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diff --git a/docs/chent-25.png b/docs/chent-25.png Binary files differdeleted file mode 100644 index 4485326..0000000 --- a/docs/chent-25.png +++ /dev/null diff --git a/docs/chent.html b/docs/chent.html deleted file mode 100644 index 0f4a43d..0000000 --- a/docs/chent.html +++ /dev/null @@ -1,180 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>chent. chents 0.2-3</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">chents 0.2-3</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>An R6 class for chemical entities with associated data</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="symbol">chent</span></pre> - - <div class="Format"> - <h2>Format</h2> - - <p>An <code><a href='http://www.rdocumentation.org/packages/R6/topics/R6Class'>R6Class</a></code> generator object</p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>The class is initialised with an identifier. Chemical information is retrieved from -the internet. Additionally, it can be generated using RDKit if RDKit and its -python bindings are installed and configured for use with PythonInR.</p> - - </div> - - <div class="Fields"> - <h2>Fields</h2> - - <p></p> - - <p><dl> -<dt><code>identifier</code></dt><dd>The identifier that was used to initiate the object, with attribute 'source'</dd></p> - - <p><dt><code>inchikey</code></dt><dd>InChI Key, with attribute 'source'</dd></p> - - <p><dt><code>smiles</code></dt><dd>SMILES code, with attribute 'source'</dd></p> - - <p><dt><code>mw</code></dt><dd>Molecular weight, with attribute 'source'</dd></p> - - <p><dt><code>pubchem</code></dt><dd>List of information retreived from PubChem</dd></p> - - <p><dt><code>rdkit</code></dt><dd>List of information obtained with RDKit, if installed and -configured for use with PythonInR</dd></p> - - <p><dt><code>Picture</code></dt><dd>Graph as a <code><a href='http://www.rdocumentation.org/packages/grImport/topics/picture'>picture</a></code> object obtained using grImport</dd></p> - - <p><dt><code>chyaml</code></dt><dd>List of information obtained from a YAML file</dd></p> - - <p><dt><code>degradation</code></dt><dd>List of degradation endpoints</dd></p> - - <p></dl></p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="symbol">oct</span> <span class="assignement"><-</span> <span class="symbol">chent</span><span class="keyword">$</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/methods/topics/new'>new</a></span><span class="keyword">(</span><span class="string">"1-octanol"</span><span class="keyword">,</span> <span class="argument">smiles</span> <span class="argument">=</span> <span class="string">"CCCCCCCCO"</span><span class="keyword">)</span></div> -<strong class='message'>PubChem:</strong> -<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</strong> -<strong class='message'>Found 1 entries in PubChem, using the first one.</strong> -<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,ExactMass,MonoisotopicMass,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,HeavyAtomCount,IsotopeAtomCount,AtomStereoCount,DefinedAtomStereoCount,UndefinedAtomStereoCount,BondStereoCount,DefinedBondStereoCount,UndefinedBondStereoCount,CovalentUnitCount,Volume3D,XStericQuadrupole3D,YStericQuadrupole3D,ZStericQuadrupole3D,FeatureCount3D,FeatureAcceptorCount3D,FeatureDonorCount3D,FeatureAnionCount3D,FeatureCationCount3D,FeatureRingCount3D,FeatureHydrophobeCount3D,ConformerModelRMSD3D,EffectiveRotorCount3D,ConformerCount3D,Fingerprint2D/JSON</strong> -<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</strong> -<strong class='message'>Loading required namespace: PythonInR</strong> -<strong class='message'> -Initialize Python Version 2.7.9 (default, Jun 29 2016, 13:11:10) -[GCC 4.9.2] -</strong> -<strong class='message'>Trying to get chemical information from RDKit using user SMILES -CCCCCCCCO</strong> -<strong class='message'>Did not find chyaml file ./1-octanol.yaml</strong> -<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="symbol">oct</span><span class="keyword">)</span></div> -<div class='output'><chent> -Identifier $identifier 1-octanol -InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N -SMILES string $smiles: - user PubChem_Canonical - "CCCCCCCCO" "CCCCCCCCO" -Molecular weight $mw: 130.2 -PubChem synonyms (up to 10): - [1] "957" "1-octanol" "Octan-1-ol" "octanol" - [5] "N-octanol" "Octyl alcohol" "Capryl alcohol" "n-Octyl alcohol" - [9] "caprylic alcohol" "111-87-5" -</div> -<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">oct</span><span class="keyword">)</span></div> -<div class='input'><span class="symbol">caffeine</span> <span class="assignement"><-</span> <span class="symbol">chent</span><span class="keyword">$</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/methods/topics/new'>new</a></span><span class="keyword">(</span><span class="string">"caffeine"</span><span class="keyword">)</span></div> -<strong class='message'>PubChem:</strong> -<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</strong> -<strong class='message'>Found 1 entries in PubChem, using the first one.</strong> -<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,ExactMass,MonoisotopicMass,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,HeavyAtomCount,IsotopeAtomCount,AtomStereoCount,DefinedAtomStereoCount,UndefinedAtomStereoCount,BondStereoCount,DefinedBondStereoCount,UndefinedBondStereoCount,CovalentUnitCount,Volume3D,XStericQuadrupole3D,YStericQuadrupole3D,ZStericQuadrupole3D,FeatureCount3D,FeatureAcceptorCount3D,FeatureDonorCount3D,FeatureAnionCount3D,FeatureCationCount3D,FeatureRingCount3D,FeatureHydrophobeCount3D,ConformerModelRMSD3D,EffectiveRotorCount3D,ConformerCount3D,Fingerprint2D/JSON</strong> -<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</strong> -<strong class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES -CN1C=NC2=C1C(=O)N(C(=O)N2C)C</strong> -<strong class='message'>Did not find chyaml file ./caffeine.yaml</strong> -<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="symbol">caffeine</span><span class="keyword">)</span></div> -<div class='output'><chent> -Identifier $identifier caffeine -InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N -SMILES string $smiles: - PubChem_Canonical -"CN1C=NC2=C1C(=O)N(C(=O)N2C)C" -Molecular weight $mw: 194.2 -PubChem synonyms (up to 10): - [1] "2519" "caffeine" - [3] "1,3,7-Trimethylxanthine" "Methyltheobromine" - [5] "Guaranine" "Cafeina" - [7] "Koffein" "Mateina" - [9] "Thein" "Theine" -</div> -<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">caffeine</span><span class="keyword">)</span></div> -<p><img src='chent-25.png' alt='' width='540' height='400' /></p></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>chent</li> - </ul> - <ul> - <li>data</li> - </ul> --> - - - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
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#fff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:.5;filter:alpha(opacity=50)}.carousel-control.right{right:15px;left:auto}.carousel-control:hover{color:#fff;text-decoration:none;opacity:.9;filter:alpha(opacity=90)}.carousel-caption{position:absolute;right:0;bottom:0;left:0;padding:10px 15px 5px;background:#333;background:rgba(0,0,0,0.75)}.carousel-caption h4,.carousel-caption p{color:#fff}.hero-unit{padding:60px;margin-bottom:30px;background-color:#eee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;letter-spacing:-1px;color:inherit}.hero-unit p{font-size:18px;font-weight:200;line-height:27px;color:inherit}.pull-right{float:right}.pull-left{float:left}.hide{display:none}.show{display:block}.invisible{visibility:hidden} diff --git a/docs/css/highlight.css b/docs/css/highlight.css deleted file mode 100644 index cd3ead6..0000000 --- a/docs/css/highlight.css +++ /dev/null @@ -1,28 +0,0 @@ -/* Syntax highlighting ---------------------------------------------------- */ - -pre .input { - border-left: 3px solid #ccc; - padding-left: 0.5em; -} -pre .output { - background-color: #eee; -} - -.number {color:rgb(21,20,181);} -.functioncall {color:#264D66 ;} -.string {color:#375D81 ;} -.keyword {font-weight:bolder ;color:black;} -.argument {color:#264D66 ;} -.comment {color: #4C886B;} -.formalargs {color: #264D66;} -.eqformalargs {color:#264D66;} -.slot {font-style:italic;} -.symbol {color:black ;} -.prompt {color:black ;} - -pre img { - background-color: #fff; - border: 1px solid #ccc; - display: block; - margin: 0.5em auto 0.5em auto; -} diff --git a/docs/css/staticdocs.css b/docs/css/staticdocs.css deleted file mode 100644 index 15d7408..0000000 --- a/docs/css/staticdocs.css +++ /dev/null @@ -1,25 +0,0 @@ -h2 {padding-top: 20px} - -.icon img { - float: right; - border: 1px solid #ccc; -} -.index .internal {display: none;} -ul.index li {margin-bottom: 0.5em; clear: both;} - -footer { - margin-top: 45px; - padding: 35px 0 36px; - border-top: 1px solid #e5e5e5; -} -footer p { - margin-bottom: 0; - color: #555; -} - -.sidebar h2 { - font-size: 1.1em; - padding-top: 0.5em; -} - -.sidebar li {margin-bottom: 0.5em;} diff --git a/docs/draw_svg.chent.html b/docs/draw_svg.chent.html deleted file mode 100644 index 4f781f1..0000000 --- a/docs/draw_svg.chent.html +++ /dev/null @@ -1,101 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>draw_svg.chent. chents 0.2-3</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">chents 0.2-3</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Draw SVG graph from a chent object using RDKit</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="functioncall"><a href='draw_svg.chent.html'>draw_svg.chent</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">,</span> <span class="argument">width</span> <span class="argument">=</span> <span class="number">300</span><span class="keyword">,</span> <span class="argument">height</span> <span class="argument">=</span> <span class="number">150</span><span class="keyword">,</span> - <span class="argument">filename</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/paste'>paste0</a></span><span class="keyword">(</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/names'>names</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">$</span><span class="symbol">identifier</span><span class="keyword">)</span><span class="keyword">,</span> <span class="string">".svg"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">subdir</span> <span class="argument">=</span> <span class="string">"svg"</span><span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>x</dt> - <dd>The chent object to be plotted</dd> - <dt>width</dt> - <dd>The desired width in pixels</dd> - <dt>height</dt> - <dd>The desired height in pixels</dd> - <dt>filename</dt> - <dd>The filename</dd> - <dt>subdir</dt> - <dd>The path to which the file should be written</dd> - </dl> - - <div class="Description"> - <h2>Description</h2> - - <p>Draw SVG graph from a chent object using RDKit</p> - - </div> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>draw_svg.chent</li> - </ul> - <ul> - - </ul> --> - - - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
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'width' : 'height' - } - - , show: function () { - var dimension - , scroll - , actives - , hasData - - if (this.transitioning) return - - dimension = this.dimension() - scroll = $.camelCase(['scroll', dimension].join('-')) - actives = this.$parent && this.$parent.find('> .accordion-group > .in') - - if (actives && actives.length) { - hasData = actives.data('collapse') - if (hasData && hasData.transitioning) return - actives.collapse('hide') - hasData || actives.data('collapse', null) - } - - this.$element[dimension](0) - this.transition('addClass', $.Event('show'), 'shown') - this.$element[dimension](this.$element[0][scroll]) - } - - , hide: function () { - var dimension - if (this.transitioning) return - dimension = this.dimension() - this.reset(this.$element[dimension]()) - this.transition('removeClass', $.Event('hide'), 'hidden') - this.$element[dimension](0) - } - - , reset: function (size) { - var dimension = this.dimension() - - this.$element - .removeClass('collapse') - [dimension](size || 'auto') - [0].offsetWidth - - this.$element[size !== null ? 'addClass' : 'removeClass']('collapse') - - return this - } - - , transition: function (method, startEvent, completeEvent) { - var that = this - , complete = function () { - if (startEvent.type == 'show') that.reset() - that.transitioning = 0 - that.$element.trigger(completeEvent) - } - - this.$element.trigger(startEvent) - - if (startEvent.isDefaultPrevented()) return - - this.transitioning = 1 - - this.$element[method]('in') - - $.support.transition && this.$element.hasClass('collapse') ? - this.$element.one($.support.transition.end, complete) : - complete() - } - - , toggle: function () { - this[this.$element.hasClass('in') ? 'hide' : 'show']() - } - - } - - - /* COLLAPSIBLE PLUGIN DEFINITION - * ============================== */ - - $.fn.collapse = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('collapse') - , options = typeof option == 'object' && option - if (!data) $this.data('collapse', (data = new Collapse(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.collapse.defaults = { - toggle: true - } - - $.fn.collapse.Constructor = Collapse - - - /* COLLAPSIBLE DATA-API - * ==================== */ - - $(function () { - $('body').on('click.collapse.data-api', '[data-toggle=collapse]', function ( e ) { - var $this = $(this), href - , target = $this.attr('data-target') - || e.preventDefault() - || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '') //strip for ie7 - , option = $(target).data('collapse') ? 'toggle' : $this.data() - $(target).collapse(option) - }) - }) - -}(window.jQuery);/* ============================================================ - * bootstrap-dropdown.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#dropdowns - * ============================================================ - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================ */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* DROPDOWN CLASS DEFINITION - * ========================= */ - - var toggle = '[data-toggle="dropdown"]' - , Dropdown = function (element) { - var $el = $(element).on('click.dropdown.data-api', this.toggle) - $('html').on('click.dropdown.data-api', function () { - $el.parent().removeClass('open') - }) - } - - Dropdown.prototype = { - - constructor: Dropdown - - , toggle: function (e) { - var $this = $(this) - , $parent - , selector - , isActive - - if ($this.is('.disabled, :disabled')) return - - selector = $this.attr('data-target') - - if (!selector) { - selector = $this.attr('href') - selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 - } - - $parent = $(selector) - $parent.length || ($parent = $this.parent()) - - isActive = $parent.hasClass('open') - - clearMenus() - - if (!isActive) $parent.toggleClass('open') - - return false - } - - } - - function clearMenus() { - $(toggle).parent().removeClass('open') - } - - - /* DROPDOWN PLUGIN DEFINITION - * ========================== */ - - $.fn.dropdown = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('dropdown') - if (!data) $this.data('dropdown', (data = new Dropdown(this))) - if (typeof option == 'string') data[option].call($this) - }) - } - - $.fn.dropdown.Constructor = Dropdown - - - /* APPLY TO STANDARD DROPDOWN ELEMENTS - * =================================== */ - - $(function () { - $('html').on('click.dropdown.data-api', clearMenus) - $('body') - .on('click.dropdown', '.dropdown form', function (e) { e.stopPropagation() }) - .on('click.dropdown.data-api', toggle, Dropdown.prototype.toggle) - }) - -}(window.jQuery);/* ========================================================= - * bootstrap-modal.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#modals - * ========================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================= */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* MODAL CLASS DEFINITION - * ====================== */ - - var Modal = function (content, options) { - this.options = options - this.$element = $(content) - .delegate('[data-dismiss="modal"]', 'click.dismiss.modal', $.proxy(this.hide, this)) - } - - Modal.prototype = { - - constructor: Modal - - , toggle: function () { - return this[!this.isShown ? 'show' : 'hide']() - } - - , show: function () { - var that = this - , e = $.Event('show') - - this.$element.trigger(e) - - if (this.isShown || e.isDefaultPrevented()) return - - $('body').addClass('modal-open') - - this.isShown = true - - escape.call(this) - backdrop.call(this, function () { - var transition = $.support.transition && that.$element.hasClass('fade') - - if (!that.$element.parent().length) { - that.$element.appendTo(document.body) //don't move modals dom position - } - - that.$element - .show() - - if (transition) { - that.$element[0].offsetWidth // force reflow - } - - that.$element.addClass('in') - - transition ? - that.$element.one($.support.transition.end, function () { that.$element.trigger('shown') }) : - that.$element.trigger('shown') - - }) - } - - , hide: function (e) { - e && e.preventDefault() - - var that = this - - e = $.Event('hide') - - this.$element.trigger(e) - - if (!this.isShown || e.isDefaultPrevented()) return - - this.isShown = false - - $('body').removeClass('modal-open') - - escape.call(this) - - this.$element.removeClass('in') - - $.support.transition && this.$element.hasClass('fade') ? - hideWithTransition.call(this) : - hideModal.call(this) - } - - } - - - /* MODAL PRIVATE METHODS - * ===================== */ - - function hideWithTransition() { - var that = this - , timeout = setTimeout(function () { - that.$element.off($.support.transition.end) - hideModal.call(that) - }, 500) - - this.$element.one($.support.transition.end, function () { - clearTimeout(timeout) - hideModal.call(that) - }) - } - - function hideModal(that) { - this.$element - .hide() - .trigger('hidden') - - backdrop.call(this) - } - - function backdrop(callback) { - var that = this - , animate = this.$element.hasClass('fade') ? 'fade' : '' - - if (this.isShown && this.options.backdrop) { - var doAnimate = $.support.transition && animate - - this.$backdrop = $('<div class="modal-backdrop ' + animate + '" />') - .appendTo(document.body) - - if (this.options.backdrop != 'static') { - this.$backdrop.click($.proxy(this.hide, this)) - } - - if (doAnimate) this.$backdrop[0].offsetWidth // force reflow - - this.$backdrop.addClass('in') - - doAnimate ? - this.$backdrop.one($.support.transition.end, callback) : - callback() - - } else if (!this.isShown && this.$backdrop) { - this.$backdrop.removeClass('in') - - $.support.transition && this.$element.hasClass('fade')? - this.$backdrop.one($.support.transition.end, $.proxy(removeBackdrop, this)) : - removeBackdrop.call(this) - - } else if (callback) { - callback() - } - } - - function removeBackdrop() { - this.$backdrop.remove() - this.$backdrop = null - } - - function escape() { - var that = this - if (this.isShown && this.options.keyboard) { - $(document).on('keyup.dismiss.modal', function ( e ) { - e.which == 27 && that.hide() - }) - } else if (!this.isShown) { - $(document).off('keyup.dismiss.modal') - } - } - - - /* MODAL PLUGIN DEFINITION - * ======================= */ - - $.fn.modal = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('modal') - , options = $.extend({}, $.fn.modal.defaults, $this.data(), typeof option == 'object' && option) - if (!data) $this.data('modal', (data = new Modal(this, options))) - if (typeof option == 'string') data[option]() - else if (options.show) data.show() - }) - } - - $.fn.modal.defaults = { - backdrop: true - , keyboard: true - , show: true - } - - $.fn.modal.Constructor = Modal - - - /* MODAL DATA-API - * ============== */ - - $(function () { - $('body').on('click.modal.data-api', '[data-toggle="modal"]', function ( e ) { - var $this = $(this), href - , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 - , option = $target.data('modal') ? 'toggle' : $.extend({}, $target.data(), $this.data()) - - e.preventDefault() - $target.modal(option) - }) - }) - -}(window.jQuery);/* =========================================================== - * bootstrap-tooltip.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#tooltips - * Inspired by the original jQuery.tipsy by Jason Frame - * =========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* TOOLTIP PUBLIC CLASS DEFINITION - * =============================== */ - - var Tooltip = function (element, options) { - this.init('tooltip', element, options) - } - - Tooltip.prototype = { - - constructor: Tooltip - - , init: function (type, element, options) { - var eventIn - , eventOut - - this.type = type - this.$element = $(element) - this.options = this.getOptions(options) - this.enabled = true - - if (this.options.trigger != 'manual') { - eventIn = this.options.trigger == 'hover' ? 'mouseenter' : 'focus' - eventOut = this.options.trigger == 'hover' ? 'mouseleave' : 'blur' - this.$element.on(eventIn, this.options.selector, $.proxy(this.enter, this)) - this.$element.on(eventOut, this.options.selector, $.proxy(this.leave, this)) - } - - this.options.selector ? - (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) : - this.fixTitle() - } - - , getOptions: function (options) { - options = $.extend({}, $.fn[this.type].defaults, options, this.$element.data()) - - if (options.delay && typeof options.delay == 'number') { - options.delay = { - show: options.delay - , hide: options.delay - } - } - - return options - } - - , enter: function (e) { - var self = $(e.currentTarget)[this.type](this._options).data(this.type) - - if (!self.options.delay || !self.options.delay.show) return self.show() - - clearTimeout(this.timeout) - self.hoverState = 'in' - this.timeout = setTimeout(function() { - if (self.hoverState == 'in') self.show() - }, self.options.delay.show) - } - - , leave: function (e) { - var self = $(e.currentTarget)[this.type](this._options).data(this.type) - - if (this.timeout) clearTimeout(this.timeout) - if (!self.options.delay || !self.options.delay.hide) return self.hide() - - self.hoverState = 'out' - this.timeout = setTimeout(function() { - if (self.hoverState == 'out') self.hide() - }, self.options.delay.hide) - } - - , show: function () { - var $tip - , inside - , pos - , actualWidth - , actualHeight - , placement - , tp - - if (this.hasContent() && this.enabled) { - $tip = this.tip() - this.setContent() - - if (this.options.animation) { - $tip.addClass('fade') - } - - placement = typeof this.options.placement == 'function' ? - this.options.placement.call(this, $tip[0], this.$element[0]) : - this.options.placement - - inside = /in/.test(placement) - - $tip - .remove() - .css({ top: 0, left: 0, display: 'block' }) - .appendTo(inside ? this.$element : document.body) - - pos = this.getPosition(inside) - - actualWidth = $tip[0].offsetWidth - actualHeight = $tip[0].offsetHeight - - switch (inside ? placement.split(' ')[1] : placement) { - case 'bottom': - tp = {top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2} - break - case 'top': - tp = {top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2} - break - case 'left': - tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth} - break - case 'right': - tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width} - break - } - - $tip - .css(tp) - .addClass(placement) - .addClass('in') - } - } - - , isHTML: function(text) { - // html string detection logic adapted from jQuery - return typeof text != 'string' - || ( text.charAt(0) === "<" - && text.charAt( text.length - 1 ) === ">" - && text.length >= 3 - ) || /^(?:[^<]*<[\w\W]+>[^>]*$)/.exec(text) - } - - , setContent: function () { - var $tip = this.tip() - , title = this.getTitle() - - $tip.find('.tooltip-inner')[this.isHTML(title) ? 'html' : 'text'](title) - $tip.removeClass('fade in top bottom left right') - } - - , hide: function () { - var that = this - , $tip = this.tip() - - $tip.removeClass('in') - - function removeWithAnimation() { - var timeout = setTimeout(function () { - $tip.off($.support.transition.end).remove() - }, 500) - - $tip.one($.support.transition.end, function () { - clearTimeout(timeout) - $tip.remove() - }) - } - - $.support.transition && this.$tip.hasClass('fade') ? - removeWithAnimation() : - $tip.remove() - } - - , fixTitle: function () { - var $e = this.$element - if ($e.attr('title') || typeof($e.attr('data-original-title')) != 'string') { - $e.attr('data-original-title', $e.attr('title') || '').removeAttr('title') - } - } - - , hasContent: function () { - return this.getTitle() - } - - , getPosition: function (inside) { - return $.extend({}, (inside ? {top: 0, left: 0} : this.$element.offset()), { - width: this.$element[0].offsetWidth - , height: this.$element[0].offsetHeight - }) - } - - , getTitle: function () { - var title - , $e = this.$element - , o = this.options - - title = $e.attr('data-original-title') - || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title) - - return title - } - - , tip: function () { - return this.$tip = this.$tip || $(this.options.template) - } - - , validate: function () { - if (!this.$element[0].parentNode) { - this.hide() - this.$element = null - this.options = null - } - } - - , enable: function () { - this.enabled = true - } - - , disable: function () { - this.enabled = false - } - - , toggleEnabled: function () { - this.enabled = !this.enabled - } - - , toggle: function () { - this[this.tip().hasClass('in') ? 'hide' : 'show']() - } - - } - - - /* TOOLTIP PLUGIN DEFINITION - * ========================= */ - - $.fn.tooltip = function ( option ) { - return this.each(function () { - var $this = $(this) - , data = $this.data('tooltip') - , options = typeof option == 'object' && option - if (!data) $this.data('tooltip', (data = new Tooltip(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.tooltip.Constructor = Tooltip - - $.fn.tooltip.defaults = { - animation: true - , placement: 'top' - , selector: false - , template: '<div class="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>' - , trigger: 'hover' - , title: '' - , delay: 0 - } - -}(window.jQuery); -/* =========================================================== - * bootstrap-popover.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#popovers - * =========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * =========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* POPOVER PUBLIC CLASS DEFINITION - * =============================== */ - - var Popover = function ( element, options ) { - this.init('popover', element, options) - } - - - /* NOTE: POPOVER EXTENDS BOOTSTRAP-TOOLTIP.js - ========================================== */ - - Popover.prototype = $.extend({}, $.fn.tooltip.Constructor.prototype, { - - constructor: Popover - - , setContent: function () { - var $tip = this.tip() - , title = this.getTitle() - , content = this.getContent() - - $tip.find('.popover-title')[this.isHTML(title) ? 'html' : 'text'](title) - $tip.find('.popover-content > *')[this.isHTML(content) ? 'html' : 'text'](content) - - $tip.removeClass('fade top bottom left right in') - } - - , hasContent: function () { - return this.getTitle() || this.getContent() - } - - , getContent: function () { - var content - , $e = this.$element - , o = this.options - - content = $e.attr('data-content') - || (typeof o.content == 'function' ? o.content.call($e[0]) : o.content) - - return content - } - - , tip: function () { - if (!this.$tip) { - this.$tip = $(this.options.template) - } - return this.$tip - } - - }) - - - /* POPOVER PLUGIN DEFINITION - * ======================= */ - - $.fn.popover = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('popover') - , options = typeof option == 'object' && option - if (!data) $this.data('popover', (data = new Popover(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.popover.Constructor = Popover - - $.fn.popover.defaults = $.extend({} , $.fn.tooltip.defaults, { - placement: 'right' - , content: '' - , template: '<div class="popover"><div class="arrow"></div><div class="popover-inner"><h3 class="popover-title"></h3><div class="popover-content"><p></p></div></div></div>' - }) - -}(window.jQuery);/* ============================================================= - * bootstrap-scrollspy.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#scrollspy - * ============================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* SCROLLSPY CLASS DEFINITION - * ========================== */ - - function ScrollSpy( element, options) { - var process = $.proxy(this.process, this) - , $element = $(element).is('body') ? $(window) : $(element) - , href - this.options = $.extend({}, $.fn.scrollspy.defaults, options) - this.$scrollElement = $element.on('scroll.scroll.data-api', process) - this.selector = (this.options.target - || ((href = $(element).attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 - || '') + ' .nav li > a' - this.$body = $('body') - this.refresh() - this.process() - } - - ScrollSpy.prototype = { - - constructor: ScrollSpy - - , refresh: function () { - var self = this - , $targets - - this.offsets = $([]) - this.targets = $([]) - - $targets = this.$body - .find(this.selector) - .map(function () { - var $el = $(this) - , href = $el.data('target') || $el.attr('href') - , $href = /^#\w/.test(href) && $(href) - return ( $href - && href.length - && [[ $href.position().top, href ]] ) || null - }) - .sort(function (a, b) { return a[0] - b[0] }) - .each(function () { - self.offsets.push(this[0]) - self.targets.push(this[1]) - }) - } - - , process: function () { - var scrollTop = this.$scrollElement.scrollTop() + this.options.offset - , scrollHeight = this.$scrollElement[0].scrollHeight || this.$body[0].scrollHeight - , maxScroll = scrollHeight - this.$scrollElement.height() - , offsets = this.offsets - , targets = this.targets - , activeTarget = this.activeTarget - , i - - if (scrollTop >= maxScroll) { - return activeTarget != (i = targets.last()[0]) - && this.activate ( i ) - } - - for (i = offsets.length; i--;) { - activeTarget != targets[i] - && scrollTop >= offsets[i] - && (!offsets[i + 1] || scrollTop <= offsets[i + 1]) - && this.activate( targets[i] ) - } - } - - , activate: function (target) { - var active - , selector - - this.activeTarget = target - - $(this.selector) - .parent('.active') - .removeClass('active') - - selector = this.selector - + '[data-target="' + target + '"],' - + this.selector + '[href="' + target + '"]' - - active = $(selector) - .parent('li') - .addClass('active') - - if (active.parent('.dropdown-menu')) { - active = active.closest('li.dropdown').addClass('active') - } - - active.trigger('activate') - } - - } - - - /* SCROLLSPY PLUGIN DEFINITION - * =========================== */ - - $.fn.scrollspy = function ( option ) { - return this.each(function () { - var $this = $(this) - , data = $this.data('scrollspy') - , options = typeof option == 'object' && option - if (!data) $this.data('scrollspy', (data = new ScrollSpy(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.scrollspy.Constructor = ScrollSpy - - $.fn.scrollspy.defaults = { - offset: 10 - } - - - /* SCROLLSPY DATA-API - * ================== */ - - $(function () { - $('[data-spy="scroll"]').each(function () { - var $spy = $(this) - $spy.scrollspy($spy.data()) - }) - }) - -}(window.jQuery);/* ======================================================== - * bootstrap-tab.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#tabs - * ======================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ======================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* TAB CLASS DEFINITION - * ==================== */ - - var Tab = function ( element ) { - this.element = $(element) - } - - Tab.prototype = { - - constructor: Tab - - , show: function () { - var $this = this.element - , $ul = $this.closest('ul:not(.dropdown-menu)') - , selector = $this.attr('data-target') - , previous - , $target - , e - - if (!selector) { - selector = $this.attr('href') - selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 - } - - if ( $this.parent('li').hasClass('active') ) return - - previous = $ul.find('.active a').last()[0] - - e = $.Event('show', { - relatedTarget: previous - }) - - $this.trigger(e) - - if (e.isDefaultPrevented()) return - - $target = $(selector) - - this.activate($this.parent('li'), $ul) - this.activate($target, $target.parent(), function () { - $this.trigger({ - type: 'shown' - , relatedTarget: previous - }) - }) - } - - , activate: function ( element, container, callback) { - var $active = container.find('> .active') - , transition = callback - && $.support.transition - && $active.hasClass('fade') - - function next() { - $active - .removeClass('active') - .find('> .dropdown-menu > .active') - .removeClass('active') - - element.addClass('active') - - if (transition) { - element[0].offsetWidth // reflow for transition - element.addClass('in') - } else { - element.removeClass('fade') - } - - if ( element.parent('.dropdown-menu') ) { - element.closest('li.dropdown').addClass('active') - } - - callback && callback() - } - - transition ? - $active.one($.support.transition.end, next) : - next() - - $active.removeClass('in') - } - } - - - /* TAB PLUGIN DEFINITION - * ===================== */ - - $.fn.tab = function ( option ) { - return this.each(function () { - var $this = $(this) - , data = $this.data('tab') - if (!data) $this.data('tab', (data = new Tab(this))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.tab.Constructor = Tab - - - /* TAB DATA-API - * ============ */ - - $(function () { - $('body').on('click.tab.data-api', '[data-toggle="tab"], [data-toggle="pill"]', function (e) { - e.preventDefault() - $(this).tab('show') - }) - }) - -}(window.jQuery);/* ============================================================= - * bootstrap-typeahead.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#typeahead - * ============================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================ */ - - -!function($){ - - "use strict"; // jshint ;_; - 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\ No newline at end of file diff --git a/docs/pai.html b/docs/pai.html deleted file mode 100644 index 61b1722..0000000 --- a/docs/pai.html +++ /dev/null @@ -1,134 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>pai. chents 0.2-3</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">chents 0.2-3</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>An R6 class for pesticidal active ingredients and associated data</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="symbol">pai</span></pre> - - <div class="Format"> - <h2>Format</h2> - - <p>An <code><a href='http://www.rdocumentation.org/packages/R6/topics/R6Class'>R6Class</a></code> generator object</p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>The class is initialised with an identifier which is generally an ISO common name. -Additional chemical information is retrieved from the internet.</p> - - </div> - - <div class="Fields"> - <h2>Fields</h2> - - <p></p> - - <p><dl> -<dt><code>iso</code></dt><dd>ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides</dd></p> - - <p><dt><code>alanwood</code></dt><dd>List of information retreived from www.alanwood.net/pesticides</dd></p> - - <p></dl></p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="symbol">atr</span> <span class="assignement"><-</span> <span class="symbol">pai</span><span class="keyword">$</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/methods/topics/new'>new</a></span><span class="keyword">(</span><span class="string">"atrazine"</span><span class="keyword">)</span></div> -<strong class='message'>alanwood.net:</strong> -<strong class='message'>Querying atrazine.html</strong> -<strong class='message'>PubChem:</strong> -<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</strong> -<strong class='message'>Found 1 entries in PubChem, using the first one.</strong> -<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,ExactMass,MonoisotopicMass,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,HeavyAtomCount,IsotopeAtomCount,AtomStereoCount,DefinedAtomStereoCount,UndefinedAtomStereoCount,BondStereoCount,DefinedBondStereoCount,UndefinedBondStereoCount,CovalentUnitCount,Volume3D,XStericQuadrupole3D,YStericQuadrupole3D,ZStericQuadrupole3D,FeatureCount3D,FeatureAcceptorCount3D,FeatureDonorCount3D,FeatureAnionCount3D,FeatureCationCount3D,FeatureRingCount3D,FeatureHydrophobeCount3D,ConformerModelRMSD3D,EffectiveRotorCount3D,ConformerCount3D,Fingerprint2D/JSON</strong> -<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</strong> -<strong class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES -CCNC1=NC(=NC(=N1)Cl)NC(C)C</strong> -<strong class='message'>Did not find chyaml file ./atrazine.yaml</strong> -<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="symbol">atr</span><span class="keyword">)</span></div> -<div class='output'><pai> with ISO common name $iso atrazine -<chent> -Identifier $identifier atrazine -InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N -SMILES string $smiles: - PubChem_Canonical -"CCNC1=NC(=NC(=N1)Cl)NC(C)C" -Molecular weight $mw: 215.7 -PubChem synonyms (up to 10): - [1] "2256" "atrazine" "1912-24-9" "Fenatrol" "Atranex" "Atred" - [7] "Atazinax" "Atrasine" "Chromozin" "Gesaprim" -</div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>pai</li> - </ul> - <ul> - <li>data</li> - </ul> --> - - - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/plot.chent-12.png b/docs/plot.chent-12.png Binary files differdeleted file mode 100644 index 4485326..0000000 --- a/docs/plot.chent-12.png +++ /dev/null diff --git a/docs/plot.chent.html b/docs/plot.chent.html deleted file mode 100644 index 1b1c5b7..0000000 --- a/docs/plot.chent.html +++ /dev/null @@ -1,123 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>plot.chent. chents 0.2-3</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">chents 0.2-3</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Plot method for chent objects</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="comment"># S3 method for chent</span> -<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>x</dt> - <dd>The chent object to be plotted</dd> - <dt>...</dt> - <dd>Further arguments passed to <code><a href='http://www.rdocumentation.org/packages/grImport/topics/grid.picture'>grid.picture</a></code></dd> - </dl> - - <div class="Description"> - <h2>Description</h2> - - <p>Plot method for chent objects</p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="symbol">caffeine</span> <span class="assignement"><-</span> <span class="symbol">chent</span><span class="keyword">$</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/methods/topics/new'>new</a></span><span class="keyword">(</span><span class="string">"caffeine"</span><span class="keyword">)</span></div> -<strong class='message'>PubChem:</strong> -<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</strong> -<strong class='message'>Found 1 entries in PubChem, using the first one.</strong> -<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,ExactMass,MonoisotopicMass,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,HeavyAtomCount,IsotopeAtomCount,AtomStereoCount,DefinedAtomStereoCount,UndefinedAtomStereoCount,BondStereoCount,DefinedBondStereoCount,UndefinedBondStereoCount,CovalentUnitCount,Volume3D,XStericQuadrupole3D,YStericQuadrupole3D,ZStericQuadrupole3D,FeatureCount3D,FeatureAcceptorCount3D,FeatureDonorCount3D,FeatureAnionCount3D,FeatureCationCount3D,FeatureRingCount3D,FeatureHydrophobeCount3D,ConformerModelRMSD3D,EffectiveRotorCount3D,ConformerCount3D,Fingerprint2D/JSON</strong> -<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</strong> -<strong class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES -CN1C=NC2=C1C(=O)N(C(=O)N2C)C</strong> -<strong class='message'>Did not find chyaml file ./caffeine.yaml</strong> -<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="symbol">caffeine</span><span class="keyword">)</span></div> -<div class='output'><chent> -Identifier $identifier caffeine -InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N -SMILES string $smiles: - PubChem_Canonical -"CN1C=NC2=C1C(=O)N(C(=O)N2C)C" -Molecular weight $mw: 194.2 -PubChem synonyms (up to 10): - [1] "2519" "caffeine" - [3] "1,3,7-Trimethylxanthine" "Methyltheobromine" - [5] "Guaranine" "Cafeina" - [7] "Koffein" "Mateina" - [9] "Thein" "Theine" -</div> -<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">caffeine</span><span class="keyword">)</span></div> -<p><img src='plot.chent-12.png' alt='' width='540' height='400' /></p></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>plot.chent</li> - </ul> - <ul> - - </ul> --> - - - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. 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\ No newline at end of file diff --git a/docs/pp.html b/docs/pp.html deleted file mode 100644 index 087141a..0000000 --- a/docs/pp.html +++ /dev/null @@ -1,111 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>pp. chents 0.2-3</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">chents 0.2-3</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>R6 class for holding a product with at least one active ingredient</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="symbol">pp</span></pre> - - <div class="Format"> - <h2>Format</h2> - - <p>An <code><a href='http://www.rdocumentation.org/packages/R6/topics/R6Class'>R6Class</a></code> generator object.</p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>An R6 class for holding information about a product with at least one active ingredient</p> - - </div> - - <div class="Fields"> - <h2>Fields</h2> - - <p></p> - - <p><dl> -<dt><code>name</code></dt><dd>The name of the product</dd></p> - - <p><dt><code>ais</code></dt><dd>A list of active ingredients</dd></p> - - <p><dt><code>concentrations</code></dt><dd>The concentration of the ais</dd></p> - - <p><dt><code>concentration_units</code></dt><dd>Defaults to g/L</dd></p> - - <p></dl></p> - - </div> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>pp</li> - </ul> - <ul> - <li>data</li> - </ul> --> - - - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/print.chent.html b/docs/print.chent.html deleted file mode 100644 index 714bf4d..0000000 --- a/docs/print.chent.html +++ /dev/null @@ -1,95 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>print.chent. chents 0.2-3</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">chents 0.2-3</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Printing method for chent objects</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="comment"># S3 method for chent</span> -<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>x</dt> - <dd>The chent object to be printed</dd> - <dt>...</dt> - <dd>Further arguments for compatibility with the S3 method</dd> - </dl> - - <div class="Description"> - <h2>Description</h2> - - <p>Printing method for chent objects</p> - - </div> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>print.chent</li> - </ul> - <ul> - - </ul> --> - - - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/print.pai.html b/docs/print.pai.html deleted file mode 100644 index 910f0e2..0000000 --- a/docs/print.pai.html +++ /dev/null @@ -1,95 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>print.pai. chents 0.2-3</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">chents 0.2-3</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Printing method for pai objects (pesticidal active ingredients)</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="comment"># S3 method for pai</span> -<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>x</dt> - <dd>The chent object to be printed</dd> - <dt>...</dt> - <dd>Further arguments for compatibility with the S3 method</dd> - </dl> - - <div class="Description"> - <h2>Description</h2> - - <p>Printing method for pai objects (pesticidal active ingredients)</p> - - </div> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>print.pai</li> - </ul> - <ul> - - </ul> --> - - - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/reference.html b/docs/reference.html deleted file mode 100644 index 52c537d..0000000 --- a/docs/reference.html +++ /dev/null @@ -1,99 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>Function reference. chents 0.2-3</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">chents 0.2-3</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <div class="row"> - <div class="span8"> - <h2>Function reference</h2> - - <h3>Class definitions</h3> - <p>R6 classes and their methods</p> - - - <ul class="index"> - - <li> - <code><a href="chent.html">chent</a></code><br />An R6 class for chemical entities with associated data</li> - - <li> - <code><a href="pai.html">pai</a></code><br />An R6 class for pesticidal active ingredients and associated data</li> - - <li> - <code><a href="pp.html">pp</a></code><br />R6 class for holding a product with at least one active ingredient</li> - - </ul> - <h3>Other</h3> - - - <ul class="index"> - - <li> - <code><a href="draw_svg.chent.html">draw_svg.chent</a></code><br />Draw SVG graph from a chent object using RDKit</li> - - <li> - <code><a href="plot.chent.html">plot.chent</a></code><br />Plot method for chent objects</li> - - <li> - <code><a href="print.chent.html">print.chent</a></code><br />Printing method for chent objects</li> - - <li> - <code><a href="print.pai.html">print.pai</a></code><br />Printing method for pai objects (pesticidal active ingredients)</li> - - </ul> - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
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