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Adding documentation for the PrincipalComponentAnalysis EnsembleMetric #52

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1eed1f8
Adding ensemble metrics to sidebars.
vmullig Feb 8, 2022
9156829
Updating main RosettaScripts page.
vmullig Feb 8, 2022
35cb717
Adding page for CentralTendency metric.
vmullig Feb 8, 2022
cc023e6
Updating auto-generated docs.
vmullig Feb 8, 2022
a18aca6
Adding auto-generated ensemble metric docs.
vmullig Feb 8, 2022
3e8cc7f
Updating CentralTendency ensemble metric doc.
vmullig Feb 8, 2022
0e5918f
Working on documentation for EnsembleMetrics.
vmullig Feb 10, 2022
b3730e1
Fleshing out EnsembleMetric documentation.
vmullig Feb 10, 2022
97d7892
Updating auto-generated docs.
vmullig Feb 10, 2022
ca9eebd
Adding note about accessing named values.
vmullig Feb 10, 2022
bbfdb09
Adding note about filtering.
vmullig Feb 10, 2022
9dd6e89
Revising text slightly.
vmullig Feb 10, 2022
9629b4b
Adding note about MPI mode.
vmullig Feb 10, 2022
3301900
Adding example of internal generation mode.
vmullig Feb 10, 2022
a5778bb
Adding note about multithreading.
vmullig Feb 10, 2022
a045962
Updating note about multi-threading.
vmullig Feb 11, 2022
eb93e85
Adding example for mode 3.
vmullig Feb 11, 2022
62a9158
Add EnsembleFilter docs to filter list.
vmullig Feb 11, 2022
d38608f
Moving some filters that were in the wrong folder.
vmullig Feb 11, 2022
11215f2
Adding documentation for EnsembleFilter.
vmullig Feb 11, 2022
b7e9ef7
Minor typos.
vmullig Feb 11, 2022
fc6e674
Expanding note about mode.
vmullig Feb 11, 2022
08dc81e
Minor tweak.
vmullig Feb 11, 2022
0b2cc38
Merge remote-tracking branch 'origin/master' into vmullig/ensemble_me…
vmullig Feb 25, 2022
af0cded
Updating note about MPI.
vmullig Feb 25, 2022
41dacf1
Updating CentralTendency and FragmentScore auto-generated docs.
vmullig Feb 25, 2022
faa5e70
Merge branch 'vmullig/ensemble_metric_doc' into vmullig/ensemble_metr…
vmullig Feb 25, 2022
4d5dc12
Adding auto-generated docs for the PCA ensemble metric.
vmullig Feb 25, 2022
a282ac4
Updating EnsembleMetrics page.
vmullig Feb 25, 2022
7e6a155
Updating CentralTendency page.
vmullig Feb 25, 2022
5e5eabc
Initial commit of PrincipalComponentAnalysis page.
vmullig Feb 25, 2022
22503cc
Merge remote-tracking branch 'origin/master' into vmullig/ensemble_me…
vmullig Mar 11, 2022
99146f7
Updating auto-generated docs.
vmullig Mar 11, 2022
e23b820
Merge branch 'vmullig/ensemble_metric_doc' into vmullig/ensemble_metr…
vmullig Mar 11, 2022
af0a491
Merge remote-tracking branch 'origin/master' into vmullig/ensemble_me…
vmullig Apr 18, 2022
4fa4729
Update documentation with mention of support in MPIFileBufJobDistribu…
vmullig Apr 18, 2022
2549d1b
Merge remote-tracking branch 'origin/master' into vmullig/ensemble_me…
vmullig Apr 27, 2022
bfe5514
Merge branch 'vmullig/ensemble_metric_doc' into vmullig/ensemble_metr…
vmullig Apr 27, 2022
f2cbac0
Merge remote-tracking branch 'origin/master' into vmullig/ensemble_me…
vmullig Jul 2, 2022
9c8700e
Merge branch 'vmullig/ensemble_metric_doc' into vmullig/ensemble_metr…
vmullig Jul 2, 2022
802ce09
Merge remote-tracking branch 'origin/master' into vmullig/ensemble_me…
vmullig Oct 11, 2022
1aed331
Merge branch 'vmullig/ensemble_metric_doc' into vmullig/ensemble_metr…
vmullig Oct 11, 2022
b922fd9
Merge branch 'vmullig/ensemble_metric_mpi_docs' into vmullig/pca_metr…
vmullig Oct 11, 2022
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Minor typos.
  • Loading branch information
vmullig committed Feb 11, 2022
commit b7e9ef79447b69e504b0ca3e0f2f8c1add90e04a
Original file line number Diff line number Diff line change
@@ -112,7 +112,7 @@ In this example, the input is a cyclic peptide (provided with the `-in:file:s` c

### 2.2 Example of internal generation mode

This example is similar to the example above, only this time, we load one or more cyclic peptides (provided with the `-in:file:s` or `-in:file:l` commandline options), generate a conformational ensemble for each peptide _in memory_, without writing all structures to disk, and perform ensemble analysis on that ensemble, filtering on the results with the [[EnsembleMetric]].
This example is similar to the example above, only this time, we load one or more cyclic peptides (provided with the `-in:file:s` or `-in:file:l` commandline options), generate a conformational ensemble for each peptide _in memory_, without writing all structures to disk, and perform ensemble analysis on that ensemble, filtering on the results with the [[EnsembleFilter]].

```xml
<ROSETTASCRIPTS>
@@ -215,7 +215,6 @@ This example is similar to the example above, only this time, we load one or mor
</PROTOCOLS>
<OUTPUT scorefxn="r15" />
</ROSETTASCRIPTS>

```

#### 2.2.1 Multi-threading