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@Gundura
Gundura authored Sep 21, 2022
1 parent 494d311 commit 77c6193
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Showing 4 changed files with 28 additions and 30 deletions.
52 changes: 25 additions & 27 deletions POTATO_GUI.py
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Original file line number Diff line number Diff line change
Expand Up @@ -539,7 +539,7 @@ def analyze_steps():
for i in treeview_df.index:
# part before first step is fitted with a single WLC model (ds part)
if treeview_df['Step number'][i] == 1:
j = i
j = treeview_df['Step number'][i]
ds_fit_dict_TOMATO, TOMATO_area_ds, real_step_start = fitting_ds(filename_TOMATO, input_settings, export_data, input_fitting, float(treeview_df['Step start'][i]), Force_Distance_TOMATO, der_arr_TOMATO, [], 1)
ds_fit_region_end = real_step_start

Expand All @@ -550,7 +550,7 @@ def analyze_steps():
stiff_ds_variable.set(ds_fit_dict_TOMATO['St_ds'])

tree_results.insert("", "end", iid='{}no step'.format(timestamp), values=(
filename_TOMATO,
entryText_filename.get(),
i,
'',
'',
Expand Down Expand Up @@ -580,12 +580,9 @@ def analyze_steps():

# fit the other ss parts
elif treeview_df['Step number'][i] > 1:
j = i
j = treeview_df['Step number'][i]
fit_ss, f_fitting_region_ss, d_fitting_region_ss, ss_fit_dict_TOMATO, area_ss_fit_start, area_ss_fit_end = fitting_ss(filename_TOMATO, input_settings, export_data, input_fitting, float(treeview_df['Step end'][i - 1]), float(treeview_df['Step start'][i]), Force_Distance_TOMATO, 1, 1, der_arr_TOMATO, [], 1)

real_step_start = np.where(Force_Distance_TOMATO[:, 0] == f_fitting_region_ss[-1])
real_step_start = real_step_start[0][0]

fit.append(fit_ss)
start_force_ss.append(f_fitting_region_ss)
start_distance_ss.append(d_fitting_region_ss)
Expand All @@ -599,12 +596,12 @@ def analyze_steps():
ssLc_variable.set(ss_fit_dict_TOMATO['Lc_ss'])
stiff_ss_variable.set(ss_fit_dict_TOMATO['St_ss'])

tree_results.insert("", "end", iid='{}step{}'.format(timestamp, j), values=(
filename_TOMATO,
tree_results.insert("", "end", iid='{}step{}'.format(timestamp, j-1), values=(
entryText_filename.get(),
i,
Force_Distance_TOMATO[real_step_start, 0],
f_fitting_region_ss[0],
f_fitting_region_ss[0] - Force_Distance_TOMATO[real_step_start, 0],
(f_fitting_region_ss[0] + Force_Distance_TOMATO[real_step_start, 0]) / 2,
Force_Distance_TOMATO[real_step_start, 1],
d_fitting_region_ss[0],
d_fitting_region_ss[0] - Force_Distance_TOMATO[real_step_start, 1],
Expand All @@ -621,6 +618,9 @@ def analyze_steps():
)
)

real_step_start = np.where(Force_Distance_TOMATO[:, 0] == f_fitting_region_ss[-1])
real_step_start = real_step_start[0][0]

# plot the marked regions and fits
# model data
F_ss_model = ss_fit_dict_TOMATO['model_ss'](distance, fit_ss.params)
Expand Down Expand Up @@ -658,12 +658,12 @@ def analyze_steps():
ssLc_variable.set(ss_fit_dict_TOMATO['Lc_ss'])
stiff_ss_variable.set(ss_fit_dict_TOMATO['St_ss'])

tree_results.insert("", "end", iid='{}step{}'.format(timestamp, j + 1), values=(
filename_TOMATO,
j + 1,
tree_results.insert("", "end", iid='{}step{}'.format(timestamp, j), values=(
entryText_filename.get(),
j,
Force_Distance_TOMATO[:, 0][real_step_start],
f_fitting_region_ss[0],
f_fitting_region_ss[0] - Force_Distance_TOMATO[:, 0][real_step_start],
(f_fitting_region_ss[0] + Force_Distance_TOMATO[:, 0][real_step_start]) / 2,
Force_Distance_TOMATO[:, 1][real_step_start],
d_fitting_region_ss[0],
d_fitting_region_ss[0] - Force_Distance_TOMATO[:, 1][real_step_start],
Expand Down Expand Up @@ -694,17 +694,19 @@ def analyze_steps():

if j > 1:
for n in range(1, j):
print(start_distance_ss[n - 1][-1])
print(start_distance_ss[n][0])
work_step_n, kT_n = calc_integral(
integral_ss_fit_end[n],
integral_ss_fit_start[n - 1],
integral_ss_fit_end[n - 1],
integral_ss_fit_start[n],
start_distance_ss[n - 1][-1],
start_distance_ss[n][0],
start_force_ss[n - 1][-1],
start_force_ss[n][0]
)

tree_results.set('{}step{}'.format(timestamp, n), column='Work [pN*nm]', value=work_step_n)
tree_results.set('{}step{}'.format(timestamp, n), column='Work [kT]', value=kT_n)
print('WORK', work_step_n)
tree_results.set('{}step{}'.format(timestamp, n+1), column='Work [pN*nm]', value=work_step_n)
tree_results.set('{}step{}'.format(timestamp, n+1), column='Work [kT]', value=kT_n)

# plot the marked regions and fits
# model data
Expand Down Expand Up @@ -776,7 +778,7 @@ def export_table():
'step number',
'Force step start [pN]',
'Force step end [pN]',
'delta force [pN]',
'mean force [pN]',
'extension step start [nm]',
'extension step end [nm]',
'Step length [nm]',
Expand All @@ -800,23 +802,19 @@ def export_table():
def tab_bind(event=None):
if tabControl.index(tabControl.select()) == 4:
root.bind("<Right>", next_FD_key)
root.bind("<d>", next_FD_key)
root.bind("<Left>", previous_FD_key)
root.bind("<a>", previous_FD_key)
root.bind("<s>", start_click_key)
root.bind("<e>", end_click_key)
root.bind("<Control-s>", save_step_key)
root.bind("<f>", start_analysis_key)
root.bind("<Control-f>", start_analysis_key)
root.bind("<Delete>", delete_result)
else:
root.unbind("<Right>")
root.unbind("<d>")
root.unbind("<Left>")
root.unbind("<a>")
root.unbind("<s>")
root.unbind("<e>")
root.unbind("<Control-s>")
root.unbind("<f>")
root.unbind("<Control-f>")
root.unbind("<Delete>")

############## TOMATO functions end ###################
Expand Down Expand Up @@ -1507,7 +1505,7 @@ def select_box(*check_box):
button_reset_parameters = tk.Button(TOMATO_button_frame, text='Reset parameters', command=lambda: parameters(0, default_values_FIT, default_values_constantF) if check_box_HF == 1 else (parameters(default_values_HF, default_values_FIT, default_values_constantF) if check_box_LF == 1 else parameters(default_values_CSV, default_values_FIT, default_values_constantF)), bg='palegreen2', font=('Arial', 11, 'bold'))
button_reset_parameters.grid(row=1, column=1, padx=4, pady=4)

label_info = tk.Label(TOMATO_button_frame, text='TOMATO is unresponsive during fitting, please be patient\n\nmark step start <s>\n mark step end <e>\n save marked step <Ctrl+s>\n start analysis <f>\n delete results line <mark+del>\n next curve <Right arrow> or <d>\n previous curve <Left arrow> or <a>')
label_info = tk.Label(TOMATO_button_frame, text='TOMATO is unresponsive during fitting, please be patient\n\nmark step start <s>\n mark step end <e>\n save marked step <Ctrl+s>\n start analysis <Ctrl+f>\n delete results line <mark+del>\n next curve <Right arrow>\n previous curve <Left arrow>')
label_info.grid(row=2, column=0, padx=4, pady=4)

button_start = tk.Button(TOMATO_parameter_frame, text='Set start', command=start_click, bg='lightsteelblue2', font=('Arial', 10, 'bold'))
Expand All @@ -1533,7 +1531,7 @@ def select_box(*check_box):
'step number',
'Force step start [pN]',
'Force step end [pN]',
'delta force [pN]',
'mean force [pN]',
'extension step start [nm]',
'extension step end [nm]',
'Step length [nm]',
Expand Down
2 changes: 1 addition & 1 deletion POTATO_TOMATO.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@


def plot_TOMATO(FD):
figure1 = Figure(figsize=(9, 7), dpi=100)
figure1 = Figure(figsize=(9, 7), dpi=70)
subplot1 = figure1.add_subplot(111)

F = FD[:, 0]
Expand Down
2 changes: 1 addition & 1 deletion POTATO_config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@
'Persistance-Length ds, upper bound, nm': '80',
'Persistance-Length ds, lower bound, nm': '12',
'Persistance-Length ss, nm': '1',
'Contour-Length ds, nm': '830',
'Contour-Length ds, nm': '1250',
'Contour-Length ss, nm': '0',
'Stiffness ds, pN': '500',
'Stiffness ds, upper bound, pN': '600',
Expand Down
2 changes: 1 addition & 1 deletion POTATO_fitting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -194,7 +194,7 @@ def fitting_ss(filename_i, input_settings, export_data, input_fitting, i_start,
# contour length
fit_ss["RNA/Lc"].value = input_fitting['lc_ss']
fit_ss["RNA/Lc"].lower_bound = 0
fit_ss["RNA/Lc"].upper_bound = input_fitting['lc_ss'] + 1000
fit_ss["RNA/Lc"].upper_bound = input_fitting['lc_ss'] + 100

fit_ss["RNA/Lc"].unit = 'nm'

Expand Down

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