From 64f4c154dd8e997e88dc3617b23b37bb2d153048 Mon Sep 17 00:00:00 2001
From: Timotej Bernat <tibe3324@colorado.edu>
Date: Fri, 17 May 2024 15:28:55 -0600
Subject: [PATCH] Consolidated openfftools, openmmtool, and lammpstools as
 submodules of master "mdtools" core module

---
 polymerist/mdtools/__init__.py                                  | 1 +
 polymerist/{ => mdtools}/lammpstools/__init__.py                | 0
 polymerist/{ => mdtools}/lammpstools/lammpseval.py              | 0
 polymerist/{ => mdtools}/lammpstools/unitstyles.py              | 0
 polymerist/{ => mdtools}/openfftools/__init__.py                | 0
 polymerist/{ => mdtools}/openfftools/boxvectors.py              | 0
 polymerist/{ => mdtools}/openfftools/omminter.py                | 0
 polymerist/{ => mdtools}/openfftools/partialcharge/__init__.py  | 0
 .../{ => mdtools}/openfftools/partialcharge/chargemethods.py    | 0
 .../{ => mdtools}/openfftools/partialcharge/molchargers.py      | 0
 .../openfftools/partialcharge/rescharge/__init__.py             | 0
 .../openfftools/partialcharge/rescharge/calculation.py          | 0
 .../openfftools/partialcharge/rescharge/interface.py            | 0
 .../openfftools/partialcharge/rescharge/rctypes.py              | 0
 .../openfftools/partialcharge/rescharge/redistribution.py       | 0
 polymerist/{ => mdtools}/openfftools/partition.py               | 0
 polymerist/{ => mdtools}/openfftools/solvation/__init__.py      | 0
 polymerist/{ => mdtools}/openfftools/solvation/packing.py       | 0
 polymerist/{ => mdtools}/openfftools/solvation/physprops.py     | 0
 .../{ => mdtools}/openfftools/solvation/solvents/__init__.py    | 0
 .../openfftools/solvation/solvents/water_TIP3P.sdf              | 0
 polymerist/{ => mdtools}/openfftools/topology.py                | 0
 polymerist/{ => mdtools}/openmmtools/__init__.py                | 0
 polymerist/{ => mdtools}/openmmtools/description.py             | 0
 polymerist/{ => mdtools}/openmmtools/evaluation.py              | 0
 polymerist/{ => mdtools}/openmmtools/execution.py               | 0
 polymerist/{ => mdtools}/openmmtools/forcegroups.py             | 0
 polymerist/{ => mdtools}/openmmtools/parameters.py              | 0
 polymerist/{ => mdtools}/openmmtools/preparation.py             | 0
 polymerist/{ => mdtools}/openmmtools/reporters.py               | 0
 polymerist/{ => mdtools}/openmmtools/serialization.py           | 0
 polymerist/{ => mdtools}/openmmtools/thermo.py                  | 0
 polymerist/polymers/building.py                                 | 2 +-
 33 files changed, 2 insertions(+), 1 deletion(-)
 create mode 100644 polymerist/mdtools/__init__.py
 rename polymerist/{ => mdtools}/lammpstools/__init__.py (100%)
 rename polymerist/{ => mdtools}/lammpstools/lammpseval.py (100%)
 rename polymerist/{ => mdtools}/lammpstools/unitstyles.py (100%)
 rename polymerist/{ => mdtools}/openfftools/__init__.py (100%)
 rename polymerist/{ => mdtools}/openfftools/boxvectors.py (100%)
 rename polymerist/{ => mdtools}/openfftools/omminter.py (100%)
 rename polymerist/{ => mdtools}/openfftools/partialcharge/__init__.py (100%)
 rename polymerist/{ => mdtools}/openfftools/partialcharge/chargemethods.py (100%)
 rename polymerist/{ => mdtools}/openfftools/partialcharge/molchargers.py (100%)
 rename polymerist/{ => mdtools}/openfftools/partialcharge/rescharge/__init__.py (100%)
 rename polymerist/{ => mdtools}/openfftools/partialcharge/rescharge/calculation.py (100%)
 rename polymerist/{ => mdtools}/openfftools/partialcharge/rescharge/interface.py (100%)
 rename polymerist/{ => mdtools}/openfftools/partialcharge/rescharge/rctypes.py (100%)
 rename polymerist/{ => mdtools}/openfftools/partialcharge/rescharge/redistribution.py (100%)
 rename polymerist/{ => mdtools}/openfftools/partition.py (100%)
 rename polymerist/{ => mdtools}/openfftools/solvation/__init__.py (100%)
 rename polymerist/{ => mdtools}/openfftools/solvation/packing.py (100%)
 rename polymerist/{ => mdtools}/openfftools/solvation/physprops.py (100%)
 rename polymerist/{ => mdtools}/openfftools/solvation/solvents/__init__.py (100%)
 rename polymerist/{ => mdtools}/openfftools/solvation/solvents/water_TIP3P.sdf (100%)
 rename polymerist/{ => mdtools}/openfftools/topology.py (100%)
 rename polymerist/{ => mdtools}/openmmtools/__init__.py (100%)
 rename polymerist/{ => mdtools}/openmmtools/description.py (100%)
 rename polymerist/{ => mdtools}/openmmtools/evaluation.py (100%)
 rename polymerist/{ => mdtools}/openmmtools/execution.py (100%)
 rename polymerist/{ => mdtools}/openmmtools/forcegroups.py (100%)
 rename polymerist/{ => mdtools}/openmmtools/parameters.py (100%)
 rename polymerist/{ => mdtools}/openmmtools/preparation.py (100%)
 rename polymerist/{ => mdtools}/openmmtools/reporters.py (100%)
 rename polymerist/{ => mdtools}/openmmtools/serialization.py (100%)
 rename polymerist/{ => mdtools}/openmmtools/thermo.py (100%)

diff --git a/polymerist/mdtools/__init__.py b/polymerist/mdtools/__init__.py
new file mode 100644
index 0000000..cb78104
--- /dev/null
+++ b/polymerist/mdtools/__init__.py
@@ -0,0 +1 @@
+'''Tools for interfacing with and setting up systems for various molecular dynamics packages'''
\ No newline at end of file
diff --git a/polymerist/lammpstools/__init__.py b/polymerist/mdtools/lammpstools/__init__.py
similarity index 100%
rename from polymerist/lammpstools/__init__.py
rename to polymerist/mdtools/lammpstools/__init__.py
diff --git a/polymerist/lammpstools/lammpseval.py b/polymerist/mdtools/lammpstools/lammpseval.py
similarity index 100%
rename from polymerist/lammpstools/lammpseval.py
rename to polymerist/mdtools/lammpstools/lammpseval.py
diff --git a/polymerist/lammpstools/unitstyles.py b/polymerist/mdtools/lammpstools/unitstyles.py
similarity index 100%
rename from polymerist/lammpstools/unitstyles.py
rename to polymerist/mdtools/lammpstools/unitstyles.py
diff --git a/polymerist/openfftools/__init__.py b/polymerist/mdtools/openfftools/__init__.py
similarity index 100%
rename from polymerist/openfftools/__init__.py
rename to polymerist/mdtools/openfftools/__init__.py
diff --git a/polymerist/openfftools/boxvectors.py b/polymerist/mdtools/openfftools/boxvectors.py
similarity index 100%
rename from polymerist/openfftools/boxvectors.py
rename to polymerist/mdtools/openfftools/boxvectors.py
diff --git a/polymerist/openfftools/omminter.py b/polymerist/mdtools/openfftools/omminter.py
similarity index 100%
rename from polymerist/openfftools/omminter.py
rename to polymerist/mdtools/openfftools/omminter.py
diff --git a/polymerist/openfftools/partialcharge/__init__.py b/polymerist/mdtools/openfftools/partialcharge/__init__.py
similarity index 100%
rename from polymerist/openfftools/partialcharge/__init__.py
rename to polymerist/mdtools/openfftools/partialcharge/__init__.py
diff --git a/polymerist/openfftools/partialcharge/chargemethods.py b/polymerist/mdtools/openfftools/partialcharge/chargemethods.py
similarity index 100%
rename from polymerist/openfftools/partialcharge/chargemethods.py
rename to polymerist/mdtools/openfftools/partialcharge/chargemethods.py
diff --git a/polymerist/openfftools/partialcharge/molchargers.py b/polymerist/mdtools/openfftools/partialcharge/molchargers.py
similarity index 100%
rename from polymerist/openfftools/partialcharge/molchargers.py
rename to polymerist/mdtools/openfftools/partialcharge/molchargers.py
diff --git a/polymerist/openfftools/partialcharge/rescharge/__init__.py b/polymerist/mdtools/openfftools/partialcharge/rescharge/__init__.py
similarity index 100%
rename from polymerist/openfftools/partialcharge/rescharge/__init__.py
rename to polymerist/mdtools/openfftools/partialcharge/rescharge/__init__.py
diff --git a/polymerist/openfftools/partialcharge/rescharge/calculation.py b/polymerist/mdtools/openfftools/partialcharge/rescharge/calculation.py
similarity index 100%
rename from polymerist/openfftools/partialcharge/rescharge/calculation.py
rename to polymerist/mdtools/openfftools/partialcharge/rescharge/calculation.py
diff --git a/polymerist/openfftools/partialcharge/rescharge/interface.py b/polymerist/mdtools/openfftools/partialcharge/rescharge/interface.py
similarity index 100%
rename from polymerist/openfftools/partialcharge/rescharge/interface.py
rename to polymerist/mdtools/openfftools/partialcharge/rescharge/interface.py
diff --git a/polymerist/openfftools/partialcharge/rescharge/rctypes.py b/polymerist/mdtools/openfftools/partialcharge/rescharge/rctypes.py
similarity index 100%
rename from polymerist/openfftools/partialcharge/rescharge/rctypes.py
rename to polymerist/mdtools/openfftools/partialcharge/rescharge/rctypes.py
diff --git a/polymerist/openfftools/partialcharge/rescharge/redistribution.py b/polymerist/mdtools/openfftools/partialcharge/rescharge/redistribution.py
similarity index 100%
rename from polymerist/openfftools/partialcharge/rescharge/redistribution.py
rename to polymerist/mdtools/openfftools/partialcharge/rescharge/redistribution.py
diff --git a/polymerist/openfftools/partition.py b/polymerist/mdtools/openfftools/partition.py
similarity index 100%
rename from polymerist/openfftools/partition.py
rename to polymerist/mdtools/openfftools/partition.py
diff --git a/polymerist/openfftools/solvation/__init__.py b/polymerist/mdtools/openfftools/solvation/__init__.py
similarity index 100%
rename from polymerist/openfftools/solvation/__init__.py
rename to polymerist/mdtools/openfftools/solvation/__init__.py
diff --git a/polymerist/openfftools/solvation/packing.py b/polymerist/mdtools/openfftools/solvation/packing.py
similarity index 100%
rename from polymerist/openfftools/solvation/packing.py
rename to polymerist/mdtools/openfftools/solvation/packing.py
diff --git a/polymerist/openfftools/solvation/physprops.py b/polymerist/mdtools/openfftools/solvation/physprops.py
similarity index 100%
rename from polymerist/openfftools/solvation/physprops.py
rename to polymerist/mdtools/openfftools/solvation/physprops.py
diff --git a/polymerist/openfftools/solvation/solvents/__init__.py b/polymerist/mdtools/openfftools/solvation/solvents/__init__.py
similarity index 100%
rename from polymerist/openfftools/solvation/solvents/__init__.py
rename to polymerist/mdtools/openfftools/solvation/solvents/__init__.py
diff --git a/polymerist/openfftools/solvation/solvents/water_TIP3P.sdf b/polymerist/mdtools/openfftools/solvation/solvents/water_TIP3P.sdf
similarity index 100%
rename from polymerist/openfftools/solvation/solvents/water_TIP3P.sdf
rename to polymerist/mdtools/openfftools/solvation/solvents/water_TIP3P.sdf
diff --git a/polymerist/openfftools/topology.py b/polymerist/mdtools/openfftools/topology.py
similarity index 100%
rename from polymerist/openfftools/topology.py
rename to polymerist/mdtools/openfftools/topology.py
diff --git a/polymerist/openmmtools/__init__.py b/polymerist/mdtools/openmmtools/__init__.py
similarity index 100%
rename from polymerist/openmmtools/__init__.py
rename to polymerist/mdtools/openmmtools/__init__.py
diff --git a/polymerist/openmmtools/description.py b/polymerist/mdtools/openmmtools/description.py
similarity index 100%
rename from polymerist/openmmtools/description.py
rename to polymerist/mdtools/openmmtools/description.py
diff --git a/polymerist/openmmtools/evaluation.py b/polymerist/mdtools/openmmtools/evaluation.py
similarity index 100%
rename from polymerist/openmmtools/evaluation.py
rename to polymerist/mdtools/openmmtools/evaluation.py
diff --git a/polymerist/openmmtools/execution.py b/polymerist/mdtools/openmmtools/execution.py
similarity index 100%
rename from polymerist/openmmtools/execution.py
rename to polymerist/mdtools/openmmtools/execution.py
diff --git a/polymerist/openmmtools/forcegroups.py b/polymerist/mdtools/openmmtools/forcegroups.py
similarity index 100%
rename from polymerist/openmmtools/forcegroups.py
rename to polymerist/mdtools/openmmtools/forcegroups.py
diff --git a/polymerist/openmmtools/parameters.py b/polymerist/mdtools/openmmtools/parameters.py
similarity index 100%
rename from polymerist/openmmtools/parameters.py
rename to polymerist/mdtools/openmmtools/parameters.py
diff --git a/polymerist/openmmtools/preparation.py b/polymerist/mdtools/openmmtools/preparation.py
similarity index 100%
rename from polymerist/openmmtools/preparation.py
rename to polymerist/mdtools/openmmtools/preparation.py
diff --git a/polymerist/openmmtools/reporters.py b/polymerist/mdtools/openmmtools/reporters.py
similarity index 100%
rename from polymerist/openmmtools/reporters.py
rename to polymerist/mdtools/openmmtools/reporters.py
diff --git a/polymerist/openmmtools/serialization.py b/polymerist/mdtools/openmmtools/serialization.py
similarity index 100%
rename from polymerist/openmmtools/serialization.py
rename to polymerist/mdtools/openmmtools/serialization.py
diff --git a/polymerist/openmmtools/thermo.py b/polymerist/mdtools/openmmtools/thermo.py
similarity index 100%
rename from polymerist/openmmtools/thermo.py
rename to polymerist/mdtools/openmmtools/thermo.py
diff --git a/polymerist/polymers/building.py b/polymerist/polymers/building.py
index c491a39..b6ea390 100644
--- a/polymerist/polymers/building.py
+++ b/polymerist/polymers/building.py
@@ -21,7 +21,7 @@
 from ..genutils.decorators.functional import allow_string_paths
 from ..rdutils.bonding.portlib import get_linker_ids
 from ..rdutils.bonding.substitution import saturate_ports, hydrogenate_rdmol_ports
-from ..openmmtools.serialization import serialize_openmm_pdb
+from ..mdtools.openmmtools.serialization import serialize_openmm_pdb
 
 
 # CONVERSION