Index

_

__init__() (pymolar.AnalysisTask method)

A

AnalysisTask (class in pymolar) append() (pymolar.System method) apply_transform() (pymolar.Sel method) areas (pymolar.Sasa attribute)

Atom (class in pymolar) atom (pymolar.Particle attribute) atomic_number (pymolar.Atom attribute) (pymolar.Particle attribute)

B

bfactor (pymolar.Atom attribute) (pymolar.Particle attribute)

box (pymolar.Sel attribute) (pymolar.State attribute) (pymolar.System attribute)

C

chain (pymolar.Atom attribute) (pymolar.Particle attribute) charge (pymolar.Atom attribute) (pymolar.Particle attribute)

closest_image() (pymolar.PeriodicBox method) cog() (pymolar.Sel method) com() (pymolar.Sel method) coords (pymolar.Sel attribute) cur_t (pymolar.FileStats attribute)

D

distance() (pymolar.PeriodicBox method)

distance_search() (in module pymolar) distance_squared() (pymolar.PeriodicBox method)

E

elapsed_time (pymolar.FileStats attribute)

F

file_name (pymolar.FileHandler attribute) FileHandler (class in pymolar) FileStats (class in pymolar)

fit_transform() (in module pymolar) fit_transform_matching() (in module pymolar) frames_processed (pymolar.FileStats attribute)

G

get_box_extents() (pymolar.PeriodicBox method) get_group_as_sel() (pymolar.NdxFile method) get_lab_extents() (pymolar.PeriodicBox method)

get_matrix() (pymolar.PeriodicBox method) greeting() (in module pymolar) gyration() (pymolar.Sel method) gyration_pbc() (pymolar.Sel method)

I

id (pymolar.Particle attribute) index (pymolar.Sel attribute) inertia() (pymolar.Sel method) inertia_pbc() (pymolar.Sel method)

is_triclinic() (pymolar.PeriodicBox method) iter_atoms() (pymolar.Sel method) (pymolar.System method) iter_pos() (pymolar.Sel method) (pymolar.System method)

M

mass (pymolar.Atom attribute) (pymolar.Particle attribute)

min_max() (pymolar.Sel method) module pymolar

N

name (pymolar.Atom attribute) (pymolar.Particle attribute)

NdxFile (class in pymolar)

O

occupancy (pymolar.Atom attribute) (pymolar.Particle attribute)

P

Particle (class in pymolar) PeriodicBox (class in pymolar) pos (pymolar.Particle attribute) post_process() (pymolar.AnalysisTask method) pre_process() (pymolar.AnalysisTask method)

principal_transform() (pymolar.Sel method) principal_transform_pbc() (pymolar.Sel method) process_frame() (pymolar.AnalysisTask method) pymolar module

R

read() (pymolar.FileHandler method) read_state() (pymolar.FileHandler method) read_topology() (pymolar.FileHandler method) register_args() (pymolar.AnalysisTask method) remove() (pymolar.System method) replace_state_deep() (pymolar.Sel method) (pymolar.System method)

resid (pymolar.Atom attribute) (pymolar.Particle attribute) resindex (pymolar.Particle attribute) resname (pymolar.Atom attribute) (pymolar.Particle attribute) rmsd_mw() (in module pymolar) rmsd_py() (in module pymolar)

S

Sasa (class in pymolar) save() (pymolar.Sel method) (pymolar.System method) Sel (class in pymolar) SelAtomIterator (class in pymolar) SelPosIterator (class in pymolar) set_box_from() (pymolar.Sel method) (pymolar.State method) (pymolar.System method) set_same_bfactor() (pymolar.Sel method) set_same_chain() (pymolar.Sel method) set_same_mass() (pymolar.Sel method) set_same_name() (pymolar.Sel method) set_same_resid() (pymolar.Sel method) set_same_resname() (pymolar.Sel method)

shortest_vector() (pymolar.PeriodicBox method) skip_to_frame() (pymolar.FileHandler method) skip_to_last() (pymolar.FileHandler method) skip_to_time() (pymolar.FileHandler method) split_chain() (pymolar.Sel method) split_molecule() (pymolar.Sel method) split_resindex() (pymolar.Sel method) State (class in pymolar) state (pymolar.Sel attribute) (pymolar.System attribute) stats (pymolar.FileHandler attribute) SysAtomIterator (class in pymolar) SysParticleIterator (class in pymolar) SysPosIterator (class in pymolar) System (class in pymolar) system (pymolar.Sel attribute)

T

time (pymolar.Sel attribute) (pymolar.State attribute) (pymolar.System attribute) to_box_coords() (pymolar.PeriodicBox method) to_gromacs_ndx() (pymolar.Sel method) to_lab_coords() (pymolar.PeriodicBox method) to_vectors_angles() (pymolar.PeriodicBox method) Topology (class in pymolar)

topology (pymolar.Sel attribute) (pymolar.System attribute) total_area (pymolar.Sasa attribute) total_volume (pymolar.Sasa attribute) translate() (pymolar.Sel method) type_id (pymolar.Atom attribute) (pymolar.Particle attribute) type_name (pymolar.Atom attribute) (pymolar.Particle attribute)

V

volumes (pymolar.Sasa attribute)

W

whole_chains() (pymolar.Sel method) whole_residues() (pymolar.Sel method) wrap_point() (pymolar.PeriodicBox method)

write() (pymolar.FileHandler method) write_state() (pymolar.FileHandler method) write_topology() (pymolar.FileHandler method)

X

x (pymolar.Particle attribute)

Y

y (pymolar.Particle attribute)

Z

z (pymolar.Particle attribute)