mmtbx.ions.environment module

Deals with examing the atoms around a site and recognizing distinct and useful chemical environments.

class mmtbx.ions.environment.ChemicalEnvironment(i_seq, contacts, manager)

Bases: slots_getstate_setstate

Container for information summarizing a site’s chemical environment.

atom
Type:

iotbx.pdb.hierarchy.atom

contacts
Type:

list of mmtbx.ions.environment.atom_contact

contacts_no_alts
Type:

list of mmtbx.ions.environment.atom_contact

chemistry
Type:

collections.Counter of int, int

geometry
Type:

list of tuples of str, float

atom
chemistry
contacts
contacts_no_alts
geometry
get_valence(element, charge=None)

Calculates the BVS and VECSUM for a given element / charge identity.

Parameters:

  • element (str) – The element identity to calculate valences for.

  • charge (int, optional) – The charge to calculate valences for.

Returns:

  • float – Bond-valence sum (BVS).

  • float – Vector sum (VECSUM).

Notes

class mmtbx.ions.environment.ScatteringEnvironment(i_seq, manager, fo_map=None, fofc_map=None, anom_map=None, fo_density=None, fofc_density=None, anom_density=None)

Bases: slots_getstate_setstate

Container for information summarizing a site’s scattering environment.

d_min
Type:

float

wavelengeth
Type:

float

fp
Type:

float

fpp
Type:

float

b_iso
Type:

float

b_mean_hoh
Type:

float

occ
Type:

float

fo_density
Type:

tuple of float, float

fofo_density
Type:

tuple of float, float

anom_density
Type:

tuple of float, float

pai

Principal axes of inertia at site, currently unused.

Type:

float

anom_density
b_iso
b_mean_hoh
d_min
fo_density
fofc_density
fp
fpp
occ
pai
wavelength
class mmtbx.ions.environment.atom_contact(atom, vector, site_cart, rt_mx)

Bases: slots_getstate_setstate

Container for information about an interacting atom. Most of the methods are simply wrappers for frequently called operations on the atom object, but symmetry-aware.

atom
Type:

iotbx.pdb.hierarchy.atom

charge
Type:

int

element
Type:

str

rt_mx
Type:

cctbx.sgtbx.rt_mx

site_cart
Type:

tuple of float, float, float

vector
Type:

scitbx.matrix.rec

altloc()

Retrieves the alternate conformation label, if any, of the coordinating atom.

Return type:

str

atom
atom_i_seq()

Retrieves the sequence ID of the coordinating atom.

Return type:

int

atom_id_no_altloc(suppress_rt_mx=False)

Unique identifier for an atom, ignoring the altloc but taking the symmetry operator (if any) into account.

Parameters:

suppress_rt_mx (bool, optional)

Return type:

str

atom_name()

Retrieves the coordinating atom’s name (i.e. “OX1”)

Return type:

str

charge
distance()

Actual distance from target atom.

Returns:

Distance, in angstroms.

Return type:

float

distance_from(other)

Distance from another coordinating atom.

Parameters:

other (mmtbx.ions.environment.atom_contact)

Returns:

Distance, in angstroms.

Return type:

float

element
id_str(suppress_rt_mx=False)

Creates a string from the atom’s id string and the symmetry operator associated with that site.

Parameters:

suppress_rt_mx (bool, optional) – Don’t include symmetry operator information in the string.

Return type:

str

is_carboxy_terminus
property occ

Occupancy of the coordinating atom.

Return type:

float

resname()

Retrieves the residue name associated with te coordinating atom (i.e. “ARG”)

Return type:

str

rt_mx
site_cart
vector
mmtbx.ions.environment.find_nearby_atoms(i_seq, xray_structure, pdb_atoms, asu_mappings, asu_table, connectivity, far_distance_cutoff=3.0, near_distance_cutoff=1.5, filter_by_bonding=True)

Given site in the structure, return a list of nearby atoms with the supplied cutoff, and the vectors between them and the atom’s site. Takes into account symmetry operations when finding nearby sites.

Parameters:
Return type:

list of mmtbx.ions.environment.atom_contact