mmtbx.ions
index
/net/chevy/raid1/nat/src/cctbx_project/mmtbx/ions/__init__.py

# -*- coding: utf-8; py-indent-offset: 2 -*-

 
Package Contents
       
build
environment
geometry
halides
identify
parameters
svm (package)
tst_environment
tst_geometries
tst_parameters
tst_pick_approx_zn
tst_pick_ca
tst_pick_ca_svm
tst_pick_k
tst_pick_mg
tst_pickle
tst_symmetry_axis
tst_utils
tst_validate_ca
tst_validate_mg
tst_validate_zn
utils

 
Classes
       
libtbx.group_args(__builtin__.object)
metal_parameters
libtbx.slots_getstate_setstate(__builtin__.object)
parameter_server

 
class metal_parameters(libtbx.group_args)
    
Method resolution order:
metal_parameters
libtbx.group_args
__builtin__.object

Methods defined here:
__str__(self)
charge_as_int(self)
scattering_type(self)

Methods inherited from libtbx.group_args:
__call__(self)
__init__(self, **keyword_arguments)
__repr__(self)

Data descriptors inherited from libtbx.group_args:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class parameter_server(libtbx.slots_getstate_setstate)
    Class for retrieving information from ion_parameters.cif
 
 
Method resolution order:
parameter_server
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__init__(self)
calculate_valence(self, ion, donor, distance)
Calculates the single valence contribution of one ion donor pair,
separated by distance. ion and donor should be AtomGuess objects.
calculate_valences(self, ion, nearby_atoms)
Calculates all of the valence contributions between ion and each
atom of nearby_atoms, each element of which should be a tuple of an
atom and a vector from the ion's location.
 
Returns a list of vectors, whose magnitudes are equal to the valence
contributions from each donor atom.
get_charge(self, atom)
get_charges(self, atom)
Return all charges associated with element in our table.
get_element(self, atom)
get_metal_parameters(self, element)
get_valence_params(self, atom1, atom2)
is_supported_donor(self, symbol)
is_supported_element(self, symbol)

Data descriptors defined here:
params

Methods inherited from libtbx.slots_getstate_setstate:
__getstate__(self)
__setstate__(self, state)

 
Functions
       
check_supported(elements)
cif_param_as_float(param)
cif_param_as_int(param)
cif_param_as_list(param)
exp(...)
exp(x)
 
Return e raised to the power of x.

 
Data
        Auto = <libtbx.AutoType object>
DEFAULT_IONS = ['MG', 'CA', 'ZN', 'CL']
HALIDES = ['F', 'CL', 'BR', 'IOD']
SUPPORTED = ['MN', 'FE', 'CO', 'CU', 'NI', 'ZN', 'PT', 'F', 'CL', 'BR', 'IOD', 'NA', 'MG', 'K', 'CA', 'CD', 'HG']
TRANSITION_METALS = ['MN', 'FE', 'CO', 'CU', 'NI', 'ZN', 'PT']
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
server = <mmtbx.ions.parameter_server object>