Topology attributes

These tables below are generated from scripts.

Non-connectivity attributes

Atom	AtomGroup	Description	Supported formats
altLoc	altLocs	Alternate location	MMTF , PDB, ENT , PDBQT , XPDB
angles	angles		DATA , GSD , PSF , TOP, PRMTOP, PARM7 , TPR , XML
atomiccharge	atomiccharges	Atomic number	GMS
atomnum	atomnums	?	DMS
bfactor	bfactors	alias of tempfactor	MMTF
bonds	bonds		DATA , DMS , GSD , MMTF , MOL2 , PDB, ENT , PSF , TOP, PRMTOP, PARM7 , TPR , TXYZ, ARC , XML , XPDB
chainID	chainIDs	chain ID	DMS , PDB, ENT , XPDB
charge	charges	partial atomic charge	DATA , DMS , GSD , MMTF , MOL2 , PDBQT , PQR , PSF , TOP, PRMTOP, PARM7 , TPR , XML
dihedrals	dihedrals		DATA , GSD , PSF , TOP, PRMTOP, PARM7 , TPR , XML
element	elements	atom element	TOP, PRMTOP, PARM7
icode	icodes	atom insertion code	MMTF , PDB, ENT , PDBQT , PQR , XPDB
impropers	impropers		DATA , GSD , PSF , TOP, PRMTOP, PARM7 , TPR , XML
mass	masses		CONFIG , CRD , GMS , GRO , HISTORY , LAMMPSDUMP , MMTF , MOL2 , PDB, ENT , PDBQT , PQR , TXYZ, ARC , XPDB , XYZ
model	models	model number (from 0)	MMTF
molnum	molnums	[molecules] number (from 0)	TPR
moltype	moltypes	[moleculetype] name	TPR
name	names	atom names	CONFIG , CRD , DMS , GMS , GRO , GSD , HISTORY , MMTF , MOL2 , PDB, ENT , PDBQT , PQR , PSF , TOP, PRMTOP, PARM7 , TPR , TXYZ, ARC , XPDB , XYZ
occupancy	occupancies	atom occupancy	MMTF , PDB, ENT , PDBQT , XPDB
radius	radii	atomic radius	GSD , PQR , XML
record_type	record_types	ATOM / HETATM	PDB, ENT , PDBQT , PQR , XPDB
resname	resnames	residue name (except GSD has ints)	CRD , DMS , GRO , GSD , MMTF , MOL2 , PDB, ENT , PDBQT , PQR , PSF , TOP, PRMTOP, PARM7 , TPR , XPDB
tempfactor	tempfactors	B-factor	CRD , PDB, ENT , PDBQT , XPDB
type_index	type_indices	amber atom type number	TOP, PRMTOP, PARM7
type	types		CONFIG , CRD , DMS , GMS , GRO , HISTORY , PDB, ENT , PQR , XPDB , XYZ

Connectivity attributes

Atom	AtomGroup	Supported formats
bonds	bonds	DATA , DMS, GSD, MMTF , MOL2 , PDB, ENT, PSF, TOP, PRMTOP, PARM7, TPR, TXYZ, ARC , XML, XPDB
angles	angles	DATA , GSD, PSF, TOP, PRMTOP, PARM7, TPR, XML
dihedrals	dihedrals	DATA , GSD, PSF, TOP, PRMTOP, PARM7, TPR, XML
impropers	impropers	DATA , GSD, PSF, TOP, PRMTOP, PARM7, TPR, XML

Attributes by topology parser

Format	Attributes read	Attributes guessed
CRD	names, resnames, tempfactors	masses, types
HISTORY	names	masses, types
CONFIG	names	masses, types
DMS	atomnums, bonds, chainIDs, charges, names, resnames	types
GMS	atomiccharges, names	masses, types
GRO	names, resnames	masses, types
GSD	angles, bonds, charges, dihedrals, impropers, names, radii, resnames
XML	angles, bonds, charges, dihedrals, impropers, radii
DATA	angles, bonds, charges, dihedrals, impropers
MMTF	altLocs, bfactors, bonds, charges, icodes, models, names, occupancies, resnames	masses
MOL2	bonds, charges, names, resnames	masses
PDB, ENT	altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors	masses, types
PDBQT	altLocs, charges, icodes, names, occupancies, record_types, resnames, tempfactors	masses
PQR	charges, icodes, names, radii, record_types, resnames	masses, types
PSF	angles, bonds, charges, dihedrals, impropers, names, resnames
TOP, PRMTOP, PARM7	angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices	elements
TPR	angles, bonds, charges, dihedrals, impropers, molnums, moltypes, names, resnames
TXYZ, ARC	bonds, names	masses
XPDB	altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors	masses, types
XYZ	names	masses, types
LAMMPSDUMP		masses

Default values for attributes

Atom	AtomGroup	default	level	type
altLocs	altLoc	''	atom	<class 'object'>
angles	angles	No default values	atom
atomiccharges	atomiccharge	No default values	atom
atomnums	atomnum	No default values	atom
bfactors	bfactor	0.0	atom	<class 'float'>
bonds	bonds	No default values	atom
chainIDs	chainID	''	atom	<class 'object'>
charges	charge	0.0	atom	<class 'float'>
dihedrals	dihedrals	No default values	atom
elements	element	''	atom	<class 'object'>
icodes	icode	''	residue	<class 'object'>
ids	id	continuous sequence from 1 to n_atoms	atom	<class 'int'>
impropers	impropers	No default values	atom
masses	mass	0.0	atom	<class 'numpy.float64'>
models	model	No default values	segment
molnums	molnum	No default values	residue	<class 'numpy.int64'>
moltypes	moltype	No default values	residue	<class 'object'>
names	name	''	atom	<class 'object'>
occupancies	occupancy	0.0	atom	<class 'float'>
radii	radius	0.0	atom	<class 'float'>
record_types	record_type	'ATOM'	atom	<class 'object'>
resids	resid	continuous sequence from 1 to n_residues	residue	<class 'int'>
resnames	resname	''	residue	<class 'object'>
resnums	resnum	continuous sequence from 1 to n_residues	residue	<class 'int'>
segids	segid	''	segment	<class 'object'>
tempfactors	tempfactor	0.0	atom	<class 'float'>
type_indices	type_index	No default values	atom
types	type	''	atom	<class 'object'>