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Merge f028f01 into fcc6a23
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@jhprinz
jhprinz committed Feb 25, 2016
2 parents fcc6a23 + f028f01 commit ed6582c
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Showing 47 changed files with 3,332 additions and 3,101 deletions.
252 changes: 129 additions & 123 deletions examples/ipython/alanine.ipynb
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48 changes: 28 additions & 20 deletions examples/ipython/mistis_analysis.ipynb
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40 changes: 20 additions & 20 deletions examples/ipython/mistis_setup.ipynb
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63 changes: 27 additions & 36 deletions examples/ipython/mstis.ipynb
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400 changes: 200 additions & 200 deletions examples/ipython/mstis_analysis.ipynb
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120 changes: 79 additions & 41 deletions examples/ipython/mstis_bootstrap.ipynb
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545 changes: 0 additions & 545 deletions examples/ipython/multistate_system_setup.ipynb
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364 changes: 268 additions & 96 deletions examples/ipython/test_cv.ipynb
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17 changes: 15 additions & 2 deletions examples/ipython/test_netcdfplus.ipynb
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Expand Up @@ -346,7 +346,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"['bool', 'float', 'index', 'int', 'json', 'jsonobj', u'lazyobj.dict', u'lazyobj.dictimmutable', u'lazyobj.nodes', u'lazyobj.nodesnamed', u'lazyobj.nodesunique', 'lazyobj.stores', u'lazyobj.varstore', 'length', 'long', 'numpy.float32', 'numpy.float64', 'numpy.int16', 'numpy.int32', 'numpy.int64', 'numpy.int8', 'numpy.uint16', 'numpy.uint32', 'numpy.uint64', 'numpy.uint8', u'obj.dict', u'obj.dictimmutable', u'obj.nodes', u'obj.nodesnamed', u'obj.nodesunique', 'obj.stores', u'obj.varstore', 'store', 'str']\n"
"['bool', 'float', 'index', 'int', 'json', 'jsonobj', 'lazyobj', u'lazyobj.dict', u'lazyobj.dictimmutable', u'lazyobj.nodes', u'lazyobj.nodesnamed', u'lazyobj.nodesunique', 'lazyobj.stores', u'lazyobj.varstore', 'length', 'long', 'numpy.float32', 'numpy.float64', 'numpy.int16', 'numpy.int32', 'numpy.int64', 'numpy.int8', 'numpy.uint16', 'numpy.uint32', 'numpy.uint64', 'numpy.uint8', 'obj', u'obj.dict', u'obj.dictimmutable', u'obj.nodes', u'obj.nodesnamed', u'obj.nodesunique', 'obj.stores', u'obj.varstore', 'store', 'str']\n"
]
}
],
Expand Down Expand Up @@ -423,6 +423,7 @@
"int (u'pair', u'pair', u'pair')\n",
"json (u'pair', u'pair', u'pair')\n",
"jsonobj (u'pair', u'pair', u'pair')\n",
"lazyobj (u'pair', u'pair', u'pair', u'pair')\n",
"lazyobj.dict (u'pair', u'pair', u'pair')\n",
"lazyobj.dictimmutable (u'pair', u'pair', u'pair')\n",
"lazyobj.nodes (u'pair', u'pair', u'pair')\n",
Expand All @@ -447,6 +448,7 @@
"numpy.uint32 (u'pair', u'pair', u'pair')\n",
"numpy.uint64 (u'pair', u'pair', u'pair')\n",
"numpy.uint8 (u'pair', u'pair', u'pair')\n",
"obj (u'pair', u'pair', u'pair', u'pair')\n",
"obj.dict (u'pair', u'pair', u'pair')\n",
"obj.dictimmutable (u'pair', u'pair', u'pair')\n",
"obj.nodes (u'pair', u'pair', u'pair')\n",
Expand Down Expand Up @@ -488,6 +490,7 @@
"int\n",
"json\n",
"jsonobj\n",
"lazyobj\n",
"lazyobj.dict\n",
"lazyobj.dictimmutable\n",
"lazyobj.nodes\n",
Expand All @@ -512,6 +515,7 @@
"numpy.uint32\n",
"numpy.uint64\n",
"numpy.uint8\n",
"obj\n",
"obj.dict\n",
"obj.dictimmutable\n",
"obj.nodes\n",
Expand Down Expand Up @@ -1926,6 +1930,15 @@
"else:\n",
" raise RuntimeWarning('This should have produced an error')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -1944,7 +1957,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.10"
"version": "2.7.11"
}
},
"nbformat": 4,
Expand Down
68 changes: 49 additions & 19 deletions examples/ipython/test_pyemma.ipynb
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Expand Up @@ -110,9 +110,17 @@
"metadata": {
"collapsed": false
},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"(store.cvs[CollectiveVariable], 6, 6)\n"
]
}
],
"source": [
"cv.save(storage)"
"print storage.save(cv)"
]
},
{
Expand Down Expand Up @@ -203,7 +211,7 @@
},
"outputs": [],
"source": [
"nc_var = storage.variables['snapshots_cv_%d_values' % storage.idx(py_cv)]"
"nc_var = storage.variables['snapshots_cv_%d_values_fw' % storage.idx(py_cv)]"
]
},
{
Expand Down Expand Up @@ -257,13 +265,13 @@
"name": "stdout",
"output_type": "stream",
"text": [
"[ u'{\"_cls\": \"CV_Function\", \"_dict\": {\"store_cache\": true, \"name\": \"psi2\", \"f\": {\"_marshal\": \"YwMAAAADAAAAAwAAAEMAAABzHAAAAHwBAHwAAIMBAGQBABN8AgB8AACDAQBkAQATF1MoAgAAAE5pAgAAACgAAAAAKAMAAAB0BAAAAGl0ZW10AwAAAHBzaXQDAAAAcGhpKAAAAAAoAAAAAHMeAAAAPGlweXRob24taW5wdXQtOS00NGFmZmMyZGY1MzU+dAcAAABwcDJfZm5jAQAAAHMCAAAAAAE=\", \"_module_vars\": [], \"_global_vars\": []}, \"scalarize_numpy_singletons\": false, \"wrap_numpy_array\": false, \"kwargs\": {\"phi\": {\"_obj\": \"cvs\", \"_idx\": 1}, \"psi\": {\"_obj\": \"cvs\", \"_idx\": 2}}, \"requires_lists\": false, \"time_reversible\": false}}'\n",
" u'{\"_cls\": \"CV_MDTraj_Function\", \"_dict\": {\"store_cache\": true, \"name\": \"phi\", \"f\": {\"_module\": \"mdtraj.geometry.dihedral\", \"_name\": \"compute_dihedrals\"}, \"scalarize_numpy_singletons\": true, \"wrap_numpy_array\": true, \"kwargs\": {\"indices\": [[4, 6, 8, 14]]}, \"requires_lists\": true, \"time_reversible\": true}}'\n",
" u'{\"_cls\": \"CV_MDTraj_Function\", \"_dict\": {\"store_cache\": true, \"name\": \"psi\", \"f\": {\"_module\": \"mdtraj.geometry.dihedral\", \"_name\": \"compute_dihedrals\"}, \"scalarize_numpy_singletons\": true, \"wrap_numpy_array\": true, \"kwargs\": {\"indices\": [[6, 8, 14, 16]]}, \"requires_lists\": true, \"time_reversible\": true}}'\n",
" u'{\"_cls\": \"CV_Volume\", \"_dict\": {\"volume\": {\"_obj\": \"volumes\", \"_idx\": 0}, \"store_cache\": true, \"name\": \"StateA\"}}'\n",
" u'{\"_cls\": \"CV_Volume\", \"_dict\": {\"volume\": {\"_obj\": \"volumes\", \"_idx\": 1}, \"store_cache\": true, \"name\": \"StateB\"}}'\n",
" u'{\"_cls\": \"CV_Volume\", \"_dict\": {\"volume\": {\"_obj\": \"volumes\", \"_idx\": 26}, \"store_cache\": true, \"name\": \"StateX\"}}'\n",
" u'{\"_cls\": \"CV_PyEMMA_Featurizer\", \"_dict\": {\"kwargs\": {}, \"store_cache\": true, \"name\": \"pyemma\", \"featurizer\": {\"_marshal\": \"YwEAAAABAAAAAwAAAEMAAABzIAAAAHwAAGoAAHwAAGoBAHwAAGoCAIMAAIMBAIMBAAFkAABTKAEAAABOKAMAAAB0FQAAAGFkZF9pbnZlcnNlX2Rpc3RhbmNlc3QFAAAAcGFpcnN0DwAAAHNlbGVjdF9CYWNrYm9uZSgBAAAAdAEAAABmKAAAAAAoAAAAAHMeAAAAPGlweXRob24taW5wdXQtNC00Nzc0ZDhlZGRkMDA+dBAAAABweWVtbWFfZ2VuZXJhdG9yAQAAAHMCAAAAAAE=\", \"_module_vars\": [], \"_global_vars\": []}, \"topology\": {\"_obj\": \"topologies\", \"_idx\": 0}}}']\n"
"[ u'{\"_cls\": \"CV_Function\", \"_dict\": {\"name\": \"psi2\", \"f\": {\"_marshal\": \"YwMAAAADAAAAAwAAAEMAAABzHAAAAHwBAHwAAIMBAGQBABN8AgB8AACDAQBkAQATF1MoAgAAAE5pAgAAACgAAAAAKAMAAAB0BAAAAGl0ZW10AwAAAHBzaXQDAAAAcGhpKAAAAAAoAAAAAHMeAAAAPGlweXRob24taW5wdXQtOS00NGFmZmMyZGY1MzU+dAcAAABwcDJfZm5jAQAAAHMCAAAAAAE=\", \"_module_vars\": [], \"_global_vars\": []}, \"cv_store_cache\": true, \"cv_time_reversible\": false, \"cv_wrap_numpy_array\": false, \"cv_requires_lists\": false, \"cv_scalarize_numpy_singletons\": false, \"kwargs\": {\"phi\": {\"_obj\": \"cvs\", \"_idx\": 1}, \"psi\": {\"_obj\": \"cvs\", \"_idx\": 2}}}}'\n",
" u'{\"_cls\": \"CV_MDTraj_Function\", \"_dict\": {\"name\": \"phi\", \"f\": {\"_module\": \"mdtraj.geometry.dihedral\", \"_name\": \"compute_dihedrals\"}, \"cv_store_cache\": true, \"cv_time_reversible\": true, \"cv_wrap_numpy_array\": true, \"cv_requires_lists\": true, \"cv_scalarize_numpy_singletons\": true, \"kwargs\": {\"indices\": [[4, 6, 8, 14]]}}}'\n",
" u'{\"_cls\": \"CV_MDTraj_Function\", \"_dict\": {\"name\": \"psi\", \"f\": {\"_module\": \"mdtraj.geometry.dihedral\", \"_name\": \"compute_dihedrals\"}, \"cv_store_cache\": true, \"cv_time_reversible\": true, \"cv_wrap_numpy_array\": true, \"cv_requires_lists\": true, \"cv_scalarize_numpy_singletons\": true, \"kwargs\": {\"indices\": [[6, 8, 14, 16]]}}}'\n",
" u'{\"_cls\": \"CV_Volume\", \"_dict\": {\"cv_store_cache\": true, \"volume\": {\"_obj\": \"volumes\", \"_idx\": 0}, \"name\": \"StateA\"}}'\n",
" u'{\"_cls\": \"CV_Volume\", \"_dict\": {\"cv_store_cache\": true, \"volume\": {\"_obj\": \"volumes\", \"_idx\": 1}, \"name\": \"StateB\"}}'\n",
" u'{\"_cls\": \"CV_Volume\", \"_dict\": {\"cv_store_cache\": true, \"volume\": {\"_obj\": \"volumes\", \"_idx\": 26}, \"name\": \"StateX\"}}'\n",
" u'{\"_cls\": \"CV_PyEMMA_Featurizer\", \"_dict\": {\"cv_store_cache\": true, \"topology\": {\"_obj\": \"topologies\", \"_idx\": 0}, \"name\": \"pyemma\", \"featurizer\": {\"_marshal\": \"YwEAAAABAAAAAwAAAEMAAABzIAAAAHwAAGoAAHwAAGoBAHwAAGoCAIMAAIMBAIMBAAFkAABTKAEAAABOKAMAAAB0FQAAAGFkZF9pbnZlcnNlX2Rpc3RhbmNlc3QFAAAAcGFpcnN0DwAAAHNlbGVjdF9CYWNrYm9uZSgBAAAAdAEAAABmKAAAAAAoAAAAAHMeAAAAPGlweXRob24taW5wdXQtNC00Nzc0ZDhlZGRkMDA+dBAAAABweWVtbWFfZ2VuZXJhdG9yAQAAAHMCAAAAAAE=\", \"_module_vars\": [], \"_global_vars\": []}, \"kwargs\": {}}}']\n"
]
}
],
Expand All @@ -278,9 +286,19 @@
"metadata": {
"collapsed": false
},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"6\n"
]
}
],
"source": [
"py_emma_feat = storage.vars['cvs_json'][6]"
"py_cv_idx = storage.idx(py_cv)\n",
"print py_cv_idx\n",
"py_emma_feat = storage.vars['cvs_json'][py_cv_idx]"
]
},
{
Expand All @@ -305,17 +323,29 @@
"name": "stdout",
"output_type": "stream",
"text": [
"[ 4.05474138 4.04429817 4.09497976 4.05629969 4.02169132 4.08048439\n",
" 3.99784589 4.06264544 3.99345803 4.06143045 4.06058693 4.01164579\n",
" 4.07558966 4.00137377 4.09326935 4.01662636 4.01421356 4.04161978\n",
" 4.02600718 4.00666857 4.06887293 4.05741262 4.0694766 4.02478552\n",
" 4.05429459 3.99438739 3.99598861 4.0506835 3.95376158]\n"
"[[ 3.03981256 2.99009299]\n",
" [ 3.25924754 2.90155435]\n",
" [ 2.99404526 2.62719202]\n",
" [ 3.10834694 2.75153995]\n",
" [ 3.01506734 2.70448661]\n",
" [ 3.0620544 2.41997933]\n",
" [ 3.00873852 2.9390707 ]\n",
" [ 3.04612613 2.70650053]\n",
" [ 3.06516457 2.89407468]\n",
" [ 3.00530863 2.87437391]\n",
" [ 3.01655579 2.752635 ]\n",
" [ 3.12972426 2.81981134]\n",
" [ 3.05628848 2.83912849]\n",
" [ 2.97415805 2.87183213]\n",
" [ 3.03389168 2.80275726]\n",
" [ 2.91935158 2.78653932]\n",
" [ 3.02000546 2.76681828]]\n"
]
}
],
"source": [
"#! lazy\n",
"print erg[0::10,1]"
"print erg[0::25,2:4]"
]
},
{
Expand Down Expand Up @@ -344,7 +374,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.10"
"version": "2.7.11"
}
},
"nbformat": 4,
Expand Down

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