Package schrodinger :: Package application :: Package matsci :: Module amorphous

Module amorphous

Builder classes for making amorphous cells

Classes

AttachmentAtoms
AttachmentAtoms(coupler, coupler_marker, grower, grow_marker)

Box
Class that defines the region a new structure may be placed in

BoxWithInnerHull
A cubic Box object that contains an inner non-cubic region that limits the valid volume for the components to be placed in.

ScaffoldError
Class for errors involving the scaffold input

Scaffold
A Scaffold is a structure that occupies space in a cluster of molecules but is not considered part of the system itself.

BuilderWithClashDetection
The base class for the amorphous builder classes

AmorphousCellBuilder
Builder for an amorphous cell

PolymerToFragments
Save the struct and break it into fragments.

PolymerFragment

PolymerBuilderGrowInCellMixin
A mixin for classes that uses in-cell polymer grow method.

XYZVolumeGraph
Create a networkx graph to search the voids in structure.

TorsionAngler
Class to handle cycling a structure though a series of torsion values

MoietyError
Raised if there is an error in creating a Moiety subclass object

BaseMoiety
Base class for all polymer units - initiator, terminator, cascader, monomers

Terminator
A unit that terminates a chain

Cascader
A group that ends a chain but starts multiple new chains

Initiator
A group that starts the whole polymer off - can have multiple grow points, which means that multiple chains will radiate from this group (a dendrimer).

Monomer
The repeating unit that makes up the polymer chain

Moieties
A holder and manager for the various moieties that make up the polymer

Functions

[hide private]

float

get_maximum_vdw_radius(struct)
Find the maximum VDW radius of any atom in the structure

tuple

get_color(index)
Get the next color in the color list - after the defined colors, a random color is returned if index > color list length

random_rotation(struct, centroid=None, max_rotation=6.28318530718)
Randomly rotate struct in 3 dimensions

assign_markers(residue_struct)
Find and add marker atoms to the extracted structures.

networkx.Graph

create_bond_graph(struct)
Create an networkx connection graph for the atoms in struct

int

find_attached_atom_index(struct, mark_index, prop=None, propval=True)
Find the index of the atom attached to the atom with the given index, optionally setting a property/value on that atom

get_other_item(two_list, item)
In a two item list, return the item that isn't the one passed in

propagate_chain_data_from_atom(struct, chain_atom)
Set the chain data for all atoms in struct to the same data as found on atom

float

get_random_nonzero_to_one()
Get a random float: 0 > x >= 1

remove_stale_props(st)
Remove stale properties from the given structure.

Variables

[hide private]

__doc__ = ...

COLOR_BY_MOLECULE = 'molecule'

GREEN = (30, 225, 30)

RED = (225, 30, 30)

CYAN = (0, 255, 255)

MAGENTA = (225, 30, 225)

YELLOW = (255, 240, 0)

BLUE = (30, 30, 225)

PINK = (255, 152, 163)

SLATE = (111, 111, 255)

ORANGE = (234, 130, 50)

LIME = (153, 255, 0)

HOTPINK = (255, 0, 159)

YELLOWORANGE = (255, 191, 51)

DEEPTEAL = (0, 102, 255)

DARKBLUE = (0, 0, 128)

SEAFOAM = (0, 191, 127)

DARKGREEN = (34, 139, 34)

GREY = (160, 160, 160)

LIGHTBLUE = (71, 71, 255)

DEEPRED = (165, 42, 42)

OLIVE = (107, 142, 35)

COLOR_CYCLE = [(30, 225, 30), (0, 255, 255), (225, 30, 30), (2...

TWO_PI = 6.28318530718

OBEY_DENSITY = 'density'

OBEY_CLASH = 'clash'

OBEY_BOTH = 'both'

SCAFFOLD_ATOM_PROP = 'b_matsci_scaffold_atom'

OPLS2005 = 'OPLS_2005'

AMCELL_NO_SYSTEM_OUT = '-amcell.maegz'

INI = 'INI'

TRM = 'TRM'

CAS = 'CAS'

WILDCARD = '*'

DIHEDRAL_NUM = 72

CHAIN_ID_PROP = 'i_matsci_polymer_chain_id'

COUPLER_ATOM_PROP = 'b_matsci_polymer_coupler_atom'

GROWER_ATOM_PROP = 'b_matsci_polymer_grower_atom'

HEADFIRST = 'headfirst'

TAILFIRST = 'tailfirst'

TACTICITY_ISO = 'Isotactic'

TACTICITY_SYN = 'Syndiotactic'

TACTICITY_ATAC = 'Atactic'

HEAD_ATOM_PROP = 'b_matsci_polymer_head_atom'

TAIL_ATOM_PROP = 'b_matsci_polymer_tail_atom'

CASCADER_ATOM_PROP = 'b_matsci_polymer_cascader_atom'

CASCADER_MARKER_ATOM_PROP = 'b_matsci_polymer_cascader_marker_...

BRANCH_ATOM_PROP = 'b_matsci_polymer_branch_atom'

BRANCH_PCT_ATOM_PROP = 'r_matsci_polymer_branch_atom_pct'

BRANCH_GEN_ATOM_PROP = 'i_matsci_polymer_branch_atom_gen'

BRANCH_MAXGEN_ATOM_PROP = 'r_matsci_polymer_branch_atom_maxgen'

CHIRAL_BB_ATOM_PROP = 'b_matsci_polymer_chiral_bb_atom'

CHIRAL_NONE_MONOMER_PROP = 'b_matsci_polymer_monomer_chiral_none'

MARKER_START_PROP = 'b_matsci_polymer_marker_start'

MOIETY_PROP = 's_matsci_polymer_gui_moiety'

MARKER_PROP = 's_matsci_polymer_gui_marker_list'

TACTICITY_PROP = 's_matsci_polymer_gui_tacticity'

BRANCH_PCT_PROP = 'r_matsci_polymer_gui_branch_pct'

BRANCH_MAX_PROP = 'i_matsci_polymer_gui_branch_max'

BBTRANS_PROP = 'b_matsci_polymer_gui_bb_trans'

CASCADE_GEN_PROP = 'i_matsci_polymer_gui_cascade_gen'

INITIATOR = 'initiator'

TERMINATOR = 'terminator'

CASCADER = 'cascader'

MONOMERX = 'monomer_x'

DEFAULT_VDW_SCALE = 0.5

R_S = ['R', 'S']

PROP_BY_CHIRALITY = OrderedDict([('R', 'b_matsci_polymer_monom...

ATOM_PROP_MARKER_IDX = [('b_matsci_polymer_head_atom', 0), ('b...

__package__ = 'schrodinger.application.matsci'

Function Details

[hide private]

get_maximum_vdw_radius(struct)

Find the maximum VDW radius of any atom in the structure

Parameters:

struct (schrodinger.structure.Structure) - The structure to check

Returns: float

The maximum VDW radius of any atom

get_color(index)

Get the next color in the color list - after the defined colors, a random color is returned if index > color list length

Parameters:

index (int) - The index of the color to return

Returns: tuple

(R, G, B) color tuple

random_rotation(struct, centroid=None, max_rotation=6.28318530718)

Randomly rotate struct in 3 dimensions

Parameters:

struct (schrodinger.structure.Structure) - The structure to rotate
centroid (3-element numpy array) - the rotation center [x, y, z]
max_rotation (float) - The maximum rotation to perform

assign_markers(residue_struct)

Find and add marker atoms to the extracted structures.

Parameters:

residue_struct (schrodinger.structure.Structure) - The structure to add the markers to

create_bond_graph(struct)

Create an networkx connection graph for the atoms in struct

Parameters:

struct (schrodinger.structure.Structure) - The structure to create the graph for

Returns: networkx.Graph

The connection graph for the backbone atoms in struct

find_attached_atom_index(struct, mark_index, prop=None, propval=True)

Find the index of the atom attached to the atom with the given index, optionally setting a property/value on that atom

Parameters:

struct (schrodinger.structure.Structure) - The structure to search for the atom
mark_index (int) - The index of the atom that we want to find an atom attached to.
prop (str) - An atom property name
propval - The value to set prop to on the found attached atom. The type of this object depends on the type of property being set

Returns: int

The index of an atom attached to the mark_index atom. If more than one atom is attached to mark_index atom, the first one is returned.

get_other_item(two_list, item)

In a two item list, return the item that isn't the one passed in

Parameters:

two_list (list) - A list two items long
item - One of the items from two_list

Returns:

The item in two_list that is not the one passed in

propagate_chain_data_from_atom(struct, chain_atom)

Set the chain data for all atoms in struct to the same data as found on atom

Parameters:

struct (schrodinger.structure.Structure) - The structure to set atom properties on
chain_atom (schrodinger.structure._StructureAtom) - The atom object to take the chain information from. Might not be from the same structure object as struct

get_random_nonzero_to_one()

Get a random float: 0 > x >= 1

Returns: float: A floating point number in the range (0, 1]

remove_stale_props(st)

Remove stale properties from the given structure.

Parameters:

st (schrodinger.structure.Structure) - the structure from which to remove the stale properties

Variables Details

[hide private]

doc

Value:

"""
Builder classes for making amorphous cells

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

COLOR_CYCLE

Value:

[(30, 225, 30),
 (0, 255, 255),
 (225, 30, 30),
 (225, 30, 225),
 (255, 240, 0),
 (30, 30, 225),
 (255, 152, 163),
 (111, 111, 255),
...

CASCADER_MARKER_ATOM_PROP

Value:

'b_matsci_polymer_cascader_marker_atom'

PROP_BY_CHIRALITY

Value:

OrderedDict([('R', 'b_matsci_polymer_monomer_chiral_r'), ('S', 'b_mats
ci_polymer_monomer_chiral_s'), (None, 'b_matsci_polymer_monomer_chiral
_none')])

ATOM_PROP_MARKER_IDX

Value:

[('b_matsci_polymer_head_atom', 0),
 ('b_matsci_polymer_tail_atom', 1),
 ('b_matsci_polymer_cascader_atom', 2),
 ('b_matsci_polymer_branch_atom', 2)]