Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
75 commits
Select commit Hold shift + click to select a range
320e36f
[visualize] bugfix
May 3, 2018
c06c791
[bmtuils] new methods regspace_cluster_to_target_kmeans, interval_sch…
May 3, 2018
973d938
[generate] adapt to new method regspace_cluster_to_target_kmeans
May 3, 2018
f805b1e
[generate.projection_paths] think about not returning the data
May 6, 2018
5275d79
[_bmutils] New class corr_dict, uniform kmeans init, avoid geom.join …
May 6, 2018
5d0f1e7
changes for the paper figures, to be reverted later
May 6, 2018
f61759c
[bmutils] new method get_repr_atom_for_residue
May 8, 2018
4f7dca0
[visualize] fix hacky color handling
May 8, 2018
c0dc480
[_bmutils] new method atom_idxs_from_general_input
May 8, 2018
69acc71
[visualize] prepering traj() to allow for input feature
May 15, 2018
f308e37
[visualize] new method contacts() and optarg verbose for FES()
May 18, 2018
d16a90c
[_bmutils] refactor interval_schachtelung() and elimiante unused opta…
May 18, 2018
f5da7b8
[_linkutils] new class ContactInNGLWidget; link_ax_w_pos_2_nglwidget …
May 18, 2018
c1ac4e8
[_bmutils] regspace_cluster_to_target_kmeans catches non-list inputs …
May 18, 2018
248ae82
[visualize] feature() accepts only MDFeaturizer (corrected docstring)…
May 18, 2018
99f2617
[test_molPX] reduced nr input features s.t. TICA does not return rubb…
May 18, 2018
f0b2825
[test_bmutils] refactor to regspace_cluster_to_target_kmeans
May 18, 2018
6e7bfe1
[test_visualize] update to visualize.feature() taking only MDFeaturizer
May 18, 2018
f8f329f
[_bmutils] get_index_ascending_coord check for len(idxs) instead of i…
May 19, 2018
030930e
[test_visualize] minor refactor
May 19, 2018
19615ab
[test_bmutils] increase use the TestWithBPTIData class, add new tests
May 19, 2018
10f6e94
[visualize] bugfix
May 3, 2018
4c934b4
[bmtuils] new methods regspace_cluster_to_target_kmeans, interval_sch…
May 3, 2018
f7421fb
[generate] adapt to new method regspace_cluster_to_target_kmeans
May 3, 2018
6c2f99a
[generate.projection_paths] think about not returning the data
May 6, 2018
7343dfa
[_bmutils] New class corr_dict, uniform kmeans init, avoid geom.join …
May 6, 2018
a2b2b7f
changes for the paper figures, to be reverted later
May 6, 2018
4bcc967
[bmutils] new method get_repr_atom_for_residue
May 8, 2018
608339c
[visualize] fix hacky color handling
May 8, 2018
f9d4198
[_bmutils] new method atom_idxs_from_general_input
May 8, 2018
747fe02
[visualize] prepering traj() to allow for input feature
May 15, 2018
6548fcb
[visualize] new method contacts() and optarg verbose for FES()
May 18, 2018
6ba821f
[_bmutils] refactor interval_schachtelung() and elimiante unused opta…
May 18, 2018
3c4845d
[_linkutils] new class ContactInNGLWidget; link_ax_w_pos_2_nglwidget …
May 18, 2018
ab9b403
[_bmutils] regspace_cluster_to_target_kmeans catches non-list inputs …
May 18, 2018
043bef7
[visualize] feature() accepts only MDFeaturizer (corrected docstring)…
May 18, 2018
822924f
[test_molPX] reduced nr input features s.t. TICA does not return rubb…
May 18, 2018
e744038
[test_bmutils] refactor to regspace_cluster_to_target_kmeans
May 18, 2018
a9f3d5f
[test_visualize] update to visualize.feature() taking only MDFeaturizer
May 18, 2018
2f99f57
[_bmutils] get_index_ascending_coord check for len(idxs) instead of i…
May 19, 2018
d0cac78
[test_visualize] minor refactor
May 19, 2018
7f57248
[test_bmutils] increase use the TestWithBPTIData class, add new tests
May 19, 2018
c0a978b
[_bmutils] atom_idxs_from_feature() refactor doc
May 19, 2018
813ef1c
[test_bmutils] refactored TestAtomIndices to TestIndexGeneralInput
May 19, 2018
04b60ff
[_bmutils] deprecated regspace_cluster_to_target (was not in the API)
May 19, 2018
27b9f2f
[_bmutils] save_traj_wrapper() avoids using join() (faster)
May 19, 2018
5ad7257
[test_bmutils] finish adapting to TestWithBPTIData and copying trajs …
May 19, 2018
b3628ad
[visualize] minor refactor
May 20, 2018
2210279
[test_bmutils] refactored test_colors into test_bmutils
May 20, 2018
49281cf
[tests] increased coverage
May 20, 2018
0694384
[_bmtutils] add_atom_idxs_widget raises Exception for more than 4 atoms
May 22, 2018
d2e8663
[tests] increased coverage
May 22, 2018
7faddb4
Merge branch 'allow_input_feats' of https://github.com/markovmodel/mo…
May 22, 2018
22abf4b
[visualize] merge-conflict deleted lazy import of pyplot, now it's ba…
May 22, 2018
cc4ebcd
[notebooks] updated notebooks to new code
May 22, 2018
e6cfbbc
[visualize] contacts() avoid using itertools for index generation, ad…
May 23, 2018
b4b681b
[_linkutils] ContactInNGLWidget refactor
May 23, 2018
c6a233e
[tests] increase coverage
May 23, 2018
2cfebfc
Merge branch 'master' into allow_input_feats
May 23, 2018
432f3ad
[meta.yml] add nose to the reqs
May 23, 2018
197e09b
[test_visualize] remove the evil Agg backend
May 23, 2018
6e78d0c
agg f
marscher May 23, 2018
f27c596
[_bmutills] interval_schachtelung new optarg maxiter to avoid infinit…
May 25, 2018
ff3aaf5
[tests] remove useless import
May 25, 2018
1e16f06
[docs] documented visualize.contacts()
May 25, 2018
3855e37
[tests] added the duration flag
May 25, 2018
bb01921
[notebooks] updated and included visualize.MSM method
May 28, 2018
0864fc5
[visualize] new method MSM
May 28, 2018
af6a9d8
[visualize] MSM minor bugifx
May 28, 2018
fa8d2ed
[_linkutils] minor in docstring
May 30, 2018
876e5cc
[visualize] sample() makes a copy of input (otherwise it gets altered…
May 30, 2018
df93fbc
[docs] updated
May 30, 2018
843f827
[tests] visualize.MSM() extensively tested
May 30, 2018
56ba6b9
[notebooks] updated
May 30, 2018
7f30a3a
[notebooks] opsin data
May 31, 2018
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion devtools/conda-recipe/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -27,10 +27,11 @@ test:
requires:
- pytest-cov
- nbval
- nose >= 1
imports:
- molpx
commands:
- pytest -vv --pyargs molpx --cov=molpx --cov-report=xml --current-env --nbval-lax
- pytest -vv --pyargs molpx --cov=molpx --cov-report=xml --current-env --nbval-lax --duration=10
- cp coverage.xml /tmp # [linux]

about:
Expand Down
7 changes: 5 additions & 2 deletions doc/source/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -49,14 +49,17 @@ def __getattribute__(self, item):
'pyemma.coordinates.data.featurization.distances',
'nglview',
'matplotlib',
'matplotlib.pyplot',
'matplotlib.widgets',
'matplotlib.figure',
'matplotlib.axes',
'matplotlib.cm',
'matplotlib.patches',
'matplotlib.colors',
'IPython.display',
'sklearn.mixture',
'scipy.spatial',
'scipy.spatial.distance',
'six.moves.urllib.request',
'numpy',
# fixme: can not mock ipywidgets because of multi-inheritance within molpx
Expand Down Expand Up @@ -392,7 +395,7 @@ def __getattribute__(self, item):
intersphinx_mapping = {'pyemma': ('http://www.emma-project.org/latest/', None),
'matplotlib': ('http://matplotlib.org/', None),
'mdtraj': ('http://mdtraj.org/latest/', None),
#'pylab' : ('http://matplotlib.org/api/', None),
'pyplot' : ('http://matplotlib.org/api/', None),
'nglview' : ('http://arose.github.io/nglview/latest/', None)
}

Expand All @@ -408,7 +411,7 @@ def __getattribute__(self, item):
nbfiles = [
'0.molPX_quick_intro_Ala2.ipynb',
'1.molPX_and_PyEMMA_Features.ipynb',
'2.molPX_TICA_BPTI.ipynb',
'2.molPX_TICA_and_MSMs_BPTI.ipynb',
'3.molPX_TICA_Ala2.ipynb',
'4.molPX_metadynamics_Di-Ala.ipynb'
]
Expand Down
3 changes: 2 additions & 1 deletion doc/source/index_visualize.rst
Original file line number Diff line number Diff line change
Expand Up @@ -20,9 +20,10 @@ The methods offered by this module are:
.. autosummary::

molpx.visualize.FES
molpx.visualize.sample
molpx.visualize.traj
molpx.visualize.sample
molpx.visualize.correlations
molpx.visualize.MSM
molpx.visualize.feature

.. automodule:: molpx.visualize
Expand Down
Loading