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update image rendering method in vmd script #17

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update image rendering method in vmd script #17

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a722da6
update image rendering method in vmd script
ftclark3 Sep 2, 2025
4ac4285
add option to write vmd script but not launch vmd
ftclark3 Sep 2, 2025
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5 changes: 3 additions & 2 deletions frustratometer/classes/Frustratometer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -291,7 +291,7 @@ def auc(self):
"""
return frustration.compute_auc(self.roc())

def vmd(self, sequence: str = None, single:Union[str,np.array] = 'singleresidue', pair:Union[str,np.array] = 'mutational',
def vmd(self, sequence: str = None, single:Union[str,np.array] = 'singleresidue', pair:Union[str,np.array] = 'mutational', launch_vmd:bool = True,
aa_freq:np.array = None, correction:int = 0, max_connections:Union[int,None] = None, movie_name=None, still_image_name=None):
"""
Calculates frustration indices and superimposes frustration patterns onto PDB structure using the VMD software.
Expand Down Expand Up @@ -322,7 +322,8 @@ def vmd(self, sequence: str = None, single:Union[str,np.array] = 'singleresidue'
-self.frustration(kind=single, sequence=sequence, aa_freq=aa_freq),
-self.frustration(kind=pair, sequence=sequence, aa_freq=aa_freq),
max_connections=max_connections, movie_name=movie_name, still_image_name=still_image_name)
frustration.call_vmd(self.pdb_file, tcl_script)
if launch_vmd:
frustration.call_vmd(self.pdb_file, tcl_script)

def view_pair_frustration(self, sequence:str = None, pair:str = 'mutational', aa_freq:np.array = None):
"""
Expand Down
7 changes: 4 additions & 3 deletions frustratometer/frustration/frustration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1025,9 +1025,10 @@ def write_tcl_script(pdb_file: Union[Path,str], chain: str, mask: np.array, dist
exit
''')
elif still_image_name:
# file type choices other than ppm may work; see https://www.ks.uiuc.edu/Research/vmd/current/ug/node147.html
fo.write(f'set output "{still_image_name}"' + '''
render snapshot $output
exit
render format TachyonInternal PPM
render TachyonInternal $output
''')
fo.close()
return tcl_script
Expand Down Expand Up @@ -1573,4 +1574,4 @@ def compute_energy_sliding_window(seq: str,
'frustration': frustration_sw
}

return results
return results
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