build

The main purpose of Pestifer is to prepare simulation-ready systems. The build subcommand is used to run a system preparation from a configuration file. The configuration file describes the tasks that should be performed to prepare the system, and the order in which they should be performed.

Note

run is accepted as a synonym for build for backwards compatibility.

$ pestifer build config.yaml

Here config.yaml is the name of the configuration file that describes the system preparation. Minimally, a pestifer config file for a build must have a tasks directive that specifies the ordered list of tasks the build should perform.

The first task must be one of a fetch or a continuation or a merge. fetch is used when you begin a run from an externally provided structure file (a PDB or mmCIF/PDBx-format file), while continuation is used when you begin a run from an already prepared system state, represented by PDB, PSF, and XSC files. merge is used when you want to combine two or more system states into a single state, for example to combine a protein structure with a ligand structure. The final task must be a terminate, which is responsible for writing out the final system state and any associated files, and optionally packaging the system for production elsewhere. In between, you can have any number of tasks that perform various operations on the system state, such as building the PSF, running minimization or MD simulations, or performing various manipulations of the system (e.g. ligation, cleavage, solvation, etc.).

Generally, each task is responsible for one or more changes of the system state, and Pestifer ensures that every task knows the current state of the system when it begins. Here is an example of a task list that begins from the X-ray crystal structure of the bovine pancreatic trypsin inhibitor structure (PDB ID 6pti), builds the PSF and PDB, then subjects that state to minimization and a short NVT MD simulation, and finally packaging for production elsewhere.

tasks:
  - fetch:
     - sourceID: 6pti
  - psfgen:
  - md:
      ensemble: minimize
  - md:
      ensemble: NVT
  - terminate:
      basename: my_system
      package:
        basename: prod_system
        md:
          ensemble: NPT

pestifer build begins by parsing the configuration file, and then it sets up a Controller object that manages the tasks. The controller executes each task in the order specified in the configuration file, and it handles any dependencies between tasks. If a task fails, the controller will stop the build and report the error.

        graph TD;
   A[Config] --> C{Next task?};
   subgraph group Controller [Controller];
      C --> Yes --> D[Run task];
      D -->|Success| C;
      D -->|Failure| F[Report error];
   end
   C --> No --> E[End];
   F --> E;
    

Execution flow for the pestifer controller

Detailed explanation of some selected common tasks you can use is below.

• fetch
• continuation
• merge
• psfgen
• validate
• pdb2pqr
• md
• manipulate
• ligate
• cleave
• solvate
• make_membrane_system
• ring_check
• terminate

Please consult the Configuration Reference pages for tasks, for a full list of available pestifer build tasks.

We provide several Examples that show a variety of task lists.