Package schrodinger :: Package application :: Package desmond :: Module fep_struc :: Class Struc

Class Struc

object --+
         |
        Struc

Known Subclasses:

SchrodStruc

Instance Methods

[hide private]

__init__(self)
x.__init__(...) initializes x; see help(type(x)) for signature

__str__(self)
str(x)

_atom(self, index)
Returns the `index'-th atom.

id(self)
Returns the ID of this structure.

set_id(self, id)
Sets the ID for this structure.

copy(self)

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

title(self)

set_title(self, new_title)

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

is_chiral_atom(self, atom_index)
Returns true if the atom indicated by atom_index is chiral; otherwise, false.

list of int

chiral_atoms(self)
Returns the indices of the chiral atoms.

set of int

ring_atoms(self)
Returns a set of ring atoms.

list of int

bonded_atoms(self, atom_index)
Returns a list of atom indices of atoms bonded to the indicated atom.

total_charge(self)
Returns the total charge of the structure.

delete_atom(self, atom_index)
Deletes a atom.

smarts(self)
Returns a SMARTS string of this structure.

smiles(self)
Returns a SMILES string of this structure.

write(filename, format, mode='a')
Writes this structure into a file in the designated format.

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__: (inherited documentation)

str(self)
(Informal representation operator)

str(x)

Overrides: object.__str__: (inherited documentation)

is_chiral_atom(self, atom_index)

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

Parameters:

atom_index (int) - Atom index

chiral_atoms(self)

Returns the indices of the chiral atoms.

Returns: list of int: A list of atom indices

ring_atoms(self)

Returns a set of ring atoms.

Returns: set of int: A set of atom indices

bonded_atoms(self, 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

Returns: list of int

A list of atom indices of atoms bonded to the indicated atom

delete_atom(self, 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

write(filename, 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 Struc

__init__(self) (Constructor)

__str__(self) (Informal representation operator)

is_chiral_atom(self, atom_index)

chiral_atoms(self)

ring_atoms(self)

bonded_atoms(self, atom_index)

delete_atom(self, atom_index)

write(filename, format, mode='a')

init(self)
(Constructor)

str(self)
(Informal representation operator)

write(filename, format, mode=`'a'`)