schrodinger.application.matsci.rxn_path module

Classes and functions for generating reaction paths.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.rxn_path.ParserWrapper(scriptname, description)

Bases: object

Manages the argparse module to parse user command line arguments.

JOB_NAME = 'rxnpath'
REACTANT = 'reactant'
PRODUCT = 'product'
TS = 'ts'
REACTANT_LIKE = 'reactant_like'
MIDWAY = 'midway'
PRODUCT_LIKE = 'product_like'
PRESUMED_TS = 'midway'
PRESUMED_TS_CHOICES = ['reactant_like', 'midway', 'product_like']
DENSEAROUND = False
SAMPLE_DEFAULT = [10.0]
SUPPORTEDINEXTS = ['.mae', '.mae.gz', '.maegz']
FVAL_KEYS = ['reactant', 'reactant_like', 'midway', 'product_like', 'product']
FVAL_VALUES = [0.0, 0.25, 0.5, 0.75, 1.0]
FVAL_DICT = {'midway': 0.5, 'product': 1.0, 'product_like': 0.75, 'reactant': 0.0, 'reactant_like': 0.25}
NUMDENSEPOINTS = 10
STEPDENSEPOINTS = 0.02
BONDWEIGHT = 1000.0
ANGLEWEIGHT = 1000.0
DIHEDRALWEIGHT = 1000.0
CARTESIANWEIGHT = 1000.0
PENALTYWEIGHT = 1.0
MIXPREVIOUS = 0.5
MIXPREVIOUSMIN = 0.0
MIXPREVIOUSMAX = 1.0
CARTESIAN = 'cartesian'
DISTANCE = 'distance'
INTERNAL = 'internal'
INTERPOLATIONCHOICES = ['internal', 'distance', 'cartesian']
BEFORESUPERPOSITION = 'beforesuperposition'
AFTERSUPERPOSITION = 'aftersuperposition'
GUESSCHOICES = ['beforesuperposition', 'aftersuperposition']
CONNECTIVITYCHOICES = ['reactant', 'ts', 'product']
NORXNCOMPLEX = False
VDWSCALE = 1.0
REORDER = False
REVERSE_INTERPOLATION = False
__init__(scriptname, description)

Create a ParserWrapper object 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__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.rxn_path', '__doc__': '\n Manages the argparse module to parse user command line arguments.\n ', 'JOB_NAME': 'rxnpath', 'REACTANT': 'reactant', 'PRODUCT': 'product', 'TS': 'ts', 'REACTANT_LIKE': 'reactant_like', 'MIDWAY': 'midway', 'PRODUCT_LIKE': 'product_like', 'PRESUMED_TS': 'midway', 'PRESUMED_TS_CHOICES': ['reactant_like', 'midway', 'product_like'], 'DENSEAROUND': False, 'SAMPLE_DEFAULT': [10.0], 'SUPPORTEDINEXTS': ['.mae', '.mae.gz', '.maegz'], 'FVAL_KEYS': ['reactant', 'reactant_like', 'midway', 'product_like', 'product'], 'FVAL_VALUES': [0.0, 0.25, 0.5, 0.75, 1.0], 'FVAL_DICT': OrderedDict([('reactant', 0.0), ('reactant_like', 0.25), ('midway', 0.5), ('product_like', 0.75), ('product', 1.0)]), 'NUMDENSEPOINTS': 10, 'STEPDENSEPOINTS': 0.02, 'BONDWEIGHT': 1000.0, 'ANGLEWEIGHT': 1000.0, 'DIHEDRALWEIGHT': 1000.0, 'CARTESIANWEIGHT': 1000.0, 'PENALTYWEIGHT': 1.0, 'MIXPREVIOUS': 0.5, 'MIXPREVIOUSMIN': 0.0, 'MIXPREVIOUSMAX': 1.0, 'CARTESIAN': 'cartesian', 'DISTANCE': 'distance', 'INTERNAL': 'internal', 'INTERPOLATIONCHOICES': ['internal', 'distance', 'cartesian'], 'BEFORESUPERPOSITION': 'beforesuperposition', 'AFTERSUPERPOSITION': 'aftersuperposition', 'GUESSCHOICES': ['beforesuperposition', 'aftersuperposition'], 'CONNECTIVITYCHOICES': ['reactant', 'ts', 'product'], 'NORXNCOMPLEX': False, 'VDWSCALE': 1.0, 'REORDER': False, 'REVERSE_INTERPOLATION': False, '__init__': <function ParserWrapper.__init__>, 'loadIt': <function ParserWrapper.loadIt>, 'parseArgs': <function ParserWrapper.parseArgs>, '__dict__': <attribute '__dict__' of 'ParserWrapper' objects>, '__weakref__': <attribute '__weakref__' of 'ParserWrapper' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.rxn_path'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.matsci.rxn_path.CheckInput

Bases: object

Check user input.

PAIRS = [('[]', ''), ('][', '-'), ('[', ''), (']', ''), (';', ''), (' ', '_')]
COMBIGLD_REPLACEMENTS = {' ': '_', ';': '', '[': '', '[]': '', ']': '', '][': '-'}
TITLEKEY = 's_m_title'
ENTRYNAMEKEY = 's_m_entry_name'
checkJobName(job_name, logger=None)

Check job_name option.

Parameters:
  • job_name (str) – name of job
  • logger (logging.getLogger) – output logger
Return type:

str
Returns:

job_name, name of job
checkInputFiles(inputfiles, logger)

Check input files.

Parameters:
  • inputfiles (list of str) – all provided input files
  • logger (logging.getLogger) – output logger
checkStructures(logger=None, *allstructures)

Check structures.

Parameters:
  • logger (logging.getLogger) – output logger
  • allstructures (tuple of schrodinger.structure.Structure) – all provided structures
Return type:

list of schrodinger.structure.Structure
Returns:

structures, updated list of structures
checkStructurePairs(reorder, logger=None, *allstructures)

Check reactant and product pairs of structures.

Parameters:
  • reorder (boolean) – normalize the atomic ordering
  • logger (logging.getLogger) – output logger
  • allstructures (tuple of schrodinger.structure.Structure) – all provided structure
Return type:

list of schrodinger.structure.Structure
Returns:

structures, updated list of structures
checkSample(sample, logger=None)

Check sample option.

Parameters:
  • sample (list of float) – sample points
  • logger (logging.getLogger) – output logger
Return type:

list of floats
Returns:

sample, sample points
checkPresumedTs(presumed_ts, logger=None)

Check the location of the presumed ts.

Parameters:
  • presumed_ts (str) – gives the location of the presumed ts
  • logger (logging.getLogger) – output logger
Return type:

str
Returns:

presumed_ts, the location of the presumed ts
checkInterpolation(interpolation, logger=None)

Check interpolation option.

Parameters:
  • interpolation (str) – coordinate system used for interpolating
  • logger (logging.getLogger) – output logger
Return type:

str
Returns:

interpolation, coordinate system used for interpolating
checkMixPrevious(mixprevious, logger=None)

Check mixprevious option.

Parameters:
  • mixprevious (float) – mixing weight of solution from previous path point
  • logger (logging.getLogger) – output logger
Return type:

float
Returns:

mixprevious, mixing weight of solution from previous path point
checkGuess(guess, logger=None)

Check guess option.

Parameters:
  • guess (str) – type of guess solution
  • logger (logging.getLogger) – output logger
Return type:

str
Returns:

guess, type of guess solution
checkConnectivity(connectivity, logger=None)

Check connectivity option.

Parameters:
  • connectivity (str) – type of connectivity
  • logger (logging.getLogger) – output logger
Return type:

str
Returns:

connectivity, type of connectivity
checkNoRxnComplex(norxncomplex, vdwscale, logger=None)

Check norxncomplex and vdwscale options.

Parameters:
  • norxncomplex (boolean) – disable preprocessing into a reaction complex
  • vdwscale (float) – scales the intermolecular distance
  • logger (logging.getLogger) – output logger
Return type:

boolean, float
Returns:

norxncomplex, vdwscale, disable preprocessing into a reaction complex and scales the intermolecular distance
checkReorder(reorder, logger=None)

Check reorder option.

Parameters:
  • reorder (boolean) – normalize the atomic ordering
  • logger (logging.getLogger) – output logger
Return type:

boolean
Returns:

reorder, normalize the atomic ordering
checkReverseInterpolation(reverse_interpolation, logger=None)

Check reverse interpolation option.

Parameters:
  • reverse_interpolation (boolean) – interpolate the reaction path in reverse
  • logger (logging.getLogger) – output logger
Return type:

boolean
Returns:

reverse_interpolation, interpolate the reaction path in reverse
checkWeights(bondweight, angleweight, dihedralweight, cartesianweight, penaltyweight, logger=None)

Check weights, i.e. bondweight, angleweight, dihedralweight, cartesianweight, and penaltyweight.

Parameters:
  • bondweight (float) – weight of the bond term
  • angleweight (float) – weight of the angle term
  • dihedralweight (float) – weight of the dihedral term
  • cartesianweight (float) – weight of the Cartesian term
  • penaltyweight (float) – weight of the bond penalty term
  • logger (logging.getLogger) – output logger

:rtype float, float, float, float, float :return: bondweight, angleweight, dihedralweight, cartesianweight,

penaltyweight, weights of the bond, angle, dihedral, Cartesian, and penalty terms
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.rxn_path', '__doc__': '\n Check user input.\n ', 'PAIRS': [('[]', ''), ('][', '-'), ('[', ''), (']', ''), (';', ''), (' ', '_')], 'COMBIGLD_REPLACEMENTS': OrderedDict([('[]', ''), ('][', '-'), ('[', ''), (']', ''), (';', ''), (' ', '_')]), 'TITLEKEY': 's_m_title', 'ENTRYNAMEKEY': 's_m_entry_name', 'checkJobName': <function CheckInput.checkJobName>, 'checkInputFiles': <function CheckInput.checkInputFiles>, 'checkStructures': <function CheckInput.checkStructures>, 'checkStructurePairs': <function CheckInput.checkStructurePairs>, 'checkSample': <function CheckInput.checkSample>, 'checkPresumedTs': <function CheckInput.checkPresumedTs>, 'checkInterpolation': <function CheckInput.checkInterpolation>, 'checkMixPrevious': <function CheckInput.checkMixPrevious>, 'checkGuess': <function CheckInput.checkGuess>, 'checkConnectivity': <function CheckInput.checkConnectivity>, 'checkNoRxnComplex': <function CheckInput.checkNoRxnComplex>, 'checkReorder': <function CheckInput.checkReorder>, 'checkReverseInterpolation': <function CheckInput.checkReverseInterpolation>, 'checkWeights': <function CheckInput.checkWeights>, '__dict__': <attribute '__dict__' of 'CheckInput' objects>, '__weakref__': <attribute '__weakref__' of 'CheckInput' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.rxn_path'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.matsci.rxn_path.Coord(indicies, names, value)

Bases: object

Manage the properties of an internal coordinate.

BOND = 'bond'
ANGLE = 'angle'
DIHEDRAL = 'dihedral'
__init__(indicies, names, value)

Create a Coord instance.

Parameters:
  • indiciees – atomic indicies
  • names (list of str) – atomic names
  • value (list of float) – value(s) of the internal coordinate in units of Angstrom or degree
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.rxn_path', '__doc__': '\n Manage the properties of an internal coordinate.\n ', 'BOND': 'bond', 'ANGLE': 'angle', 'DIHEDRAL': 'dihedral', '__init__': <function Coord.__init__>, '__dict__': <attribute '__dict__' of 'Coord' objects>, '__weakref__': <attribute '__weakref__' of 'Coord' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.rxn_path'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.matsci.rxn_path.InternalCoords

Bases: object

Manage the internal coordinates of a structure.

ZMATNUMBER = 1
__init__()

Create an InternalCoords instance.

getZmatrix(astructure)

Get the Z-matrix for the structure.

Parameters:astructure (schrodinger.structure.Structure) – the structure
getDmatrix(astructure)

Get the distance matrix for the structure.

Parameters:astructure (schrodinger.structure.Structure) – the structure
printInternals(headermsg, maxindexwidth, logger)

Formatted print of header followed by the internal coordinates.

Parameters:
  • headermsg (str) – header
  • maxindexwidth (int) – number of characters in the largest atom index
  • logger (logging.getLogger) – output logger
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.rxn_path', '__doc__': '\n Manage the internal coordinates of a structure.\n ', 'ZMATNUMBER': 1, '__init__': <function InternalCoords.__init__>, 'getZmatrix': <function InternalCoords.getZmatrix>, 'getDmatrix': <function InternalCoords.getDmatrix>, 'printInternals': <function InternalCoords.printInternals>, '__dict__': <attribute '__dict__' of 'InternalCoords' objects>, '__weakref__': <attribute '__weakref__' of 'InternalCoords' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.rxn_path'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

schrodinger.application.matsci.rxn_path.max_pair_vdw_distance(astructure)

Find the largest atom-atom VDW distance in a structure.

Parameters:astructure (schrodinger.structure.Structure) – the structure
Return type:int, int, float
Returns:atom1, atom2, maxdistance, atom1 and atom2 are the first and second atom indicies and maxdistance is the largest distance. If input structure is a single atom then just return that atom index twice followed by twice its VDW radius, i.e. the atomic diameter.
schrodinger.application.matsci.rxn_path.add_temp_hydrogen(astructure, index)

To the given structure add a temporary hydrogen to the atom with the given index. This function is more robust than structutils.build.add_hydrogens.

Parameters:
  • astructure (schrodinger.structure.Structure) – the structure containing the atom to which a hydrogen will be added
  • index (int) – the index of the atom to which to add the hydrogen
Return type:

int
Returns:

the index of the added temporary hydrogen
class schrodinger.application.matsci.rxn_path.ReactionCoords

Bases: object

Manage reaction coordinates.

REACTIONBONDTHRESH = 0.05
REACTIONANGLETHRESH = 1.0
REACTIONDIHEDRALTHRESH = 1.0
REVOLUTION = 360
HALFREVOLUTION = 180
REVOLUTIONTHRESH = 10
REACTANTPREFIX = 'pre-'
PRODUCTPREFIX = 'post-'
__init__()

Create a ReactionCoords instance.

getNormalOrdering(reactant, product, logger=None)

Attempt to normalize the atomic ordering between reactants and products.

Parameters:
Return type:

schrodinger.structure.Structure, schrodinger.structure.Structure
Returns:

newreactant, newproduct, if defined specifies the reordered reactant and product structures
makeRxnComplex(reactant, product, vdwscale, logger=None)

For certain bimolecular reactions preprocess reactants and products into reaction complexes.

Parameters:
Return type:

schrodinger.structure.Structure, schrodinger.structure.Structure
Returns:

newreactant, newproduct, if defined specifies the reactant and product structures in the created reaction complex
collectInternals(reactant, product, rinternals, pinternals, logger=None)

Find the redundant internal coordinates by merging the coordinates defined in the reactant and product.

Parameters:
getReactionInternals(rinternals, pinternals, reactioninternals)

Determine the reactive redundant internal coordinates.

Parameters:
runSuperposition(reactant, product, reactioninternals, logger=None)

Superpose the product structure on to the reactant structure using the non-reactive atoms, i.e. those that do not define any reactive redundant internal coordinate.

Parameters:
Return type:

list of ints, float
Returns:

tosuperpose, armsd, atom indicies used to superpose and the final RMSD
getCartesianCoords(astructure)

Get the Cartesian coordinates of a structure as a 3N dimensional list of floats.

Parameters:astructure (schrodinger.structure.Structure) – structure
Return type:list of float
Returns:cartesians, the 3N Cartesian coordinates ordered like [x1, y1, z1, x2, …, zN]
prepare(reactant, product, interpolation, norxncomplex, vdwscale, samplepoints, logger=None)

Prepare reaction coordinates.

Parameters:
  • reactant (schrodinger.structure.Structure) – reactant
  • product (schrodinger.structure.Structure) – product
  • interpolation (str) – coordinate system used for interpolating
  • norxncomplex (boolean) – disable preprocessing into a reaction complex
  • vdwscale (float) – scales the intermolecular distance
  • samplepoints (list of float) – reaction path sample points
  • logger (logging.getLogger) – output logger
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.rxn_path', '__doc__': '\n Manage reaction coordinates.\n ', 'REACTIONBONDTHRESH': 0.05, 'REACTIONANGLETHRESH': 1.0, 'REACTIONDIHEDRALTHRESH': 1.0, 'REVOLUTION': 360, 'HALFREVOLUTION': 180, 'REVOLUTIONTHRESH': 10, 'REACTANTPREFIX': 'pre-', 'PRODUCTPREFIX': 'post-', '__init__': <function ReactionCoords.__init__>, 'getNormalOrdering': <function ReactionCoords.getNormalOrdering>, 'makeRxnComplex': <function ReactionCoords.makeRxnComplex>, 'collectInternals': <function ReactionCoords.collectInternals>, 'getReactionInternals': <function ReactionCoords.getReactionInternals>, 'runSuperposition': <function ReactionCoords.runSuperposition>, 'getCartesianCoords': <function ReactionCoords.getCartesianCoords>, 'prepare': <function ReactionCoords.prepare>, '__dict__': <attribute '__dict__' of 'ReactionCoords' objects>, '__weakref__': <attribute '__weakref__' of 'ReactionCoords' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.rxn_path'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.matsci.rxn_path.Point(index, fval, name, astructure, internals, cartesians)

Bases: object

Collect properties of reaction path points.

__init__(index, fval, name, astructure, internals, cartesians)

Create a Point instance.

Parameters:
  • index (int) – path point index
  • fval (float) – path point value
  • name (str) – path point name
  • astructure (schrodinger.structure.Structure) – structure
  • internals (InternalCoords) – path point internal coordinates
  • cartesians (list of float) – the 3N Cartesian coordinates ordered like [x1, y1, z1, x2, …, zN]
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.rxn_path', '__doc__': '\n Collect properties of reaction path points.\n ', '__init__': <function Point.__init__>, '__dict__': <attribute '__dict__' of 'Point' objects>, '__weakref__': <attribute '__weakref__' of 'Point' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.rxn_path'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.matsci.rxn_path.ReactionPath

Bases: object

Generate reaction path.

FVALINCREMENT = 0.001
NORMTHRESH = 1e-12
BONDPENALTYTHRESH = 1000000000.0
DIFFLOWTHRESH = 10.0
DIFFHIGHVAL = 1000000000.0
RXNINDEX = 'i_matsci_RXN_Index'
RXNCOORD = 'r_matsci_RXN_Coord'
REACTIVEATOM = 'b_matsci_Reactive_Atom'
__init__()

Create a ReactionPath instance.

getSamplePoints(sample, densearound, presumed_ts)

Determine the final set of sampling points.

Parameters:
  • sample (list of float) – points to be interpolated
  • densearound (bool) – include additional sampling points at specific regions
  • presumed_ts (str) – location of presumed ts
Return type:

list of floats
Returns:

samplepoints, the list of points to be sampled.
getReactiveAtoms(reactant, product)

Determine the reactive atoms, i.e. those which have changed Cartesian positions in the superposed reactant/product pair.

Parameters:
Return type:

list of int
Returns:

reactiveatoms, reactive atoms
interpolateReactionCoords(pointindex, fval, connectivity, rpoint, ppoint, reactiveatoms, logger=None)

Interpolate reaction coordinates between the reactant and product for this sample point.

Parameters:
  • pointindex (int) – sample point index
  • fval (float) – interpolated reaction path point
  • connectivity (str) – specifies the type of connectivity
  • rpoint (Point) – reactant information
  • ppoint (Point) – product information
  • reactiveatoms (list of ints) – reactive atoms
  • logger (logging.getLogger) – output logger
Return type:

Point
Returns:

ipoint, interpolated point information
getInitialGuess(cartesians, reactiveatoms)

Obtain the initial guess Cartesians for the non-linear least squares solver. The guess is the interpolated Cartesian coordinates for the reactive atoms.

Parameters:
  • cartesians (list of floats) – all interpolated Cartesian coordinates
  • reactiveatoms (list of ints) – atom indicies of reactive atoms
Return type:

list of floats
Returns:

guessparams, interpolated Cartesian coordinates of the reactive atoms
doNonLinearFit(ipoint, guessparams, reactiveatoms, mixprevious, logger=None)

Using the interpolated redundant internal coordinates and interpolated Cartesian coordinates obtain the final set of Cartesian coordinates for this reaction path point by minimizing a sum-of-squares error function using non-linear least sqaures, i.e.

error = sum_{bonds} bondweight*(r(a,b) - r^{i}(a,b))**2
  • sum_{angles} angleweight*(theta(a,b,c) - theta^{i}(a,b,c))**2
  • sum_{dihedrals} dihedralweight*(tau(a,b,c,d) - tau^{i}(a,b,c,d))**2
  • sum_{atoms} cartweight*[(x(a) - x^{i}(a))**2 + (y(a) - y^{i}(a))**2
  • (z(a) - z^{i}(a))**2]

where those variables marked with “^{i}” are the interpolated quantities and where

r(a,b) = r(x(a), y(a), z(a), x(b), y(b), z(b)) = norm(vec(a,b)) theta(a,b,c) = arccos[(vec(a,b) dot vec(c,b))/(norm(vec(a,b))*norm(vec(c,b)))] tau(a,b,c,d) = arccos[((vec(c,b) cross vec(a,b)) dot (vec(d,c) cross vec(b,c)))

/ (norm((vec(c,b) cross vec(a,b)))*norm((vec(d,c) cross vec(b,c))))]

The 3N Cartesian coordinates, x(a), y(a), z(a), x(b), …, z(N), are choosen so as to minimize the error.

Parameters:
  • ipoint (Point) – interpolated point information
  • guessparams (list of floats) – initial parameters, i.e. Cartesian coordinates of the reactive atoms
  • reactiveatoms (list of ints) – atomic indicies of reactive atoms
  • mixprevious (float) – specifies to what extent the optimized Cartesian coordinates from the previous reaction path point are mixed with the coordinates determined by interpolation at the current point.
  • logger (logging.getLogger) – output logger
Return type:

list
Returns:

optcartesians, non-linear-optimized Cartesian coordinates for this sample point.
getInterpolatedStructure(ipoint, optcartesians, reactiveatoms, tosuperpose, fval, connectivity, presumed_ts, rpoint, ppoint)

Build the schrodinger.structure.Structure object from the optimized Cartesian coordinates for the interpolated structure at this sample point and update the internal and Cartesian coordinates in the Point object.

Parameters:
  • ipoint (Point) – interpolated point information
  • optcartesians (list of floats) – optimized Cartesian coordinates for the reactive atoms
  • reactiveatoms (list of ints) – atom indicies of reactive atoms.
  • tosuperpose (list of ints) – contains the atom indicies of the atoms used in the superposition.
  • fval (float) – The interpolated reaction path point.
  • connectivity (str) – specifies the type of connectivity
  • presumed_ts (str) – specifies the location of the presumed ts
  • rpoint (Point) – reactant information
  • ppoint (Point) – product information
Return type:

list of floats, InternalCoords object
Returns:

optcartesianssuperposed, reactiveinternals, the optimized Cartesian coordinates for the reactive atoms after superposition on to the reactant structure and an object containing the interpolated and calculated reactive internal coordinates.
runIt(reactant, product, job_name='rxnpath', sample=[10.0], presumed_ts='midway', densearound=False, bondweight=1000.0, angleweight=1000.0, dihedralweight=1000.0, cartesianweight=1000.0, penaltyweight=1.0, interpolation='cartesian', mixprevious=0.5, guess='beforesuperposition', connectivity='ts', norxncomplex=False, vdwscale=1.0, reorder=False, reverse_interpolation=False, logger=None)

Function to orchestrate calculation of the reaction path.

Parameters:
  • reactant (schrodinger.structure.Structure) – reactant
  • product (schrodinger.structure.Structure) – product
  • job_name (str) – name of job
  • sample (list of floats) – contains either the list of sample points or the number of points to sample as a “decimal-less” float.
  • presumed_ts (str) – gives the location of the presumed ts.
  • densearound (bool) – Specifies if additional sampling points should be included in the interpolation.
  • bondweight (float) – Specifies the weight of the bonding term in the objective function which is minimized using non-linear least squares.
  • angleweight (float) – Specifies the weight of the angle term in the objective function which is minimized using non-linear least squares.
  • dihedralweight (float) – Specifies the weight of the dihedral term in the objective function which is minimized using non-linear least squares.
  • cartesianweight (float) – Specifies the weight of the Cartesian term in the objective function which is minimized using non-linear least squares.
  • penaltyweight (float) – Specifies the weight of the bond penalty term in the objective function which is minimized using non-linear least squares.
  • interpolation (str) – specifies the coordinate system in which the reaction path points are interpolated.
  • mixprevious (float) – specifies to what extent the optimized Cartesian coordinates from the previous reaction path point are mixed with the coordinates determined by interpolation at the current point.
  • guess (str) – specifies the type of solution guess generated from the optimized Cartesian coordinates of the previous reaction path point.
  • connectivity (str) – specifies the type of connectivity to use in defining the structure objects of points along the reaction path.
  • norxncomplex (boolean) – Disables the preprocessing of reactants and products into reaction complexes for certain bimolecular reactions.
  • vdwscale (float) – Scales the inter-molecular VDW distance used to separate reactant or product structures when forming reaction complexes for certain bimolecular reactions.
  • reorder (boolean) – Specifies to run the protocol to normalize the atom ordering in the reactants and products.
  • reverse_interpolation (boolean) – interpolate the reaction in reverse
  • logger (a logging.getLogger object) – The output logger for this script.
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.rxn_path', '__doc__': '\n Generate reaction path.\n ', 'FVALINCREMENT': 0.001, 'NORMTHRESH': 1e-12, 'BONDPENALTYTHRESH': 1000000000.0, 'DIFFLOWTHRESH': 10.0, 'DIFFHIGHVAL': 1000000000.0, 'RXNINDEX': 'i_matsci_RXN_Index', 'RXNCOORD': 'r_matsci_RXN_Coord', 'REACTIVEATOM': 'b_matsci_Reactive_Atom', '__init__': <function ReactionPath.__init__>, 'getSamplePoints': <function ReactionPath.getSamplePoints>, 'getReactiveAtoms': <function ReactionPath.getReactiveAtoms>, 'interpolateReactionCoords': <function ReactionPath.interpolateReactionCoords>, 'getInitialGuess': <function ReactionPath.getInitialGuess>, 'doNonLinearFit': <function ReactionPath.doNonLinearFit>, 'getInterpolatedStructure': <function ReactionPath.getInterpolatedStructure>, 'runIt': <function ReactionPath.runIt>, '__dict__': <attribute '__dict__' of 'ReactionPath' objects>, '__weakref__': <attribute '__weakref__' of 'ReactionPath' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.rxn_path'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)