Code

Add morph support#9

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Dialpuri merged 51 commits intomasterDialpuri/Sails:masterfrom add-morph-supportDialpuri/Sails:add-morph-supportCopy head branch name to clipboardNov 23, 2024

+320-55

Commits

Commits on Oct 31, 2024

• Added infrastructure for sails-morph start

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  4bb85ef

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• Added infrastructure for sails-morph start

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  34fb71d

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• Added infrastructure for sails-morph start

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  1e5d763

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• Added infrastructure for sails-morph start

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  cf97c42

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Commits on Nov 22, 2024

• Rebased onto master (temp)

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  9e7142f

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• Added sails-wurcs command line exec

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  f6f144f

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• Made sugars appear in unique list in order

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  0bb8364

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• Added sugar order part of WURCS code

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  1e8178c

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• Added WURCS linkage string formulation

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• Added DFS with glycosites

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• Added sorting for donor sets in Sails JSON

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  e595d76

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• Reordered residue order and linkage list using DFS

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• Added pseudoglycan to ensure a distinction is made from a real Glycan and a non-positioned Glycan

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• Added string split function to Utils

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  f7ed0cf

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• Added WURCS parsing code

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  20d320f

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• Added WURCS interface methods and cmdline arguments

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  bc6f041

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• Refactored some WURCS parsing methods and added ability to add a Glycan created by a WURCS to a gemmi structure

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  f163fde

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• Added Utiltity function to get last chain in a gemmi Structure

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  70918c6

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• Changed add_residue to take in a gemmi::Atom rather than gemmi::Atom* as if you had multiple clusters the position of the second residue would be wrong.

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  3c4eac3

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• Changed name of glycosite from residue to site

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• Add Triangle SNFG shape

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• Add triangle SNFG shape to options

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• Add triangle cpp file to CMakeLists.txt

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  6205ceb

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• Updated FUC in data.json

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  b80e4d3

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• Added special positioning for FUC residues

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  7261893

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• Added special key value pair to data.json and sails-json parser

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  7a2a7bb

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• Added special to ResidueData

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  c9150ae

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• Added dimanond shape to SNFG Shapes

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  13ea6cc

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• Added exotic shapes to data.json

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  a05f0e8

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• Added diamond to SNFG factory

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• Added diamond header file

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• Added diamond to CMakeLists.txt

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  74d0c5e

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• Updated test conditions for donor label

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  4b45d7c

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• Added check to log calculation to ensure a deleted residue doesn't have it's RSCC calculated

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• Added Emscripten target in CMakeLists for cross-compiling

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• Added ZLIB requirement for python

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  53fdb6d

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• Fixed JSON merge bug

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  9f60394

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• Rebased onto master

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  2bfbbce

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• Fixed merge bug with find_wurcs

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  8e3f46b

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Commits on Nov 23, 2024

• Improved command line interface

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  f1a7471

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• Added morph toplevel flow

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  1c2c97a

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• Added replace_residue and get_monomer_only static functions to Sails::Model

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  ed647c7

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• Created Sails::Morph functionality

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  c2ebbb7

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• Created Sails::Morph functionality

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  5edc6f4

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• Created Sails::Morph functionality

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  b719bb1

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• Added star to 1C4 MAN WURCS

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  4915ddf

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• Added morph to __init__

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  4665f85

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• Swapped pyproject.toml

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• Swapped pyproject.toml

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• Removed CLANG from test.yml

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• Removed template for superpose_atoms

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