becksteinlab / propkatraj

pKa estimates for proteins using an ensemble approach

README: propkatraj

propkatraj.py can be used to computationally estimate pKa values for protein residues. We use an ensemble approach where many different conformations are sampled with equilibrium molecular dynamics simulations. We then apply the fast heuristic pKa predictor PROPKA 3 to individual frames of the trajectory. By analysing the statistics of the pKa predictions a more consistent picture emerges than from a pKa prediction of a single static conformation.

Required software

• PROPKA 3 (used as a Python package)
• MDAnalysis
• pandas

See INSTALL.md for how to install everything.

Usage

The propkatraj.PropkaTraj class contains all functionality. Import it with

from propkatraj import PropkaTraj

It takes a MDAnalysis.AtomGroup or MDAnalysis.Universe instance as an argument to initialize and runs PROPKA on each frame of the trajectory when calling the run() method. See help(PropkaTraj) for more details.

pkatraj = PropkaTraj(atomgroup, select='protein', skip_failure=False)

   Runs :program:`propka` on the titrateable residues of the selected AtomGroup
   on each frame in the trajectory.
   
   Parameters
   ----------
   atomgroup : :class:`MDAnalysis.Universe` or :class:`MDAnalysis.AtomGroup`
       Group of atoms containing the residues for pKa analysis. Please note
       that :class:`MDAnalysis.UpdatingAtomGroup` are not supported and will
       be automatically converted to :class:`MDAnalysis.AtomGroup`.
   select : str
       Selection string to use for selecting a subsection of atoms to use
       from the input ``atomgroup``. Note: passing non-protein residues to
       :program:`propka` may lead to incorrect results (see notes). [`protein`]
   skip_failure : bool
       If set to ``True``, skip frames where :program:`propka` fails. A list
       of failed frames is made available in
       :attr:`PropkaTraj.failed_frames_log`. If ``False`` raise a
       RuntimeError exception on those frames. [`False`]


    Notes
    -----
    Currently only the default behaviour supplemented with the `--quiet` flag
    of :program:`propka` is used.

    Temporary :program:`propka` files are written in the current working
    directory. This will leave a ``current.pka`` and ``current.propka_input``
    file. These are the temporary files for the final frame and can be removed
    safely.

    Current known issues:

    1. Due to the current behaviour of the MDAnalysis PDBWriter, non-protein
       atoms are written to PDBs using `ATOM` records instead of `HETATM`.
       This is likely to lead to undefined behaviour in :program:`propka`,
       which will likely expect `HETATM` inputs. We recommend users to only
       pass protein atoms for now. See the following issue for more details:
       https://github.com/Becksteinlab/propkatraj/issues/24


pkatraj.run()

   Perform the calculation

   Parameters
   ----------
   start : int, optional
      start frame of analysis
   stop : int, optional
      stop frame of analysis
   step : int, optional
      number of frames to skip between each analysed frame
   verbose : bool, optional
      Turn on verbosity

Calling the run() method creates a pandas.DataFrame, accessed through results.pkas, which contains the time as the first column and the residue numbers as subsequent columns. For each time step, the predicted pKa value for this residue is stored. Process the DataFrame to obtain statistics as shown in the Documentation. For example, you can get a summary of the statistics of the timeseries in the following manner:

pkatraj.results.pkas.describe()

Documentation

See the Jupyter notebook docs/propkatraj-example.ipynb for how to use propkatraj.PropkaTraj on an example trajectory and how to plot the data with seaborn.

Citation

If you use propkatraj in published work please cite Reference 1 for PROPKA 3.1 and Reference 2 for the ensemble method itself. Reference 3 is for the software if you need a specific software citation.

1. C. R. Søndergaard, M. H. M. Olsson, M. Rostkowski, and J. H. Jensen. Improved treatment of ligands and coupling effects in empirical calculation and rationalization of pKa values. J Chemical Theory and Computation, 7(7):2284–2295, 2011. doi: 10.1021/ct200133y.

2. C. Lee, S. Yashiro, D. L. Dotson, P. Uzdavinys, S. Iwata, M. S. P. Sansom, C. von Ballmoos, O. Beckstein, D. Drew, and A. D. Cameron. Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights. J Gen Physiol, 144(6):529–544, 2014. doi: 10.1085/jgp.201411219.

3. David Dotson, Irfan Alibay, Rick Sexton, Shujie Fan, Armin Zijajo, Oliver Beckstein. (2020). Becksteinlab/propkatraj: 1.1.x. Zenodo. https://doi.org/10.5281/zenodo.3228425

Contact

Please raise issues in the issue tracker.

propkatraj's Issues

doc notebook does not display in nbviewer

When looking at the notebook through nbviewer https://nbviewer.jupyter.org/github/Becksteinlab/propkatraj/blob/master/docs/propkatraj-example.ipynb I get

400 : Bad Request

{'model_id': '34dd1b2989df48a98da0566d926d6a68', 'version_major': 2, 'version_minor': 0} is not valid under any of the given schemas Failed validating 'oneOf' in display_data['properties']['data']['patternProperties']['^(?!application/json$)[a-zA-Z0-9]+/[a-zA-Z0-9\\-\\+\\.]+$']: On instance['cells'][13]['outputs'][0]['data']['application/vnd.jupyter.widget-view+json']: {'model_id': '34dd1b2989df48a98da0566d926d6a68', 'version_major': 2, 'version_minor': 0}

Not sure why this is happening.

ProgressMeter removal in MDAnalysis 2.0

As the progressmeter has now been replaced by the progressbar, the following will fail from 2.0 onwards:

propkatraj/propkatraj/propkatraj.py

Line 61 in 2abd91f

pm = mda.lib.log.ProgressMeter(universe.trajectory.n_frames,

I would be interested in attempting to refactor the code to use AnalysisBase instead if there is any interest in doing so.

add zenodo badge

I enabled zenodo but need to make a pre-release to trigger the first DOI minting and get a URL for the badge.

pip installation

The package is pip installable and is published on PyPi https://pypi.python.org/pypi/propkatraj . However, PROPKA is not pip-installable yet (see jensengroup/propka#16 ).

Once jensengroup/propka#16 is solved, add a note to INSTALL.md that one can simply

pip install propkatraj

2.0.0 release

With #36, the get_propka function is removed. Per the deprecation warning, this means a release of 2.0.0 is needed.

Release checklist

• addressed all issues for 2.0.0 milestone
• updated release (PR #50 )
• tagged as 2.0.0
• tested package
• created new release on GitHub
• upload to test.pypi.org (create package on test.pypi.org first, add @IAlibay and @orbeckst as admins)
• test the test.pypi package
• upload pypi package

remove deprecated functionality

For a 2.0 release, remove deprecated stuff

• get_propka
• Python ≤ 3.5 (six, future etc can go)

Bump dependencies

• MDAnalysis ≥ 1.0
• propka ≥ 3.2
• Python ≥ 3.6 (in setup.py and remove jobs from Travis CI)

remove CRON CI codecov

See MDAnalysis/cookiecutter-mdakit#54

Solution: don't run codecov on CRON CI

Make python support 3.9+

Now that MDA has dropped 3.8, we should also move ahead with removing 3.8 support.

Python 3.9 CI failing due to MDAnalysis develop supporting different py than stable

related to this: MDAnalysis/cookiecutter-mdakit#110

See MDAnalysis/PathSimAnalysis#19 for how to fix.

Reformat for MDAnalysis 2.0

I've been neglecting propkatraj a little bit, I don't think it's compatible with MDAnalysis 2.0. - Needs investigating and fixing (probably post ACS)

Fix coveragerc to not try to cover things that we don't need to check

Our coverage is artificially low, we can fix coveragerc to exclude anything that isn't under (e.g. everything that isn't in propkatraj.py or propkatraj/tests.

We can also quickly add an nbval test (alongside the standard CI test action) to run the examples through - although that's not a coverage thing.

use CODECOV_TOKEN

We had some spurious codecov.io upload issues. Sometimes this can be improved by using a codecov token

• add CODECOV_TOKEN as secret to repository
• use CODECOV_TOKEN in the codecov step

get_propka will fail with file generated via `fetch_mmtf`

As the the "filename" for the PDB stream relies on universe.filename universes without filenames set, e.g. when using fetch_mmtf will cause get_propka to fail.

Code to reproduce behaviour:

import MDAnalysis as mda
import propkatraj

u = mda.fetch_mmtf('4LYI')

pkatraj = propkatraj.get_propka(u)

Note; this might not need fixing, in the AnalysisBase update I would like to switch to using os.path.curdir.

conda-forge package

It would be nice to be able to install from conda-forge.

uses writeout=False which is not in propka 3.1

propkatraj.get_propka(s, sel='protein')

fails with

Time (ps): 0.0

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-11-dc948db1b97b> in <module>()
----> 1 propkatraj.get_propka(s, sel='protein')

/nfs/homes/azjajo/Projects/Staph_Member/David/propkatraj.pyc in get_propka(sim, sel, start, stop, step)
     55         # we feed the stream to propka, and it reads it as if it were a file on
     56         # disk
---> 57         mol = pk.single(pstream, None, writeout=False)
     58         pstream.close(force=True)  # deallocate
     59 

TypeError: single() got an unexpected keyword argument 'writeout'

only use one "main" branch

There's not a ton of activity here so let's simplify and just do development on a main branch.

• merge dev into current master
• rename master -> main
• add main branch protection and required status checks
• update badges

Error running propkatraj as in tutorial

I am following the Jupyter notebook tutorial (docs/propkatraj-example.ipynb) and when I type
pkas = propkatraj.get_propka(u) I get the following error. I am not sure what the problem is. Many thanks

pkas = propkatraj.get_propka(u)
1/98 t= 1.000 ps [ 1.0%]/Users/nehade/anaconda3/lib/python3.5/site-packages/MDAnalysis/coordinates/PDB.py:892: UserWarning: Found no information for attr: 'altLocs' Using default value of ' '
"".format(attrname, default))
/Users/nehade/anaconda3/lib/python3.5/site-packages/MDAnalysis/coordinates/PDB.py:892: UserWarning: Found no information for attr: 'icodes' Using default value of ' '
"".format(attrname, default))
/Users/nehade/anaconda3/lib/python3.5/site-packages/MDAnalysis/coordinates/PDB.py:892: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0'
"".format(attrname, default))
/Users/nehade/anaconda3/lib/python3.5/site-packages/MDAnalysis/coordinates/PDB.py:892: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0'
"".format(attrname, default))

Traceback (most recent call last):
File "/Users/nehade/.local/lib/python3.5/site-packages/PROPKA-3.1-py3.5.egg/propka/lib.py", line 37, in open_file_for_reading
TypeError: invalid file: <NamedStream(<_io.StringIO object at 0x110245c18>, /Users/nehade/anaconda3/lib/python3.5/site-packages/MDAnalysisTests/data/current.pdb)>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "", line 1, in
File "/Users/nehade/.local/lib/python3.5/site-packages/propkatraj/propkatraj.py", line 82, in get_propka
mol = pk.single(pstream, optargs=['--quiet'])
File "/Users/nehade/.local/lib/python3.5/site-packages/PROPKA-3.1-py3.5.egg/propka/run.py", line 30, in single
File "/Users/nehade/.local/lib/python3.5/site-packages/PROPKA-3.1-py3.5.egg/propka/molecular_container.py", line 41, in init
File "/Users/nehade/.local/lib/python3.5/site-packages/PROPKA-3.1-py3.5.egg/propka/pdb.py", line 40, in read_pdb
printed but the debugger's state is not changed.
File "/Users/nehade/.local/lib/python3.5/site-packages/PROPKA-3.1-py3.5.egg/propka/pdb.py", line 91, in get_atom_lines_from_pdb
def find_function(funcname, filename):
File "/Users/nehade/.local/lib/python3.5/site-packages/PROPKA-3.1-py3.5.egg/propka/lib.py", line 39, in open_file_for_reading
OSError: Cannot find file /Users/nehade/anaconda3/lib/python3.5/site-packages/MDAnalysisTests/data/current.pdb

Get_propka docs reference MDS

Docs say function returns sim but actually is a DataFrame.

Be stricter on the protein residue check

Currently the code will throw a warning if it finds any non-protein atoms in the residue selection. However the "protein residue" definition in MDA is quite loose, my understanding is that propka only really accepts these:

https://github.com/jensengroup/propka/blob/831e7380689b05892645012766671e2df8a644d8/propka/lib.py#L20-L23

What would we think about making the check more stringent so that if it finds anything not in that dictionary it throws a warning to telling users to consider renaming residues to their standard value if necessary?

Comparison against standard propka call fails (HETATM issue)

This is an upstream issue, but probably should be documented whilst the MDA parser has this current behaviour.

Expected

Passing a PDB to propka or propkatraj should give the same predicted pkas

Actual outcome

When passing 4LYI (everyone's favourite BRD4 model), the results will differ significantly for GLU 151, 154, and 163.

The cause for this is that the MDA PDBWriter will output everything with ATOM records whilst the native PDB has HETATM entries for the small molecules/ions/solvent. This causes the difference in results seen here (manualy hand-editing the output of a MDA PDBWriter file for 4LYI makes things work again).

I'm not versed enough in the internal workings for propka 3.1+ to know why HETATM and ATOMS are handled differently, maybe @orbeckst has more insights here?

release 1.1

Last release to work with PROPKA 3.1 and Python 2.7.

Afterwards it will be >= PROPKA 3.2 and Python >= 3.6, see #20

Add powered by MDAnalysis badge

As per the title - mainly a reminder to add it in the next PR 🙃

add doc badge to README

Online docs were added #38 . We should have a standard badge on the README for people to easily find the docs.

AttributeError: module 'propkatraj' has no attribute 'get_propka'

Hi

I am having issues running propkatraj and I think it's related to my local propkatraj or Propka installation because the error I get is

AttributeError: module 'propkatraj' has no attribute 'get_propka'

(I get no error about the module not being found)

I have MDAnalysis 2.5 installed (on a MacOS 10.15) and that works fine. I have install propka and propkatraj using

pip install propka==3.1
pip install propkatraj

No error messages during the installation

I tried a very stripped-back test script (see attached) but I can't even call the function help(propkatraj.get_propka)

Any help would be much appreciated.

thanks from Australia
Evelyne

I came across this older issue
#18

I checked the lib.py in /Users/evelyne/opt/anaconda3/lib/python3.9/site-packages/propka/lib.py and as far as I can tell the required code for the function open_file_for_reading is there
pka_test.txt

remove MDSynthesis dependency

The propkatraj.py script uses MDSynthesis. Should we retain this dependency or make it more bare-bones?

@dotsdl , have you got an opinion?

Docs no longer deploy properly

Looks like the action was based on calling setup.py this needs to be changed to using sphinx-build or equivalent.

Fix license

Says GPLv3 in some places, says GPLv2 in others. Need to pick one and choose.

allow skipping of frames where PROPKA fails

If PROPKA fails for mysterious reasons then we want to have the option to move on and skip frames.

requirements

• keyword argument that allows ignoring failing frames (skip_failing = True)
• use try/except to skip
• log frames that fail
• log error message at end if any frames were skipped and summarize the percentage of skipped frames

design notes

Put a try/except around https://github.com/Becksteinlab/propkatraj/blob/master/propkatraj/propkatraj.py#L74 together with the logging.

• If skip_failing = False then raise the exception.
• If skip_failing = True then log error and continue

Something like

try:
        mol = pk.single(pstream, optargs=['--quiet'])
except IndexError as err:
        if not skip_failing:
            raise
        else:
            # log ...
            # continue the loop at the next frame, not sure if this
            # is working....
            continue
finally:
       pstream.close(force=True) # deallocate

(IndexError is the PROPKA error that @rsexton2 encounters.)

standard setuptools installation

It should be possible to install this script with its dependencies in a standard Pythonic manner.

Current dependencies

• numpy
• pandas
• MDAnalysis
• MDSynthesis
• PROPKA 3.1 — not on PyPi, no releases on GitHub.

api doc formatting of argument lists messed up

In https://becksteinlab.github.io/propkatraj/api.html , the argument name and type are not separated.

citing

add notes on citing

• 2014 JGP paper
• PROPKA 3.1 paper

Latest propka no compatible with MDA < 1.0: AttributeError: 'PropkaTraj' object has no attribute 'times'

I have recieved an error message when I run pkatraj.run(verbose=True, start=300, stop=500, step=20).

I have checked the trajectory and they are all fine. Not too sure what's going on..

AttributeError Traceback (most recent call last)
in
----> 1 pkatraj.run(verbose=True, start=300, stop=500, step=20)

~/.local/lib/python3.7/site-packages/MDAnalysis/analysis/base.py in run(self, start, stop, step, verbose)
198 self._pm.echo(self._frame_index)
199 logger.info("Finishing up")
--> 200 self._conclude()
201 return self
202

~/anaconda3/lib/python3.7/site-packages/propkatraj/propkatraj.py in _conclude(self)
226 logging.warning(wmsg)
227
--> 228 self.pkas = pd.DataFrame(self._pkas, index=pd.Float64Index(self.times,
229 name='time'), columns=self._columns)

Thank you so much for your help in advance.

Best wishes

Will

PROPKA failure 'None_type'

PROPKA fails with the following error:

1 rsexton@chipbacca:~/Projects/pKa_Prediction/propkatraj/propkatraj⟫ ipython wt_pkas.py %run
    1/100001 t=       0.000 ps  [  0.0%]/usr/local/lib/python2.7/dist-packages/MDAnalysis/coordinates/PDB.py:892: UserWarning: Found no information for attr: 'altLocs'
Using default value of ' '
  "".format(attrname, default))
/usr/local/lib/python2.7/dist-packages/MDAnalysis/coordinates/PDB.py:892: UserWarning: Found no information for attr: 'icodes' Using default value of ' '
  "".format(attrname, default))
/usr/local/lib/python2.7/dist-packages/MDAnalysis/coordinates/PDB.py:892: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0'
  "".format(attrname, default))
/usr/local/lib/python2.7/dist-packages/MDAnalysis/coordinates/PDB.py:892: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0'
  "".format(attrname, default))
 1415/100001 t=    1414.000 ps  [  1.4%]WARNING:root:/nfs/homes/rsexton/Projects/pKa_Prediction/wt/md/md_centered_nowater_nopbc.xtc (failure 0): failing frame 1414
 1587/100001 t=    1586.000 ps  [  1.6%]WARNING:root:/nfs/homes/rsexton/Projects/pKa_Prediction/wt/md/md_centered_nowater_nopbc.xtc (failure 1): failing frame 1586
 2157/100001 t=    2156.000 ps  [  2.2%]---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
/nfs/homes/rsexton/Projects/pKa_Prediction/propkatraj/propkatraj/wt_pkas.py in <module>()
      6
      7
----> 8 pkas = propkatraj.get_propka(u, sel='protein', step=1, skip_failure=True)
      9 pkas.to_csv('wt_pkas.csv')
     10
/nfs/homes/rsexton/Projects/pKa_Prediction/propkatraj/propkatraj/propkatraj.pyc in get_propka(universe, sel, start, stop, step, skip_failure)
     80         # disk
     81         try:
---> 82                mol = pk.single(pstream, optargs=['--quiet'])
     83         except IndexError as err:
     84                if not skip_failure:
/nfs/homes/rsexton/.local/lib/python2.7/site-packages/propka/run.pyc in single(pdbfile, optargs)
     29                                                                                                                                                       [280/2594]
     30     my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
---> 31     my_molecule.calculate_pka()
     32     my_molecule.write_pka()
     33     return my_molecule
/nfs/homes/rsexton/.local/lib/python2.7/site-packages/propka/molecular_container.pyc in calculate_pka(self)
    122         # calculate for each conformation
    123         for name in self.conformation_names:
--> 124             self.conformations[name].calculate_pka(self.version, self.options)
    125
    126         # find non-covalently coupled groups
/nfs/homes/rsexton/.local/lib/python2.7/site-packages/propka/conformation_container.pyc in calculate_pka(self, version, options)
    186
    187         # setting remaining non-iterative and iterative side-chain & Coulomb interaction determinants
--> 188         propka.determinants.setDeterminants(self.get_sidechain_groups(), version=version, options=options)
    189
    190         # calculating the total pKa values
/nfs/homes/rsexton/.local/lib/python2.7/site-packages/propka/determinants.pyc in setDeterminants(propka_groups, version, options)
     32                     propka.iterative.addtoDeterminantList(group1, group2, distance, iterative_interactions, version=version)
     33                 elif interaction_type == 'N':
---> 34                     addDeterminants(group1, group2, distance, version)
     35
     36
/nfs/homes/rsexton/.local/lib/python2.7/site-packages/propka/determinants.pyc in addDeterminants(group1, group2, distance, version)
     45
     46     # side-chain determinant
---> 47     addSidechainDeterminants(group1, group2, version)
     48
     49     # Coulomb determinant
/nfs/homes/rsexton/.local/lib/python2.7/site-packages/propka/determinants.pyc in addSidechainDeterminants(group1, group2, version)
     58     """
     59
---> 60     hbond_interaction = version.hydrogen_bond_interaction(group1, group2)
     61
     62     if hbond_interaction:
/nfs/homes/rsexton/.local/lib/python2.7/site-packages/propka/version.pyc in hydrogen_bond_interaction(self, group1, group2)
     24     # side chains                                                                                                                                     [238/2594]
     25     def hydrogen_bond_interaction(self, group1, group2):
---> 26         return self.hydrogen_bond_interaction_model(group1, group2, self)
     27
     28     def calculateSideChainEnergy(self, distance, dpka_max, cutoff, weight, f_angle):
/nfs/homes/rsexton/.local/lib/python2.7/site-packages/propka/calculations.pyc in hydrogen_bond_interaction(group1, group2, version)
    625     weight = version.calculatePairWeight(group1.Nmass, group2.Nmass)
    626
--> 627     exception, value = version.checkExceptions(group1, group2)
    628     #exception = False # circumventing exception
    629     if exception == True:
/nfs/homes/rsexton/.local/lib/python2.7/site-packages/propka/version.pyc in checkExceptions(self, group1, group2)
     45     # exceptions
     46     def checkExceptions(self, group1, group2):
---> 47         return self.exception_check_method(self, group1, group2)
     48
     49     def setup_bonding_and_protonation(self, molecular_container):
/nfs/homes/rsexton/.local/lib/python2.7/site-packages/propka/calculations.pyc in checkExceptions(version, group1, group2)
    751
    752     if   (resType1 == "COO" and resType2 == "ARG"):
--> 753         exception, value = checkCooArgException(group1, group2, version)
    754     elif (resType1 == "ARG" and resType2 == "COO"):
    755         exception, value = checkCooArgException(group2, group1, version)
/nfs/homes/rsexton/.local/lib/python2.7/site-packages/propka/calculations.pyc in checkCooArgException(group_coo, group_arg, version)
    798         # find the closest interaction pair
    799         [closest_coo_atom, distance, closest_arg_atom] = get_smallest_distance(atoms_coo, atoms_arg)
--> 800         [dpka_max, cutoff] = version.get_hydrogen_bond_parameters(closest_coo_atom,closest_arg_atom)
    801      # calculate and sum up interaction energy
    802         f_angle = 1.00
/nfs/homes/rsexton/.local/lib/python2.7/site-packages/propka/version.pyc in get_hydrogen_bond_parameters(self, atom1, atom2)
     88     def get_hydrogen_bond_parameters(self, atom1, atom2):
     89         dpka_max = self.parameters.sidechain_interaction
---> 90         cutoff   = self.parameters.sidechain_cutoffs.get_value(atom1.group_type, atom2.group_type)
     91         return [dpka_max, cutoff]
     92
AttributeError: 'NoneType' object has no attribute 'group_type'

The files used to produce the error are attached below.
error_traj_top.zip

The following two .pdb files were both produced by GROMACS. PROPKA works with one and not the other, where the only noticeable difference is one of the files contains Na and Cl ions.
pass_fail.zip

Review/update to work with propka >= 3.3.0

The new propka 3.2.0 release breaks the internal API in parts. To check

• run.single() still works
• getting the information from the molecular container still works
• increase minimum propka version in setup.py

Python 3 cannot deal with cStringIO

propkatraj/propkatraj/propkatraj.py

Line 74 in f9d2886

pstream = mda.lib.util.NamedStream(cStringIO.StringIO(), newname)

Use

from six import StringIO

(and delete the line import cStringIO)
and then

pstream = mda.lib.util.NamedStream(StringIO(), newname)

Also add "six" to

propkatraj/setup.py

Line 28 in f9d2886

install_requires=['numpy', 'pandas', 'MDAnalysis', 'propka']

as

install_requires=['numpy', 'pandas', 'six', 'MDAnalysis', 'propka'] 

Passing an index array fails

The current code should support passing an array index instead of a string selection.

However the following will cause a TypeError.

The reason for this is here:

propkatraj/propkatraj/propkatraj.py

Line 53 in 2abd91f

elif isinstance(sel, (list, np.array)):

The latter should be np.ndarray not np.array.

Suggestion: the fix is quite trivial so it's not an issue, but I would suggest relying on users passing atomgroups instead of universes, with the default selection string being None (if a selection string is even needed). That way the responsibility is on users to pass the right thing?

sphinx docs fail to build with `python setup.py build_sphinx`

The docs action fails:

$ python setup.py build_sphinx
error: invalid command 'build_sphinx'

See https://github.com/Becksteinlab/propkatraj/actions/runs/4964078889/jobs/8883897113

parallelize with pmda

Create a parallel version based on pmda.parallel.ParallelAnalysisBase.

(Thanks to @dotsdl for the suggestion.)

add AUTHORS file

AUTHORS to record contributors.

review current repo for 0.1.0 release

@dotsdl and @azjajo – please have a look at the repo and let me know if anything needs to be changed/added. (PRs or direct commits are welcome).

I tested the installation instructions in a virtual env and everything works with MDA 0.16.0 and current MDSynthesis as well as PROPKA 3.1. master.

If you are happy I cut a 0.1.0 release (and possibly add citation information).

Add propka 3.4 support

propkatraj currently pins propka to v3.1

add new pypi maintainers

invitation sent

• add @ianmkenney as maintainer for PyPi
• add @IAlibay as maintainer

invitation accepted

• @ianmkenney
• @IAlibay

Upgrade documentation

Upgrade documentation to Sphinx, hosted on GitHub pages.