Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
41 commits
Select commit Hold shift + click to select a range
211ac22
Initial setup
adeshusa Mar 7, 2026
4e7065c
Initial Setup
adeshusa Mar 7, 2026
492bfb4
Merge pull request #1 from adeshusa/Adesh
adeshusa Mar 7, 2026
d1bd140
completed methods 5 and 6 in Archive Utils/ - Needs refinement with t…
Shreyas765 Mar 8, 2026
e844457
Method 7
vamagowni Mar 13, 2026
7a054f8
added methods 1 and 2 as well as additional methods to convert vizfol…
adeshusa Mar 13, 2026
ccd6bcb
Merge pull request #3 from adeshusa/Adesh
adeshusa Mar 13, 2026
5152e4e
Merge pull request #2 from adeshusa/Varenya
adeshusa Mar 19, 2026
996b21e
Revert "Merge pull request #2 from adeshusa/Varenya"
adeshusa Mar 19, 2026
791304a
Methods 7 and 8
vamagowni Mar 19, 2026
167e6c0
Merge pull request #4 from adeshusa/Varenya
adeshusa Mar 20, 2026
d41eb32
updated methods 5 and 6 following the completion of pre-requisites
Shreyas765 Mar 22, 2026
a3f79ff
Refractored activation storage functions (part 1 and 2)
Shreyas765 Apr 21, 2026
e8411fb
spec for walk through and diagrams as well as further requirements
adeshusa Apr 22, 2026
3639cf9
Refactoring methods 3, 4, & 6
katamyra Apr 22, 2026
4322f83
Merge branch 'main' of https://github.com/adeshusa/issue-40
katamyra Apr 22, 2026
21738fd
refactor step #5, adding meta data
adeshusa Apr 22, 2026
138b7d6
refactor added
adeshusa Apr 22, 2026
59e91ad
Merge remote-tracking branch 'origin' into Adesh
adeshusa Apr 22, 2026
c4c7696
resolved merge conflicts
adeshusa Apr 22, 2026
937ed0d
Merge pull request #6 from adeshusa/Adesh
adeshusa Apr 22, 2026
72ceb1f
Refactoring method 8
vamagowni Apr 24, 2026
25dd3db
Merge pull request #7 from adeshusa/Varenya
vamagowni Apr 24, 2026
246208d
refactoring
adeshusa Apr 27, 2026
ba5dc3e
Merge branch 'main' of https://github.com/adeshusa/issue-40
adeshusa Apr 27, 2026
7671751
rebranched outline.py into 3
adeshusa Apr 27, 2026
498b0f1
Merge pull request #8 from adeshusa/Adesh
adeshusa Apr 27, 2026
4e08124
Renamed archive + also turned it into an external module
katamyra Apr 27, 2026
761256d
Merge pull request #9 from adeshusa/module-refactor
katamyra Apr 27, 2026
2e6baed
Added cli.py to use the archive through command line
katamyra Apr 27, 2026
48ac047
new spec
adeshusa Apr 27, 2026
0ba73e7
Merge pull request #10 from adeshusa/Adesh
adeshusa Apr 27, 2026
4073d4d
alignment changes
adeshusa Apr 27, 2026
416faff
added unit test cases for working archive append API
Shreyas765 Apr 28, 2026
a60078b
Fixed the old code, made bug changes, created new updated test file, …
katamyra Apr 28, 2026
04d141a
Merge pull request #11 from adeshusa/divergent-code-fixes
katamyra Apr 28, 2026
6ffa9b5
Created a base line demo that we can use for the video
katamyra Apr 28, 2026
99a41f4
Merge pull request #12 from adeshusa/demo
katamyra Apr 28, 2026
e626083
Added more info into demo
katamyra Apr 28, 2026
b616933
Merge pull request #13 from adeshusa/demo-updates
katamyra Apr 28, 2026
f532bd0
Removed old folder
katamyra Apr 28, 2026
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Binary file added archive/1UBQ_result_model_1_ptm.pickle
Binary file not shown.
106 changes: 106 additions & 0 deletions archive/ARCHITECTURE_DIAGRAM.xml
Original file line number Diff line number Diff line change
@@ -0,0 +1,106 @@
<mxfile host="app.diagrams.net" agent="Mozilla/5.0">
<diagram id="archive-utilities-architecture" name="Archive Utilities Architecture">
<mxGraphModel dx="792" dy="479" grid="1" gridSize="10" guides="1" tooltips="1" connect="1" arrows="1" fold="1" page="1" pageScale="1" pageWidth="1200" pageHeight="800" background="#ffffff" math="0" shadow="0">
<root>
<mxCell id="0" />
<mxCell id="1" parent="0" />
<mxCell id="input-layer" parent="1" style="swimlane;html=1;childLayout=stackLayout;resizeParent=1;resizeParentMax=0;startSize=30;horizontalStack=0;fontSize=12;fontStyle=1;fillColor=#D3E4F7;strokeColor=#2C3E50;strokeWidth=2;" value="Input Layer" vertex="1">
<mxGeometry height="180" width="200" x="50" y="50" as="geometry" />
</mxCell>
<mxCell id="pickle" parent="input-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=11;" value="Pickle Files" vertex="1">
<mxGeometry height="50" width="200" y="30" as="geometry" />
</mxCell>
<mxCell id="pytorch" parent="input-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=11;" value="PyTorch Tensors" vertex="1">
<mxGeometry height="50" width="200" y="80" as="geometry" />
</mxCell>
<mxCell id="numpy" parent="input-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=11;" value="NumPy Arrays" vertex="1">
<mxGeometry height="50" width="200" y="130" as="geometry" />
</mxCell>
<mxCell id="ingest-layer" parent="1" style="swimlane;html=1;childLayout=stackLayout;resizeParent=1;resizeParentMax=0;startSize=30;horizontalStack=0;fontSize=12;fontStyle=1;fillColor=#E8F4F8;strokeColor=#2C3E50;strokeWidth=2;" value="Ingestion Layer" vertex="1">
<mxGeometry height="180" width="250" x="350" y="50" as="geometry" />
</mxCell>
<mxCell id="pickle-ingest" parent="ingest-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=11;" value="ingest_output_pkl()&#xa;key_matches traceability" vertex="1">
<mxGeometry height="50" width="250" y="30" as="geometry" />
</mxCell>
<mxCell id="tensor-conv" parent="ingest-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=11;" value="tensor_to_numpy()" vertex="1">
<mxGeometry height="50" width="250" y="80" as="geometry" />
</mxCell>
<mxCell id="text-ingest" parent="ingest-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=11;" value="ingest_attention_txt()" vertex="1">
<mxGeometry height="50" width="250" y="130" as="geometry" />
</mxCell>
<mxCell id="storage-layer" parent="1" style="swimlane;html=1;childLayout=stackLayout;resizeParent=1;resizeParentMax=0;startSize=30;horizontalStack=1;fontSize=12;fontStyle=1;fillColor=#FFF4E6;strokeColor=#2C3E50;strokeWidth=2;" value="Storage Layer (overwrite=False)" vertex="1">
<mxGeometry height="120" width="550" x="50" y="280" as="geometry" />
</mxCell>
<mxCell id="store-meta" parent="storage-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=10;" value="store_metadata()" vertex="1">
<mxGeometry height="120" width="110" as="geometry" />
</mxCell>
<mxCell id="store-single" parent="storage-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=10;" value="store_single_representation()" vertex="1">
<mxGeometry height="120" width="110" x="110" as="geometry" />
</mxCell>
<mxCell id="store-pair" parent="storage-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=10;" value="store_pair_representation()" vertex="1">
<mxGeometry height="120" width="110" x="220" as="geometry" />
</mxCell>
<mxCell id="store-attn" parent="storage-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=10;" value="store_attention()" vertex="1">
<mxGeometry height="120" width="110" x="330" as="geometry" />
</mxCell>
<mxCell id="store-struct" parent="storage-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=10;" value="store_structure_coordinates()" vertex="1">
<mxGeometry height="120" width="110" x="440" as="geometry" />
</mxCell>
<mxCell id="archive-layer" parent="1" style="swimlane;html=1;childLayout=stackLayout;resizeParent=1;resizeParentMax=0;startSize=30;horizontalStack=1;fontSize=12;fontStyle=1;fillColor=#E8F5E9;strokeColor=#2C3E50;strokeWidth=2;" value="VizFold 1.0 Archive" vertex="1">
<mxGeometry height="100" width="550" x="50" y="480" as="geometry" />
</mxCell>
<mxCell id="archive-meta" parent="archive-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=10;fontStyle=1;" value="metadata/" vertex="1">
<mxGeometry height="100" width="110" as="geometry" />
</mxCell>
<mxCell id="archive-repr" parent="archive-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=10;fontStyle=1;" value="representations/&#xa;single/ pair/" vertex="1">
<mxGeometry height="100" width="110" x="110" as="geometry" />
</mxCell>
<mxCell id="archive-attn" parent="archive-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=10;fontStyle=1;" value="attention/&#xa;by type" vertex="1">
<mxGeometry height="100" width="110" x="220" as="geometry" />
</mxCell>
<mxCell id="archive-struct" parent="archive-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=10;fontStyle=1;" value="structure/&#xa;atom_positions&#xa;atom_mask, ptm" vertex="1">
<mxGeometry height="100" width="110" x="330" as="geometry" />
</mxCell>
<mxCell id="archive-sparse" parent="archive-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=10;fontStyle=1;" value="Sparse Storage&#xa;layer_00,01...(skips ok)" vertex="1">
<mxGeometry height="100" width="110" x="440" as="geometry" />
</mxCell>
<mxCell id="validate-layer" parent="1" style="swimlane;html=1;childLayout=stackLayout;resizeParent=1;resizeParentMax=0;startSize=30;horizontalStack=0;fontSize=12;fontStyle=1;fillColor=#F3E5F5;strokeColor=#2C3E50;strokeWidth=2;" value="Validation Layer" vertex="1">
<mxGeometry height="120" width="260" x="50" y="650" as="geometry" />
</mxCell>
<mxCell id="strict-mode" parent="validate-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=10;" value="strict=True&#xa;All components required&#xa;Production-ready" vertex="1">
<mxGeometry height="120" width="130" as="geometry" />
</mxCell>
<mxCell id="lenient-mode" parent="validate-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=10;" value="strict=False&#xa;Warnings only&#xa;Partial/Development" vertex="1">
<mxGeometry height="120" width="130" x="130" as="geometry" />
</mxCell>
<mxCell id="output-layer" parent="1" style="swimlane;html=1;childLayout=stackLayout;resizeParent=1;resizeParentMax=0;startSize=30;horizontalStack=0;fontSize=12;fontStyle=1;fillColor=#FFF9C4;strokeColor=#2C3E50;strokeWidth=2;" value="Output States" vertex="1">
<mxGeometry height="150" width="200" x="400" y="650" as="geometry" />
</mxCell>
<mxCell id="partial" parent="output-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=11;fontStyle=1;" value="Partial" vertex="1">
<mxGeometry height="40" width="200" y="30" as="geometry" />
</mxCell>
<mxCell id="valid" parent="output-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=11;fontStyle=1;" value="Valid" vertex="1">
<mxGeometry height="40" width="200" y="70" as="geometry" />
</mxCell>
<mxCell id="invalid" parent="output-layer" style="text;html=1;align=center;verticalAlign=middle;fillColor=none;strokeColor=none;fontSize=11;fontStyle=1;" value="Invalid" vertex="1">
<mxGeometry height="40" width="200" y="110" as="geometry" />
</mxCell>
<mxCell id="conn1" edge="1" parent="1" source="input-layer" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;endArrow=classic;strokeColor=#2C3E50;strokeWidth=2;" target="ingest-layer">
<mxGeometry relative="1" as="geometry" />
</mxCell>
<mxCell id="conn2" edge="1" parent="1" source="ingest-layer" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;endArrow=classic;strokeColor=#2C3E50;strokeWidth=2;" target="storage-layer">
<mxGeometry relative="1" as="geometry" />
</mxCell>
<mxCell id="conn3" edge="1" parent="1" source="storage-layer" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;endArrow=classic;strokeColor=#2C3E50;strokeWidth=2;" target="archive-layer">
<mxGeometry relative="1" as="geometry" />
</mxCell>
<mxCell id="conn4" edge="1" parent="1" source="archive-layer" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;endArrow=classic;strokeColor=#2C3E50;strokeWidth=2;" target="validate-layer">
<mxGeometry relative="1" as="geometry" />
</mxCell>
<mxCell id="conn5" edge="1" parent="1" source="validate-layer" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;endArrow=classic;strokeColor=#2C3E50;strokeWidth=2;" target="output-layer">
<mxGeometry relative="1" as="geometry" />
</mxCell>
</root>
</mxGraphModel>
</diagram>
</mxfile>
Loading