Merge pull request #170 from martimunicoy/devel

peleffy 1.4.2 release
martimunicoy · Jun 13, 2022 · 09a1862 · 09a1862
2 parents 8ad949b + 5ee3484
commit 09a1862
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diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
@@ -8,6 +8,22 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
 
+1.4.2 - Compatibility fixes for latest RDKit and Schrodinger versions
+---------------------------------------------------------------------
+
+This is a micro release of peleffy that fixes several bugs related with latest versions of RDKit and Schrodinger. Affected modules are rotamer libraries, the runner and parser of the ffld server, and the alchemistry package. It also adds some minor improvements to log handlers.
+
+New features
+""""""""""""
+- `PR #166 <https://github.com/martimunicoy/peleffy/pull/166>`_: New options for log handlers.
+
+Bugfixes
+""""""""
+- `PR #167 <https://github.com/martimunicoy/peleffy/pull/167>`_: Bug fixes for rotamer libraries and affected tests
+- `PR #168 <https://github.com/martimunicoy/peleffy/pull/168>`_: Compatibility changes for the ffld server shipped with latest Schrodinger version
+- `PR #169 <https://github.com/martimunicoy/peleffy/pull/169>`_: Support new RDKit versions.
+
+
 1.4.1 - Bug fixes for heteromolecules extraction
 ---------------------------------------------------------
 

diff --git a/examples/alchemistry/ethylene_to_chlorofom.ipynb b/examples/alchemistry/ethylene_to_chlorofom.ipynb
@@ -467,7 +467,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -481,9 +481,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.10"
+   "version": "3.8.12"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}
diff --git a/peleffy/data/tests/alchemical_0.rot.assign b/peleffy/data/tests/alchemical_0.rot.assign
@@ -1,4 +1,4 @@
 rot assign res HYB &
-   sidelib FREE30 _N1_ _C4_ &
+   sidelib FREE30 _C4_ _N1_ &
      newgrp &
-   sidelib FREE30 _C5_ _C4_ &
+   sidelib FREE30 _C4_ _C5_ &
diff --git a/peleffy/data/tests/alchemical_1.rot.assign b/peleffy/data/tests/alchemical_1.rot.assign
@@ -1,5 +1,5 @@
 rot assign res HYB &
-   sidelib FREE30 _C4_ _N1_ &
+   sidelib FREE30 _N1_ _C4_ &
    sidelib FREE30 _C4_ _C5_ &
      newgrp &
-   sidelib FREE30 _C6_ _N1_ &
+   sidelib FREE30 _N1_ _C6_ &
diff --git a/peleffy/data/tests/alchemical_2.rot.assign b/peleffy/data/tests/alchemical_2.rot.assign
@@ -1,2 +1,2 @@
 rot assign res HYB &
-   sidelib FREE30 _N1_ _C6_ &
+   sidelib FREE30 _C6_ _N1_ &
diff --git a/peleffy/data/tests/alchemical_structure.pdb b/peleffy/data/tests/alchemical_structure.pdb
@@ -34,10 +34,10 @@ CONECT    3   12   13   14
 CONECT    4   15   16   17
 CONECT    5    6   18   19
 CONECT    6    7    7    8
-CONECT   20   21   25
+CONECT   20   21   21   25
 CONECT   21   22   26
-CONECT   22   23   27
+CONECT   22   23   23   27
 CONECT   23   24   28
-CONECT   24   25   29
+CONECT   24   25   25   29
 CONECT   25   30
 END
diff --git a/peleffy/forcefield/parameters.py b/peleffy/forcefield/parameters.py
@@ -1200,6 +1200,12 @@ def from_ffld_output(molecule, ffld_output):
 
         params['charges'] = unit.Quantity(charges, unit.elementary_charge)
 
+        # Check params is not empty (it would mean that ffld_server failed)
+        if len(params['atom_types']) == 0:
+            raise ValueError(f"ffld server did not produce a valid output. " +
+                             f"Instead, the following output was obtained: " +
+                             f"{ffld_output}")
+
         opls_parameters_wrapper = OPLS2005ParameterWrapper(params)
         OPLS2005ParameterWrapper._add_SGBNP_solvent_parameters(
             opls_parameters_wrapper)