Model Server
Model Server is a tool for preprocessing and querying macromolecular structure data.
Installing and Running
Getting the code (use node 8+):
git clone https://github.com/molstar/molstar-proto
npm installCustomize configuration at src/server/model/config.ts to point to your data and which custom properties to include (see the Custom Properties section). Alternatively, the config can be edited in the compiled version in build/node_modules/servers/model/config.js.
Afterwards, build the project:
npm run build(or run watch mode for automatic rebuilds: npm run watch)
Running the server locally for testing:
npm run model-serveror
node build/node_modules/servers/model/serverIn production it is a good idea to use a service that will keep the server running, such as forever.js.
Memory issues
Sometimes nodejs might run into problems with memory. This is usually resolved by adding the --max-old-space-size=8192 parameter.
Preprocessor
The preprocessor application allows to add custom data to CIF files and/or convert CIF to BinaryCIF. See the Custom Properties section for providing custom properties.
Usage
The app works in two modes: single files and folders.
Single files:
node build\node_modules\servers\model\preprocess -i input.cif [-oc output.cif] [-ob output.bcif] [--cfg config.json]Folder:
node build\node_modules\servers\model\preprocess -fin input_folder [-foc output_cif_folder] [-fob output_bcif_folder] [--cfg config.json]Config
The config speficies the maximum number of processes to use (in case of folder processing) and defines sources and parameters for custom properties.
Example:
{
"numProcesses": 4,
"customProperties": {
"sources": [
"./properties/pdbe"
],
"params": {
"PDBe": {
"UseFileSource": false,
"API": {
"residuewise_outlier_summary": "https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry",
"preferred_assembly": "https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary",
"struct_ref_domain": "https://www.ebi.ac.uk/pdbe/api/mappings/sequence_domains"
}
}
}
}
}Custom Properties
It is possible to provide property descriptors that transform data to internal representation and define how it should be exported into one or mode CIF categories. Examples of this are located in the mol-model-props module and are linked to the server in the config and servers/model/properties.
Local Mode
The server can be run in local/file based mode:
node build/node_modules/servers/model/server jobs.jsonwhere jobs.json is an array of
type LocalInput = {
input: string,
output: string,
query: QueryName,
modelNums?: number[],
params?: any,
binary?: boolean
}[]For example
[
{
"input": "c:/test/quick/1tqn.cif",
"output": "c:/test/quick/localapi/1tqn_full.cif",
"query": "full"
},
{
"input": "c:/test/quick/1tqn.cif",
"output": "c:/test/quick/localapi/1tqn_full.bcif",
"query": "full",
"params": {}
},
{
"input": "c:/test/quick/1cbs_updated.cif",
"output": "c:/test/quick/localapi/1cbs_ligint.cif",
"query": "residueInteraction",
"params": {
"atom_site": { "label_comp_id": "REA" }
}
}
]