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.
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
perf: features.contact #220
Merged
Merged
Changes from all commits
Commits
Show all changes
38 commits
Select commit
Hold shift + click to select a range
ffcd1f2
numpy -> np
DaniBodor 9d48d0c
distance, covalent, samechain
DaniBodor 209e8c5
electrostatic
DaniBodor 4a3fda8
temporary testing notebook
DaniBodor 2ea2ae9
update to notebook
DaniBodor c2c084c
epsilon fix
DaniBodor 5b68522
vdw potentials
DaniBodor df66ac8
added option to raise/override UnknownAtomError inside the forcefield…
DaniBodor 5f1f636
removed obsolete code from add residue features
DaniBodor 6f1f040
simplified functions for get potentials
DaniBodor 6a0766f
check for inter vs intra parameters
DaniBodor 93d832e
minor changes to get_potentials functions
DaniBodor be7ce66
aligned pdb.py (i think obsolete to be deleted)
DaniBodor adb8605
untracking notebook
DaniBodor 66c6218
simplified atomic contacts calculations
DaniBodor b51c0ff
deleted obsolete code and renamed functions
DaniBodor 67e2a59
docstrings and linting
DaniBodor 9aace17
commented on some unused functions
DaniBodor 61ee8ba
deleted obsolete functions
DaniBodor 4688b0f
convert naming to internal functions
DaniBodor d3b4021
removed optional UnknownAtomError in forcefield
DaniBodor 24c9f9f
unused imports
DaniBodor 0005a27
assign SAMERES feature in atomic models
DaniBodor c4f77a7
prospector
DaniBodor 53d6370
prospector
DaniBodor 2bc1eb2
Merge pull request #221 from DeepRank/obsolete_pdb_code
DaniBodor 54ba328
removed more unused functions
DaniBodor b81b385
passing distances instead of recalculating
DaniBodor 5cf9606
prettier np function
DaniBodor c98c8d7
updated LJ potentials functions
DaniBodor b921bfd
add_features with one-shot calculations
DaniBodor 8bdd933
updated coulomb function
DaniBodor fb51b7b
updated doc strings
DaniBodor c7c5a67
fixed minor bug
DaniBodor 945cd47
linting
DaniBodor 1df1922
Merge pull request #226 from DeepRank/atomiccontact_speed
DaniBodor bf3a136
Merge branch 'main' into add_features_for_residues
DaniBodor 63e1af1
Merge branch 'add_features_for_residues' of github.com:DeepRank/deepr…
DaniBodor File filter
Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Don't we need type_ var?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
It's used for getting the right vanderwaals parameters from the table file.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
As far as I could see it was only used internally by the
get_vanderwaals_parameters
function. However, this function basically did nothing else than read the type_ and get the parameters, so instead I mergedget_type
intoget_vanderwaals_parameters
.I tested that old and new
add_features
functions (from atomic_contact, which uses this) give the exact same result on ~5 test cases, so am fairly confident that it is still being read correctly.