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Bond angles dihedrals #139

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Bond angles dihedrals #139

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5dcba38
bond angles dihedrals backbone code
brittyscience Jun 7, 2024
520e16c
path registry and code revisions
brittyscience Jun 8, 2024
3b1539f
revised class descriptions for clarity
brittyscience Jun 8, 2024
6829a49
merge from main
brittyscience Jun 8, 2024
06d5561
unit test
brittyscience Jun 9, 2024
64e64b9
minor changes to the bond_angle file
brittyscience Jun 9, 2024
a142cf9
minor changes to the bond_angle file
brittyscience Jun 9, 2024
5019578
added try except to every run function
brittyscience Jun 9, 2024
fd600b9
Merge branch 'main' into bond_angles_dihedrals
brittyscience Jun 12, 2024
327925d
a hopeful small correction to pass the git check
brittyscience Jun 13, 2024
847f764
updated the toools to include Ram plot.
brittyscience Jun 14, 2024
e732d23
added type hint, added graphs, save to path and file, added helper f…
brittyscience Jun 16, 2024
7ebb3a4
updated unit test
brittyscience Jun 21, 2024
7de6997
Co-authored-by: Quinny Campbell <[email protected]>
brittyscience Jun 24, 2024
244de1c
did some tweaking to try to get unit test to be functional.
brittyscience Jun 24, 2024
615b895
waving white flag. Need a second set of eyes to see what I am missin…
brittyscience Jun 25, 2024
7cb976b
Merge branch 'main' into bond_angles_dihedrals
Jgmedina95 Jan 23, 2025
16c0be9
ComputeAngle tool implementation
Jgmedina95 Jan 24, 2025
5467132
removing unnecesary angle tools
Jgmedina95 Jan 24, 2025
59071e3
adding small peptide traj in conftest.py
Jgmedina95 Jan 24, 2025
15b7ccc
adding initial tests that check correct workflow for angle tool
Jgmedina95 Jan 24, 2025
52aae41
redoing chi angle analysis for computeangle tools
Jgmedina95 Jan 27, 2025
f834550
typo
Jgmedina95 Jan 27, 2025
01ebab5
fixing input error (Removing path registry as input) in the analyze a…
Jgmedina95 Jan 28, 2025
777797d
fixing typos and input descriptions
Jgmedina95 Jan 28, 2025
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25 changes: 25 additions & 0 deletions mdagent/tools/base_tools/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,15 @@
from .analysis_tools.bond_angles_dihedrals_tool import (
ComputeAngles,
ComputeChi1,
ComputeChi2,
ComputeChi3,
ComputeChi4,
ComputeDihedrals,
ComputeOmega,
ComputePhi,
ComputePsi,
RamachandranPlot,
)
from .analysis_tools.distance_tools import ContactsTool, DistanceMatrixTool
from .analysis_tools.inertia import MomentOfInertia
from .analysis_tools.pca_tools import PCATool
Expand Down Expand Up @@ -63,6 +75,18 @@
"GetSubunitStructure",
"GetTurnsBetaSheetsHelices",
"GetUniprotID",
"ComputeAngles",
"ComputeChi1",
"ComputeChi2",
"ComputeChi3",
"ComputeChi4",
"ComputeDihedrals",
"ComputeOmega",
"ComputePhi",
"ComputePsi",
"ListRegistryPaths",
"MapPath2Name",
"ModifyBaseSimulationScriptTool",
"ComputeLPRMSD",
"ComputeRMSD",
"ComputeRMSF",
Expand All @@ -80,6 +104,7 @@
"RadiusofGyrationAverage",
"RadiusofGyrationPerFrame",
"RadiusofGyrationPlot",
"RamachandranPlot",
"RDFTool",
"RMSDCalculator",
"Scholar2ResultLLM",
Expand Down
22 changes: 22 additions & 0 deletions mdagent/tools/base_tools/analysis_tools/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,15 @@
from .bond_angles_dihedrals_tool import (
ComputeAngles,
ComputeChi1,
ComputeChi2,
ComputeChi3,
ComputeChi4,
ComputeDihedrals,
ComputeOmega,
ComputePhi,
ComputePsi,
RamachandranPlot,
)
from .distance_tools import ContactsTool, DistanceMatrixTool
from .inertia import MomentOfInertia
from .pca_tools import PCATool
Expand All @@ -9,6 +21,15 @@
from .vis_tools import VisFunctions, VisualizeProtein

__all__ = [
"ComputeAngles",
"ComputeChi1",
"ComputeChi2",
"ComputeChi3",
"ComputeChi4",
"ComputeDihedrals",
"ComputeOmega",
"ComputePhi",
"ComputePsi",
"ComputeLPRMSD",
"ComputeRMSD",
"ComputeRMSF",
Expand All @@ -20,6 +41,7 @@
"RadiusofGyrationAverage",
"RadiusofGyrationPerFrame",
"RadiusofGyrationPlot",
"RamachandranPlot",
"RMSDCalculator",
"SimulationOutputFigures",
"SolventAccessibleSurfaceArea",
Expand Down
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