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Amber-MD / cpptraj

Biomolecular simulation trajectory/data analysis.
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Data that pytraj currently doesn't have access to but would like to #177

Open hainm opened 8 years ago

hainm commented 8 years ago

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.

drroe commented 8 years ago

72 seems like it belongs under this umbrella.

hainm commented 8 years ago

Native contact

    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'
...
#                     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 commented 8 years ago

Select dihedral, angle (bond too?) from Topology

The output should be ready to used for further calculation.

         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", ...)

hainm commented 8 years ago

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 commented 8 years ago

cluster analysis

hainm commented 8 years ago

Action.Help()

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

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.

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 commented 4 years ago

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