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 prody.atomic.fields.Field(name, dtype, **kwargs)[source]

Atomic data 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

getDocstr(meth, plural=True, selex=True)[source]: Returns documentation string for the 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