Galaxy |

Changeset 4:de4c80d17527 (2020-07-28)

Previous changeset 3:015ccbd1ad68 (2020-04-09) Next changeset 5:a5f4b80e6769 (2020-10-19)

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

modified:
change_title_to_metadata_value.py
cheminfolib.py
distance_finder.py
macros.xml
multi_obgrep.py
ob_addh.py
ob_filter.py
ob_genProp.py
ob_prepare_ligands.xml
ob_remIons.py
ob_spectrophore_search.py
remove_protonation_state.py
subsearch.py
test-data/ob_convert_on_CID2244.cml
test-data/ob_convert_on_CID2244.pdb
test-data/ob_depiction_svg_on_8_mol.svg
test-data/ob_prepare_ligands1.pdbqt
test-data/ob_prepare_ligands2.pdbqt
test-data/split1.pdbqt
test-data/split2.pdbqt

diff -r 015ccbd1ad68 -r de4c80d17527 change_title_to_metadata_value.py
--- a/change_title_to_metadata_value.py Thu Apr 09 10:10:31 2020 -0400
+++ b/change_title_to_metadata_value.py Tue Jul 28 08:40:43 2020 -0400

@@ -9,13 +9,13 @@
import os
import sys
import argparse
-import openbabel
-openbabel.obErrorLog.StopLogging()
-import pybel
import random
import string

+from openbabel import openbabel, pybel
+openbabel.obErrorLog.StopLogging()
+
def main():
parser = argparse.ArgumentParser(
description="Change the title from a molecule file to metadata \

diff -r 015ccbd1ad68 -r de4c80d17527 cheminfolib.py
--- a/cheminfolib.py Thu Apr 09 10:10:31 2020 -0400
+++ b/cheminfolib.py Tue Jul 28 08:40:43 2020 -0400

@@ -13,8 +13,8 @@
     print('psycopg2 is not available. It is currently used in the pgchem wrappers, that are not shipped with default CTB')

try:
-    import pybel
-    import openbabel
+    from openbabel import openbabel, pybel
+    openbabel.obErrorLog.StopLogging()
except:
     print('OpenBabel could not be found. A few functions are not available without OpenBabel.')

diff -r 015ccbd1ad68 -r de4c80d17527 distance_finder.py
--- a/distance_finder.py Thu Apr 09 10:10:31 2020 -0400
+++ b/distance_finder.py Tue Jul 28 08:40:43 2020 -0400

@@ -12,10 +12,10 @@
# there would be properties for distance1, distance2 and distance3.

import argparse, os, sys, math
+
from openbabel import pybel

-
def log(*args, **kwargs):
"""Log output to STDERR
"""

diff -r 015ccbd1ad68 -r de4c80d17527 macros.xml
--- a/macros.xml Thu Apr 09 10:10:31 2020 -0400
+++ b/macros.xml Tue Jul 28 08:40:43 2020 -0400

@@ -1,9 +1,9 @@
<macros>
-    <token name="@VERSION@">2.4.2.2</token>
+    <token name="@TOOL_VERSION@">3.1.1</token>

     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.4.1">openbabel</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">openbabel</requirement>
             <requirement type="package" version="3">python</requirement>
             <yield />
         </requirements>

diff -r 015ccbd1ad68 -r de4c80d17527 multi_obgrep.py
--- a/multi_obgrep.py Thu Apr 09 10:10:31 2020 -0400
+++ b/multi_obgrep.py Tue Jul 28 08:40:43 2020 -0400

@@ -6,15 +6,14 @@
"""
import sys, os
import argparse
-import openbabel
-openbabel.obErrorLog.StopLogging()
-import pybel
import multiprocessing
import tempfile
import subprocess
import shutil
import shlex

+from openbabel import openbabel, pybel
+openbabel.obErrorLog.StopLogging()
def parse_command_line():
parser = argparse.ArgumentParser()
parser.add_argument('-i', '--infile', required=True, help='Molecule file.')

diff -r 015ccbd1ad68 -r de4c80d17527 ob_addh.py
--- a/ob_addh.py Thu Apr 09 10:10:31 2020 -0400
+++ b/ob_addh.py Tue Jul 28 08:40:43 2020 -0400

@@ -5,9 +5,9 @@
"""
import sys, os
import argparse
-import openbabel
+
+from openbabel import openbabel, pybel
openbabel.obErrorLog.StopLogging()
-import pybel

def parse_command_line(argv):
parser = argparse.ArgumentParser()

diff -r 015ccbd1ad68 -r de4c80d17527 ob_filter.py
--- a/ob_filter.py Thu Apr 09 10:10:31 2020 -0400
+++ b/ob_filter.py Tue Jul 28 08:40:43 2020 -0400

@@ -10,9 +10,9 @@
import argparse
import cheminfolib
import json
-import pybel
import shlex, subprocess

+from openbabel import pybel
cheminfolib.pybel_stop_logging()

def parse_command_line():

diff -r 015ccbd1ad68 -r de4c80d17527 ob_genProp.py
--- a/ob_genProp.py Thu Apr 09 10:10:31 2020 -0400
+++ b/ob_genProp.py Tue Jul 28 08:40:43 2020 -0400

@@ -8,9 +8,9 @@
import argparse
import openbabel
openbabel.obErrorLog.StopLogging()
-import pybel
import cheminfolib

+from openbabel import pybel

def parse_command_line(argv):
parser = argparse.ArgumentParser()

diff -r 015ccbd1ad68 -r de4c80d17527 ob_prepare_ligands.xml
--- a/ob_prepare_ligands.xml Thu Apr 09 10:10:31 2020 -0400
+++ b/ob_prepare_ligands.xml Tue Jul 28 08:40:43 2020 -0400

[

@@ -1,7 +1,8 @@
-<tool id="prepare_ligands_for_docking" name="Prepare ligands for docking" version="@VERSION@.0">
+<tool id="prepare_ligands_for_docking" name="Prepare ligands for docking" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
     <description>Tool to prepare ligands for docking with tools like Autodock Vina</description>
     <macros>
         <import>macros.xml</import>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive"><![CDATA[

diff -r 015ccbd1ad68 -r de4c80d17527 ob_remIons.py
--- a/ob_remIons.py Thu Apr 09 10:10:31 2020 -0400
+++ b/ob_remIons.py Tue Jul 28 08:40:43 2020 -0400

@@ -6,9 +6,9 @@
"""
import sys, os
import argparse
-import openbabel
+
+from openbabel import openbabel, pybel
openbabel.obErrorLog.StopLogging()
-import pybel

def parse_command_line():
parser = argparse.ArgumentParser()

diff -r 015ccbd1ad68 -r de4c80d17527 ob_spectrophore_search.py
--- a/ob_spectrophore_search.py Thu Apr 09 10:10:31 2020 -0400
+++ b/ob_spectrophore_search.py Tue Jul 28 08:40:43 2020 -0400

@@ -6,12 +6,11 @@
"""
import sys, os
import argparse
-import openbabel
-openbabel.obErrorLog.StopLogging()
-import pybel
import math
import numpy as np

+from openbabel import openbabel, pybel
+openbabel.obErrorLog.StopLogging()
#TODO get rid of eval()

global spectrophore

diff -r 015ccbd1ad68 -r de4c80d17527 remove_protonation_state.py
--- a/remove_protonation_state.py Thu Apr 09 10:10:31 2020 -0400
+++ b/remove_protonation_state.py Tue Jul 28 08:40:43 2020 -0400

diff -r 015ccbd1ad68 -r de4c80d17527 subsearch.py
--- a/subsearch.py Thu Apr 09 10:10:31 2020 -0400
+++ b/subsearch.py Tue Jul 28 08:40:43 2020 -0400

@@ -6,14 +6,14 @@
"""
import sys, os
import argparse
-import openbabel
-openbabel.obErrorLog.StopLogging()
-import pybel
import multiprocessing
import tempfile
import subprocess
import shutil

+from openbabel import openbabel, pybel
+openbabel.obErrorLog.StopLogging()
+
def parse_command_line():
parser = argparse.ArgumentParser()
parser.add_argument('-i', '--infile', required=True, help='Molecule file.')

diff -r 015ccbd1ad68 -r de4c80d17527 test-data/ob_convert_on_CID2244.cml
--- a/test-data/ob_convert_on_CID2244.cml Thu Apr 09 10:10:31 2020 -0400
+++ b/test-data/ob_convert_on_CID2244.cml Tue Jul 28 08:40:43 2020 -0400

@@ -1,27 +1,27 @@
<?xml version="1.0"?>
<molecule id="id2244" xmlns="http://www.xml-cml.org/schema">
  <atomArray>
-  <atom id="a1" elementType="O" x2="3.732000" y2="-0.060000"/>
-  <atom id="a2" elementType="O" x2="6.330100" y2="1.440000"/>
-  <atom id="a3" elementType="O" x2="4.598100" y2="1.440000"/>
-  <atom id="a4" elementType="O" x2="2.866000" y2="-1.560000"/>
-  <atom id="a5" elementType="C" x2="4.598100" y2="-0.560000"/>
-  <atom id="a6" elementType="C" x2="5.464100" y2="-0.060000"/>
-  <atom id="a7" elementType="C" x2="4.598100" y2="-1.560000"/>
-  <atom id="a8" elementType="C" x2="6.330100" y2="-0.560000"/>
-  <atom id="a9" elementType="C" x2="5.464100" y2="-2.060000"/>
-  <atom id="a10" elementType="C" x2="6.330100" y2="-1.560000"/>
-  <atom id="a11" elementType="C" x2="5.464100" y2="0.940000"/>
-  <atom id="a12" elementType="C" x2="2.866000" y2="-0.560000"/>
-  <atom id="a13" elementType="C" x2="2.000000" y2="-0.060000"/>
-  <atom id="a14" elementType="H" x2="4.061100" y2="-1.870000"/>
-  <atom id="a15" elementType="H" x2="6.867100" y2="-0.250000"/>
-  <atom id="a16" elementType="H" x2="5.464100" y2="-2.680000"/>
-  <atom id="a17" elementType="H" x2="6.867100" y2="-1.870000"/>
-  <atom id="a18" elementType="H" x2="2.310000" y2="0.476900"/>
-  <atom id="a19" elementType="H" x2="1.463100" y2="0.250000"/>
-  <atom id="a20" elementType="H" x2="1.690000" y2="-0.596900"/>
-  <atom id="a21" elementType="H" x2="6.330100" y2="2.060000"/>
+  <atom id="a1" elementType="O" hydrogenCount="0" x2="3.732000" y2="-0.060000"/>
+  <atom id="a2" elementType="O" hydrogenCount="1" x2="6.330100" y2="1.440000"/>
+  <atom id="a3" elementType="O" hydrogenCount="0" x2="4.598100" y2="1.440000"/>
+  <atom id="a4" elementType="O" hydrogenCount="0" x2="2.866000" y2="-1.560000"/>
+  <atom id="a5" elementType="C" hydrogenCount="0" x2="4.598100" y2="-0.560000"/>
+  <atom id="a6" elementType="C" hydrogenCount="0" x2="5.464100" y2="-0.060000"/>
+  <atom id="a7" elementType="C" hydrogenCount="1" x2="4.598100" y2="-1.560000"/>
+  <atom id="a8" elementType="C" hydrogenCount="1" x2="6.330100" y2="-0.560000"/>
+  <atom id="a9" elementType="C" hydrogenCount="1" x2="5.464100" y2="-2.060000"/>
+  <atom id="a10" elementType="C" hydrogenCount="1" x2="6.330100" y2="-1.560000"/>
+  <atom id="a11" elementType="C" hydrogenCount="0" x2="5.464100" y2="0.940000"/>
+  <atom id="a12" elementType="C" hydrogenCount="0" x2="2.866000" y2="-0.560000"/>
+  <atom id="a13" elementType="C" hydrogenCount="3" x2="2.000000" y2="-0.060000"/>
+  <atom id="a14" elementType="H" hydrogenCount="0" x2="4.061100" y2="-1.870000"/>
+  <atom id="a15" elementType="H" hydrogenCount="0" x2="6.867100" y2="-0.250000"/>
+  <atom id="a16" elementType="H" hydrogenCount="0" x2="5.464100" y2="-2.680000"/>
+  <atom id="a17" elementType="H" hydrogenCount="0" x2="6.867100" y2="-1.870000"/>
+  <atom id="a18" elementType="H" hydrogenCount="0" x2="2.310000" y2="0.476900"/>
+  <atom id="a19" elementType="H" hydrogenCount="0" x2="1.463100" y2="0.250000"/>
+  <atom id="a20" elementType="H" hydrogenCount="0" x2="1.690000" y2="-0.596900"/>
+  <atom id="a21" elementType="H" hydrogenCount="0" x2="6.330100" y2="2.060000"/>
  </atomArray>
  <bondArray>
   <bond atomRefs2="a1 a5" order="1"/>

diff -r 015ccbd1ad68 -r de4c80d17527 test-data/ob_convert_on_CID2244.pdb
--- a/test-data/ob_convert_on_CID2244.pdb Thu Apr 09 10:10:31 2020 -0400
+++ b/test-data/ob_convert_on_CID2244.pdb Tue Jul 28 08:40:43 2020 -0400

@@ -1,5 +1,5 @@
COMPND    2244
-AUTHOR    GENERATED BY OPEN BABEL 2.3.90
+AUTHOR    GENERATED BY OPEN BABEL 3.1.0
HETATM    1  O   UNL     1       3.732  -0.060   0.000  1.00  0.00           O
HETATM    2  O   UNL     1       6.330   1.440   0.000  1.00  0.00           O
HETATM    3  O   UNL     1       4.598   1.440   0.000  1.00  0.00           O
@@ -23,16 +23,16 @@
HETATM   21  H   UNL     1       6.330   2.060   0.000  1.00  0.00           H
CONECT    1    5   12
CONECT    2   11   21
-CONECT    3   11
-CONECT    4   12
-CONECT    5    1    6    7
-CONECT    6    5    8   11
-CONECT    7    5    9   14
-CONECT    8    6   10   15
-CONECT    9    7   10   16
-CONECT   10    8    9   17
-CONECT   11    2    3    6
-CONECT   12    1    4   13
+CONECT    3   11   11
+CONECT    4   12   12
+CONECT    5    1    6    7    7
+CONECT    6    5    8    8   11
+CONECT    7    5    5    9   14
+CONECT    8    6    6   10   15
+CONECT    9    7   10   10   16
+CONECT   10    8    9    9   17
+CONECT   11    2    3    3    6
+CONECT   12    1    4    4   13
CONECT   13   12   18   19   20
CONECT   14    7
CONECT   15    8

diff -r 015ccbd1ad68 -r de4c80d17527 test-data/ob_depiction_svg_on_8_mol.svg
--- a/test-data/ob_depiction_svg_on_8_mol.svg Thu Apr 09 10:10:31 2020 -0400
+++ b/test-data/ob_depiction_svg_on_8_mol.svg Tue Jul 28 08:40:43 2020 -0400

b'@@ -7,44 +7,44 @@\n <g transform="translate(0,0)">\n <svg width="33.3333" height="33.3333" x="0" y="0" viewBox="0 0 300 258.564"\n font-family="sans-serif" stroke="rgb(0,0,0)" stroke-width="4" stroke-linecap="round">\n-<line x1="103.0" y1="191.6" x2="103.0" y2="205.6" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="97.0" y1="191.6" x2="97.0" y2="205.6" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="112.8" y1="182.5" x2="124.9" y2="189.5" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="109.8" y1="187.7" x2="121.9" y2="194.7" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="180.0" y1="109.3" x2="207.0" y2="109.3" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="223.0" y1="122.3" x2="223.0" y2="136.3" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="217.0" y1="122.3" x2="217.0" y2="136.3" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="233.0" y1="106.3" x2="247.0" y2="106.3" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="233.0" y1="112.3" x2="247.0" y2="112.3" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="220.0" y1="96.3" x2="220.0" y2="82.3" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="160.0" y1="74.6" x2="173.5" y2="51.3" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="180.0" y1="109.3" x2="160.0" y2="143.9" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="160.0" y1="143.9" x2="120.0" y2="143.9" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="154.0" y1="136.7" x2="126.0" y2="136.7" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="120.0" y1="143.9" x2="100.0" y2="109.3" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="100.0" y1="109.3" x2="120.0" y2="74.6" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="109.2" y1="107.7" x2="123.2" y2="83.4" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="120.0" y1="74.6" x2="160.0" y2="74.6" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="160.0" y1="74.6" x2="180.0" y2="109.3" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="156.8" y1="83.4" x2="170.8" y2="107.7" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="120.0" y1="143.9" x2="106.5" y2="167.3" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="87.0" y1="178.6" x2="73.0" y2="178.6" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="53.5" y1="167.3" x2="40.0" y2="143.9" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="40.0" y1="143.9" x2="53.5" y2="120.5" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="73.0" y1="109.3" x2="100.0" y2="109.3" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<text x="94.000000" y="186.564065" fill="rgb(178,178,0)" stroke="rgb(178,178,0)" stroke-width="1" font-size="16" >S</text>\n-<text x="174.000000" y="48.000000" fill="rgb(30,239,30)" stroke="rgb(30,239,30)" stroke-width="1" font-size="16" >Cl</text>\n-<text x="216.000000" y="77.282032" fill="rgb(12,12,255)" stroke="rgb(12,12,255)" stroke-width="1" font-size="16" >NH</text>\n-<text x="240.000000" y="80.962032" fill="rgb(12,12,255)" stroke="rgb(12,12,255)" stroke-width="1" font-size="13" >2</text>\n-<text x="254.000000" y="117.282032" fill="rgb(255,12,12)" stroke="rgb(255,12,12)" stroke-width="1" font-size="16" >O</text>\n-<text x="214.000000" y="157.282032" fill="rgb(255,12,12)" stroke="rgb(255,12,12)" stroke-width="1" font-size="16" >O</text>\n-<text x="214.000000" y="117.282032" fill="rgb(178,178,0)" stroke="rgb(178,178,0)" stroke-width="1" font-size="16" >S</text>\n-<text x="54.000000" y="186.564065" fill="rgb(12,12,255)" stroke="rgb(12,12,255)" stroke-width="1" font-size="16" >N</text>\n-<text x="54.000000" y="202.564065" fill="rgb(12,12,255)" stroke="rgb(12,12,255)" stroke-width="1" font-size="16" >H</text>\n-<text x="128.641016" y="206.564065" fill="rgb(255,12,12)" stroke="rgb(255,12,12)" stroke-width="1" font-size="16" >O</text>\n-<text x="94.000000" y="226.564065" fill="rgb(255,12,12)" stroke="rgb(255,12,12)" stroke-width="1" font-size="16" >O</text>\n-<text x="54.000000" y="117.282032" fill="rgb(12,12,255)" stroke="rgb(12,12,255)" stroke-width="'..b'roke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="83.4" y1="63.2" x2="107.7" y2="49.2" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="109.3" y1="40.0" x2="143.9" y2="60.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="143.9" y1="60.0" x2="143.9" y2="100.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="136.7" y1="66.0" x2="136.7" y2="94.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="143.9" y1="100.0" x2="109.3" y2="120.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="109.3" y1="120.0" x2="74.6" y2="100.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="107.7" y1="110.8" x2="83.4" y2="96.8" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<line x1="74.6" y1="100.0" x2="74.6" y2="60.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n-<text x="68.641016" y="228.000000" fill="rgb(255,12,12)" stroke="rgb(255,12,12)" stroke-width="1" font-size="16" >O</text>\n-<text x="103.282032" y="168.000000" fill="rgb(255,12,12)" stroke="rgb(255,12,12)" stroke-width="1" font-size="16" >O</text>\n-<text x="172.564065" y="168.000000" fill="rgb(255,12,12)" stroke="rgb(255,12,12)" stroke-width="1" font-size="16" >O</text>\n-<text x="218.005081" y="85.888000" fill="rgb(255,12,12)" stroke="rgb(255,12,12)" stroke-width="1" font-size="16" >_</text>\n-<text x="207.205081" y="108.000000" fill="rgb(255,12,12)" stroke="rgb(255,12,12)" stroke-width="1" font-size="16" >O</text>\n+<line x1="40.0" y1="160.0" x2="74.6" y2="180.0" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="77.6" y1="180.0" x2="77.6" y2="207.0" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="71.6" y1="180.0" x2="71.6" y2="207.0" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="74.6" y1="180.0" x2="98.0" y2="166.5" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="109.3" y1="147.0" x2="109.3" y2="120.0" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="143.9" y1="100.0" x2="178.6" y2="120.0" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="181.6" y1="120.0" x2="181.6" y2="147.0" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="175.6" y1="120.0" x2="175.6" y2="147.0" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="178.6" y1="120.0" x2="201.9" y2="106.5" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="74.6" y1="60.0" x2="109.3" y2="40.0" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="83.4" y1="63.2" x2="107.7" y2="49.2" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="109.3" y1="40.0" x2="143.9" y2="60.0" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="143.9" y1="60.0" x2="143.9" y2="100.0" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="136.7" y1="66.0" x2="136.7" y2="94.0" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="143.9" y1="100.0" x2="109.3" y2="120.0" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="109.3" y1="120.0" x2="74.6" y2="100.0" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="107.7" y1="110.8" x2="83.4" y2="96.8" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<line x1="74.6" y1="100.0" x2="74.6" y2="60.0" opacity="1.0" stroke="rgb(0,0,0)" stroke-width="4.0"/>\n+<text x="68.641016" y="228.000000" fill="rgb(255,12,12)" stroke-width="0" font-weight="bold" font-size="16" >O</text>\n+<text x="103.282032" y="168.000000" fill="rgb(255,12,12)" stroke-width="0" font-weight="bold" font-size="16" >O</text>\n+<text x="172.564065" y="168.000000" fill="rgb(255,12,12)" stroke-width="0" font-weight="bold" font-size="16" >O</text>\n+<text x="218.005081" y="85.888000" fill="rgb(255,12,12)" stroke-width="0" font-weight="bold" font-size="16" >_</text>\n+<text x="207.205081" y="108.000000" fill="rgb(255,12,12)" stroke-width="0" font-weight="bold" font-size="16" >O</text>\n </svg>\n </g>\n <text text-anchor="middle" font-size="2.000000" fill ="black" font-family="sans-serif"\n'

diff -r 015ccbd1ad68 -r de4c80d17527 test-data/ob_prepare_ligands1.pdbqt
--- a/test-data/ob_prepare_ligands1.pdbqt Thu Apr 09 10:10:31 2020 -0400
+++ b/test-data/ob_prepare_ligands1.pdbqt Tue Jul 28 08:40:43 2020 -0400

@@ -6,36 +6,36 @@
REMARK                            x       y       z     vdW  Elec       q    Type
REMARK                         _______ _______ _______ _____ _____    ______ ____
ROOT
-ATOM      1  C   UNL     1      -3.701   0.824   0.000  0.00  0.00    +0.163 A
-ATOM      2  N   UNL     1      -2.491   1.539   0.000  0.00  0.00    -0.223 NA
-ATOM      3  C   UNL     1      -1.227   0.824   0.000  0.00  0.00    +0.124 A
-ATOM      4  C   UNL     1      -1.227  -0.605   0.000  0.00  0.00    +0.196 A
-ATOM      5  O   UNL     1       0.000  -1.319   0.000  0.00  0.00    -0.432 OA
-ATOM      6  C   UNL     1       1.227  -0.605   0.000  0.00  0.00    +0.230 A
-ATOM      7  N   UNL     1       2.473  -1.319   0.000  0.00  0.00    -0.220 NA
-ATOM      8  C   UNL     1       3.737  -0.605   0.000  0.00  0.00    +0.114 A
-ATOM      9  C   UNL     1       3.737   0.824   0.000  0.00  0.00    +0.021 A
-ATOM     10  C   UNL     1       2.473   1.539   0.000  0.00  0.00    +0.017 A
-ATOM     11  C   UNL     1      -2.491  -1.319   0.000  0.00  0.00    +0.169 A
-ATOM     12  N   UNL     1      -2.506  -2.820   0.000  0.00  0.00    -0.308 N
-ATOM     13  C   UNL     1      -3.813  -3.555   0.000  0.00  0.00    +0.134 C
-ATOM     14  C   UNL     1      -3.831  -5.055   0.000  0.00  0.00    +0.178 C
-ATOM     15  O   UNL     1      -2.540  -5.820   0.000  0.00  0.00    -0.377 OA
-ATOM     16  C   UNL     1      -1.233  -5.085   0.000  0.00  0.00    +0.178 C
-ATOM     17  C   UNL     1      -1.216  -3.585   0.000  0.00  0.00    +0.134 C
-ATOM     18  C   UNL     1       1.227   0.824   0.000  0.00  0.00    +0.066 A
-ATOM     19  N   UNL     1      -3.701  -0.605   0.000  0.00  0.00    -0.209 NA
+ATOM      1  C   UNL     1      -3.701   0.824   0.000  0.00  0.00    +0.000 A
+ATOM      2  N   UNL     1      -3.701  -0.605   0.000  0.00  0.00    +0.000 NA
+ATOM      3  C   UNL     1      -2.491  -1.319   0.000  0.00  0.00    +0.000 A
+ATOM      4  N   UNL     1      -2.506  -2.820   0.000  0.00  0.00    +0.000 N
+ATOM      5  C   UNL     1      -1.216  -3.585   0.000  0.00  0.00    +0.000 C
+ATOM      6  C   UNL     1      -1.233  -5.085   0.000  0.00  0.00    +0.000 C
+ATOM      7  O   UNL     1      -2.540  -5.820   0.000  0.00  0.00    +0.000 OA
+ATOM      8  C   UNL     1      -3.831  -5.055   0.000  0.00  0.00    +0.000 C
+ATOM      9  C   UNL     1      -3.813  -3.555   0.000  0.00  0.00    +0.000 C
+ATOM     10  C   UNL     1      -1.227  -0.605   0.000  0.00  0.00    +0.000 A
+ATOM     11  O   UNL     1       0.000  -1.319   0.000  0.00  0.00    +0.000 OA
+ATOM     12  C   UNL     1       1.227  -0.605   0.000  0.00  0.00    +0.000 A
+ATOM     13  N   UNL     1       2.473  -1.319   0.000  0.00  0.00    +0.000 NA
+ATOM     14  C   UNL     1       3.737  -0.605   0.000  0.00  0.00    +0.000 A
+ATOM     15  C   UNL     1       3.737   0.824   0.000  0.00  0.00    +0.000 A
+ATOM     16  C   UNL     1       2.473   1.539   0.000  0.00  0.00    +0.000 A
+ATOM     17  C   UNL     1       1.227   0.824   0.000  0.00  0.00    +0.000 A
+ATOM     18  C   UNL     1      -1.227   0.824   0.000  0.00  0.00    +0.000 A
+ATOM     19  N   UNL     1      -2.491   1.539   0.000  0.00  0.00    +0.000 NA
ENDROOT
-BRANCH   1  22
-ATOM     20  C   UNL     1      -7.602   1.560   0.000  0.00  0.00    +0.118 A
-ATOM     21  C   UNL     1      -6.301   0.814   0.000  0.00  0.00    +0.057 A
-ATOM     22  C   UNL     1      -5.004   1.568   0.000  0.00  0.00    +0.023 A
-ATOM     23  C   UNL     1      -5.009   3.068   0.000  0.00  0.00    +0.012 A
-ATOM     24  C   UNL     1      -6.310   3.814   0.000  0.00  0.00    +0.004 A
-ATOM     25  C   UNL     1      -7.607   3.060   0.000  0.00  0.00    +0.045 A
+BRANCH   1  24
+ATOM     20  C   UNL     1      -7.602   1.560   0.000  0.00  0.00    +0.000 A
+ATOM     21  C   UNL     1      -7.607   3.060   0.000  0.00  0.00    +0.000 A
+ATOM     22  C   UNL     1      -6.310   3.814   0.000  0.00  0.00    +0.000 A
+ATOM     23  C   UNL     1      -5.009   3.068   0.000  0.00  0.00    +0.000 A
+ATOM     24  C   UNL     1      -5.004   1.568   0.000  0.00  0.00    +0.000 A
+ATOM     25  C   UNL     1      -6.301   0.814   0.000  0.00  0.00    +0.000 A
BRANCH  20  26
-ATOM     26  O   UNL     1      -8.640   0.957   0.000  0.00  0.00    -0.507 OA
-ATOM     27  H   UNL     1      -9.453   1.423   0.000  0.00  0.00    +0.292 HD
+ATOM     26  O   UNL     1      -8.640   0.957   0.000  0.00  0.00    +0.000 OA
+ATOM     27  H   UNL     1      -9.453   1.423   0.000  0.00  0.00    +0.000 HD
ENDBRANCH  20  26
-ENDBRANCH   1  22
+ENDBRANCH   1  24
TORSDOF 2

diff -r 015ccbd1ad68 -r de4c80d17527 test-data/ob_prepare_ligands2.pdbqt
--- a/test-data/ob_prepare_ligands2.pdbqt Thu Apr 09 10:10:31 2020 -0400
+++ b/test-data/ob_prepare_ligands2.pdbqt Tue Jul 28 08:40:43 2020 -0400

@@ -10,55 +10,55 @@
REMARK                            x       y       z     vdW  Elec       q    Type
REMARK                         _______ _______ _______ _____ _____    ______ ____
ROOT
-ATOM      1  C   UNL     1      -2.650   2.250   0.000  0.00  0.00    +0.191 C
-ATOM      2  C   UNL     1      -1.830   0.930   0.000  0.00  0.00    +0.174 C
-ATOM      3  N   UNL     1      -0.980  -0.780   0.000  0.00  0.00    -0.307 N
-ATOM      4  C   UNL     1       0.240  -1.440   0.000  0.00  0.00    +0.077 A
-ATOM      5  C   UNL     1       0.240  -2.770   0.000  0.00  0.00    +0.015 A
-ATOM      6  C   UNL     1       1.430  -3.470   0.000  0.00  0.00    -0.008 A
-ATOM      7  C   UNL     1       2.660  -2.750   0.000  0.00  0.00    +0.052 A
-ATOM      8  C   UNL     1       2.680  -1.460   0.000  0.00  0.00    +0.022 A
-ATOM      9  C   UNL     1       3.790   0.560   0.000  0.00  0.00    +0.008 A
-ATOM     10  C   UNL     1       2.640   1.240   0.000  0.00  0.00    +0.052 A
-ATOM     11  N   UNL     1       1.490   0.540   0.000  0.00  0.00    -0.311 N
-ATOM     12  C   UNL     1       0.500   2.180   0.000  0.00  0.00    +0.224 C
-ATOM     13  C   UNL     1      -0.240   3.520   0.000  0.00  0.00    +0.080 C
-ATOM     14  C   UNL     1       2.640   2.590   0.000  0.00  0.00    +0.026 A
-ATOM     15  C   UNL     1       3.810   3.290   0.000  0.00  0.00    +0.002 A
-ATOM     16  C   UNL     1       4.960   2.630   0.000  0.00  0.00    +0.001 A
-ATOM     17  C   UNL     1       4.960   1.280   0.000  0.00  0.00    +0.010 A
-ATOM     18  C   UNL     1       3.850  -3.630   0.000  0.00  0.00    +0.245 C
-ATOM     19  O   UNL     1       4.997  -3.278   0.000  0.00  0.00    -0.270 OA
-ATOM     20  N   UNL     1       3.260  -5.080   0.000  0.00  0.00    -0.307 N
-ATOM     21  H   UNL     1       3.779  -5.916   0.000  0.00  0.00    +0.149 HD
-ATOM     22  C   UNL     1       1.760  -4.970   0.000  0.00  0.00    +0.141 C
-ATOM     23  C   UNL     1      -2.130  -2.790   0.000  0.00  0.00    +0.008 A
-ATOM     24  C   UNL     1      -3.340  -3.470   0.000  0.00  0.00    +0.010 A
-ATOM     25  C   UNL     1      -4.580  -2.770   0.000  0.00  0.00    +0.001 A
-ATOM     26  C   UNL     1      -4.550  -1.480   0.000  0.00  0.00    +0.002 A
-ATOM     27  C   UNL     1      -3.320  -0.760   0.000  0.00  0.00    +0.026 A
-ATOM     28  C   UNL     1       1.450  -0.760   0.000  0.00  0.00    +0.077 A
-ATOM     29  C   UNL     1      -2.130  -1.460   0.000  0.00  0.00    +0.053 A
-ATOM     30  C   UNL     1      -3.030   0.930   0.000  0.00  0.00    +0.069 C
-ATOM     31  O   UNL     1      -1.060   2.180   0.000  0.00  0.00    -0.328 OA
-ATOM     32  C   UNL     1      -1.810   3.500   0.000  0.00  0.00    +0.114 C
+ATOM      1  C   UNL     1      -2.650   2.250   0.000  0.00  0.00    +0.000 C
+ATOM      2  C   UNL     1      -1.810   3.500   0.000  0.00  0.00    +0.000 C
+ATOM      3  C   UNL     1      -0.240   3.520   0.000  0.00  0.00    +0.000 C
+ATOM      4  C   UNL     1       0.500   2.180   0.000  0.00  0.00    +0.000 C
+ATOM      5  O   UNL     1      -1.060   2.180   0.000  0.00  0.00    +0.000 OA
+ATOM      6  C   UNL     1      -1.830   0.930   0.000  0.00  0.00    +0.000 C
+ATOM      7  C   UNL     1      -3.030   0.930   0.000  0.00  0.00    +0.000 C
+ATOM      8  N   UNL     1      -0.980  -0.780   0.000  0.00  0.00    +0.000 N
+ATOM      9  C   UNL     1      -2.130  -1.460   0.000  0.00  0.00    +0.000 A
+ATOM     10  C   UNL     1      -3.320  -0.760   0.000  0.00  0.00    +0.000 A
+ATOM     11  C   UNL     1      -4.550  -1.480   0.000  0.00  0.00    +0.000 A
+ATOM     12  C   UNL     1      -4.580  -2.770   0.000  0.00  0.00    +0.000 A
+ATOM     13  C   UNL     1      -3.340  -3.470   0.000  0.00  0.00    +0.000 A
+ATOM     14  C   UNL     1      -2.130  -2.790   0.000  0.00  0.00    +0.000 A
+ATOM     15  C   UNL     1       0.240  -2.770   0.000  0.00  0.00    +0.000 A
+ATOM     16  C   UNL     1       1.430  -3.470   0.000  0.00  0.00    +0.000 A
+ATOM     17  C   UNL     1       1.760  -4.970   0.000  0.00  0.00    +0.000 C
+ATOM     18  N   UNL     1       3.260  -5.080   0.000  0.00  0.00    +0.000 N
+ATOM     19  C   UNL     1       3.850  -3.630   0.000  0.00  0.00    +0.000 C
+ATOM     20  O   UNL     1       4.997  -3.278   0.000  0.00  0.00    +0.000 OA
+ATOM     21  C   UNL     1       2.660  -2.750   0.000  0.00  0.00    +0.000 A
+ATOM     22  C   UNL     1       2.680  -1.460   0.000  0.00  0.00    +0.000 A
+ATOM     23  C   UNL     1       3.790   0.560   0.000  0.00  0.00    +0.000 A
+ATOM     24  C   UNL     1       4.960   1.280   0.000  0.00  0.00    +0.000 A
+ATOM     25  C   UNL     1       4.960   2.630   0.000  0.00  0.00    +0.000 A
+ATOM     26  C   UNL     1       3.810   3.290   0.000  0.00  0.00    +0.000 A
+ATOM     27  C   UNL     1       2.640   2.590   0.000  0.00  0.00    +0.000 A
+ATOM     28  C   UNL     1       2.640   1.240   0.000  0.00  0.00    +0.000 A
+ATOM     29  N   UNL     1       1.490   0.540   0.000  0.00  0.00    +0.000 N
+ATOM     30  C   UNL     1       1.450  -0.760   0.000  0.00  0.00    +0.000 A
+ATOM     31  C   UNL     1       0.240  -1.440   0.000  0.00  0.00    +0.000 A
+ATOM     32  H   UNL     1       3.779  -5.916   0.000  0.00  0.00    +0.000 HD
ENDROOT
-BRANCH  32  33
-ATOM     33  N   UNL     1      -2.551   4.803   0.000  0.00  0.00    -0.295 N
-ATOM     34  C   UNL     1      -4.052   4.814   0.000  0.00  0.00    +0.247 C
-ATOM     35  O   UNL     1      -4.659   3.778   0.000  0.00  0.00    -0.270 OA
-ATOM     36  C   UNL     1      -1.944   5.838   0.000  0.00  0.00    +0.132 C
-BRANCH  34  37
-ATOM     37  C   UNL     1      -4.794   6.118   0.000  0.00  0.00    +0.037 A
-ATOM     38  C   UNL     1      -4.033   7.411   0.000  0.00  0.00    +0.013 A
-ATOM     39  C   UNL     1      -4.772   8.716   0.000  0.00  0.00    +0.001 A
+BRANCH   2  33
+ATOM     33  N   UNL     1      -2.551   4.803   0.000  0.00  0.00    +0.000 N
+ATOM     34  C   UNL     1      -1.944   5.838   0.000  0.00  0.00    +0.000 C
+ATOM     35  C   UNL     1      -4.052   4.814   0.000  0.00  0.00    +0.000 C
+ATOM     36  O   UNL     1      -4.659   3.778   0.000  0.00  0.00    +0.000 OA
+BRANCH  35  37
+ATOM     37  C   UNL     1      -4.794   6.118   0.000  0.00  0.00    +0.000 A
+ATOM     38  C   UNL     1      -6.294   6.131   0.000  0.00  0.00    +0.000 A
+ATOM     39  C   UNL     1      -7.033   7.436   0.000  0.00  0.00    +0.000 A
ATOM     40  C   UNL     1      -6.272   8.729   0.000  0.00  0.00    +0.000 A
-ATOM     41  C   UNL     1      -7.033   7.436   0.000  0.00  0.00    +0.001 A
-ATOM     42  C   UNL     1      -6.294   6.131   0.000  0.00  0.00    +0.013 A
-ENDBRANCH  34  37
-ENDBRANCH  32  33
+ATOM     41  C   UNL     1      -4.772   8.716   0.000  0.00  0.00    +0.000 A
+ATOM     42  C   UNL     1      -4.033   7.411   0.000  0.00  0.00    +0.000 A
+ENDBRANCH  35  37
+ENDBRANCH   2  33
BRANCH   1  44
-ATOM     43  C   UNL     1      -4.720   3.343   0.000  0.00  0.00    +0.194 C
-ATOM     44  O   UNL     1      -4.147   2.289   0.000  0.00  0.00    -0.373 OA
+ATOM     43  C   UNL     1      -4.720   3.343   0.000  0.00  0.00    +0.000 C
+ATOM     44  O   UNL     1      -4.147   2.289   0.000  0.00  0.00    +0.000 OA
ENDBRANCH   1  44
TORSDOF 3

diff -r 015ccbd1ad68 -r de4c80d17527 test-data/split1.pdbqt
--- a/test-data/split1.pdbqt Thu Apr 09 10:10:31 2020 -0400
+++ b/test-data/split1.pdbqt Tue Jul 28 08:40:43 2020 -0400

@@ -7,24 +7,24 @@
REMARK                            x       y       z     vdW  Elec       q    Type
REMARK                         _______ _______ _______ _____ _____    ______ ____
ROOT
-ATOM      1  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.149 A
-ATOM      2  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.038 A
-ATOM      3  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.003 A
+ATOM      1  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 A
+ATOM      2  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 A
+ATOM      3  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 A
ATOM      4  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 A
-ATOM      5  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.004 A
-ATOM      6  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.049 A
+ATOM      5  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 A
+ATOM      6  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 A
ENDROOT
BRANCH   6   7
-ATOM      7  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.076 C
-ATOM      8  O   UNL     1       0.000   0.000   0.000  0.00  0.00    -0.544 OA
-ATOM      9  O   UNL     1       0.000   0.000   0.000  0.00  0.00    -0.544 OA
+ATOM      7  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 C
+ATOM      8  O   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 OA
+ATOM      9  O   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 OA
ENDBRANCH   6   7
BRANCH   1  10
-ATOM     10  O   UNL     1       0.000   0.000   0.000  0.00  0.00    -0.424 OA
+ATOM     10  O   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 OA
BRANCH  10  12
-ATOM     11  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.122 C
-ATOM     12  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.322 C
-ATOM     13  O   UNL     1       0.000   0.000   0.000  0.00  0.00    -0.250 OA
+ATOM     11  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 C
+ATOM     12  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 C
+ATOM     13  O   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 OA
ENDBRANCH  10  12
ENDBRANCH   1  10
TORSDOF 3

diff -r 015ccbd1ad68 -r de4c80d17527 test-data/split2.pdbqt
--- a/test-data/split2.pdbqt Thu Apr 09 10:10:31 2020 -0400
+++ b/test-data/split2.pdbqt Tue Jul 28 08:40:43 2020 -0400