Merge pull request #34 from molssi-seamm/dev

Dev
molssi-seamm · Jun 21, 2024 · 065e582 · 065e582
2 parents 29913be + aae55df
commit 065e582
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Showing 19 changed files with 44 additions and 37 deletions.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -1,6 +1,10 @@
 =======
 History
 =======
+2024.6.21 -- Switching to RDKit for SMILES
+    * Using RDKit for SMILES since we found some issues with OpenBabel, and also the
+      atom typing uses RDKit, so this is more compatible.
+
 2024.3.19 -- Updated installer for new scheme
     * packmol-step-installer now uses the new scheme, which supports both Conda and
       Docker installation.

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -10,7 +10,9 @@ dependencies:
 
   # SEAMM
   - seamm
+  - seamm-installer
   - pyyaml
+  - rdkit
   - tabulate
 
   # Testing
@@ -21,7 +23,7 @@ dependencies:
   - pytest-cov
 
   # Integration testing
-  - packmol==20.2.2
+  # - packmol==20.2.2
 
   # Documentation
   - pydata-sphinx-theme

diff --git a/packmol_step/packmol.py b/packmol_step/packmol.py
@@ -421,7 +421,7 @@ def round_copies(n_copies, molecules):
             if source == "SMILES":
                 tmp_system = tmp_db.create_system(name=definition)
                 tmp_configuration = tmp_system.create_configuration(name="default")
-                tmp_configuration.from_smiles(definition)
+                tmp_configuration.from_smiles(definition, rdkit=True)
                 if ff is not None:
                     ff.assign_forcefield(tmp_configuration)
             elif source == "configuration":

diff --git a/requirements.txt b/requirements.txt
@@ -1,3 +1,4 @@
 seamm
 seamm_exec
+rdkit
 tabulate
diff --git a/tests/outputs/test_10_20_Å_spherical_region_with_solvent_around_solute.inp b/tests/outputs/test_10_20_Å_spherical_region_with_solvent_around_solute.inp
@@ -5,7 +5,7 @@ connect yes
 structure input_1.pdb
    inside sphere 0.0 0.0 0.0 10.0000
    center
-   fixed -0.6957 2.0477 -0.1418 0.0 0.0 0.0
+   fixed -0.0189 -0.1051 -0.0281 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb

diff --git a/tests/outputs/test_11_spherical_region_with_solvent_thickness_around_solute.inp b/tests/outputs/test_11_spherical_region_with_solvent_thickness_around_solute.inp
@@ -3,12 +3,12 @@ output packmol.pdb
 filetype pdb
 connect yes
 structure input_1.pdb
-   inside sphere 0.0 0.0 0.0 14.5277
+   inside sphere 0.0 0.0 0.0 14.5778
    center
-   fixed -0.6957 2.0477 -0.1418 0.0 0.0 0.0
+   fixed -0.0043 -0.0362 -0.0348 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb
-   inside sphere 0.0 0.0 0.0 14.5277
-   number 421
+   inside sphere 0.0 0.0 0.0 14.5778
+   number 425
 end structure
diff --git a/tests/outputs/test_11_spherical_region_with_solvent_thickness_around_solute.out b/tests/outputs/test_11_spherical_region_with_solvent_thickness_around_solute.out
@@ -13,13 +13,13 @@
     the molecule. The number of molecules of the fluid will be obtained  by
     using the density 1.0 g/ml.
 
-Created a spherical region with a diameter of 29.06 Å with the solute and 421.0 solvent molecules
+Created a spherical region with a diameter of 29.16 Å with the solute and 425.0 solvent molecules
 
     +-------------+------------------+---------------+----------+------------+
     |  Component  | Structure        |   Requested % |   Number | Actual %   |
     |-------------+------------------+---------------+----------+------------|
     |   solute    | c1ccccc1c2ccccc2 |               |        1 |            |
-    |    fluid    | O                |       100.000 |      421 | 100.000    |
+    |    fluid    | O                |       100.000 |      425 | 100.000    |
     +-------------+------------------+---------------+----------+------------+
 
-There are a total of 1285 atoms in the cell giving a density of 1.0006 g/ml.
+There are a total of 1297 atoms in the cell giving a density of 0.99949 g/ml.
diff --git a/tests/outputs/test_12_cubic_region_with_solvent_thickness_around_solute.inp b/tests/outputs/test_12_cubic_region_with_solvent_thickness_around_solute.inp
@@ -3,12 +3,12 @@ output packmol.pdb
 filetype pdb
 connect yes
 structure input_1.pdb
-   inside cube 0.0 0.0 0.0 28.4724
+   inside cube 0.0 0.0 0.0 29.2609
    center
-   fixed 14.0639 16.2839 14.3271 0.0 0.0 0.0
+   fixed 14.6244 14.6137 14.6231 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb
-   inside cube 0.0 0.0 0.0 28.4724
-   number 763
+   inside cube 0.0 0.0 0.0 29.2609
+   number 829
 end structure
diff --git a/tests/outputs/test_12_cubic_region_with_solvent_thickness_around_solute.out b/tests/outputs/test_12_cubic_region_with_solvent_thickness_around_solute.out
@@ -13,13 +13,13 @@
     the molecule. The number of molecules of the fluid will be obtained  by
     using the density 1.0 g/ml.
 
-Created a cubic region 28.47 Å on a side with the solute and 763.0 solvent molecules
+Created a cubic region 29.26 Å on a side with the solute and 829.0 solvent molecules
 
     +-------------+------------------+---------------+----------+------------+
     |  Component  | Structure        |   Requested % |   Number | Actual %   |
     |-------------+------------------+---------------+----------+------------|
     |   solute    | c1ccccc1c2ccccc2 |               |        1 |            |
-    |    fluid    | O                |       100.000 |      763 | 100.000    |
+    |    fluid    | O                |       100.000 |      829 | 100.000    |
     +-------------+------------------+---------------+----------+------------+
 
-There are a total of 2311 atoms in the cell giving a density of 0.99998 g/ml.
+There are a total of 2509 atoms in the cell giving a density of 1.0001 g/ml.
diff --git a/tests/outputs/test_13_cubic_cell_with_solvent_thickness_around_solute.inp b/tests/outputs/test_13_cubic_cell_with_solvent_thickness_around_solute.inp
@@ -3,12 +3,12 @@ output packmol.pdb
 filetype pdb
 connect yes
 structure input_1.pdb
-   inside cube 1.0000 1.0000 1.0000 16.4724
+   inside cube 1.0000 1.0000 1.0000 17.2164
    center
-   fixed 8.0639 10.2839 8.3271 0.0 0.0 0.0
+   fixed 8.6069 8.5960 8.6042 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb
-   inside cube 1.0000 1.0000 1.0000 16.4724
-   number 202
+   inside cube 1.0000 1.0000 1.0000 17.2164
+   number 229
 end structure
diff --git a/tests/outputs/test_13_cubic_cell_with_solvent_thickness_around_solute.out b/tests/outputs/test_13_cubic_cell_with_solvent_thickness_around_solute.out
@@ -13,13 +13,13 @@
     the molecule. The number of molecules of the fluid will be obtained  by
     using the density 1.0 g/ml.
 
-Created a periodic cubic cell 18.47 Å on a side with the solute and 202.0 solvent molecules
+Created a periodic cubic cell 19.22 Å on a side with the solute and 229.0 solvent molecules
 
     +-------------+------------------+---------------+----------+------------+
     |  Component  | Structure        |   Requested % |   Number | Actual %   |
     |-------------+------------------+---------------+----------+------------|
     |   solute    | c1ccccc1c2ccccc2 |               |        1 |            |
-    |    fluid    | O                |       100.000 |      202 | 100.000    |
+    |    fluid    | O                |       100.000 |      229 | 100.000    |
     +-------------+------------------+---------------+----------+------------+
 
-There are a total of 628 atoms in the cell giving a density of 0.9993 g/ml.
+There are a total of 709 atoms in the cell giving a density of 1.0015 g/ml.
diff --git a/tests/outputs/test_14_rectangular_cell_with_solvent_thickness_around_solute.inp b/tests/outputs/test_14_rectangular_cell_with_solvent_thickness_around_solute.inp
@@ -3,12 +3,12 @@ output packmol.pdb
 filetype pdb
 connect yes
 structure input_1.pdb
-   inside cube 1.0000 1.0000 1.0000 16.4724
+   inside cube 1.0000 1.0000 1.0000 17.2792
    center
-   fixed 8.0639 10.2839 8.3271 0.0 0.0 0.0
+   fixed 8.6363 8.6450 8.6389 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb
-   inside cube 1.0000 1.0000 1.0000 16.4724
-   number 202
+   inside cube 1.0000 1.0000 1.0000 17.2792
+   number 231
 end structure
diff --git a/tests/outputs/test_14_rectangular_cell_with_solvent_thickness_around_solute.out b/tests/outputs/test_14_rectangular_cell_with_solvent_thickness_around_solute.out
@@ -13,13 +13,13 @@
     the molecule. The number of molecules of the fluid will be obtained  by
     using the density 1.0 g/ml.
 
-Created a periodic cubic cell 18.47 Å on a side with the solute and 202.0 solvent molecules
+Created a periodic cubic cell 19.28 Å on a side with the solute and 231.0 solvent molecules
 
     +-------------+------------------+---------------+----------+------------+
     |  Component  | Structure        |   Requested % |   Number | Actual %   |
     |-------------+------------------+---------------+----------+------------|
     |   solute    | c1ccccc1c2ccccc2 |               |        1 |            |
-    |    fluid    | O                |       100.000 |      202 | 100.000    |
+    |    fluid    | O                |       100.000 |      231 | 100.000    |
     +-------------+------------------+---------------+----------+------------+
 
-There are a total of 628 atoms in the cell giving a density of 0.9993 g/ml.
+There are a total of 715 atoms in the cell giving a density of 1.0001 g/ml.
diff --git a/tests/outputs/test_15_rectangular_cell_with_Ideal_gas_around_solute.inp b/tests/outputs/test_15_rectangular_cell_with_Ideal_gas_around_solute.inp
@@ -5,7 +5,7 @@ connect yes
 structure input_1.pdb
    inside box 1.0000 1.0000 1.0000 25.3153 52.6305 79.9458
    center
-   fixed 13.4853 29.3630 41.0638 0.0 0.0 0.0
+   fixed 13.6630 27.3240 40.9699 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb

diff --git a/tests/outputs/test_1_spherical_region.inp b/tests/outputs/test_1_spherical_region.inp
@@ -5,7 +5,7 @@ connect yes
 structure input_1.pdb
    inside sphere 0.0 0.0 0.0 13.3688
    center
-   fixed -0.6957 2.0477 -0.1418 0.0 0.0 0.0
+   fixed -0.0074 0.0650 0.0012 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb

diff --git a/tests/outputs/test_3_cubic_region.inp b/tests/outputs/test_3_cubic_region.inp
@@ -5,7 +5,7 @@ connect yes
 structure input_1.pdb
    inside cube 0.0 0.0 0.0 21.5504
    center
-   fixed 10.6029 12.8229 10.8661 0.0 0.0 0.0
+   fixed 10.7916 10.7737 10.7750 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb

diff --git a/tests/outputs/test_4_periodic_cubic_cell.inp b/tests/outputs/test_4_periodic_cubic_cell.inp
@@ -5,7 +5,7 @@ connect yes
 structure input_1.pdb
    inside cube 1.0000 1.0000 1.0000 19.5504
    center
-   fixed 10.6029 12.8229 10.8661 0.0 0.0 0.0
+   fixed 10.7627 10.7772 10.7756 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb

diff --git a/tests/outputs/test_8_10x20x30_ang_region_1k_atoms_biphenyl_solute.inp b/tests/outputs/test_8_10x20x30_ang_region_1k_atoms_biphenyl_solute.inp
@@ -5,7 +5,7 @@ connect yes
 structure input_1.pdb
    inside box 0.0 0.0 0.0 10.0000 20.0000 30.0000
    center
-   fixed 4.8276 12.0477 15.0909 0.0 0.0 0.0
+   fixed 4.9978 10.0181 14.9962 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb

diff --git a/tests/outputs/test_9_10x20x30_ang_cell_1k_atoms_biphenyl_solute.inp b/tests/outputs/test_9_10x20x30_ang_cell_1k_atoms_biphenyl_solute.inp
@@ -5,7 +5,7 @@ connect yes
 structure input_1.pdb
    inside box 1.0000 1.0000 1.0000 8.0000 18.0000 28.0000
    center
-   fixed 3.8276 11.0477 14.0909 0.0 0.0 0.0
+   fixed 4.0105 9.0004 13.9970 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb