Members
color_val
stage
viewer
visible_components
xmlhttp
- Source:
Methods
expandPDB(tree)
function allows webserver to load for a second to retrieve data associated to a PDB (eg. maybe split into chains, cartoon view, stick view, etc.) TODO: NEED TO ADD DATA CHANGES AFTER EXPANSION
Parameters:
| Name | Type | Description |
|---|---|---|
tree |
smart-tree |
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(async) getXML(id, files, cnt)
Asynchronous load using XMLHttpRequest.
- Setup xmlhttp with functions and requests to be called upon send(). First get list of files[] containing all files to be viewed, and open all. When a file is "ready", format XML and then load data. TODO: No need to format for now but left here just in case. Recursive getXML() call to loop through all files. TODO: Recursion isn't great but it works here, so I'll leave it. Finally, send() requests to server.
Parameters:
| Name | Type | Description |
|---|---|---|
id |
string | |
files |
string | |
cnt |
int | index for surf object |
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loadData(file)
Function to load surf files.
After loading, we make arrays of vertices, normals, and faces.
We then create a custom object using these 3 arrays.
This code essentially takes care of all the viewer loading
and rendering that need to be done.
Parameters:
| Name | Type | Description |
|---|---|---|
file |
string |
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(async) loadHBond(File)
Async function to load hydrogen bond files.
After loading, we make an array of vertices and pair together the vertices that form each hydrogen bond. We then create a custom object composed of cylinders using the vertex pairs.
Parameters:
| Name | Type | Description |
|---|---|---|
File |
string | name in uploads folder. |
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loadPDB(id, pdb_file)
####################################################### Utils for PDB file loading #######################################################
Parameters:
| Name | Type | Description |
|---|---|---|
id |
string | name to set object in NGL |
pdb_file |
string | file name in uploads folder |
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makeTree(tree, id, files)
Creates tree from a list of files
Parameters:
| Name | Type | Description |
|---|---|---|
tree |
smart-tree | |
id |
string | |
files |
string |
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(async) set_up_tree(dir)
Sets up the file tree
Parameters:
| Name | Type | Description |
|---|---|---|
dir |
string | Directory where files are located |
treeSelectionEventHandler(tree, dir_list) → {None}
treeSelectionEventHandler() handles visibility of objects when the associated index of the file tree is checked or unchecked using an eventListener().
Parameters:
| Name | Type | Description |
|---|---|---|
tree |
smart-tree | |
dir_list |
Array.<string> |
Returns:
- Type
- None
viewData(face, file, normal, vertex)
Function to view surf objects after loading
Set colors and add objects to stage here. This function is called at the end of loadData()
Parameters:
| Name | Type | Description |
|---|---|---|
face |
Array.<int> | |
file |
string | |
normal |
Array.<int> | |
vertex |
Array.<int> |
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viewHBond(file, bonds, bondPairs)
Function to view hydrogen bonds after loading data
Set colors and add objects to stage here. This function is called at the end of loadHBond()
Parameters:
| Name | Type | Description |
|---|---|---|
file |
string | |
bonds |
Array.<array> | |
bondPairs |
Array.<array> |
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