Model Server

Provides access to molecular 1D, 2D, and 3D (sub-)structure models of molecules. Substructures are described by the mol-script (MolQL) language. It has the ability to include additional data to mmCIF “on the fly”, e.g. integrate primary PDB archival data from Chemical Component Dictionary (CCD), Protonation Variants Companion Dictionary (PVCD) and Biologically Interesting moleculeReference Dictionary (BIRD).

Example

node lib/commonjs/servers/model/server --sourceMap pdb-bcif '/opt/data/bcif/${id}.bcif'

Usage

Argument	Description
--version, -v	Show program's version number and exit.
--cfg	JSON config file path. If a property is not specified, cmd line param/OS variable/default value are used.
--printCfg	Print current config for validation and exit.
--cfgTemplate	Prints default JSON config template to be modified and exit.
--apiPrefix	Specify the prefix of the API, i.e. <host>/<apiPrefix>/<API queries>
--defaultPort	Specify the port the server is running on
--cacheMaxSizeInBytes	Read structures are cached, this specifies the cache size, 0 for off.
--cacheEntryTimeoutMs	Specify in ms how long to keep entries in cache.
--requestTimeoutMs	The maximum number of ms the server spends on a request.
--queryTimeoutMs	The maximum time the server dedicates to executing a query in ms. Does not include the time it takes to read and export the data.
--shutdownTimeoutMinutes	Server will shut down after this amount of minutes, 0 for off.
--shutdownTimeoutVarianceMinutes	Modifies the shutdown timer by +/- timeoutVarianceMinutes (to avoid multiple instances shutting at the same time)
--maxQueryManyQueries	Maximum number of queries allowed by the query-many at a time
--defaultSource	modifies which 'sourceMap' source to use by default
--sourceMap	Map ids for a source to a file path. Example: pdb-bcif '../../data/bcif/${id}.bcif' - JS expressions can be used inside ${}, e.g. ${id.substr(1, 2)}/${id}.mdb Can be specified multiple times. The SOURCE variable (e.g. pdb-bcif) is arbitrary and depends on how you plan to use the server. Supported formats: cif, bcif, cif.gz, bcif.gz
--sourceMapUrl	Same as --sourceMap but for URL. --sourceMapUrl src url format Example: pdb-cif "https://www.ebi.ac.uk/pdbe/entry-files/download/${id}_updated.cif" cif Supported formats: cif, bcif, cif.gz, bcif.gz

node lib/commonjs/servers/model/server [-h] [-v]
        [--cfg CFG]
        [--printCfg]
        [--cfgTemplate]
        [--apiPrefix PREFIX]
        [--defaultPort PORT]
        [--cacheMaxSizeInBytes CACHE_SIZE]
        [--cacheEntryTimeoutMs CACHE_TIMEOUT]
        [--requestTimeoutMs REQUEST_TIMEOUT]
        [--queryTimeoutMs QUERY_TIMEOUT]
        [--shutdownTimeoutMinutes TIME]
        [--shutdownTimeoutVarianceMinutes VARIANCE]
        [--maxQueryManyQueries QUERY_MANY_LIMIT]
        [--defaultSource DEFAULT_SOURCE]
        [--sourceMap SOURCE PATH]
        [--sourceMapUrl SOURCE PATH SOURCE_MAP_FORMAT]

Production Use

In production, it is required 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 Example

The preprocessor application allows addiing custom data to CIF files and/or convert CIF to BinaryCIF.

node lib/commonjs/servers/model/preprocess

Preprocessor Usage

Argument	Description
--input, -i	Input filename
--outCIF, -oc	Output CIF filename
--outBCIF, -ob	Output BinaryCIF filename
--cfg, -c	Config file path
--folderIn, -fin	Convert folder
--folderOutCIF, -foc	Convert folder text output
--folderOutBCIF, -fob	Convert folder binary output
--folderNumProcesses, -fp	Convert folder number processes

Example cfg.json:

{ 
    "numProcesses": 1, 
    "customProperties": { 
        "sources": [ "wwpdb" ], 
        "params": { 
            "wwPDB": { 
                "chemCompBondTablePath": "./build/data/ccb.bcif"
            }
        }
    }
}

Local Mode

The server can be run in local/file based mode using

node lib/commonjs/servers/model/query

Custom Properties

This feature is still in development.

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.

From NPM

npm install --production molstar
cd ./model-server 

(or node node_modules\.bin\model-server in Windows).

The NPM package contains all the tools mentioned in the previous sections as "binaries":

• model-server
• model-server-query
• model-server-preprocess