AttributeError: 'Namespace' object has no attribute 'outCsvFile' and not plots

[stephaneabel]

HI all

I have the data from gmx_clusterByFeatures with the following commands bot in a bash script

/ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/install_noMPI/bin/gmx_clusterByFeatures hole -f /ccc/store/cont003/drf/abel01/MDs_GENCI_2017/GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2/XTC/1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_Along_Z_Axis_Rotated_afterFit_Center.xtc -s 1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_fake_reoriented.tpr -n System.ndx -o 1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_hole_radius_along_Z.dat -pdb 1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_hole_sphpdb.pdb -b 229000 -e 230000 -fit -sample 0.5 -cvect 0 0 1 -rad bondi

And I would like to obtain and image of the results so I use the following command

/ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/install_noMPI/bin/gmx_clusterByFeatures holeplot -i 1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_hole_radius_along_Z.dat -csv 1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_hole_radius_along_Z.csv -xmin 0 -xmax 15 -ax Z -resplot -b 229000 -e 230000 -ymin 0 -ymax 15 --output 1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_hole_radius_along_Z.pdf -fs 14 -dpi 300 -rlsize 10

But I obtain the error and no pdf file is generated
Traceback (most recent call last):
File "/ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/install_noMPI/bin/gmx_clusterByFeatures", line 8, in
gmx_clusterByFeatures.main.main()
File "/ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/gmx_clusterByFeatures-master/gmx_clusterByFeatures/main.py", line 79, in main
holeplot.main()
File "/ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/gmx_clusterByFeatures-master/gmx_clusterByFeatures/holeplot.py", line 170, in main
holeProcessor.plot_radius_residues(outputFile, csvfile=args.outCsvFile, violinplot=args.violinplot,
AttributeError: 'Namespace' object has no attribute 'outCsvFile'

See also the file attached.

Could you help me to resolve this problem

Thank you
GrA_SDS_hole.4602493e.TXT

[rjdkmr]

This is a bug in code. I will look into it. You may use without csvfile as output for meantime. It will anyway print the values on display terminal.

You have not used either -cpoint or -catmid with hole command. It will use COM of radius group. And use -pdb option for only one frame to check whether cavity is identified correctly.

[stephaneabel]

Thank you Dr Kumar

You have not used either -cpoint or -catmid with hole command. It will use COM of radius group. And use -pdb option for only one frame to check whether cavity is identified correctly.
OK I have used these options in my calculations.

But I still have a problem to obtain the average radius of the channel for plotting the pore lining surface as for instance in figure 3A in the following paper (10.1080/19336950.2017.1306163)

Do you have an idea when the bug in the "holeplot.py" will be corrected ?

Thanks again

Stéphane

[rjdkmr]

To make surface for average-radius, here is a link which could help: http://www.holeprogram.org/doc/index.html#_producing_a_colored_dot_surface_and_visualizing_in_vmd. You can use pdb file obtained from -pdb option in place of hole_out.sph in the above link. I do not know how average value can be visualized as sph (or pdb) file generated for each frame. You may take a pdb file and replace manually all radius value with average value and then procedures given in above link might work for visualization of average radius.

I will try to correct csvfile problem in this weekend.

[rjdkmr]

You may also try to correct the csvfile error as follows:
Open holeplot.py file and go to line no. 204 and add dest="outCsvFile" as shown below:

parser.add_argument('-csv', '--out-csv', action='store', dest="outCsvFile",
                        type=str, metavar='output.csv', 
                        help=outCsvFileHelp)

It should work after this correction.

[stephaneabel]

Thank you for your response.
With the help of the information provided in the link your suggested I was able to resolve the my problem and output the average lining surface

[stephaneabel]

You may also try to correct the csvfile error as follows:
Open holeplot.py file and go to line no. 204 and add dest="outCsvFile" as shown below:

parser.add_argument('-csv', '--out-csv', action='store', dest="outCsvFile",
                        type=str, metavar='output.csv', 
                        help=outCsvFileHelp)

It should work after this correction.
After the modification, the holeplot program seems to work but crash before to finish the calculation with the following error (see also the file attached):

---

abel@is154919:~/MDs_GramicidinA/GrA_65SDS_Water_rep1_2/Hole_Analysis$ ./Do_HolePlot_Analysis.bash

Reading file : 1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_hole_radius_along_Z.dat
Reading frame 0 at time 200000.000
Maximum axis range is: (0.000 to 15.000)
Reading frame 3000 at time 215075.000
Finishid reading.... Total number of frame read = 3895
After removing axis points with any missing data:

Axis Mean radius Std. deviation

---

---

Traceback (most recent call last):
File "/gmx_clusterByFeatures/install_noMPI/bin/gmx_clusterByFeatures", line 8, in
gmx_clusterByFeatures.main.main()
File "/home/abel/gmx_clusterByFeatures/gmx_clusterByFeatures/main.py", line 79, in main
holeplot.main()
File "/home/abel/gmx_clusterByFeatures/gmx_clusterByFeatures/holeplot.py", line 173, in main
rlabelsize=args.rlabelsize, dpi=args.dpi)
File "/home/abel/gmx_clusterByFeatures/gmx_clusterByFeatures/holeOutputProcessor.py", line 380, in plot_radius_residues
ax1.plot(self.axis_value, self.average.values(), '-r')
File "/usr/local/lib/python3.6/dist-packages/matplotlib/axes/_axes.py", line 1665, in plot
lines = [*self._get_lines(*args, data=data, **kwargs)]
File "/usr/local/lib/python3.6/dist-packages/matplotlib/axes/_base.py", line 225, in call
yield from self._plot_args(this, kwargs)
File "/usr/local/lib/python3.6/dist-packages/matplotlib/axes/_base.py", line 391, in _plot_args
x, y = self._xy_from_xy(x, y)
File "/usr/local/lib/python3.6/dist-packages/matplotlib/axes/_base.py", line 270, in _xy_from_xy
"have shapes {} and {}".format(x.shape, y.shape))
ValueError: x and y must have same first dimension, but have shapes (0,) and (1,)

---

The command I used
"$MYSOURCE"/gmx_clusterByFeatures holeplot -i my_radius_along_Z.dat -xmin 0 -xmax 15 -ax Z -endrad 5.0 -do 90 --out-csv output.csv -resplot -b 200000 -e 230000 -ymin 0 -ymax 15 --output my_radius_radius_along_Z.pdf -fs 14 -dpi 300 -rlsize 1

Thanks again
error.txt

[stephaneabel]

Re Hello
I have finally resolved the problem mentioned above and obtained the *csv and *.png file I want with the following command:
"$MYSOURCE"/gmx_clusterByFeatures holeplot -i MYRAD_radius_along_Z.dat -ax Z -endrad 5.0 -do 90 -vplot --out-csv MYRAD_radius_along_Z_Holeplot.csv --residues-plot -rfreq 50 -b 200000 -e 300000 --output MYRAD_radius_along_Z_Holeplot.png -gap 1 -fs 14 -dpi 300 -rlsize 10 -wd 8 -ht 8

"$MYSOURCE"/gmx_clusterByFeatures holeplot -i my_radius_along_Z.dat -xmin 0 -endrad 5.0 -do 90 --out-csv output.csv -resplot -b 200000 -e 230000 -ymin 0 -ymax 15 --output my_radius_radius_along_Z.pdf -fs 14 -dpi 300 -rlsize 1