Skip to content

Refactoring of Peptide Tools and upgrade of pIChemiSt #4

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Open
wants to merge 67 commits into
base: master
Choose a base branch
from
Open

Refactoring of Peptide Tools and upgrade of pIChemiSt #4

wants to merge 67 commits into from

Conversation

ghiander
Copy link
Collaborator

No description provided.

ghiander and others added 30 commits December 3, 2024 12:20
@ghiander
makefile to create branch
6f6c31d
@ghiander
basic peptools tests for cli
00a3e8c
@ghiander
created main modules
013bc8e
@ghiander
runtime params
98c3b74
@ghiander
more tests
4ec4600
@ghiander
removed sys exit
d69550d
@frolov-pchem
fix the booleans for arguments
1a9aad8
@ghiander
integrated changes from pi_fasta
fbd5a22
@ghiander
Merge branch 'refactor/peptools' of https://github.com/AstraZeneca/pe…
2953e3f 
…ptide-tools into refactor/peptools
@ghiander
multi-line tests for smiles and fasta
1f00b4d
@ghiander
use of textwrap
3fd8e2a
@ghiander
rebased pichemist changes from master
a7a9a59
@ghiander
tests for new pichemist, pull apart input generation
9c11438
@ghiander
multiline polish
445d7b1
@ghiander
io tests
9c89e31
@ghiander
unpicking io into submodules
268de2b
@ghiander
fasta submodule polish
f5693be
@ghiander
finalised polishing of input generation
9dc66f7
@ghiander
some calc wrappers, polish, unpicking
18e30bb
@ghiander
ec polish
cd89c05
@ghiander
rearranging, pichemist wrapper
71ede8d
@ghiander
separate io and runtime params
c52cdea
@ghiander
created param set
54dd1e0
@ghiander
output into io, dep cleanup
54b68dd
@ghiander
removed fasta chem functions
2de1233
@ghiander
added license
a0ad3ac
@ghiander
moved params into submodule, ref file renaming
543ec79
@ghiander
main wrapper, polish, fasta out unpicking
fc31900
@ghiander
fixed fasta seq input + test, some readme
ddc01cd
@ghiander
polish cli
bb40f83
ghiander and others added 24 commits December 20, 2024 07:51
@ghiander
api cleanup, OutputFragAttribute
c2ba0b5
@frolov-pchem
Fix inout_type for peptide_tools call of pichemist
c00f88d
@ghiander
removed diacid stubs, api cleanup, linting
c4d0243
@ghiander
integrated new pichemist with peptools; decommission of pifasta; pept…
5c31618 
…ools tests broken
@ghiander
pichemist mol overrides fasta; pifasta removal from peptools
33dd45b
@ghiander
pichemist fasta termini capping fixes
b70735e
@ghiander
added all capped test to pichemist
f5fd8ff
@ghiander
fixed and increased test coverage peptools
aa58f87
@ghiander
Merge pull request #3 from AstraZeneca/feature/pifasta-decomm
2c7032c 
Feature/pifasta decomm
@ghiander
cleanup, stubs for descriptors and liabilities
eaf92b6
@ghiander
integration of liabilities and molecular descriptors
33c192c
@ghiander
linting of liabilities and mol descriptors
b5e498e
@frolov-pchem
Update liabilities
172d93f
@frolov-pchem
Bridge the server with refactored pbackend. Fix generate_fragment_ima…
8b118be 
…ges flag in pIChemiSt.
@ghiander
biopython dep; polishing of deprecated code
dfa9fdf
@ghiander
clean up
b1c53a0
@ghiander
pre-commit; polishing peptools
1fa78bd
@ghiander
license update
f38bf5b
@ghiander
pichemist: some polishing, flake8 to pre-commit
07e0847
@ghiander
peptools: refactor of io output section
fc228a7
@ghiander
pichemist: flaking
991fa10
@ghiander
licenses
9628b03
@ghiander
peptools: flaking
1792689
@ghiander
polishing readmes
5e781bf
@ghiander ghiander requested a review from frolov-pchem April 17, 2025 16:13
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@frolov-pchem frolov-pchem Awaiting requested review from frolov-pchem

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@ghiander @frolov-pchem