Alex Izvorski
fb50d37665
Fix formal charge reading from pdb files; store formal charges in topology ( #4630 )
...
* fix formal charge reading and writing in pdb files; store formal charge in topology
* use formalCharge in public api
* permissive reading
* fix writing
* fix
* add test for formal charges
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Co-authored-by: Alex Izvorski <alex@genesistherapeutics.ai >
2024-09-02 07:53:58 -07:00
Peter Eastman
889baef66e
writeFile() accepts a filename instead of a file object ( #4162 )
2023-08-02 13:59:55 -07:00
Peter Eastman
79740ece0a
Use hex for large atom and residue IDs in PDB files ( #3522 )
2022-03-22 11:55:56 -07:00
Peter Eastman
5cfa489f92
Improved handling of atoms with alternate locations ( #3270 )
...
* Improved handling of atoms with alternate locations
* Fixed a test failure caused by an invalid PDB file
2021-10-05 15:09:13 -07:00
Peter Eastman
e53bdc5eab
Top level Python module is now "openmm" ( #3000 )
...
* Top level Python module is now "openmm"
* Updated module names in examples
* Updated module names in documentation
* Updated module in CI scripts
* Added deprecation warning
2021-02-01 09:40:37 -08:00
peastman
68eb50bd3c
Fixed test case
2020-06-04 15:34:06 -07:00
tic20
a52611a84e
Ensuring opened files are properly closed
2019-02-19 11:19:11 +00:00
peastman
d11c2f67ba
Handle PDB files with altlocs correctly
2018-05-22 13:34:37 -07:00
Rafal P. Wiewiora
197eac7443
rearrange TestPdbFile.py
2016-01-09 18:34:17 -05:00
Rafal P. Wiewiora
58d0c54811
tests
2016-01-09 18:13:12 -05:00
Robert T. McGibbon
920d3d4b1b
Update TestPdbFile.py
2015-08-12 15:36:19 -07:00
Robert McGibbon
408cfe6cf4
Fix two tests for python3
2015-08-12 15:31:48 -07:00
peastman
9fee45f98a
Added test for binary PDB streams
2015-02-27 14:32:36 -08:00
Peter Eastman
30a5370239
More support for triclinic boxes
2015-02-10 11:18:17 -08:00
Peter Eastman
0a0f021469
Continuing triclinic box support in Python layer
2015-02-09 13:28:15 -08:00
