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MSM Test Notebook 1 - Markov Models.html
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<!DOCTYPE html>
<html>
<head><meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>MSM Test Notebook 1 - Markov Models</title><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"></script>
<style type="text/css">
pre { line-height: 125%; }
td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
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td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
.highlight .hll { background-color: var(--jp-cell-editor-active-background) }
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<style type="text/css">
/*-----------------------------------------------------------------------------
| Copyright (c) Jupyter Development Team.
| Distributed under the terms of the Modified BSD License.
|----------------------------------------------------------------------------*/
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*/
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scrollbar-color: rgb(var(--jp-scrollbar-thumb-color))
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}
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background-color: transparent;
}
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.CodeMirror-hscrollbar::-webkit-scrollbar-thumb,
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/*
* Phosphor
*/
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max-height: 16px;
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border-top: 1px solid #a0a0a0;
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max-width: 16px;
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background-color: #f0f0f0;
background-position: center center;
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max-height: 15px;
min-width: 15px;
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}
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background-color: #dadada;
}
.lm-ScrollBar-button.lm-mod-active {
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background-size: 17px;
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background-size: 17px;
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.lm-ScrollBar-button[data-action='increment'] {
background-image: var(--jp-icon-caret-down);
background-size: 17px;
}
/*-----------------------------------------------------------------------------
| Copyright (c) Jupyter Development Team.
| Copyright (c) 2014-2017, PhosphorJS Contributors
|
| Distributed under the terms of the BSD 3-Clause License.
|
| The full license is in the file LICENSE, distributed with this software.
|----------------------------------------------------------------------------*/
/* <DEPRECATED> */ .p-Widget, /* </DEPRECATED> */
.lm-Widget {
box-sizing: border-box;
position: relative;
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/* <DEPRECATED> */ .p-Widget.p-mod-hidden, /* </DEPRECATED> */
.lm-Widget.lm-mod-hidden {
display: none !important;
}
/*-----------------------------------------------------------------------------
| Copyright (c) Jupyter Development Team.
| Copyright (c) 2014-2017, PhosphorJS Contributors
|
| Distributed under the terms of the BSD 3-Clause License.
|
| The full license is in the file LICENSE, distributed with this software.
|----------------------------------------------------------------------------*/
/* <DEPRECATED> */ .p-CommandPalette, /* </DEPRECATED> */
.lm-CommandPalette {
display: flex;
flex-direction: column;
-webkit-user-select: none;
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-ms-user-select: none;
user-select: none;
}
/* <DEPRECATED> */ .p-CommandPalette-search, /* </DEPRECATED> */
.lm-CommandPalette-search {
flex: 0 0 auto;
}
/* <DEPRECATED> */ .p-CommandPalette-content, /* </DEPRECATED> */
.lm-CommandPalette-content {
flex: 1 1 auto;
margin: 0;
padding: 0;
min-height: 0;
overflow: auto;
list-style-type: none;
}
/* <DEPRECATED> */ .p-CommandPalette-header, /* </DEPRECATED> */
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overflow: hidden;
white-space: nowrap;
text-overflow: ellipsis;
}
/* <DEPRECATED> */ .p-CommandPalette-item, /* </DEPRECATED> */
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flex-direction: row;
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/* <DEPRECATED> */ .p-CommandPalette-itemContent, /* </DEPRECATED> */
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/* <DEPRECATED> */ .p-CommandPalette-itemShortcut, /* </DEPRECATED> */
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text-overflow: ellipsis;
}
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border:1px solid transparent;
background-color: transparent;
position: absolute;
z-index:1;
right:3%;
top: 0;
bottom: 0;
margin: auto;
padding: 7px 0;
display: none;
vertical-align: middle;
outline: 0;
cursor: pointer;
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.lm-close-icon:after {
content: "X";
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width: 15px;
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text-align: center;
color:#000;
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cursor: pointer;
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/*-----------------------------------------------------------------------------
| Copyright (c) Jupyter Development Team.
| Copyright (c) 2014-2017, PhosphorJS Contributors
|
| Distributed under the terms of the BSD 3-Clause License.
|
| The full license is in the file LICENSE, distributed with this software.
|----------------------------------------------------------------------------*/
/* <DEPRECATED> */ .p-DockPanel, /* </DEPRECATED> */
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}
/* <DEPRECATED> */ .p-DockPanel-handle, /* </DEPRECATED> */
.lm-DockPanel-handle {
z-index: 2;
}
/* <DEPRECATED> */ .p-DockPanel-handle.p-mod-hidden, /* </DEPRECATED> */
.lm-DockPanel-handle.lm-mod-hidden {
display: none !important;
}
/* <DEPRECATED> */ .p-DockPanel-handle:after, /* </DEPRECATED> */
.lm-DockPanel-handle:after {
position: absolute;
top: 0;
left: 0;
width: 100%;
height: 100%;
content: '';
}
/* <DEPRECATED> */
.p-DockPanel-handle[data-orientation='horizontal'],
/* </DEPRECATED> */
.lm-DockPanel-handle[data-orientation='horizontal'] {
cursor: ew-resize;
}
/* <DEPRECATED> */
.p-DockPanel-handle[data-orientation='vertical'],
/* </DEPRECATED> */
.lm-DockPanel-handle[data-orientation='vertical'] {
cursor: ns-resize;
}
/* <DEPRECATED> */
.p-DockPanel-handle[data-orientation='horizontal']:after,
/* </DEPRECATED> */
.lm-DockPanel-handle[data-orientation='horizontal']:after {
left: 50%;
min-width: 8px;
transform: translateX(-50%);
}
/* <DEPRECATED> */
.p-DockPanel-handle[data-orientation='vertical']:after,
/* </DEPRECATED> */
.lm-DockPanel-handle[data-orientation='vertical']:after {
top: 50%;
min-height: 8px;
transform: translateY(-50%);
}
/* <DEPRECATED> */ .p-DockPanel-overlay, /* </DEPRECATED> */
.lm-DockPanel-overlay {
z-index: 3;
box-sizing: border-box;
pointer-events: none;
}
/* <DEPRECATED> */ .p-DockPanel-overlay.p-mod-hidden, /* </DEPRECATED> */
.lm-DockPanel-overlay.lm-mod-hidden {
display: none !important;
}
/*-----------------------------------------------------------------------------
| Copyright (c) Jupyter Development Team.
| Copyright (c) 2014-2017, PhosphorJS Contributors
|
| Distributed under the terms of the BSD 3-Clause License.
|
| The full license is in the file LICENSE, distributed with this software.
|----------------------------------------------------------------------------*/
/* <DEPRECATED> */ .p-Menu, /* </DEPRECATED> */
.lm-Menu {
z-index: 10000;
position: absolute;
white-space: nowrap;
overflow-x: hidden;
overflow-y: auto;
outline: none;
-webkit-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
user-select: none;
}
/* <DEPRECATED> */ .p-Menu-content, /* </DEPRECATED> */
.lm-Menu-content {
margin: 0;
padding: 0;
display: table;
list-style-type: none;
}
/* <DEPRECATED> */ .p-Menu-item, /* </DEPRECATED> */
.lm-Menu-item {
display: table-row;
}
/* <DEPRECATED> */
.p-Menu-item.p-mod-hidden,
.p-Menu-item.p-mod-collapsed,
/* </DEPRECATED> */
.lm-Menu-item.lm-mod-hidden,
.lm-Menu-item.lm-mod-collapsed {
display: none !important;
}
/* <DEPRECATED> */
.p-Menu-itemIcon,
.p-Menu-itemSubmenuIcon,
/* </DEPRECATED> */
.lm-Menu-itemIcon,
.lm-Menu-itemSubmenuIcon {
display: table-cell;
text-align: center;
}
/* <DEPRECATED> */ .p-Menu-itemLabel, /* </DEPRECATED> */
.lm-Menu-itemLabel {
display: table-cell;
text-align: left;
}
/* <DEPRECATED> */ .p-Menu-itemShortcut, /* </DEPRECATED> */
.lm-Menu-itemShortcut {
display: table-cell;
text-align: right;
}
/*-----------------------------------------------------------------------------
| Copyright (c) Jupyter Development Team.
| Copyright (c) 2014-2017, PhosphorJS Contributors
|
| Distributed under the terms of the BSD 3-Clause License.
|
| The full license is in the file LICENSE, distributed with this software.
|----------------------------------------------------------------------------*/
/* <DEPRECATED> */ .p-MenuBar, /* </DEPRECATED> */
.lm-MenuBar {
outline: none;
-webkit-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
user-select: none;
}
/* <DEPRECATED> */ .p-MenuBar-content, /* </DEPRECATED> */
.lm-MenuBar-content {
margin: 0;
padding: 0;
display: flex;
flex-direction: row;
list-style-type: none;
}
/* <DEPRECATED> */ .p--MenuBar-item, /* </DEPRECATED> */
.lm-MenuBar-item {
box-sizing: border-box;
}
/* <DEPRECATED> */
.p-MenuBar-itemIcon,
.p-MenuBar-itemLabel,
/* </DEPRECATED> */
.lm-MenuBar-itemIcon,
.lm-MenuBar-itemLabel {
display: inline-block;
}
/*-----------------------------------------------------------------------------
| Copyright (c) Jupyter Development Team.
| Copyright (c) 2014-2017, PhosphorJS Contributors
|
| Distributed under the terms of the BSD 3-Clause License.
|
| The full license is in the file LICENSE, distributed with this software.
|----------------------------------------------------------------------------*/
/* <DEPRECATED> */ .p-ScrollBar, /* </DEPRECATED> */
.lm-ScrollBar {
display: flex;
-webkit-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
user-select: none;
}
/* <DEPRECATED> */
.p-ScrollBar[data-orientation='horizontal'],
/* </DEPRECATED> */
.lm-ScrollBar[data-orientation='horizontal'] {
flex-direction: row;
}
/* <DEPRECATED> */
.p-ScrollBar[data-orientation='vertical'],
/* </DEPRECATED> */
.lm-ScrollBar[data-orientation='vertical'] {
flex-direction: column;
}
/* <DEPRECATED> */ .p-ScrollBar-button, /* </DEPRECATED> */
.lm-ScrollBar-button {
box-sizing: border-box;
flex: 0 0 auto;
}
/* <DEPRECATED> */ .p-ScrollBar-track, /* </DEPRECATED> */
.lm-ScrollBar-track {
box-sizing: border-box;
position: relative;
overflow: hidden;
flex: 1 1 auto;
}
/* <DEPRECATED> */ .p-ScrollBar-thumb, /* </DEPRECATED> */
.lm-ScrollBar-thumb {
box-sizing: border-box;
position: absolute;
}
/*-----------------------------------------------------------------------------
| Copyright (c) Jupyter Development Team.
| Copyright (c) 2014-2017, PhosphorJS Contributors
|
| Distributed under the terms of the BSD 3-Clause License.
|
| The full license is in the file LICENSE, distributed with this software.
|----------------------------------------------------------------------------*/
/* <DEPRECATED> */ .p-SplitPanel-child, /* </DEPRECATED> */
.lm-SplitPanel-child {
z-index: 0;
}
/* <DEPRECATED> */ .p-SplitPanel-handle, /* </DEPRECATED> */
.lm-SplitPanel-handle {
z-index: 1;
}
/* <DEPRECATED> */ .p-SplitPanel-handle.p-mod-hidden, /* </DEPRECATED> */
.lm-SplitPanel-handle.lm-mod-hidden {
display: none !important;
}
/* <DEPRECATED> */ .p-SplitPanel-handle:after, /* </DEPRECATED> */
.lm-SplitPanel-handle:after {
position: absolute;
top: 0;
left: 0;
width: 100%;
height: 100%;
content: '';
}
/* <DEPRECATED> */
.p-SplitPanel[data-orientation='horizontal'] > .p-SplitPanel-handle,
/* </DEPRECATED> */
.lm-SplitPanel[data-orientation='horizontal'] > .lm-SplitPanel-handle {
cursor: ew-resize;
}
/* <DEPRECATED> */
.p-SplitPanel[data-orientation='vertical'] > .p-SplitPanel-handle,
/* </DEPRECATED> */
.lm-SplitPanel[data-orientation='vertical'] > .lm-SplitPanel-handle {
cursor: ns-resize;
}
/* <DEPRECATED> */
.p-SplitPanel[data-orientation='horizontal'] > .p-SplitPanel-handle:after,
/* </DEPRECATED> */
.lm-SplitPanel[data-orientation='horizontal'] > .lm-SplitPanel-handle:after {
left: 50%;
min-width: 8px;
transform: translateX(-50%);
}
/* <DEPRECATED> */
.p-SplitPanel[data-orientation='vertical'] > .p-SplitPanel-handle:after,
/* </DEPRECATED> */
.lm-SplitPanel[data-orientation='vertical'] > .lm-SplitPanel-handle:after {
top: 50%;
min-height: 8px;
transform: translateY(-50%);
}
/*-----------------------------------------------------------------------------
| Copyright (c) Jupyter Development Team.
| Copyright (c) 2014-2017, PhosphorJS Contributors
|
| Distributed under the terms of the BSD 3-Clause License.
|
| The full license is in the file LICENSE, distributed with this software.
|----------------------------------------------------------------------------*/
/* <DEPRECATED> */ .p-TabBar, /* </DEPRECATED> */
.lm-TabBar {
display: flex;
-webkit-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
user-select: none;
}
/* <DEPRECATED> */ .p-TabBar[data-orientation='horizontal'], /* </DEPRECATED> */
.lm-TabBar[data-orientation='horizontal'] {
flex-direction: row;
}
/* <DEPRECATED> */ .p-TabBar[data-orientation='vertical'], /* </DEPRECATED> */
.lm-TabBar[data-orientation='vertical'] {
flex-direction: column;
}
/* <DEPRECATED> */ .p-TabBar-content, /* </DEPRECATED> */
.lm-TabBar-content {
margin: 0;
padding: 0;
display: flex;
flex: 1 1 auto;
list-style-type: none;
}
/* <DEPRECATED> */
.p-TabBar[data-orientation='horizontal'] > .p-TabBar-content,
/* </DEPRECATED> */
.lm-TabBar[data-orientation='horizontal'] > .lm-TabBar-content {
flex-direction: row;
}
/* <DEPRECATED> */
.p-TabBar[data-orientation='vertical'] > .p-TabBar-content,
/* </DEPRECATED> */
.lm-TabBar[data-orientation='vertical'] > .lm-TabBar-content {
flex-direction: column;
}
/* <DEPRECATED> */ .p-TabBar-tab, /* </DEPRECATED> */
.lm-TabBar-tab {
display: flex;
flex-direction: row;
box-sizing: border-box;
overflow: hidden;
}
/* <DEPRECATED> */
.p-TabBar-tabIcon,
.p-TabBar-tabCloseIcon,
/* </DEPRECATED> */
.lm-TabBar-tabIcon,
.lm-TabBar-tabCloseIcon {
flex: 0 0 auto;
}
/* <DEPRECATED> */ .p-TabBar-tabLabel, /* </DEPRECATED> */
.lm-TabBar-tabLabel {
flex: 1 1 auto;
overflow: hidden;
white-space: nowrap;
}
.lm-TabBar-tabInput {
user-select: all;
width: 100%;
box-sizing : border-box;
}
/* <DEPRECATED> */ .p-TabBar-tab.p-mod-hidden, /* </DEPRECATED> */
.lm-TabBar-tab.lm-mod-hidden {
display: none !important;
}
/* <DEPRECATED> */ .p-TabBar.p-mod-dragging .p-TabBar-tab, /* </DEPRECATED> */
.lm-TabBar.lm-mod-dragging .lm-TabBar-tab {
position: relative;
}
/* <DEPRECATED> */
.p-TabBar.p-mod-dragging[data-orientation='horizontal'] .p-TabBar-tab,
/* </DEPRECATED> */
.lm-TabBar.lm-mod-dragging[data-orientation='horizontal'] .lm-TabBar-tab {
left: 0;
transition: left 150ms ease;
}
/* <DEPRECATED> */
.p-TabBar.p-mod-dragging[data-orientation='vertical'] .p-TabBar-tab,
/* </DEPRECATED> */
.lm-TabBar.lm-mod-dragging[data-orientation='vertical'] .lm-TabBar-tab {
top: 0;
transition: top 150ms ease;
}
/* <DEPRECATED> */
.p-TabBar.p-mod-dragging .p-TabBar-tab.p-mod-dragging,
/* </DEPRECATED> */
.lm-TabBar.lm-mod-dragging .lm-TabBar-tab.lm-mod-dragging {
transition: none;
}
/*-----------------------------------------------------------------------------
| Copyright (c) Jupyter Development Team.
| Copyright (c) 2014-2017, PhosphorJS Contributors
|
| Distributed under the terms of the BSD 3-Clause License.
|
| The full license is in the file LICENSE, distributed with this software.
|----------------------------------------------------------------------------*/
/* <DEPRECATED> */ .p-TabPanel-tabBar, /* </DEPRECATED> */
.lm-TabPanel-tabBar {
z-index: 1;
}
/* <DEPRECATED> */ .p-TabPanel-stackedPanel, /* </DEPRECATED> */
.lm-TabPanel-stackedPanel {
z-index: 0;
}
/*-----------------------------------------------------------------------------
| Copyright (c) Jupyter Development Team.
| Copyright (c) 2014-2017, PhosphorJS Contributors
|
| Distributed under the terms of the BSD 3-Clause License.
|
| The full license is in the file LICENSE, distributed with this software.
|----------------------------------------------------------------------------*/
@charset "UTF-8";
html{
-webkit-box-sizing:border-box;
box-sizing:border-box; }
*,
*::before,
*::after{
-webkit-box-sizing:inherit;
box-sizing:inherit; }
body{
font-size:14px;
font-weight:400;
letter-spacing:0;
line-height:1.28581;
text-transform:none;
color:#182026;
font-family:-apple-system, "BlinkMacSystemFont", "Segoe UI", "Roboto", "Oxygen", "Ubuntu", "Cantarell", "Open Sans", "Helvetica Neue", "Icons16", sans-serif; }
p{
margin-bottom:10px;
margin-top:0; }
small{
font-size:12px; }
strong{
font-weight:600; }
::-moz-selection{
background:rgba(125, 188, 255, 0.6); }
::selection{
background:rgba(125, 188, 255, 0.6); }
.bp3-heading{
color:#182026;
font-weight:600;
margin:0 0 10px;
padding:0; }
.bp3-dark .bp3-heading{
color:#f5f8fa; }
h1.bp3-heading, .bp3-running-text h1{
font-size:36px;
line-height:40px; }
h2.bp3-heading, .bp3-running-text h2{
font-size:28px;
line-height:32px; }
h3.bp3-heading, .bp3-running-text h3{
font-size:22px;
line-height:25px; }
h4.bp3-heading, .bp3-running-text h4{
font-size:18px;
line-height:21px; }
h5.bp3-heading, .bp3-running-text h5{
font-size:16px;
line-height:19px; }
h6.bp3-heading, .bp3-running-text h6{
font-size:14px;
line-height:16px; }
.bp3-ui-text{
font-size:14px;
font-weight:400;
letter-spacing:0;
line-height:1.28581;
text-transform:none; }
.bp3-monospace-text{
font-family:monospace;
text-transform:none; }
.bp3-text-muted{
color:#5c7080; }
.bp3-dark .bp3-text-muted{
color:#a7b6c2; }
.bp3-text-disabled{
color:rgba(92, 112, 128, 0.6); }
.bp3-dark .bp3-text-disabled{
color:rgba(167, 182, 194, 0.6); }
.bp3-text-overflow-ellipsis{
overflow:hidden;
text-overflow:ellipsis;
white-space:nowrap;