schrodinger.application.jaguar.scan module

Support functions and classes for Jaguar scans.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.jaguar.scan.Scan(var_name, initial=None, final=None, steps=None, step_size=None, at_values=None)

Bases: object

A class for storing information about geometry scan variables.

precision = 0.001

__init__(var_name, initial=None, final=None, steps=None, step_size=None, at_values=None)

This constructor can be used for two different types of scans - regular and irregular. For regular scans, the ‘initial’ argument must be specified along with two out of the three arguments ‘final,’ ‘steps,’ or ‘step_size.’ For irregular scans, the only argument that should be specified is ‘at_values.’

Attributes

var_name (str)

The name of the variable the scan is based on.

initial (float)

The starting point for a scan.

final (float)

The final point for a scan.

steps (float)

The number of steps in the scan

step_size (float)

The step size of a regular scan.

at_values (sequence of floats)

Specific values at which a

final

final scan value

initial

initial scan value

steps

number of steps in the scan

step_size

step size (None for ‘at values’ scans)

at_values

an array of the scan values for ‘at values’ scans

__eq__(other)

Equality comparison only looks at numeric quantities, not the variable name.

__ne__(other)

Return self!=value.

static parse(zvarstring)

Parse a scan definition string and return a Scan object.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.jaguar.scan', '__doc__': '\n A class for storing information about geometry scan variables.\n\n ', 'precision': 0.001, '__init__': <function Scan.__init__>, '_getFinal': <function Scan._getFinal>, 'final': <property object>, '_getInitial': <function Scan._getInitial>, 'initial': <property object>, '_getSteps': <function Scan._getSteps>, 'steps': <property object>, '_getStepSize': <function Scan._getStepSize>, 'step_size': <property object>, '_getAtValues': <function Scan._getAtValues>, 'at_values': <property object>, '__eq__': <function Scan.__eq__>, '__ne__': <function Scan.__ne__>, 'parse': <staticmethod object>, '__dict__': <attribute '__dict__' of 'Scan' objects>, '__weakref__': <attribute '__weakref__' of 'Scan' objects>, '__hash__': None})

__dir__() → list

default dir() implementation

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__ = None

__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.jaguar.scan'

__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)