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dwhswensondwhswenson
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Revert "Merge remote-tracking branch 'upstream/master' into replica_networks"
This reverts commit f03ee6b, reversing changes made to 8d788d9.
1 parent f03ee6b commit 7abbe34

37 files changed

Lines changed: 2856 additions & 3548 deletions

‎examples/alanine/ala_dipeptide_example.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -71,7 +71,7 @@
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snap = engine.current_snapshot
7272
engine.storage.snapshots.save(snap, 0)
7373
engine.initialized = True
74-
SampleGeneratingMover.engine = engine
74+
PathMover.engine = engine
7575

7676
# this generates an order parameter (callable) object named psi (so if
7777
# we call `psi(trajectory)` we get a list of the values of psi for each

‎examples/alanine/ala_dipeptide_pathmovertest.py‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -74,7 +74,7 @@
7474
snap = engine.current_snapshot
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engine.storage.snapshots.save(snap, 0)
7676
engine.initialized = True
77-
SampleGeneratingMover.engine = engine
77+
PathMover.engine = engine
7878

7979
# this generates an order parameter (callable) object named psi (so if
8080
# we call `psi(trajectory)` we get a list of the values of psi for each
@@ -189,8 +189,8 @@
189189
print third_set[0].__dict__
190190
print third_set.__dict__
191191

192-
print second_path.results
193-
print first_path.results
192+
print second_path.samples
193+
print first_path.samples
194194

195195

196196
mover3 = CollapseMove(SequentialMover([
@@ -204,7 +204,7 @@
204204

205205
third_path = mover3.move(third_set)
206206

207-
print third_path.results
207+
print third_path.samples
208208
print str(third_path)
209209
print str(third_path.opened)
210210
print len(third_path)

‎examples/alanine/ala_dipeptide_simple.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -67,7 +67,7 @@
6767
snap = engine.current_snapshot
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engine.storage.snapshots.save(snap, 0)
6969
engine.initialized = True
70-
SampleGeneratingMover.engine = engine
70+
PathMover.engine = engine
7171

7272
# this generates an order parameter (callable) object named psi (so if
7373
# we call `psi(trajectory)` we get a list of the values of psi for each

‎examples/ipython/alanine.ipynb‎

Lines changed: 51 additions & 94 deletions
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‎examples/ipython/mstis_analysis.ipynb‎

Lines changed: 19 additions & 55 deletions
Original file line numberDiff line numberDiff line change
@@ -25,66 +25,28 @@
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"collapsed": false,
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"scrolled": true
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},
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"outputs": [],
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"source": [
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"mstis = storage.networks.load(0)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {
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"collapsed": false
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Multiple State TIS Network:\n",
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"RETISTransition: Out B\n",
46-
"B -> B or all states except B\n",
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"Interface: 0.0<opB<0.04\n",
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"Interface: 0.0<opB<0.09\n",
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"Interface: 0.0<opB<0.16\n",
50-
"RETISTransition: Out A\n",
51-
"A -> A or all states except A\n",
52-
"Interface: 0.0<opA<0.04\n",
53-
"Interface: 0.0<opA<0.09\n",
54-
"Interface: 0.0<opA<0.16\n",
55-
"RETISTransition: Out C\n",
56-
"C -> C or all states except C\n",
57-
"Interface: 0.0<opC<0.04\n",
58-
"Interface: 0.0<opC<0.09\n",
59-
"Interface: 0.0<opC<0.16\n",
60-
"\n"
30+
"ename": "TypeError",
31+
"evalue": "object.__new__(): not enough arguments",
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"output_type": "error",
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"traceback": [
34+
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
35+
"\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
36+
"\u001b[0;32m<ipython-input-2-6388b15d781e>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmstis\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mstorage\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnetworks\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
37+
"\u001b[0;32m/Users/dwhs/Dropbox/msm-tis/openpathsampling/storage/object_storage.pyc\u001b[0m in \u001b[0;36minner\u001b[0;34m(self, idx, *args, **kwargs)\u001b[0m\n\u001b[1;32m 1204\u001b[0m \u001b[0;31m# the class method directly it is not bound yet and so we need to include the self! Took me some time to\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1205\u001b[0m \u001b[0;31m# understand and figure that out\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1206\u001b[0;31m \u001b[0mobj\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mn_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1207\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mobj\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1208\u001b[0m \u001b[0;31m# update cache there might have been a change due to naming\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
38+
"\u001b[0;32m/Users/dwhs/Dropbox/msm-tis/openpathsampling/storage/object_storage.pyc\u001b[0m in \u001b[0;36minner\u001b[0;34m(self, idx, *args, **kwargs)\u001b[0m\n\u001b[1;32m 1272\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1273\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1274\u001b[0;31m \u001b[0mobj\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mn_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1275\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1276\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mhasattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'idx'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
39+
"\u001b[0;32m/Users/dwhs/Dropbox/msm-tis/openpathsampling/storage/object_storage.pyc\u001b[0m in \u001b[0;36mload\u001b[0;34m(self, idx)\u001b[0m\n\u001b[1;32m 546\u001b[0m '''\n\u001b[1;32m 547\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 548\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload_json\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0midx_dimension\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m'_json'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0midx\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 549\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 550\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mclear_cache\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
40+
"\u001b[0;32m/Users/dwhs/Dropbox/msm-tis/openpathsampling/storage/object_storage.pyc\u001b[0m in \u001b[0;36mload_json\u001b[0;34m(self, name, idx)\u001b[0m\n\u001b[1;32m 921\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 922\u001b[0m \u001b[0msimplified\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0myaml\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mjson_string\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 923\u001b[0;31m \u001b[0mobj\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msimplifier\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuild\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msimplified\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 924\u001b[0m \u001b[0msetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'json'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mjson_string\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 925\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
41+
"\u001b[0;32m/Users/dwhs/Dropbox/msm-tis/openpathsampling/storage/storage.pyc\u001b[0m in \u001b[0;36mbuild\u001b[0;34m(self, obj)\u001b[0m\n\u001b[1;32m 571\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 572\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 573\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mStorableObjectJSON\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuild\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
42+
"\u001b[0;32m/Users/dwhs/Dropbox/msm-tis/openpathsampling/todict.pyc\u001b[0m in \u001b[0;36mbuild\u001b[0;34m(self, obj)\u001b[0m\n\u001b[1;32m 212\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mobj\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'_cls'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclass_list\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 213\u001b[0m \u001b[0mattributes\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuild\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'_dict'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 214\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclass_list\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'_cls'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_dict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mattributes\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 215\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 216\u001b[0m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Cannot create obj of class \"'\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mobj\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'_cls'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m+\u001b[0m \u001b[0;34m'\". Class is not registered as creatable!'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
43+
"\u001b[0;32m/Users/dwhs/Dropbox/msm-tis/openpathsampling/analysis/network.py\u001b[0m in \u001b[0;36mfrom_dict\u001b[0;34m(dct)\u001b[0m\n\u001b[1;32m 62\u001b[0m \u001b[0;34m@\u001b[0m\u001b[0mstaticmethod\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 63\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mfrom_dict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdct\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 64\u001b[0;31m \u001b[0mnetwork\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mMSTISNetwork\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__new__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 65\u001b[0m \u001b[0mnetwork\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_state\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdct\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'from_state'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 66\u001b[0m \u001b[0mnetwork\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmovers\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdct\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'movers'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
44+
"\u001b[0;31mTypeError\u001b[0m: object.__new__(): not enough arguments"
6145
]
6246
}
6347
],
6448
"source": [
65-
"print mstis"
66-
]
67-
},
68-
{
69-
"cell_type": "code",
70-
"execution_count": 5,
71-
"metadata": {
72-
"collapsed": false
73-
},
74-
"outputs": [
75-
{
76-
"data": {
77-
"text/plain": [
78-
"u''"
79-
]
80-
},
81-
"execution_count": 5,
82-
"metadata": {},
83-
"output_type": "execute_result"
84-
}
85-
],
86-
"source": [
87-
"mstis._name"
49+
"mstis = storage.networks.load(0)"
8850
]
8951
},
9052
{
@@ -94,7 +56,9 @@
9456
"collapsed": true
9557
},
9658
"outputs": [],
97-
"source": []
59+
"source": [
60+
"print mstis"
61+
]
9862
}
9963
],
10064
"metadata": {

‎examples/ipython/multistate_system_setup.ipynb‎

Lines changed: 48 additions & 14 deletions
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