schrodinger.application.desmond.fep_struc module¶

Defines a `Struc’ class as a generic represention of molecular structure

class schrodinger.application.desmond.fep_struc.Struc¶

Bases: object

__init__()¶: Initialize self. See help(type(self)) for accurate signature.

__str__()¶: Return str(self).

id()¶: Returns the ID of this structure.

set_id(id)¶: Sets the ID for this structure.

copy()¶

extract(indices)¶: Return a new structure object which contains the atoms of the current structure that appear in the specified list.

title()¶

set_title(new_title)¶

heavy_atoms()¶: Returns a list of indices of heavy atoms (viz non-hydrogen atoms).

is_chiral_atom(atom_index)¶

Returns true if the atom indicated by atom_index is chiral; otherwise, false.

Parameters:	atom_index (`int`) – Atom index

chiral_atoms()¶

Returns the indices of the chiral atoms.

Return type:	`list` of `int`
Returns:	A list of atom indices

ring_atoms()¶

Returns a set of ring atoms.

Return type:	`set` of `int`
Returns:	A set of atom indices

bonded_atoms(atom_index)¶

Returns a list of atom indices of atoms bonded to the indicated atom.

Parameters:	atom_index (`int`) – A single index or a list of indices of the atoms to be deleted
Return type:	`list` of `int`
Returns:	A list of atom indices of atoms bonded to the indicated atom

total_charge()¶: Returns the total charge of the structure.

delete_atom(atom_index)¶

Deletes a atom.

Parameters:	atom_index (`int` or `list` of `int`) – A single index or a list of indices of the atoms to be deleted

smarts()¶: Returns a SMARTS string of this structure.

smiles()¶: Returns a SMILES string of this structure.

write(format, mode='a')¶

Writes this structure into a file in the designated format.

Parameters:	mode (`char`, ‘a’ \| ‘w’) – When a file of the same name exists, this determines whether to overwrite (‘w’) or append (‘a’) to the file.

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.fep_struc', '__doc__': '\n\n ', '__init__': <function Struc.__init__>, '__str__': <function Struc.__str__>, '_atom': <function Struc._atom>, 'id': <function Struc.id>, 'set_id': <function Struc.set_id>, 'copy': <function Struc.copy>, 'extract': <function Struc.extract>, 'title': <function Struc.title>, 'set_title': <function Struc.set_title>, 'heavy_atoms': <function Struc.heavy_atoms>, 'is_chiral_atom': <function Struc.is_chiral_atom>, 'chiral_atoms': <function Struc.chiral_atoms>, 'ring_atoms': <function Struc.ring_atoms>, 'bonded_atoms': <function Struc.bonded_atoms>, 'total_charge': <function Struc.total_charge>, 'delete_atom': <function Struc.delete_atom>, 'smarts': <function Struc.smarts>, 'smiles': <function Struc.smiles>, 'write': <function Struc.write>, '__dict__': <attribute '__dict__' of 'Struc' objects>, '__weakref__': <attribute '__weakref__' of 'Struc' 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.desmond.fep_struc'¶

__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

__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.desmond.fep_struc.SchrodStruc(struc)¶

Bases: schrodinger.application.desmond.fep_struc.Struc

A `Struc’ subclass based on Schrodinger’s infrastructure

__init__(struc)¶: `struc’ should be a `schrodinger.structure.Structure’ object.

__setstate__(dict)¶

copy()¶: Returns a copy of this structure.

extract(indices)¶: Return a new structure object which contains the atoms of the current structure that appear in the specified list.

title()¶: Returns the title of this structure. (Normally title’s a user-friendly description)

set_title(new_title)¶: Sets a new title to this structure.

heavy_atoms()¶: Returns a list of indices of heavy atoms (viz non-hydrogen atoms).

is_chiral_atom(atom_index)¶

Returns true if the atom indicated by atom_index is chiral; otherwise, false.

Parameters:	atom_index (`int`) – Atom index

chiral_atoms()¶

Returns the indices of the chiral atoms.

Return type:	`list` of `int`
Returns:	A list of atom indices

ring_atoms(aromaticity=0, group=False)¶

Returns ring atoms.

Parameters:	aromaticity (`int` -1, 0, 1) – -1 = non-aromatic, 0 = all, 1 = aromatic. Make the function return the specified type of ring atoms. group (`bool`) – If true, returns a list of `set` objects, each of which is a set of indices of atoms in the same ring; otherwise, returns a single set containing indices of all selected ring atoms.

:rtype : set of int or a list of set of int :return : A set or a list of sets of atom indices