Atom Flags

This module defines atom flags that are used in Atom Selections. You can read this page in interactive sessions using help(flags).

Flag labels can be used in atom selections:

In [1]: from prody import *

In [2]: p = parsePDB('1ubi')

In [3]: p.select('protein')
Out[3]: <Selection: 'protein' from 1ubi (602 atoms)>

Flag labels can be combined with dot operator as follows to make selections:

In [4]: p.protein
Out[4]: <Selection: 'protein' from 1ubi (602 atoms)>

In [5]: p.protein.acidic  # selects acidic residues
Out[5]: <Selection: '(acidic) and (protein)' from 1ubi (94 atoms)>

Flag labels can be prefixed with 'is' to check whether all atoms in an Atomic instance are flagged the same way:

In [6]: p.protein.ishetero
Out[6]: False

In [7]: p.water.ishetero
Out[7]: True

Flag labels can also be used to make quick atom counts:

In [8]: p.numAtoms()
Out[8]: 683

In [9]: p.numAtoms('protein')
Out[9]: 602

In [10]: p.numAtoms('water')
Out[10]: 81

Protein

protein
aminoacid

indicates the twenty standard amino acids (stdaa) and some non-standard amino acids (nonstdaa) described below. Residue must also have an atom named 'CA' in addition to having a qualifying residue name.

stdaa

indicates the standard amino acid residues: ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, and VAL

nonstdaa

indicates one of the following residues:

ASX (B)	asparagine or aspartic acid
GLX (Z)	glutamine or glutamic acid
CSO (C)	S-hydroxycysteine
HIP (H)	ND1-phosphohistidine
HSD (H)	prototropic tautomer of histidine, H on ND1 (CHARMM)
HSE (H)	prototropic tautomer of histidine, H on NE2 (CHARMM)
HSP (H)	protonated histidine
MSE	selenomethionine
SEC (U)	selenocysteine
SEP (S)	phosphoserine
TPO (T)	phosphothreonine
PTR (Y)	O-phosphotyrosine
XLE (J)	leucine or isoleucine
XAA (X)	unspecified or unknown

You can modify the list of non-standard amino acids using addNonstdAminoacid(), delNonstdAminoacid(), and listNonstdAAProps().

calpha
ca

Cα atoms of protein residues, same as selection 'name CA and protein'

backbone
bb

non-hydrogen backbone atoms of protein residues, same as selection 'name CA C O N and protein'

backbonefull
bbfull

backbone atoms of protein residues, same as selection 'name CA C O N H H1 H2 H3 OXT and protein'

sidechain
sc

side-chain atoms of protein residues, same as selection 'protein and not backbonefull'

acidic

residues ASP, GLU, HSP, PHD, PTR, SEP, TPO

acyclic

residues ALA, ARG, ASN, ASP, ASX, CSO, CYS, CYX, GLN, GLU, GLX, GLY, LE, LEU, LYS, MET, MSE, PHD, SEC, SEP, SER, THR, TPO, VAL, XLE

aliphatic

residues ALA, GLY, ILE, LEU, PRO, VAL, XLE

aromatic

residues HIS, PHE, PTR, TRP, TYR

basic

residues ARG, HID, HIE, HIP, HIS, HSD, HSE, LYS

buried

residues ALA, CYS, CYX, ILE, LEU, MET, MSE, PHE, SEC, TRP, VAL, XLE

charged

residues ARG, ASP, GLU, HIS, LYS

cyclic

residues HID, HIE, HIP, HIS, HSD, HSE, HSP, PHE, PRO, PTR, TRP, TYR

hydrophobic

residues ALA, ILE, LEU, MET, PHE, PRO, TRP, VAL, XLE

large

residues ARG, GLN, GLU, GLX, HID, HIE, HIP, HIS, HSD, HSE, HSP, ILE, EU, LYS, MET, MSE, PHD, PHE, PTR, SEP, TPO, TRP, TYR, XLE

medium

residues ASN, ASP, ASX, CSO, CYS, CYX, PRO, SEC, THR, VAL

neutral

residues ALA, ASN, CSO, CYS, CYX, GLN, GLY, ILE, LEU, MET, MSE, PHE, RO, SEC, SER, THR, TRP, TYR, VAL

polar

residues ARG, ASN, ASP, ASX, CSO, CYS, CYX, GLN, GLU, GLX, GLY, HID, IE, HIP, HIS, HSD, HSE, HSP, LYS, PHD, PTR, SEC, SEP, SER, THR, PO, TYR

small

residues ALA, GLY, SER

surface

residues ARG, ASN, ASP, ASX, CSO, GLN, GLU, GLX, GLY, HID, HIE, HIP, IS, HSD, HSE, HSP, LYS, PHD, PRO, PTR, SEP, SER, THR, TPO, TYR

Nucleic

nucleic

indicates nucleobase, nucleotide, and some nucleoside derivatives that are described below, so it is same as 'nucleobase or nucleotide or nucleoside'.

nucleobase

indicates ADE (adenine), GUN (guanine), CYT (cytosine), THY (thymine), and URA (uracil).

nucleotide

indicates residues with the following names:

DA	2’-deoxyadenosine-5’-monophosphate
DC	2’-deoxycytidine-5’-monophosphate
DG	2’-deoxyguanosine-5’-monophosphate
DT	2’-deoxythymidine-5’-monophosphate
DU	2’-deoxyuridine-5’-monophosphate
A	adenosine-5’-monophosphate
C	cytidine-5’-monophosphate
G	guanosine-5’-monophosphate
T	2’-deoxythymidine-5’-monophosphate
U	uridine-5’-monophosphate

nucleoside

indicates following nucleoside derivatives that are recognized by PDB:

AMP	adenosine monophosphate
ADP	adenosine-5’-diphosphate
ATP	adenosine-5’-triphosphate
CDP	cytidine-5’-diphosphate
CTP	cytidine-5’-triphosphate
GMP	guanosine
GDP	guanosine-5’-diphosphate
GTP	guanosine-5’-triphosphate
TMP	thymidine-5’-phosphate
TTP	thymidine-5’-triphosphate
UMP	2’-deoxyuridine 5’-monophosphate
UDP	uridine 5’-diphosphate
UTP	uridine 5’-triphosphate

at

same as selection 'resname ADE A THY T'

cg

same as selection 'resname CYT C GUN G'

purine

same as selection 'resname ADE A GUN G'

pyrimidine

same as selection 'resname CYT C THY T URA U'

Heteros

hetero

indicates anything other than a protein or a nucleic residue, i.e. 'not (protein or nucleic)'.

hetatm

is available when atomic data is parsed from a PDB or similar format file and indicates atoms that are marked 'HETATM' in the file.

water

indices HOH and DOD recognized by PDB and also WAT, TIP3, H2O, OH2, TIP, TIP2, and TIP4 recognized by molecular dynamics (MD) force fields.

Previously used water types HH0, OHH, and SOL conflict with other compounds in the PDB, so are removed from the definition of this flag.

ion

indicates the following ions most of which are recognized by the PDB and others by MD force fields.

		PDB	Source	Conflict
AL	aluminum	Yes
BA	barium	Yes
CA	calcium	Yes
CD	cadmium	Yes
CL	chloride	Yes
CO	cobalt (ii)	Yes
CS	cesium	Yes
CU	copper (ii)	Yes
CU1	copper (i)	Yes
CUA	dinuclear copper	Yes
HG	mercury (ii)	Yes
IN	indium (iii)	Yes
IOD	iodide	Yes
K	potassium	Yes
MG	magnesium	Yes
MN3	manganese (iii)	Yes
NA	sodium	Yes
PB	lead (ii)	Yes
PT	platinum (ii)	Yes
RB	rubidium	Yes
TB	terbium (iii)	Yes
TL	thallium (i)	Yes
WO4	thungstate (vi)	Yes
YB	ytterbium (iii)	Yes
ZN	zinc	Yes
CAL	calcium	No	CHARMM	Yes
CES	cesium	No	CHARMM	Yes
CLA	chloride	No	CHARMM	Yes
POT	potassium	No	CHARMM	Yes
SOD	sodium	No	CHARMM	Yes
ZN2	zinc	No	CHARMM	No

Ion identifiers that are obsoleted by PDB (MO3, MO4, MO5, MO6, NAW, OC7, and ZN1) are removed from this definition.

lipid

indicates GPE, LPP, OLA, SDS, and STE from PDB, and also POPC, LPPC, POPE, DLPE, PCGL, STEA, PALM, OLEO, DMPC from CHARMM force field.

sugar

indicates BGC, GLC, and GLO from PDB, and also AGLC from CHARMM.

heme

indicates 1FH, 2FH, DDH, DHE, HAS, HDD, HDE, HDM, HEA, HEB, HEC, HEM, HEO, HES, HEV, NTE, SRM, and VER from PDB, and also HEMO and HEMR from CHARMM.

pdbter

is available when atomic data is parsed from a PDB format file and indicates atoms that were followed by 'TER' record.

Elements

Following elements found in proteins are recognized by applying regular expressions to atom names:

carbon

carbon atoms, same as 'name "C.*" and not ion'

nitrogen

nitrogen atoms, same as 'name "N.*" and not ion'

oxygen

oxygen atoms, same as 'name "O.*" and not ion'

sulfur

sulfur atoms, same as 'name "S.*" and not ion'

hydrogen

hydrogen atoms, same as 'name "[1-9]?H.*" and not ion'

noh
heavy

non hydrogen atoms, same as 'not hydrogen

'not ion' is appended to above definitions to avoid conflicts with ion atoms.

Structure

Following secondary structure flags are defined but before they can be used, secondary structure assignments must be made.

extended

extended conformation, same as 'secondary E'

helix

α-helix conformation, same as 'secondary H'

helix310

3_10-helix conformation, same as 'secondary G'

helixpi

π-helix conformation, same as 'secondary I'

turn

hydrogen bonded turn conformation, same as 'secondary T'

bridge

isolated beta-bridge conformation, same as 'secondary B'

bend

bend conformation, same as 'secondary S'

coil

not in one of above conformations, same as 'secondary C'

Others

all

indicates all atoms, returns a new view of the instance

none

indicates no atoms, returns None

dummy

indicates dummy atoms in an AtomMap

mapped

indicates mapped atoms in an AtomMap

Functions

The following functions can be used to customize flag definitions:

• flagDefinition()
• addNonstdAminoacid()
• delNonstdAminoacid()
• listNonstdAAProps()

flagDefinition(*arg, **kwarg)

Learn, change, or reset Atom Flags definitions.

Learn a definition

Calling this function with no arguments will return list of flag names whose definitions you can learn:

In [1]: flagDefinition()
Out[1]: 
['acidic',
 'acyclic',
 'aliphatic',
 'aminoacid',
 'aromatic',
 'at',
 'backbone',
 'backbonefull',
 'basic',
 'bb',
 'bbfull',
 'buried',
 'carbon',
 'cg',
 'charged',
 'cyclic',
 'heme',
 'hydrogen',
 'hydrophobic',
 'ion',
 'large',
 'lipid',
 'medium',
 'neutral',
 'nitrogen',
 'nonstdaa',
 'nucleic',
 'nucleobase',
 'nucleoside',
 'nucleotide',
 'oxygen',
 'polar',
 'protein',
 'purine',
 'pyrimidine',
 'small',
 'stdaa',
 'sugar',
 'sulfur',
 'surface',
 'water']

Passing a flag name will return its definition:

In [2]: flagDefinition('backbone')
Out[2]: ['C', 'CA', 'N', 'O']

In [3]: flagDefinition('hydrogen')
Out[3]: '[0-9]?H.*'

Change a definition

Calling the function with editable=True argument will return flag names those definitions that can be edited:

In [4]: flagDefinition(editable=True)
Out[4]: 
['at',
 'backbone',
 'backbonefull',
 'bb',
 'bbfull',
 'carbon',
 'cg',
 'heme',
 'hydrogen',
 'ion',
 'lipid',
 'nitrogen',
 'nucleobase',
 'nucleoside',
 'nucleotide',
 'oxygen',
 'purine',
 'pyrimidine',
 'sugar',
 'sulfur',
 'water']

Pass an editable flag name with its new definition:

In [5]: flagDefinition(nitrogen='N.*')

In [6]: flagDefinition(backbone=['CA', 'C', 'O', 'N'])

In [7]: flagDefinition(nucleobase=['ADE', 'CYT', 'GUN', 'THY', 'URA'])

Note that the type of the new definition must be the same as the type of the old definition. Flags with editable definitions are: at, backbone, backbonefull, bb, bbfull, carbon, cg, heme, hydrogen, ion, lipid, nitrogen, nucleobase, nucleoside, nucleotide, oxygen, purine, pyrimidine, sugar, sulfur, and water

Reset definitions

Pass reset keyword as follows to restore all default definitions of editable flags and also non-standard amino acids.

In [8]: flagDefinition(reset='all')

Or, pass a specific editable flag label to restore its definition:

In [9]: flagDefinition(reset='nitrogen')

listNonstdAAProps(resname)

Returns properties of non-standard amino acid resname.

In [1]: listNonstdAAProps('PTR')
Out[1]: ['acidic', 'aromatic', 'cyclic', 'large', 'polar', 'surface']

getNonstdProperties(resname)

Deprecated for removal in v1.4, use listNonstdAAProps() instead.

addNonstdAminoacid(resname, *properties)

Add non-standard amino acid resname with properties selected from:

• cyclic: acyclic, or cyclic
• charge: acidic, basic, or neutral
• depth: buried, or surface
• hydrophobicity: hydrophobic, or polar
• aromaticity: aliphatic, or aromatic
• size: large, medium, or small

In [1]: addNonstdAminoacid('PTR', 'acidic', 'aromatic', 'cyclic', 'large',
   ...: 'polar', 'surface')
   ...: 

Default set of non-standard amino acids can be restored as follows:

In [2]: flagDefinition(reset='nonstdaa')

delNonstdAminoacid(resname)

Delete non-standard amino acid resname.

In [1]: delNonstdAminoacid('PTR')

In [2]: flagDefinition('nonstdaa')
Out[2]: 
['ASX',
 'CSB',
 'CSO',
 'CYX',
 'GLX',
 'HID',
 'HIE',
 'HIP',
 'HSD',
 'HSE',
 'HSP',
 'MEN',
 'MSE',
 'PHD',
 'SEC',
 'SEP',
 'TPO',
 'XAA',
 'XLE']

Default set of non-standard amino acids can be restored as follows:

In [3]: flagDefinition(reset='nonstdaa')