Add missing documentation and test data files

.gitignore

@@ -3,7 +3,4 @@ build/
 dist/
 *.pyc
 *pycache*
-Lib
-nMOLDYN/Trajectories
 nMOLDYN/win32_files/*.exe
-nMOLDYN/Doc

nMOLDYN/Doc/API/HTML/epydoc.js

@@ -0,0 +1,293 @@
+function toggle_private() {
+        // Search for any private/public links on this page.  Store
+        // their old text in "cmd," so we will know what action to
+        // take; and change their text to the opposite action.
+        var cmd = "?";
+        var elts = document.getElementsByTagName("a");
+        for(var i=0; i<elts.length; i++) {
+          if (elts[i].className == "privatelink") {
+            cmd = elts[i].innerHTML;
+            elts[i].innerHTML = ((cmd && cmd.substr(0,4)=="show")?
+                                    "hide&nbsp;private":"show&nbsp;private");
+          }
+        }
+        // Update all DIVs containing private objects.
+        var elts = document.getElementsByTagName("div");
+        for(var i=0; i<elts.length; i++) {
+          if (elts[i].className == "private") {
+            elts[i].style.display = ((cmd && cmd.substr(0,4)=="hide")?"none":"block");
+          }
+          else if (elts[i].className == "public") {
+            elts[i].style.display = ((cmd && cmd.substr(0,4)=="hide")?"block":"none");
+          }
+        }
+        // Update all table rows containing private objects.  Note, we
+        // use "" instead of "block" becaue IE & firefox disagree on what
+        // this should be (block vs table-row), and "" just gives the
+        // default for both browsers.
+        var elts = document.getElementsByTagName("tr");
+        for(var i=0; i<elts.length; i++) {
+          if (elts[i].className == "private") {
+            elts[i].style.display = ((cmd && cmd.substr(0,4)=="hide")?"none":"");
+          }
+        }
+        // Update all list items containing private objects.
+        var elts = document.getElementsByTagName("li");
+        for(var i=0; i<elts.length; i++) {
+          if (elts[i].className == "private") {
+            elts[i].style.display = ((cmd && cmd.substr(0,4)=="hide")?
+                                        "none":"");
+          }
+        }
+        // Update all list items containing private objects.
+        var elts = document.getElementsByTagName("ul");
+        for(var i=0; i<elts.length; i++) {
+          if (elts[i].className == "private") {
+            elts[i].style.display = ((cmd && cmd.substr(0,4)=="hide")?"none":"block");
+          }
+        }
+        // Set a cookie to remember the current option.
+        document.cookie = "EpydocPrivate="+cmd;
+      }
+function show_private() {
+        var elts = document.getElementsByTagName("a");
+        for(var i=0; i<elts.length; i++) {
+          if (elts[i].className == "privatelink") {
+            cmd = elts[i].innerHTML;
+            if (cmd && cmd.substr(0,4)=="show")
+                toggle_private();
+          }
+        }
+      }
+function getCookie(name) {
+        var dc = document.cookie;
+        var prefix = name + "=";
+        var begin = dc.indexOf("; " + prefix);
+        if (begin == -1) {
+          begin = dc.indexOf(prefix);
+          if (begin != 0) return null;
+        } else
+        { begin += 2; }
+        var end = document.cookie.indexOf(";", begin);
+        if (end == -1)
+        { end = dc.length; }
+        return unescape(dc.substring(begin + prefix.length, end));
+      }
+function setFrame(url1, url2) {
+          parent.frames[1].location.href = url1;
+          parent.frames[2].location.href = url2;
+      }
+function checkCookie() {
+        var cmd=getCookie("EpydocPrivate");
+        if (cmd && cmd.substr(0,4)!="show" && location.href.indexOf("#_") < 0)
+            toggle_private();
+      }
+function toggleCallGraph(id) {
+        var elt = document.getElementById(id);
+        if (elt.style.display == "none")
+            elt.style.display = "block";
+        else
+            elt.style.display = "none";
+      }
+function expand(id) {
+  var elt = document.getElementById(id+"-expanded");
+  if (elt) elt.style.display = "block";
+  var elt = document.getElementById(id+"-expanded-linenums");
+  if (elt) elt.style.display = "block";
+  var elt = document.getElementById(id+"-collapsed");
+  if (elt) { elt.innerHTML = ""; elt.style.display = "none"; }
+  var elt = document.getElementById(id+"-collapsed-linenums");
+  if (elt) { elt.innerHTML = ""; elt.style.display = "none"; }
+  var elt = document.getElementById(id+"-toggle");
+  if (elt) { elt.innerHTML = "-"; }
+}
+
+function collapse(id) {
+  var elt = document.getElementById(id+"-expanded");
+  if (elt) elt.style.display = "none";
+  var elt = document.getElementById(id+"-expanded-linenums");
+  if (elt) elt.style.display = "none";
+  var elt = document.getElementById(id+"-collapsed-linenums");
+  if (elt) { elt.innerHTML = "<br />"; elt.style.display="block"; }
+  var elt = document.getElementById(id+"-toggle");
+  if (elt) { elt.innerHTML = "+"; }
+  var elt = document.getElementById(id+"-collapsed");
+  if (elt) {
+    elt.style.display = "block";
+
+    var indent = elt.getAttribute("indent");
+    var pad = elt.getAttribute("pad");
+    var s = "<tt class='py-lineno'>";
+    for (var i=0; i<pad.length; i++) { s += "&nbsp;" }
+    s += "</tt>";
+    s += "&nbsp;&nbsp;<tt class='py-line'>";
+    for (var i=0; i<indent.length; i++) { s += "&nbsp;" }
+    s += "<a href='#' onclick='expand(\"" + id;
+    s += "\");return false'>...</a></tt><br />";
+    elt.innerHTML = s;
+  }
+}
+
+function toggle(id) {
+  elt = document.getElementById(id+"-toggle");
+  if (elt.innerHTML == "-")
+      collapse(id); 
+  else
+      expand(id);
+  return false;
+}
+
+function highlight(id) {
+  var elt = document.getElementById(id+"-def");
+  if (elt) elt.className = "py-highlight-hdr";
+  var elt = document.getElementById(id+"-expanded");
+  if (elt) elt.className = "py-highlight";
+  var elt = document.getElementById(id+"-collapsed");
+  if (elt) elt.className = "py-highlight";
+}
+
+function num_lines(s) {
+  var n = 1;
+  var pos = s.indexOf("\n");
+  while ( pos > 0) {
+    n += 1;
+    pos = s.indexOf("\n", pos+1);
+  }
+  return n;
+}
+
+// Collapse all blocks that mave more than `min_lines` lines.
+function collapse_all(min_lines) {
+  var elts = document.getElementsByTagName("div");
+  for (var i=0; i<elts.length; i++) {
+    var elt = elts[i];
+    var split = elt.id.indexOf("-");
+    if (split > 0)
+      if (elt.id.substring(split, elt.id.length) == "-expanded")
+        if (num_lines(elt.innerHTML) > min_lines)
+          collapse(elt.id.substring(0, split));
+  }
+}
+
+function expandto(href) {
+  var start = href.indexOf("#")+1;
+  if (start != 0 && start != href.length) {
+    if (href.substring(start, href.length) != "-") {
+      collapse_all(4);
+      pos = href.indexOf(".", start);
+      while (pos != -1) {
+        var id = href.substring(start, pos);
+        expand(id);
+        pos = href.indexOf(".", pos+1);
+      }
+      var id = href.substring(start, href.length);
+      expand(id);
+      highlight(id);
+    }
+  }
+}
+
+function kill_doclink(id) {
+  var parent = document.getElementById(id);
+  parent.removeChild(parent.childNodes.item(0));
+}
+function auto_kill_doclink(ev) {
+  if (!ev) var ev = window.event;
+  if (!this.contains(ev.toElement)) {
+    var parent = document.getElementById(this.parentID);
+    parent.removeChild(parent.childNodes.item(0));
+  }
+}
+
+function doclink(id, name, targets_id) {
+  var elt = document.getElementById(id);
+
+  // If we already opened the box, then destroy it.
+  // (This case should never occur, but leave it in just in case.)
+  if (elt.childNodes.length > 1) {
+    elt.removeChild(elt.childNodes.item(0));
+  }
+  else {
+    // The outer box: relative + inline positioning.
+    var box1 = document.createElement("div");
+    box1.style.position = "relative";
+    box1.style.display = "inline";
+    box1.style.top = 0;
+    box1.style.left = 0;
+
+    // A shadow for fun
+    var shadow = document.createElement("div");
+    shadow.style.position = "absolute";
+    shadow.style.left = "-1.3em";
+    shadow.style.top = "-1.3em";
+    shadow.style.background = "#404040";
+
+    // The inner box: absolute positioning.
+    var box2 = document.createElement("div");
+    box2.style.position = "relative";
+    box2.style.border = "1px solid #a0a0a0";
+    box2.style.left = "-.2em";
+    box2.style.top = "-.2em";
+    box2.style.background = "white";
+    box2.style.padding = ".3em .4em .3em .4em";
+    box2.style.fontStyle = "normal";
+    box2.onmouseout=auto_kill_doclink;
+    box2.parentID = id;
+
+    // Get the targets
+    var targets_elt = document.getElementById(targets_id);
+    var targets = targets_elt.getAttribute("targets");
+    var links = "";
+    target_list = targets.split(",");
+    for (var i=0; i<target_list.length; i++) {
+        var target = target_list[i].split("=");
+        links += "<li><a href='" + target[1] + 
+               "' style='text-decoration:none'>" +
+               target[0] + "</a></li>";
+    }
+
+    // Put it all together.
+    elt.insertBefore(box1, elt.childNodes.item(0));
+    //box1.appendChild(box2);
+    box1.appendChild(shadow);
+    shadow.appendChild(box2);
+    box2.innerHTML =
+        "Which <b>"+name+"</b> do you want to see documentation for?" +
+        "<ul style='margin-bottom: 0;'>" +
+        links + 
+        "<li><a href='#' style='text-decoration:none' " +
+        "onclick='kill_doclink(\""+id+"\");return false;'>"+
+        "<i>None of the above</i></a></li></ul>";
+  }
+  return false;
+}
+
+function get_anchor() {
+          var href = location.href;
+          var start = href.indexOf("#")+1;
+          if ((start != 0) && (start != href.length))
+              return href.substring(start, href.length);
+      }
+function redirect_url(dottedName) {
+          // Scan through each element of the "pages" list, and check
+          // if "name" matches with any of them.
+          for (var i=0; i<pages.length; i++) {
+
+              // Each page has the form "<pagename>-m" or "<pagename>-c";
+              // extract the <pagename> portion & compare it to dottedName.
+              var pagename = pages[i].substring(0, pages[i].length-2);
+              if (pagename == dottedName.substring(0,pagename.length)) {
+
+                  // We've found a page that matches `dottedName`;
+                  // construct its URL, using leftover `dottedName`
+                  // content to form an anchor.
+                  var pagetype = pages[i].charAt(pages[i].length-1);
+                  var url = pagename + ((pagetype=="m")?"-module.html":
+                                                        "-class.html");
+                  if (dottedName.length > pagename.length)
+                      url += "#" + dottedName.substring(pagename.length+1,
+                                                        dottedName.length);
+                  return url;
+              }
+          }
+      }