Merge pull request #152 from martimunicoy/devel

peleffy 1.3.4 release
martimunicoy · Sep 20, 2021 · c3874d4 · c3874d4
2 parents fe4308c + 04ad69d
commit c3874d4
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diff --git a/devtools/conda/meta.yaml b/devtools/conda/meta.yaml
@@ -24,7 +24,7 @@ requirements:
     - networkx
     - rdkit
     - ambertools
-    - openff-toolkit==0.9.2
+    - openff-toolkit==0.10.0
 
 about:
   home: https://github.com/martimunicoy/peleffy

diff --git a/devtools/envs/standard.yaml b/devtools/envs/standard.yaml
@@ -13,4 +13,4 @@ dependencies:
   - ipython
   - ambertools
   - rdkit
-  - openff-toolkit==0.9.2
+  - openff-toolkit==0.10.0
diff --git a/docs/index.rst b/docs/index.rst
@@ -7,6 +7,8 @@ are:
 
 * The following force field from the `Open Force Field toolkit <https://github.com/openforcefield/openforcefield>`_:
 
+  * openff_unconstrained-2.0.0.offxml
+
   * openff_unconstrained-1.3.0.offxml
 
   * openff_unconstrained-1.2.1.offxml

diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
@@ -7,6 +7,22 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``minor`` increments add features but do not break API compatibility
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
+
+1.3.4 - Current development
+---------------------------------------------------------
+
+This is a micro release of peleffy that solves a minor bug in the OPLS2005 parametrization. It also adds support for the new openff-2.0.0.
+
+New features
+""""""""""""
+- `PR #151 <https://github.com/martimunicoy/peleffy/pull/151>`_: Add support for openff-2.0.0.
+
+Bugfixes
+""""""""
+- `PR #149 <https://github.com/martimunicoy/peleffy/pull/149>`_: Minor error when parsing ffld output file.
+- `PR #153 <https://github.com/martimunicoy/peleffy/pull/153>`_: Fix parameters inconsistencies.
+
+
 1.3.3 - Explicit hydrogens support
 ---------------------------------------------------------
 

diff --git a/peleffy/data/tests/ETL_opls2005_parameters.json b/peleffy/data/tests/ETL_opls2005_parameters.json
@@ -123,14 +123,7 @@
             "spring_constant": "340.0 * angstrom**-2 * mole**-1 * kilocalorie"
         }
     ],
-    "charges": [
-        "-0.23 * elementary_charge",
-        "-0.23 * elementary_charge",
-        "0.115 * elementary_charge",
-        "0.115 * elementary_charge",
-        "0.115 * elementary_charge",
-        "0.115 * elementary_charge"
-    ],
+    "charges": "[-0.23, -0.23, 0.115, 0.115, 0.115, 0.115] * elementary_charge",
     "epsilons": [
         "0.076 * mole**-1 * kilocalorie",
         "0.076 * mole**-1 * kilocalorie",
@@ -227,4 +220,4 @@
         "1.25 * angstrom",
         "1.25 * angstrom"
     ]
-}
+}
diff --git a/peleffy/data/tests/MET_opls2005_parameters.json b/peleffy/data/tests/MET_opls2005_parameters.json
@@ -111,13 +111,7 @@
             "spring_constant": "340.0 * angstrom**-2 * mole**-1 * kilocalorie"
         }
     ],
-    "charges": [
-        "-0.24 * elementary_charge",
-        "0.06 * elementary_charge",
-        "0.06 * elementary_charge",
-        "0.06 * elementary_charge",
-        "0.06 * elementary_charge"
-    ],
+    "charges": "[-0.24, 0.06, 0.06, 0.06, 0.06] * elementary_charge",
     "epsilons": [
         "0.066 * mole**-1 * kilocalorie",
         "0.03 * mole**-1 * kilocalorie",
@@ -148,4 +142,4 @@
         "1.25 * angstrom",
         "1.25 * angstrom"
     ]
-}
+}
diff --git a/peleffy/data/tests/MET_parameters_to_json.json b/peleffy/data/tests/MET_parameters_to_json.json
@@ -1,3 +1,4 @@
+#openff_unconstrained-2.0.0.offxml
 {
     "GBSA_radii": [],
     "GBSA_scales": [],
@@ -20,43 +21,43 @@
             "atom1_idx": 1,
             "atom2_idx": 0,
             "atom3_idx": 2,
-            "eq_angle": "110.2468561538 * degree",
-            "spring_constant": "33.78875634641 * mole**-1 * radian**-2 * kilocalorie"
+            "eq_angle": "115.6030999533 * degree",
+            "spring_constant": "48.776492647595 * mole**-1 * radian**-2 * kilocalorie"
         },
         {
             "atom1_idx": 1,
             "atom2_idx": 0,
             "atom3_idx": 3,
-            "eq_angle": "110.2468561538 * degree",
-            "spring_constant": "33.78875634641 * mole**-1 * radian**-2 * kilocalorie"
+            "eq_angle": "115.6030999533 * degree",
+            "spring_constant": "48.776492647595 * mole**-1 * radian**-2 * kilocalorie"
         },
         {
             "atom1_idx": 1,
             "atom2_idx": 0,
             "atom3_idx": 4,
-            "eq_angle": "110.2468561538 * degree",
-            "spring_constant": "33.78875634641 * mole**-1 * radian**-2 * kilocalorie"
+            "eq_angle": "115.6030999533 * degree",
+            "spring_constant": "48.776492647595 * mole**-1 * radian**-2 * kilocalorie"
         },
         {
             "atom1_idx": 2,
             "atom2_idx": 0,
             "atom3_idx": 3,
-            "eq_angle": "110.2468561538 * degree",
-            "spring_constant": "33.78875634641 * mole**-1 * radian**-2 * kilocalorie"
+            "eq_angle": "115.6030999533 * degree",
+            "spring_constant": "48.776492647595 * mole**-1 * radian**-2 * kilocalorie"
         },
         {
             "atom1_idx": 2,
             "atom2_idx": 0,
             "atom3_idx": 4,
-            "eq_angle": "110.2468561538 * degree",
-            "spring_constant": "33.78875634641 * mole**-1 * radian**-2 * kilocalorie"
+            "eq_angle": "115.6030999533 * degree",
+            "spring_constant": "48.776492647595 * mole**-1 * radian**-2 * kilocalorie"
         },
         {
             "atom1_idx": 3,
             "atom2_idx": 0,
             "atom3_idx": 4,
-            "eq_angle": "110.2468561538 * degree",
-            "spring_constant": "33.78875634641 * mole**-1 * radian**-2 * kilocalorie"
+            "eq_angle": "115.6030999533 * degree",
+            "spring_constant": "48.776492647595 * mole**-1 * radian**-2 * kilocalorie"
         }
     ],
     "atom_names": [
@@ -77,35 +78,35 @@
         {
             "atom1_idx": 0,
             "atom2_idx": 1,
-            "eq_dist": "1.094223427522 * angstrom",
-            "spring_constant": "376.8940758588 * angstrom**-2 * mole**-1 * kilocalorie"
+            "eq_dist": "1.093899492634 * angstrom",
+            "spring_constant": "370.04670688625 * angstrom**-2 * mole**-1 * kilocalorie"
         },
         {
             "atom1_idx": 0,
             "atom2_idx": 2,
-            "eq_dist": "1.094223427522 * angstrom",
-            "spring_constant": "376.8940758588 * angstrom**-2 * mole**-1 * kilocalorie"
+            "eq_dist": "1.093899492634 * angstrom",
+            "spring_constant": "370.04670688625 * angstrom**-2 * mole**-1 * kilocalorie"
         },
         {
             "atom1_idx": 0,
             "atom2_idx": 3,
-            "eq_dist": "1.094223427522 * angstrom",
-            "spring_constant": "376.8940758588 * angstrom**-2 * mole**-1 * kilocalorie"
+            "eq_dist": "1.093899492634 * angstrom",
+            "spring_constant": "370.04670688625 * angstrom**-2 * mole**-1 * kilocalorie"
         },
         {
             "atom1_idx": 0,
             "atom2_idx": 4,
-            "eq_dist": "1.094223427522 * angstrom",
-            "spring_constant": "376.8940758588 * angstrom**-2 * mole**-1 * kilocalorie"
+            "eq_dist": "1.093899492634 * angstrom",
+            "spring_constant": "370.04670688625 * angstrom**-2 * mole**-1 * kilocalorie"
         }
     ],
     "charges": "[-0.077576, 0.019394, 0.019394, 0.019394, 0.019394] * elementary_charge",
     "epsilons": [
-        "0.1094 * mole**-1 * kilocalorie",
-        "0.0157 * mole**-1 * kilocalorie",
-        "0.0157 * mole**-1 * kilocalorie",
-        "0.0157 * mole**-1 * kilocalorie",
-        "0.0157 * mole**-1 * kilocalorie"
+        "0.1088406109251 * mole**-1 * kilocalorie",
+        "0.01577948280971 * mole**-1 * kilocalorie",
+        "0.01577948280971 * mole**-1 * kilocalorie",
+        "0.01577948280971 * mole**-1 * kilocalorie",
+        "0.01577948280971 * mole**-1 * kilocalorie"
     ],
     "gammas": [
         null,
@@ -117,17 +118,17 @@
     "impropers": [],
     "propers": [],
     "sigmas": [
-        "3.3996695084235347 * angstrom",
-        "2.649532787749369 * angstrom",
-        "2.649532787749369 * angstrom",
-        "2.649532787749369 * angstrom",
-        "2.649532787749369 * angstrom"
+        "3.3795317616266205 * angstrom",
+        "2.6445434132681247 * angstrom",
+        "2.6445434132681247 * angstrom",
+        "2.6445434132681247 * angstrom",
+        "2.6445434132681247 * angstrom"
     ],
     "vdW_radii": [
-        "1.6998347542117673 * angstrom",
-        "1.3247663938746845 * angstrom",
-        "1.3247663938746845 * angstrom",
-        "1.3247663938746845 * angstrom",
-        "1.3247663938746845 * angstrom"
+        "1.6897658808133103 * angstrom",
+        "1.3222717066340623 * angstrom",
+        "1.3222717066340623 * angstrom",
+        "1.3222717066340623 * angstrom",
+        "1.3222717066340623 * angstrom"
     ]
 }
diff --git a/peleffy/forcefield/calculators.py b/peleffy/forcefield/calculators.py
@@ -172,7 +172,7 @@ def get_partial_charges(self):
         # Extract number of atoms in molecule
         n_atoms = len(self.molecule.get_pdb_atom_names())
 
-        return [unit.Quantity(0.0, unit.elementary_charge), ] * n_atoms
+        return unit.Quantity([0.0, ] * n_atoms, unit.elementary_charge)
 
     def assign_partial_charges(self, parameters):
         """