103D\n-\n- 16 18 0 0 1 0 0 0 0 0999 V2000\n- 37.7170 -43.6430 74.0280 C 0 0 2 0 0 0 0 0 0 0 0 0\n- 37.8920 -43.5790 72.3070 S 0 0 0 0 0 0 0 0 0 0 0 0\n- 39.4300 -42.8130 72.4390 C 0 0 2 0 0 0 0 0 0 0 0 0\n- 39.8650 -42.8270 73.7550 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 38.8060 -43.0840 74.6470 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 39.9700 -42.2960 71.2010 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 41.2160 -42.5530 70.7350 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 41.8690 -43.1380 71.1830 H 0 0 0 0 0 0 0 0 0 0 0 0\n- 41.4450 -41.8960 69.5690 N 0 0 0 0 0 0 0 0 0 0 0 0\n- 40.3280 -41.2160 69.3100 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 39.3870 -41.4300 70.3060 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.5520 -45.3650 74.9520 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 34.6300 -44.6830 76.1060 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.1360 -43.9290 76.2750 S 0 0 0 0 0 0 0 0 0 0 0 0\n- 36.5430 -44.2440 74.6330 C 0 0 1 0 0 0 0 0 0 0 0 0\n- 35.6320 -45.0890 74.0590 C 0 0 0 0 0 0 0 0 0 0 0 0\n- 1 15 1 0 0 0 0\n- 1 5 1 1 0 0 0\n- 2 3 1 0 0 0 0\n- 2 1 1 0 0 0 0\n- 3 6 1 1 0 0 0\n- 3 4 1 0 0 0 0\n- 4 5 1 0 0 0 0\n- 7 8 1 0 0 0 0\n- 7 6 1 0 0 0 0\n- 9 7 1 0 0 0 0\n- 10 9 2 0 0 0 0\n- 10 11 1 0 0 0 0\n- 11 6 2 0 0 0 0\n- 12 13 1 0 0 0 0\n- 13 14 1 0 0 0 0\n- 15 16 1 6 0 0 0\n- 15 14 1 0 0 0 0\n- 16 12 1 0 0 0 0\n-M END\n-> <MODEL>\n-9\n-\n-> <REMARK>\n- VINA RESULT: -4.6 5.569 8.005\n- Name = \n- 2 active torsions:\n- status: ('A' for Active; 'I' for Inactive)\n- 1 A between atoms: C_5 and C_7\n- 2 A between atoms: C_10 and C_11\n- x y z vdW Elec q Type\n- _______ _______ _______ _____ _____ ______ ____\n-\n-> <TORSDO>\n-F 2\n-\n-> <SCORE>\n--4.6\n-\n-> <RMSD_LB>\n-5.569\n-\n-> <RMSD_UB>\n-8.005\n-\n-$$$$\n"

diff -r 7b2f205b3f68 -r 7a871df65202 test-data/ligand_docked.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ligand_docked.sdf Tue Jul 28 08:13:41 2020 -0400

b"@@ -0,0 +1,639 @@\n+=\n+ OpenBabel07272015383D\n+\n+ 18 19 0 0 1 0 0 0 0 0999 V2000\n+ 34.9430 -44.6790 75.3760 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.9810 -45.3120 74.1360 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 33.8000 -45.4860 73.4300 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 32.5650 -45.0460 73.9280 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.5600 -44.4150 75.1790 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 33.7310 -44.2300 75.8970 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 31.3080 -45.2470 73.1490 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.1600 -44.5040 73.4380 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 28.9830 -44.6880 72.7230 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 28.9280 -45.6270 71.7060 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 30.0510 -46.3710 71.4040 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 31.2300 -46.1900 72.1180 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 36.0990 -44.4850 76.1000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.4420 -44.6700 76.3250 C 0 0 0 0 0 1 0 0 0 0 0 0\n+ 37.3130 -44.2430 75.3990 C 0 0 2 0 0 3 0 0 0 0 0 0\n+ 37.3440 -42.7630 75.0270 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.7170 -42.4800 73.8720 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.9800 -41.9400 75.8900 O 0 0 0 0 0 1 0 0 0 0 0 0\n+ 1 6 1 0 0 0 0\n+ 1 13 1 0 0 0 0\n+ 2 1 2 0 0 0 0\n+ 3 4 2 0 0 0 0\n+ 3 2 1 0 0 0 0\n+ 4 5 1 0 0 0 0\n+ 5 6 2 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 7 4 1 0 0 0 0\n+ 9 8 2 0 0 0 0\n+ 10 9 1 0 0 0 0\n+ 11 10 2 0 0 0 0\n+ 11 12 1 0 0 0 0\n+ 12 7 2 0 0 0 0\n+ 15 13 1 0 0 0 0\n+ 15 14 1 1 0 0 0\n+ 16 15 1 0 0 0 0\n+ 16 18 1 0 0 0 0\n+ 17 16 2 0 0 0 0\n+M END\n+> <MODEL>\n+1\n+\n+> <REMARK>\n+ VINA RESULT: -6.3 0.000 0.000\n+ Name = \n+ 5 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_8\n+ 2 A between atoms: C_2 and C_13\n+ 3 A between atoms: C_8 and C_9\n+ 4 A between atoms: C_8 and O_18\n+ 5 A between atoms: C_10 and O_18\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-6.3\n+\n+> <RMSD_LB>\n+0.000\n+\n+> <RMSD_UB>\n+0.000\n+\n+$$$$\n+=\n+ OpenBabel07272015383D\n+\n+ 18 19 0 0 1 0 0 0 0 0999 V2000\n+ 32.0500 -45.3100 74.1090 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.9770 -45.9810 73.3150 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 34.3280 -45.8550 73.6020 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 34.7920 -45.0680 74.6660 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.8350 -44.4060 75.4450 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 32.4790 -44.5220 75.1760 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 36.2510 -44.9480 74.9520 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.1130 -46.0300 74.7440 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 38.4720 -45.9310 75.0130 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 38.9980 -44.7470 75.5040 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 38.1650 -43.6660 75.7140 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 36.8040 -43.7630 75.4470 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 30.7000 -45.4190 73.8560 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.0680 -44.0450 72.8440 C 0 0 0 0 0 1 0 0 0 0 0 0\n+ 30.2080 -45.0170 72.5830 C 0 0 2 0 0 3 0 0 0 0 0 0\n+ 29.7880 -46.2760 71.8300 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.6430 -46.7120 72.0560 O 0 0 0 0 0 1 0 0 0 0 0 0\n+ 30.6060 -46.7740 71.0310 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 6 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 2 1 2 0 0 0 0\n+ 3 4 2 0 0 0 0\n+ 4 7 1 0 0 0 0\n+ 4 5 1 0 0 0 0\n+ 6 5 2 0 0 0 0\n+ 7 12 1 0 0 0 0\n+ 8 7 2 0 0 0 0\n+ 8 9 1 0 "..b" 0 0 3 0 0 0 0 0 0\n+ 32.1990 -40.0210 79.2400 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 34.0870 -45.2390 75.8130 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.6280 -46.0800 73.6550 C 0 0 0 0 0 1 0 0 0 0 0 0\n+ 34.4040 -45.0340 74.4410 C 0 0 2 0 0 3 0 0 0 0 0 0\n+ 35.9180 -45.1470 74.2960 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.4550 -46.1740 74.7550 O 0 0 0 0 0 1 0 0 0 0 0 0\n+ 36.5160 -44.2200 73.7140 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 6 2 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 2 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 7 1 0 0 0 0\n+ 5 4 2 0 0 0 0\n+ 6 5 1 0 0 0 0\n+ 7 12 2 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 8 9 2 0 0 0 0\n+ 9 10 1 0 0 0 0\n+ 11 10 2 0 0 0 0\n+ 12 11 1 0 0 0 0\n+ 13 1 1 0 0 0 0\n+ 15 14 1 6 0 0 0\n+ 15 13 1 0 0 0 0\n+ 16 15 1 0 0 0 0\n+ 16 17 1 0 0 0 0\n+ 18 16 2 0 0 0 0\n+M END\n+> <MODEL>\n+8\n+\n+> <REMARK>\n+ VINA RESULT: -5.1 4.047 6.722\n+ Name = \n+ 5 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_8\n+ 2 A between atoms: C_2 and C_13\n+ 3 A between atoms: C_8 and C_9\n+ 4 A between atoms: C_8 and O_18\n+ 5 A between atoms: C_10 and O_18\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-5.1\n+\n+> <RMSD_LB>\n+4.047\n+\n+> <RMSD_UB>\n+6.722\n+\n+$$$$\n+=\n+ OpenBabel07272015383D\n+\n+ 18 19 0 0 1 0 0 0 0 0999 V2000\n+ 34.7830 -43.5140 77.4980 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.4850 -42.9340 78.5520 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 34.8800 -41.9340 79.2970 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 33.5800 -41.4840 79.0200 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.9010 -42.0860 77.9530 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 33.4900 -43.0900 77.1990 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 32.9520 -40.4040 79.8370 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.6620 -39.9490 79.5500 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 31.0700 -38.9400 80.3000 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 31.7620 -38.3580 81.3500 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 33.0380 -38.7940 81.6500 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 33.6320 -39.8030 80.9010 C 0 0 0 0 0 3 0 0 0 0 0 0\n+ 35.3540 -44.5150 76.7420 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.8330 -45.5620 74.6810 C 0 0 0 0 0 1 0 0 0 0 0 0\n+ 35.7350 -44.2270 75.4010 C 0 0 2 0 0 3 0 0 0 0 0 0\n+ 37.0480 -43.4510 75.4500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.0400 -42.2980 74.9780 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.0320 -44.0110 75.9720 O 0 0 0 0 0 1 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 2 0 0 0 0\n+ 4 3 1 0 0 0 0\n+ 4 7 1 0 0 0 0\n+ 5 4 2 0 0 0 0\n+ 6 1 2 0 0 0 0\n+ 6 5 1 0 0 0 0\n+ 7 12 1 0 0 0 0\n+ 8 7 2 0 0 0 0\n+ 8 9 1 0 0 0 0\n+ 9 10 2 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 12 11 2 0 0 0 0\n+ 13 1 1 0 0 0 0\n+ 15 14 1 6 0 0 0\n+ 15 16 1 0 0 0 0\n+ 15 13 1 0 0 0 0\n+ 16 18 1 0 0 0 0\n+ 17 16 2 0 0 0 0\n+M END\n+> <MODEL>\n+9\n+\n+> <REMARK>\n+ VINA RESULT: -5.0 4.531 6.799\n+ Name = \n+ 5 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_8\n+ 2 A between atoms: C_2 and C_13\n+ 3 A between atoms: C_8 and C_9\n+ 4 A between atoms: C_8 and O_18\n+ 5 A between atoms: C_10 and O_18\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-5.0\n+\n+> <RMSD_LB>\n+4.531\n+\n+> <RMSD_UB>\n+6.799\n+\n+$$$$\n"