Commit Graph

29 Commits

Author SHA1 Message Date
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