PeleTasks

A peleSimulation has a “PeleTasks” block. It is an array comprised of all the tasks that the program has to carry out before a command (usually a simulation) is considered to be finished [1]. Each task is a block, so it should be enclosed in curly braces.

Contents:

Pele_parameters and algorithms

It can redefine both Pele_parameters and algorithms (e.g. ligandPerturbation, ANM, sideChainPrediction, Minimization…).

If an algorithm is defined at PeleTask level, it uses this one instead of the one at peleSimulation level.

Example

Side chain prediction is defined at peleSimulation level, so, unless overriden, this algorithm is going to be used thorughout all the simulation. However, the first PeleTask redefines it, so the latter one is going to be used for that specific task.

"commands": [
        {
            "commandType": "peleSimulation",
            ...
             "SideChainPrediction": {
                "algorithm": "zhexin"
                },
                "parameters": {
                    "randomize": false,
                    "numberOfIterations": 1
                }
            },
            ...
            "PeleTasks": [
                {
                    ...
                     "SideChainPrediction": {
                        "algorithm": "zhexin"
                        },
                        "parameters": {
                            "randomize": true,
                            "numberOfIterations": 3
                        }
                    },
                    ...
                },
                ...
            ]
]

Constraints

A PELE Task can include additional constraints to those already defined for the complete PELE simulation. Check the Constraints section.

metrics

It is an array that contains all the metrics to be measured in that task.

Check the metrics documentation for more information.

jumpif/jumpController block

Makes explorer jump if certain conditions are met.

Check the jumpController documentation for more information.

parametersChanges

Array of conditions that make some defined parameters to be changed.

Check the dynamic changes section for more information.

exitCondition

When the condition is met, it makes the task finish.

Check the exit conditions section for more information.

Footnotes