New Method visualize.contacts and extensive testing#47

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gph82 wants to merge 75 commits intomasterfrom

allow_input_feats

Commits on May 3, 2018

Commits on May 6, 2018

[generate.projection_paths] think about not returning the data
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[_bmutils] New class corr_dict, uniform kmeans init, avoid geom.join in save_traj
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changes for the paper figures, to be reverted later
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Commits on May 8, 2018

[bmutils] new method get_repr_atom_for_residue
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[visualize] fix hacky color handling
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[_bmutils] new method atom_idxs_from_general_input
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Commits on May 15, 2018

[visualize] prepering traj() to allow for input feature
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Commits on May 18, 2018

Commits on May 19, 2018

Commits on May 22, 2018

[visualize] bugfix

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[bmtuils] new methods regspace_cluster_to_target_kmeans, interval_schachtelung, regspace_from_distance_matrix

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[generate] adapt to new method regspace_cluster_to_target_kmeans

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[generate.projection_paths] think about not returning the data

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gph82
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[_bmutils] New class corr_dict, uniform kmeans init, avoid geom.join in save_traj

gph82
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gph82
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changes for the paper figures, to be reverted later

gph82
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gph82
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[bmutils] new method get_repr_atom_for_residue
gph82
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[visualize] fix hacky color handling
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[_bmutils] new method atom_idxs_from_general_input
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[visualize] prepering traj() to allow for input feature
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[visualize] new method contacts() and optarg verbose for FES()

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[_bmutils] refactor interval_schachtelung() and elimiante unused optarg in get_repr_atom_for_residue()

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[_linkutils] new class ContactInNGLWidget; link_ax_w_pos_2_nglwidget handles "_CtcsInWid"; ClickOnAxisListener handles ContactInNGLWidgets, recomputes kdtree on zooming

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[_bmutils] regspace_cluster_to_target_kmeans catches non-list inputs and listyfies

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[visualize] feature() accepts only MDFeaturizer (corrected docstring) and slice(idxs) for lists

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[test_molPX] reduced nr input features s.t. TICA does not return rubbish with so few frames

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[test_bmutils] refactor to regspace_cluster_to_target_kmeans

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[test_visualize] update to visualize.feature() taking only MDFeaturizer

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[_bmutils] get_index_ascending_coord check for len(idxs) instead of idxs==[]
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[test_visualize] minor refactor
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[test_bmutils] increase use the TestWithBPTIData class, add new tests
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[_bmutils] atom_idxs_from_feature() refactor doc
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[test_bmutils] refactored TestAtomIndices to TestIndexGeneralInput
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[_bmutils] deprecated regspace_cluster_to_target (was not in the API)
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[_bmutils] save_traj_wrapper() avoids using join() (faster)
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[test_bmutils] finish adapting to TestWithBPTIData and copying trajs (instead of joining)
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[visualize] minor refactor
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[test_bmutils] refactored test_colors into test_bmutils
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[tests] increased coverage
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[_bmtutils] add_atom_idxs_widget raises Exception for more than 4 atoms
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[tests] increased coverage
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Merge branch 'allow_input_feats' of https://github.com/markovmodel/molPX into allow_input_feats
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[visualize] merge-conflict deleted lazy import of pyplot, now it's back to lazy
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[notebooks] updated notebooks to new code
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Commits on May 23, 2018

Commits on May 25, 2018

[_bmutills] interval_schachtelung new optarg maxiter to avoid infinite loops
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[tests] remove useless import
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[docs] documented visualize.contacts()
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[tests] added the duration flag
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Commits on May 28, 2018

[notebooks] updated and included visualize.MSM method
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[visualize] new method MSM
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[visualize] MSM minor bugifx
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Commits on May 30, 2018

[_linkutils] minor in docstring
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[visualize] sample() makes a copy of input (otherwise it gets altered) and MSM() refactor and documented
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[docs] updated
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[tests] visualize.MSM() extensively tested
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[notebooks] updated
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Commits on May 31, 2018

[notebooks] opsin data
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