7 Commits

Author SHA1 Message Date
Greg Landrum
af4e6c05ec strip whitespace from embedParametersToJSON() (#8989)
* strip whitespace from embedParametersToJSON()

* update expected results in python tests

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Co-authored-by: = <=>
2025-12-04 06:57:08 +01:00
Niels Maeder
bc4fffda7b Embed Parameters to JSON (#8977)
* add function to convert embedParams to json

* add catch test

* add function to python wrapper

* test python function

* update copyright

* undo formatting and cleanup

* more cleanup

* remove the map flag and added round trip

* add bounds mat output

* run clang-format
2025-11-29 05:19:44 +01:00
Nikitas Rontsis
f20b83bc64 Conformer embedding timeout (#8110)
* Conformer embedding timeout

* Add README for patching

* Don't raise Exception but set EmbedFailureCauses on timeout.

* Fix

* Remove wrongly added README

* Debug segfault

* Improve logging of failures

* Fix pointer reference

* Don't use optional
2025-01-13 10:08:25 +01:00
Greg Landrum
81af0dbd63 add option to symmetrize conjugated terminal groups when RMS pruning conformers (#7270)
* expose symmetrizeTerminalAtoms() to the public API

* support symmetrizing terminal groups in RMS pruning in confgen

* add that to the python wrapper

* add backwards compatibility note

* allow JSON config of the new option
2024-03-19 04:38:29 +01:00
Greg Landrum
ec8e637ecd add option to use sequential random seeds in the conformer generator (#6639) 2023-08-19 19:19:56 +02:00
hjuinj
8857bf8a69 Add custom distance bounds parameter for ETKDG conformer generation (#4516)
* add custom parameter  to tune the relative weights of distance bounds to all the other force terms during ETKDG conformer generation

* fixes as per reviewer comments
2021-09-16 12:32:10 +02:00
Greg Landrum
f829c877d8 MinimalLib: add CFFI interface (#4018)
* hello world works

* more

* more
minimallib needs to be tested

* parse substructure parameters from JSON

* add substruct search and parameters

* add descriptors

* register more descriptors

* fingerprints, first pass

* stop outputting tiny coord vals

* support generating 2d coords

* coordgen testing

* return nulls

* initial 3d support; add/removeHs; cleanup

* Embedding parameters from JSON

* update

* pattern fp, fps as bytes

* use json to configure MFP

* use json to configure rdkit and pattern fps

* aligned 2d coords

* parsing options

* options for writers

* rename remove_hs

* get this working on windows (kind of)

* silence some msvc warnings

* cmake updates

* update python tests

* add the CFFI code to CI builds

* cleanup line ending mess?

* a couple small fixes

* make this work with URF

* support coordMap in the 3D coordinate generation

* updates in response to review
2021-04-15 21:33:52 +02:00