Index

A | B | C | D | E | F | G | H | I | J | K | L | M | N | P | R | S | T | U | V | W | X

A

acorr() (in module pytraj)

(in module pytraj.all_actions)

ActionList (class in pytraj.c_action.actionlist)

add() (pytraj.c_action.actionlist.ActionList method)

add_angles (pytraj.topology.Topology attribute)

add_atom() (pytraj.core.c_core.AtomMask method)

(pytraj.topology.Topology method)

add_atom_range() (pytraj.core.c_core.AtomMask method)

add_atoms() (pytraj.core.c_core.AtomMask method)

add_bonds (pytraj.topology.Topology attribute)

add_dihedrals (pytraj.topology.Topology attribute)

add_selected_indices() (pytraj.core.c_core.AtomMask method)

align_principal_axis() (in module pytraj.all_actions)

(pytraj.trajectory.Trajectory method)

angle() (in module pytraj)

angle_indices (pytraj.topology.Topology attribute)

angles (pytraj.topology.Topology attribute)

append() (pytraj.trajectory.Trajectory method)

append_xyz() (pytraj.frame.Frame method)

(pytraj.trajectory.Trajectory method)

ArgList (class in pytraj.core.c_core)

as_2darray() (in module pytraj.tools)

as_3darray() (in module pytraj.tools)

at() (pytraj.trajectory.Trajectory method)

(pytraj.trajectory_iterator.TrajectoryIterator method)

atom() (pytraj.frame.Frame method)

(pytraj.topology.Topology method)

atom_indices() (pytraj.topology.Topology method)

atom_names (pytraj.topology.Topology attribute)

atomic_number (pytraj.topology.SimplifiedAtom attribute)

atomlist (pytraj.topology.Topology attribute)

AtomMask (class in pytraj.core.c_core)

atoms (pytraj.topology.SimplifiedTopology attribute)

(pytraj.topology.Topology attribute)

autoimage() (in module pytraj), [1]

(in module pytraj.all_actions)
(pytraj.trajectory.Trajectory method)

B

bfactors() (in module pytraj)
block_average() (in module pytraj.tools)
bond_indices (pytraj.topology.Topology attribute)
bonds (pytraj.topology.Topology attribute)

box (pytraj.frame.Frame attribute)

(pytraj.topology.Topology attribute)

box() (in module pytraj.vector)

boxcenter() (in module pytraj.vector)

C

calc_angle() (in module pytraj.all_actions)
calc_atomiccorr() (in module pytraj.all_actions)
calc_atomicfluct() (in module pytraj.all_actions)
calc_bfactors() (in module pytraj.all_actions)
calc_center_of_geometry() (in module pytraj.all_actions)
calc_center_of_mass() (in module pytraj.all_actions)
calc_COM() (in module pytraj.all_actions)
calc_diffusion() (in module pytraj.all_actions)
calc_dihedral() (in module pytraj.all_actions)
calc_distance() (in module pytraj.all_actions)
calc_distance_rmsd() (in module pytraj.all_actions)
calc_grid() (in module pytraj.all_actions)
calc_jcoupling() (in module pytraj.all_actions)
calc_matrix() (in module pytraj.all_actions)
calc_mindist() (in module pytraj.all_actions)
calc_molsurf() (in module pytraj.all_actions)
calc_multidihedral() (in module pytraj.all_actions)
calc_multivector() (in module pytraj.all_actions)
calc_pairdist() (in module pytraj.all_actions)
calc_pairwise_distance() (in module pytraj.all_actions)
calc_pairwise_rmsd() (in module pytraj.all_actions)
calc_pca() (in module pytraj.all_actions)
calc_radgyr() (in module pytraj.all_actions)
calc_rdf() (in module pytraj.all_actions)
calc_rmsd_nofit() (in module pytraj.all_actions)
calc_rotation_matrix() (in module pytraj.all_actions)

calc_surf() (in module pytraj.all_actions)

calc_vector() (in module pytraj)

(in module pytraj.all_actions)

calc_volmap() (in module pytraj.all_actions)

calc_volume() (in module pytraj.all_actions)

calc_watershell() (in module pytraj.all_actions)

center() (in module pytraj)

(in module pytraj.vector)
(pytraj.trajectory.Trajectory method)

center_of_geometry() (in module pytraj)

(pytraj.frame.Frame method)

center_of_mass() (in module pytraj)

(pytraj.frame.Frame method)

charge (pytraj.topology.SimplifiedAtom attribute)

(pytraj.topology.Topology attribute)

check_structure() (in module pytraj.all_actions)

check_topology() (pytraj.c_action.actionlist.ActionList method)

closest() (in module pytraj)

(in module pytraj.all_actions)

Command (class in pytraj.core.c_core)

command_is() (pytraj.core.c_core.ArgList method)

compose() (in module pytraj.tools)

compute() (pytraj.c_action.actionlist.ActionList method)

(pytraj.CpptrajState method)
(pytraj.core.c_core.CpptrajState method)

concat_dict() (in module pytraj.tools)

CoordinateInfo (class in pytraj.core.c_core)

coordinates (pytraj.frame.Frame attribute)

copy() (pytraj.core.c_core.NameType method)

(pytraj.frame.Frame method)
(pytraj.topology.Topology method)
(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)

correl() (in module pytraj.matrix)

corrplane() (in module pytraj.vector)

count() (pytraj.topology.SimplifiedAtom method)

(pytraj.topology.SimplifiedResidue method)
(pytraj.topology.SimplifiedTopology method)

covar() (in module pytraj.matrix)

CpptrajState (class in pytraj)

(class in pytraj.core.c_core)

crank() (in module pytraj)

D

data (pytraj.c_action.actionlist.ActionList attribute)

(pytraj.CpptrajState attribute)
(pytraj.core.c_core.CpptrajState attribute)
(pytraj.hbond_.DatasetHBond attribute)

datafilelist (pytraj.core.c_core.CpptrajState attribute)

(pytraj.CpptrajState attribute)

DatasetHBond (class in pytraj.hbond_)

datasetlist (pytraj.core.c_core.CpptrajState attribute)

(pytraj.CpptrajState attribute)

diagonalize() (in module pytraj.matrix)

dict_to_ndarray() (in module pytraj.tools)

dihcovar() (in module pytraj.matrix)

dihedral() (in module pytraj)

dihedral_indices (pytraj.topology.Topology attribute)

dihedrals (pytraj.topology.Topology attribute)

dipole() (in module pytraj.vector)

dir_() (in module pytraj.tools)

dispatch() (in module pytraj)

(pytraj.core.c_core.Command method)

dist() (in module pytraj.matrix)

distance() (in module pytraj)

distcovar() (in module pytraj.matrix)

do() (in module pytraj.c_action.actionlist)

donor_acceptor (pytraj.hbond_.DatasetHBond attribute)

dssp() (in module pytraj)

E

element (pytraj.topology.SimplifiedAtom attribute)

estimate_size() (in module pytraj.tools)

F

filelist (pytraj.trajectory_iterator.TrajectoryIterator attribute)

FileName (class in pytraj.core.c_core)

filename (pytraj.topology.Topology attribute)

(pytraj.trajectory_iterator.TrajectoryIterator attribute)

filename() (pytraj.topology.ParmFile method)

find_lib() (in module pytraj.tools)

first_atom_index (pytraj.topology.SimplifiedResidue attribute)

flatten() (in module pytraj.tools)

force (pytraj.frame.Frame attribute)
Frame (class in pytraj.frame)
FrameIterator (class in pytraj.frameiter)
from_dict() (pytraj.topology.Topology method)
from_iterable() (pytraj.trajectory.Trajectory class method)
fullname (pytraj.core.c_core.FileName attribute)

G

get_amber_mask() (pytraj.hbond_.DatasetHBond method)
get_average_frame() (in module pytraj.all_actions)
get_key_double() (pytraj.core.c_core.ArgList method)
get_key_int() (pytraj.core.c_core.ArgList method)
get_next_double() (pytraj.core.c_core.ArgList method)
get_next_integer() (pytraj.core.c_core.ArgList method)
get_next_mask() (pytraj.core.c_core.ArgList method)
get_next_string() (pytraj.core.c_core.ArgList method)

get_next_tag() (pytraj.core.c_core.ArgList method)
get_state() (pytraj.core.c_core.Command method)
get_state_from_string() (pytraj.core.c_core.Command method)
get_string_key() (pytraj.core.c_core.ArgList method)
get_velocity() (in module pytraj.all_actions)
grep_key() (in module pytraj.tools)
groupby() (in module pytraj.tools)

H

has_box() (pytraj.core.c_core.CoordinateInfo method)

(pytraj.frame.Frame method)
(pytraj.topology.Topology method)

has_force() (pytraj.core.c_core.CoordinateInfo method)

(pytraj.frame.Frame method)

has_key() (pytraj.core.c_core.ArgList method)

has_replica_dims() (pytraj.core.c_core.CoordinateInfo method)

has_temp() (pytraj.core.c_core.CoordinateInfo method)

has_time() (pytraj.core.c_core.CoordinateInfo method)
has_vel() (pytraj.core.c_core.CoordinateInfo method)
has_velocity() (pytraj.frame.Frame method)
hbond() (in module pytraj.hbond_)

I

idea() (in module pytraj.matrix)

index (pytraj.topology.SimplifiedAtom attribute)

(pytraj.topology.SimplifiedResidue attribute)

index() (pytraj.topology.SimplifiedTopology method)

indices (pytraj.core.c_core.AtomMask attribute)

indices_bonded_to() (pytraj.topology.Topology method)

invert_mask() (pytraj.core.c_core.AtomMask method)

is_() (pytraj.frame.Frame method)

is_empty() (pytraj.core.c_core.ArgList method)

(pytraj.core.c_core.AtomMask method)
(pytraj.topology.Topology method)

iterchunk() (in module pytraj)

(pytraj.trajectory_iterator.TrajectoryIterator method)

iterframe() (in module pytraj)

(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)

iteritems() (in module pytraj.tools)

iterload() (in module pytraj.io)

iterload_remd() (in module pytraj.io)

J

jcoupling() (in module pytraj)

join() (pytraj.topology.Topology method)

K

kmeans() (in module pytraj.cluster), [1]

L

last_atom_index (pytraj.topology.SimplifiedResidue attribute)

load() (in module pytraj.io)

(pytraj.topology.Topology method)
(pytraj.trajectory.Trajectory method)

load_batch() (in module pytraj)

load_cpptraj_file() (in module pytraj.io)

load_ParmEd() (in module pytraj.io)

load_pdb_rcsb() (in module pytraj.io)

load_pipeline() (in module pytraj)
load_remd() (in module pytraj.io)
load_sample_data() (in module pytraj.io)
load_topology() (in module pytraj.io)
lowestcurve() (in module pytraj.all_actions)

M

make_fake_topology() (in module pytraj.tools)

make_structure() (in module pytraj.all_actions)

mask_expression() (pytraj.core.c_core.AtomMask method)

mask_string (pytraj.core.c_core.AtomMask attribute)

mass (pytraj.frame.Frame attribute)

(pytraj.topology.SimplifiedAtom attribute)
(pytraj.topology.Topology attribute)

match() (pytraj.core.c_core.NameType method)

mean_and_error() (in module pytraj.tools)

mean_structure() (in module pytraj.all_actions)

merge_coordinates() (in module pytraj.tools)

merge_frame_from_trajs() (in module pytraj.tools)

merge_frames() (in module pytraj.tools)

merge_trajs() (in module pytraj.tools)
metadata (pytraj.trajectory_iterator.TrajectoryIterator attribute)
mindist() (in module pytraj)
minimage() (in module pytraj.vector)
moleculelist (pytraj.topology.Topology attribute)
molnum (pytraj.topology.SimplifiedAtom attribute)
mols (pytraj.topology.Topology attribute)
molsurf() (in module pytraj)
moving_average() (in module pytraj.tools)
multidihedral() (in module pytraj)
mwcovar() (in module pytraj.matrix)

N

n_args (pytraj.core.c_core.ArgList attribute)

n_atoms (pytraj.core.c_core.AtomMask attribute)

(pytraj.frame.Frame attribute)
(pytraj.frameiter.FrameIterator attribute)
(pytraj.topology.Topology attribute)
(pytraj.trajectory.Trajectory attribute)
(pytraj.trajectory_iterator.TrajectoryIterator attribute)

n_frames (pytraj.c_action.actionlist.ActionList attribute)

(pytraj.frame.Frame attribute)
(pytraj.frameiter.FrameIterator attribute)
(pytraj.trajectory.Trajectory attribute)
(pytraj.trajectory_iterator.TrajectoryIterator attribute)

n_grams() (in module pytraj.tools)

n_mols (pytraj.topology.Topology attribute)

n_residues (pytraj.topology.Topology attribute)

n_selected (pytraj.core.c_core.AtomMask attribute)

n_solvents (pytraj.topology.Topology attribute)

name (pytraj.topology.SimplifiedAtom attribute)

(pytraj.topology.SimplifiedResidue attribute)

NameType (class in pytraj.core.c_core)

nastruct() (in module pytraj)

native_contacts() (in module pytraj.all_actions)

P

pairwise_rmsd() (in module pytraj)

ParmFile (class in pytraj.topology)

pipe() (in module pytraj.c_action.actionlist)

pmap() (in module pytraj.parallel.multiprocessing_)

pmap_mpi() (in module pytraj.parallel.mpi)

principal() (in module pytraj.vector)

principal_axes() (in module pytraj)

(in module pytraj.all_actions)

projection() (in module pytraj.all_actions)

pucker() (in module pytraj.all_actions)

pytraj (module)

pytraj.all_actions (module)

pytraj.c_action.actionlist (module)

pytraj.cluster (module)

pytraj.core.c_core (module)
pytraj.frame (module)
pytraj.frameiter (module)
pytraj.hbond_ (module)
pytraj.io (module)
pytraj.matrix (module)
pytraj.parallel.mpi (module)
pytraj.parallel.multiprocessing_ (module)
pytraj.tools (module)
pytraj.topology (module)
pytraj.trajectory (module)
pytraj.trajectory_iterator (module)
pytraj.vector (module)

R

radgyr() (in module pytraj)

randomize_ions() (in module pytraj)

(in module pytraj.all_actions)

read_gaussian_output() (in module pytraj.tools)

read_json() (in module pytraj.io)

read_parm() (in module pytraj.io)

read_pickle() (in module pytraj.io)

read_to_array() (in module pytraj.tools)

readparm() (pytraj.topology.ParmFile method)

replace_asterisk() (pytraj.core.c_core.NameType method)

replicate_cell() (in module pytraj)

(in module pytraj.all_actions)

resid (pytraj.topology.SimplifiedAtom attribute)

residue() (pytraj.topology.Topology method)

residue_names (pytraj.topology.Topology attribute)

residuelist (pytraj.topology.Topology attribute)

residues (pytraj.topology.SimplifiedTopology attribute)

(pytraj.topology.Topology attribute)

resname (pytraj.topology.SimplifiedAtom attribute)

reverse() (pytraj.trajectory.Trajectory method)

rmsd() (in module pytraj), [1]

(in module pytraj.all_actions)
(in module pytraj.tools)
(pytraj.frame.Frame method)

rmsd_1darray() (in module pytraj.tools)

rmsd_nofit() (pytraj.frame.Frame method)

rmsd_perres() (in module pytraj)

(in module pytraj.all_actions)

rmsfit() (pytraj.frame.Frame method)

(pytraj.trajectory.Trajectory method)

rotate() (in module pytraj)

(in module pytraj.all_actions)
(pytraj.trajectory.Trajectory method)

rotate_dihedral() (in module pytraj)

run() (in module pytraj)

(pytraj.CpptrajState method)
(pytraj.core.c_core.CpptrajState method)

S

save() (in module pytraj.io)

(pytraj.frameiter.FrameIterator method)
(pytraj.topology.Topology method)
(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)

scale() (in module pytraj)

(in module pytraj.all_actions)
(pytraj.trajectory.Trajectory method)

search_hbonds() (in module pytraj)

search_neighbors() (in module pytraj)

(in module pytraj.all_actions)

select() (in module pytraj)

(pytraj.topology.Topology method)

select_atoms() (in module pytraj)

selected_indices() (pytraj.core.c_core.AtomMask method)

set_cpptraj_verbose() (in module pytraj)

set_dihedral() (in module pytraj.all_actions)

set_distance_mask_reference() (pytraj.topology.Topology method)

set_integer_mask() (pytraj.topology.Topology method)

set_mass() (pytraj.frame.Frame method)

set_nobox() (pytraj.frame.Frame method)

(pytraj.topology.Topology method)

set_solvent() (pytraj.topology.Topology method)

shape (pytraj.frame.Frame attribute)

(pytraj.trajectory.Trajectory attribute)
(pytraj.trajectory_iterator.TrajectoryIterator attribute)

show() (in module pytraj)

show_versions() (in module pytraj)

SimplifiedAtom (class in pytraj.topology)

SimplifiedResidue (class in pytraj.topology)

SimplifiedTopology (class in pytraj.topology)

simplify() (pytraj.topology.Topology method)

size (pytraj.frame.Frame attribute)

split() (in module pytraj.tools)

split_and_write_traj() (in module pytraj.tools)

split_traj_by_residues() (in module pytraj.tools)

start_new_mol() (pytraj.topology.Topology method)

strip() (in module pytraj)

(pytraj.frame.Frame method)
(pytraj.topology.Topology method)
(pytraj.trajectory.Trajectory method)

summary() (pytraj.topology.Topology method)

superpose() (in module pytraj), [1]

(pytraj.trajectory.Trajectory method)

swap_atoms (pytraj.frame.Frame attribute)

T

temperature (pytraj.frame.Frame attribute)

temperatures (pytraj.trajectory_iterator.TrajectoryIterator attribute)

time (pytraj.frame.Frame attribute)

timecorr() (in module pytraj)

(in module pytraj.all_actions)

to_buffer() (pytraj.core.c_core.NameType method)

to_dataframe() (pytraj.topology.Topology method)

to_dict() (pytraj.hbond_.DatasetHBond method)

(pytraj.topology.Topology method)

to_json() (in module pytraj.io)

to_ndarray() (pytraj.frame.Frame method)

to_parmed() (pytraj.topology.Topology method)

to_pickle() (in module pytraj.io)

top (pytraj.frame.Frame attribute)

(pytraj.trajectory.Trajectory attribute)
(pytraj.trajectory_iterator.TrajectoryIterator attribute)

Topology (class in pytraj.topology)

topology (pytraj.trajectory.Trajectory attribute)

(pytraj.trajectory_iterator.TrajectoryIterator attribute)

total_solute_hbonds() (pytraj.hbond_.DatasetHBond method)

traj_box() (pytraj.core.c_core.CoordinateInfo method)

Trajectory (class in pytraj.trajectory)

TrajectoryIterator (class in pytraj.trajectory_iterator)

transform() (in module pytraj)

(in module pytraj.all_actions)
(pytraj.trajectory.Trajectory method)

translate() (in module pytraj)

(in module pytraj.all_actions)
(pytraj.trajectory.Trajectory method)

truncated_name (pytraj.core.c_core.NameType attribute)

type (pytraj.topology.SimplifiedAtom attribute)

U

ucellx() (in module pytraj.vector)
ucelly() (in module pytraj.vector)

ucellz() (in module pytraj.vector)

unitcells (pytraj.trajectory.Trajectory attribute)

(pytraj.trajectory_iterator.TrajectoryIterator attribute)

V

values (pytraj.hbond_.DatasetHBond attribute)
vdw_radii (pytraj.topology.Topology attribute)
vector_mask() (in module pytraj.vector)

velocity (pytraj.frame.Frame attribute)
volume() (in module pytraj)

W

watershell() (in module pytraj)
write_parm() (in module pytraj.io)

write_traj() (in module pytraj)

(in module pytraj.io)

writeparm() (pytraj.topology.ParmFile method)

X

xcorr() (in module pytraj)

(in module pytraj.all_actions)

xyz (pytraj.frame.Frame attribute)

(pytraj.trajectory.Trajectory attribute)
(pytraj.trajectory_iterator.TrajectoryIterator attribute)