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', keep_edge_atoms=False, cov_offset=0.45, intact_molecules=None, fract_offset=0.0001, no_pbc_bonding=False, logger=None)
Create an instance.

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

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 the atoms should be translated to the first unit cell.

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.

setUnitCellLowerBounds(self)
Set the lower bounds of the unit cell.

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.

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.

bool

cellFromOuterLayer(self, indexa, indexb, indexc, ncella, ncellb, ncellc)
Return True if the query cell is in the outer layer of cells of a super cell build with three or more cells along each lattice vector.

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

int, int, int

increaseExtentsBy(self, extra)
Increase the extents by some amount.

dict or None

getIntactMolecules(self, crystal_super_cell)
Get the original super cell including intact molecules at the boundary from the larger super cell.

translateSupercell(self, delta_a, delta_b, delta_c)
Translate the super cell by the given amount along each of the lattice vectors and update the fractional coordinates.

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

dict

getRealPBCBonds(self, ncella, ncellb, ncellc)
From all bonds made in building the crystal super cell (plus two extra unit cell along each lattice vector), obtain only those bonds that involve the outer layer of cells bonded to the inner cells.

tuple, int

getImageCellInfo(self, real_cell, ncella, ncellb, ncellc)
Given the real cell tuple return both the image cell tuple as well as the number of cells between the real and image according to a traversal path of c then b then a.

int

getImageAtomIndex(self, real_index, ncella, ncellb, ncellc, real_cell=None)
Return the image atom index from the real atom index.

list

getImageAtomsForRealPBCBonds(self, real_pbc_bonds, ncella, ncellb, ncellc)
For all real PBC bonds collect the image atom indices for the outside atoms and return a list of unique tuples containing information about both real and image bonds.

dict

getAromaticPBCRingBonds(self, bonding_triples, ncella, ncellb, ncellc)
For all aromatic rings that cross the PBC collect and return a dictionary containing bonding and bond order information for real and image rings.

makePBCBonds(self, bonding_triples)
Make the PBC bonds.

setAromaticPBCRingBonds(self, aromatic_pbc_ring_bonds)
Set the bond orders for aromatic PBC ring bonds.

trimOuterCells(self, ncella, ncellb, ncellc)
Remove the extra layer of outer cells from the crystal super cell.

handlePBCBonding(self, ncella, ncellb, ncellc)
Handle the PBC bonding.

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'

LATTICE_VECTOR_A_KEY = 's_matsci_Lattice_Vector_A/(3*Ang.)'

LATTICE_VECTOR_B_KEY = 's_matsci_Lattice_Vector_B/(3*Ang.)'

LATTICE_VECTOR_C_KEY = 's_matsci_Lattice_Vector_C/(3*Ang.)'

LATTICE_VECTOR_COORDS = 6

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'

FORMULA_ENTRY_PATTERN = re.compile(r'([A-Z][a-z]?)(\d*)')

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'`, keep_edge_atoms=False, cov_offset=0.45, intact_molecules=None, fract_offset=0.0001, no_pbc_bonding=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
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
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 the atoms should be translated to the first unit cell.

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.

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

cellFromOuterLayer(self, indexa, indexb, indexc, ncella, ncellb, ncellc)

Return True if the query cell is in the outer layer of cells of a super cell build with three or more cells along each lattice vector.

Parameters:

indexa (int) - query index along a
indexb (int) - query index along b
indexc (int) - query index along c
ncella (int) - the number of cells along a
ncellb (int) - the number of cells along b
ncellc (int) - the number of cells along c

Returns: bool

True if the query cell is in the outer layer of cells, False otherwise

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

increaseExtentsBy(self, extra)

Increase the extents by some amount.

Parameters:

extra (int) - the amount by which to increase the extents

Returns: int, int, int

ncella, ncellb, ncellc, the numbers of unit cells to generate along lattice vector a, b, and c

getIntactMolecules(self, crystal_super_cell)

Get the original super cell including intact molecules at the boundary from the larger super cell.

Parameters:

crystal_super_cell (schrodinger.Structure.structure) - the structure object for the supercell

Returns: dict or None

renumber map for deleted atoms or None if no atoms were deleted

translateSupercell(self, delta_a, delta_b, delta_c)

Translate the super cell by the given amount along each of the lattice vectors and update the fractional coordinates.

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

buildCrystalSuperCellWithIntactMolecules(self, ncella, ncellb, ncellc)

Build a crystal super cell while keeping intact molecules at the unit cell boundaries.

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

getRealPBCBonds(self, ncella, ncellb, ncellc)

From all bonds made in building the crystal super cell (plus two extra unit cell along each lattice vector), obtain only those bonds that involve the outer layer of cells bonded to the inner cells.

Parameters:

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

Returns: dict

real PBC bonds, keys are tuples of super cell pairs (where each of the two pairs is another tuple containing a triple of integer cell indices), values are lists of bonding atom index pairs that span the boundary of the cell pair, this boundary can be a face, edge, or corner, these results are ordered like (outer cell, inner cell): [ (outer index, inner index), ...]

getImageCellInfo(self, real_cell, ncella, ncellb, ncellc)

Given the real cell tuple return both the image cell tuple as well as the number of cells between the real and image according to a traversal path of c then b then a.

Parameters:

real_cell (tuple) - a triple of real cell indices
ncella (int) - the number of unit cells along lattice vector a
ncellb (int) - the number of unit cells along lattice vector b
ncellc (int) - the number of unit cells along lattice vector c

Returns: tuple, int

a triple of image cell indices and the number of cells between real and image

getImageAtomIndex(self, real_index, ncella, ncellb, ncellc, real_cell=None)

Return the image atom index from the real atom index.

Parameters:

real_index (int) - the super cell index of the query real atom
ncella (int) - the number of unit cells along lattice vector a
ncellb (int) - the number of unit cells along lattice vector b
ncellc (int) - the number of unit cells along lattice vector c
real_cell (tuple or None) - a triple of cell indicies for the query real atom, if None then will be determined using the fractional coordinates of the query atom

Returns: int

the super cell index of the image atom

getImageAtomsForRealPBCBonds(self, real_pbc_bonds, ncella, ncellb, ncellc)

For all real PBC bonds collect the image atom indices for the outside atoms and return a list of unique tuples containing information about both real and image bonds.

Parameters:

real_pbc_bonds (dict) - real PBC bonds, keys are tuples of super cell pairs ordered like (outer cell, inner cell), values are lists of (outer index, inner index) bonding atom index pairs that span the boundary of the cell pair
ncella (int) - the number of unit cells along lattice vector a
ncellb (int) - the number of unit cells along lattice vector b
ncellc (int) - the number of unit cells along lattice vector c

Returns: list

contains unique real and image bonding tuples, where each tuple is an atom index triple like (real outside, real inside, image inside)

getAromaticPBCRingBonds(self, bonding_triples, ncella, ncellb, ncellc)

For all aromatic rings that cross the PBC collect and return a dictionary containing bonding and bond order information for real and image rings.

Parameters:

bonding_triples (list) - contains PBC bonding information as unique tuples with (1) outside atom index for a PBC bond, (2) inside atom index for a PBC bond, and (3) the inside image of (1).
ncella (int) - the number of unit cells along lattice vector a
ncellb (int) - the number of unit cells along lattice vector b
ncellc (int) - the number of unit cells along lattice vector c

Returns: dict

keys tuples containing two two-index tuples for real and image bonding atom pairs that are for bonds in aromatic rings that cross the PBC, values are real bond orders for that bond

makePBCBonds(self, bonding_triples)

Make the PBC bonds.

Parameters:

bonding_triples (list) - contains PBC bonding information as unique tuples with (1) outside atom index for a PBC bond, (2) inside atom index for a PBC bond, and (3) the inside image of (1).

setAromaticPBCRingBonds(self, aromatic_pbc_ring_bonds)

Set the bond orders for aromatic PBC ring bonds.

Parameters:

aromatic_pbc_ring_bonds (dict) - keys tuples containing two two-index tuples for real and image bonding atom pairs that are for bonds in aromatic rings that cross the PBC, values are real bond orders for that bond

trimOuterCells(self, ncella, ncellb, ncellc)

Remove the extra layer of outer cells from the crystal super cell.

Parameters:

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

handlePBCBonding(self, ncella, ncellb, ncellc)

Handle the PBC bonding.

Parameters:

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

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.]])