Merge pull request #39 from molssi-seamm/dev

seamm · web-flow · commit af5f226e6d0f · 2025-01-29T16:26:51.000-05:00
Bugfixes: executable and SMILES
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -1,6 +1,10 @@
 =======
 History
 =======
+2025.1.29 -- Bugfixes: executable and SMILES
+    * The configuration for the executable was not set up correctly.
+    * There was a bug due to change in the SMILES interface for configurations.
+      
 2024.7.25 -- Bugfix: initial setup of packmol.ini file
     * The initial setup of the packmol.ini file did not add the information for
       Conda. This release fixes that problem.
diff --git a/packmol_step/packmol.py b/packmol_step/packmol.py
@@ -247,8 +247,8 @@ def run(self):
             else:
                 txt_config = Configuration(path)
                 txt_config.add_section(executor_type)
-                txt_config.add_value(executor_type, "installation", "local")
-                txt_config.add_value(executor_type, "code", str(path))
+                txt_config.set_value(executor_type, "installation", "local")
+                txt_config.set_value(executor_type, "code", str(path))
                 txt_config.save()
                 full_config.read(ini_dir / "packmol.ini")
 
@@ -433,7 +433,7 @@ 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, rdkit=True)
+                tmp_configuration.from_smiles(definition, flavor="openbabel")
                 if ff is not None:
                     ff.assign_forcefield(tmp_configuration)
             elif source == "configuration":
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 -0.0309 -0.0697 -0.0322 0.0 0.0 0.0
+   fixed -0.6957 2.0477 -0.1418 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 14.5687
+   inside sphere 0.0 0.0 0.0 14.5277
    center
-   fixed 0.0302 -0.1685 0.0129 0.0 0.0 0.0
+   fixed -0.6957 2.0477 -0.1418 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb
-   inside sphere 0.0 0.0 0.0 14.5687
-   number 424
+   inside sphere 0.0 0.0 0.0 14.5277
+   number 421
 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 29.14 Å with the solute and 424.0 solvent molecules
+Created a spherical region with a diameter of 29.06 Å with the solute and 421.0 solvent molecules
 
     +-------------+------------------+---------------+----------+------------+
     |  Component  | Structure        |   Requested % |   Number | Actual %   |
     |-------------+------------------+---------------+----------+------------|
     |   solute    | c1ccccc1c2ccccc2 |               |        1 |            |
-    |    fluid    | O                |       100.000 |      424 | 100.000    |
+    |    fluid    | O                |       100.000 |      421 | 100.000    |
     +-------------+------------------+---------------+----------+------------+
 
-There are a total of 1294 atoms in the cell giving a density of 0.99906 g/ml.
+There are a total of 1285 atoms in the cell giving a density of 1.0006 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 29.1850
+   inside cube 0.0 0.0 0.0 28.4724
    center
-   fixed 14.6157 14.5994 14.5991 0.0 0.0 0.0
+   fixed 14.0639 16.2839 14.3271 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb
-   inside cube 0.0 0.0 0.0 29.1850
-   number 822
+   inside cube 0.0 0.0 0.0 28.4724
+   number 763
 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 29.18 Å on a side with the solute and 822.0 solvent molecules
+Created a cubic region 28.47 Å on a side with the solute and 763.0 solvent molecules
 
     +-------------+------------------+---------------+----------+------------+
     |  Component  | Structure        |   Requested % |   Number | Actual %   |
     |-------------+------------------+---------------+----------+------------|
     |   solute    | c1ccccc1c2ccccc2 |               |        1 |            |
-    |    fluid    | O                |       100.000 |      822 | 100.000    |
+    |    fluid    | O                |       100.000 |      763 | 100.000    |
     +-------------+------------------+---------------+----------+------------+
 
-There are a total of 2488 atoms in the cell giving a density of 0.99951 g/ml.
+There are a total of 2311 atoms in the cell giving a density of 0.99998 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 17.0750
+   inside cube 1.0000 1.0000 1.0000 16.4724
    center
-   fixed 8.5324 8.5449 8.5430 0.0 0.0 0.0
+   fixed 8.0639 10.2839 8.3271 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb
-   inside cube 1.0000 1.0000 1.0000 17.0750
-   number 223
+   inside cube 1.0000 1.0000 1.0000 16.4724
+   number 202
 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 19.08 Å on a side with the solute and 223.0 solvent molecules
+Created a periodic cubic cell 18.47 Å on a side with the solute and 202.0 solvent molecules
 
     +-------------+------------------+---------------+----------+------------+
     |  Component  | Structure        |   Requested % |   Number | Actual %   |
     |-------------+------------------+---------------+----------+------------|
     |   solute    | c1ccccc1c2ccccc2 |               |        1 |            |
-    |    fluid    | O                |       100.000 |      223 | 100.000    |
+    |    fluid    | O                |       100.000 |      202 | 100.000    |
     +-------------+------------------+---------------+----------+------------+
 
-There are a total of 691 atoms in the cell giving a density of 0.99807 g/ml.
+There are a total of 628 atoms in the cell giving a density of 0.9993 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 17.1247
+   inside cube 1.0000 1.0000 1.0000 16.4724
    center
-   fixed 8.5765 8.5850 8.5614 0.0 0.0 0.0
+   fixed 8.0639 10.2839 8.3271 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb
-   inside cube 1.0000 1.0000 1.0000 17.1247
-   number 225
+   inside cube 1.0000 1.0000 1.0000 16.4724
+   number 202
 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 19.12 Å on a side with the solute and 225.0 solvent molecules
+Created a periodic cubic cell 18.47 Å on a side with the solute and 202.0 solvent molecules
 
     +-------------+------------------+---------------+----------+------------+
     |  Component  | Structure        |   Requested % |   Number | Actual %   |
     |-------------+------------------+---------------+----------+------------|
     |   solute    | c1ccccc1c2ccccc2 |               |        1 |            |
-    |    fluid    | O                |       100.000 |      225 | 100.000    |
+    |    fluid    | O                |       100.000 |      202 | 100.000    |
     +-------------+------------------+---------------+----------+------------+
 
-There are a total of 697 atoms in the cell giving a density of 0.99887 g/ml.
+There are a total of 628 atoms in the cell giving a density of 0.9993 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 13.6616 27.3213 40.9757 0.0 0.0 0.0
+   fixed 13.4853 29.3630 41.0638 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 0.0269 0.1283 -0.0216 0.0 0.0 0.0
+   fixed -0.6957 2.0477 -0.1418 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 10.7897 10.7676 10.7743 0.0 0.0 0.0
+   fixed 10.6029 12.8229 10.8661 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 10.7661 10.7778 10.7743 0.0 0.0 0.0
+   fixed 10.6029 12.8229 10.8661 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 4.9959 10.0322 14.9967 0.0 0.0 0.0
+   fixed 4.8276 12.0477 15.0909 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 3.9805 8.9732 13.9961 0.0 0.0 0.0
+   fixed 3.8276 11.0477 14.0909 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb
