schrodinger.pipeline.input module¶

Classes for writing Pipeline input files.

class schrodinger.pipeline.input.Writer(filename=None, comment=None)¶

Bases: object

Class for writing pipeline input files.

__init__(filename=None, comment=None)¶: Initialize self. See help(type(self)) for accurate signature.

write(filename=None)¶: Serialize the job parameters to a file.

addVar(vname, vclass, data, comment=None)¶

Add a variable of name vname and class vclass. For vclass of “PhaseDB” and “Grid”, data should be a single path; for vclass of “Structures”, data should be a list of files.

The argument comment is ignored.

userOutput(varname)¶: Append output parameter descriptors to self.userouts.

setStructureOutput(varname)¶: Set structure output to varname (overwriting the previous one, if any). The structures from this variable will be imported into Maestro when incorporating.

addStage(sname, sclass, inputs, outputs, keywords=None, comment=None)¶

Add a stage.

The comment argument is ignored.

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.pipeline.input', '__doc__': '\n Class for writing pipeline input files.\n\n ', '__init__': <function Writer.__init__>, 'write': <function Writer.write>, 'addVar': <function Writer.addVar>, 'userOutput': <function Writer.userOutput>, 'setStructureOutput': <function Writer.setStructureOutput>, 'addStage': <function Writer.addStage>, '__dict__': <attribute '__dict__' of 'Writer' objects>, '__weakref__': <attribute '__weakref__' of 'Writer' 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.pipeline.input'¶

__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.pipeline.input.LinearWriter(filename, comment=None)¶

Bases: schrodinger.pipeline.input.Writer

Class for writing linear stage maps (ones with no branches).

__init__(filename, comment=None)¶: Initialize self. See help(type(self)) for accurate signature.

addVar(vname, vclass, files, comment=None)¶

addStage(sname, sclass, output, keywords=None, comment=None)¶

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.pipeline.input', '__doc__': '\n Class for writing linear stage maps (ones with no branches).\n\n ', '__init__': <function LinearWriter.__init__>, 'addVar': <function LinearWriter.addVar>, 'addStage': <function LinearWriter.addStage>})¶

__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).