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internal go contact map#643

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csbrasnett wants to merge 30 commits intomastermarrink-lab/vermouth-martinize:masterfrom Go-contact-mapmarrink-lab/vermouth-martinize:Go-contact-mapCopy head branch name to clipboard

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Commits on Nov 21, 2024

• basis of implementation

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  8591a5a

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Commits on Nov 26, 2024

• basic implementation of go model

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Commits on Dec 6, 2024

• implementation of working go model with flexible CLI

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Commits on Dec 7, 2024

• change to using _res_serial attribute, so we can deal with > 1 chain

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Commits on Dec 12, 2024

• fix contact map calculation

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• Merge branch 'master' into Go-contact-map

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Commits on Dec 16, 2024

• change implementation to using KDTree.

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• tidy up for readability and testing, added comments and docstrings

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Commits on Dec 18, 2024

• addressed smaller comments. atom2res now significantly faster with prearranged dictionary

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Commits on Dec 20, 2024

• changed to run the processor on molecule not system.

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• fixed deferred file writing and corrected associated cli

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• made small corrections.

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Commits on Jan 3, 2025

• fix test_read_go_map.py

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• fix test_go_structure_bias.py

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• fixed the reading/generation check for go map

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• changed make_surface to _make_surface, shouldn't need function externally

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• first tests for contact map generation. Improved PROTEIN map handling to ensure test coverage

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• more tests for contact map generation. refactored some contact_map functions. added more information to test_molecule.

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• more contact map generation tests for main contact finding functions.

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• sorted out written contact map checking

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Commits on Jan 6, 2025

• processor tests for contact map generation

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• Update docs with new arguments

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• correct logic for go_write_file

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• add CLI for backbone and go atomnames as per #585

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• Hacked an error raise for #642 if chain-resid pair for go model not found in molecule

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• fixed tests

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• added integration test for internal contact map calculation

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Commits on Jan 10, 2025

• update docs with additional arguments for go bead placement

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Commits on Jan 13, 2025

• add test to check that warning raised when chain ids in contact map not found

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Commits on Jan 16, 2025

• add note about using multiple go models in documentation

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