cpptraj: list of things to write to Dataset

[hainm]

• clustering

This is stdout

#Clustering: 10 clusters 401 frames
#Cluster 0 has average-distance-to-centroid 1.115112
#Cluster 1 has average-distance-to-centroid 1.058091
#Cluster 2 has average-distance-to-centroid 1.136221
#Cluster 3 has average-distance-to-centroid 0.769939
#Cluster 4 has average-distance-to-centroid 0.770699
#Cluster 5 has average-distance-to-centroid 0.825140
#Cluster 6 has average-distance-to-centroid 0.502964
#Cluster 7 has average-distance-to-centroid 0.622283
#Cluster 8 has average-distance-to-centroid 0.556346
#Cluster 9 has average-distance-to-centroid 0.594979
#DBI: 0.471646
#pSF: 4271.368183
#Algorithm: HierAgglo linkage average-linkage nclusters 10 epsilon 1.79769e+308
#Representative frames: 385 5 217 187 255 70 32 39 23 116

TODO: need to write different clusters to different files for pytraj too.

• Representative frames: Dataset_Integer
• centroid distane

[hainm]

• Action_Principal

In [8]: cat principal.in
parm ../Test_IRED/1IEE_A_prot.prmtop
noprogress
trajin ../Test_IRED/1IEE_A_test.mdcrd 1 10
principal * dorotation mass out principal.dat
trajout Ctest.pdb pdb

In [9]: s = pt.io.load_cpptraj_file('./principal.in')

In [10]: s
Out[10]: <pytraj.core.CpptrajState.CpptrajState at 0x2aaac9dd91f8>

In [11]: s.run()
Out[11]: 0

In [12]: s.da
s.datafilelist  s.datasetlist

In [12]: s.datasetlist
Out[12]: <pytraj.DataSetList with 0 datasets>

updated need to specify a name so cpptraj can dump data internally. Need to fix anyway.

[hainm]

• Analysis_CrankShaft too?