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thermo analysis tools #131

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thermo analysis tools #131

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c254a54
first draft of thermo tools, still need registry implmentation, add t…
SamCox822 May 15, 2024
47bec5c
merge main into thermo-analyses
SamCox822 Jun 13, 2024
64e3c75
updated tools, need to write unit tests
SamCox822 Jun 13, 2024
ced15cd
minor fixes, also removed a tool
SamCox822 Jun 29, 2024
f11f378
tools done, agent is having trouble with multi-input though
SamCox822 Jun 29, 2024
8c91474
Merge branch 'main' into thermo-analyses
SamCox822 Jun 29, 2024
632d0f5
getting charges from traj using openmm
SamCox822 Jun 29, 2024
3522778
formatting and fixed overloaded var
SamCox822 Jun 29, 2024
4ab42a3
i forgot to actually push the format fix
SamCox822 Jun 29, 2024
5dbb624
let agent provide forcefield
SamCox822 Jun 29, 2024
4590bb4
merge main into branch & etc.
SamCox822 Jun 29, 2024
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10 changes: 10 additions & 0 deletions mdagent/tools/base_tools/__init__.py
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Expand Up @@ -19,6 +19,12 @@
ComputeRelativeShapeAntisotropy,
SummarizeProteinStructure,
)
from .analysis_tools.thermo_tools import (
ComputeDipoleMoments,
ComputeIsothermalCompressabilityKappaT,
ComputeMassDensity,
ComputeStaticDielectric,
)
from .analysis_tools.vis_tools import VisFunctions, VisualizeProtein
from .preprocess_tools.clean_tools import CleaningToolFunction
from .preprocess_tools.packing import PackMolTool
Expand Down Expand Up @@ -102,6 +108,10 @@
"VisFunctions",
"VisualizeProtein",
"get_pdb",
"ComputeDipoleMoments",
"ComputeStaticDielectric",
"ComputeIsothermalCompressabilityKappaT",
"ComputeMassDensity",
"CleaningToolFunction",
"SetUpandRunFunction",
"ModifyBaseSimulationScriptTool",
Expand Down
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