schrodinger.application.matsci.freevolume module

Analyzes free volume in a structure

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.freevolume.GridRadius(grid, radius)

Bases: tuple

__add__

Return self+value.

__class__

alias of builtins.type

__contains__

Return key in self.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__

Return self[key].

__getnewargs__()

Return self as a plain tuple. Used by copy and pickle.

__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.

__iter__

Implement iter(self).

__le__

Return self<=value.

__len__

Return len(self).

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.freevolume'
__mul__

Return self*value.n

__ne__

Return self!=value.

static __new__(_cls, grid, radius)

Create new instance of GridRadius(grid, radius)

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__()

Return a nicely formatted representation string

__rmul__

Return self*value.

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ()
__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).

count(value) → integer -- return number of occurrences of value
grid

Alias for field number 0

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

radius

Alias for field number 1

exception schrodinger.application.matsci.freevolume.FatalCoordinateError

Bases: Exception

Raised if something is wrong with matching the current coordinates to the ones used to compute free volume. Typically and atom number or element mismatch

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.freevolume', '__doc__': '\n Raised if something is wrong with matching the current coordinates to the\n ones used to compute free volume. Typically and atom number or element\n mismatch\n ', '__weakref__': <attribute '__weakref__' of 'FatalCoordinateError' 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.freevolume'
__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).

__setstate__()
__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).

__suppress_context__
__traceback__
__weakref__

list of weak references to the object (if defined)

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.application.matsci.freevolume.get_free_volume_structure(struct)

Get the structure that the free volume calculation was run on

Parameters:struct (schrodinger.structure.Structure) – The structure that contains the properties that point to the free volume structure
Return type:schrodinger.structure.Structure or None
Returns:The structure from the free volume calculation or None if it couldn’t be found (due to missing property or file)
schrodinger.application.matsci.freevolume.check_coordinates_changed(struct)

Check that the given structure matches the structure the free volume calculation was run on. In addition to basic number/type of atoms, the coordinates must also be the same since the void data has XYZ information incorporated in it.

Parameters:struct (schrodinger.structure.Structure) – The structure that contains the properties that point to the free volume structure
Return type:schrodinger.structure.Structure, False, or None
Returns:False if the structures match (number of atoms, elements and XYZ), Structure if the coordinates do not match - in this case the returned structure is a structure with the original free volume coordinates suitable for passing to fix_free_volume_coordinates, None if the free volume structure couldn’t be found (due to missing property or file)
Raises:FatalCoordinateError – If something unfixable does not match between the two structures, such as number of atoms or elements
schrodinger.application.matsci.freevolume.fix_free_volume_coordinates(struct, fv_struct=None)

Change the coordinates of struct to be those from the free volume calculation. Note that this assumes check_coordinates_changed has been called first (and the results dealt with).

The structure is modified in-place

Parameters:

not given, the structure obtained by get_free_volume_structure will be used.

Get atom indexes for atoms that are either crosslinkable, crosslinked or both.

Parameters:struct (schrodinger.structure.Structure) – The structure to look for atoms in.
Return type:set, set, set
Returns:In order, indexes for atoms that are both crosslinked AND crosslinkable, atoms that are crosslinkable, atoms that are crosslinked. The sets are mutually exclusive.
schrodinger.application.matsci.freevolume.get_atom_layers(atom, origin, num_layers, layer_width, axis)

Get the range of layers that the given atom would intersect.

Parameters:
  • atom (schrodinger.structure._StructureAtom) – The atom to find the layers for
  • origin (float) – The offset to add to each layer because the system starts at a point other than zero. The offset is along the axis defined by the axis parameter.
  • num_layers (int) – The number of layers
  • layer_width (float) – The width of each layer
  • axis (int) – 0, 1 or 2 to indicate the layers are cross sections of the X, Y or Z axis
Return type:

list
Returns:

Each item of the list is a layer the atom intersects based on its VdW radius
schrodinger.application.matsci.freevolume.extract_grid_and_radius(word)

Given a string, extract the floating point grid spacing and probe radius values

Parameters:word (str) – The string to extract the grid & radius from
Return type:GridRadius
Returns:The GridRadius namedtuple with the extracted values
schrodinger.application.matsci.freevolume.get_grid_radius_property_values(struct, propbase)

Get all the grid and radius values for properties on the structure that begin with the given base string.

Parameters:
  • struct (schrodinger.structure.Structure) – The structure to extract the properties from
  • propbase (str) – The starting string for properties to search for
Return type:

dict
Returns:

Keys are GridRadius instances, values are the property value for that set of grid/radius values.
schrodinger.application.matsci.freevolume.get_file_data(struct, propbase, file_reader, override_path=None)

Use file_reader to extract the data from the files specified by the given structure properties

Parameters:
  • struct (schrodinger.structure.Structure) – The structure to get data for
  • propbase (str) – The starting string for properties to search for
  • file_reader (callable) – The function that will read the data from the file
  • override_path (str or None) – If given, look for files in this directory rather than the one specified in the structure property
Return type:

(OrderedDict, list)
Returns:

Keys of the dict are GridRadius objects, values are the data extracted from the file for that set of Grid and Radius values. keys are orderd by (radius, grid) sort order. Each item of the list is a str that gives the path of a file that could not be located.
schrodinger.application.matsci.freevolume.read_volume_file(path)

Read the void volume data file located at path

Parameters:path (str) – The path to the file
Return type:list
Returns:The volumes from the file, each item is a float
schrodinger.application.matsci.freevolume.read_void_file(path)

Read the void data file located at path

Parameters:path (str) – The path to the file
Return type:dict
Returns:Keys are INFO and VOIDS. INFO value is a VoidInfo object, VOIDS

value is a list of Void objects sorted from largest to smallest.

schrodinger.application.matsci.freevolume.get_volume_data(struct, path=None)

Get all the volume data available for the given structure

Parameters:
  • struct (schrodigner.structure.Structure) – The structure to get volume data for
  • path (str or None) – If given, look for files in this directory rather than the one specified in the structure property
Return type:

(See read_volume_file function, list)
Returns:

The volume data collected from struct, and a list of paths to files that could not be read
schrodinger.application.matsci.freevolume.get_voids_data(struct, path=None)

Get all the void data available for the given structure

Parameters:
  • struct (schrodigner.structure.Structure) – The structure to get volume data for
  • path (str or None) – If given, look for files in this directory rather than the one specified in the structure property
Return type:

(See read_void_file function, list)
Returns:

The volume data collected from struct, and a list of paths to the files that could not be read.
class schrodinger.application.matsci.freevolume.JsonObject

Bases: object

Base class for custom objects that can be serialized and deserialized by json

jsonData()

Return a json-serializable object for this instance

Return type:dict
Returns:A json-serializable object for this instance
classmethod fromJsonData(data)

Create a new VoidInfo object from json data

Parameters:data (dict) – A dict such as returned by the jsonData method
Return type:class
Returns:A new class object created using the data in dict
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.freevolume', '__doc__': '\n Base class for custom objects that can be serialized and deserialized by\n json\n ', 'jsonData': <function JsonObject.jsonData>, 'fromJsonData': <classmethod object>, '__dict__': <attribute '__dict__' of 'JsonObject' objects>, '__weakref__': <attribute '__weakref__' of 'JsonObject' 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.freevolume'
__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.freevolume.VoidInfo(origin, numxyz, spacing, periodic, probe)

Bases: schrodinger.application.matsci.freevolume.JsonObject

Holds general information about the void calculation

__init__(origin, numxyz, spacing, periodic, probe)

Create a VoidInfo object

Parameters:
  • origin (iterable) – The x, y, z coordinates of the grid origin
  • numxyz (iterable) – The number of gridpoints in the x, y and z direction
  • spacing (iterable) – The spacing of gridpoints in the x, y and z direction
  • periodic (bool) – Whether the grid is periodic
  • probe (float) – The probe radius used in the void calculation
getNodeXYZ(node)

Get the xyz coordinates a node represents

Parameters:node (tuple) – A graph node (a, b, c) for coordinate a, b, c in the grid
Return type:list
Returns:[x, y, z] coordinates of the node
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.freevolume', '__doc__': '\n Holds general information about the void calculation\n ', '__init__': <function VoidInfo.__init__>, 'getNodeXYZ': <function VoidInfo.getNodeXYZ>})
__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.freevolume'
__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)

classmethod fromJsonData(data)

Create a new VoidInfo object from json data

Parameters:data (dict) – A dict such as returned by the jsonData method
Return type:class
Returns:A new class object created using the data in dict
jsonData()

Return a json-serializable object for this instance

Return type:dict
Returns:A json-serializable object for this instance
class schrodinger.application.matsci.freevolume.Void(size=0, volume=0, nodes=None)

Bases: schrodinger.application.matsci.freevolume.JsonObject

Holds information about a single Void

__init__(size=0, volume=0, nodes=None)

Create a Void instance

Parameters:
  • size (int) – The number of nodes in the void
  • volume (float) – The volume the void represents
  • nodes (iterable) – The collection of grid nodes that make up the void
__eq__(other)
__lt__(other)
getSurfaceNodes(vinfo)

Find all the surface nodes in the void

Parameters:vinfo (VoidInfo) – The VoidInfo object used to compute the void
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.freevolume', '__doc__': '\n Holds information about a single Void\n ', '__init__': <function Void.__init__>, '__eq__': <function Void.__eq__>, '__lt__': <function Void.__lt__>, 'getSurfaceNodes': <function Void.getSurfaceNodes>, '__hash__': None, '__gt__': <function _gt_from_lt>, '__le__': <function _le_from_lt>, '__ge__': <function _ge_from_lt>})
__dir__() → list

default dir() implementation

__format__()

default object formatter

__ge__(other, NotImplemented=NotImplemented)

Return a >= b. Computed by @total_ordering from (not a < b).

__getattribute__

Return getattr(self, name).

__gt__(other, NotImplemented=NotImplemented)

Return a > b. Computed by @total_ordering from (not a < b) and (a != b).

__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__(other, NotImplemented=NotImplemented)

Return a <= b. Computed by @total_ordering from (a < b) or (a == b).

__module__ = 'schrodinger.application.matsci.freevolume'
__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)

classmethod fromJsonData(data)

Create a new VoidInfo object from json data

Parameters:data (dict) – A dict such as returned by the jsonData method
Return type:class
Returns:A new class object created using the data in dict
jsonData()

Return a json-serializable object for this instance

Return type:dict
Returns:A json-serializable object for this instance
exception schrodinger.application.matsci.freevolume.FreeVolumeException

Bases: Exception

Raised if something goes wrong with computing the Free Volume

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.freevolume', '__doc__': '\n Raised if something goes wrong with computing the Free Volume\n ', '__weakref__': <attribute '__weakref__' of 'FreeVolumeException' 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.freevolume'
__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).

__setstate__()
__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).

__suppress_context__
__traceback__
__weakref__

list of weak references to the object (if defined)

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.matsci.freevolume.FreeVolumeDriver(grid=0.25, probe=1.4, generic_title='free_volume', logger=None, verbose=True)

Bases: object

Driver to compute Free Volume

__init__(grid=0.25, probe=1.4, generic_title='free_volume', logger=None, verbose=True)

Create a FreeVolumeDriver instance

Parameters:
  • grid (float) – The requested grid spacing
  • probe (float) – The probe radius
  • generic_title (str) – The title to use if a structure does not have one
  • logger (None or logging.logger) – If None, no logging will be done and FreeVolumeException

will be raised if an error occurs. If a logger, logging will be done and the system will exit on an error.

Parameters:verbose (bool) – Turns on additional logging
log(msg, is_verbose=False, **kwargs)

Log a message if logging is being used

Parameters:msg (str) – The message to log

Additonal keyword arguments are passed to textlogger.log_msg

logError(msg, **kwargs)

Log an error message if logging is being used and exit, otherwise raise an Exception.

Parameters:msg (str) – The message to log

Additonal keyword arguments are passed to textlogger.log_error

Raises:
findFreeVolume(struct)

Find the free volume in the structure. Results are stored as properties on the structure

Parameters:

struct (schrodinger.structure.Structure) – The structure to find the free volume in
Raises:
  • FreeVolumeException – if the PBC dimensions are too small or memory usage grows too large and no logger exists
  • SystemExit – if the PBC dimensions are too small or memory usage grows too large and a logger exists
getVoidVolumes()

Get the volume of each void

Return type:list
Returns:A list of void volumes. Each item is a float.
defineVoids()

Define all the voids found in the structure

volumeOfGraph()

Get the current total volume of the graph

Return type:float
Returns:The volume of all the remaining nodes in the graph
writeFiles(basename=None)

Write all the data to files

The actual node graph is written to a pkl file

The void data is written to a json file

The volumes are written to a simple text file, one volume per line

The structure is written to a Maestro file

Parameters:basename (str) – Use this instead of the structure title as the base file name
Return type:str, str, str
Returns:The paths to the files written (volume file, void file, graph file)
clearGraph()

Clear out the graph for this driver to preserve memory space

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.freevolume', '__doc__': ' Driver to compute Free Volume ', '__init__': <function FreeVolumeDriver.__init__>, 'log': <function FreeVolumeDriver.log>, 'logError': <function FreeVolumeDriver.logError>, 'findFreeVolume': <function FreeVolumeDriver.findFreeVolume>, 'getVoidVolumes': <function FreeVolumeDriver.getVoidVolumes>, 'defineVoids': <function FreeVolumeDriver.defineVoids>, 'volumeOfGraph': <function FreeVolumeDriver.volumeOfGraph>, 'writeFiles': <function FreeVolumeDriver.writeFiles>, '_formFileNamesAndProps': <function FreeVolumeDriver._formFileNamesAndProps>, 'clearGraph': <function FreeVolumeDriver.clearGraph>, '__dict__': <attribute '__dict__' of 'FreeVolumeDriver' objects>, '__weakref__': <attribute '__weakref__' of 'FreeVolumeDriver' 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.freevolume'
__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)