issues with cylindrical-density

[VBurns]

I've been trying to use cylindrical-density.py and i keep getting with error:

cylindrical-density.py foo.prmtop foo-centered.mdcrd 'name == "CA"' 'resname == "PC" || resname == "PA" || resname == "OL"' -25 25 50 10 30 20

/usr/local/bin/cylindrical-density.py foo.prmtop foo-centered.mdcrd name == "CA" resname == "PC" || resname == "PA" || resname == "OL" -25 25 50 10 30 20

Traceback (most recent call last): File "/usr/local/bin/cylindrical-density.py", line 106, in hist[rbin, zbin] += 1.0 IndexError: index 50 is out of bounds for axis 1 with size 50

LOOS has been set up with python3, so i know it's not the python version. I don't know where the problem is.

[agrossfield]

That certainly looks like a bug, and not in any way your fault. I'll take a look at it today

[agrossfield]

I think I fixed it -- unlucky roundoff. Can you check out the fix-cyl-density branch and see if it fixes it for you?

If you don't want to do that, you can edit cylindrical-density.py (or copy it and edit the new version), so that the offending line (line 106) is replaced by this:

if (0 <= rbin < rnum_bins) and (0 <= zbin < znum_bins): hist[rbin, zbin] += 1.0

Let me know, so I can merge and close the issue if this is it (or delve deeper if it isn't).

Alan

[VBurns]

It's works. Thank you so much Alan!

[agrossfield]

Awesome. I’ll merge it tonight.

Alan

---

Dr. Alan Grossfield Associate Professor Department of Biochemistry and Biophysics University of Rochester Medical Center 610 Elmwood Ave, Box 712 Rochester, NY 14642 Phone: 585 276 4193 http://membrane.urmc.rochester.edu https://orcid.org/0000-0002-5877-2789

On Oct 24, 2019, at 4:41 PM, VBurns notifications@github.com<mailto:notifications@github.com> wrote:

It's works. Thank you so much Alan!

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[agrossfield]

Fix is merged in