d5a43b2b6b
fixed relative imports (language_level=2), need to be explicit for python3 (language_level=3)
2025-05-23 21:52:11 +02:00
Niels Müller
a7e02ba47c
Save Local Tpology with TPXReader for Gmx Whole Function
2019-10-25 14:06:41 +02:00
Niels Müller
92addd3148
Implement Gromacs internal Whole Procedure
2019-10-25 09:55:20 +02:00
Niels Müller
b8b61380c8
Include Gromacs internal function for making Frames Whole
2019-10-24 12:45:13 +02:00
Niels Müller
fa7e3347d9
Make sure too close XTC Files.
2019-10-18 14:43:13 +02:00
Niels Mueller
a820741ec3
Clean up Code
2019-10-08 15:08:52 +02:00
Niels Mueller
27fc2cbbcc
Remove c source from index.
2019-10-08 15:05:45 +02:00
Niels Mueller
b0d373c9cb
Enables time info for XTCReader
2019-10-08 15:03:40 +02:00
Niels Mueller
025cf3fe6f
Add function to write/append xtc files.
2019-10-08 15:01:02 +02:00
Niels Müller
47e78cce6c
Change coordinates property to positions, according to mdanalysis.
2017-11-14 13:43:59 +01:00
Niels Müller
d178df5c7f
Add function to read single xtc frmames.
2017-08-18 13:22:58 +02:00
Niels Müller
edc1bd759a
Added option to ignore timestamps when loading xtc indexfiles.
2017-06-30 14:34:57 +02:00
Niels Müller
896b3ff900
Merge branch 'gromacs-2016'
2017-04-25 13:13:53 +02:00
Niels Müller
99ebc9134a
Import exceptions from global module.
2017-04-25 13:13:15 +02:00
Niels Müller
e52768e6de
Improvements!
2017-02-02 14:01:37 +01:00
Niels Müller
b0bc90fa6c
More topology handling.
2016-11-09 12:57:49 +01:00
Niels Müller
108200cea8
Use python array instead of numpy array for appending data.
2016-10-07 10:21:30 +02:00
Niels Müller
9cf16bc602
Enabled & functioning edrfile reader.
2016-09-27 15:46:05 +02:00
Niels Müller
db06925a0d
Remove redundant basedefinitions
2016-09-27 13:59:52 +02:00
Niels Müller
80e0519942
Fix type conversion bug in xtcreader.
2016-09-27 13:50:08 +02:00
Niels Müller
ad482006b0
Switched to Headers fo the Gromacs-2016 branch.
2016-09-27 12:28:11 +02:00
Niels Müller
f4e2501142
Clarified docs.
2016-06-27 15:29:24 +02:00
Niels Müller
b56bc4b41e
Fixed typo.
2016-06-22 14:48:18 +02:00
Niels Müller
e280afb076
Return iterative resisue ids from tpr files.
...
Since Gromacs doesn't care about the residue number in gro files, they are
not stored in the tpr files and thus have to be reproduced by hand.
This solution increases the residue index with each new molecule.
2016-06-22 14:47:24 +02:00
Niels Müller
cd562c269a
Generate xtc index in pygmx.open if necessary.
2016-06-13 11:34:33 +02:00
Niels Müller
cabd68f287
Pointer was dissolved in the wrong order.
...
This led to wrong atom names and eventually to seg faults.
2016-06-09 10:50:16 +02:00
Niels Müller
b3f4de0567
Make filename a public attribute of XTCReader.
2016-06-07 16:21:36 +02:00
Niels Müller
9c00242e2c
Module errors that collects all exceptions.
2016-06-07 16:20:38 +02:00
Niels Müller
0033cede6d
Clean up __init__.py
2016-06-07 11:15:04 +02:00
Niels Müller
3c3c1edb34
Remove generated Cython files from index.
2016-06-07 11:08:04 +02:00
Niels Müller
f072cf3fb6
Import XTCReader in global package.
2016-06-06 17:00:02 +02:00
Niels Müller
208a51acfe
Catch some possible seg faults when opening invalid xtc files.
2016-06-06 16:59:16 +02:00
Niels Müller
98757efe13
Implemnted xtcindex file handling for XTCReader.
2016-06-06 13:57:19 +02:00
Niels Müller
8d3d09fcc9
Ignore Cython c files.
2016-06-03 13:06:56 +02:00
Niels Müller
a601636d55
Moved gromacs module from mdevaluate to pygmx
2016-06-03 12:34:36 +02:00
Niels Müller
eeb5c607f8
Remove enxio for now.
2016-06-02 13:51:51 +02:00
Niels Müller
ff92b01e3e
Reduce verbosity when reading tpr files.
2016-04-23 19:13:39 +02:00
Niels Müller
56c38cb46b
Bundle commit of all recent changes on pygmx.
2016-03-30 11:52:02 +02:00
Niels Müller
21e6594c07
Use gromacs 5.1 release (instead of master)
2016-03-16 14:54:53 +01:00
Niels Müller
58d5d3a6c4
First draft of a python wrapper for gromacs library
2016-03-16 13:07:02 +01:00
