Expand description
Builder functions sharing the textual parser’s typed IR.
Functions§
- all
- Every atom.
- alpha_
helix - Alpha-helix residues.
- aromatic
- Aromatic atoms.
- backbone
- Protein backbone atoms.
- bend
- Bend residues.
- bfactor
- Temperature-factor column.
- bridge
- Isolated beta-bridge residues.
- by_
residue - Whole residues containing
targetatoms. - chain
- Chain identifier column.
- coil
- Assigned coil residues, excluding unknown.
- glycans
- Saccharide atoms.
- heavy
- Non-hydrogen atoms.
- helix
- All helices, including polyproline-II and deposited other helices.
- helix_
310 - Three-ten helix residues.
- hetero
- Heterogeneous atoms.
- hydrogen
- Hydrogen atoms.
- ions
- Ion atoms.
- is_
protein - Protein atoms.
- ligands
- Non-polymer ligand atoms.
- lipids
- Lipid atoms.
- name
- Atom name column.
- none
- No atoms.
- nonpolar_
hydrogen - Hydrogen atoms not bonded to N, O or S, including unbonded H. Requires available bonds.
- nucleic
- Nucleic-acid atoms.
- nucleic_
backbone - Nucleic-acid backbone atoms.
- nucleic_
base - Nucleic-acid base atoms.
- nucleic_
sugar - Nucleic-acid sugar atoms.
- occupancy
- Occupancy column.
- pi_
helix - Pi-helix residues.
- plddt_
confident - Atoms whose pLDDT is above 70 and at most 90.
- plddt_
low - Atoms whose pLDDT is above 50 and at most 70.
- plddt_
very_ high - Atoms whose pLDDT is above 90.
- plddt_
very_ low - Atoms whose pLDDT is at most 50.
- polar_
hydrogen - Hydrogen atoms bonded to N, O or S in the full topology. Requires available bonds.
- polymer
- Polymer atoms.
- polyproline
- Polyproline-II helix residues.
- residues_
within - Whole residues within
radiusoftarget. - resname
- Residue name column.
- sheet
- Beta strands and isolated bridges.
- sidechain
- Protein side-chain atoms.
- strand
- Beta-ladder residues only.
- turn
- Hydrogen-bonded turn residues.
- water
- Water atoms.
- within
- Atoms within
radiusoftarget. - x
- X coordinate.