changeset 12:43167f164076 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:37:32 -0400
parents 716dcb5bbb71
children f697d9601273
files change_title_to_metadata_value.py cheminfolib.py distance_finder.py macros.xml multi_obgrep.py ob_addh.py ob_addh.xml ob_filter.py ob_genProp.py 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
diffstat 20 files changed, 595 insertions(+), 626 deletions(-) [+]
line wrap: on
line diff
--- a/change_title_to_metadata_value.py	Thu Apr 09 10:06:25 2020 -0400
+++ b/change_title_to_metadata_value.py	Tue Jul 28 08:37:32 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 \
--- a/cheminfolib.py	Thu Apr 09 10:06:25 2020 -0400
+++ b/cheminfolib.py	Tue Jul 28 08:37:32 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.')
 
--- a/distance_finder.py	Thu Apr 09 10:06:25 2020 -0400
+++ b/distance_finder.py	Tue Jul 28 08:37:32 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
     """
--- a/macros.xml	Thu Apr 09 10:06:25 2020 -0400
+++ b/macros.xml	Tue Jul 28 08:37:32 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>
--- a/multi_obgrep.py	Thu Apr 09 10:06:25 2020 -0400
+++ b/multi_obgrep.py	Tue Jul 28 08:37:32 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.')
--- a/ob_addh.py	Thu Apr 09 10:06:25 2020 -0400
+++ b/ob_addh.py	Tue Jul 28 08:37:32 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()
--- a/ob_addh.xml	Thu Apr 09 10:06:25 2020 -0400
+++ b/ob_addh.xml	Tue Jul 28 08:37:32 2020 -0400
@@ -1,8 +1,9 @@
-<tool id="openbabel_addh" name="Add hydrogen atoms" version="@VERSION@.0">
+<tool id="openbabel_addh" name="Add hydrogen atoms" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
     <description>at a certain pH value</description>
     <!--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@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
--- a/ob_filter.py	Thu Apr 09 10:06:25 2020 -0400
+++ b/ob_filter.py	Tue Jul 28 08:37:32 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():
--- a/ob_genProp.py	Thu Apr 09 10:06:25 2020 -0400
+++ b/ob_genProp.py	Tue Jul 28 08:37:32 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()
--- a/ob_remIons.py	Thu Apr 09 10:06:25 2020 -0400
+++ b/ob_remIons.py	Tue Jul 28 08:37:32 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()
--- a/ob_spectrophore_search.py	Thu Apr 09 10:06:25 2020 -0400
+++ b/ob_spectrophore_search.py	Tue Jul 28 08:37:32 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
--- a/remove_protonation_state.py	Thu Apr 09 10:06:25 2020 -0400
+++ b/remove_protonation_state.py	Tue Jul 28 08:37:32 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()
--- a/subsearch.py	Thu Apr 09 10:06:25 2020 -0400
+++ b/subsearch.py	Tue Jul 28 08:37:32 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.')
--- a/test-data/ob_convert_on_CID2244.cml	Thu Apr 09 10:06:25 2020 -0400
+++ b/test-data/ob_convert_on_CID2244.cml	Tue Jul 28 08:37:32 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"/>
--- a/test-data/ob_convert_on_CID2244.pdb	Thu Apr 09 10:06:25 2020 -0400
+++ b/test-data/ob_convert_on_CID2244.pdb	Tue Jul 28 08:37:32 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                                                      
--- a/test-data/ob_depiction_svg_on_8_mol.svg	Thu Apr 09 10:06:25 2020 -0400
+++ b/test-data/ob_depiction_svg_on_8_mol.svg	Tue Jul 28 08:37:32 2020 -0400
@@ -7,44 +7,44 @@
 <g transform="translate(0,0)">
 <svg width="33.3333" height="33.3333" x="0" y="0" viewBox="0 0 300 258.564"
 font-family="sans-serif" stroke="rgb(0,0,0)" stroke-width="4"  stroke-linecap="round">
-<line x1="103.0" y1="191.6" x2="103.0" y2="205.6" stroke="rgb(0,0,0)"  stroke-width="4.0"/>
-<line x1="97.0" y1="191.6" x2="97.0" y2="205.6" stroke="rgb(0,0,0)"  stroke-width="4.0"/>
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-<line x1="223.0" y1="122.3" x2="223.0" y2="136.3" stroke="rgb(0,0,0)"  stroke-width="4.0"/>
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--- a/test-data/ob_prepare_ligands1.pdbqt	Thu Apr 09 10:06:25 2020 -0400
+++ b/test-data/ob_prepare_ligands1.pdbqt	Tue Jul 28 08:37:32 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
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-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
--- a/test-data/ob_prepare_ligands2.pdbqt	Thu Apr 09 10:06:25 2020 -0400
+++ b/test-data/ob_prepare_ligands2.pdbqt	Tue Jul 28 08:37:32 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
--- a/test-data/split1.pdbqt	Thu Apr 09 10:06:25 2020 -0400
+++ b/test-data/split1.pdbqt	Tue Jul 28 08:37:32 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
--- a/test-data/split2.pdbqt	Thu Apr 09 10:06:25 2020 -0400
+++ b/test-data/split2.pdbqt	Tue Jul 28 08:37:32 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