A script that's pruporse is to create tbl restrain files from assigned NOESY signals. The assigment is read from a csv file with a format shown below:
HydrogenPair,AssignedNOESYIntensity
NH1 - NH2,m
NH2 - NH5,s
NH7 - NH1,w
To use the class you've to create its object instance with
two arguments noecsv_fname, sequence_fname and restwrite_fname as in
the example below.
The script also allows for generation of .tbl restrain files that have ambigiously defined
atoms (e.g. from signals that can be asssigned either between hydrogens H1, H2 or H1, H3).
To use this option, in the CSV file don't specify its number e.g. if you take the example at the beginning,
then instead of writting NH1 - NH2,m, you write NH - NH2,m or NH1 - NH,m.
To limit number of such combinations, specify one_atom_max_limit=N, where N is number of combinations
for one atom - atom pair. E.g. if there would be 9 combinations for a pair and N=3, then the program
would crash with appropiate message. Atoms with such a large combinations should be avoided, especially
with other atoms with such a large number of combinations, because the total number of comb. grows as N! (or N factorial).
from noesytorestrains import TblFileMaker
tblfm = TblFileMaker(noecsv_fname='noe.csv',
restwrite_fname='rest.tbl',
sequence_fname='sequence.seq',
one_atom_max_limit=1)
tblfm.read_noecsv()
tblfm.save_tbl()
The script is used as it is, imported directly from the directory, where the repository was cloned into.
- Python 3.5 or above
- Cardinality package (
https://pypi.org/project/cardinality/)