Package schrodinger :: Package application :: Package matsci :: Package nano :: Module particle

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Module particle

Classes

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ParserWrapper
Manages the argparse module to parse user command line arguments.

CheckInput
Manage checking user input.

Nanoparticle
Manage the building of a nanoparticle.

Functions

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list of str

get_lattice_properties()
Get the properties which are required for defining a crystal structure

bool

check_if_lattice_properties_exist(struct, keys=None)
Check if the structure has all the required crystal lattice properties

str

format_alignment_ids(num_unique)
Return a formatted collection of shapes and alignment axis IDs.

tuple

group_subtuples_by_key_and_value(atuple)
Take a tuple of two-element subtuples and group them by both key and value and collect into subsubtuples.

dict

build_kwargs(kwargs_list, defaults, acceptable_keys=None, token_separator=TOKEN_SEPARATOR, key_value_separator=KEY_VALUE_SEPARATOR, all_choices=None)
Build the kwargs dictionary from an unformatted and unvalidated list of kwargs.

Variables

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__doc__ = ...

_version = '$Revision 0.0 $'

DEFAULT_SHAPE = 'cube'

ALL_SHAPES = shapes.SHAPES_NAMES_TO_OBJECTS_DICT.keys()

OUTFILE_SUFFIX = '-out'

FRAGMENT_NAME = 'FRAGMENT_NAME'

TERM_FRAG = 'hydrogen'

TERM_FRAGS = ['none', 'hydrogen', 'oxide', 'hydroxyl', 'fluoro...

TERM_DICT = OrderedDict([('none', ['', '']), ('hydrogen', ['',...

TERM_DIRECTION = 'forward'

TERM_BOND_LENGTH = 1.50

REPRESENTATION_KEY = 'i_m_representation'

REPRESENTATION = 3

FROM_REP_KEY = 'i_m_from_rep'

TO_REP_KEY = 'i_m_to_rep'

NANOPARTICLE_NATOMS_KEY = 'i_matsci_Nanoparticle_Natoms'

NANOPARTICLE_VOLUME_KEY = 'r_matsci_Volume/Ang.^3'

NANOPARTICLE_SURFACE_AREA_KEY = 'r_matsci_Surface_Area/Ang.^2'

NANOPARTICLE_CIRCUMRADIUS_KEY = 'r_matsci_Circumradius/Ang.'

NANOPARTICLE_DENSITY_KEY = 'r_matsci_Density/g/cm^3'

NANOPARTICLE_TEMPLATE = 'b_matsci_Nanoparticle_Template'

ORIGINAL_ATOM_KEY = 'b_matsci_np_gui_original_atom'

NUM_DECIMAL = 4

CM_TO_ANGSTROM = float(100000000)

TOKEN_SEPARATOR = ','

KEY_VALUE_SEPARATOR = '='

AXIS_KEY = 'axis'

VECTOR_KEY = 'vector'

BASIS_KEY = 'basis'

HKL_VALUE = 'hkl'

ABC_VALUE = 'abc'

XYZ_VALUE = 'xyz'

ALIGNMENT_KEYS = [AXIS_KEY, VECTOR_KEY, BASIS_KEY]

BASIS_VALUES = [HKL_VALUE, ABC_VALUE, XYZ_VALUE]

PRIMARY_ALIGNMENT_DEFAULT = OrderedDict([(AXIS_KEY, '1'), (VEC...

SECONDARY_ALIGNMENT_DEFAULT = OrderedDict([(AXIS_KEY, '1'), (V...

dict_to_str = lambda x:

PRIMARY_ALIGNMENT_DEFAULT_LIST = dict_to_str(PRIMARY_ALIGNMENT...

SECONDARY_ALIGNMENT_DEFAULT_LIST = dict_to_str(SECONDARY_ALIGN...

INCLUDE_AXES_DEFAULT = False
hash(x)

VERTICES_DEFAULT = []

ALLOW_FRAGMENTS = False
hash(x)

Function Details

[hide private]

get_lattice_properties()

Get the properties which are required for defining a crystal structure

Returns: list of str: Each item in the list is a structure property that is required to be present if a crystal structure is defined

check_if_lattice_properties_exist(struct, keys=None)

Check if the structure has all the required crystal lattice properties

Parameters:

struct (schrodinger.structure.Structure) - The structure to check
keys (list) - The list of crystal properties to check. If not given, the default set of crystal properties from get_lattice_properties will be checked

Returns: bool

If all the requested properties are present on the structure

format_alignment_ids(num_unique)

Return a formatted collection of shapes and alignment axis IDs.

Parameters:

num_unique (str) - the shape attr to format

Returns: str

the formatted string

group_subtuples_by_key_and_value(atuple)

Take a tuple of two-element subtuples and group them by both key and value and collect into subsubtuples. For example, take ((1, 2), (1, 3), (4, 5), (6, 7), (8, 7)) and return (((1), (2, 3)), ((4), (5)), ((6, 8), (7))).

Parameters:

atuple (tuple) - contains two-element tuples

Returns: tuple

contains two-element tuples each of which contains a keys tuple and a values tuple

build_kwargs(kwargs_list, defaults, acceptable_keys=None, token_separator=TOKEN_SEPARATOR, key_value_separator=KEY_VALUE_SEPARATOR, all_choices=None)

Build the kwargs dictionary from an unformatted and unvalidated list of kwargs.

Parameters:

kwargs_list (list) - list of strings that contain kwargs in one form or another
defaults (dict) - default kwargs to be updated
acceptable_keys (list) - list of acceptable keys
token_separator (str) - the separator used for tokens
key_value_separator (str) - the separator used in key-value pairs
all_choices (dict) - if the values of certain keys are limited then collect those options here in lists for validation purposes

Returns: dict

dictionary of kwargs, formatted, validated, and contains unspecified defaults

Variables Details

[hide private]

doc

Value:

"""
Classes and functions to create nanoparticles.

Copyright Schrodinger, LLC.  All rights reserved."""

TERM_FRAGS

Value:

['none',
 'hydrogen',
 'oxide',
 'hydroxyl',
 'fluoro',
 'chloro',
 'bromo',
 'carbonyl',
...

TERM_DICT

Value:

OrderedDict([('none', ['', '']), ('hydrogen', ['', '']), ('oxide', ['o
rganic', 'Hydroxide']), ('hydroxyl', ['organic', 'Hydroxyl']), ('fluor
o', ['diverse_fragments', 'fluoro']), ('chloro', ['diverse_fragments',
 'chloro']), ('bromo', ['diverse_fragments', 'bromo']), ('carbonyl', [
'organic', 'Carbonyl']), ('methyl', ['organic', 'Methyl']), ('carboxyl
', ['organic', 'Acid(C->O)']), ('amine', ['organic', 'Amine']), ('plan
ar amine', ['organic', 'Planar_Amine']), ('silyl', ['organic', 'Silyl'
]), ('thiol', ['organic', 'Thiol']), ('phosphyl', ['organic', 'Phosphy
...

PRIMARY_ALIGNMENT_DEFAULT

Value:

OrderedDict([(AXIS_KEY, '1'), (VECTOR_KEY, '1.0 0.0 0.0'), (BASIS_KEY,
 HKL_VALUE)])

SECONDARY_ALIGNMENT_DEFAULT

Value:

OrderedDict([(AXIS_KEY, '1'), (VECTOR_KEY, '0.0 1.0 0.0'), (BASIS_KEY,
 ABC_VALUE)])

PRIMARY_ALIGNMENT_DEFAULT_LIST

Value:

dict_to_str(PRIMARY_ALIGNMENT_DEFAULT)

SECONDARY_ALIGNMENT_DEFAULT_LIST

Value:

dict_to_str(SECONDARY_ALIGNMENT_DEFAULT)