Package schrodinger :: Package application :: Package desmond :: Module gui :: Class _AtomGroup

Class _AtomGroup

object --+
         |
        _AtomGroup

Represents the data of the atom group table? Of the Misc tab of the Advanced Options dialog

Instance Methods

[hide private]

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

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

Static Methods

[hide private]

_default_group_selector(grp)

_condense_atom_group(grp, group_selector)

get_asl(raw_grp)
Returns an ASL string for a given group of atoms ('raw_grp').

get_atom_grp(structs)
Given a list of component CTs (`structs'), returns a list of '_AtomGroup' objects

del_all_atom_grp(structs)

inject_atom_grp(structs, atom_grp)
Updates the atom-level properties on the given model CTs based on the given atom group list, and returns the list of modified structs.

get_restr(structs)
Return a list of AtomGroups for restraints in the given model CTs.

_restr_grp_selector(grp)

resize_restr_block(ffh, size)
Resizes the "ffio_restraints" block, i.e., changes the number of entries of the block.

set_restr(ffh, i, k, i_atom, x, y, z)

set_restr_block(ct, restr)

inject_restr(structs, restr_grp)
Sets up the restraints in the given components CTs based on the state of the given restraint group.

Class Variables

[hide private]

FROZEN_NAME = "frozen"

PREDEFINED_GROUP_NAME = []

PREFIX_NAME = "i_ffio_grp_"

PREFIX_NAME_LEN = len(PREFIX_NAME)

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, name)
(Constructor)

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

Overrides: object.__init__: (inherited documentation)

get_asl(raw_grp)
Static Method

Returns an ASL string for a given group of atoms ('raw_grp').

Parameters:

raw_grp - Must be an iterable of 2-element tuples. The first element of the tuple is the entry ID, the second is the atom ID within the entry.

resize_restr_block(ffh, size)
Static Method

Resizes the "ffio_restraints" block, i.e., changes the number of entries of the block.

What will happen?

If the new size is the same as the existing size, nothing changes.
If the new size is smaller, the entries at the end of the block will be deleted.
If the new size is larger, new entries will be appended. These new entries will have undetermined values.

Parameters:

ffh - The handle of the ffio block.
size - The wanted size of the restraint block.

Class _AtomGroup

__init__(self, name) (Constructor)

get_asl(raw_grp) Static Method

resize_restr_block(ffh, size) Static Method

init(self, name)
(Constructor)

get_asl(raw_grp)
Static Method

resize_restr_block(ffh, size)
Static Method