Update Voronota-LT, add alternative modes to Voronoi analysis. (#456)

Version 0.9.4 of Voronota-LT has an improved API and a new ability
to update the tessellation without fully rebuilding it when possible.

The Voronoi analysis class now has adjustable running mode.
The class implementation makes use of the "pImpl" idiom.

Examples collection now contains "voronota" directory with
polymer-based and peptide based multichain simulation
configuration files and the corresponding output logs.

Author: kliment-olechnovic

docs/_docs/analysis.md

@@ -377,6 +377,7 @@ The algorithm is significantly faster than the above `sasa` analysis.
 `nstep`        | Interval between samples
 `nskip=0`      | Number of initial steps excluded from the analysis
 `file`         | Optionally stream surface area for each `nstep` to file (`.dat|.dat.gz`)
+`mode=full`    | Running mode: `full`, `interchain`, `updateable`
 `radius=1.4`   | Probe radius (Å)
 
 

docs/schema.yml

@@ -1312,6 +1312,11 @@ properties:
                             type: string
                             pattern: "(.*?)\\.(dat|dat.gz)$"
                             description: "Streaming filename (.dat|.dat.gz)"
+                        mode:
+                            type: string
+                            enum: ["full", "interchain", "updateable"]
+                            default: "full"
+                            description: "Running mode"
                     required: [nstep]
                     additionalProperties: false