choderalab / torsionfit Goto Github PK

Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.

License: MIT License

Python 18.54% Batchfile 0.01% Shell 0.11% Rich Text Format 81.35%

bayesian-inference nsf-grant-che-1738979 forcefield torsions force-field forcefield-parameterization uncertainty-quantification

torsionfit's Introduction

Torsionfit

A toolkit for Bayesian torsion parameterization for molecular mechanics forcefields.

License

This software is licences under the MIT Licence, a permissive open source license.

Warning

Please beware that this code is currently experimental and under active development. If you are using this code, be aware that it is not guaranteed to provide the correct results, the documentation and testing is incomplete and the API can change without notice.

Installation

torsionfit will eventually be made conda installable. To install:

python setup.py install

dependencies are listed here

Manifest

torsionfit/ - Package containing code for Bayesian torsion fitting
devtools/ - Continuous integration and package utilities

Examples and data for using torsionfit are in torsionfit_examples

Authors

Chaya D. Stern <[email protected]>
John D. Chodera <[email protected]>

torsionfit's People

Contributors

Stargazers

Watchers

Forkers

chayast jchodera hainm somous-jhzhao layeqa

torsionfit's Issues

Celery example config file

Hello,

I see references to using celery for job submission, would it be possible to see an example of the config file in documentation (under examples). ? Thanks!

Brandon Walker

pymc installation

When pymc 2.3.4 is installed with setup.py

ImportError                               Traceback (most recent call last)
<ipython-input-1-5f262cfcb99b> in <module>()
----> 1 import pymc

/Users/sternc1/anaconda/lib/python2.7/site-packages/pymc-2.3.4-py2.7-macosx-10.9-x86_64.egg/pymc/__init__.pyc in <module>()
     28 from .PyMCObjects import *
     29 from .InstantiationDecorators import *
---> 30 from .CommonDeterministics import *
     31 from .NumpyDeterministics import *
     32 from .distributions import *

/Users/sternc1/anaconda/lib/python2.7/site-packages/pymc-2.3.4-py2.7-macosx-10.9-x86_64.egg/pymc/CommonDeterministics.py in <module>()
     19 import inspect
     20 import types
---> 21 from .utils import safe_len, stukel_logit, stukel_invlogit, logit, invlogit, value, find_element
     22 from copy import copy
     23 import sys

/Users/sternc1/anaconda/lib/python2.7/site-packages/pymc-2.3.4-py2.7-macosx-10.9-x86_64.egg/pymc/utils.py in <module>()
     12 from copy import copy
     13 from .PyMCObjects import Variable
---> 14 from . import flib
     15 import pdb
     16 from numpy.linalg.linalg import LinAlgError

ImportError: dlopen(/Users/sternc1/anaconda/lib/python2.7/site-packages/pymc-2.3.4-py2.7-macosx-10.9-x86_64.egg/pymc/flib.so, 2): Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1/libgfortran.3.dylib
  Referenced from: /Users/sternc1/anaconda/lib/python2.7/site-packages/pymc-2.3.4-py2.7-macosx-10.9-x86_64.egg/pymc/flib.so
  Reason: image not found

When pymc is installed with conda conda install pymc=2.3.4 everything works.
This seems to be a pymc issue thought.

I can start working on parallelizing sampling over fragments, but I'm not sure how much that will speed things up.

travis error

I can reproduce this failure on my machine:

======================================================================
ERROR: Failure: ValueError (zero-size array to reduction operation minimum which has no identity)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/torsionfit/tests/test_torsionFitModel.py", line 30, in <module>
    model = TorsionFitModel(param, stream, frag, platform=platform)
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/torsionfit/TorsionFitModel.py", line 101, in __init__
    def mm_energy(pymc_parameters=self.pymc_parameters, param=param):
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/pymc/InstantiationDecorators.py", line 250, in deterministic
    return instantiate_n(__func__)
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/pymc/InstantiationDecorators.py", line 243, in instantiate_n
    return Deterministic(parents=parents, **kwds)
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/pymc/PyMCObjects.py", line 442, in __init__
    verbose=verbose)
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/pymc/Node.py", line 219, in __init__
    Node.__init__(self, doc, name, parents, cache_depth, verbose=verbose)
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/pymc/Node.py", line 129, in __init__
    self.parents = parents
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/pymc/Node.py", line 152, in _set_parents
    self.gen_lazy_function()
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/pymc/PyMCObjects.py", line 453, in gen_lazy_function
    self._value.force_compute()
  File "LazyFunction.pyx", line 257, in pymc.LazyFunction.LazyFunction.force_compute (pymc/LazyFunction.c:2409)
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/torsionfit/TorsionFitModel.py", line 106, in mm_energy
    platform=self.platform)
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/torsionfit/TorsionScanSet.py", line 252, in compute_energy
    self.mm_energy -= self.mm_energy.min() + Quantity(value=float(offset.value), unit=kilojoules_per_mole)
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/simtk/unit/quantity.py", line 560, in min
    mymin = self._value.min(*args, **kwargs)
  File "/Users/choderaj/miniconda/envs/_test/lib/python2.7/site-packages/numpy/core/_methods.py", line 29, in _amin
    return umr_minimum(a, axis, None, out, keepdims)
ValueError: zero-size array to reduction operation minimum which has no identity

----------------------------------------------------------------------

Move to open-forcefield-group org?

It might be good to start to migrate this toolkit to the open-forcefield-group org.

I can transfer the repository once we're ready to do so, and the old URL will still redirect there.

Problems creating table

After changing tables.parameters.MAX_COLUMNS I stop getting the warning but still get this error

Traceback (most recent call last):
  File "example.py", line 33, in <module>
    sampler.sample(iter=10000)
  File "/home/chayas/anaconda/lib/python2.7/site-packages/pymc/MCMC.py", line 277, in sample
    Sampler.sample(self, iter, length, verbose)
  File "/home/chayas/anaconda/lib/python2.7/site-packages/pymc/Model.py", line 243, in sample
    self.db._initialize(self._funs_to_tally, length)
  File "/home/chayas/anaconda/lib/python2.7/site-packages/pymc/database/hdf5.py", line 444, in _initialize
    expectedrows=length)
  File "/home/chayas/anaconda/lib/python2.7/site-packages/tables/file.py", line 1067, in create_table
    chunkshape=chunkshape, byteorder=byteorder)
  File "/home/chayas/anaconda/lib/python2.7/site-packages/tables/table.py", line 867, in __init__
    byteorder, _log)
  File "/home/chayas/anaconda/lib/python2.7/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/chayas/anaconda/lib/python2.7/site-packages/tables/node.py", line 269, in __init__
    self._v_objectid = self._g_create()
  File "/home/chayas/anaconda/lib/python2.7/site-packages/tables/table.py", line 1019, in _g_create
    self._v_new_title, self.filters.complib or '', obversion)
  File "tableextension.pyx", line 212, in tables.tableextension.Table._create_table (tables/tableextension.c:3079)
tables.exceptions.HDF5ExtError: Problems creating the table
Closing remaining open files:fragments.db.hdf5...done