Index

_

__and__() (protutils.atom.AtomCollection method) __contains__() (protutils.atom.AtomCollection method) __dict__ (protutils.atom.Atom attribute) (protutils.atom.AtomCollection attribute) (protutils.residue.Residue attribute) (protutils.residue.Residues attribute) __eq__() (protutils.atom.Atom method) (protutils.atom.AtomCollection method) __getitem__() (protutils.atom.AtomCollection method) (protutils.residue.Residue method) (protutils.residue.Residues method) __hash__() (protutils.atom.Atom method) __iand__() (protutils.atom.AtomCollection method) __init__() (protutils.atom.Atom method) (protutils.atom.AtomCollection method) (protutils.bgf.BGFAtom method) (protutils.bgf.BGFFile method) (protutils.pdb.PDBAtom method) (protutils.pdb.PDBResidue method) (protutils.pdb.PDBResidues method) (protutils.pqr.PQRAtom method) (protutils.pqr.PQRFile method) (protutils.residue.Residue method) (protutils.residue.Residues method) __ior__() (protutils.atom.AtomCollection method)

__iter__() (protutils.atom.AtomCollection method) __ixor__() (protutils.atom.AtomCollection method) __len__() (protutils.atom.AtomCollection method) __module__ (protutils.atom.Atom attribute) (protutils.atom.AtomCollection attribute) (protutils.bgf.BGFAtom attribute) (protutils.bgf.BGFFile attribute) (protutils.pdb.PDBAtom attribute) (protutils.pdb.PDBFile attribute) (protutils.pdb.PDBResidue attribute) (protutils.pdb.PDBResidues attribute) (protutils.pqr.PQRAtom attribute) (protutils.pqr.PQRFile attribute) (protutils.residue.Residue attribute) (protutils.residue.Residues attribute) __or__() (protutils.atom.AtomCollection method) __repr__() (protutils.atom.Atom method) (protutils.atom.AtomCollection method) (protutils.bgf.BGFAtom method) (protutils.pdb.PDBAtom method) (protutils.pqr.PQRAtom method) __weakref__ (protutils.atom.Atom attribute) (protutils.atom.AtomCollection attribute) (protutils.residue.Residue attribute) (protutils.residue.Residues attribute) __xor__() (protutils.atom.AtomCollection method)

A

add_connections_from_line() (protutils.bgf.BGFAtom method) (protutils.pdb.PDBAtom method) add_connections_from_list() (protutils.atom.Atom method) align() (protutils.atom.AtomCollection method) aligned_rmsd() (protutils.atom.AtomCollection method)

angle() (protutils.atom.Atom static method) assign() (protutils.atom.AtomCollection method) Atom (class in protutils.atom) AtomCollection (class in protutils.atom)

B

backbone() (protutils.atom.AtomCollection method) BGFAtom (class in protutils.bgf)

BGFFile (class in protutils.bgf)

C

cealign() (protutils.atom.AtomCollection method) chains (protutils.atom.AtomCollection attribute)

cross() (protutils.atom.Atom static method)

D

dihedral() (protutils.atom.Atom static method) dist() (protutils.atom.Atom static method)

distance() (protutils.atom.Atom method) dot() (protutils.atom.Atom static method)

E

exclude() (protutils.atom.AtomCollection method)

F

fetch() (protutils.pdb.PDBFile class method) fetch_ligand() (protutils.pdb.PDBFile class method) fftypes (protutils.bgf.BGFFile attribute)

from_atoms() (protutils.pdb.PDBResidue class method) (protutils.residue.Residue class method) from_file() (protutils.bgf.BGFFile class method) (protutils.pdb.PDBFile class method) (protutils.pqr.PQRFile class method) from_line() (protutils.bgf.BGFAtom class method) (protutils.pdb.PDBAtom class method) (protutils.pqr.PQRAtom class method)

G

get_next() (protutils.pdb.PDBResidue method) (protutils.residue.Residue method) get_prev() (protutils.pdb.PDBResidue method) (protutils.residue.Residue method)

groupby_residue() (protutils.atom.AtomCollection method)

L

ligand() (protutils.atom.AtomCollection method)

N

new_coordinates() (protutils.atom.AtomCollection method)

nomalize() (protutils.atom.Atom static method)

O

orient() (protutils.atom.AtomCollection method)

P

PDBAtom (class in protutils.pdb) PDBFile (class in protutils.pdb) PDBResidue (class in protutils.pdb) PDBResidues (class in protutils.pdb) phi() (protutils.residue.Residues method) PQRAtom (class in protutils.pqr) PQRFile (class in protutils.pqr)

protein() (protutils.atom.AtomCollection method) protutils.atom (module) protutils.bgf (module) protutils.pdb (module) protutils.pqr (module) protutils.residue (module) psi() (protutils.residue.Residues method)

R

ramachandran_plot() (protutils.atom.AtomCollection method) (protutils.pdb.PDBFile method) (protutils.residue.Residues method) remove_protons() (protutils.atom.AtomCollection method) renumber_atoms() (protutils.atom.AtomCollection method) renumber_residues() (protutils.atom.AtomCollection method) resi (protutils.atom.AtomCollection attribute)

Residue (class in protutils.residue) Residues (class in protutils.residue) residues (protutils.atom.AtomCollection attribute) rmsd() (protutils.atom.AtomCollection method)

S

select() (protutils.atom.AtomCollection method) sequence (protutils.atom.AtomCollection attribute)

set_movable() (protutils.bgf.BGFFile method) sidechains() (protutils.atom.AtomCollection method)

T

to_pdb() (protutils.bgf.BGFFile method) (protutils.pqr.PQRFile method)

W

within() (protutils.atom.AtomCollection method) write_bgf() (protutils.bgf.BGFFile method) write_pdb() (protutils.bgf.BGFFile method) (protutils.pdb.PDBFile method) (protutils.pqr.PQRFile method)

write_pqr() (protutils.pqr.PQRFile method) writeline() (protutils.bgf.BGFAtom method) (protutils.pdb.PDBAtom method) (protutils.pqr.PQRAtom method)