molssi / mmic Goto Github PK

Traceback (most recent call last):        
File "/home/******/Project/MMIC/lab/01_Issue/to_file_error_01.py", line 17, in <module> error_repeat_compute.compute(inp)
File "/home/******/miniconda3/envs/mmic/lib/python3.9/site-packages/mmic/components/base/base_component.py", line 74, in compute
cls.output(**exec_output.dict())
File "pydantic/main.py", line 406, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for error_output 
molecule
Model data inconsistent with stored hash code! (type=assertion_error) 

import mmelemental
from mmelemental.models import Molecule
import tempfile
import mm_data
import gromacs

mol = mmelemental.models.Molecule.from_file(mm_data.mols["water-mol.json"])
gro_file = tempfile.NamedTemporaryFile(suffix=".gro").name
box_gro_file = tempfile.NamedTemporaryFile(suffix=".gro").name
mol.to_file(gro_file, translator="mmic_parmed") 

gromacs.editconf(f=gro_file, d=2, o=box_gro_file)

mol = Molecule.from_file(box_gro_file, translator="mmic_parmed")

import mmelemental 
import tempfile
import mm_data
import to_file_error_02
from to_file_error_02 import error_repeat_compute

mol = mmelemental.models.Molecule.from_file(mm_data.mols["water-mol.json"])
gro_file = tempfile.NamedTemporaryFile(suffix=".gro").name
mol.to_file(gro_file, translator="mmic_parmed")

inp = to_file_error_02.error_input(
	molecule = gro_file,
	schema_name = "error",
	schema_version = 1.0,
	)

error_repeat_compute.compute(inp)

import mmelemental
from mmelemental.models import Molecule
from cmselemental.models.procedures import InputProc, OutputProc
import tempfile
import mm_data
from pydantic import Field
from typing import Dict, Optional, List, Tuple
import gromacs
from mmic.components.blueprints import GenericComponent
from cmselemental.util.decorators import classproperty

__all__ = ["error_repeat_compute"]


class error_input(InputProc):

    molecule: str = Field(None, description="molecule used for repeating the error")


class error_output(OutputProc):

    molecule: Molecule = Field(
        None, description="molecule used for repeating the error"
    )


class error_repeat_compute(GenericComponent):
    @classproperty
    def input(cls):
        return error_input

    @classproperty
    def output(cls):
        return error_output

    @classproperty
    def version(cls) -> str:
        """Finds program, extracts version, returns normalized version string.
		Returns
		-------
		str
			Return a valid, safe python version string.
		"""
        return ""

    def execute(
        self,
        inputs: error_input,
        extra_outfiles: Optional[List[str]] = None,
        extra_commands: Optional[List[str]] = None,
        scratch_name: Optional[str] = None,
        timeout: Optional[int] = None,
    ) -> Tuple[bool, error_output]:

        if isinstance(inputs, dict):
            inputs = self.input(**inputs)

        mol_file = inputs.molecule
        #boxed_gro_file = tempfile.NamedTemporaryFile(suffix=".gro").name
        #gromacs.editconf(f=mol_file, d=2, o=boxed_gro_file)
        #mol = Molecule.from_file(boxed_gro_file, translator="mmic_parmed")
        mol = Molecule.from_file(inputs.molecule, translator="mmic_parmed")

        return (True, error_output(molecule=mol, success=True, schema_name = "error", schema_version =1.0))