packmol_step package

Submodules

packmol_step.installer module

Installer for the PACKMOL plug-in.

This handles any further installation needed after installing the Python package packmol-step.

class packmol_step.installer.Installer(logger=<Logger packmol_step.installer (WARNING)>)

Bases: InstallerBase

Handle further installation needed after installing packmol-step.

The Python package packmol-step should already be installed, using pip, conda, or similar. This plug-in-specific installer then checks for the PACKMOL executable, installing it if needed, and registers its location in seamm.ini.

There are a number of ways to determine which are the correct PACKMOL executables to use. The aim of this installer is to help the user locate the executables. There are a number of possibilities

1. The correct executables are already available.

   1. If they are already registered in seamm.ini there is nothing else to do.

   2. They may be in the current path, in which case they need to be added to seamm.ini.

   3. If a module system is in use, a module may need to be loaded to give access to PACKMOL.

   4. They cannot be found automatically, so the user needs to locate the executables for the installer.

2. PACKMOL is not installed on the machine. In this case they can be installed in a Conda environment. There is one choice

   1. They can be installed in a separate environment, seamm-packmol by default.

check()

Check the status of the Packmol installation.

exe_version(config)

Get the version of the PACKMOL executable.

Parameters:

config (dict) – Dictionary of options for running Packmol

Returns:

The version reported by the executable, or ‘unknown’.

Return type:

“Packmol”, str

install()

Install Packmol in a conda environment.

show()

Show the status of the Packmol installation.

uninstall()

Uninstall the Packmol installation.

update()

Updates the Packmol installation.

packmol_step.packmol module

A step for building fluids with Packmol in a SEAMM flowchart

class packmol_step.packmol.Packmol(flowchart=None, extension=None)

Bases: Node

create_parser()

Setup the command-line / config file parser

description_text(P=None)

Return a short description of this step.

Return a nicely formatted string describing what this step will do.

Keyword Arguments:

P – a dictionary of parameter values, which may be variables or final values. If None, then the parameters values will be used as is.

static get_input(P, system_db, tmp_db, context, ff=None)

Create the input for Packmol.

property git_revision

The git version of this module.

run()

Run a Packmol building step

property version

The semantic version of this module.

packmol_step.packmol.bounding_box(points)

packmol_step.packmol.bounding_sphere(points)

A fast, approximate method for finding the sphere containing a set of points.

See https://www.researchgate.net/publication/242453691_An_Efficient_Bounding_Sphere

This method is approximate. While the sphere is guaranteed to contain all the points it is a few percent larger than necessary on average.

packmol_step.packmol_parameters module

Control parameters for Packmol, currently for packing fluids

class packmol_step.packmol_parameters.PackmolParameters(defaults={}, data=None)

Bases: Parameters

The control parameters for Packmol packing fluids

amounts = ('rounding this number of atoms', 'rounding this number of molecules', 'using the density', 'using the Ideal Gas Law')

amounts_for_density = ('rounding this number of atoms', 'rounding this number of molecules')

amounts_for_layer = ('using the density', 'using the Ideal Gas Law')

parameters = {'a': {'default': 20, 'default_units': 'Å', 'description': 'a:', 'enumeration': (), 'format_string': '.1f', 'help_text': 'The length of the first side of the box.', 'kind': 'float'}, 'a_ratio': {'default': 1, 'default_units': '', 'description': 'a ratio:', 'enumeration': (), 'format_string': '.1f', 'help_text': 'The ratio for the first side of the box.', 'kind': 'float'}, 'approximate number of atoms': {'default': 2000, 'default_units': '', 'description': 'Approximate number of atoms:', 'enumeration': (), 'format_string': 'd', 'help_text': 'The approximate number of atoms packed into the cell. This will be rounded to give whole molecules', 'kind': 'integer'}, 'approximate number of molecules': {'default': 100, 'default_units': '', 'description': 'Approximate number of molecules:', 'enumeration': (), 'format_string': 'd', 'help_text': 'The approximate number of molecules to pack in the cell.', 'kind': 'integer'}, 'assign forcefield': {'default': 'If not assigned', 'default_units': '', 'description': 'Assign forcefield:', 'enumeration': ('If not assigned', 'Always', 'No'), 'format_string': 's', 'help_text': 'Whether to assign the forcefield to the molecules.', 'kind': 'enum'}, 'b': {'default': 20, 'default_units': 'Å', 'description': 'b:', 'enumeration': (), 'format_string': '.1f', 'help_text': 'The length of the second side of the box.', 'kind': 'float'}, 'b_ratio': {'default': 1, 'default_units': '', 'description': 'b ratio:', 'enumeration': (), 'format_string': '.1f', 'help_text': 'The ratio for the second side of the box.', 'kind': 'float'}, 'c': {'default': 20, 'default_units': 'Å', 'description': 'c:', 'enumeration': (), 'format_string': '.1f', 'help_text': 'The length of the third side of the box.', 'kind': 'float'}, 'c_ratio': {'default': 1, 'default_units': '', 'description': 'c ratio:', 'enumeration': (), 'format_string': '.1f', 'help_text': 'The ratio for the third side of the box.', 'kind': 'float'}, 'density': {'default': 0.7, 'default_units': 'g/ml', 'description': 'Density:', 'enumeration': (), 'format_string': '.1f', 'help_text': 'The target density of the cell.', 'kind': 'float'}, 'diameter': {'default': 20.0, 'default_units': 'Å', 'description': 'The diameter:', 'enumeration': (), 'format_string': '.1f', 'help_text': 'The diameter of the sphere or cylinder.', 'kind': 'float'}, 'dimensions': {'default': 'calculated from the density', 'default_units': '', 'description': 'The dimensions will be', 'enumeration': ('given explicitly', 'calculated from the volume', 'calculated from the solute dimensions', 'calculated from the density', 'calculated using the Ideal Gas Law'), 'format_string': 's', 'help_text': 'How to get the dimensions of the region', 'kind': 'enumeration'}, 'edge length': {'default': 20, 'default_units': 'Å', 'description': 'Length of the cube edge:', 'enumeration': (), 'format_string': '.1f', 'help_text': 'The length of the cube edge.', 'kind': 'float'}, 'fluid amount': {'default': 'rounding this number of atoms', 'default_units': '', 'description': 'Get number of fluid molecules by', 'enumeration': ('rounding this number of atoms', 'rounding this number of molecules'), 'format_string': 's', 'help_text': 'How to get the number of fluid molecules', 'kind': 'enumeration'}, 'gap': {'default': 2.0, 'default_units': 'Å', 'description': 'Gap around cell:', 'enumeration': (), 'format_string': '.1f', 'help_text': 'Since Packmol does not support periodic systems we will build a box with this gap around the atoms, then make it periodic. The gap ensures that molecules at the boundary do not hit images', 'kind': 'float'}, 'molecules': {'default': [], 'default_units': None, 'description': 'The molecules', 'enumeration': (), 'format_string': '', 'help_text': 'An internal place to put the molecule definitions.', 'kind': 'list'}, 'periodic': {'default': 'No', 'default_units': '', 'description': 'Create periodic system:', 'enumeration': ('Yes', 'No'), 'format_string': 's', 'help_text': 'Whether to create a periodic system or not.', 'kind': 'boolean'}, 'pressure': {'default': 1.0, 'default_units': 'atm', 'description': 'P:', 'enumeration': (), 'format_string': '.2f', 'help_text': 'The pressure using an ideal gas model (PV=nRT).', 'kind': 'float'}, 'shape': {'default': 'spherical', 'default_units': '', 'description': 'Shape of the region:', 'enumeration': ('cubic', 'rectangular', 'spherical'), 'format_string': 's', 'help_text': 'The shape of the desired region.', 'kind': 'enumeration'}, 'solvent thickness': {'default': 10.0, 'default_units': 'Å', 'description': 'Solvent thickness:', 'enumeration': (), 'format_string': '.1f', 'help_text': 'The thickness of the layer of solvent around the solute', 'kind': 'float'}, 'temperature': {'default': 298.15, 'default_units': 'K', 'description': 'T:', 'enumeration': (), 'format_string': '.2f', 'help_text': 'The temperature using an ideal gas model (PV=nRT).', 'kind': 'float'}, 'volume': {'default': 8.0, 'default_units': 'nm^3', 'description': 'The volume of the cell:', 'enumeration': (), 'format_string': '.1f', 'help_text': 'The volume of the target cell.', 'kind': 'float'}}

periodic_shapes = ('cubic', 'rectangular')

shapes = ('cubic', 'rectangular', 'spherical')

packmol_step.packmol_step module

Helper class needed for the stevedore integration. Needs to provide a description() method that returns a dict containing a description of this node, and a factory() method for creating the graphical and non-graphical nodes.

class packmol_step.packmol_step.PackmolStep(flowchart=None, gui=None)

Bases: object

create_node(flowchart=None, **kwargs)

Return the new node object

create_tk_node(canvas=None, **kwargs)

Return the graphical Tk node object

description()

Return a description of what this extension does

my_description = {'description': 'An interface for Packmol', 'group': 'Building', 'name': 'Packmol'}

packmol_step.tk_packmol module

The graphical part of a Packmol step

class packmol_step.tk_packmol.TkPackmol(tk_flowchart=None, node=None, canvas=None, x=None, y=None, w=200, h=50)

Bases: TkNode

Graphical interface for using Packmol for fluid boxes

add_molecule()

Add a new row to the molecule table.

create_dialog()

Create the dialog!

handle_dialog(result)

Do the right thing when the dialog is closed.

remove_molecule(row)

Remove a molecule entry from the table.

Parameters:

row (int) – The row in the table to remove. Note the first molecule is at row 1.

reset_dialog(widget=None)

Layout the widgets in the dialog contingent on the parameter values.

reset_molecules()

Layout the table of molecules to use.

right_click(event)

Probably need to add our dialog…

Module contents

packmol_step A step for building fluid boxes using Packmol