This module defines atomic data fields. You can read this page in interactive sessions using help(fields).
Data parsed from PDB and other supported files for these fields are stored in AtomGroup instances. Available data fields are listed in the table below. Atomic classes, such as Selection, offer get and set for handling parsed data:
Many of these data fields can be used to make Atom Selections. Following table lists definitions of fields and selection examples. Note that fields noted as read only do not have a set method.
alternate location indicator
E.g.: 'altloc A B', 'altloc _'
β-value (temperature factor)
E.g.: 'beta 555.55', 'beta 0 to 500', 'beta 0:500', 'beta < 500'
chain identifier
E.g.: 'chain A', 'chid A B C', 'chain _'
partial charge
E.g.: 'charge 1', 'abs(charge) == 1', 'charge < 0'
chain index (read only)
E.g.: 'chindex 0'
element symbol
E.g.: 'element C O N'
fragment index (read only)
E.g.: 'fragindex 0', 'fragment 1'
insertion code
E.g.: 'icode A', 'icode _'
mass
E.g.: '12 <= mass <= 13.5'
name
E.g.: 'name CA CB'
number of bonds (read only)
E.g.: 'numbonds 0', 'numbonds 1'
occupancy value
E.g.: 'occupancy 1', 'occupancy > 0'
radius
E.g.: 'radii < 1.5', 'radii ** 2 < 2.3'
residue index (read only)
E.g.: 'resindex 0'
residue name
E.g.: 'resname ALA GLY'
residue number
E.g.: 'resnum 1 2 3', 'resnum 120A 120B', 'resnum 10 to 20', 'resnum 10:20:2', 'resnum < 10'
secondary structure assignment
E.g.: 'secondary H E', 'secstr H E'
segment index (read only)
E.g.: 'segindex 0'
segment name
E.g.: 'segment PROT', 'segname PROT'
serial number (from file)
E.g.: 'serial 1 2 3', 'serial 1 to 10', 'serial 1:10:2', 'serial < 10'
type
E.g.: 'type CT1 CT2 CT3'
Atomic data field.
deprecated method name
deprecated method name in plural form
description of data field, used in documentation
plural form for documentation
data type (primitive Python types)
True when there are flags associated with the data field
atomic get/set method name
get/set method name in plural form
data field name used in atom selections
expected dimension of the data array
read-only attribute without a set method
list of selection string examples
synonym used in atom selections