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Topology attributes

Lily Wang edited this page Nov 6, 2019 · 3 revisions

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'>
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