Index

A

add_atom() (chemfiles.Frame method) add_bond() (chemfiles.Frame method) (chemfiles.Topology method) add_configuration() (in module chemfiles.misc) add_residue() (chemfiles.Frame method) add_velocities() (chemfiles.Frame method)

angle() (chemfiles.Frame method) angles (chemfiles.Topology property) (chemfiles.UnitCell property) angles_count() (chemfiles.Topology method) Atom (class in chemfiles) atomic_number (chemfiles.Atom property)

B

BondOrder (class in chemfiles) bonds (chemfiles.Topology property) bonds_count() (chemfiles.Topology method)

bonds_order() (chemfiles.Topology method) bonds_orders (chemfiles.Topology property) buffer() (chemfiles.MemoryTrajectory method)

C

cell (chemfiles.Frame property) CellShape (class in chemfiles) charge (chemfiles.Atom property) chemfiles.misc module ChemfilesError

ChemfilesWarning clear_bonds() (chemfiles.Frame method) (chemfiles.Topology method) close() (chemfiles.MemoryTrajectory method) (chemfiles.Trajectory method) covalent_radius (chemfiles.Atom property)

D

dihedral() (chemfiles.Frame method) dihedrals (chemfiles.Topology property)

dihedrals_count() (chemfiles.Topology method) distance() (chemfiles.Frame method)

E

evaluate() (chemfiles.Selection method)

F

ffi (chemfiles.MemoryTrajectory property) (chemfiles.Trajectory property) FormatMetadata (class in chemfiles.misc) formats_list() (in module chemfiles.misc) Frame (class in chemfiles)

from_const_ptr() (chemfiles.MemoryTrajectory class method) (chemfiles.Trajectory class method) from_mutable_ptr() (chemfiles.MemoryTrajectory class method) (chemfiles.Trajectory class method) full_name (chemfiles.Atom property)

G

guess_bonds() (chemfiles.Frame method)

guess_format() (in module chemfiles.misc)

H

has_velocities() (chemfiles.Frame method)

I

id (chemfiles.Residue property)

impropers (chemfiles.Topology property) impropers_count() (chemfiles.Topology method)

L

lengths (chemfiles.UnitCell property) list_properties() (chemfiles.Atom method) (chemfiles.Frame method) (chemfiles.Residue method)

M

mass (chemfiles.Atom property) matrix (chemfiles.UnitCell property) MemoryTrajectory (class in chemfiles)

module chemfiles.misc mut_ptr (chemfiles.MemoryTrajectory property) (chemfiles.Trajectory property)

N

name (chemfiles.Atom property) (chemfiles.Residue property)

nsteps (chemfiles.MemoryTrajectory property) (chemfiles.Trajectory property)

O

out_of_plane() (chemfiles.Frame method)

P

path (chemfiles.MemoryTrajectory property) (chemfiles.Trajectory property) positions (chemfiles.Frame property) properties_count() (chemfiles.Atom method) (chemfiles.Frame method) (chemfiles.Residue method)

ptr (chemfiles.MemoryTrajectory property) (chemfiles.Trajectory property)

R

read() (chemfiles.MemoryTrajectory method) (chemfiles.Trajectory method) read_step() (chemfiles.MemoryTrajectory method) (chemfiles.Trajectory method) remove() (chemfiles.Frame method) remove_bond() (chemfiles.Frame method) (chemfiles.Topology method)

Residue (class in chemfiles) residue_for_atom() (chemfiles.Topology method) residues_linked() (chemfiles.Topology method) resize() (chemfiles.Frame method) (chemfiles.Topology method)

S

Selection (class in chemfiles) set_cell() (chemfiles.MemoryTrajectory method) (chemfiles.Trajectory method) set_topology() (chemfiles.MemoryTrajectory method) (chemfiles.Trajectory method)

set_warnings_callback() (in module chemfiles.misc) shape (chemfiles.UnitCell property) size (chemfiles.Selection property) step (chemfiles.Frame property) string (chemfiles.Selection property)

T

topology (chemfiles.Frame property) Topology (class in chemfiles)

Trajectory (class in chemfiles) type (chemfiles.Atom property)

U

UnitCell (class in chemfiles)

V

vdw_radius (chemfiles.Atom property)

velocities (chemfiles.Frame property) volume (chemfiles.UnitCell property)

W

wrap() (chemfiles.UnitCell method)

write() (chemfiles.MemoryTrajectory method) (chemfiles.Trajectory method)