Bugfix: initial setup of packmol.ini file

HISTORY.rst

@@ -1,6 +1,10 @@
 =======
 History
 =======
+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.
+
 2024.6.29 -- Bugfix: bonding incorrect in some cases.
     * The use of PDB with Packmol could in some cases lead to multiple bonds in the
       wrong place. This release fixes that problem.

packmol_step/packmol.py

@@ -6,6 +6,7 @@
 import importlib
 import logging
 import math
+import os
 from pathlib import Path
 import pprint
 import shutil
@@ -16,7 +17,7 @@
 from molsystem import SystemDB
 import seamm
 import seamm_util
-from seamm_util import ureg, Q_, units_class  # noqa: F401
+from seamm_util import Configuration, ureg, Q_, units_class  # noqa: F401
 import seamm_util.printing as printing
 from seamm_util.printing import FormattedText as __
 import packmol_step
@@ -220,14 +221,19 @@ def run(self):
         ini_dir = Path(seamm_options["root"]).expanduser()
         path = ini_dir / "packmol.ini"
 
-        if path.exists():
-            full_config.read(ini_dir / "packmol.ini")
-
-        # If the section we need doesn't exists, get the default
-        if not path.exists() or executor_type not in full_config:
+        # If the config file doesn't exists, get the default
+        if not path.exists():
             resources = importlib.resources.files("packmol_step") / "data"
             ini_text = (resources / "packmol.ini").read_text()
-            full_config.read_string(ini_text)
+            txt_config = Configuration(path)
+            txt_config.from_string(ini_text)
+
+            # Work out the conda info needed
+            txt_config.set_value("local", "conda", os.environ["CONDA_EXE"])
+            txt_config.set_value("local", "conda-environment", "seamm-packmol")
+            txt_config.save()
+
+        full_config.read(ini_dir / "packmol.ini")
 
         # Getting desperate! Look for an executable in the path
         if executor_type not in full_config:
@@ -239,17 +245,12 @@ def run(self):
                     "in the path!"
                 )
             else:
-                full_config[executor_type] = {
-                    "installation": "local",
-                    "code": str(path),
-                }
-
-        # If the ini file does not exist, write it out!
-        if not path.exists():
-            with path.open("w") as fd:
-                full_config.write(fd)
-            printer.normal(f"Wrote the Packmol configuration file to {path}")
-            printer.normal("")
+                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.save()
+                full_config.read(ini_dir / "packmol.ini")
 
         config = dict(full_config.items(executor_type))
 

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 -0.0189 -0.1051 -0.0281 0.0 0.0 0.0
+   fixed -0.0309 -0.0697 -0.0322 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb

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 14.5778
+   inside sphere 0.0 0.0 0.0 14.5687
    center
-   fixed -0.0043 -0.0362 -0.0348 0.0 0.0 0.0
+   fixed 0.0302 -0.1685 0.0129 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb
-   inside sphere 0.0 0.0 0.0 14.5778
-   number 425
+   inside sphere 0.0 0.0 0.0 14.5687
+   number 424
 end structure

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 29.16 Å with the solute and 425.0 solvent molecules
+Created a spherical region with a diameter of 29.14 Å with the solute and 424.0 solvent molecules
 
     +-------------+------------------+---------------+----------+------------+
     |  Component  | Structure        |   Requested % |   Number | Actual %   |
     |-------------+------------------+---------------+----------+------------|
     |   solute    | c1ccccc1c2ccccc2 |               |        1 |            |
-    |    fluid    | O                |       100.000 |      425 | 100.000    |
+    |    fluid    | O                |       100.000 |      424 | 100.000    |
     +-------------+------------------+---------------+----------+------------+
 
-There are a total of 1297 atoms in the cell giving a density of 0.99949 g/ml.
+There are a total of 1294 atoms in the cell giving a density of 0.99906 g/ml.

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 29.2609
+   inside cube 0.0 0.0 0.0 29.1850
    center
-   fixed 14.6244 14.6137 14.6231 0.0 0.0 0.0
+   fixed 14.6157 14.5994 14.5991 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb
-   inside cube 0.0 0.0 0.0 29.2609
-   number 829
+   inside cube 0.0 0.0 0.0 29.1850
+   number 822
 end structure

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 29.26 Å on a side with the solute and 829.0 solvent molecules
+Created a cubic region 29.18 Å on a side with the solute and 822.0 solvent molecules
 
     +-------------+------------------+---------------+----------+------------+
     |  Component  | Structure        |   Requested % |   Number | Actual %   |
     |-------------+------------------+---------------+----------+------------|
     |   solute    | c1ccccc1c2ccccc2 |               |        1 |            |
-    |    fluid    | O                |       100.000 |      829 | 100.000    |
+    |    fluid    | O                |       100.000 |      822 | 100.000    |
     +-------------+------------------+---------------+----------+------------+
 
-There are a total of 2509 atoms in the cell giving a density of 1.0001 g/ml.
+There are a total of 2488 atoms in the cell giving a density of 0.99951 g/ml.

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 17.2164
+   inside cube 1.0000 1.0000 1.0000 17.0750
    center
-   fixed 8.6069 8.5960 8.6042 0.0 0.0 0.0
+   fixed 8.5324 8.5449 8.5430 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb
-   inside cube 1.0000 1.0000 1.0000 17.2164
-   number 229
+   inside cube 1.0000 1.0000 1.0000 17.0750
+   number 223
 end structure

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 19.22 Å on a side with the solute and 229.0 solvent molecules
+Created a periodic cubic cell 19.08 Å on a side with the solute and 223.0 solvent molecules
 
     +-------------+------------------+---------------+----------+------------+
     |  Component  | Structure        |   Requested % |   Number | Actual %   |
     |-------------+------------------+---------------+----------+------------|
     |   solute    | c1ccccc1c2ccccc2 |               |        1 |            |
-    |    fluid    | O                |       100.000 |      229 | 100.000    |
+    |    fluid    | O                |       100.000 |      223 | 100.000    |
     +-------------+------------------+---------------+----------+------------+
 
-There are a total of 709 atoms in the cell giving a density of 1.0015 g/ml.
+There are a total of 691 atoms in the cell giving a density of 0.99807 g/ml.

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 17.2792
+   inside cube 1.0000 1.0000 1.0000 17.1247
    center
-   fixed 8.6363 8.6450 8.6389 0.0 0.0 0.0
+   fixed 8.5765 8.5850 8.5614 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb
-   inside cube 1.0000 1.0000 1.0000 17.2792
-   number 231
+   inside cube 1.0000 1.0000 1.0000 17.1247
+   number 225
 end structure

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 19.28 Å on a side with the solute and 231.0 solvent molecules
+Created a periodic cubic cell 19.12 Å on a side with the solute and 225.0 solvent molecules
 
     +-------------+------------------+---------------+----------+------------+
     |  Component  | Structure        |   Requested % |   Number | Actual %   |
     |-------------+------------------+---------------+----------+------------|
     |   solute    | c1ccccc1c2ccccc2 |               |        1 |            |
-    |    fluid    | O                |       100.000 |      231 | 100.000    |
+    |    fluid    | O                |       100.000 |      225 | 100.000    |
     +-------------+------------------+---------------+----------+------------+
 
-There are a total of 715 atoms in the cell giving a density of 1.0001 g/ml.
+There are a total of 697 atoms in the cell giving a density of 0.99887 g/ml.

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 13.6630 27.3240 40.9699 0.0 0.0 0.0
+   fixed 13.6616 27.3213 40.9757 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb

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 -0.0074 0.0650 0.0012 0.0 0.0 0.0
+   fixed 0.0269 0.1283 -0.0216 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb

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 10.7916 10.7737 10.7750 0.0 0.0 0.0
+   fixed 10.7897 10.7676 10.7743 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb

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 10.7627 10.7772 10.7756 0.0 0.0 0.0
+   fixed 10.7661 10.7778 10.7743 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb

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 4.9978 10.0181 14.9962 0.0 0.0 0.0
+   fixed 4.9959 10.0322 14.9967 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb

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 4.0105 9.0004 13.9970 0.0 0.0 0.0
+   fixed 3.9805 8.9732 13.9961 0.0 0.0 0.0
    number 1
 end structure
 structure input_2.pdb