schrodinger.application.matsci.nano.tube module¶
Classes and functions for building single- and multi-walled nanotubes.
Copyright Schrodinger, LLC. All rights reserved.
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class
schrodinger.application.matsci.nano.tube.
CheckInput
¶ Bases:
schrodinger.application.matsci.nano.check.CheckInput
Check user input.
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checkAll
(element1, element2, bondlength, nindex, mindex, ncells, no_double_bonds, termfrag, min_term_frags, up_to_nindex, up_to_mindex, nwalls, wallsep, logger=None)¶ Manage all checks.
Parameters: - element1 (str) – elemental symbol of the first atom
- element2 (str) – elemental symbol of the second atom
- bondlength (float) – bond length between the first and second atoms in Angstrom
- nindex (int) – first chiral index
- mindex (int) – second chiral index
- ncells (int) – number of unit cells
- no_double_bonds (bool) – disable the formation of double bonds
- termfrag (str) – terminate the lattice with a given fragment
- min_term_frags (bool) – minimize the geometry of terminating fragments
- up_to_nindex (bool) – enumerate nanotube structures on the n-index
- up_to_mindex (bool) – enumerate nanotube structures on the m-index
- nwalls (int) – number of walls in a multi-wall nanotube
- wallsep (float) – wall separation in Angstrom for a multi-wall nanotube
- logger (logging.getLogger) – output logger
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DEFAULTMSG
= '\n You have specified a value for flag %s that is not supported. Values\n must be %s. Proceeding with the default value of %s.'¶
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MIDFIX
= '-'¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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checkBilayerSep
(bilayersep, logger=None)¶
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checkBilayerShift
(bilayershift, logger=None)¶
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checkBilayerStackType
(stacktype, logger=None)¶
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checkBondlength
(bondlength, logger=None)¶
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checkCellDims
(ncell1, ncell2, logger=None)¶
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checkEdgetypes
(edgetype1, edgetype2, logger=None)¶
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checkElements
(element1, element2, logger=None)¶
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checkExistingFile
(infile)¶ Check if the infile already exists and find a new name if it does.
Parameters: infile (str) – file name to check Return type: str Returns: outfile, if infile is bad return new file name
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checkIndicies
(nindex, mindex, logger=None)¶ Check n-index and m-index.
Parameters: - nindex (int) – the first chiral index
- mindex (int) – the second chiral index
- logger (logging.getLogger) – output logger
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checkMaeExt
(infile)¶ Check that the infile has a supported Maestro extension.
Parameters: infile (str) – file name to check Return type: str Returns: outfile, if infile is bad return its basename plus constants.DEFAULT_MAE_EXT
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checkNumBilayers
(nbilayers, logger=None)¶
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checkNumCells
(ncells, logger=None)¶ Check the number of unit cells.
Parameters: - ncells (int) – the number of unit cells
- logger (logging.getLogger) – output logger
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checkNumWalls
(nwalls, logger=None)¶ Check the number of walls.
Parameters: - nwalls (int) – the number of walls
- logger (logging.getLogger) – output logger
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checkTermFrag
(termfrag, logger=None)¶
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checkUpToIndex
(up_to_nindex, up_to_mindex, logger=None)¶ Check the enumeration options.
Parameters: - up_to_nindex (bool) – enumerate on the n-index
- up_to_mindex (bool) – enumerate on the m-index
- logger (logging.getLogger) – output logger
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checkWallSep
(wallsep, logger=None)¶ Check the desired wall separation.
Parameters: - wallsep (float) – wall separation in Angstrom
- logger (logging.getLogger) – output logger
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class
schrodinger.application.matsci.nano.tube.
Rectangle
(origin, bottom, left, end)¶ Bases:
object
Manage the properties of a rectangle.
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INSIDETHRESH
= 1e-05¶
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__init__
(origin, bottom, left, end)¶ Create an instance.
Parameters: - origin (numpy.array) – lower left point
- bottom (numpy.array) – lower right point
- left (numpy.array) – upper left point
- end (numpy.array) – upper right point
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linear_equation
(ixy, fxy, x)¶ Return y = m*x + b for m and b from the line formed by initial point ixy and final point fxy.
Parameters: - ixy (numpy.array) – initial point on line
- fxy (numpy.array) – final point on line
- x (float) – domain argument
Return type: float
Returns: y, range value
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insideRectangle
(xy, logger=None)¶ Return boolean specifying if the provided plane coordinates lie within the boundary.
Parameters: - xy (numpy.array) – plane coordinates
- logger (logging.getLogger) – output logger
Return type: bool, bool
Returns: insidex, insidey, inside the x-boundary or not, same for y-boundary
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class
schrodinger.application.matsci.nano.tube.
NanoSheet
(nanotube_sheet_obj)¶ Bases:
object
Create a sheet.HoneycombLattice that is large enough so that the nanotube sheet can be cut out from it.
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ANGLEMEDIUM
= 1.0471975511965976¶
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__init__
(nanotube_sheet_obj)¶ Create an instance.
Parameters: nanotube_sheet_obj (NanoTubeSheet) – contains parameters of the nanotube sheet
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defineVectors
()¶ Define HoneycombLattice and NanoTubeSheet lattice, etc. vectors.
Return type: numpy.array, numpy.array Returns: lattvec1, lattvec2, the HoneycombLattice lattice vectors
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getGrowParams
(lattvec1, lattvec2)¶ Get HoneycombLattice grow parameters.
Parameters: - lattvec1 (numpy.array) – lattice vector 1
- lattvec2 (numpy.array) – lattice vector 2
Return type: float, numpy.array, float, numpy.array
Returns: grow1len, grow1unit, grow2len, grow2unit, the lengths and unit vectors of the grow vectors
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changeBasis
(grow1unit, grow2unit)¶ Change the basis of the NanoTubeSheet to that of the NanoSheet.
Parameters: - grow1unit (numpy.array) – unit vector of first grow vector
- grow2unit (numpy.array) – unit vector of second grow vector
Return type: float, float
Returns: coef1, coef2, coefficients of the end vector in the grow basis
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defineDimensions
(coef1, grow1len, coef2, grow2len)¶ Define the dimensions of the NanoSheet.
Parameters: - coef1 (float) – coefficient of end vector on first grow vector
- grow1len (float) – length of first grow vector
- coef2 (float) – coefficient of end vector on second grow vector
- grow2len (float) – length of second grow vector
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rotateNanoSheet
()¶ Rotate the nanosheet so that lattice edge 1 is along the x-axis.
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getNanoSheet
(logger=None)¶ Get the sheet.HoneycombLattice from which the nanotube sheet will be cut.
Parameters: logger (logging.getLogger) – output logger
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class
schrodinger.application.matsci.nano.tube.
NanoTubeSheet
(element1, element2, bondlength, nindex, mindex, ncells)¶ Bases:
object
Preprocess a nanosheet into a nanotube sheet which will be rolled up into a nanotube.
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ZEROVEC
= array([0., 0.])¶
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__init__
(element1, element2, bondlength, nindex, mindex, ncells)¶ Create an instance.
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redefineLatticeVecs
(lattvec1, lattvec2)¶ Redefine lattice vectors according to Dresselhaus.
Parameters: - lattvec1 (numpy.array) – first lattice vector
- lattvec2 (numpy.array) – second lattice vector
Return type: numpy.array, numpy.array
Returns: nlattvec1, nlattvec2, first and second lattice vectors redefined
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getTubeVectors
()¶ Return chiral and translation vectors for the nanotube sheet.
Return type: numpy.array, numpy.array Returns: chiral, translat, tube vectors
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renumberAtomLists
(renumbermap)¶ Apply the given renumbering map to the terminating and matching atom lists.
Parameters: renumbermap (dict) – maps old indicies into new indicies
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cutOutNanoSheet
(logger=None)¶ Cut out the nanotube sheet from the nanosheet.
Parameters: logger (logging.getLogger) – output logger
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delDanglingTermAtoms
()¶ Remove dangling atoms from the top and bottom of the nanotube sheet.
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delZigZagMatchAtoms
(logger=None)¶ Remove overlapping match atoms for the zigzag case.
Parameters: logger (logging.getLogger) – output logger
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delChiralMatchAtoms
(logger=None)¶ Remove overlapping match atoms for the chiral case.
Parameters: logger (logging.getLogger) – output logger
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buildNanoTubeSheet
(termfrag, use_finite_bos=True, logger=None)¶ Build the nanotube sheet.
Parameters: - termfrag (str) – terminate the lattice with a given fragment
- use_finite_bos (bool) – use a bond order protocol meant for finite molecules
- logger (logging.getLogger) – output logger
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class
schrodinger.application.matsci.nano.tube.
NanoTube
(element1, element2, bondlength, no_double_bonds, nindex, mindex, ncells, termfrag, min_term_frags)¶ Bases:
object
Create a nanotube by rolling up a nanotube sheet.
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TITLEKEY
= 's_m_title'¶
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ENTRYKEY
= 's_m_entry_name'¶
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TITLENAME
= 'nanotube'¶
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NINDEX
= 'i_matsci_N_Index'¶
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MINDEX
= 'i_matsci_M_Index'¶
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NCELLS
= 'i_matsci_N_Cells'¶
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RADIUS
= 'r_matsci_Radius/Ang.'¶
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LENGTH
= 'r_matsci_Length/Ang.'¶
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TWOPI
= 6.283185307179586¶
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MSGWIDTH
= 50¶
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NUMDECIMAL
= 3¶
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A_VACUUM
= 3.35¶
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C_VACUUM
= 3.35¶
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__init__
(element1, element2, bondlength, no_double_bonds, nindex, mindex, ncells, termfrag, min_term_frags)¶ Create an instance.
Parameters: - element1 (str) – elemental symbol of the first atom
- element2 (str) – elemental symbol of the second atom
- bondlength (float) – bond length between the first and second atoms in Angstrom
- no_double_bonds (bool) – disable the formation of double bonds
- nindex (int) – first chiral index
- mindex (int) – second chiral index
- ncells (int) – number of unit cells
- termfrag (str) – terminate the lattice with a given fragment
- min_term_frags (bool) – minimize the geometry of terminating fragments
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getChiralAngle
(logger=None)¶ Determine the chiral angle of the tube in degrees where the chiral angle is angle(lattvec1, chiral) and is in [0.0, 30.0], 0.0 for zigzag and 30.0 for armchair and the rest are chiral.
Parameters: logger (logging.getLogger) – output logger
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tubularizeNanoTubeSheet
(logger=None)¶ Tubularize the nanotube sheet.
Parameters: logger (logging.getLogger) – output logger
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rotateTube
(logger=None)¶ Rotate the nanotube so that the tube axis is the translation vector.
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preprocessMatchAtoms
(inmatch)¶ Dangling match atoms require two bonding partners so make those atom indicies redundant in the list.
Parameters: inmatch (list of ints) – non-redundant list Return type: list of ints Returns: outmatch, redundant list
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bondMatchingEdges
(matchleft, matchright)¶ Properly bond the left and right edges which meet each other after rolling.
Parameters: - matchleft (list of ints) – indicies of atoms on the left
- matchright (list of ints) – indicies of atoms on the right
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doTermination
(nanosheet_obj, fragment)¶ Terminate the nanotube. Do this by hijacking the HoneycombLattice instance and overwriting some attributes.
Parameters: - nanosheet_obj (sheet.HoneycombLattice) – contains information shared between this instance and the nanotube instance
- fragment (str) – fragment name
Return type: list of ints
Returns: nanosheet_obj.frozenatoms, those fragment atoms bound to the nanotube
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doBondOrders
(logger=None)¶ Assign bond orders to the nanotube.
Parameters: logger (logging.getLogger) – output logger
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removeHydrogens
()¶ Remove all hydrogens from the structure.
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minTerminatingFrags
(nanosheet_obj)¶ Minimize terminating fragments. Do this by hijacking the HoneycombLattice instance and overwriting some attributes.
Parameters: nanosheet_obj (sheet.HoneycombLattice) – contains information shared between this instance and the nanotube instance
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handleProps
(chorus_properties)¶ Handle the structure properties of the tube.
Parameters: chorus_properties (list) – contains the nine chorus properties, i.e. ax, ay, az, bx, …, cz
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printProps
(logger=None)¶ Print the properties of this nanotube.
Parameters: logger (logging.getLogger) – output logger
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getChorusPBC
()¶ Return the chorus box PBC.
Return type: list Returns: contains the nine chorus properties, i.e. ax, ay, az, bx, …, cz
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translateTube
()¶ Translate the tube so that it is inside the box.
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buildTube
(use_finite_bos=True, logger=None)¶ Build a tube.
Parameters: - use_finite_bos (bool) – use a bond order protocol meant for finite molecules
- logger (logging.getLogger) – output logger
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class
schrodinger.application.matsci.nano.tube.
MultiWalledNanoTube
(innertube, nwalls, wallsep)¶ Bases:
object
Build a multi-walled nanotube by assembling specific NanoTubes.
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NWALLS
= 'i_matsci_N_Walls'¶
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WALLSEP
= 'r_matsci_Wall_Sep./Ang.'¶
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MSGWIDTH
= 50¶
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__init__
(innertube, nwalls, wallsep)¶ Create an instance.
Parameters: - innertube (NanoTube) – tube object of inner most tube
- nwalls (int) – number of walls in the multi-walled tube
- wallsep (float) – wall separation in Angstrom for the multi-walled tube.
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getOuterChiralIndicies
(wallindex, logger=None)¶ Get the chiral indicies for this outer tube.
Parameters: - wallindex (int) – index of this outer tube
- logger (logging.getLogger) – output logger
Return type: int, int
Return type: nindex, mindex, chiral indicies for outer tube
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getOuterTubeVectors
(nindex, mindex)¶ Return the tube vectors for the given (n, m).
Parameters: - nindex (int) – first chiral index
- mindex (int) – second chiral index
Return type: numpy.array, numpy.array
Returns: chiral, translat, the tube vectors
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findLargestTranslat
()¶ Return the length of the wall with the longest translation vector.
Return type: float Returns: tmax, length of longest vector in Angstrom
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getNumUnitCells
(translat)¶ Return the number of unit cells to use for the given wall.
Parameters: translat (numpy.array) – translation vector of the given wall Return type: int Returns: ncells, the number of cells to use for the given wall
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alignCenterCollect
()¶ Align and center the tubes and collect tubes into a single structure.
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getTubeSpacings
()¶ Determine actual tube spacings in units of Ang.
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handleProps
()¶ Handle the structure properties of the multi-walled tube.
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printProps
(logger=None)¶ Print the properties of this multi-walled nanotube.
Parameters: logger (logging.getLogger) – output logger
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buildMultiWallTube
(use_finite_bos=True, logger=None)¶ Assemble the multi-walled tube.
Parameters: - use_finite_bos (bool) – use a bond order protocol meant for finite molecules
- logger (logging.getLogger) – output logger
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class
schrodinger.application.matsci.nano.tube.
NanoTubes
(element1='C', element2='C', bondlength=1.418, no_double_bonds=False, nindex=6, mindex=6, ncells=1, termfrag='hydrogen', min_term_frags=False, up_to_nindex=False, up_to_mindex=False, nwalls=1, wallsep=3.35, orient=False, logger=None)¶ Bases:
object
Main class for making nanotubes.
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MSGWIDTH
= 50¶
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__init__
(element1='C', element2='C', bondlength=1.418, no_double_bonds=False, nindex=6, mindex=6, ncells=1, termfrag='hydrogen', min_term_frags=False, up_to_nindex=False, up_to_mindex=False, nwalls=1, wallsep=3.35, orient=False, logger=None)¶ Parameters: - element1 (str) – elemental symbol of the first atom
- element2 (str) – elemental symbol of the second atom
- bondlength (float) – bond length between the first and second atoms in Angstrom
- no_double_bonds (bool) – disable the formation of double bonds
- nindex (int) – first chiral index
- mindex (int) – second chiral index
- ncells (int) – number of unit cells
- termfrag (str) – terminate the lattice with a given fragment
- min_term_frags (bool) – minimize the geometry of terminating fragments
- up_to_nindex (bool) – enumerate nanotube structures on the n-index
- up_to_mindex (bool) – enumerate nanotube structures on the m-index
- nwalls (int) – number of walls in a multi-wall nanotube
- wallsep (float) – wall separation in Angstrom in a multi-wall nanotube
- orient (bool) – whether to orient the sheets for Maestro
- logger (logging.getLogger) – output logger
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printJobParams
(logger=None)¶ Print job parameters.
Parameters: logger (logging.getLogger) – output logger
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makeSingleWalledTubes
(use_finite_bos=True, logger=None)¶ Make single-walled nanotubes.
Parameters: - use_finite_bos (bool) – use a bond order protocol meant for finite molecules
- logger (logging.getLogger) – output logger
Return type: list of NanoTube
Returns: singletubes, contains all created single-walled tubes
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printSingleWalledTubes
(logger=None)¶ Formatted print of single-walled tubes.
Parameters: logger (logging.getLogger) – output logger
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makeMultiWalledTubes
(use_finite_bos=True, logger=None)¶ Make multi-walled nanotubes.
Parameters: - use_finite_bos (bool) – use a bond order protocol meant for finite molecules
- logger (logging.getLogger) – output logger
Return type: list of MultiWalledNanoTube
Returns: multitubes, contains all created multi-walled tubes
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printMultiWalledTubes
(logger=None)¶ Formatted print of multi-walled tubes.
Parameters: logger (logging.getLogger) – output logger
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schrodinger.application.matsci.nano.tube.
remove_pbc
(astructure)¶ Remove the PBC definitions from the given structure.
Parameters: astructure (schrodinger.structure.Structure) – the structure for which to remove the PBC