Consolidated openfftools, openmmtool, and lammpstools as submodules o…

…f master "mdtools" core module
timbernat · May 17, 2024 · 64f4c15 · 64f4c15
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diff --git a/polymerist/mdtools/__init__.py b/polymerist/mdtools/__init__.py
@@ -0,0 +1 @@
+'''Tools for interfacing with and setting up systems for various molecular dynamics packages'''
diff --git a/polymerist/lammpstools/__init__.py → polymerist/mdtools/lammpstools/__init__.py b/polymerist/lammpstools/__init__.py → polymerist/mdtools/lammpstools/__init__.py
diff --git a/polymerist/lammpstools/lammpseval.py → polymerist/mdtools/lammpstools/lammpseval.py b/polymerist/lammpstools/lammpseval.py → polymerist/mdtools/lammpstools/lammpseval.py
diff --git a/polymerist/lammpstools/unitstyles.py → polymerist/mdtools/lammpstools/unitstyles.py b/polymerist/lammpstools/unitstyles.py → polymerist/mdtools/lammpstools/unitstyles.py
diff --git a/polymerist/openfftools/__init__.py → polymerist/mdtools/openfftools/__init__.py b/polymerist/openfftools/__init__.py → polymerist/mdtools/openfftools/__init__.py
diff --git a/polymerist/openfftools/boxvectors.py → polymerist/mdtools/openfftools/boxvectors.py b/polymerist/openfftools/boxvectors.py → polymerist/mdtools/openfftools/boxvectors.py
diff --git a/polymerist/openfftools/omminter.py → polymerist/mdtools/openfftools/omminter.py b/polymerist/openfftools/omminter.py → polymerist/mdtools/openfftools/omminter.py
diff --git a/...ist/openfftools/partialcharge/__init__.py → ...ols/openfftools/partialcharge/__init__.py b/...ist/openfftools/partialcharge/__init__.py → ...ols/openfftools/partialcharge/__init__.py
diff --git a/...penfftools/partialcharge/chargemethods.py → ...penfftools/partialcharge/chargemethods.py b/...penfftools/partialcharge/chargemethods.py → ...penfftools/partialcharge/chargemethods.py
diff --git a/.../openfftools/partialcharge/molchargers.py → .../openfftools/partialcharge/molchargers.py b/.../openfftools/partialcharge/molchargers.py → .../openfftools/partialcharge/molchargers.py
diff --git a/...tools/partialcharge/rescharge/__init__.py → ...tools/partialcharge/rescharge/__init__.py b/...tools/partialcharge/rescharge/__init__.py → ...tools/partialcharge/rescharge/__init__.py
diff --git a/...ls/partialcharge/rescharge/calculation.py → ...ls/partialcharge/rescharge/calculation.py b/...ls/partialcharge/rescharge/calculation.py → ...ls/partialcharge/rescharge/calculation.py
diff --git a/...ools/partialcharge/rescharge/interface.py → ...ools/partialcharge/rescharge/interface.py b/...ools/partialcharge/rescharge/interface.py → ...ools/partialcharge/rescharge/interface.py
diff --git a/...ftools/partialcharge/rescharge/rctypes.py → ...ftools/partialcharge/rescharge/rctypes.py b/...ftools/partialcharge/rescharge/rctypes.py → ...ftools/partialcharge/rescharge/rctypes.py
diff --git a/...partialcharge/rescharge/redistribution.py → ...partialcharge/rescharge/redistribution.py b/...partialcharge/rescharge/redistribution.py → ...partialcharge/rescharge/redistribution.py
diff --git a/polymerist/openfftools/partition.py → polymerist/mdtools/openfftools/partition.py b/polymerist/openfftools/partition.py → polymerist/mdtools/openfftools/partition.py
diff --git a/polymerist/openfftools/solvation/__init__.py → ...mdtools/openfftools/solvation/__init__.py b/polymerist/openfftools/solvation/__init__.py → ...mdtools/openfftools/solvation/__init__.py
diff --git a/polymerist/openfftools/solvation/packing.py → .../mdtools/openfftools/solvation/packing.py b/polymerist/openfftools/solvation/packing.py → .../mdtools/openfftools/solvation/packing.py
diff --git a/...merist/openfftools/solvation/physprops.py → ...dtools/openfftools/solvation/physprops.py b/...merist/openfftools/solvation/physprops.py → ...dtools/openfftools/solvation/physprops.py
diff --git a/...penfftools/solvation/solvents/__init__.py → ...penfftools/solvation/solvents/__init__.py b/...penfftools/solvation/solvents/__init__.py → ...penfftools/solvation/solvents/__init__.py
diff --git a/...ftools/solvation/solvents/water_TIP3P.sdf → ...ftools/solvation/solvents/water_TIP3P.sdf b/...ftools/solvation/solvents/water_TIP3P.sdf → ...ftools/solvation/solvents/water_TIP3P.sdf
diff --git a/polymerist/openfftools/topology.py → polymerist/mdtools/openfftools/topology.py b/polymerist/openfftools/topology.py → polymerist/mdtools/openfftools/topology.py
diff --git a/polymerist/openmmtools/__init__.py → polymerist/mdtools/openmmtools/__init__.py b/polymerist/openmmtools/__init__.py → polymerist/mdtools/openmmtools/__init__.py
diff --git a/polymerist/openmmtools/description.py → ...merist/mdtools/openmmtools/description.py b/polymerist/openmmtools/description.py → ...merist/mdtools/openmmtools/description.py
diff --git a/polymerist/openmmtools/evaluation.py → polymerist/mdtools/openmmtools/evaluation.py b/polymerist/openmmtools/evaluation.py → polymerist/mdtools/openmmtools/evaluation.py
diff --git a/polymerist/openmmtools/execution.py → polymerist/mdtools/openmmtools/execution.py b/polymerist/openmmtools/execution.py → polymerist/mdtools/openmmtools/execution.py
diff --git a/polymerist/openmmtools/forcegroups.py → ...merist/mdtools/openmmtools/forcegroups.py b/polymerist/openmmtools/forcegroups.py → ...merist/mdtools/openmmtools/forcegroups.py
diff --git a/polymerist/openmmtools/parameters.py → polymerist/mdtools/openmmtools/parameters.py b/polymerist/openmmtools/parameters.py → polymerist/mdtools/openmmtools/parameters.py
diff --git a/polymerist/openmmtools/preparation.py → ...merist/mdtools/openmmtools/preparation.py b/polymerist/openmmtools/preparation.py → ...merist/mdtools/openmmtools/preparation.py
diff --git a/polymerist/openmmtools/reporters.py → polymerist/mdtools/openmmtools/reporters.py b/polymerist/openmmtools/reporters.py → polymerist/mdtools/openmmtools/reporters.py
diff --git a/polymerist/openmmtools/serialization.py → ...rist/mdtools/openmmtools/serialization.py b/polymerist/openmmtools/serialization.py → ...rist/mdtools/openmmtools/serialization.py
diff --git a/polymerist/openmmtools/thermo.py → polymerist/mdtools/openmmtools/thermo.py b/polymerist/openmmtools/thermo.py → polymerist/mdtools/openmmtools/thermo.py
diff --git 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
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		'''Tools for interfacing with and setting up systems for various molecular dynamics packages'''