Skip to content
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

new version for pdb2pdbqt #117

Merged
merged 38 commits into from
Aug 6, 2024
Merged

new version for pdb2pdbqt #117

merged 38 commits into from
Aug 6, 2024

Conversation

zhangplpl
Copy link
Contributor

No description provided.

@Hong-Rui
Copy link
Collaborator

Hong-Rui commented Apr 7, 2024

Supported new features:

  1. Unified protein residue topology templates for standard amino acids.
  2. Support 40 popular non-standard amino acid templates from Schrodinger's internal templates, including lots of C-ter and N-ters.
  3. Drop all MGLTools and openbabel dependencies in protein preprocessing parts.
  4. Support Receptor PDB standardizations prior to PDBQT format generation.
  5. Automatic AD4 map and autogrid4 runs in PDBQT generation process, with use of our own gpf and receptor clean algorithm, if ad4 options got specified.
  6. Support receptor preparation for covalent docking, and flex res.
  7. Support receptor preparation in case crystal water, cofactors are specified to be included.

@caic99 caic99 requested a review from dp-yuanyn April 7, 2024 10:18
@zhengh96 zhengh96 self-requested a review April 7, 2024 10:36
zhangplpl and others added 24 commits April 7, 2024 18:36
@zhangplpl
del docking_grids_generator_old.py and schrodinger_atom_types.py, cha…
9ac7aa8 
…nged protein_pdbqt_writer.py
@zhangplpl
del protein_prep/pdb2pdbqt.py
4393607
@zhangplpl
changed import path
4891458
@zhangplpl
changed test_receptor_processor.py
b729f9e
@zhangplpl
changed test_proprep.py and for mcdock.py del pdb2pdbqt add receptor_…
183dbd8 
…processor
[bugfix] escape some pyright warnings and fix ad4 option parsing in a…
089cc4f 
…utogrid runner
[feature] rename file names for templates
310ac93
[bugfix] add missing import
507218f
[bugfix] add required dependencies
3311fcc
@zhangplpl
pyproject.toml: add some dir; mcdock.py,unidock_pipeline.py: Path-->str
767e023
@zhangplpl
unidock.py: del line 37
0ff8f65
@Hong-Rui
Merge branch 'main' into main
32c0890
[bugfix] ad4 map path
9988cd0
[feature] receptor preprocessor options, deprecated PDBQT file format…
466fd4f 
… as receptor input
@Hong-Rui
Merge branch 'main' into main
84c66d3
[feature] dependencies
41bdee1
@zhangplpl
add_argument
cc1bcdb
@zhangplpl
change receptor_preprocessor_runner.py args.covalent_residue_atom_info
dec951e
[feature] remove autogrid runner usage
292ac50
[bugfix] autogrid ruuner remove
8eaae7d
[feature] ad4 map unit test
378ef40
[bugfix] receptor processor option
62eb726
[bugfix] pocket option
0cca15a
[bugfix] receptor option
e009169
@zhengh96 zhengh96 merged commit e98f756 into dptech-corp:main Aug 6, 2024
4 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@dp-yuanyn dp-yuanyn dp-yuanyn approved these changes

@zhengh96 zhengh96 Awaiting requested review from zhengh96

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

Successfully merging this pull request may close these issues.
4 participants
@zhangplpl @Hong-Rui @dp-yuanyn @zhengh96