# -*- coding: utf-8 -*- """Non-graphical part of the Custom step in a SEAMM flowchart""" import logging import os import custom_step import seamm import seamm_util.printing as printing from seamm_util.printing import FormattedText as __ logger = logging.getLogger(__name__) job = printing.getPrinter() printer = printing.getPrinter('Custom') class cd: """Context manager for changing the current working directory""" def __init__(self, newPath): self.newPath = os.path.expanduser(newPath) def __enter__(self): self.savedPath = os.getcwd() os.chdir(self.newPath) def __exit__(self, etype, value, traceback): os.chdir(self.savedPath) class Custom(seamm.Node): def __init__(self,
# -*- coding: utf-8 -*- """Run a vibrational frequency calculation in MOPAC""" import logging import seamm import seamm_util.printing as printing from seamm_util.printing import FormattedText as __ import mopac_step logger = logging.getLogger(__name__) job = printing.getPrinter() printer = printing.getPrinter('mopac') class IR(mopac_step.Energy): def __init__(self, flowchart=None, title='IR Spectrum', extension=None): """Initialize the node""" logger.debug('Creating IR {}'.format(self)) super().__init__(flowchart=flowchart, title=title, extension=extension) self.parameters = mopac_step.IRParameters() self.description = 'Infrared (vibrational) spectroscopy calculation' def description_text(self, P): """Prepare information about what this node will do """ text = ('Harmonic vibrational calculation using {hamiltonian}, ' 'with the SCF converged to ')
the job, and should be used very sparingly, typically to echo what this step will do in the initial summary of the job. 'printer' sends output to the file 'step.out' in this steps working directory, and is used for all normal output from this step. """ import logging import seamm from seamm_util import ureg, Q_ # noqa: F401 import seamm_util.printing as printing from seamm_util.printing import FormattedText as __ import cassandra_step logger = logging.getLogger(__name__) job = printing.getPrinter() printer = printing.getPrinter('lammps') class Cassandra(seamm.Node): def __init__(self, flowchart=None, title='Cassandra', extension=None): """A Cassandra step in a MolSSI flowchart. You may wish to change the title above, which is the string displayed in the box representing the step in the flowchart. Keyword arguments: """ logger.debug('Creating Cassandra {}'.format(self))
import system_step import seamm from seamm_util import ureg, Q_ # noqa: F401 import seamm_util.printing as printing from seamm_util.printing import FormattedText as __ # In addition to the normal logger, two logger-like printing facilities are # defined: 'job' and 'printer'. 'job' send output to the main job.out file for # the job, and should be used very sparingly, typically to echo what this step # will do in the initial summary of the job. # # 'printer' sends output to the file 'step.out' in this steps working # directory, and is used for all normal output from this step. logger = logging.getLogger(__name__) job = printing.getPrinter() printer = printing.getPrinter('System') class System(seamm.Node): """ The non-graphical part of a System step in a flowchart. Attributes ---------- parser : configargparse.ArgParser The parser object. options : tuple It contains a two item tuple containing the populated namespace and the list of remaining argument strings.
import logging from pathlib import PurePath, Path import textwrap from .formats.registries import get_format_metadata import read_structure_step from .read import read import seamm from seamm import data # noqa: F401 from seamm_util import ureg, Q_ # noqa: F401 import seamm_util.printing as printing from seamm_util.printing import FormattedText as __ from .utils import guess_extension logger = logging.getLogger(__name__) job = printing.getPrinter() printer = printing.getPrinter("Read Structure") class ReadStructure(seamm.Node): def __init__(self, flowchart=None, title="Read Structure", extension=None): """A step for Read Structure in a SEAMM flowchart. You may wish to change the title above, which is the string displayed in the box representing the step in the flowchart. Parameters: flowchart: The flowchart that contains this step. title: The name displayed in the flowchart. extension: ??
import logging import os.path from pathlib import PurePath import numpy as np import pandas from tabulate import tabulate import seamm import seamm_util.printing as printing from seamm_util import ureg, Q_, units_class # noqa: F401 import table_step logger = logging.getLogger(__name__) job = printing.getPrinter() printer = printing.getPrinter("table") class Table(seamm.Node): def __init__(self, flowchart=None, extension=None): """Setup the non-graphical part of the Table step in SEAMM. Keyword arguments: """ logger.debug("Creating Table {}".format(self)) # Initialize our parent class super().__init__(flowchart=flowchart, title="Table", extension=extension,
""" import logging from pathlib import PurePath import read_structure_step from .write import write import seamm from seamm import data # noqa: F401 from seamm_util import ureg, Q_ # noqa: F401 import seamm_util.printing as printing from seamm_util.printing import FormattedText as __ from .utils import guess_extension logger = logging.getLogger(__name__) job = printing.getPrinter() printer = printing.getPrinter("Write Structure") class WriteStructure(seamm.Node): def __init__(self, flowchart=None, title="Write Structure", extension=None): """A step for Write Structure in a SEAMM flowchart. You may wish to change the title above, which is the string displayed in the box representing the step in the flowchart. Parameters: flowchart: The flowchart that contains this step.
import configargparse import mendeleev import seamm from seamm import data import seamm_util from seamm_util import ureg, Q_, units_class # noqa: F401 from seamm_util import pdbfile import seamm_util.printing as printing from seamm_util.printing import FormattedText as __ from seamm_util.water_models import Water import solvate_step logger = logging.getLogger(__name__) job = printing.getPrinter() printer = printing.getPrinter('solvate') class Solvate(seamm.Node): def __init__(self, flowchart=None, extension=None): """Setup the main Solvate step Keyword arguments: """ logger.debug('Handling arguments in Solvate {}'.format(self)) # Argument/config parsing self.parser = configargparse.ArgParser(auto_env_var_prefix='', default_config_files=[
import set_cell_step import seamm from seamm_util import ureg, Q_ # noqa: F401 import seamm_util.printing as printing from seamm_util.printing import FormattedText as __ # In addition to the normal logger, two logger-like printing facilities are # defined: 'job' and 'printer'. 'job' send output to the main job.out file for # the job, and should be used very sparingly, typically to echo what this step # will do in the initial summary of the job. # # 'printer' sends output to the file 'step.out' in this steps working # directory, and is used for all normal output from this step. logger = logging.getLogger(__name__) job = printing.getPrinter() printer = printing.getPrinter('Set Cell') class SetCell(seamm.Node): """ The non-graphical part of a Set Cell step in a flowchart. Attributes ---------- parser : configargparse.ArgParser The parser object. options : tuple It contains a two item tuple containing the populated namespace and the list of remaining argument strings.
import seamm_antechamber import seamm from seamm_util import ureg, Q_ # noqa: F401 import seamm_util.printing as printing from seamm_util.printing import FormattedText as __ # In addition to the normal logger, two logger-like printing facilities are # defined: 'job' and 'printer'. 'job' send output to the main job.out file for # the job, and should be used very sparingly, typically to echo what this step # will do in the initial summary of the job. # # 'printer' sends output to the file 'step.out' in this steps working # directory, and is used for all normal output from this step. logger = logging.getLogger(__name__) job = printing.getPrinter() printer = printing.getPrinter('Antechamber') ANTECHAMBER = "/Users/meliseo/Scratch/antechamber/amber20_src/bin/antechamber" class Antechamber: """ The non-graphical part of a Antechamber step in a flowchart. Attributes ---------- parser : configargparse.ArgParser The parser object. options : tuple
from seamm_util.printing import FormattedText as __ import rdkit import rdkit.Chem import rdkit.Chem.AllChem import re # In addition to the normal logger, two logger-like printing facilities are # defined: 'job' and 'printer'. 'job' send output to the main job.out file for # the job, and should be used very sparingly, typically to echo what this step # will do in the initial summary of the job. # # 'printer' sends output to the file 'step.out' in this steps working # directory, and is used for all normal output from this step. logger = logging.getLogger(__name__) job = printing.getPrinter() printer = printing.getPrinter('seamm_default_atomtyping') class SeammDefaultAtomtyping: """ The non-graphical part of a seamm_default_atomtyping step in a flowchart. Attributes ---------- parser : configargparse.ArgParser The parser object. options : tuple It contains a two item tuple containing the populated namespace and the list of remaining argument strings.