ProtoCaller.IO.PDB.Chain module¶
-
class
ProtoCaller.IO.PDB.Chain.
Chain
(residues=None)¶ Bases:
ProtoCaller.IO.PDB.Residue.Residue
,ProtoCaller.Utils.ConditionalList.ConditionalList
Represents a single Chain in a PDB file.
- Parameters
atoms ([ProtoCaller.IO.PDB.Residue.Residue]) – A list of residues.
-
chainID
¶ Chain identifier.
- Type
str
-
property
numberOfAtoms
¶ Returns the number of atoms.
- Type
int
-
property
numberOfResidues
¶ Returns the number of Residues.
- Type
int
-
purgeAtoms
(atoms, mode)¶ Removes or keeps the selected atoms.
- Parameters
atoms ([ProtoCaller.IO.PDB.Atom.Atom]) – Atoms to be removed or kept
mode (str) – One of “keep” and “discard” - either keeps only the selection or discards the latter.
-
purgeEmpty
()¶ Removes empty elements.
-
purgeResidues
(residues, mode)¶ Removes or keeps the selected residues.
- Parameters
atoms ([ProtoCaller.IO.PDB.Atom.Atom]) – Residues to be removed or kept
mode (str) – One of “keep” and “discard” - either keeps only the selection or discards the latter.
-
reNumberAtoms
(start=1, custom_serials=None)¶ Renumbers the atoms.
- Parameters
start (int, optional) – Initial index.
custom_serials ([int] or None, optional) – A list of custom indices. If None, atoms are renumbered sequentially.
-
reNumberResidues
(start=1, custom_resSeqs=None, custom_iCodes=None)¶ Renumbers the residues.
- Parameters
start (int, optional) – Initial index.
custom_resSeqs ([int] or None, optional) – A list of custom resSeqs. If None, residues are renumbered sequentially.
custom_iCodes ([str] or None, optional) – A list of custom iCodes. If None, residues are renumbered sequentially.
-
property
sequence
¶ Returns the single-character sequence of the amino acids in the chain. Missing amino acids are not taken into account.
- Type
str
-
property
type
¶ “chain” if it has amino acid residues and “molecules” otherwise.
- Type
str
- Type
Returns the type of the chain