import scadnano as sc
design = sc.Design.from_scadnano_file('240210 zigzag growth.sc')
design.write_oxview_file()
This is the error:
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
Cell In[3], line 4
1 import scadnano as sc
3 design = sc.Design.from_scadnano_file('240210 zigzag growth.sc')
----> 4 design.write_oxview_file()
File C:\Dropbox\git\scadnano-python-package\scadnano\scadnano.py:7877, in Design.write_oxview_file(self, directory, filename, warn_duplicate_strand_names, use_strand_colors)
7862 def write_oxview_file(self, directory: str = '.', filename: Optional[str] = None,
7863 warn_duplicate_strand_names: bool = True, use_strand_colors: bool = True) -> None:
7864 """Writes an oxView file rerpesenting this design.
7865
7866 :param directory:
(...)
7875 of the strand.
7876 """
-> 7877 oxvsystem = self.to_oxview_format(warn_duplicate_strand_names=warn_duplicate_strand_names,
7878 use_strand_colors=use_strand_colors)
7879 write_file_same_name_as_running_python_script(json.dumps(oxvsystem), 'oxview', directory, filename)
File C:\Dropbox\git\scadnano-python-package\scadnano\scadnano.py:7772, in Design.to_oxview_format(self, warn_duplicate_strand_names, use_strand_colors)
7770 import datetime
7771 self._check_legal_design(warn_duplicate_strand_names)
-> 7772 system = _convert_design_to_oxdna_system(self)
7774 oxview_strands: List[Dict[str, Any]] = []
7775 nuc_count = 0
File C:\Dropbox\git\scadnano-python-package\scadnano\scadnano.py:9145, in _convert_design_to_oxdna_system(design)
9141 elif isinstance(domain, Loopout):
9142 # we place the loopout nucleotides at temporary nonsense positions and orientations
9143 # these will be updated later, for now we just need the base
9144 for _ in range(domain.length):
-> 9145 base = seq[i]
9146 center = _OxdnaVector()
9147 normal = _OxdnaVector(0, -1, 0)
IndexError: string index out of range
One clue is that the loop variable _ is unused, and each iteration of the loop is accessing the same symbol seq[i] of the domain's sequence. So it might be that the fix is to replace lines 9144 and 9145 with
The following design
240210 zigzag growth.sc.txt
raises an exception when executing
This is the error:
One clue is that the loop variable
_
is unused, and each iteration of the loop is accessing the same symbolseq[i]
of the domain's sequence. So it might be that the fix is to replace lines 9144 and 9145 with