38 lines
1.2 KiB
Python
38 lines
1.2 KiB
Python
"""
|
|
Python wrapper for the gromacs library for their file formats.
|
|
|
|
Currently this supports xtc and tpr files within the `open` function.
|
|
Trajectories in trr format may be read with `.gromacs.reader.TRRReader`, which is experimental.
|
|
"""
|
|
|
|
import os
|
|
|
|
from .tpxio import TPXReader
|
|
from .xtcio import XTCReader, read_xtcframe
|
|
from .enxio import EDRFile
|
|
from .errors import FileTypeError
|
|
from .gromacs.reader import index_filename_for_xtc
|
|
from .gromacs.xtcindex import index_xtcfile
|
|
|
|
FILE_EXTENSIONS = {
|
|
'xtc': XTCReader,
|
|
'tpr': TPXReader,
|
|
'edr': EDRFile,
|
|
}
|
|
|
|
|
|
def open(filename, ignore_index_timestamps=False):
|
|
"""Open a supported gromacs file. Currently supported file formats: tpr, xtc."""
|
|
ext = filename.split('.')[-1]
|
|
if ext in FILE_EXTENSIONS:
|
|
if ext in ['xtc']:
|
|
indexfile = index_filename_for_xtc(filename)
|
|
if not os.path.exists(indexfile):
|
|
print('Generating Index for xtc file. This may take a while...')
|
|
index_xtcfile(filename)
|
|
return FILE_EXTENSIONS[ext](filename, indexfile, ignore_timestamps=ignore_index_timestamps)
|
|
else:
|
|
return FILE_EXTENSIONS[ext](filename)
|
|
else:
|
|
raise FileTypeError('Filetype {} not supported by pygmx.'.format(ext))
|