Package schrodinger :: Package application :: Package matsci :: Module clusterstruct :: Class SpeciesData

Class SpeciesData

object --+
         |
        SpeciesData

Tracks information about each chemically distinct molecule in a system

Instance Methods

[hide private]

__init__(self, struct, smiles)
Create a SpeciesData instance

addMember(self, stindex, molnumber)
Add a new member of this species

isMember(self, stindex, molnumber)
Check if a molecule is a member of this species

addCharges(self, struct, prop='r_j_ESP_Charges')
Add atomic charge information to this SpeciesData object (does not actually add the charges as properties to structures).

schrodinger.structure.Structure

getSampleStructure(self, struct_iterator)
Get a sample structure for this species

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, struct, smiles)
(Constructor)

Create a SpeciesData instance

Parameters:

struct (schrodinger.structure.Structure) - The structure of this species
smiles (str) - The unique smiles string for this species

Overrides: object.__init__

addMember(self, stindex, molnumber)

Add a new member of this species

Parameters:

stindex (int) - The structure index this member comes from. It is up to the calling code to generate and make use of this value.
molnumber (int) - The molecule number in the structure that is a member of this species

isMember(self, stindex, molnumber)

Check if a molecule is a member of this species

Parameters:

stindex (int) - The structure index this molecule comes from.
molnumber (int) - The molecule number that is being checked

addCharges(self, struct, prop=`'r_j_ESP_Charges'`)

Add atomic charge information to this SpeciesData object (does not actually add the charges as properties to structures). The element and charge for every atom are stored as a tuple in the charges list. The element is stored to help ensure that any future structure the charges are applied to has the same atom ordering as struct.

Parameters:

struct (schrodinger.structure.Structure) - The structure of this species. Used to determine the element of each atom and the charge of each atom.
prop (str) - The property name to use to obtain charges from each atom in struct

getSampleStructure(self, struct_iterator)

Get a sample structure for this species

Parameters:

struct_iterator (iterable) - An iterable of schrodinger.structure.Structure objects used to create this SpeciesData object

Returns: schrodinger.structure.Structure

A structure object representing a molecule of this species

Class SpeciesData

__init__(self, struct, smiles) (Constructor)

addMember(self, stindex, molnumber)

isMember(self, stindex, molnumber)

addCharges(self, struct, prop='r_j_ESP_Charges')

getSampleStructure(self, struct_iterator)

init(self, struct, smiles)
(Constructor)

addCharges(self, struct, prop=`'r_j_ESP_Charges'`)