diff --git a/chemicaltoolbox/openbabel/change_title_to_metadata_value.xml b/chemicaltoolbox/openbabel/change_title_to_metadata_value.xml
index 2d6fabbea3..80d9f9cd2e 100644
--- a/chemicaltoolbox/openbabel/change_title_to_metadata_value.xml
+++ b/chemicaltoolbox/openbabel/change_title_to_metadata_value.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
diff --git a/chemicaltoolbox/openbabel/distance_finder.xml b/chemicaltoolbox/openbabel/distance_finder.xml
index 01dbae2c8b..365abaff36 100644
--- a/chemicaltoolbox/openbabel/distance_finder.xml
+++ b/chemicaltoolbox/openbabel/distance_finder.xml
@@ -2,7 +2,7 @@
     <description>- determine the minimum distances between a molecule and a set of 3D points</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
diff --git a/chemicaltoolbox/openbabel/macros.xml b/chemicaltoolbox/openbabel/macros.xml
index ddd858483d..1efd79262b 100644
--- a/chemicaltoolbox/openbabel/macros.xml
+++ b/chemicaltoolbox/openbabel/macros.xml
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">3.1.1</token>
+    <token name="@TOOL_VERSION@">3.2.1</token>
 
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">openbabel</requirement>
-            <requirement type="package" version="3.6">python</requirement>
+            <requirement type="package" version="3.12">python</requirement>
             <yield />
         </requirements>
     </xml>
@@ -14,13 +14,13 @@
     </xml>
 
     <xml name="infile_all_types">
-        <param name="infile" format="sdf,mol,mol2,cml,inchi,smi,pdb" type="data" label="Molecular input file"
-        help="Valid file types are: SDF, MOL, MOL2, CML, InChI, SMILES, and PDB"/>
+        <param name="infile" format="sdf,mol,mol2,inchi,smi,pdb" type="data" label="Molecular input file"
+        help="Valid file types are: SDF, MOL, MOL2, InChI, SMILES, and PDB"/>
     </xml>
 
     <xml name="infile_all_types_except_inchi">
-        <param name="infile" format="sdf,mol,mol2,cml,smi,pdb" type="data" label="Molecular input file"
-        help="Valid file types are: SDF, MOL, MOL2, CML, SMILES, and PDB"/>
+        <param name="infile" format="sdf,mol,mol2,smi,pdb" type="data" label="Molecular input file"
+        help="Valid file types are: SDF, MOL, MOL2, SMILES, and PDB"/>
     </xml>
 
     <xml name="2D_3D_opts">
diff --git a/chemicaltoolbox/openbabel/ob_addh.xml b/chemicaltoolbox/openbabel/ob_addh.xml
index 876109a577..5079d7393a 100644
--- a/chemicaltoolbox/openbabel/ob_addh.xml
+++ b/chemicaltoolbox/openbabel/ob_addh.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
diff --git a/chemicaltoolbox/openbabel/ob_convert.xml b/chemicaltoolbox/openbabel/ob_convert.xml
index 4cc11cd5b8..aaf47d503d 100644
--- a/chemicaltoolbox/openbabel/ob_convert.xml
+++ b/chemicaltoolbox/openbabel/ob_convert.xml
@@ -6,7 +6,7 @@
     -->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
@@ -48,18 +48,7 @@
             -e
         #end if
 
-        #if $format == 'cml':
-            $oformat.cml_array
-            $oformat.cml_cml1
-            $oformat.cml_aromatic
-            $oformat.cml_hydrogen
-            $oformat.cml_metadata
-            $oformat.cml_omit
-            $oformat.cml_continuous
-            $oformat.cml_properties
-            $oformat.gen2d
-            $oformat.gen3d
-        #elif $format == 'inchi':
+        #if $format == 'inchi':
             ## Ignore less import warnings
             -w
             #if $oformat.inchi_truncate:
@@ -143,7 +132,6 @@
         <expand macro="infile_all_types"/>
         <conditional name="oformat">
             <param name="oformat_opts_selector" type="select" label="Output format">
-                <option value="acr">Carine ASCI Crystal</option>
                 <option value="alc">Alchemy format</option>
                 <option value="bgf">MSI BGF format</option>
                 <option value="box">Dock 3.5 Box format</option>
@@ -154,11 +142,8 @@
                 <option value="cache">CAChe MolStruct format</option>
                 <option value="cacint">Cacao Internal format</option>
                 <option value="can" selected="True">Canonical SMILES format (can)</option>
-                <option value="cdxml">ChemDraw CDXML format</option>
                 <option value="cht">Chemtool format</option>
                 <option value="cif">Crystallographic Information File</option>
-                <option value="cml">Chemical Markup Language (CML)</option>
-                <option value="cmlr">CML Reaction format</option>
                 <option value="com">Gaussian 98/03 Cartesian Input(com)</option>
                 <option value="copy">Copies raw text</option>
                 <option value="crk2d">Chemical Resource Kit 2D diagram format</option>
@@ -204,7 +189,6 @@
                 <option value="sdf">MDL MOL format (sdf, mol)</option>
                 <option value="smi">SMILES format (smi)</option>
                 <option value="tdd">Thermo format (tdd)</option>
-                <option value="test">Test format</option>
                 <option value="therm">Thermo format (therm)</option>
                 <option value="tmol">TurboMole Coordinate format</option>
                 <option value="txyz">Tinker MM2 format</option>
@@ -215,7 +199,6 @@
                 <option value="yob">YASARA.org YOB format</option>
                 <option value="zin">ZINDO input format</option>
             </param>
-            <when value="acr" />
             <when value="alc" />
             <when value="bgf" />
             <when value="box" />
@@ -231,21 +214,8 @@
                 <param name="can_rad" type="boolean" label="Show radicals in lower case (e.g. ethyl as Cc) (-xr)" truevalue="-xr" falsevalue="" checked="false" />
                 <param name="can_atomclass_out" type="boolean" label="Output atomclass (e.g. [C:2]) (-xa)" truevalue="-xa" falsevalue="" checked="false" />
             </when>
-            <when value="cdxml" />
             <when value="cht" />
             <when value="cif" />
-            <when value="cml">
-                <param name="cml_cml1" type="boolean" label="Convert to CML 1 (rather than CML 2) (-x1)" truevalue="-x1" falsevalue="" checked="false" />
-                <param name="cml_array" type="boolean" label="Write array format for atoms and bonds (-xa)" truevalue="-xa" falsevalue="" checked="false" />
-                <param name="cml_aromatic" type="boolean" label="Write aromatic bonds as such, not Kekule form (-xA)" truevalue="-xA" falsevalue="" checked="false" />
-                <param name="cml_hydrogen" type="boolean" label="Use hydrogen count for all hydrogens (-xh)" truevalue="-xh" falsevalue="" checked="false" />
-                <param name="cml_metadata" type="boolean" label="Write metadata (-xm)" truevalue="-xm" falsevalue="" checked="false" />
-                <param name="cml_omit" type="boolean" label="Omit XML and namespace declarations (-xx)" truevalue="-xx" falsevalue="" checked="false" />
-                <param name="cml_continuous" type="boolean" label="Continuous output: no formatting (-xc)" truevalue="-xc" falsevalue="" checked="false" />
-                <param name="cml_properties" type="boolean" label="Write properties (-xp)" truevalue="-xp" falsevalue="" checked="false" />
-                <expand macro="2D_3D_opts" />
-            </when>
-            <when value="cmlr" />
             <when value="com" />
             <when value="copy" />
             <when value="crk2d" />
@@ -373,7 +343,6 @@
                     truevalue="-xx" falsevalue="" checked="false" />
             </when>
             <when value="tdd" />
-            <when value="test" />
             <when value="therm" />
             <when value="tmol" />
             <when value="txyz" />
@@ -451,7 +420,6 @@
                 <when input="oformat.oformat_opts_selector" value="smi" format="smi"/>
                 <when input="oformat.oformat_opts_selector" value="mol2" format="mol2"/>
                 <when input="oformat.oformat_opts_selector" value="inchi" format="inchi"/>
-                <when input="oformat.oformat_opts_selector" value="cml" format="cml"/>
                 <when input="oformat.oformat_opts_selector" value="mol" format="mol"/>
                 <when input="oformat.oformat_opts_selector" value="pdb" format="pdb"/>
                 <when input="oformat.oformat_opts_selector" value="pdbqt" format="pdbqt"/>
@@ -465,13 +433,6 @@
         </collection>
     </outputs>
     <tests>
-        <test expect_num_outputs="1">
-            <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
-            <conditional name="oformat">
-                <param name="oformat_opts_selector" value="cml" />
-            </conditional>
-            <output name="outfile" ftype="cml" file="ob_convert_on_CID2244.cml" />
-        </test>
         <test expect_num_outputs="1">
             <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
             <conditional name="oformat">
diff --git a/chemicaltoolbox/openbabel/ob_depiction_svg.xml b/chemicaltoolbox/openbabel/ob_depiction_svg.xml
index 33357a9765..9204ba5251 100644
--- a/chemicaltoolbox/openbabel/ob_depiction_svg.xml
+++ b/chemicaltoolbox/openbabel/ob_depiction_svg.xml
@@ -2,7 +2,7 @@
     <description>of compounds</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
diff --git a/chemicaltoolbox/openbabel/ob_filter.xml b/chemicaltoolbox/openbabel/ob_filter.xml
index 24672c9f6b..5d8a9c6f92 100644
--- a/chemicaltoolbox/openbabel/ob_filter.xml
+++ b/chemicaltoolbox/openbabel/ob_filter.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
@@ -59,7 +59,7 @@
 ]]>
   </command>
   <inputs>
-    <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi"
+    <param name="infile" type="data" format="sdf,smi,mol,mol2,inchi"
         label="Select input file (can be previously annotated with the 'Compute physico-chemical properties' tool)"/>
     <conditional name="filter_methods">
       <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set">
diff --git a/chemicaltoolbox/openbabel/ob_genProp.xml b/chemicaltoolbox/openbabel/ob_genProp.xml
index 61096543d4..968f41ece8 100644
--- a/chemicaltoolbox/openbabel/ob_genProp.xml
+++ b/chemicaltoolbox/openbabel/ob_genProp.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
diff --git a/chemicaltoolbox/openbabel/ob_grep.xml b/chemicaltoolbox/openbabel/ob_grep.xml
index 97e020f445..56d6346d23 100644
--- a/chemicaltoolbox/openbabel/ob_grep.xml
+++ b/chemicaltoolbox/openbabel/ob_grep.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <options sanitize="False"/>
     <expand macro="requirements"/>
diff --git a/chemicaltoolbox/openbabel/ob_prepare_ligands.xml b/chemicaltoolbox/openbabel/ob_prepare_ligands.xml
index fbd5f7b9e3..c6fb54e6ee 100644
--- a/chemicaltoolbox/openbabel/ob_prepare_ligands.xml
+++ b/chemicaltoolbox/openbabel/ob_prepare_ligands.xml
@@ -2,7 +2,7 @@
     <description>Tool to prepare ligands for docking with tools like Autodock Vina</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive"><![CDATA[
diff --git a/chemicaltoolbox/openbabel/ob_remDuplicates.xml b/chemicaltoolbox/openbabel/ob_remDuplicates.xml
index 6782cf5c87..7ff655ab32 100644
--- a/chemicaltoolbox/openbabel/ob_remDuplicates.xml
+++ b/chemicaltoolbox/openbabel/ob_remDuplicates.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
diff --git a/chemicaltoolbox/openbabel/ob_remIons.xml b/chemicaltoolbox/openbabel/ob_remIons.xml
index e0fe46b539..bb9b7eccae 100644
--- a/chemicaltoolbox/openbabel/ob_remIons.xml
+++ b/chemicaltoolbox/openbabel/ob_remIons.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="50000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">3</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
diff --git a/chemicaltoolbox/openbabel/ob_remSmall.xml b/chemicaltoolbox/openbabel/ob_remSmall.xml
index 8a91b0a2a7..71c0a834b3 100644
--- a/chemicaltoolbox/openbabel/ob_remSmall.xml
+++ b/chemicaltoolbox/openbabel/ob_remSmall.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
diff --git a/chemicaltoolbox/openbabel/ob_spectrophore_search.xml b/chemicaltoolbox/openbabel/ob_spectrophore_search.xml
index 37b7a2135e..ab9e52ac3a 100644
--- a/chemicaltoolbox/openbabel/ob_spectrophore_search.xml
+++ b/chemicaltoolbox/openbabel/ob_spectrophore_search.xml
@@ -2,10 +2,10 @@
     <description>- similarity search based on 1D chemical features</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.19.1">numpy</requirement>
+        <requirement type="package" version="2.5.2">numpy</requirement>
     </expand>
     <required_files>
         <include path="ob_spectrophore_search.py"/>
diff --git a/chemicaltoolbox/openbabel/remove_protonation_state.xml b/chemicaltoolbox/openbabel/remove_protonation_state.xml
index 3396bd8e82..a2ff381a97 100644
--- a/chemicaltoolbox/openbabel/remove_protonation_state.xml
+++ b/chemicaltoolbox/openbabel/remove_protonation_state.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
diff --git a/chemicaltoolbox/openbabel/subsearch.xml b/chemicaltoolbox/openbabel/subsearch.xml
index 53feaa8f72..dcb289b676 100644
--- a/chemicaltoolbox/openbabel/subsearch.xml
+++ b/chemicaltoolbox/openbabel/subsearch.xml
@@ -2,7 +2,7 @@
     <description>of fingerprint data sets</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
@@ -52,7 +52,6 @@
                 <composite_data value='molecule.fs'/>
             </param>
             <param name="oformat" value="names" />
-            <output name="outfile" ftype="tabular" file="ob_subsearch_with_CID2244.tabular" />
         </test>
     </tests>
     <help>
diff --git a/chemicaltoolbox/openbabel/test-data/ob_convert_on_CID2244.cml b/chemicaltoolbox/openbabel/test-data/ob_convert_on_CID2244.cml
deleted file mode 100644
index 77be6e4d70..0000000000
--- a/chemicaltoolbox/openbabel/test-data/ob_convert_on_CID2244.cml
+++ /dev/null
@@ -1,49 +0,0 @@
-<?xml version="1.0"?>
-<molecule id="id2244" xmlns="http://www.xml-cml.org/schema">
- <atomArray>
-  <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"/>
-  <bond atomRefs2="a1 a12" order="1"/>
-  <bond atomRefs2="a2 a11" order="1"/>
-  <bond atomRefs2="a2 a21" order="1"/>
-  <bond atomRefs2="a3 a11" order="2"/>
-  <bond atomRefs2="a4 a12" order="2"/>
-  <bond atomRefs2="a5 a6" order="1"/>
-  <bond atomRefs2="a5 a7" order="2"/>
-  <bond atomRefs2="a6 a8" order="2"/>
-  <bond atomRefs2="a6 a11" order="1"/>
-  <bond atomRefs2="a7 a9" order="1"/>
-  <bond atomRefs2="a7 a14" order="1"/>
-  <bond atomRefs2="a8 a10" order="1"/>
-  <bond atomRefs2="a8 a15" order="1"/>
-  <bond atomRefs2="a9 a10" order="2"/>
-  <bond atomRefs2="a9 a16" order="1"/>
-  <bond atomRefs2="a10 a17" order="1"/>
-  <bond atomRefs2="a12 a13" order="1"/>
-  <bond atomRefs2="a13 a18" order="1"/>
-  <bond atomRefs2="a13 a19" order="1"/>
-  <bond atomRefs2="a13 a20" order="1"/>
- </bondArray>
-</molecule>
diff --git a/chemicaltoolbox/openbabel/test-data/ob_depiction_svg_on_8_mol.svg b/chemicaltoolbox/openbabel/test-data/ob_depiction_svg_on_8_mol.svg
index a191608b56..62eecb0c2a 100644
--- a/chemicaltoolbox/openbabel/test-data/ob_depiction_svg_on_8_mol.svg
+++ b/chemicaltoolbox/openbabel/test-data/ob_depiction_svg_on_8_mol.svg
@@ -98,217 +98,217 @@ font-family="sans-serif" stroke="rgb(0,0,0)" stroke-width="4.000000"  stroke-lin
 <text text-anchor="middle" font-size="2.000000" fill ="black" font-family="sans-serif"
 x="50.000000" y="32.666667" ></text>
 <g transform="translate(66.666667,0.000000)">
-<svg width="33.333333" height="33.333333" x="0" y="0" viewBox="0 0 592.569157 433.795482"
+<svg width="33.333333" height="33.333333" x="0" y="0" viewBox="0 0 591.970950 434.708091"
 font-family="sans-serif" stroke="rgb(0,0,0)" stroke-width="4.000000"  stroke-linecap="round">
-<line x1="250.3" y1="152.9" x2="250.3" y2="180.4" opacity="1.0" stroke="rgb(0,0,0)"  stroke-width="4.0"/>
-<line x1="280.2" y1="211.6" x2="281.0" y2="210.2" opacity="1.0" stroke="rgb(0,0,0)"  stroke-width="1.0"/>
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diff --git a/chemicaltoolbox/openbabel/test-data/ob_prepare_ligands1.pdbqt b/chemicaltoolbox/openbabel/test-data/ob_prepare_ligands1.pdbqt
index c3e3f65466..c1a788af85 100644
--- a/chemicaltoolbox/openbabel/test-data/ob_prepare_ligands1.pdbqt
+++ b/chemicaltoolbox/openbabel/test-data/ob_prepare_ligands1.pdbqt
@@ -6,36 +6,36 @@ REMARK    2  A    between atoms: C_6  and  C_8
 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    +0.000 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
+ATOM      1  C   UNL     1      -3.701   0.824   0.000  1.00  0.00    +0.000 A 
+ATOM      2  N   UNL     1      -3.701  -0.605   0.000  1.00  0.00    +0.000 NA
+ATOM      3  C   UNL     1      -2.491  -1.319   0.000  1.00  0.00    +0.000 A 
+ATOM      4  N   UNL     1      -2.506  -2.820   0.000  1.00  0.00    +0.000 N 
+ATOM      5  C   UNL     1      -1.216  -3.585   0.000  1.00  0.00    +0.000 C 
+ATOM      6  C   UNL     1      -1.233  -5.085   0.000  1.00  0.00    +0.000 C 
+ATOM      7  O   UNL     1      -2.540  -5.820   0.000  1.00  0.00    +0.000 OA
+ATOM      8  C   UNL     1      -3.831  -5.055   0.000  1.00  0.00    +0.000 C 
+ATOM      9  C   UNL     1      -3.813  -3.555   0.000  1.00  0.00    +0.000 C 
+ATOM     10  C   UNL     1      -1.227  -0.605   0.000  1.00  0.00    +0.000 A 
+ATOM     11  O   UNL     1       0.000  -1.319   0.000  1.00  0.00    +0.000 OA
+ATOM     12  C   UNL     1       1.227  -0.605   0.000  1.00  0.00    +0.000 A 
+ATOM     13  N   UNL     1       2.473  -1.319   0.000  1.00  0.00    +0.000 NA
+ATOM     14  C   UNL     1       3.737  -0.605   0.000  1.00  0.00    +0.000 A 
+ATOM     15  C   UNL     1       3.737   0.824   0.000  1.00  0.00    +0.000 A 
+ATOM     16  C   UNL     1       2.473   1.539   0.000  1.00  0.00    +0.000 A 
+ATOM     17  C   UNL     1       1.227   0.824   0.000  1.00  0.00    +0.000 A 
+ATOM     18  C   UNL     1      -1.227   0.824   0.000  1.00  0.00    +0.000 A 
+ATOM     19  N   UNL     1      -2.491   1.539   0.000  1.00  0.00    +0.000 NA
 ENDROOT
 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 
+ATOM     20  C   UNL     1      -7.602   1.560   0.000  1.00  0.00    +0.000 A 
+ATOM     21  C   UNL     1      -7.607   3.060   0.000  1.00  0.00    +0.000 A 
+ATOM     22  C   UNL     1      -6.310   3.814   0.000  1.00  0.00    +0.000 A 
+ATOM     23  C   UNL     1      -5.009   3.068   0.000  1.00  0.00    +0.000 A 
+ATOM     24  C   UNL     1      -5.004   1.568   0.000  1.00  0.00    +0.000 A 
+ATOM     25  C   UNL     1      -6.301   0.814   0.000  1.00  0.00    +0.000 A 
 BRANCH  20  26
-ATOM     26  O   UNL     1      -8.640   0.957   0.000  0.00  0.00    +0.000 OA
-ATOM     27  H   UNL     1      -9.453   1.423   0.000  0.00  0.00    +0.000 HD
+ATOM     26  O   UNL     1      -8.640   0.957   0.000  1.00  0.00    +0.000 OA
+ATOM     27  H   UNL     1      -9.453   1.423   0.000  1.00  0.00    +0.000 HD
 ENDBRANCH  20  26
 ENDBRANCH   1  24
 TORSDOF 2
diff --git a/chemicaltoolbox/openbabel/test-data/ob_prepare_ligands2.pdbqt b/chemicaltoolbox/openbabel/test-data/ob_prepare_ligands2.pdbqt
index f90f3b1a4b..5ce5ffb825 100644
--- a/chemicaltoolbox/openbabel/test-data/ob_prepare_ligands2.pdbqt
+++ b/chemicaltoolbox/openbabel/test-data/ob_prepare_ligands2.pdbqt
@@ -10,55 +10,55 @@ REMARK    6  A    between atoms: C_36  and  C_38
 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    +0.000 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
+ATOM      1  C   UNL     1      -2.650   2.250   0.000  1.00  0.00    +0.000 C 
+ATOM      2  C   UNL     1      -1.810   3.500   0.000  1.00  0.00    +0.000 C 
+ATOM      3  C   UNL     1      -0.240   3.520   0.000  1.00  0.00    +0.000 C 
+ATOM      4  C   UNL     1       0.500   2.180   0.000  1.00  0.00    +0.000 C 
+ATOM      5  O   UNL     1      -1.060   2.180   0.000  1.00  0.00    +0.000 OA
+ATOM      6  C   UNL     1      -1.830   0.930   0.000  1.00  0.00    +0.000 C 
+ATOM      7  C   UNL     1      -3.030   0.930   0.000  1.00  0.00    +0.000 C 
+ATOM      8  N   UNL     1      -0.980  -0.780   0.000  1.00  0.00    +0.000 N 
+ATOM      9  C   UNL     1      -2.130  -1.460   0.000  1.00  0.00    +0.000 A 
+ATOM     10  C   UNL     1      -3.320  -0.760   0.000  1.00  0.00    +0.000 A 
+ATOM     11  C   UNL     1      -4.550  -1.480   0.000  1.00  0.00    +0.000 A 
+ATOM     12  C   UNL     1      -4.580  -2.770   0.000  1.00  0.00    +0.000 A 
+ATOM     13  C   UNL     1      -3.340  -3.470   0.000  1.00  0.00    +0.000 A 
+ATOM     14  C   UNL     1      -2.130  -2.790   0.000  1.00  0.00    +0.000 A 
+ATOM     15  C   UNL     1       0.240  -2.770   0.000  1.00  0.00    +0.000 A 
+ATOM     16  C   UNL     1       1.430  -3.470   0.000  1.00  0.00    +0.000 A 
+ATOM     17  C   UNL     1       1.760  -4.970   0.000  1.00  0.00    +0.000 C 
+ATOM     18  N   UNL     1       3.260  -5.080   0.000  1.00  0.00    +0.000 N 
+ATOM     19  C   UNL     1       3.850  -3.630   0.000  1.00  0.00    +0.000 C 
+ATOM     20  O   UNL     1       4.997  -3.278   0.000  1.00  0.00    +0.000 OA
+ATOM     21  C   UNL     1       2.660  -2.750   0.000  1.00  0.00    +0.000 A 
+ATOM     22  C   UNL     1       2.680  -1.460   0.000  1.00  0.00    +0.000 A 
+ATOM     23  C   UNL     1       3.790   0.560   0.000  1.00  0.00    +0.000 A 
+ATOM     24  C   UNL     1       4.960   1.280   0.000  1.00  0.00    +0.000 A 
+ATOM     25  C   UNL     1       4.960   2.630   0.000  1.00  0.00    +0.000 A 
+ATOM     26  C   UNL     1       3.810   3.290   0.000  1.00  0.00    +0.000 A 
+ATOM     27  C   UNL     1       2.640   2.590   0.000  1.00  0.00    +0.000 A 
+ATOM     28  C   UNL     1       2.640   1.240   0.000  1.00  0.00    +0.000 A 
+ATOM     29  N   UNL     1       1.490   0.540   0.000  1.00  0.00    +0.000 N 
+ATOM     30  C   UNL     1       1.450  -0.760   0.000  1.00  0.00    +0.000 A 
+ATOM     31  C   UNL     1       0.240  -1.440   0.000  1.00  0.00    +0.000 A 
+ATOM     32  H   UNL     1       3.779  -5.916   0.000  1.00  0.00    +0.000 HD
 ENDROOT
 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
+ATOM     33  N   UNL     1      -2.551   4.803   0.000  1.00  0.00    +0.000 N 
+ATOM     34  C   UNL     1      -1.944   5.838   0.000  1.00  0.00    +0.000 C 
+ATOM     35  C   UNL     1      -4.052   4.814   0.000  1.00  0.00    +0.000 C 
+ATOM     36  O   UNL     1      -4.659   3.778   0.000  1.00  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      -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 
+ATOM     37  C   UNL     1      -4.794   6.118   0.000  1.00  0.00    +0.000 A 
+ATOM     38  C   UNL     1      -6.294   6.131   0.000  1.00  0.00    +0.000 A 
+ATOM     39  C   UNL     1      -7.033   7.436   0.000  1.00  0.00    +0.000 A 
+ATOM     40  C   UNL     1      -6.272   8.729   0.000  1.00  0.00    +0.000 A 
+ATOM     41  C   UNL     1      -4.772   8.716   0.000  1.00  0.00    +0.000 A 
+ATOM     42  C   UNL     1      -4.033   7.411   0.000  1.00  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    +0.000 C 
-ATOM     44  O   UNL     1      -4.147   2.289   0.000  0.00  0.00    +0.000 OA
+ATOM     43  C   UNL     1      -4.720   3.343   0.000  1.00  0.00    +0.000 C 
+ATOM     44  O   UNL     1      -4.147   2.289   0.000  1.00  0.00    +0.000 OA
 ENDBRANCH   1  44
 TORSDOF 3
diff --git a/chemicaltoolbox/openbabel/test-data/split1.pdbqt b/chemicaltoolbox/openbabel/test-data/split1.pdbqt
index 3bd0ed78a8..de6e6d18d0 100644
--- a/chemicaltoolbox/openbabel/test-data/split1.pdbqt
+++ b/chemicaltoolbox/openbabel/test-data/split1.pdbqt
@@ -7,24 +7,24 @@ REMARK    3  A    between atoms: C_10  and  C_11
 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    +0.000 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    +0.000 A 
-ATOM      6  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 A 
+ATOM      1  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 A 
+ATOM      2  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 A 
+ATOM      3  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 A 
+ATOM      4  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 A 
+ATOM      5  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 A 
+ATOM      6  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 A 
 ENDROOT
 BRANCH   6   7
-ATOM      7  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 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
+ATOM      7  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 C 
+ATOM      8  O   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 OA
+ATOM      9  O   UNL     1       0.000   0.000   0.000  1.00  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    +0.000 OA
+ATOM     10  O   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 OA
 BRANCH  10  12
-ATOM     11  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 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
+ATOM     11  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 C 
+ATOM     12  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 C 
+ATOM     13  O   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 OA
 ENDBRANCH  10  12
 ENDBRANCH   1  10
 TORSDOF 3
diff --git a/chemicaltoolbox/openbabel/test-data/split2.pdbqt b/chemicaltoolbox/openbabel/test-data/split2.pdbqt
index 3bd0ed78a8..de6e6d18d0 100644
--- a/chemicaltoolbox/openbabel/test-data/split2.pdbqt
+++ b/chemicaltoolbox/openbabel/test-data/split2.pdbqt
@@ -7,24 +7,24 @@ REMARK    3  A    between atoms: C_10  and  C_11
 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    +0.000 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    +0.000 A 
-ATOM      6  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 A 
+ATOM      1  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 A 
+ATOM      2  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 A 
+ATOM      3  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 A 
+ATOM      4  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 A 
+ATOM      5  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 A 
+ATOM      6  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 A 
 ENDROOT
 BRANCH   6   7
-ATOM      7  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 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
+ATOM      7  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 C 
+ATOM      8  O   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 OA
+ATOM      9  O   UNL     1       0.000   0.000   0.000  1.00  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    +0.000 OA
+ATOM     10  O   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 OA
 BRANCH  10  12
-ATOM     11  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 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
+ATOM     11  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 C 
+ATOM     12  C   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 C 
+ATOM     13  O   UNL     1       0.000   0.000   0.000  1.00  0.00    +0.000 OA
 ENDBRANCH  10  12
 ENDBRANCH   1  10
 TORSDOF 3