schrodinger.application.matsci.nano.particle module¶

Classes and functions to create nanoparticles.

schrodinger.application.matsci.nano.particle.dict_to_str(x)¶

schrodinger.application.matsci.nano.particle.get_lattice_properties()¶

Get the properties which are required for defining a crystal structure

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

schrodinger.application.matsci.nano.particle.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

Return type

bool

Returns

If all the requested properties are present on the structure

schrodinger.application.matsci.nano.particle.format_alignment_ids(num_unique)¶

Return a formatted collection of shapes and alignment axis IDs.

Parameters: num_unique (str) – the shape attr to format
Return type: str
Returns: the formatted string

class schrodinger.application.matsci.nano.particle.ParserWrapper(scriptname, description)¶

Bases: object

Manages the argparse module to parse user command line arguments.

__init__(scriptname, description)¶

Create a ParserWrapper instance and process it.

Parameters

scriptname (str) – name of this script
description (str) – description of this script

loadIt()¶: Load ParserWrapper with options.

parseArgs(args)¶

Parse the command line arguments.

Parameters: args (tuple) – command line arguments

class schrodinger.application.matsci.nano.particle.CheckInput¶

Bases: object

Manage checking user input.

checkShapeParams(shape, params, logger=None)¶

Check the specified shape and shape parameters.

Parameters

shape (str) – the shape of nanoparticle
params (list) – contains floats specifying the shapes geometry
logger (logging.Logger) – output logger

checkAlignment(shape, primary_alignment, secondary_alignment, logger=None)¶

Check the specified alignment.

Parameters

shape (str) – the shape of nanoparticle
primary_alignment (dict) – dictionary defining the primary alignment
secondary_alignment (dict) – dictionary defining the secondary alignment
logger (logging.Logger) – output logger

Return type

dict, dict

Returns

the final primary and secondary alignment dictionaries

schrodinger.application.matsci.nano.particle.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
Return type: tuple
Returns: contains two-element tuples each of which contains a keys tuple and a values tuple

class schrodinger.application.matsci.nano.particle.Nanoparticle(supercell, shape='cube', origin=None, params=None, overwrite_vertices=[], primary_alignment_dict={'axis': '1', 'basis': 'hkl', 'vector': '1.0 0.0 0.0'}, secondary_alignment_dict={'axis': '1', 'basis': 'abc', 'vector': '0.0 1.0 0.0'}, include_axes=False, term_frag='hydrogen', term_bond_length=1.5, allow_fragments=False, com_inclusion=False, logger=None, no_term_faces=None)¶

Bases: object

Manage the building of a nanoparticle.

MSGWIDTH = 100¶

__init__(supercell, shape='cube', origin=None, params=None, overwrite_vertices=[], primary_alignment_dict={'axis': '1', 'basis': 'hkl', 'vector': '1.0 0.0 0.0'}, secondary_alignment_dict={'axis': '1', 'basis': 'abc', 'vector': '0.0 1.0 0.0'}, include_axes=False, term_frag='hydrogen', term_bond_length=1.5, allow_fragments=False, com_inclusion=False, logger=None, no_term_faces=None)¶

Create an instance.

Parameters

supercell (schrodinger.structure.Structure) – the crystalline supercell from which to cut the nanaparticle
shape (str) – the shape of the nanoparticle
origin (list) – list of three floats specifying the origin of the shape in the crystal
params (list) – list of parameters defining the specified shape
overwrite_vertices (list) – vertices to overwrite those of the created shape, just of list of floats
primary_alignment_dict (dict) – a dictionary defining the primary alignment
secondary_alignment_dict (dict) – a dictionary defining the secondary alignment
include_axes (bool) – include unit vectors for the primary and secondary alignment axes in the template
term_frag (str) – the fragment by which to terminate the nanoparticle
term_bond_length (float) – the bond length of the bond connecting the nanoparticle with the fragment
allow_fragments (bool) – specify if molecular fragments are allowed at the boundary of the nanoparticle
com_inclusion (bool) – True if center of mass determines if molecules are inside the particle, False if the determination is if any atom is inside the particle
logger (logging.Logger) – output logger
no_term_faces (list) – by default when terminating polyhedral nanoparticles all faces are considered, this option specifies that the given integer faces not be terminated (integers start at zero)

checkInput()¶: Check user input.

setMoleculeCompletion()¶: Set whether or not molecules should be completed at the nanoparticle boundary.

isInside(aatom)¶

Return whether or not the given atom is inside the shape. If the given atom has not yet been categorized then categorize it and append the result to the collections.

Parameters: aatom (schrodinger.structure._StructureAtom) – the atom in question
Return type: bool
Returns: True if the atom is inside the shape, False otherwise

checkIntersectingBond(atom1, atom2)¶

Check if the bond given by the specified atoms can be intersected by the shape of nanoparticle. We will only be either keeping a single atom from this bond (no termination) or using it to terminate with a fragment that is expected to connect via a single bond.

Parameters

atom1 (int) – the first atom index of the bond
atom2 (int) – the second atom index of the bond

partitionAtoms()¶: Return three non-overlapping lists of atom indices, (1) for atoms inside the shape, (2) for atoms belonging to bonds which intersect the shape boundary (a (inside, outside) tuple of atom indices for the intersecting bonds), and (3) for atoms that lie outside of shape.

removeAndRenumber(to_remove=None, renumber_map=None)¶

Remove the specified atoms from the nanoparticle and renumber all collections of indices or just renumber the collections using the specified renumber map.

Parameters

to_remove (list or none) – indices of atoms to remove
renumber_map (dict or none) – a renumber map to use in renumbering collections

cutAwayExcess()¶: Remove the unneeded atoms from the crystalline supercell.

handleOneToMany(inside_index, outside_indices)¶

Handle the one to many situation, i.e. a single atom inside the region of interest bonded to multiple atoms outside of the region of interest.

Parameters

inside_index (int) – the index of the inside atom
outside_indices (list) – the indices of the outside atoms

handleManyToOne(inside_indices, outside_index)¶

Handle the many to one situation, i.e. multiple atoms inside the region of interest are bonded to a single atom that is outside of the region of interest.

Parameters

inside_indices (list) – the indices of the inside atoms
outside_index (int) – the index of the outside atom

Return type

list

Returns

contains (inside, outside) tuples of newly created bonds

configureBonds()¶: Configure the nanoparticle bonds that intersect the shape.

doTermination()¶: Terminate the nanoparticle.

setNanoparticleProperties()¶: Set nanoparticle properties.

printParams()¶: Log the parameters.

getAlignmentVector(alignment_dict)¶

Return the alignment vector.

Parameters: alignment_dict (dict) – defines the alignment
Return type: numpy.array
Returns: the vector on which to align

translateToPlane()¶: Translate the shape object so that the reference face is coplanar with the requested crystal plane.

overwriteVertices()¶: Overwrite the vertices of the shape object.

runIt(template_only=False)¶

Create the nanoparticle.

Parameters: template_only (bool) – If True, the method will return immediately after the template is created and before the nanoparticle has been fully synthesized. Using this parameter means that the .template structure is valid but no .nanoparticle structure is created - the .nanoparticle property will be set to None.

schrodinger.application.matsci.nano.particle.build_kwargs(kwargs_list, defaults, acceptable_keys=None, token_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

Return type

dict

Returns

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

schrodinger.application.matsci.nano.particle.set_representation(astructure)¶

Set the representation of the given structure.

Parameters: astructure (schrodinger.structure.Structure) – the structure to set the representation for