Local simulations

examples/assign_parameters_from_openff/terphenyl_mop/octamer/assign_terphenyl_oct.ipynb

@@ -5377,9 +5377,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python [conda env:terphenyl] *",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "conda-env-terphenyl-py"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -5391,7 +5391,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.12"
+   "version": "3.9.13"
   }
  },
  "nbformat": 4,

examples/build_polymer/mop/mop_decamer_mbuild.gro

@@ -1,4 +1,4 @@
-Great Red Oystrich Makes All Chemists Sane
+Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
   461
     1DEC      C    1  -0.300  -0.491   0.012
     1DEC      O    2  -0.388  -0.541  -0.064

examples/build_polymer/mop/mop_decamer_mbuild.mol

@@ -1,5 +1,5 @@
 mop_decamer_mbuild.pdb
- OpenBabel12132212253D
+ OpenBabel04062318113D
 
 461490  0  0  1  0  0  0  0  0999 V2000
    -3.0020   -4.9110    0.1170 C   0  0  0  0  0  0  0  0  0  0  0  0

examples/build_polymer/mop/mop_dimer_mbuild.gro

@@ -1,4 +1,4 @@
-Gromacs Runs On Most of All Computer Systems
+GRowing Old MAkes el Chrono Sweat
   109
     1DIM      C    1  -0.300  -0.491   0.012
     1DIM      O    2  -0.388  -0.541  -0.064

examples/build_polymer/mop/mop_dimer_mbuild.mol

@@ -1,5 +1,5 @@
 mop_dimer_mbuild.pdb
- OpenBabel12132212253D
+ OpenBabel04062318103D
 
 109114  0  0  1  0  0  0  0  0999 V2000
    -3.0020   -4.9110    0.1170 C   0  0  0  0  0  0  0  0  0  0  0  0

examples/build_polymer/mop/mop_hexamer_mbuild.gro

@@ -1,4 +1,4 @@
-God Rules Over Mankind, Animals, Cosmos and Such
+Good gRace! Old Maple Actually Chews Slate
   285
     1HEX      C    1  -0.300  -0.491   0.012
     1HEX      O    2  -0.388  -0.541  -0.064

examples/build_polymer/mop/mop_hexamer_mbuild.mol

@@ -1,5 +1,5 @@
 mop_hexamer_mbuild.pdb
- OpenBabel12132212253D
+ OpenBabel04062318113D
 
 285302  0  0  1  0  0  0  0  0999 V2000
    -3.0020   -4.9110    0.1170 C   0  0  0  0  0  0  0  0  0  0  0  0

examples/build_polymer/mop/mop_octamer_mbuild.gro

@@ -1,4 +1,4 @@
-S  C  A  M  O  R  G
+Gyas ROwers Mature At Cryogenic Speed
   373
     1OCT      C    1  -0.300  -0.491   0.012
     1OCT      O    2  -0.388  -0.541  -0.064

examples/build_polymer/mop/mop_octamer_mbuild.mol

@@ -1,5 +1,5 @@
 mop_octamer_mbuild.pdb
- OpenBabel12132212253D
+ OpenBabel04062318113D
 
 373396  0  0  1  0  0  0  0  0999 V2000
    -3.0020   -4.9110    0.1170 C   0  0  0  0  0  0  0  0  0  0  0  0

examples/build_polymer/mop/mop_tetramer_mbuild.gro

@@ -1,4 +1,4 @@
-Grunge ROck MAChoS
+Great Red Owns Many ACres of Sand 
   197
     1TET      C    1  -0.300  -0.491   0.012
     1TET      O    2  -0.388  -0.541  -0.064

examples/build_polymer/mop/mop_tetramer_mbuild.mol

@@ -1,5 +1,5 @@
 mop_tetramer_mbuild.pdb
- OpenBabel12132212253D
+ OpenBabel04062318113D
 
 197208  0  0  1  0  0  0  0  0999 V2000
    -3.0020   -4.9110    0.1170 C   0  0  0  0  0  0  0  0  0  0  0  0

examples/build_polymer/mop/mop_trimer_mbuild.gro

@@ -1,4 +1,4 @@
-Grunge ROck MAChoS
+GROningen Mixture of Alchemy and Childrens' Stories
   153
     1TRI      C    1  -0.300  -0.491   0.012
     1TRI      O    2  -0.388  -0.541  -0.064

examples/build_polymer/mop/mop_trimer_mbuild.mol

@@ -1,5 +1,5 @@
 mop_trimer_mbuild.pdb
- OpenBabel12132212253D
+ OpenBabel04062318113D
 
 153161  0  0  1  0  0  0  0  0999 V2000
    -3.0020   -4.9110    0.1170 C   0  0  0  0  0  0  0  0  0  0  0  0

fastentrypoints.py

@@ -0,0 +1,112 @@
+# noqa: D300,D400
+# Copyright (c) 2016, Aaron Christianson
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# 1. Redistributions of source code must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+#    notice, this list of conditions and the following disclaimer in the
+#    documentation and/or other materials provided with the distribution.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+# TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+'''
+Monkey patch setuptools to write faster console_scripts with this format:
+
+    import sys
+    from mymodule import entry_function
+    sys.exit(entry_function())
+
+This is better.
+
+(c) 2016, Aaron Christianson
+http://github.com/ninjaaron/fast-entry_points
+'''
+from setuptools.command import easy_install
+import re
+TEMPLATE = r'''
+# -*- coding: utf-8 -*-
+# EASY-INSTALL-ENTRY-SCRIPT: '{3}','{4}','{5}'
+__requires__ = '{3}'
+import re
+import sys
+
+from {0} import {1}
+
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
+    sys.exit({2}())
+'''.lstrip()
+
+
+@classmethod
+def get_args(cls, dist, header=None):  # noqa: D205,D400
+    """
+    Yield write_script() argument tuples for a distribution's
+    console_scripts and gui_scripts entry points.
+    """
+    if header is None:
+        # pylint: disable=E1101
+        header = cls.get_header()
+    spec = str(dist.as_requirement())
+    for type_ in 'console', 'gui':
+        group = type_ + '_scripts'
+        for name, ep in dist.get_entry_map(group).items():
+            # ensure_safe_name
+            if re.search(r'[\\/]', name):
+                raise ValueError("Path separators not allowed in script names")
+            script_text = TEMPLATE.format(
+                ep.module_name, ep.attrs[0], '.'.join(ep.attrs),
+                spec, group, name)
+            # pylint: disable=E1101
+            args = cls._get_script_args(type_, name, header, script_text)
+            for res in args:
+                yield res
+
+
+# pylint: disable=E1101
+easy_install.ScriptWriter.get_args = get_args
+
+
+def main():
+    import os
+    import shutil
+    import sys
+    dests = sys.argv[1:] or ['.']
+    filename = re.sub(r'\.pyc$', '.py', __file__)
+
+    for dst in dests:
+        shutil.copy(filename, dst)
+        manifest_path = os.path.join(dst, 'MANIFEST.in')
+        setup_path = os.path.join(dst, 'setup.py')
+
+        # Insert the include statement to MANIFEST.in if not present
+        with open(manifest_path, 'a+') as manifest:
+            manifest.seek(0)
+            manifest_content = manifest.read()
+            if 'include fastentrypoints.py' not in manifest_content:
+                manifest.write(('\n' if manifest_content else '') +
+                               'include fastentrypoints.py')
+
+        # Insert the import statement to setup.py if not present
+        with open(setup_path, 'a+') as setup:
+            setup.seek(0)
+            setup_content = setup.read()
+            if 'import fastentrypoints' not in setup_content:
+                setup.seek(0)
+                setup.truncate()
+                setup.write('import fastentrypoints\n' + setup_content)