Atom Data Fields

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.

altloc

alternate location indicator

E.g.: 'altloc A B', 'altloc _'

beta

β-value (temperature factor)

E.g.: 'beta 555.55', 'beta 0 to 500', 'beta 0:500', 'beta < 500'

chain
chid

chain identifier

E.g.: 'chain A', 'chid A B C', 'chain _'

charge

partial charge

E.g.: 'charge 1', 'abs(charge) == 1', 'charge < 0'

chindex

chain index (read only)

E.g.: 'chindex 0'

element

element symbol

E.g.: 'element C O N'

fragindex
fragment

fragment index (read only)

E.g.: 'fragindex 0', 'fragment 1'

icode

insertion code

E.g.: 'icode A', 'icode _'

mass

mass

E.g.: '12 <= mass <= 13.5'

name

name

E.g.: 'name CA CB'

numbonds

number of bonds (read only)

E.g.: 'numbonds 0', 'numbonds 1'

occupancy

occupancy value

E.g.: 'occupancy 1', 'occupancy > 0'

radius

radius

E.g.: 'radii < 1.5', 'radii ** 2 < 2.3'

resindex

residue index (read only)

E.g.: 'resindex 0'

resname

residue name

E.g.: 'resname ALA GLY'

resnum
resid

residue number

E.g.: 'resnum 1 2 3', 'resnum 120A 120B', 'resnum 10 to 20', 'resnum 10:20:2', 'resnum < 10'

secclass

secondary structure class

E.g.: 'secclass 2', 'secclass -1'

secid

secondary structure identifier

E.g.: 'secid A B', 'secid 1 2'

secindex

secondary structure index

E.g.: 's', 'e', 'c', 'i', 'n', 'd', 'e', 'x', ' ', '2'

secondary
secstr

secondary structure assignment

E.g.: 'secondary H E', 'secstr H E'

segindex

segment index (read only)

E.g.: 'segindex 0'

segment
segname

segment name

E.g.: 'segment PROT', 'segname PROT'

serial

serial number (from file)

E.g.: 'serial 1 2 3', 'serial 1 to 10', 'serial 1:10:2', 'serial < 10'

siguij

standard deviations for anisotropic temperature factor

type

type

E.g.: 'type CT1 CT2 CT3'

class Field(name, dtype, **kwargs)

Atomic data field.

getDocstr(meth, plural=True, selex=True)

Returns documentation string for the field.

call

list of AtomGroup methods to call when getMethod is called

depr

deprecated method name

depr_pl

deprecated method name in plural form

desc

description of data field, used in documentation

doc

internal variable name used as key for AtomGroup _data

doc_pl

plural form for documentation

dtype

data type (primitive Python types)

flags

True when there are flags associated with the data field

meth

atomic get/set method name

meth_pl

get/set method name in plural form

name

data field name used in atom selections

ndim

expected dimension of the data array

none

AtomGroup attributes to be set None, when setMethod is called

private

define only _getMethod for AtomGroup to be used by Select class

readonly

read-only attribute without a set method

selstr

list of selection string examples

synonym

synonym used in atom selections