Source code for aiida_gromacs.calculations.pdb2gmx

"""
Calculations provided by aiida_gromacs.

This calculation configures the ability to use the 'gmx pdb2gmx' executable.
"""
from aiida.common import CalcInfo, CodeInfo
from aiida.engine import CalcJob
from aiida.orm import SinglefileData
from aiida.plugins import DataFactory

Pdb2gmxParameters = DataFactory("gromacs.pdb2gmx")




class Pdb2gmxCalculation(CalcJob):
    """
    AiiDA calculation plugin wrapping the 'gmx pdb2gmx' executable.

    AiiDA plugin wrapper for converting PDB files to GRO files.
    """



    @classmethod
    def define(cls, spec):
        """Define inputs and outputs of the calculation."""
        # yapf: disable
        super().define(spec)

        # set default values for AiiDA options
        # TODO: something changed about withmpi in aiida-2.4.0, needs investigation.
        spec.inputs['metadata']['options']['withmpi'].default = False
        spec.inputs['metadata']['options']['resources'].default = {
            'num_machines': 1,
            'num_mpiprocs_per_machine': 1,
        }
        
        # Required inputs.
        spec.inputs['metadata']['options']['parser_name'].default = 'gromacs.pdb2gmx'
        spec.input('metadata.options.output_filename', valid_type=str, default='pdb2gmx.out')
        spec.input('pdbfile', valid_type=SinglefileData, help='Input structure.')
        spec.input('parameters', valid_type=Pdb2gmxParameters, help='Command line parameters for gmx pdb2gmx')

        # Default outputs.
        spec.output('stdout', valid_type=SinglefileData, help='stdout')
        spec.output('grofile', valid_type=SinglefileData, help='Output forcefield compliant file.')
        spec.output('topfile', valid_type=SinglefileData, help='Output forcefield compliant file.')
        spec.output('itpfile', valid_type=SinglefileData, help='Output forcefield compliant file.')
        
        # Optional outputs.
        spec.output('n_file', required=False, valid_type=SinglefileData, help='Output index file')
        spec.output('q_file', required=False, valid_type=SinglefileData, help='Output Structure file')

        spec.exit_code(300, 'ERROR_MISSING_OUTPUT_FILES', message='Calculation did not produce all expected output files.')




    def prepare_for_submission(self, folder):
        """
        Create input files.

        :param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files
            needed by the calculation.
        :return: `aiida.common.datastructures.CalcInfo` instance
        """
        codeinfo = CodeInfo()

        # Setup data structures for files.
        output_options = ["o", "p", "i", "n", "q"] 
        output_files = []

        # Add output files to retrieve list.
        output_files.append(self.metadata.options.output_filename)
        for item in output_options:
            if item in self.inputs.parameters:
                output_files.append(self.inputs.parameters[item])


        codeinfo.cmdline_params = self.inputs.parameters.cmdline_params(
            pdbfile=self.inputs.pdbfile.filename
        )
        codeinfo.code_uuid = self.inputs.code.uuid
        codeinfo.stdout_name = self.metadata.options.output_filename
        codeinfo.withmpi = self.inputs.metadata.options.withmpi

        # Prepare a `CalcInfo` to be returned to the engine
        calcinfo = CalcInfo()
        calcinfo.codes_info = [codeinfo]
        calcinfo.local_copy_list = [
            (
                self.inputs.pdbfile.uuid,
                self.inputs.pdbfile.filename,
                self.inputs.pdbfile.filename,
            ),
        ]
        calcinfo.retrieve_list = output_files

        return calcinfo