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It can be used directly with the preconfigured +list of functional groups as listed in `Functional Group Tree`_ or by +specifying your own patterns using :py:class:`~fgutils.fgconfig.FGConfig` +and :py:class:`~fgutils.fgconfig.FGConfigProvider`. + +Get functional groups in molecule +================================= + +Common functional groups of a molecule can be retrieved by the +:py:class:`~fgutils.query.FGQuery` class. The query can directly use the +molecules SMILES or the molecular graph representation of the compound as +networkx graph. The following example demonstrates how to get the functional +groups from *acetylsalicylic acid*:: + + >>> from fgutils import FGQuery + + >>> smiles = "O=C(C)Oc1ccccc1C(=O)O" # acetylsalicylic acid + >>> query = FGQuery() + >>> query.get(smiles) + [("ester", [0, 1, 3]), ("carboxylic_acid", [10, 11, 12])] + + +Get changing groups in reaction +=============================== + +The extended :ref:`graph-syntax` enables the description of reaction +mechanisms by specifying bond changes in ``<>`` brackets. Functional group +patterns can therefor also specify bond changes. Querying bond changes can be +used to look for a changing functional groups in a reaction. The following +example demonstrates how to check for a nucleophilic addition-elimination +reaction on a carbonyl group:: + + >>> from fgutils.query import FGQuery, FGConfig + + >>> smiles = "[C:1][C:2](=[O:3])[O:4][C:5].[O:6]>>[C:1][C:2](=[O:3])[O:6].[O:4][C:5]" + >>> fgconfig = FGConfig(name="carbonyl-AE", pattern="C(=O)(<0,1>R)<1,0>R") + >>> query = FGQuery(config=fgconfig, require_implicit_hydrogen=False) + >>> query.get(smiles) + [("carbonyl-AE", [2, 3, 4, 6])] + + +Functional Group Tree +===================== + +.. code-block:: + + Functional Group Parents Pattern + ---------------------------------------------------------------------------- + ether [ROOT] ROR + ├── ketal [ether] RC(OR)(OR)R + │ ├── acetal [ketal] RC(OC)(OC)H + │ └── hemiketal [ketal, alcohol] RC(OH)(OR)R + │ └── hemiacetal [hemiketal] RC(OC)(OH)H + ├── epoxid [ether] RC(R)1C(R)(R)O1 + ├── ester [ketone, ether] RC(=O)OR + │ ├── anhydride [ester] RC(=O)OC(=O)R + │ ├── peroxy_acid [ester, peroxide] RC(=O)OOH + │ ├── carbamate [amide, ester] ROC(=O)N(R)R + │ └── carboxylic_acid [ester, alcohol] RC(=O)OH + ├── alcohol [ether] COH + │ ├── hemiketal [ketal, alcohol] RC(OH)(OR)R + │ │ └── hemiacetal [hemiketal] RC(OC)(OH)H + │ ├── carboxylic_acid [ester, alcohol] RC(=O)OH + │ ├── enol [alcohol] C=COH + │ ├── primary_alcohol [alcohol] CCOH + │ │ └── secondary_alcohol [primary_alcohol] C(C)(C)OH + │ │ └── tertiary_alcohol [secondary_alcohol] C(C)(C)(C)OH + │ └── phenol [alcohol] C:COH + └── peroxide [ether] ROOR + └── peroxy_acid [ester, peroxide] RC(=O)OOH + thioether [ROOT] RSR + └── thioester [ketone, thioether] RC(=O)SR + amine [ROOT] RN(R)R + ├── amide [ketone, amine] RC(=O)N(R)R + │ └── carbamate [amide, ester] ROC(=O)N(R)R + └── anilin [amine] C:CN(R)R + carbonyl [ROOT] C(=O) + ├── ketene [carbonyl] RC(R)=C=O + └── ketone [carbonyl] RC(=O)R + ├── amide [ketone, amine] RC(=O)N(R)R + │ └── carbamate [amide, ester] ROC(=O)N(R)R + ├── thioester [ketone, thioether] RC(=O)SR + ├── ester [ketone, ether] RC(=O)OR + │ ├── anhydride [ester] RC(=O)OC(=O)R + │ ├── peroxy_acid [ester, peroxide] RC(=O)OOH + │ ├── carbamate [amide, ester] ROC(=O)N(R)R + │ └── carboxylic_acid [ester, alcohol] RC(=O)OH + ├── acyl_chloride [ketone] RC(=O)Cl + └── aldehyde [ketone] RC(=O)H + nitrose [ROOT] RN=O + └── nitro [nitrose] RN(=O)O + nitrile [ROOT] RC#N diff --git a/_sources/getting_started.rst.txt b/_sources/getting_started.rst.txt new file mode 100644 index 0000000..ca35171 --- /dev/null +++ b/_sources/getting_started.rst.txt @@ -0,0 +1,15 @@ +=============== +Getting Started +=============== + +Installation +============ + + +Query Functional Groups +======================= + + + +A Simple Reaction Proxy +======================= diff --git a/_sources/graph_syntax.rst.txt b/_sources/graph_syntax.rst.txt new file mode 100644 index 0000000..df55f4a --- /dev/null +++ b/_sources/graph_syntax.rst.txt @@ -0,0 +1,186 @@ +.. _graph-syntax: + +============ +Graph Syntax +============ + +FGUtils has its own graph description language. The syntax is closely related +to the SMILES format for molecules and reactions. It is kind of an extenstion +to SMILES to support modeling ITS graphs and reaction patterns. To convert the +SMILES-like description into a graph object use the +:py:class:`~fgutils.parse.Parser` class. The Caffeine molecular graph can be +obtained as follows:: + + import matplotlib.pyplot as plt + from fgutils import Parser + from fgutils.vis import plot_as_mol + + parser = Parser() + mol = parser("CN1C=NC2=C1C(=O)N(C(=O)N2C)C") + + fig, ax = plt.subplots(1, 1) + plot_as_mol(mol, ax) + plt.show() + +.. image:: figures/caffeine_example.png + :width: 300 + +Besides parsing common SMILES it is possible to generate molecule-like graphs +with more abstract nodes, i.e., arbitrary node labels. Arbitrary node labels +are surrounded by ``{}`` (e.g. ``{label}``). This abstract labeling can be used +to substitute nodes with specific patterns. In this context the labels are +group names of :py:class:`~fgutils.proxy.ProxyGroup` objects. A ProxyGroup +defines a set of sub-graphs to be replaced for the labeled node. This can be +done by using a :py:class:`~fgutils.proxy.Proxy`. Propyl acetate can be created +by replacing the labeled node with the propyl group:: + + import matplotlib.pyplot as plt + from fgutils import Parser + from fgutils.proxy import MolProxy, ProxyGroup + from fgutils.vis import GraphVisualizer + + pattern = "CC(=O)O{propyl}" + propyl_group = ProxyGroup("propyl", "CCC") + parser = Parser() + proxy = MolProxy(pattern, propyl_group, parser=parser) + + g = parser(pattern) + mol = next(proxy) + + vis = GraphVisualizer() + fig, ax = plt.subplots(1, 2, dpi=100, figsize=(12, 3)) + vis.plot(g, ax[0], title="Core Pattern") + vis.plot(mol, ax[1], title="Generated Molecule") + plt.show() + +.. image:: figures/labeled_node_example.png + :width: 600 + + +.. note:: + + A node can have more than one label. This can be done by separating the + labels with a comma, e.g.: ``{label_1,label_2}``. + +In the example above the ProxyGroup has only one subgraph pattern. In general, +a ProxyGroup is a collection of several possible subgraphs from which one is +selected when a new sample is instantiated. To get more information on how +graphs are sample take a look at the :py:class:`~fgutils.proxy.GraphSampler` +class and the :py:class:`~fgutils.proxy.ProxyGroup` constructor. By default a +pattern has one anchor at index 0. If you need more control over how a subgraph +is inserted into a parent graph you can instantiate the +:py:class:`~fgutils.proxy.ProxyGraph` class. For a ProxyGraph you can provide a +list of anchor node indices. The insertion of the subgraph into the parent +depends on the number of anchor nodes in the subgraph and the number of edges +to the labeled node in the parent. The first edge in the parent connects to the +first anchor node in the subgraph and so forth. The following example +demonstrates the insertion with multiple anchor nodes:: + + import matplotlib.pyplot as plt + from fgutils.proxy import MolProxy, ProxyGroup, ProxyGraph, Parser + from fgutils.vis import GraphVisualizer + + pattern = "N{g}C{g}(O)C" + g_1 = ProxyGroup("g", ProxyGraph("C1CCCCC1", anchor=[1, 3])) + g_2 = ProxyGroup("g", ProxyGraph("C1CCCCC1", anchor=[1, 3, 4])) + + parser = Parser() + proxy1 = MolProxy(pattern, g_1) + proxy2 = MolProxy(pattern, g_2) + + parent_graph = parser(pattern) + mol1 = next(proxy1) + mol2 = next(proxy2) + + vis = GraphVisualizer(show_edge_labels=False) + fig, ax = plt.subplots(1, 3, dpi=200, figsize=(20, 3)) + vis.plot(parent_graph, ax[0], title="parent") + vis.plot(mol1, ax[1], title="2 anchor nodes") + vis.plot(mol2, ax[2], title="3 anchor nodes") + plt.show() + +.. image:: figures/multiple_anchor_example.png + :width: 1000 + +Another extension to the SMILES notation is the encoding of bond changes. This +feature is required to model reaction mechanisms as ITS graph. Changing bonds +are surrounded by ``<>`` (e.g. ``<1, 2>`` for the formation of a double bond +from a single bond). The extended notation allows the automated generation of +reaction examples with complete atom-to-atom maps. The following code snippet +demonstrates the generation of a few Diels-Alder reactions. The **diene** and +**dienophile** groups can of course be extended to increase varaity of the +samples:: + + + import random + import matplotlib.pyplot as plt + from fgutils.proxy import ProxyGroup, ProxyGraph, ReactionProxy + from fgutils.proxy_collection.common import common_groups + from fgutils.vis import plot_reaction, plot_its + from fgutils.chem.its import get_its + + + electron_donating_group = ProxyGroup( + "electron_donating_group", + ["{methyl}", "{ethyl}", "{propyl}", "{aryl}", "{amine}"], + ) + electron_withdrawing_group = ProxyGroup( + "electron_withdrawing_group", + ["{alkohol}", "{ether}", "{aldehyde}", "{ester}", "{nitrile}"], + ) + diene_group = ProxyGroup( + "diene", + ProxyGraph("C<2,1>C<1,2>C<2,1>C{electron_donating_group}", anchor=[0, 3]), + ) + dienophile_group = ProxyGroup( + "dienophile", + ProxyGraph("C<2,1>C{electron_withdrawing_group}", anchor=[0, 1]), + ) + groups = common_groups + [ + electron_donating_group, + electron_withdrawing_group, + diene_group, + dienophile_group, + ] + + proxy = ReactionProxy("{diene}1<0,1>{dienophile}<0,1>1", groups) + + n = 4 + fig, ax = plt.subplots(n, 2, width_ratios=[2, 1], figsize=(20, n * 4)) + for i, (g, h) in enumerate(random.sample(list(proxy), n)): + plot_reaction(g, h, ax[i, 0], title="Reaction") + plot_its(get_its(g, h), ax[i, 1], title="ITS Graph") + plt.tight_layout() + plt.show() + +.. image:: figures/diels_alder_example.png + :width: 1000 + +This proxy can now generate Diels-Alder reaction samples. A few of the results +are shown in the figure above. On the left side the reaction and on the right +side the resulting ITS. The results are balanced and have complete atom-to-atom +maps. The atom-to-atom maps are correct as long as the configuration makes +sence in the chemical domain. Note that the synthesizability of the generated +samples can not be guaranteed. It soley depends on what ProxyGroups and +ProxyGraphs are configured. For a comprehensive Diels-Alder reaction proxy take +a look at the +:py:class:`~fgutils.proxy_collection.diels_alder_proxy.DielsAlderProxy` class +and the section TODO. This class is also able to generate negative Diels-Alder +reaction samples, i.e., reactions where a Diels-Alder graph transformation rule +is theoretically applicable but the reaction will never happen in reality. + +.. note:: + + The ``electron_donating_group`` and ``electron_withdrawing_group`` serve as + a collection of other groups to simplify the notation. They consist of a + single node with multiple labels. When iterating the next sample from the + proxy the labeled nodes get replaced by the pattern from one of the groups. + The group/label is chosen randomly with uniform distribution. + + +.. warning:: + + The call ``list(proxy)`` will generate all possible instantiations at once. + Depending on the configuration this can take a long time to complete. If the + core ProxyGroup graph sampling is not unique this can even result in an + endless loop. diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 0000000..b14f042 --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,16 @@ +.. FGUtils documentation master file, created by + sphinx-quickstart on Tue Aug 20 09:10:34 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to FGUtils's documentation! +=================================== + +.. toctree:: + :maxdepth: 1 + + getting_started + functional_groups + graph_syntax + proxy_collection + references diff --git a/_sources/proxy_collection.rst.txt b/_sources/proxy_collection.rst.txt new file mode 100644 index 0000000..6cb0be7 --- /dev/null +++ b/_sources/proxy_collection.rst.txt @@ -0,0 +1,96 @@ +================ +Proxy Collection +================ + + +.. _diels-alder_reaction_proxy: + +Diels-Alder Reaction Proxy +========================== + +The class +:py:class:`~fgutils.proxy_collection.diels_alder_proxy.DielsAlderProxy` +implements a comprehensive Diels-Alder reaction generation proxy. It generates +ring formation reaction samples between diene and dienophile molecules. It can +also be used to generate negative reaction samples, i.e., reactions where a +Diels-Alder graph transformation rule is theoretically applicable but the +reaction will never happen in reality. + +The Diels-Alder Reaction proxy has the following reaction center graphs +configured (ProxyGraphs of the *core* ProxyGroup). Node labels show the atom +type or group name and the node index and edge labels depict the bond type. +Bond changes are depicted as tuples ``(,)`` where the first +entry is the bond in the reactants and the second entry is the bond in the +product. + + +.. image:: figures/proxy_collection_DAReactionProxy.png + :width: 1000 + +The **Intra Molecular Center** is used to generate intra molecular Diels-Alder +reactions. It depicts the entire reaction center. It's easy to identify the [4 ++ 2] cycloaddition reaction center between the diene part (C=CC=C, node 0-3) +and the dienophile part (C=C, node 5-6). Diene and dienophile are connected +by node 4, a graph from the **intra_mol_bridge** group. The **Inter Molecular +Center** depicts the abstracted reaction center for inter molecular Diels-Alder +reactions. + +.. note:: + + Have you noticed that the **Inter Molecular Center** is a multi graph (it + has multiple edges between two vertices)? Molecular graphs are never multi + graphs, the bond order is represented as label on the unique edge between + two atoms. However, to represent this abstract form of the reaction center + it's necessary to have independent edges for both single bond formations. + To parse this type of graphs you must set the ``use_multigraph=True`` + argument in :py:class:`~fgutils.parse.Parser`. + +The next level of abstraction are the **diene** and **dienophile** ProxyGroups. +They provide the structures depicted in the following two figures, +respectively. Anchor nodes, the nodes where the substructures connect to the +parent, are surrounded by ``[]``. + +**Graphs from the diene group:** + +.. image:: figures/proxy_collection_DAReactionProxy_diene.png + :width: 1000 + +**Graphs from the dienophile group:** + +.. image:: figures/proxy_collection_DAReactionProxy_dienophile.png + :width: 1000 + +**Graphs from the electron_donating_group:** + +.. image:: figures/proxy_collection_DAReactionProxy_EDG.png + :width: 1000 + +**Graphs from the electron_withdrawing_group:** + +.. image:: figures/proxy_collection_DAReactionProxy_EWG.png + :width: 1000 + +**A few of the 10470 Diels-Alder reactions generated by the proxy:** + +.. image:: figures/proxy_collection_DAReactionProxy_DA_reactions.png + :width: 1000 + +Invalid Sample Generation (negative data) +----------------------------------------- + +The :py:class:`~fgutils.proxy_collection.diels_alder_proxy.DielsAlderProxy` +provides the functionality to generate Diels-Alder counter examples, i.e., +reactions where based on the structure a Diels-Alder graph transformation rule +would be applicable but the reaction can not happen because the diene is for +example in a fixed s-trans conformation. + +**Graphs from the (s-trans) diene group:** + +.. image:: figures/proxy_collection_DAReactionProxy_s-trans_diene.png + :width: 1000 + +**A few of the 12875 INVALID Diels-Alder reactions generated by the proxy +(negative data):** + +.. image:: figures/proxy_collection_DAReactionProxy_DA_reactions_neg.png + :width: 1000 diff --git a/_sources/references.rst.txt b/_sources/references.rst.txt new file mode 100644 index 0000000..a9ea2b8 --- /dev/null +++ b/_sources/references.rst.txt @@ -0,0 +1,44 @@ +========== +References +========== + +fgconfig +======== + +.. automodule:: fgutils.fgconfig + :members: + +utils +===== + +.. automodule:: fgutils.utils + :members: + +query +===== + +.. automodule:: fgutils.query + :members: + +parse +===== + +.. automodule:: fgutils.parse + :members: + + +proxy +===== + +.. automodule:: fgutils.proxy + :members: + + +proxy_collection +================ + +.. automodule:: fgutils.proxy_collection.common + :members: + +.. automodule:: fgutils.proxy_collection.diels_alder_proxy + :members: diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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+ float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; 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+ +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/functional_groups.html b/functional_groups.html new file mode 100644 index 0000000..2d9b8f3 --- /dev/null +++ b/functional_groups.html @@ -0,0 +1,209 @@ + + + + + + + Functional Groups — FGUtils documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Functional Groups

+

FGUtils provides a class FGQuery to retrieve a +molecules functional groups. It can be used directly with the preconfigured +list of functional groups as listed in Functional Group Tree or by +specifying your own patterns using FGConfig +and FGConfigProvider.

+
+

Get functional groups in molecule

+

Common functional groups of a molecule can be retrieved by the +FGQuery class. The query can directly use the +molecules SMILES or the molecular graph representation of the compound as +networkx graph. The following example demonstrates how to get the functional +groups from acetylsalicylic acid:

+
>>> from fgutils import FGQuery
+
+>>> smiles = "O=C(C)Oc1ccccc1C(=O)O"  # acetylsalicylic acid
+>>> query = FGQuery()
+>>> query.get(smiles)
+[("ester", [0, 1, 3]), ("carboxylic_acid", [10, 11, 12])]
+
+
+
+
+

Get changing groups in reaction

+

The extended Graph Syntax enables the description of reaction +mechanisms by specifying bond changes in <> brackets. Functional group +patterns can therefor also specify bond changes. Querying bond changes can be +used to look for a changing functional groups in a reaction. The following +example demonstrates how to check for a nucleophilic addition-elimination +reaction on a carbonyl group:

+
>>> from fgutils.query import FGQuery, FGConfig
+
+>>> smiles = "[C:1][C:2](=[O:3])[O:4][C:5].[O:6]>>[C:1][C:2](=[O:3])[O:6].[O:4][C:5]"
+>>> fgconfig = FGConfig(name="carbonyl-AE", pattern="C(=O)(<0,1>R)<1,0>R")
+>>> query = FGQuery(config=fgconfig, require_implicit_hydrogen=False)
+>>> query.get(smiles)
+[("carbonyl-AE", [2, 3, 4, 6])]
+
+
+
+
+

Functional Group Tree

+
Functional Group                    Parents                  Pattern
+----------------------------------------------------------------------------
+ether                               [ROOT]                   ROR
+├── ketal                           [ether]                  RC(OR)(OR)R
+│   ├── acetal                      [ketal]                  RC(OC)(OC)H
+│   └── hemiketal                   [ketal, alcohol]         RC(OH)(OR)R
+│       └── hemiacetal              [hemiketal]              RC(OC)(OH)H
+├── epoxid                          [ether]                  RC(R)1C(R)(R)O1
+├── ester                           [ketone, ether]          RC(=O)OR
+│   ├── anhydride                   [ester]                  RC(=O)OC(=O)R
+│   ├── peroxy_acid                 [ester, peroxide]        RC(=O)OOH
+│   ├── carbamate                   [amide, ester]           ROC(=O)N(R)R
+│   └── carboxylic_acid             [ester, alcohol]         RC(=O)OH
+├── alcohol                         [ether]                  COH
+│   ├── hemiketal                   [ketal, alcohol]         RC(OH)(OR)R
+│   │   └── hemiacetal              [hemiketal]              RC(OC)(OH)H
+│   ├── carboxylic_acid             [ester, alcohol]         RC(=O)OH
+│   ├── enol                        [alcohol]                C=COH
+│   ├── primary_alcohol             [alcohol]                CCOH
+│   │   └── secondary_alcohol       [primary_alcohol]        C(C)(C)OH
+│   │       └── tertiary_alcohol    [secondary_alcohol]      C(C)(C)(C)OH
+│   └── phenol                      [alcohol]                C:COH
+└── peroxide                        [ether]                  ROOR
+    └── peroxy_acid                 [ester, peroxide]        RC(=O)OOH
+thioether                           [ROOT]                   RSR
+└── thioester                       [ketone, thioether]      RC(=O)SR
+amine                               [ROOT]                   RN(R)R
+├── amide                           [ketone, amine]          RC(=O)N(R)R
+│   └── carbamate                   [amide, ester]           ROC(=O)N(R)R
+└── anilin                          [amine]                  C:CN(R)R
+carbonyl                            [ROOT]                   C(=O)
+├── ketene                          [carbonyl]               RC(R)=C=O
+└── ketone                          [carbonyl]               RC(=O)R
+    ├── amide                       [ketone, amine]          RC(=O)N(R)R
+    │   └── carbamate               [amide, ester]           ROC(=O)N(R)R
+    ├── thioester                   [ketone, thioether]      RC(=O)SR
+    ├── ester                       [ketone, ether]          RC(=O)OR
+    │   ├── anhydride               [ester]                  RC(=O)OC(=O)R
+    │   ├── peroxy_acid             [ester, peroxide]        RC(=O)OOH
+    │   ├── carbamate               [amide, ester]           ROC(=O)N(R)R
+    │   └── carboxylic_acid         [ester, alcohol]         RC(=O)OH
+    ├── acyl_chloride               [ketone]                 RC(=O)Cl
+    └── aldehyde                    [ketone]                 RC(=O)H
+nitrose                             [ROOT]                   RN=O
+└── nitro                           [nitrose]                RN(=O)O
+nitrile                             [ROOT]                   RC#N
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/genindex.html b/genindex.html new file mode 100644 index 0000000..d84be43 --- /dev/null +++ b/genindex.html @@ -0,0 +1,312 @@ + + + + + + Index — FGUtils documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ B + | D + | F + | G + | M + | P + | R + | S + +
+

B

+ + + +
+ +

D

+ + +
+ +

F

+ + + +
+ +

G

+ + + +
+ +

M

+ + + +
+ +

P

+ + + +
+ +

R

+ + + +
+ +

S

+ + + +
+ + + +
+
+
+ +
+ +
+

© Copyright 2024, Klaus Weinbauer.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/getting_started.html b/getting_started.html new file mode 100644 index 0000000..0dce65b --- /dev/null +++ b/getting_started.html @@ -0,0 +1,128 @@ + + + + + + + Getting Started — FGUtils documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Getting Started

+
+

Installation

+
+
+

Query Functional Groups

+
+
+

A Simple Reaction Proxy

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/graph_syntax.html b/graph_syntax.html new file mode 100644 index 0000000..a9c71c9 --- /dev/null +++ b/graph_syntax.html @@ -0,0 +1,283 @@ + + + + + + + Graph Syntax — FGUtils documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Graph Syntax

+

FGUtils has its own graph description language. The syntax is closely related +to the SMILES format for molecules and reactions. It is kind of an extenstion +to SMILES to support modeling ITS graphs and reaction patterns. To convert the +SMILES-like description into a graph object use the +Parser class. The Caffeine molecular graph can be +obtained as follows:

+
import matplotlib.pyplot as plt
+from fgutils import Parser
+from fgutils.vis import plot_as_mol
+
+parser = Parser()
+mol = parser("CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
+
+fig, ax = plt.subplots(1, 1)
+plot_as_mol(mol, ax)
+plt.show()
+
+
+_images/caffeine_example.png +

Besides parsing common SMILES it is possible to generate molecule-like graphs +with more abstract nodes, i.e., arbitrary node labels. Arbitrary node labels +are surrounded by {} (e.g. {label}). This abstract labeling can be used +to substitute nodes with specific patterns. In this context the labels are +group names of ProxyGroup objects. A ProxyGroup +defines a set of sub-graphs to be replaced for the labeled node. This can be +done by using a Proxy. Propyl acetate can be created +by replacing the labeled node with the propyl group:

+
import matplotlib.pyplot as plt
+from fgutils import Parser
+from fgutils.proxy import MolProxy, ProxyGroup
+from fgutils.vis import GraphVisualizer
+
+pattern = "CC(=O)O{propyl}"
+propyl_group = ProxyGroup("propyl", "CCC")
+parser = Parser()
+proxy = MolProxy(pattern, propyl_group, parser=parser)
+
+g = parser(pattern)
+mol = next(proxy)
+
+vis = GraphVisualizer()
+fig, ax = plt.subplots(1, 2, dpi=100, figsize=(12, 3))
+vis.plot(g, ax[0], title="Core Pattern")
+vis.plot(mol, ax[1], title="Generated Molecule")
+plt.show()
+
+
+_images/labeled_node_example.png +
+

Note

+

A node can have more than one label. This can be done by separating the +labels with a comma, e.g.: {label_1,label_2}.

+
+

In the example above the ProxyGroup has only one subgraph pattern. In general, +a ProxyGroup is a collection of several possible subgraphs from which one is +selected when a new sample is instantiated. To get more information on how +graphs are sample take a look at the GraphSampler +class and the ProxyGroup constructor. By default a +pattern has one anchor at index 0. If you need more control over how a subgraph +is inserted into a parent graph you can instantiate the +ProxyGraph class. For a ProxyGraph you can provide a +list of anchor node indices. The insertion of the subgraph into the parent +depends on the number of anchor nodes in the subgraph and the number of edges +to the labeled node in the parent. The first edge in the parent connects to the +first anchor node in the subgraph and so forth. The following example +demonstrates the insertion with multiple anchor nodes:

+
import matplotlib.pyplot as plt
+from fgutils.proxy import MolProxy, ProxyGroup, ProxyGraph, Parser
+from fgutils.vis import GraphVisualizer
+
+pattern = "N{g}C{g}(O)C"
+g_1 = ProxyGroup("g", ProxyGraph("C1CCCCC1", anchor=[1, 3]))
+g_2 = ProxyGroup("g", ProxyGraph("C1CCCCC1", anchor=[1, 3, 4]))
+
+parser = Parser()
+proxy1 = MolProxy(pattern, g_1)
+proxy2 = MolProxy(pattern, g_2)
+
+parent_graph = parser(pattern)
+mol1 = next(proxy1)
+mol2 = next(proxy2)
+
+vis = GraphVisualizer(show_edge_labels=False)
+fig, ax = plt.subplots(1, 3, dpi=200, figsize=(20, 3))
+vis.plot(parent_graph, ax[0], title="parent")
+vis.plot(mol1, ax[1], title="2 anchor nodes")
+vis.plot(mol2, ax[2], title="3 anchor nodes")
+plt.show()
+
+
+_images/multiple_anchor_example.png +

Another extension to the SMILES notation is the encoding of bond changes. This +feature is required to model reaction mechanisms as ITS graph. Changing bonds +are surrounded by <> (e.g. <1, 2> for the formation of a double bond +from a single bond). The extended notation allows the automated generation of +reaction examples with complete atom-to-atom maps. The following code snippet +demonstrates the generation of a few Diels-Alder reactions. The diene and +dienophile groups can of course be extended to increase varaity of the +samples:

+
import random
+import matplotlib.pyplot as plt
+from fgutils.proxy import ProxyGroup, ProxyGraph, ReactionProxy
+from fgutils.proxy_collection.common import common_groups
+from fgutils.vis import plot_reaction, plot_its
+from fgutils.chem.its import get_its
+
+
+electron_donating_group = ProxyGroup(
+    "electron_donating_group",
+    ["{methyl}", "{ethyl}", "{propyl}", "{aryl}", "{amine}"],
+)
+electron_withdrawing_group = ProxyGroup(
+    "electron_withdrawing_group",
+    ["{alkohol}", "{ether}", "{aldehyde}", "{ester}", "{nitrile}"],
+)
+diene_group = ProxyGroup(
+    "diene",
+    ProxyGraph("C<2,1>C<1,2>C<2,1>C{electron_donating_group}", anchor=[0, 3]),
+)
+dienophile_group = ProxyGroup(
+    "dienophile",
+    ProxyGraph("C<2,1>C{electron_withdrawing_group}", anchor=[0, 1]),
+)
+groups = common_groups + [
+    electron_donating_group,
+    electron_withdrawing_group,
+    diene_group,
+    dienophile_group,
+]
+
+proxy = ReactionProxy("{diene}1<0,1>{dienophile}<0,1>1", groups)
+
+n = 4
+fig, ax = plt.subplots(n, 2, width_ratios=[2, 1], figsize=(20, n * 4))
+for i, (g, h) in enumerate(random.sample(list(proxy), n)):
+    plot_reaction(g, h, ax[i, 0], title="Reaction")
+    plot_its(get_its(g, h), ax[i, 1], title="ITS Graph")
+plt.tight_layout()
+plt.show()
+
+
+_images/diels_alder_example.png +

This proxy can now generate Diels-Alder reaction samples. A few of the results +are shown in the figure above. On the left side the reaction and on the right +side the resulting ITS. The results are balanced and have complete atom-to-atom +maps. The atom-to-atom maps are correct as long as the configuration makes +sence in the chemical domain. Note that the synthesizability of the generated +samples can not be guaranteed. It soley depends on what ProxyGroups and +ProxyGraphs are configured. For a comprehensive Diels-Alder reaction proxy take +a look at the +DielsAlderProxy class +and the section TODO. This class is also able to generate negative Diels-Alder +reaction samples, i.e., reactions where a Diels-Alder graph transformation rule +is theoretically applicable but the reaction will never happen in reality.

+
+

Note

+

The electron_donating_group and electron_withdrawing_group serve as +a collection of other groups to simplify the notation. They consist of a +single node with multiple labels. When iterating the next sample from the +proxy the labeled nodes get replaced by the pattern from one of the groups. +The group/label is chosen randomly with uniform distribution.

+
+
+

Warning

+

The call list(proxy) will generate all possible instantiations at once. +Depending on the configuration this can take a long time to complete. If the +core ProxyGroup graph sampling is not unique this can even result in an +endless loop.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000..be0b280 --- /dev/null +++ b/index.html @@ -0,0 +1,121 @@ + + + + + + + Welcome to FGUtils’s documentation! — FGUtils documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Welcome to FGUtils’s documentation!

+
+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000..6afd909 Binary files /dev/null and b/objects.inv differ diff --git a/proxy_collection.html b/proxy_collection.html new file mode 100644 index 0000000..e951432 --- /dev/null +++ b/proxy_collection.html @@ -0,0 +1,181 @@ + + + + + + + Proxy Collection — FGUtils documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Proxy Collection

+
+

Diels-Alder Reaction Proxy

+

The class +DielsAlderProxy +implements a comprehensive Diels-Alder reaction generation proxy. It generates +ring formation reaction samples between diene and dienophile molecules. It can +also be used to generate negative reaction samples, i.e., reactions where a +Diels-Alder graph transformation rule is theoretically applicable but the +reaction will never happen in reality.

+

The Diels-Alder Reaction proxy has the following reaction center graphs +configured (ProxyGraphs of the core ProxyGroup). Node labels show the atom +type or group name and the node index and edge labels depict the bond type. +Bond changes are depicted as tuples (<bond_g>,<bond_h>) where the first +entry is the bond in the reactants and the second entry is the bond in the +product.

+_images/proxy_collection_DAReactionProxy.png +

The Intra Molecular Center is used to generate intra molecular Diels-Alder +reactions. It depicts the entire reaction center. It’s easy to identify the [4 ++ 2] cycloaddition reaction center between the diene part (C=CC=C, node 0-3) +and the dienophile part (C=C, node 5-6). Diene and dienophile are connected +by node 4, a graph from the intra_mol_bridge group. The Inter Molecular +Center depicts the abstracted reaction center for inter molecular Diels-Alder +reactions.

+
+

Note

+

Have you noticed that the Inter Molecular Center is a multi graph (it +has multiple edges between two vertices)? Molecular graphs are never multi +graphs, the bond order is represented as label on the unique edge between +two atoms. However, to represent this abstract form of the reaction center +it’s necessary to have independent edges for both single bond formations. +To parse this type of graphs you must set the use_multigraph=True +argument in Parser.

+
+

The next level of abstraction are the diene and dienophile ProxyGroups. +They provide the structures depicted in the following two figures, +respectively. Anchor nodes, the nodes where the substructures connect to the +parent, are surrounded by [].

+

Graphs from the diene group:

+_images/proxy_collection_DAReactionProxy_diene.png +

Graphs from the dienophile group:

+_images/proxy_collection_DAReactionProxy_dienophile.png +

Graphs from the electron_donating_group:

+_images/proxy_collection_DAReactionProxy_EDG.png +

Graphs from the electron_withdrawing_group:

+_images/proxy_collection_DAReactionProxy_EWG.png +

A few of the 10470 Diels-Alder reactions generated by the proxy:

+_images/proxy_collection_DAReactionProxy_DA_reactions.png +
+

Invalid Sample Generation (negative data)

+

The DielsAlderProxy +provides the functionality to generate Diels-Alder counter examples, i.e., +reactions where based on the structure a Diels-Alder graph transformation rule +would be applicable but the reaction can not happen because the diene is for +example in a fixed s-trans conformation.

+

Graphs from the (s-trans) diene group:

+_images/proxy_collection_DAReactionProxy_s-trans_diene.png +

A few of the 12875 INVALID Diels-Alder reactions generated by the proxy +(negative data):

+_images/proxy_collection_DAReactionProxy_DA_reactions_neg.png +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/py-modindex.html b/py-modindex.html new file mode 100644 index 0000000..cb87a60 --- /dev/null +++ b/py-modindex.html @@ -0,0 +1,160 @@ + + + + + + Python Module Index — FGUtils documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Python Module Index
    • +
  • +
    • +
+
+
+
+
+ + +

Python Module Index

+ +
+ f +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
 
+ f
+ fgutils +
    + fgutils.fgconfig +
    + fgutils.parse +
    + fgutils.proxy +
    + fgutils.proxy_collection.common +
    + fgutils.proxy_collection.diels_alder_proxy +
    + fgutils.query +
    + fgutils.utils +
+ + +
+
+
+ +
+ +
+

© Copyright 2024, Klaus Weinbauer.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/references.html b/references.html new file mode 100644 index 0000000..33f9444 --- /dev/null +++ b/references.html @@ -0,0 +1,755 @@ + + + + + + + References — FGUtils documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

References

+
+

fgconfig

+
+
+class fgutils.fgconfig.FGConfig(name: str | None = None, pattern: str | None = None, parser: Parser | None = None, group_atoms: list[int] | None = None, anti_pattern: str | list[str] = [], depth: int | None = None, len_exclude_nodes: list[str] = ['R'])
+

Functional group configuration class.

+
+
Parameters:
+
    +

  • name – The name of the functional gruop.

    • +

  • pattern – The structural description of the functional group.

    • +

  • parser – (optional) A parser to use to convert the pattern into a +structure.

    • +

  • group_atoms – (optional) A list of indices indicating with nodes in +the pattern belong to the functional group. A pattern might have some +wildcard nodes attached that are required to match but do not belong to +the group. (Default = all nodes)

    • +

  • anti_pattern – (optional) A list of anti patterns that must not be +matched. (Default = None)

    • +

  • depth – (optional) The maximal depth to check the patterns. (Default += max(pattern, anti_pattern)

    • +

  • len_exclude_nodes – (optional) Node types that should be excluded in +the pattern length. (Default = [“R”] - wildcard pattern)

    • +
+
+
+
+
+property pattern_len: int
+

The number of nodes of the functional group structure. Nodes +specified in len_exclude_nodes are not included.

+
+ +
+ +
+
+class fgutils.fgconfig.FGConfigProvider(config: FGConfig | list[dict] | list[FGConfig] | None = None, mapper: PermutationMapper | None = None)
+

Provider for functional group configs.

+
+
Parameters:
+
    +

  • config – A FGConfig object or a list of config objects. The +configurations can also be passed as dictionaries.

    • +

  • mapper – (optional) A PermutationMapper to use.

    • +
+
+
+
+
+get_by_name(name: str) → FGConfig
+

Get the functional group config by name.

+
+
Returns:
+

Returns the FGConfig instance.

+
+
+
+ +
+
+get_tree() → list[FGTreeNode]
+

Get the functional groups hirachically organized in a tree. +Functional groups are ordered based on their structure. A group is +another groups child if its structure is more specific, i.e., the +parent structure is a subgraph of the child. A child can have multiple +parents and a parent can have multiple childs.

+
+
Returns:
+

Returns the list of root groups.

+
+
+
+ +
+ +
+
+

utils

+
+
+fgutils.utils.split_its(graph: Graph) → tuple[Graph, Graph]
+

Split an ITS graph into reactant graph G and product graph H.

+
+
Parameters:
+

graph – ITS graph to split up.

+
+
Returns:
+

Tuple of two graphs (G, H).

+
+
+
+ +
+
+

query

+
+
+class fgutils.query.FGQuery(mapper: PermutationMapper | None = None, config: FGConfig | list[FGConfig] | FGConfigProvider | None = None, require_implicit_hydrogen: bool = True)
+

Class to get functional groups from a molecule.

+
+
Parameters:
+
    +

  • mapper – (optional) The permutation mapper to use.

    • +

  • config_provider – (optional) A functional group config provider. If +not specified the default functional group collection will be used.

    • +

  • require_implicit_hydrogen – Flag to specify if implicit hydrogens are +required for the query. This usually depends on the provided FGConfigs. +If the configured functional group patterns do not require hydrogens +this can be set to false. (Default = True)

    • +
+
+
+
+
+get(value) → list[tuple[str, list[int]]]
+

Get all functional groups from a molecule. The query returns two +functional groups for acetylsalicylic acid:

+
>>> smiles = "O=C(C)Oc1ccccc1C(=O)O" # acetylsalicylic acid
+>>> query = FGQuery()
+>>> query.get(smiles)
+[('ester', [0, 1, 3]), ('carboxylic_acid', [10, 11, 12])]
+
+
+
+
Parameters:
+

value – This is either a graph or SMILES as string.

+
+
Returns:
+

Returns a list of tuples. The first element in a tuple is the +functional group name and the second element is a list of node +indices that belong to this functional group +(functional_group_name, [idx_1, idx_2, ...]).

+
+
+
+ +
+ +
+
+

parse

+
+
+class fgutils.parse.Parser(use_multigraph=False, init_aam=False, verbose=False)
+

Class to convert a SMILES like graph description into a NetworkX graph.

+

Example for parsing acetic acid:

+
>>> parser = Parser()
+>>> g = parser("CC(O)=O")
+Graph with 4 nodes and 3 edges
+
+
+
+
Parameters:
+
    +

  • use_multigraph – Flag to specify if the resulting graph object should +be of type networkx.MultiGraph or networkx.Graph. The difference is +that a MultiGraph can have more than one edge between two nodes. For +parsing molecule like graphs this is not necessary because bond types +are encoded as edge labels. (Default = False)

    • +

  • verbose – Flag to print information during parsing. (Default = False)

    • +
+
+
+
+
+parse(pattern: str, idx_offset: int = 0)
+

Method to parse a SMILES like graph pattern.

+
+
Parameters:
+
    +

  • pattern – The pattern to convert into a graph. The pattern is a +tree-like description of the graph. It is strongly oriented at the +SMILES notation.

    • +

  • idx_offset – The index offset argument provides the starting +value for the consecutive node numbering. (Default = 0)

    • +
+
+
Returns:
+

Returns the converted graph object.

+
+
+
+ +
+ +
+
+

proxy

+
+
+class fgutils.proxy.GraphSampler(unique=False)
+

Base class for sampling ProxyGraphs.

+
+
Parameters:
+

unique – If set to true each graph is only returned once. (Default = +False)

+
+
+
+
+sample(graphs: list[ProxyGraph], group_name=None) → list[ProxyGraph] | None
+

Method to retrive a new sample from a list of graphs. If unique is set +to true the first graph that was not yet returned is selected. None is +returned if all graphs have been selected. If unique is false all +graphs are returned each time the function is called.

+
+
Parameters:
+
    +

  • graphs – A list of graphs to sample from.

    • +

  • group_name – (optional) The group name is an optional argument. +It’s not necessary to specify it if it’s not needed.

    • +
+
+
Returns:
+

Returns one or more graphs from the list or None if sampling +should stop.

+
+
+
+ +
+ +
+
+class fgutils.proxy.MolProxy(core: str | list[str] | ProxyGroup, groups: ProxyGroup | list[ProxyGroup] | dict[str, ProxyGroup], parser: Parser | None = None)
+

Proxy to generate molecules.

+
+
Parameters:
+
    +

  • core – A pattern string or ProxyGroup representing the core graph. +For example a specific functional group.

    • +

  • groups – A list of groups to expand the core graph with.

    • +

  • parser – (optional) The parser to convert patterns into structures.

    • +
+
+
+
+ +
+
+class fgutils.proxy.Proxy(core: str | list[str] | ProxyGroup, groups: ProxyGroup | list[ProxyGroup] | dict[str, ProxyGroup], enable_aam: bool = True, parser: Parser | None = None)
+

Proxy is a generator class. It extends a specific core graph by a set +of subgraphs (groups). This class implements the iterator interface so it +can be used in a for loop to generate samples:

+
>>> proxy = Proxy("C{g}", ProxyGroup("g", ["C", "O", "N"]))
+>>> for graph in proxy:
+>>>    print([d["symbol"] for n, d in graph.nodes(data=True)])
+['C', 'C']
+['C', 'O']
+['C', 'N']
+
+
+
+
Parameters:
+
    +

  • core – A pattern string or ProxyGroup representing the core graph. +For example a specific functional group or a reaction center.

    • +

  • groups – A list of groups to expand the core graph with.

    • +

  • enable_aam – Flag to specify if the ‘aam’ label is set in the result +graph. (Default = True)

    • +

  • parser – (optional) The parser to convert patterns into structures.

    • +
+
+
+
+
+static from_dict(config: dict) → Proxy
+

Load Proxy from dict config. The expected JSON format is:

+
{
+    "core": <pattern>,
+    "groups": <groups> # for expected format take a
+    # look at ProxyGroup.from_dict()
+}
+
+
+
+
Parameters:
+

config – The configuration dictionary. E.g. loaded from JSON

+
+
Returns:
+

The instantiated Proxy.

+
+
+
+ +
+
+get_next()
+

Get the next sample.

+
+
Returns:
+

A generated graph.

+
+
+
+ +
+
+property groups: list[ProxyGroup]
+

The list of ProxyGroups. This can be set with values of the +following type: ProxyGroup | list[ProxyGroup] | dict[str, +ProxyGroup]

+
+ +
+ +
+
+class fgutils.proxy.ProxyGraph(pattern: str, anchor: list[int] = [0], name: str | None = None, **kwargs)
+

ProxyGraph is essentially a subgraph used to expand molecules. If the node +that is replaced by the pattern has more edges than the pattern has +anchors, the last anchor will be used multiple times. In the default case +the first node in the pattern will connect to all the neighboring nodes of +the replaced node.

+
+
Parameters:
+
    +

  • pattern – String representation of the graph.

    • +

  • anchor – A list of indices in the pattern that are used to +connect to the parent graph. (Default = [0])

    • +

  • name – A name for the graph. This is just for visualization and +debugging.

    • +

  • kwargs – Keyword arguments are used as graph properties. Specify +whatever you need.

    • +
+
+
+
+ +
+
+class fgutils.proxy.ProxyGroup(name, graphs: str | list[str] | ProxyGraph | list[ProxyGraph], sampler=None, unique=False)
+

ProxyGroup is a collection of patterns that can be replaced for a labeled +node in a graph. The node label is the respective group name where one of +the patterns will be replaced

+
+
Parameters:
+
    +

  • name – The name of the group.

    • +

  • graphs – (optional) A list of subgraphs or a list of graph +descriptions. The patterns are converted to ProxyGraphs with one anchor +at index 0. Use ProxyGraph objects if you need more control over how +subgraphs are instantiated.

    • +

  • sampler – (optional) An object or a function to retrive individual +graphs from the list. The expected function interface is: +func(list[ProxyGraph]) -> list[ProxyGraph]. Implement the +__call__ method if you use a class. The function can have an +optional keyword argument group_name.

    • +

  • unique – Argument to specify if graphs can be returned multiple +times. This only takes effect if sampler is not set. (Default = False)

    • +
+
+
+
+
+static from_dict(config: dict) → dict[str, ProxyGroup]
+

Load ProxyGroups from dict config. The expected JSON format is:

+
{
+    "group_name_1": <pattern>,
+    "group_name_2": [<pattern>],
+    "group_name_3": <group_config> # for expected format take a
+    # look at ProxyGroup.from_dict_single()
+}
+
+
+
+
Parameters:
+

config – The configuration dictionary. E.g. loaded from JSON +file.

+
+
Returns:
+

Returns a mapping dictionary of ProxyGroups where the key is +the group name and the value is the ProxyGroup object.

+
+
+
+ +
+
+static from_dict_single(name: str, config: dict) → ProxyGroup
+

Load a single ProxyGroup object from configuration. The expected +JSON format is one of the following:

+
{
+    # short form
+    "graphs": <pattern>,
+    "graphs": [<pattern>],
+    "graphs": {"pattern": <pattern>, "anchor": list[int]},
+    # complete config
+    "graphs": [{
+            "pattern": <pattern>,
+            "anchor": list[int],
+            <any_key>: <any_value>
+        }],
+
+    # <pattern> is the SMILES-like graph description of type str
+}
+
+
+

It’s possible to specify additional properties on graphs. These can be +used for example by custom samplers to implement some logic or +dependencies between groups.

+
+
Parameters:
+
    +

  • name – The name of the ProxyGroup.

    • +

  • config – The configuration dictionary. E.g. loaded from JSON +file.

    • +
+
+
Returns:
+

The instantiated ProxyGroup.

+
+
+
+ +
+
+property graphs: list[ProxyGraph]
+

The list of ProxyGraphs. This can be set with values of the +following type: str | list[str] | ProxyGraph | list[ProxyGraph]

+
+ +
+
+sample_graphs() → list[ProxyGraph] | None
+

Sample graphs. This method uses the sampler to select a list of +graphs.

+
+
Returns:
+

A list of ProxyGraph objects or None if there is nothing more +to sample.

+
+
+
+ +
+ +
+
+class fgutils.proxy.ReactionProxy(core: str | list[str] | ProxyGroup, groups: ProxyGroup | list[ProxyGroup] | dict[str, ProxyGroup], enable_aam: bool = True, parser: Parser | None = None)
+

Proxy to generate reactions.

+
+
Parameters:
+
    +

  • core – A pattern string or ProxyGroup representing the core graph. +For example a specific functional group or a reaction center.

    • +

  • groups – A list of groups to expand the core graph with.

    • +

  • enable_aam – Flag to specify if the ‘aam’ label is set in the result +graph. (Default = True)

    • +

  • parser – (optional) The parser to convert patterns into structures.

    • +
+
+
+
+
+get_next()
+

Generate a new reaction sample. The reaction proxy returns two graphs G +and H. G is the reactant graph and H is the product graph.

+
+
Returns:
+

A tuple of two graphs (G, H) representing the reaction G +→ H.

+
+
+
+ +
+ +
+
+fgutils.proxy.build_graphs(core: ProxyGraph, groups: dict[str, ProxyGroup], parser: Parser)
+

Replace labeled nodes in the core graph with groups. For each labeled +node the respective group is used to replace the node by the specified +subgraphs.

+
+
Parameters:
+
    +

  • core – The parent graph with labeled nodes.

    • +

  • groups – A list of groups to replace the labeled nodes in the core +graph with. The dictionary keys must be the group names.

    • +

  • parser – The parser that is used to convert graph patterns into +graphs.

    • +
+
+
Returns:
+

Returns a list of graphs with replaced nodes.

+
+
+
+ +
+
+fgutils.proxy.build_group_tree(core: ProxyGroup, groups: ProxyGroup | list[ProxyGroup], parser=None) → Graph
+

Constructs a tree of all possible graph instantiations. The number of leave +nodes in this tree is the number of possible samples.

+
+
Parameters:
+
    +

  • core – The ProxyGroup that serves as core group.

    • +

  • groups – A list of groups to replace labeled nodes.

    • +

  • parser – (optional) A parser to use for conversion from pattern to +structures.

    • +
+
+
Returns:
+

Returns the construction tree as nx.Graph object.

+
+
+
+ +
+
+fgutils.proxy.replace_next_node(graph, groups: dict[str, ProxyGroup], parser: Parser)
+

Replace the next labeled node in graph with the respective group.

+
+
Parameters:
+
    +

  • graph – The graph where a node should be replace by a subgraph.

    • +

  • groups – A mapping dictionary of groups to replace the labeled nodes +in the parent with. The dictionary keys must be the group name.

    • +

  • parser – The parser to use to convert the pattern into structure.

    • +
+
+
Returns:
+

Returns a list of new graphs where the first labeled node is +replaced. None is returned if no replaceable labeled node is left.

+
+
+
+ +
+
+fgutils.proxy.replace_node(graph, node, replacement_graph: ProxyGraph, parser: Parser)
+

Replace node in graph with replacement_graph converted by the parser.

+
+
Parameters:
+
    +

  • graph – The graph where a node should be replace by a subgraph.

    • +

  • node – The node to replace in graph.

    • +

  • replacement_graph – The subgraph that is inserted instead of the +node.

    • +

  • parser – The parser to convert the pattern into structure.

    • +
+
+
Returns:
+

Returns a new graph with node replace by +replacement_graph.

+
+
+
+ +
+
+

proxy_collection

+
+
+class fgutils.proxy_collection.diels_alder_proxy.DielsAlderProxy(enable_aam=True, neg_sample=False)
+

A proxy for the generation of Diels-Alder reaction samples and +counter-samples. The proxy returns two graphs G and H as tuple. G is the +reactant graph and H is the product graph. For a comprehensive description +of the proxy configuration read section Diels-Alder Reaction Proxy.

+
+
Parameters:
+
    +

  • enable_aam – Flag to specify if the aam label is set in the +result graphs. (Default = True)

    • +

  • neg_sample – If set to true the proxy will exclusively generate +negative samples, i.e., reactions where a Diels-Alder graph +transformation rule is theoretically applicable but the reaction will +never happen in reality. (Default = False)

    • +
+
+
+
+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/search.html b/search.html new file mode 100644 index 0000000..2b229e4 --- /dev/null +++ b/search.html @@ -0,0 +1,125 @@ + + + + + + Search — FGUtils documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Search
    • +
  • +
    • +
+
+
+
+
+ + + + +
+ +
+ +
+
+
+ +
+ +
+

© Copyright 2024, Klaus Weinbauer.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + + + + + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js new file mode 100644 index 0000000..9f5097e --- /dev/null +++ b/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"A Simple Reaction Proxy": [[1, "a-simple-reaction-proxy"]], "Diels-Alder Reaction Proxy": [[4, "diels-alder-reaction-proxy"]], "Functional Group Tree": [[0, "functional-group-tree"]], "Functional Groups": [[0, null]], "Get changing groups in reaction": [[0, "get-changing-groups-in-reaction"]], "Get functional groups in molecule": [[0, "get-functional-groups-in-molecule"]], "Getting Started": [[1, null]], "Graph Syntax": [[2, null]], "Installation": [[1, "installation"]], "Invalid Sample Generation (negative data)": [[4, "invalid-sample-generation-negative-data"]], "Proxy Collection": [[4, null]], "Query Functional Groups": [[1, "query-functional-groups"]], "References": [[5, null]], "Welcome to FGUtils\u2019s documentation!": [[3, null]], "fgconfig": [[5, 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