Package schrodinger :: Package application :: Package matsci :: Package nano :: Module xtal :: Class Crystal

Class Crystal

object --+
         |
        Crystal

Main class for generating crystals.

Instance Methods

[hide private]

__init__(self, asymmetric_unit, space_group=None, a_param=None, b_param=None, c_param=None, alpha_param=None, beta_param=None, gamma_param=None, ncella=1, ncellb=1, ncellc=1, origin=[0.0, 0.0, 0.0], bonding='none', bond_orders='none', translate='none', translate_type='atoms', keep_edge_atoms=False, cov_offset=0.45, intact_molecules=None, fract_offset=0.0001, no_pbc_bonding=False, use_existing_pbc_bonds=False, logger=None)
Create an instance.

handleSettings(self)
Handle the settings of this crystal build.

handleIntactMoleculesSettings(self)
Handle the settings for intact molecules.

bool

doBonding(self)
Determine if this script should handle the bonding both inside and between unit cells.

bool

doBondOrders(self)
Determine if this script should handle the assignment of bond orders both inside and between unit cells.

bool

doTranslation(self)
Determine if a translation to the first unit cell should be performed.

getLatticeParameters(self)
Get lattice parameters.

checkInputParams(self)
Check input parameters.

updateLatticeProperties(self)
Update the lattice properties for the asymmetric unit structure.

setAsuColor(self)
Set the color scheme to use for the ASU structure.

mmcrystal handle

setCrystalSymmetry(self)
Set the crystal symmetry.

determineBasisVectors(self)
Determine the lattice vectors in the cartesian basis and the cartesian vectors in the lattice basis.

buildCrystalUnitCell(self, mmcrystal_handle)
Build a crystal unit cell.

labelSymEquivPos(self)
Label the symmetry equivalent positions.

labelAsuAtoms(self, astructure)
Label the atoms that make up an ASU, i.e.

completeUnitCellBoundary(self, astructure)
Complete the unit cell boundary so that atoms are defined on both edges.

doPropertyEvaluation(self)
Compute some properties of the unit cell.

setStructureProperties(self)
Set some structure properties.

setChorusProperties(self, astructure, ncella=1, ncellb=1, ncellc=1)
Set the chorus structure properties on the given structure.

printCrystalParams(self)
Print some crystal parameters.

updateFractionals(self, next_cell, indexa, indexb, indexc)
Update the fractional coordinates of the next unit cell.

setAsuAtomsFalse(self, astructure)
Set the ASU atom labels to false for this structure.

buildCrystalSuperCell(self, ncella, ncellb, ncellc)
Build a crystal super cell.

list

getIntactExtents(self)
Return the extents needed to un-PBC-ify all disconnected molecules in the unit cell, i.e.

list

getBaseExtents(self)
Return the base extents, these plus those extents needed for intact molecules specify the size of the super cell to be built.

list

getFinalExtents(self, extra_a, extra_b, extra_c)
Return the final extents to use for building the super cell from which to collect intact molecules.

disableConnectabilities(self, pbc_bonds)
Disable the connectabilities of all PBC bonds that belong to infinite molecules.

trimCell(self, cell, to_keep)
Delete all atoms in the given cell except those in the provided list.

getIntactMolecules(self, extra_a, extra_b, extra_c)
Collect intact molecules from the super cell.

translateIntactMolecules(self, delta_a, delta_b, delta_c)
Translate the intact molecules.

uniquifyMolecules(self)
Uniquify the molecules.

getPBCBonds(self, cell)
Return a PBCBonds object for the given cell.

extendUniqueIntactMolecules(self)
Extend the unique intact molecules.

buildCrystalSuperCellWithIntactMolecules(self)
Build a crystal super cell while keeping intact molecules at the unit cell boundaries.

orchestrate(self)
Orchestrate the construction of the crystal.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

SPACE_GROUP_KEY = 's_pdb_PDB_CRYST1_Space_Group'

A_KEY = 'r_pdb_PDB_CRYST1_a'

B_KEY = 'r_pdb_PDB_CRYST1_b'

C_KEY = 'r_pdb_PDB_CRYST1_c'

ALPHA_KEY = 'r_pdb_PDB_CRYST1_alpha'

BETA_KEY = 'r_pdb_PDB_CRYST1_beta'

GAMMA_KEY = 'r_pdb_PDB_CRYST1_gamma'

SPACE_GROUP_ID_KEY = 'i_matsci_Space_Group_ID'

CHORUS_BOX_BASE_KEY = 'r_chorus_box_'

CHORUS_BOX_AX_KEY = 'r_chorus_box_ax'

CHORUS_BOX_AY_KEY = 'r_chorus_box_ay'

CHORUS_BOX_AZ_KEY = 'r_chorus_box_az'

CHORUS_BOX_BX_KEY = 'r_chorus_box_bx'

CHORUS_BOX_BY_KEY = 'r_chorus_box_by'

CHORUS_BOX_BZ_KEY = 'r_chorus_box_bz'

CHORUS_BOX_CX_KEY = 'r_chorus_box_cx'

CHORUS_BOX_CY_KEY = 'r_chorus_box_cy'

CHORUS_BOX_CZ_KEY = 'r_chorus_box_cz'

CHORUS_BOX_A_KEYS = ['r_chorus_box_ax', 'r_chorus_box_ay', 'r_...

CHORUS_BOX_B_KEYS = ['r_chorus_box_bx', 'r_chorus_box_by', 'r_...

CHORUS_BOX_C_KEYS = ['r_chorus_box_cx', 'r_chorus_box_cy', 'r_...

NUM_DECIMAL_COORDS = 4

MSGWIDTH = 80

GENERAL_VEC_1 = matrix([[ 1...

GENERAL_VEC_2 = matrix([[ 0...

GENERAL_VEC_3 = matrix([[ 0...

F1F2F3_FORMAT = '(%.4f, %.4f, %.4f)'

F1F2F3_KEY = 's_matsci_f1f2f3'

F1_KEY = 'r_matsci_f1'

F2_KEY = 'r_matsci_f2'

F3_KEY = 'r_matsci_f3'

FRACT_KEYS = ['r_matsci_f1', 'r_matsci_f2', 'r_matsci_f3']

SYMMETRY_LABEL_KEY = 'i_matsci_Symmetry_Label'

ASU_LABEL_KEY = 'b_matsci_ASU_Atom'

CM_TO_ANGSTROM = 100000000.0

UNIT_CELL_FORMULA_KEY = 's_m_Unit_Cell_Formula'

UNIT_CELL_VOLUME_KEY = 'r_m_Unit_Cell_Volume/Ang.^3'

UNIT_CELL_DENSITY_KEY = 'r_m_Unit_Cell_Density/g/cm^3'

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, asymmetric_unit, space_group=None, a_param=None, b_param=None, c_param=None, alpha_param=None, beta_param=None, gamma_param=None, ncella=1, ncellb=1, ncellc=1, origin=`[`0.0`,` 0.0`,` 0.0`]`, bonding=`'none'`, bond_orders=`'none'`, translate=`'none'`, translate_type=`'atoms'`, keep_edge_atoms=False, cov_offset=0.45, intact_molecules=None, fract_offset=0.0001, no_pbc_bonding=False, use_existing_pbc_bonds=False, logger=None)
(Constructor)

Create an instance.

Parameters:

asymmetric_unit (schrodinger.Structure.structure) - the ASU
space_group (str) - the full or short Hermann-Mauguin symbol of the space group
a_param (float) - the lattice parameter a in Angstrom
b_param (float) - the lattice parameter b in Angstrom
c_param (float) - the lattice parameter c in Angstrom
alpha_param (float) - the lattice parameter alpha in degrees
beta_param (float) - the lattice parameter beta in degrees
gamma_param (float) - the lattice parameter gamma in degrees
ncella (int) - the number of unit cells to generate along lattice vector a
ncellb (int) - the number of unit cells to generate along lattice vector b
ncellc (int) - the number of unit cells to generate along lattice vector c
origin (list) - the origin of the unit cell, i.e. list of three floats
bonding (str) - specifies how the bonding should be handled, takes a string in BONDING_CHOICES
bond_orders (str) - specifies how the bond orders should be handled, takes a string in BOND_ORDERS_CHOICES
translate (str) - specifies how the translation to the first unit cell should be handled, takes a string in TRANSLATE_CHOICES
translate_type (str) - specifies what to translate when translating
keep_edge_atoms (bool) - whether or not to keep redundant edge atoms
cov_offset (float) - the maximum distance for drawn bonds is the sum of the covalent radii of the two atoms plus this offset in angstrom
intact_molecules (str) - specify how molecules should be clipped at the unit or super cell boundaries
fract_offset (float) - the threshold used to compare floating point fractional coordinate values and in particular those that are on the cell boundary
no_pbc_bonding (bool) - disable the creation of PBC bonds
use_existing_pbc_bonds (bool) - rather than recalculating PBC bonds use existing PBC bonds
logger (logging.getLogger) - output logger

Overrides: object.__init__

doBonding(self)

Determine if this script should handle the bonding both inside and between unit cells.

Returns: bool: True if this script should handle the bonding, False otherwise.

doBondOrders(self)

Determine if this script should handle the assignment of bond orders both inside and between unit cells.

Returns: bool: True if this script should handle the assignment, False otherwise.

doTranslation(self)

Determine if a translation to the first unit cell should be performed.

Returns: bool: True if this translation should be performed, False otherwise.

setCrystalSymmetry(self)

Set the crystal symmetry.

Returns: mmcrystal handle: mmcrystal_handle, mmcrystal handle with symmetry set

determineBasisVectors(self)

Determine the lattice vectors in the cartesian basis and the cartesian vectors in the lattice basis. Also determine the reciprocal lattice vectors.

buildCrystalUnitCell(self, mmcrystal_handle)

Build a crystal unit cell.

Parameters:

mmcrystal_handle - mmcrystal handle with symmetry set

labelAsuAtoms(self, astructure)

Label the atoms that make up an ASU, i.e. the symmetry unique atoms.

Parameters:

astructure (schrodinger.Structure.structure) - the structure whose atoms will be labeled

completeUnitCellBoundary(self, astructure)

Complete the unit cell boundary so that atoms are defined on both edges.

Parameters:

astructure (schrodinger.Structure.structure) - the structure object for which the boundary will be completed

doPropertyEvaluation(self)

Compute some properties of the unit cell. In order for the properties to be consistent with their standard definitions the provided unit cell must be void of the redundant edge, meaning that the fractionals must be defined on n < f < n + 1 rather than n < f <= n + 1, as well as any other redundancies.

setChorusProperties(self, astructure, ncella=1, ncellb=1, ncellc=1)

Set the chorus structure properties on the given structure.

Parameters:

astructure (schrodinger.structure.Structure) - the structure that needs the chorus properties
ncella (int) - the number of cells along a
ncellb (int) - the number of cells along b
ncellc (int) - the number of cells along c

updateFractionals(self, next_cell, indexa, indexb, indexc)

Update the fractional coordinates of the next unit cell.

Parameters:

next_cell (schrodinger.Structure.structure) - the structure object to be updated
indexa (int) - the a-position of this cell
indexb (int) - the b-position of this cell
indexc (int) - the c-position of this cell

setAsuAtomsFalse(self, astructure)

Set the ASU atom labels to false for this structure.

Parameters:

astructure (schrodinger.Structure.structure) - the structure object to be updated

buildCrystalSuperCell(self, ncella, ncellb, ncellc)

Build a crystal super cell.

Parameters:

ncella (int) - the number of unit cells to generate along lattice vector a
ncellb (int) - the number of unit cells to generate along lattice vector b
ncellc (int) - the number of unit cells to generate along lattice vector c

getIntactExtents(self)

Return the extents needed to un-PBC-ify all disconnected molecules in the unit cell, i.e. these are the minimum extents needed to create an intact view for all molecules in the cell.

Returns: list: contains extents along the a, b, and c lattice vectors

getBaseExtents(self)

Return the base extents, these plus those extents needed for intact molecules specify the size of the super cell to be built.

Returns: list: contains extents along the a, b, and c lattice vectors

getFinalExtents(self, extra_a, extra_b, extra_c)

Return the final extents to use for building the super cell from which to collect intact molecules.

Parameters:

extra_a (int) - the number of extra extents to create along a
extra_b (int) - the number of extra extents to create along b
extra_c (int) - the number of extra extents to create along c

Returns: list

contains extents along the a, b, and c lattice vectors

disableConnectabilities(self, pbc_bonds)

Disable the connectabilities of all PBC bonds that belong to infinite molecules.

Parameters:

pbc_bonds (PBCBonds) - contains all PBC bonds

trimCell(self, cell, to_keep)

Delete all atoms in the given cell except those in the provided list.

Parameters:

cell (schrodinger.Structure.structure) - the cell from which to delete atoms
to_keep (list) - atoms to keep

getIntactMolecules(self, extra_a, extra_b, extra_c)

Collect intact molecules from the super cell.

Parameters:

extra_a (int) - the number of extra extents created along a
extra_b (int) - the number of extra extents created along b
extra_c (int) - the number of extra extents created along c

translateIntactMolecules(self, delta_a, delta_b, delta_c)

Translate the intact molecules.

Parameters:

delta_a (int) - amount to translate along a
delta_b (int) - amount to translate along b
delta_c (int) - amount to translate along c

getPBCBonds(self, cell)

Return a PBCBonds object for the given cell.

Parameters:

cell (schrodinger.Structure.structure) - the cell for which PBCBonds will be returned

Class Variable Details

[hide private]

CHORUS_BOX_A_KEYS

Value:

['r_chorus_box_ax', 'r_chorus_box_ay', 'r_chorus_box_az']

CHORUS_BOX_B_KEYS

Value:

['r_chorus_box_bx', 'r_chorus_box_by', 'r_chorus_box_bz']

CHORUS_BOX_C_KEYS

Value:

['r_chorus_box_cx', 'r_chorus_box_cy', 'r_chorus_box_cz']

GENERAL_VEC_1

Value:

matrix([[ 1.],
        [ 0.],
        [ 0.]])

GENERAL_VEC_2

Value:

matrix([[ 0.],
        [ 1.],
        [ 0.]])

GENERAL_VEC_3

Value:

matrix([[ 0.],
        [ 0.],
        [ 1.]])