Recent ProDy updates to Cavi-Finder branch - #9

Update ProDy's readthedocs

updated README shield with correct link

…ording-in-DruGUI-2.0's-GUI

Update gui.py

Co-authored-by: AnthonyBogetti <34397256+AnthonyBogetti@users.noreply.github.com>

Co-authored-by: AnthonyBogetti <34397256+AnthonyBogetti@users.noreply.github.com>

Co-authored-by: AnthonyBogetti <34397256+AnthonyBogetti@users.noreply.github.com>

updated spring constants

…nner_radius for ease of use

…e channels slithering on surface are clear artifacts, no need for switch that would enable thier production

they were move out of the calcChannels signature into **kwargs, listed in
a CHANNELS_ADVANCED_OPTIONS table inside the function. They are settings a
normal run never touches, and the signature is long enough already. Unknown keywords raise TypeError instead of being ignored, so a misspelled
option is reported rather than silently falling back to its default. All these args options remain documented among the arguments, under a note that they are accepted as keywords only.

…er CA atom. Previously, since nucleic acids, ligands, cofactors and ions have no CA, they were dropped from the lining reports entirely, and a channel lined by no protein raised

AttributeError (e.g. on ribosome). Residues now come from the hierarchical view. Water is excluded unless include_water=True,. one_letter_aa translates only amino acids and nucleotides. Labels carry the chain (ASP108:A) unless include_chain=False, without which a residue number is not an identifier in an oligomer. An object with no lining is reported as "channelN: None" rather than skipped.

…not its centre. Previously, distA was measured from the probe centre, but the probe is a sphere whose radius varies along the object, so the reach past the wall was distA - r: a second shell was collected where an object is narrow and the wall was missed entirely where it is wide. The criterion is now |v - x| <= r + distA, and distA defaults to 2.5, which keeps channel reports close to their previous size; the distance still runs to the atom centre, so a touching atom sits at about one van der Waals radius. Channel and pore radii come from the radius spline, which also removes repetitive analysis of PDB file with each channel, making it about five times faster. Cavity vertices carry no radius, so the inscribed radius is recomputed against the atoms the tessellation used (water excluded); hence a vertex cannot lie inside one of those atoms, so a negative radius is reported as a mismatch between the cavities and the atoms given, rather than clamped away. + Minor refactors.

…(), not str.replace() to avoid cases wehn separate channel/cavity files were named by filename.replace('.pqr','_chl0.pqr'), which rewrites every occurrence of the extension anywhere in the path. An output directory called run.pqr/ was renamed along with the file, so the write failed after the combined file had already been produced; a name carrying no extension matched neither replace, so every object overwrote the previous one and the combined file with it; and a name holding both extensions was numbered twice. The new _numberedPath() helper numbers the file's own name only and leaves the directories alone.

CaviTracer: clearer parameter names, per-residue lining, and output-path fixes

…undant Code

…face cavities

…ion]

CaviTracer - additonal functions and multoprocessing

…xes and changes

ClustENM: multi-start (setAtoms accepts a list of AtomGroups) + optional fixer

Trajectory Clustering, Statistical Analysis, and Visualization Tools