diff --git a/docs/.buildinfo b/docs/.buildinfo index e5937fa..732018b 100644 --- a/docs/.buildinfo +++ b/docs/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: a8e686330cd82d1e1e428ef58223c494 +config: dc0dc5212cfdc73f6c712028918bddd0 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/.doctrees/_about/index.doctree b/docs/.doctrees/_about/index.doctree index 5d511d0..1c0fbce 100644 Binary files a/docs/.doctrees/_about/index.doctree and b/docs/.doctrees/_about/index.doctree differ diff --git a/docs/.doctrees/_api_reference/index.doctree b/docs/.doctrees/_api_reference/index.doctree index 6ad0c13..1cc64ae 100644 Binary files a/docs/.doctrees/_api_reference/index.doctree and b/docs/.doctrees/_api_reference/index.doctree differ diff --git a/docs/.doctrees/_installation/index.doctree b/docs/.doctrees/_installation/index.doctree index 806eab8..bd43c59 100644 Binary files a/docs/.doctrees/_installation/index.doctree and b/docs/.doctrees/_installation/index.doctree differ diff --git a/docs/.doctrees/_tutorial/index.doctree b/docs/.doctrees/_tutorial/index.doctree index e5ab4ba..8cc19d2 100644 Binary files a/docs/.doctrees/_tutorial/index.doctree and b/docs/.doctrees/_tutorial/index.doctree differ diff --git a/docs/.doctrees/index.doctree b/docs/.doctrees/index.doctree index 298f521..e80aef5 100644 Binary files a/docs/.doctrees/index.doctree and b/docs/.doctrees/index.doctree differ diff --git a/docs/_about/index.html b/docs/_about/index.html index d521407..826c0b4 100644 --- a/docs/_about/index.html +++ b/docs/_about/index.html @@ -1,10 +1,10 @@ - + - Issues — SERD 0.1.1 documentation + Issues — SERD 0.1.2 documentation diff --git a/docs/_api_reference/index.html b/docs/_api_reference/index.html index 4528f3a..9069e7f 100644 --- a/docs/_api_reference/index.html +++ b/docs/_api_reference/index.html @@ -1,10 +1,10 @@ - + - SERD.detect — SERD 0.1.1 documentation + SERD.detect — SERD 0.1.2 documentation @@ -278,7 +278,7 @@

SERD.r2gfloat], optional) – A limit of distance to define an edge between two solvent-exposed residues, by default None. If None, cutoff depends on selection argument. If “CA”, cutoff is 10.0. If “CB”, cutoff is 8.0.

  • intraresidual (bool, optional) – Whether to consider intraresidual contacts to create adjacency matrix, by default False.

    • -

  • weighted_edges (bool, False) – Whether to include the interresidual distances as edge weights, by default False.

    • +

  • weighted_edges (bool, optional) – Whether to include the distances as weight of the edges.

    • Returns:
    diff --git a/docs/_installation/index.html b/docs/_installation/index.html index 15a1b70..e62f807 100644 --- a/docs/_installation/index.html +++ b/docs/_installation/index.html @@ -1,10 +1,10 @@ - + - Requirements — SERD 0.1.1 documentation + Requirements — SERD 0.1.2 documentation diff --git a/docs/_modules/SERD/SERD.html b/docs/_modules/SERD/SERD.html index 419b129..771488f 100644 --- a/docs/_modules/SERD/SERD.html +++ b/docs/_modules/SERD/SERD.html @@ -3,7 +3,7 @@ - SERD.SERD — SERD 0.1.1 documentation + SERD.SERD — SERD 0.1.2 documentation @@ -874,8 +874,8 @@

    Source code for SERD.SERD

             If None, cutoff depends on selection argument. If "CA", cutoff is 10.0. If "CB", cutoff is 8.0.
     intraresidual : bool, optional
         Whether to consider intraresidual contacts to create adjacency matrix, by default False.
-    weighted_edges : bool, False
-        Whether to include the interresidual distances as edge weights, by default False.
+    weighted_edges : bool, optional
+        Whether to include the distances as weight of the edges.
 
     Returns
     -------
@@ -926,6 +926,15 @@ 
    Source code for SERD.SERD
         # Create networkx.Graph
     G = networkx.Graph()
     G.add_edges_from(numpy.argwhere(adjacency))
+    if weighted_edges:
+        weighted_edges = [
+            (edges[0], edges[1], distance[edges[0]][edges[1]])
+            for edges in G.edges(data=True)
+        ]
+        G.add_weighted_edges_from(weighted_edges)
+    else:
+        weighted_edges = [(edges[0], edges[1], 1.0) for edges in G.edges(data=True)]
+        G.add_weighted_edges_from(weighted_edges)
 
     # Add interresidual distances as edge weights
     if weighted_edges:
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
index 461c76c..34c39da 100644
--- a/docs/_modules/index.html
+++ b/docs/_modules/index.html
@@ -3,7 +3,7 @@
 
   
   
-  Overview: module code — SERD 0.1.1 documentation
+  Overview: module code — SERD 0.1.2 documentation
       
       
     
diff --git a/docs/_modules/pyKVFinder/utils.html b/docs/_modules/pyKVFinder/utils.html
index 09e2f7d..ba6731d 100644
--- a/docs/_modules/pyKVFinder/utils.html
+++ b/docs/_modules/pyKVFinder/utils.html
@@ -3,7 +3,7 @@
 
   
   
-  pyKVFinder.utils — SERD 0.1.1 documentation
+  pyKVFinder.utils — SERD 0.1.2 documentation
       
       
     
@@ -353,7 +353,7 @@ 
    Source code for pyKVFinder.utils
                 line = line.split()
             if len(line) == 4:
                 # Get PDB information
-                atom_symbol = line[0]
+                atom_symbol = line[0].upper()
                 x = float(line[1])
                 y = float(line[2])
                 z = float(line[3])
diff --git a/docs/_static/basic.css b/docs/_static/basic.css
index 4e9a9f1..0889677 100644
--- a/docs/_static/basic.css
+++ b/docs/_static/basic.css
@@ -326,6 +326,7 @@ p.sidebar-title {
 }
 nav.contents,
 aside.topic,
+
 div.admonition, div.topic, blockquote {
     clear: left;
 }
@@ -333,6 +334,7 @@ div.admonition, div.topic, blockquote {
 /* -- topics ---------------------------------------------------------------- */
 nav.contents,
 aside.topic,
+
 div.topic {
     border: 1px solid #ccc;
     padding: 7px;
@@ -373,6 +375,7 @@ 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;
@@ -382,6 +385,7 @@ div.sidebar::after,
 aside.sidebar::after,
 nav.contents::after,
 aside.topic::after,
+
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -606,6 +610,26 @@ ol.simple p,
 ul.simple p {
     margin-bottom: 0;
 }
+
+/* Docutils 0.17 and older (footnotes & citations) */
+dl.footnote > dt,
+dl.citation > dt {
+    float: left;
+    margin-right: 0.5em;
+}
+
+dl.footnote > dd,
+dl.citation > dd {
+    margin-bottom: 0em;
+}
+
+dl.footnote > dd:after,
+dl.citation > dd:after {
+    content: "";
+    clear: both;
+}
+
+/* Docutils 0.18+ (footnotes & citations) */
 aside.footnote > span,
 div.citation > span {
     float: left;
@@ -630,6 +654,8 @@ div.citation > p:last-of-type:after {
     clear: both;
 }
 
+/* Footnotes & citations ends */
+
 dl.field-list {
     display: grid;
     grid-template-columns: fit-content(30%) auto;
@@ -642,6 +668,10 @@ dl.field-list > dt {
     padding-right: 5px;
 }
 
+dl.field-list > dt:after {
+    content: ":";
+}
+
 dl.field-list > dd {
     padding-left: 0.5em;
     margin-top: 0em;
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
index 3462e59..149fa13 100644
--- a/docs/_static/documentation_options.js
+++ b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.1.1',
+    VERSION: '0.1.2',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
@@ -10,5 +10,5 @@ var DOCUMENTATION_OPTIONS = {
     SOURCELINK_SUFFIX: '.txt',
     NAVIGATION_WITH_KEYS: false,
     SHOW_SEARCH_SUMMARY: true,
-    ENABLE_SEARCH_SHORTCUTS: true,
+    ENABLE_SEARCH_SHORTCUTS: false,
 };
\ No newline at end of file
diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js
index f2fb7d5..ac4d586 100644
--- a/docs/_static/searchtools.js
+++ b/docs/_static/searchtools.js
@@ -88,7 +88,7 @@ const _displayItem = (item, highlightTerms, searchTerms) => {
   linkEl.href = linkUrl + "?" + params.toString() + anchor;
   linkEl.innerHTML = title;
   if (descr)
-    listItem.appendChild(document.createElement("span")).innerHTML =
+    listItem.appendChild(document.createElement("span")).innerText =
       " (" + descr + ")";
   else if (showSearchSummary)
     fetch(requestUrl)
@@ -155,8 +155,10 @@ const Search = {
   _pulse_status: -1,
 
   htmlToText: (htmlString) => {
-    const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
-    htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() });
+    const htmlElement = document
+      .createRange()
+      .createContextualFragment(htmlString);
+    _removeChildren(htmlElement.querySelectorAll(".headerlink"));
     const docContent = htmlElement.querySelector('[role="main"]');
     if (docContent !== undefined) return docContent.textContent;
     console.warn(
@@ -502,12 +504,11 @@ const Search = {
    * latter for highlighting it.
    */
   makeSearchSummary: (htmlText, keywords, highlightWords) => {
-    const text = Search.htmlToText(htmlText);
+    const text = Search.htmlToText(htmlText).toLowerCase();
     if (text === "") return null;
 
-    const textLower = text.toLowerCase();
     const actualStartPosition = [...keywords]
-      .map((k) => textLower.indexOf(k.toLowerCase()))
+      .map((k) => text.indexOf(k.toLowerCase()))
       .filter((i) => i > -1)
       .slice(-1)[0];
     const startWithContext = Math.max(actualStartPosition - 120, 0);
@@ -515,9 +516,9 @@ const Search = {
     const top = startWithContext === 0 ? "" : "...";
     const tail = startWithContext + 240 < text.length ? "..." : "";
 
-    let summary = document.createElement("p");
+    let summary = document.createElement("div");
     summary.classList.add("context");
-    summary.textContent = top + text.substr(startWithContext, 240).trim() + tail;
+    summary.innerText = top + text.substr(startWithContext, 240).trim() + tail;
 
     highlightWords.forEach((highlightWord) =>
       _highlightText(summary, highlightWord, "highlighted")
diff --git a/docs/_tutorial/index.html b/docs/_tutorial/index.html
index 11d4b17..9689b81 100644
--- a/docs/_tutorial/index.html
+++ b/docs/_tutorial/index.html
@@ -1,10 +1,10 @@
 
 
 
-  
+  
 
   
-  Full workflow — SERD 0.1.1 documentation
+  Full workflow — SERD 0.1.2 documentation
       
       
     
diff --git a/docs/genindex.html b/docs/genindex.html
index b94627a..874fc3f 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -3,7 +3,7 @@
 
   
   
-  Index — SERD 0.1.1 documentation
+  Index — SERD 0.1.2 documentation
       
       
     
diff --git a/docs/index.html b/docs/index.html
index 41c6d5a..8e21d5e 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -1,10 +1,10 @@
 
 
 
-  
+  
 
   
-  Welcome to SERD’s documentation! — SERD 0.1.1 documentation
+  Welcome to SERD’s documentation! — SERD 0.1.2 documentation
       
       
     
diff --git a/docs/search.html b/docs/search.html
index e9938d9..35c66f9 100644
--- a/docs/search.html
+++ b/docs/search.html
@@ -3,7 +3,7 @@
 
   
   
-  Search — SERD 0.1.1 documentation
+  Search — SERD 0.1.2 documentation
       
       
     
diff --git a/docs/searchindex.js b/docs/searchindex.js
index a83cbfc..c0961b2 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["_about/index", "_api_reference/index", "_installation/index", "_tutorial/index", "index"], "filenames": ["_about/index.rst", "_api_reference/index.rst", "_installation/index.rst", "_tutorial/index.rst", "index.rst"], "titles": ["Issues", "SERD.detect", "Requirements", "Full workflow", "Welcome to SERD\u2019s documentation!"], "terms": {"about": 0, "serd": [0, 2, 3], "packag": [0, 1, 3, 4], "us": [0, 1, 2, 3], "github": [0, 2], "project": 0, "manag": [0, 4], "pleas": 0, "help": [0, 4], "u": [0, 3], "report": [0, 4], "ani": 0, "problem": 0, "request": [0, 4], "On": [0, 2], "page": [0, 4], "you": [0, 2, 3, 4], "can": [0, 2, 3], "file": [0, 1, 3], "bug": [0, 4], "new": [0, 4], "featur": [0, 3, 4], "onli": [0, 3], "make": 0, "sure": 0, "ha": [0, 1, 3], "alreadi": 0, "been": 0, "click": 0, "search": 0, "enter": 0, "some": 0, "keyword": [0, 1], "thank": 0, "improv": 0, "wa": [0, 4], "develop": 0, "jo\u00e3o": 0, "victor": 0, "da": 0, "silva": 0, "guerra": 0, "gabriel": 0, "ernesto": 0, "jara": 0, "jos\u00e9": 0, "geraldo": 0, "de": 0, "carvalho": 0, "pereira": 0, "paulo": 0, "sergio": 0, "lope": 0, "oliveira": 0, "comput": 0, "biologi": 0, "laboratori": 0, "lbc": 0, "brazilian": 0, "bioscienc": 0, "nation": 0, "lnbio": 0, "center": 0, "research": 0, "energi": 0, "materi": 0, "cnpem": 0, "If": [0, 1, 2, 3], "have": [0, 2], "further": [0, 3], "question": 0, "inquir": 0, "wish": [0, 3], "contribut": 0, "contact": [0, 1], "jvsguerra": [0, 2], "gmail": 0, "com": [0, 2], "The": [0, 1, 2, 3], "softwar": 0, "i": [0, 1, 2, 3], "under": 0, "term": 0, "gnu": 0, "gener": [0, 1], "public": 0, "version": [0, 2], "3": [0, 2], "gpl3": 0, "distribut": 0, "hope": 0, "without": 0, "warranti": 0, "even": 0, "impli": 0, "merchant": 0, "fit": 0, "FOR": 0, "A": [0, 1], "particular": 0, "purpos": 0, "see": [0, 1, 3], "more": [0, 1, 3], "detail": [0, 1, 3], "api": [1, 3], "refer": [1, 3], "target": [1, 3], "union": 1, "str": 1, "path": 1, "surface_represent": 1, "liter": 1, "vdw": [1, 3], "se": [1, 3], "sa": 1, "step": [1, 3], "float": 1, "int": 1, "0": [1, 3], "6": [1, 3], "probe": [1, 3], "1": [1, 3], "4": [1, 3], "option": 1, "none": 1, "ignore_backbon": 1, "bool": 1, "true": 1, "nthread": 1, "verbos": 1, "fals": 1, "sourc": 1, "solvent": [1, 3, 4], "expos": [1, 3, 4], "residu": [1, 3, 4], "biomolecul": [1, 3], "paramet": 1, "pathlib": 1, "pdb": [1, 3], "xyz": [1, 3], "biomolecular": [1, 3], "structur": [1, 3], "represent": 1, "ar": [1, 3], "van": [1, 3], "der": [1, 3], "waal": [1, 3], "exclud": 1, "access": 1, "default": [1, 2], "grid": [1, 3], "space": [1, 3], "size": 1, "defin": [1, 3], "radii": [1, 3], "appli": [1, 3], "built": [1, 3, 4], "dat": [1, 3], "whether": 1, "ignor": 1, "backbon": 1, "atom": [1, 3], "c": [1, 3], "ca": [1, 3], "n": [1, 2, 3], "o": [1, 3], "when": [1, 3], "number": [1, 3], "thread": 1, "cpu_count": 1, "print": [1, 3], "extra": 1, "inform": [1, 3], "standard": 1, "output": 1, "return": [1, 3], "list": [1, 3], "type": 1, "rais": 1, "typeerror": 1, "must": [1, 3], "string": 1, "posit": 1, "real": 1, "valueerror": 1, "non": 1, "neg": 1, "integ": 1, "boolean": 1, "set": 1, "radiu": [1, 3], "valu": [1, 3], "each": [1, 3], "base": [1, 2, 3], "pykvfind": [1, 3], "graph": [1, 3], "ndarrai": 1, "fn": [1, 3], "format": 1, "node": [1, 3], "repres": [1, 3], "edg": [1, 3], "conect": [1, 3], "record": [1, 3], "networkx": 1, "class": [1, 3], "distanc": [1, 3], "smaller": 1, "than": [1, 2], "cutoff": [1, 3], "numpi": [1, 3], "arrai": [1, 3], "data": 1, "chain": [1, 3], "name": [1, 3], "coordin": [1, 3], "get": [1, 4], "3d": [1, 3], "vertic": [1, 3], "origin": [1, 3], "x": [1, 3], "axi": [1, 3], "y": [1, 3], "z": [1, 3], "identifi": [1, 3], "point": 1, "nx": 1, "ny": 1, "nz": [1, 3], "label": 1, "enclos": 1, "region": 1, "consid": 1, "incorrect": 1, "shape": 1, "It": 1, "8": [1, 3], "select": [1, 3], "cb": [1, 3], "intraresidu": 1, "weighted_edg": 1, "creat": [1, 2, 3], "from": [1, 2], "all": [1, 3], "alfa": 1, "carbon": 1, "beta": 1, "except": 1, "glycin": 1, "which": 1, "between": [1, 3], "smallest": 1, "limit": 1, "an": [1, 2, 3], "two": 1, "depend": [1, 2, 3], "argument": [1, 3], "10": 1, "adjac": 1, "matrix": 1, "includ": 1, "interresidu": 1, "weight": 1, "capri": 1, "round": 1, "28": [1, 3], "For": [1, 3], "http": [1, 2], "www": 1, "ebi": 1, "ac": [1, 3], "uk": 1, "msd": 1, "srv": 1, "round28": 1, "html": 1, "dict": 1, "read": [1, 3], "dictionari": [1, 3], "contain": [1, 3], "line": 1, "doubl": 1, "tab": 1, "separ": 1, "templat": 1, "function": [1, 3], "load": 1, "pickl": [1, 3], "binari": [1, 3], "pse": [1, 3], "pymol": [1, 2, 3], "session": [1, 3], "shown": [1, 3], "red": 1, "stick": 1, "cartoon": 1, "don": 2, "t": 2, "python": [2, 3], "v3": 2, "swig": 2, "yet": 2, "procedur": [2, 3], "differ": 2, "oper": 2, "system": 2, "linux": 2, "maco": 2, "sudo": 2, "apt": 2, "python3": 2, "brew": 2, "user": [2, 3], "prefer": [2, 3], "channel": 2, "environ": 2, "rather": 2, "recommend": 2, "myenv": 2, "activ": 2, "command": 2, "prerequisit": 2, "v2": 2, "To": 2, "latest": 2, "releas": 2, "pypi": 2, "run": [2, 3], "pip": 2, "Or": 2, "development": 2, "git": 2, "clone": 2, "tutori": 3, "thi": [3, 4], "section": 3, "introductori": 3, "overview": 3, "document": 3, "In": 3, "we": 3, "catalyt": 3, "subunit": 3, "camp": 3, "protein": 3, "kinas": 3, "cadk": 3, "detect": [3, 4], "its": 3, "expoos": 3, "first": 3, "import": 3, "exampl": 3, "1fmo": 3, "13": 3, "e": 3, "glu": 3, "14": 3, "ser": 3, "15": 3, "val": 3, "16": 3, "ly": 3, "17": 3, "18": 3, "phe": 3, "19": 3, "leu": 3, "20": 3, "ala": 3, "21": 3, "22": 3, "23": 3, "24": 3, "25": 3, "asp": 3, "26": 3, "27": 3, "29": 3, "30": 3, "trp": 3, "31": 3, "32": 3, "thr": 3, "33": 3, "pro": 3, "34": 3, "35": 3, "gln": 3, "36": 3, "asn": 3, "37": 3, "38": 3, "39": 3, "40": 3, "41": 3, "42": 3, "43": 3, "44": 3, "45": 3, "arg": 3, "46": 3, "il": 3, "47": 3, "48": 3, "49": 3, "51": 3, "53": 3, "54": 3, "56": 3, "57": 3, "58": 3, "met": 3, "59": 3, "60": 3, "61": 3, "62": 3, "hi": 3, "63": 3, "64": 3, "65": 3, "67": 3, "68": 3, "69": 3, "tyr": 3, "70": 3, "71": 3, "72": 3, "73": 3, "74": 3, "75": 3, "76": 3, "77": 3, "78": 3, "79": 3, "80": 3, "81": 3, "82": 3, "83": 3, "84": 3, "85": 3, "86": 3, "87": 3, "88": 3, "89": 3, "90": 3, "91": 3, "92": 3, "93": 3, "94": 3, "95": 3, "96": 3, "97": 3, "98": 3, "99": 3, "100": 3, "101": 3, "102": 3, "103": 3, "104": 3, "105": 3, "106": 3, "107": 3, "108": 3, "109": 3, "110": 3, "111": 3, "112": 3, "113": 3, "114": 3, "115": 3, "116": 3, "117": 3, "118": 3, "119": 3, "120": 3, "121": 3, "122": 3, "123": 3, "124": 3, "127": 3, "128": 3, "129": 3, "130": 3, "131": 3, "132": 3, "133": 3, "134": 3, "135": 3, "137": 3, "138": 3, "139": 3, "140": 3, "141": 3, "142": 3, "143": 3, "144": 3, "145": 3, "146": 3, "147": 3, "148": 3, "149": 3, "150": 3, "151": 3, "152": 3, "153": 3, "154": 3, "155": 3, "156": 3, "157": 3, "158": 3, "159": 3, "160": 3, "161": 3, "162": 3, "163": 3, "164": 3, "165": 3, "166": 3, "167": 3, "168": 3, "169": 3, "170": 3, "171": 3, "172": 3, "173": 3, "174": 3, "175": 3, "176": 3, "177": 3, "179": 3, "180": 3, "181": 3, "182": 3, "183": 3, "184": 3, "185": 3, "187": 3, "188": 3, "189": 3, "190": 3, "191": 3, "192": 3, "194": 3, "195": 3, "196": 3, "197": 3, "tpo": 3, "198": 3, "199": 3, "cy": 3, "201": 3, "202": 3, "203": 3, "204": 3, "205": 3, "206": 3, "207": 3, "208": 3, "209": 3, "210": 3, "211": 3, "212": 3, "213": 3, "215": 3, "216": 3, "217": 3, "218": 3, "219": 3, "220": 3, "221": 3, "222": 3, "223": 3, "224": 3, "226": 3, "227": 3, "228": 3, "229": 3, "230": 3, "231": 3, "232": 3, "233": 3, "235": 3, "236": 3, "237": 3, "238": 3, "239": 3, "240": 3, "241": 3, "242": 3, "243": 3, "244": 3, "245": 3, "246": 3, "247": 3, "248": 3, "249": 3, "250": 3, "251": 3, "252": 3, "254": 3, "255": 3, "256": 3, "257": 3, "258": 3, "259": 3, "260": 3, "261": 3, "262": 3, "263": 3, "264": 3, "265": 3, "266": 3, "267": 3, "268": 3, "269": 3, "270": 3, "271": 3, "272": 3, "273": 3, "274": 3, "275": 3, "276": 3, "277": 3, "278": 3, "279": 3, "280": 3, "281": 3, "283": 3, "284": 3, "285": 3, "286": 3, "288": 3, "289": 3, "290": 3, "291": 3, "292": 3, "293": 3, "294": 3, "295": 3, "296": 3, "297": 3, "298": 3, "299": 3, "300": 3, "301": 3, "302": 3, "303": 3, "304": 3, "305": 3, "306": 3, "307": 3, "308": 3, "309": 3, "310": 3, "311": 3, "312": 3, "313": 3, "314": 3, "315": 3, "316": 3, "317": 3, "318": 3, "319": 3, "321": 3, "323": 3, "324": 3, "325": 3, "326": 3, "327": 3, "328": 3, "329": 3, "330": 3, "331": 3, "332": 3, "333": 3, "334": 3, "335": 3, "336": 3, "337": 3, "338": 3, "sep": 3, "339": 3, "340": 3, "341": 3, "342": 3, "343": 3, "345": 3, "346": 3, "347": 3, "348": 3, "349": 3, "350": 3, "still": 3, "save": [3, 4], "visual": 3, "save_sess": [3, 4], "furthermor": 3, "read_pdb": [3, 4], "g": 3, "r2g": [3, 4], "number_of_nod": 3, "number_of_edg": 3, "929": 3, "addit": 3, "g2pdb": [3, 4], "instead": 3, "fashion": 3, "below": 3, "briefli": 3, "describ": 3, "read_vdw": [3, 4], "take": 3, "contan": 3, "824": 3, "h": 3, "hn": 3, "908": 3, "387": 3, "hb1": 3, "487": 3, "1hb": 3, "hb2": 3, "2hb": 3, "hb3": 3, "3hb": 3, "6612": 3, "cg": 3, "hg2": 3, "2hg": 3, "hg3": 3, "hg1": 3, "1hg": 3, "cd": 3, "hd2": 3, "1hd": 3, "2hd": 3, "hd3": 3, "hd1": 3, "ne": 3, "he": 3, "cz": 3, "nh1": 3, "hh11": 3, "1hh1": 3, "hh12": 3, "2hh1": 3, "nh2": 3, "hh21": 3, "2hh2": 3, "hh22": 3, "1hh2": 3, "ash": 3, "od1": 3, "od2": 3, "721": 3, "0001": 3, "nd2": 3, "hd21": 3, "1hd2": 3, "hd22": 3, "2hd2": 3, "cym": 3, "sg": 3, "2": 3, "hg": 3, "cyx": 3, "glh": 3, "oe1": 3, "oe2": 3, "he2": 3, "ne2": 3, "he21": 3, "1he2": 3, "he22": 3, "2he2": 3, "gly": 3, "ha2": 3, "ha1": 3, "1ha": 3, "2ha": 3, "ha3": 3, "hid": 3, "nd1": 3, "ce1": 3, "he1": 3, "359": 3, "cd2": 3, "409": 3, "hie": 3, "hip": 3, "hb": 3, "cg2": 3, "hg21": 3, "1hg2": 3, "hg22": 3, "2hg2": 3, "hg23": 3, "3hg2": 3, "cg1": 3, "hg12": 3, "2hg1": 3, "hg13": 3, "hg11": 3, "1hg1": 3, "cd1": 3, "hd11": 3, "1hd1": 3, "hd12": 3, "2hd1": 3, "hd13": 3, "3hd1": 3, "hd23": 3, "3hd2": 3, "lyn": 3, "ce": 3, "he3": 3, "hz2": 3, "hz3": 3, "2he": 3, "1he": 3, "hz1": 3, "1hz": 3, "2hz": 3, "3hz": 3, "sd": 3, "3he": 3, "459": 3, "hz": 3, "ce2": 3, "og": 3, "og1": 3, "ne1": 3, "cz2": 3, "ch2": 3, "hh2": 3, "cz3": 3, "ce3": 3, "oh": 3, "hh": 3, "3hg1": 3, "ptr": 3, "6837": 3, "p": 3, "o1p": 3, "o2p": 3, "o3p": 3, "h2d": 3, "y1p": 3, "h1p": 3, "t1p": 3, "s1p": 3, "gen": 3, "ag": 3, "al": 3, "am": 3, "AS": 3, "AT": 3, "au": 3, "66": 3, "b": 3, "ba": 3, "BE": 3, "bh": 3, "bi": 3, "bk": 3, "br": 3, "cf": 3, "cl": 3, "cm": 3, "co": 3, "cr": 3, "cu": 3, "db": 3, "d": 3, "dy": 3, "er": 3, "eu": 3, "f": 3, "fe": 3, "fm": 3, "fr": 3, "ga": 3, "gd": 3, "ge": 3, "hf": 3, "55": 3, "ho": 3, "IN": 3, "ir": 3, "k": 3, "kr": 3, "02": 3, "la": 3, "li": 3, "lr": 3, "lu": 3, "md": 3, "mg": 3, "mn": 3, "mo": 3, "mt": 3, "na": 3, "nb": 3, "nd": 3, "ni": 3, "NO": 3, "np": 3, "pa": 3, "pb": 3, "pd": 3, "pm": 3, "po": 3, "pr": 3, "pt": 3, "pu": 3, "ra": 3, "rb": 3, "re": 3, "rf": 3, "rh": 3, "rn": 3, "ru": 3, "": 3, "09": 3, "sb": 3, "sc": 3, "9": 3, "si": 3, "sm": 3, "sn": 3, "sr": 3, "ta": 3, "tb": 3, "tc": 3, "te": 3, "06": 3, "th": 3, "ti": 3, "tl": 3, "tm": 3, "v": 3, "w": 3, "xe": 3, "yb": 3, "zn": 3, "zr": 3, "necessari": 3, "custom": 3, "read_xyz": 3, "642": 3, "858": 3, "897": 3, "357": 3, "508": 3, "878": 3, "885": 3, "624": 3, "558": 3, "234": 3, "442": 3, "dtype": 3, "u32": 3, "specifi": 3, "earlier": 3, "pass": 3, "get_vertic": [3, 4], "525": 3, "588": 3, "846": 3, "752": 3, "surfac": [3, 4], "int32": 3, "interfac": [3, 4], "start": 4, "our": 4, "requir": 4, "conda": 4, "full": 4, "workflow": 4, "stepwis": 4, "issu": 4, "scientif": 4, "team": 4, "licens": 4}, "objects": {"SERD": [[1, 0, 1, "", "detect"], [1, 0, 1, "", "g2pdb"], [1, 0, 1, "", "get_vertices"], [1, 0, 1, "", "interface"], [1, 0, 1, "", "r2g"], [1, 0, 1, "", "read_pdb"], [1, 0, 1, "", "read_vdw"], [1, 0, 1, "", "save"], [1, 0, 1, "", "save_session"], [1, 0, 1, "", "surface"]]}, "objtypes": {"0": "py:function"}, "objnames": {"0": ["py", "function", "Python function"]}, "titleterms": {"issu": 0, "scientif": 0, "team": 0, "licens": 0, "serd": [1, 4], "detect": 1, "g2pdb": 1, "get_vertic": 1, "interfac": 1, "r2g": 1, "read_vdw": 1, "read_pdb": 1, "save": 1, "save_sess": 1, "surfac": 1, "requir": 2, "packag": 2, "manag": 2, "conda": 2, "instal": [2, 4], "full": 3, "workflow": 3, "stepwis": 3, "welcom": 4, "": 4, "document": 4, "tutori": 4, "api": 4, "refer": 4, "about": 4}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 56}})
\ No newline at end of file
+Search.setIndex({"docnames": ["_about/index", "_api_reference/index", "_installation/index", "_tutorial/index", "index"], "filenames": ["_about/index.rst", "_api_reference/index.rst", "_installation/index.rst", "_tutorial/index.rst", "index.rst"], "titles": ["Issues", "SERD.detect", "Requirements", "Full workflow", "Welcome to SERD\u2019s documentation!"], "terms": {"about": 0, "serd": [0, 2, 3], "packag": [0, 1, 3, 4], "us": [0, 1, 2, 3], "github": [0, 2], "project": 0, "manag": [0, 4], "pleas": 0, "help": [0, 4], "report": [0, 4], "ani": 0, "problem": 0, "request": [0, 4], "On": [0, 2], "page": [0, 4], "you": [0, 2, 3, 4], "can": [0, 2, 3], "file": [0, 1, 3], "bug": [0, 4], "new": [0, 4], "featur": [0, 3, 4], "onli": [0, 3], "make": 0, "sure": 0, "ha": [0, 1, 3], "alreadi": 0, "been": 0, "click": 0, "search": 0, "enter": 0, "some": 0, "keyword": [0, 1], "thank": 0, "improv": 0, "wa": [0, 4], "develop": 0, "jo\u00e3o": 0, "victor": 0, "da": 0, "silva": 0, "guerra": 0, "gabriel": 0, "ernesto": 0, "jara": 0, "jos\u00e9": 0, "geraldo": 0, "de": 0, "carvalho": 0, "pereira": 0, "paulo": 0, "sergio": 0, "lope": 0, "oliveira": 0, "comput": 0, "biologi": 0, "laboratori": 0, "lbc": 0, "brazilian": 0, "bioscienc": 0, "nation": 0, "lnbio": 0, "center": 0, "research": 0, "energi": 0, "materi": 0, "cnpem": 0, "If": [0, 1, 2, 3], "have": [0, 2], "further": [0, 3], "question": 0, "inquir": 0, "wish": [0, 3], "contribut": 0, "contact": [0, 1], "jvsguerra": [0, 2], "gmail": 0, "com": [0, 2], "The": [0, 1, 2, 3], "softwar": 0, "under": 0, "term": 0, "gnu": 0, "gener": [0, 1], "public": 0, "version": [0, 2], "3": [0, 2], "gpl3": 0, "distribut": 0, "hope": 0, "without": 0, "warranti": 0, "even": 0, "impli": 0, "merchant": 0, "fit": 0, "FOR": 0, "A": [0, 1], "particular": 0, "purpos": 0, "see": [0, 1, 3], "more": [0, 1, 3], "detail": [0, 1, 3], "api": [1, 3], "refer": [1, 3], "target": [1, 3], "union": 1, "str": 1, "path": 1, "surface_represent": 1, "liter": 1, "vdw": [1, 3], "se": [1, 3], "sa": 1, "step": [1, 3], "float": 1, "int": 1, "0": [1, 3], "6": [1, 3], "probe": [1, 3], "1": [1, 3], "4": [1, 3], "option": 1, "none": 1, "ignore_backbon": 1, "bool": 1, "true": 1, "nthread": 1, "verbos": 1, "fals": 1, "sourc": 1, "solvent": [1, 3, 4], "expos": [1, 3, 4], "residu": [1, 3, 4], "biomolecul": [1, 3], "paramet": 1, "pathlib": 1, "pdb": [1, 3], "xyz": [1, 3], "biomolecular": [1, 3], "structur": [1, 3], "represent": 1, "ar": [1, 3], "van": [1, 3], "der": [1, 3], "waal": [1, 3], "exclud": 1, "access": 1, "default": [1, 2], "grid": [1, 3], "space": [1, 3], "size": 1, "defin": [1, 3], "radii": [1, 3], "appli": [1, 3], "built": [1, 3, 4], "dat": [1, 3], "whether": 1, "ignor": 1, "backbon": 1, "atom": [1, 3], "c": [1, 3], "ca": [1, 3], "n": [1, 2, 3], "o": [1, 3], "when": [1, 3], "number": [1, 3], "thread": 1, "os": [1, 3], "cpu_count": 1, "print": [1, 3], "extra": 1, "inform": [1, 3], "standard": 1, "output": 1, "return": [1, 3], "list": [1, 3], "type": 1, "rais": 1, "typeerror": 1, "must": [1, 3], "string": 1, "posit": 1, "real": 1, "valueerror": 1, "non": 1, "neg": 1, "integ": 1, "boolean": 1, "set": 1, "radiu": [1, 3], "valu": [1, 3], "each": [1, 3], "base": [1, 2, 3], "pykvfind": [1, 3], "graph": [1, 3], "ndarrai": 1, "fn": [1, 3], "format": 1, "node": [1, 3], "repres": [1, 3], "edg": [1, 3], "conect": [1, 3], "record": [1, 3], "networkx": 1, "class": [1, 3], "distanc": [1, 3], "smaller": 1, "than": [1, 2], "cutoff": [1, 3], "numpi": [1, 3], "arrai": [1, 3], "data": 1, "chain": [1, 3], "name": [1, 3], "coordin": [1, 3], "get": [1, 4], "3d": [1, 3], "vertic": [1, 3], "origin": [1, 3], "x": [1, 3], "axi": [1, 3], "y": [1, 3], "z": [1, 3], "identifi": [1, 3], "point": 1, "nx": 1, "ny": 1, "nz": [1, 3], "label": 1, "enclos": 1, "region": 1, "consid": 1, "incorrect": 1, "shape": 1, "It": 1, "8": [1, 3], "select": [1, 3], "cb": [1, 3], "intraresidu": 1, "weighted_edg": 1, "creat": [1, 2, 3], "from": [1, 2], "all": [1, 3], "alfa": 1, "carbon": 1, "beta": 1, "except": 1, "glycin": 1, "which": 1, "between": [1, 3], "smallest": 1, "limit": 1, "an": [1, 2, 3], "two": 1, "depend": [1, 2, 3], "argument": [1, 3], "10": 1, "adjac": 1, "matrix": 1, "includ": 1, "weight": 1, "capri": 1, "round": 1, "28": [1, 3], "For": [1, 3], "http": [1, 2], "www": 1, "ebi": 1, "ac": [1, 3], "uk": 1, "msd": 1, "srv": 1, "round28": 1, "html": 1, "dict": 1, "read": [1, 3], "dictionari": [1, 3], "contain": [1, 3], "line": 1, "doubl": 1, "tab": 1, "separ": 1, "templat": 1, "function": [1, 3], "load": 1, "pickl": [1, 3], "binari": [1, 3], "pse": [1, 3], "pymol": [1, 2, 3], "session": [1, 3], "shown": [1, 3], "red": 1, "stick": 1, "cartoon": 1, "don": 2, "t": 2, "python": [2, 3], "v3": 2, "swig": 2, "yet": 2, "procedur": [2, 3], "differ": 2, "oper": 2, "system": 2, "linux": 2, "maco": 2, "sudo": 2, "apt": 2, "python3": 2, "brew": 2, "user": [2, 3], "prefer": [2, 3], "channel": 2, "environ": 2, "rather": 2, "recommend": 2, "myenv": 2, "activ": 2, "command": 2, "prerequisit": 2, "v2": 2, "To": 2, "latest": 2, "releas": 2, "pypi": 2, "run": [2, 3], "pip": 2, "Or": 2, "development": 2, "git": 2, "clone": 2, "tutori": 3, "thi": [3, 4], "section": 3, "introductori": 3, "overview": 3, "document": 3, "In": 3, "we": 3, "catalyt": 3, "subunit": 3, "camp": 3, "protein": 3, "kinas": 3, "cadk": 3, "detect": [3, 4], "its": 3, "expoos": 3, "first": 3, "import": 3, "exampl": 3, "1fmo": 3, "13": 3, "e": 3, "glu": 3, "14": 3, "ser": 3, "15": 3, "val": 3, "16": 3, "ly": 3, "17": 3, "18": 3, "phe": 3, "19": 3, "leu": 3, "20": 3, "ala": 3, "21": 3, "22": 3, "23": 3, "24": 3, "25": 3, "asp": 3, "26": 3, "27": 3, "29": 3, "30": 3, "trp": 3, "31": 3, "32": 3, "thr": 3, "33": 3, "pro": 3, "34": 3, "35": 3, "gln": 3, "36": 3, "asn": 3, "37": 3, "38": 3, "39": 3, "40": 3, "41": 3, "42": 3, "43": 3, "44": 3, "45": 3, "arg": 3, "46": 3, "il": 3, "47": 3, "48": 3, "49": 3, "51": 3, "53": 3, "54": 3, "56": 3, "57": 3, "58": 3, "met": 3, "59": 3, "60": 3, "61": 3, "62": 3, "hi": 3, "63": 3, "64": 3, "65": 3, "67": 3, "68": 3, "69": 3, "tyr": 3, "70": 3, "71": 3, "72": 3, "73": 3, "74": 3, "75": 3, "76": 3, "77": 3, "78": 3, "79": 3, "80": 3, "81": 3, "82": 3, "83": 3, "84": 3, "85": 3, "86": 3, "87": 3, "88": 3, "89": 3, "90": 3, "91": 3, "92": 3, "93": 3, "94": 3, "95": 3, "96": 3, "97": 3, "98": 3, "99": 3, "100": 3, "101": 3, "102": 3, "103": 3, "104": 3, "105": 3, "106": 3, "107": 3, "108": 3, "109": 3, "110": 3, "111": 3, "112": 3, "113": 3, "114": 3, "115": 3, "116": 3, "117": 3, "118": 3, "119": 3, "120": 3, "121": 3, "122": 3, "123": 3, "124": 3, "127": 3, "128": 3, "129": 3, "130": 3, "131": 3, "132": 3, "133": 3, "134": 3, "135": 3, "137": 3, "138": 3, "139": 3, "140": 3, "141": 3, "142": 3, "143": 3, "144": 3, "145": 3, "146": 3, "147": 3, "148": 3, "149": 3, "150": 3, "151": 3, "152": 3, "153": 3, "154": 3, "155": 3, "156": 3, "157": 3, "158": 3, "159": 3, "160": 3, "161": 3, "162": 3, "163": 3, "164": 3, "165": 3, "166": 3, "167": 3, "168": 3, "169": 3, "170": 3, "171": 3, "172": 3, "173": 3, "174": 3, "175": 3, "176": 3, "177": 3, "179": 3, "180": 3, "181": 3, "182": 3, "183": 3, "184": 3, "185": 3, "187": 3, "188": 3, "189": 3, "190": 3, "191": 3, "192": 3, "194": 3, "195": 3, "196": 3, "197": 3, "tpo": 3, "198": 3, "199": 3, "cy": 3, "201": 3, "202": 3, "203": 3, "204": 3, "205": 3, "206": 3, "207": 3, "208": 3, "209": 3, "210": 3, "211": 3, "212": 3, "213": 3, "215": 3, "216": 3, "217": 3, "218": 3, "219": 3, "220": 3, "221": 3, "222": 3, "223": 3, "224": 3, "226": 3, "227": 3, "228": 3, "229": 3, "230": 3, "231": 3, "232": 3, "233": 3, "235": 3, "236": 3, "237": 3, "238": 3, "239": 3, "240": 3, "241": 3, "242": 3, "243": 3, "244": 3, "245": 3, "246": 3, "247": 3, "248": 3, "249": 3, "250": 3, "251": 3, "252": 3, "254": 3, "255": 3, "256": 3, "257": 3, "258": 3, "259": 3, "260": 3, "261": 3, "262": 3, "263": 3, "264": 3, "265": 3, "266": 3, "267": 3, "268": 3, "269": 3, "270": 3, "271": 3, "272": 3, "273": 3, "274": 3, "275": 3, "276": 3, "277": 3, "278": 3, "279": 3, "280": 3, "281": 3, "283": 3, "284": 3, "285": 3, "286": 3, "288": 3, "289": 3, "290": 3, "291": 3, "292": 3, "293": 3, "294": 3, "295": 3, "296": 3, "297": 3, "298": 3, "299": 3, "300": 3, "301": 3, "302": 3, "303": 3, "304": 3, "305": 3, "306": 3, "307": 3, "308": 3, "309": 3, "310": 3, "311": 3, "312": 3, "313": 3, "314": 3, "315": 3, "316": 3, "317": 3, "318": 3, "319": 3, "321": 3, "323": 3, "324": 3, "325": 3, "326": 3, "327": 3, "328": 3, "329": 3, "330": 3, "331": 3, "332": 3, "333": 3, "334": 3, "335": 3, "336": 3, "337": 3, "338": 3, "sep": 3, "339": 3, "340": 3, "341": 3, "342": 3, "343": 3, "345": 3, "346": 3, "347": 3, "348": 3, "349": 3, "350": 3, "still": 3, "save": [3, 4], "visual": 3, "save_sess": [3, 4], "furthermor": 3, "read_pdb": [3, 4], "g": 3, "r2g": [3, 4], "number_of_nod": 3, "number_of_edg": 3, "929": 3, "addit": 3, "g2pdb": [3, 4], "instead": 3, "fashion": 3, "below": 3, "briefli": 3, "describ": 3, "read_vdw": [3, 4], "take": 3, "contan": 3, "824": 3, "h": 3, "hn": 3, "908": 3, "387": 3, "hb1": 3, "487": 3, "1hb": 3, "hb2": 3, "2hb": 3, "hb3": 3, "3hb": 3, "6612": 3, "cg": 3, "hg2": 3, "2hg": 3, "hg3": 3, "hg1": 3, "1hg": 3, "cd": 3, "hd2": 3, "1hd": 3, "2hd": 3, "hd3": 3, "hd1": 3, "ne": 3, "he": 3, "cz": 3, "nh1": 3, "hh11": 3, "1hh1": 3, "hh12": 3, "2hh1": 3, "nh2": 3, "hh21": 3, "2hh2": 3, "hh22": 3, "1hh2": 3, "ash": 3, "od1": 3, "od2": 3, "721": 3, "0001": 3, "nd2": 3, "hd21": 3, "1hd2": 3, "hd22": 3, "2hd2": 3, "cym": 3, "sg": 3, "2": 3, "hg": 3, "cyx": 3, "glh": 3, "oe1": 3, "oe2": 3, "he2": 3, "ne2": 3, "he21": 3, "1he2": 3, "he22": 3, "2he2": 3, "gly": 3, "ha2": 3, "ha1": 3, "1ha": 3, "2ha": 3, "ha3": 3, "hid": 3, "nd1": 3, "ce1": 3, "he1": 3, "359": 3, "cd2": 3, "409": 3, "hie": 3, "hip": 3, "hb": 3, "cg2": 3, "hg21": 3, "1hg2": 3, "hg22": 3, "2hg2": 3, "hg23": 3, "3hg2": 3, "cg1": 3, "hg12": 3, "2hg1": 3, "hg13": 3, "hg11": 3, "1hg1": 3, "cd1": 3, "hd11": 3, "1hd1": 3, "hd12": 3, "2hd1": 3, "hd13": 3, "3hd1": 3, "hd23": 3, "3hd2": 3, "lyn": 3, "ce": 3, "he3": 3, "hz2": 3, "hz3": 3, "2he": 3, "1he": 3, "hz1": 3, "1hz": 3, "2hz": 3, "3hz": 3, "sd": 3, "3he": 3, "459": 3, "hz": 3, "ce2": 3, "og": 3, "og1": 3, "ne1": 3, "cz2": 3, "ch2": 3, "hh2": 3, "cz3": 3, "ce3": 3, "oh": 3, "hh": 3, "3hg1": 3, "ptr": 3, "6837": 3, "p": 3, "o1p": 3, "o2p": 3, "o3p": 3, "h2d": 3, "y1p": 3, "h1p": 3, "t1p": 3, "s1p": 3, "gen": 3, "ag": 3, "al": 3, "am": 3, "AS": 3, "AT": 3, "au": 3, "66": 3, "b": 3, "ba": 3, "BE": 3, "bh": 3, "bi": 3, "bk": 3, "br": 3, "cf": 3, "cl": 3, "cm": 3, "co": 3, "cr": 3, "cs": 3, "cu": 3, "db": 3, "ds": 3, "dy": 3, "er": 3, "es": 3, "eu": 3, "f": 3, "fe": 3, "fm": 3, "fr": 3, "ga": 3, "gd": 3, "ge": 3, "hf": 3, "55": 3, "ho": 3, "hs": 3, "i": 3, "IN": 3, "ir": 3, "k": 3, "kr": 3, "02": 3, "la": 3, "li": 3, "lr": 3, "lu": 3, "md": 3, "mg": 3, "mn": 3, "mo": 3, "mt": 3, "na": 3, "nb": 3, "nd": 3, "ni": 3, "NO": 3, "np": 3, "pa": 3, "pb": 3, "pd": 3, "pm": 3, "po": 3, "pr": 3, "pt": 3, "pu": 3, "ra": 3, "rb": 3, "re": 3, "rf": 3, "rh": 3, "rn": 3, "ru": 3, "s": 3, "09": 3, "sb": 3, "sc": 3, "9": 3, "si": 3, "sm": 3, "sn": 3, "sr": 3, "ta": 3, "tb": 3, "tc": 3, "te": 3, "06": 3, "th": 3, "ti": 3, "tl": 3, "tm": 3, "u": 3, "v": 3, "w": 3, "xe": 3, "yb": 3, "zn": 3, "zr": 3, "necessari": 3, "custom": 3, "read_xyz": 3, "642": 3, "858": 3, "897": 3, "357": 3, "508": 3, "878": 3, "885": 3, "624": 3, "558": 3, "234": 3, "442": 3, "dtype": 3, "u32": 3, "specifi": 3, "earlier": 3, "pass": 3, "get_vertic": [3, 4], "525": 3, "588": 3, "846": 3, "752": 3, "surfac": [3, 4], "int32": 3, "interfac": [3, 4], "start": 4, "our": 4, "requir": 4, "conda": 4, "full": 4, "workflow": 4, "stepwis": 4, "issu": 4, "scientif": 4, "team": 4, "licens": 4}, "objects": {"SERD": [[1, 0, 1, "", "detect"], [1, 0, 1, "", "g2pdb"], [1, 0, 1, "", "get_vertices"], [1, 0, 1, "", "interface"], [1, 0, 1, "", "r2g"], [1, 0, 1, "", "read_pdb"], [1, 0, 1, "", "read_vdw"], [1, 0, 1, "", "save"], [1, 0, 1, "", "save_session"], [1, 0, 1, "", "surface"]]}, "objtypes": {"0": "py:function"}, "objnames": {"0": ["py", "function", "Python function"]}, "titleterms": {"issu": 0, "scientif": 0, "team": 0, "licens": 0, "serd": [1, 4], "detect": 1, "g2pdb": 1, "get_vertic": 1, "interfac": 1, "r2g": 1, "read_vdw": 1, "read_pdb": 1, "save": 1, "save_sess": 1, "surfac": 1, "requir": 2, "packag": 2, "manag": 2, "conda": 2, "instal": [2, 4], "full": 3, "workflow": 3, "stepwis": 3, "welcom": 4, "s": 4, "document": 4, "tutori": 4, "api": 4, "refer": 4, "about": 4}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 56}})
\ No newline at end of file