becksteinlab / hop Goto Github PK

Right now almost all docs are in python doc strings. The strings should be all turned into restructured text and then processed with Sphinx.

With the modification "MDAnalysis>=0.7.4" in setup.py and in Hop.egg-info/requires.txt the installation works well.

At some point (maybe MDA 0.10 - 0.11 transition?) the sorting of sites by increasing volume broke.

Some issue with newer version of the Bio.PDB writer:

In [44]: density.export3D()
S --> ?
S --> ?
...
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)

/Volumes/Data/oliver/Biop/Projects/WaterNetworks/testcases/2IFB/analysis/ in ()

/Volumes/Data/oliver/Biop/Library/python/Hop/hop/sitemap.pyc in export3D(self, filename, site_labels)
   1300 
   1301         self._write_psf(filename,site_labels)       # atoms are numbered consecutively...
-> 1302         self._write_pdb(filename,site_labels)       # ..and residues correspond to sites
   1303         self._write_vmd(filename,site_labels)       # tcl code for labels in VMD
   1304 

/Volumes/Data/oliver/Biop/Library/python/Hop/hop/sitemap.pyc in _write_pdb(self, filename, site_labels)
   1334         io.set_structure(s)
   1335         pdbfile = self.filename(filename,'pdb')
-> 1336         io.save(pdbfile)
   1337 
   1338     def _write_psf(self,filename,site_labels):

/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/PDB/PDBIO.pyc in save(self, file, select, write_end)
    154                             model_residues_written=1
    155                             s=get_atom_line(atom, hetfield, segid, atom_number, resname,
--> 156                                 resseq, icode, chain_id)
    157                             fp.write(s)
    158                             atom_number=atom_number+1

/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/PDB/PDBIO.pyc in _get_atom_line(self, atom, hetfield, segid, atom_number, resname, resseq, icode, chain_id, charge)
     76             element = atom.element.strip().upper()
     77             if len(atom.element) > 2 or not element.isalpha():
---> 78                 raise ValueError("Unrecognised element %s" % repr(atom.element))
     79             element = element.rjust(2)
     80         else:

ValueError: Unrecognised element '?'
> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/PDB/PDBIO.py(78)_get_atom_line()
     77             if len(atom.element) > 2 or not element.isalpha():
---> 78                 raise ValueError("Unrecognised element %s" % repr(atom.element))
     79             element = element.rjust(2)

Remove most of the code in hop.constants and use MDAnalysis.units (which was based on hop.constants...).

hop-generate-hopgraph.py -f hoptraj.dcd -s hoptraj.psf analysis/water.pickle

fails with

...
    self._cache['sitelabels'].sort()
AttributeError: 'NodeView' object has no attribute 'sort'

To ensure minimum coding style: add

# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8

@iwelland has done major additions, which need to be merged

Serve docs from RTD instead of gh-pages.

• enable RTD
• badge to README
• remove gh-pages branch and disable outdated https://becksteinlab.github.io/hop/

via @iorga:

How can we visualize the network encoded by the file hopgraph.xgmml ? I tried with Cytoscape, it recognizes the columns etc, but the drawing shows only one big rectangle.

I also installed graphviz, but I'm not sure about how to use the modules, like "dot" for example. Is it correct to type

dot -Tpng -o x.png test.xgmml

The result is :

Warning: test.xgmml: syntax error in line 1 near '>'

Or do I have to format the xgmml file into a specific format ?

The current manual testing protocol contains a short (0.5 ns) trajectory of I-FABP. The rates that come out of running it through hop are not very believable, see discussion following #11 (comment).

We want to figure out if these rates are correctly calculated but just not converged or if there's a deeper problem.

(This is also important if we want to use a short version of the test trajectory for proper tests #2.)

In [66]: hm = HeatmapAnalysis(cg)

<type 'exceptions.AttributeError'> Traceback (most recent call last)

/mnt/denniej0/1l2x/namd_alex3/analysis/ in ()

/mnt/denniej0/1l2x/namd_alex3/analysis/build/bdist.linux-i686/egg/hop/analysis.py in init(self, hoppinggraphs, normalization, verbosity, prune)

<type 'exceptions.AttributeError'>: 'CombinedGraph' object has no attribute 'keys'

Most of the code in hop.density can be replaced with MDAnalysis.analysis.density (which originated here...).

Remove legacy code for Grid and replace with the gridDataFormats library.

Remove code to call VMD (not really needed and too complicated to maintain)

Code is broken with modern networkx > 0.99.

Needs to be upgraded. Use networkx 0.36 for the time being.

Replace own versioning with versioneer.

Should have proper unit tests to check function.

• must be added as u.trajctectory
• fails with _C_addr... missing

Currently, the sphinx docs do not build correctly with a weird

RuntimeError: sys.path must be a list of directory names

Need be fixed.

When the 2 (h and h_ref) networks are combined and then trying to graph them

In [70]: cg = hop.graph.CombinedGraph(g0=h,g1=h_ref)
In [71]: cg.plot(0,'cg_h',linewidths=(0.01,))

<type 'exceptions.ValueError'> Traceback (most recent call last)

/mnt/denniej0/1l2x/namd_alex3/analysis/ in ()

/mnt/denniej0/1l2x/namd_alex3/analysis/build/bdist.linux-i686/egg/hop/graph.py in plot(self, igraph, filename, format, use_filtered_graph, label_sites, prog, cmap, max_node_size, interactive, **drawargs)

/mnt/denniej0/1l2x/namd_alex3/analysis/build/bdist.linux-i686/egg/hop/graph.py in select_graph(self, use_filtered_graph)

<type 'exceptions.ValueError'>: No filtered graph defined; create one with CombinedGraph.filter().

The h and h_ref stats show the following:

In [63]: h_ref.stats()
Out[63]:
{'G_degree': 14.352941176470589,
'G_degree_in': 7.1764705882352944,
'G_degree_in_max': 203,
'G_degree_in_min': 1,
'G_degree_in_nobulk': 6.2118226601,
'G_degree_in_nobulk_max': 23,
'G_degree_in_nobulk_min': 1,
'G_degree_max': 406,
'G_degree_min': 2,
'G_degree_nobulk': 12.423645320197044,
'G_degree_nobulk_max': 44,
'G_degree_nobulk_min': 2,
'G_degree_out': 7.1764705882352944,
'G_degree_out_max': 203,
'G_degree_out_min': 1,
'G_degree_out_nobulk': 6.2118226601,
'G_degree_out_nobulk_max': 22,
'G_degree_out_nobulk_min': 1,
'G_edges': 1464,
'G_edges_nobulk': 1261.0,
'G_internal': 0,
'G_isolated': 0,
'G_order': 204,
'G_order_nobulk': 203,
'site_N_equivalence_sites': 3,
'site_N_subsites': 3,
'site_lifetime_avg': 16.3956265762,
'site_lifetime_max': 520.0,
'site_lifetime_med': 10.9756097561,
'site_lifetime_min': 9.88235294118,
'site_lifetime_std': 36.3143549497,
'site_occupancy_kin_avg': 0.288865545357,
'site_occupancy_kin_max': 3.81550801001,
'site_occupancy_kin_med': 0.171122994142,
'site_occupancy_kin_min': 0.045454545319,
'site_occupancy_kin_std': 0.400538382202,
'site_occupancy_rho_avg': 0.295487473986,
'site_occupancy_rho_med': 0.177807486631,
'site_occupancy_rho_std': 0.408680025598,
'site_volume_avg': 4.65500820728,
'site_volume_med': 2.0}

In [64]: h.stats()
Out[64]:
{'G_degree': 14.617647058823529,
'G_degree_in': 7.3088235294117645,
'G_degree_in_max': 203,
'G_degree_in_min': 1,
'G_degree_in_nobulk': 6.34482758621,
'G_degree_in_nobulk_max': 23,
'G_degree_in_nobulk_min': 1,
'G_degree_max': 406,
'G_degree_min': 2,
'G_degree_nobulk': 12.689655172413794,
'G_degree_nobulk_max': 46,
'G_degree_nobulk_min': 2,
'G_degree_out': 7.3088235294117645,
'G_degree_out_max': 203,
'G_degree_out_min': 1,
'G_degree_out_nobulk': 6.34482758621,
'G_degree_out_nobulk_max': 23,
'G_degree_out_nobulk_min': 1,
'G_edges': 1491,
'G_edges_nobulk': 1288.0,
'G_internal': 0,
'G_isolated': 0,
'G_order': 204,
'G_order_nobulk': 203,
'site_N_equivalence_sites': 203,
'site_N_subsites': 203,
'site_lifetime_avg': 16.5140403744,
'site_lifetime_max': 520.0,
'site_lifetime_med': 11.0880829016,
'site_lifetime_min': 9.87951807229,
'site_lifetime_std': 36.5261078654,
'site_occupancy_kin_avg': 0.304829297582,
'site_occupancy_kin_max': 3.98997325014,
'site_occupancy_kin_med': 0.179812833689,
'site_occupancy_kin_min': 0.0548128340612,
'site_occupancy_kin_std': 0.42739504416,
'site_occupancy_rho_avg': 0.295487473986,
'site_occupancy_rho_med': 0.177807486631,
'site_occupancy_rho_std': 0.408680025598,
'site_volume_avg': 4.65500820728,
'site_volume_med': 2.0}

I ran the tests https://github.com/Becksteinlab/hop/wiki/Testing (see also #11) but no transitions are detected, even though earlier versions showed them.

(hop) yngvi:TESTING oliver$ ./HOP_TESTRUN.sh
MDAnalysis  : INFO     MDAnalysis 0.18.0 STARTED logging to 'MDAnalysis.log'
Histogramming bulk=3036 solvent=3444  atoms in frame   500/500  [100.0%]
/Users/oliver/anaconda3/envs/hop/lib/python2.7/site-packages/numpy/core/fromnumeric.py:2909: RuntimeWarning: Mean of empty slice.
  out=out, **kwargs)
/Users/oliver/anaconda3/envs/hop/lib/python2.7/site-packages/numpy/core/_methods.py:80: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
MDAnalysis  : INFO     MDAnalysis STOPPED logging
MDAnalysis  : INFO     MDAnalysis 0.18.0 STARTED logging to 'MDAnalysis.log'
MDAnalysis.app: INFO     Generating hopping trajectory for density 'analysis/water.pickle'
Mapping frame   500/   500  [100.0%]
MDAnalysis.analysis.hop.trajectory: INFO     HoppingTrajectory.write(): wrote hoptraj 'analysis/hoptraj.dcd'.
MDAnalysis.analysis.hop.trajectory: INFO     HoppingTrajectory.write(): wrote hoppsf 'analysis/hoptraj.psf'.
MDAnalysis.app: INFO     Created hopping trajectory analysis/hoptraj.dcd with analysis/hoptraj.psf
MDAnalysis  : INFO     MDAnalysis STOPPED logging
MDAnalysis  : INFO     MDAnalysis 0.18.0 STARTED logging to 'MDAnalysis.log'
MDAnalysis.app: INFO     Generating hopping graph from trajectory '/Volumes/Data/oliver/Biop/Projects/Bogdan/TESTING/analysis/hoptraj.psf'/'/Volumes/Data/oliver/Biop/Projects/Bogdan/TESTING/analysis/hoptraj.dcd' ...
Analyzing hops: frame   500/500  [100.0%]
MDAnalysis.analysis.hop.graph: INFO     Building hopping graph with rate constants k1, k2 or k.
MDAnalysis.analysis.hop.graph: INFO     (Ignore 'Warning: ... maxfev = 800': then a single k is chosen automatically.)
MDAnalysis.app: INFO     Saved hopgraph as analysis/hopgraph.pickle
No handlers could be found for logger "hop.interactive"
/Users/oliver/anaconda3/envs/hop/lib/python2.7/site-packages/hop/graph.py:924: MissingDataWarning: Filtered graph contains no transitions: no plots available
  warnings.warn(msg, category=MissingDataWarning)
MDAnalysis.analysis.hop.graph: WARNING  Filtered graph contains no transitions: no plots available
MDAnalysis.app: INFO     Created hopping graph analysis/hopgraph.pickle and other files
MDAnalysis  : INFO     MDAnalysis STOPPED logging

@iwelland , is the g_flux like tool part of your PR #20? It would be good to have this available because people (occasionally) ask for an update of g_flux such as orbeckst/g_count#6.

In density.py, lines 149-155 assume that the MD trajectory will have the properties mentioned in the subject. My local version just has try/except clauses added to get around this since all that code is doing is determining metadata that as far as I can tell is not used for the Hop process.

Installing the package directly from the tar ball should work but doesn't:

easy_install Hop-0.3.0.tar.gz 

Gives the error message
Processing Hop-0.3.0.tar.gz
Running Hop-0.3.0/setup.py -q bdist_egg --dist-dir /var/folders/ja/jaE1z6Zo2RaPfE+F75CkvU+++TM/-Tmp-/easy_install-2eLMhS/Hop-0.3.0/egg-dist-tmp-ED49ho
The required version of setuptools (>=0.6c11) is not available, and can't be installed
while this script is running. Please install a more recent version first, using
'easy_install -U setuptools'.
(Currently using setuptools 0.6c9 (/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python))
error: Setup script exited with 2

The same error appears even after upgrading setuptools.

The new MDAnalysis release 0.11.0 breaks parts of the API and it is likely that hop needs to be migrated and pinned to MDAnalysis >= 0.11.0.