Data that pytraj currently doesn't have access to but would like to

[hainm]

related to https://github.com/Amber-MD/cpptraj/issues/175, https://github.com/Amber-MD/cpptraj/issues/93

I will keep updating checklist in 1st post and post the detail in following post.

• [ ] Action_NativeContact
• [ ] Select dihedral, angle (bond too?) from Topology
• [ ] Action_Checkstructure
• [ ] Cluster analysis: Representative frames
• [ ] Action.Help(): Not sure about technical issue

[drroe]

#72 seems like it belongs under this umbrella.

[hainm]

Native contact

• info about contacts

    Setup 33 native contacts:
        Atom ':1@CA' to ':2@CA'
        Atom ':1@CA' to ':11@CA'
        Atom ':1@CA' to ':12@CA'
        Atom ':2@CA' to ':3@CA'
...

• summary

#                     Contact  Nframes    Frac.      Avg    Stdev
       1          :1@OG_:1@HG      101        1     0.96 0.000365
       2        :2@NE1_:2@HE1      101        1     1.01 0.000366
       3           :1@N_:1@H2      101        1     1.01  0.00043
       4           :1@N_:1@H1      101        1     1.01 0.000364
       5           :1@N_:1@H3      101        1     1.01 0.000391
       6            :2@N_:2@H      101        1     1.01 0.000362

[hainm]

Select dihedral, angle (bond too?) from Topology

The output should be ready to used for further calculation.

• this output from cpptraj is good enough

         1:  2.000 0.00  1.0 :1@O      :1@C      :2@N      :2@H      (13,12,14,15) O -C -N -H 
E        2:  2.500 3.14  2.0 :1@O      :1@C      :2@N      :2@H      (13,12,14,15) O -C -N -H 
         3:  0.000 0.00  2.0 :1@C      :2@N      :2@CA     :2@HA     (12,14,16,17) C -N -CT-H1
        12:  0.000 0.00  2.0 :1@HA     :1@CA     :1@C      :2@N      (6,5,12,14) HP-CT-C -N 

(at least we could parse ":1@O :1@C :2@N :2@H", ...)

• we don't need 'pk phase pn` stuff. Just direct users to ParmEd.

[hainm]

Check structure

In [10]: traj = pt.load('tz2.stretched.pdb')

In [11]: pt.common_actions.check_structure(traj)
1    Warning: Atoms 222:NME_13@HH32 and 223:NME_13@HH33 are close (0.61)

The warning does not work with Jupyter notebook.

[hainm]

cluster analysis

• [ ] representative frame numbers: currently STDOUT

[hainm]

Action.Help()

@drroe How hard to turn Help to vector<string>? Sometimes need to inspect cpptraj's doc interactively. For example

• calling doc from Action_Volmap.Help

In [1]: pt.info('volmap')
        filename dx dy dz <mask> [xplor] [radscale <factor>]
        [ [[buffer <buffer>] [centermask <mask>]] | [center <x,y,z>] [size <x,y,z>] ]
        [peakcut <cutoff>] [peakfile <xyzfile>]
    filename  : Output file name
    dx, dy, dz: grid spacing in the x-, y-, and z-dimensions, respectively.
  The grid size can be determined either by the size (x,y,z in Angstroms)
  or by a rectangular prism enclosing a mask with <buffer> clearance
  in every dimension. The density is calculated from the atoms in the
  required <mask>. If a <buffer> is given, the grid is centered on the
  centermask if provided, or the required mask if not.

This works fine with Python interactive Ipython but does not work (appear) with the notebook.

• pytraj has two modes: Pythonic (for whom likes python) or cpptraj-nic (:D, for whom want to run everything completely in cpptraj (example below))

In [4]: state = pt.load_cpptraj_state('''
rms
radgyr nomax
molsurf @CA
matrix dist @CA''', traj)

In [5]: state.run()
Out[5]:
CpptrajState, include:
<datasetlist: 5 datasets>

So it's great if we (users) can view cpptraj doc.

But if it's a bit difficult to change, I am fine with using Ipython instead of Jupyter notebook for cpptraj doc.

[hainm]

@drroe Please do not work on this issue yet. I don't see specific need in pytraj right now. Thanks.