Index

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

A

acorr() (in module pytraj), [1]
(in module pytraj.all_actions)
ActionDict (class in pytraj)
ActionList (class in pytraj)
add() (pytraj.ActionList method)
add_angles (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
add_atom() (pytraj.AtomMask method)
(pytraj.Topology method)
(pytraj.core.c_core.AtomMask method)
(pytraj.topology.topology.Topology method)
add_atom_range() (pytraj.AtomMask method)
(pytraj.core.c_core.AtomMask method)
add_atoms() (pytraj.AtomMask method)
(pytraj.core.c_core.AtomMask method)
add_bonds (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
add_dihedrals (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
add_frame() (pytraj.datasets.c_datasets.DatasetCoords method)
(pytraj.datasets.c_datasets.DatasetCoordsCRD method)
(pytraj.datasets.c_datasets.DatasetCoordsRef method)
add_selected_indices() (pytraj.AtomMask method)
(pytraj.core.c_core.AtomMask method)
align_principal_axis() (in module pytraj)
(in module pytraj.all_actions)
(pytraj.Trajectory method)
(pytraj.trajectory.trajectory.Trajectory method)
allocate_frame() (pytraj.datasets.c_datasets.DatasetCoords method)
(pytraj.datasets.c_datasets.DatasetCoordsCRD method)
(pytraj.datasets.c_datasets.DatasetCoordsRef method)
AnalysisDict (class in pytraj)
angle() (in module pytraj), [1]
(in module pytraj.all_actions)
angle_indices (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
angles (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
append() (pytraj.datasets.c_datasets.DatasetCoords method)
(pytraj.Trajectory method)
(pytraj.datasets.c_datasets.DatasetCoordsCRD method)
(pytraj.datasets.c_datasets.DatasetCoordsRef method)
(pytraj.datasets.c_datasets.DatasetDouble method)
(pytraj.datasets.c_datasets.DatasetFloat method)
(pytraj.datasets.c_datasets.DatasetInteger method)
(pytraj.datasets.c_datasets.DatasetMatrix3x3 method)
(pytraj.datasets.c_datasets.DatasetMatrixDouble method)
(pytraj.datasets.c_datasets.DatasetVector method)
(pytraj.trajectory.trajectory.Trajectory method)
append_xyz() (pytraj.Frame method)
(pytraj.Trajectory method)
(pytraj.trajectory.frame.Frame method)
(pytraj.trajectory.trajectory.Trajectory method)
ArgList (class in pytraj.core.c_core)
as_2darray() (in module pytraj.utils.tools)
as_3darray() (in module pytraj.utils.tools)
aspect (pytraj.datasets.c_datasets.Dataset attribute)
(pytraj.datasets.c_datasets.Dataset1D attribute)
(pytraj.datasets.c_datasets.Dataset2D attribute)
(pytraj.datasets.c_datasets.Dataset3D attribute)
(pytraj.datasets.c_datasets.DatasetCoords attribute)
(pytraj.datasets.c_datasets.DatasetCoordsCRD attribute)
(pytraj.datasets.c_datasets.DatasetCoordsRef attribute)
(pytraj.datasets.c_datasets.DatasetDouble attribute)
(pytraj.datasets.c_datasets.DatasetFloat attribute)
(pytraj.datasets.c_datasets.DatasetGridDouble attribute)
(pytraj.datasets.c_datasets.DatasetGridFloat attribute)
(pytraj.datasets.c_datasets.DatasetInteger attribute)
(pytraj.datasets.c_datasets.DatasetMatrix3x3 attribute)
(pytraj.datasets.c_datasets.DatasetMatrixDouble attribute)
(pytraj.datasets.c_datasets.DatasetMatrixFloat attribute)
(pytraj.datasets.c_datasets.DatasetMesh attribute)
(pytraj.datasets.c_datasets.DatasetModes attribute)
(pytraj.datasets.c_datasets.DatasetString attribute)
(pytraj.datasets.c_datasets.DatasetTopology attribute)
(pytraj.datasets.c_datasets.DatasetVector attribute)
at() (pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.trajectory.Trajectory method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
Atom (class in pytraj)
atom() (pytraj.Frame method)
(pytraj.Topology method)
(pytraj.topology.topology.Topology method)
(pytraj.trajectory.frame.Frame method)
atom_indices() (pytraj.Topology method)
(pytraj.topology.topology.Topology method)
atom_names (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
atomic_number (pytraj.Atom attribute)
(pytraj.topology.topology.SimplifiedAtom attribute)
atomiccorr() (in module pytraj)
(in module pytraj.all_actions)
atomicfluct() (in module pytraj)
(in module pytraj.all_actions)
atomlist (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
AtomMask (class in pytraj)
(class in pytraj.core.c_core)
atoms (pytraj.Topology attribute)
(pytraj.topology.topology.SimplifiedTopology attribute)
(pytraj.topology.topology.Topology attribute)
autoimage() (in module pytraj), [1], [2]
(in module pytraj.all_actions)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.trajectory.Trajectory method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)

B

begin_atom (pytraj.Molecule attribute)
bfactors() (in module pytraj), [1]
(in module pytraj.all_actions)
block_average() (in module pytraj.utils.tools)
bond_indices (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
bonded_indices() (pytraj.Atom method)
bonds (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
box (pytraj.Frame attribute)
(pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
(pytraj.trajectory.frame.Frame attribute)
box() (in module pytraj.analysis.vector), [1]
boxcenter() (in module pytraj.analysis.vector), [1]

C

calc_alpha() (in module pytraj)
(in module pytraj.analysis.dihedral_analysis)
calc_beta() (in module pytraj)
(in module pytraj.analysis.dihedral_analysis)
calc_chin() (in module pytraj)
(in module pytraj.analysis.dihedral_analysis)
calc_chip() (in module pytraj)
(in module pytraj.analysis.dihedral_analysis)
calc_delta() (in module pytraj)
(in module pytraj.analysis.dihedral_analysis)
calc_epsilon() (in module pytraj)
(in module pytraj.analysis.dihedral_analysis)
calc_gamma() (in module pytraj)
(in module pytraj.analysis.dihedral_analysis)
calc_ired_vector_and_matrix() (in module pytraj.analysis.nmr)
calc_multidihedral() (in module pytraj)
(in module pytraj.analysis.dihedral_analysis)
calc_NH_order_parameters() (in module pytraj.analysis.nmr)
calc_nu1() (in module pytraj)
(in module pytraj.analysis.dihedral_analysis)
calc_nu2() (in module pytraj)
(in module pytraj.analysis.dihedral_analysis)
calc_omega() (in module pytraj)
(in module pytraj.analysis.dihedral_analysis)
calc_phi() (in module pytraj)
(in module pytraj.analysis.dihedral_analysis)
calc_psi() (in module pytraj)
(in module pytraj.analysis.dihedral_analysis)
calc_vector() (in module pytraj)
calc_zeta() (in module pytraj)
(in module pytraj.analysis.dihedral_analysis)
center() (in module pytraj), [1]
(in module pytraj.all_actions)
(in module pytraj.analysis.vector), [1]
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.trajectory.Trajectory method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
center_of_geometry() (in module pytraj), [1]
(in module pytraj.all_actions)
(pytraj.Frame method)
(pytraj.trajectory.frame.Frame method)
center_of_mass() (in module pytraj), [1]
(in module pytraj.all_actions)
(pytraj.Frame method)
(pytraj.trajectory.frame.Frame method)
chain (pytraj.Atom attribute)
charge (pytraj.Atom attribute)
(pytraj.Topology attribute)
(pytraj.topology.topology.SimplifiedAtom attribute)
(pytraj.topology.topology.Topology attribute)
check_structure() (in module pytraj)
(in module pytraj.all_actions)
close() (pytraj.TrajectoryWriter method)
closest() (in module pytraj), [1]
(in module pytraj.all_actions)
clustering_dataset() (in module pytraj.cluster)
Command (class in pytraj.core.c_core)
command_is() (pytraj.core.c_core.ArgList method)
compose() (in module pytraj.utils.tools)
compute() (pytraj.ActionList method)
concat_dict() (in module pytraj.utils.tools)
coordinates (pytraj.Frame attribute)
(pytraj.trajectory.frame.Frame attribute)
copy() (pytraj.Atom method)
(pytraj.Frame method)
(pytraj.Topology method)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.core.c_core.NameType method)
(pytraj.topology.topology.Topology method)
(pytraj.trajectory.frame.Frame method)
(pytraj.trajectory.trajectory.Trajectory method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
correl() (in module pytraj.analysis.matrix), [1]
corrplane() (in module pytraj.analysis.vector), [1]
count() (pytraj.topology.topology.SimplifiedAtom method)
(pytraj.topology.topology.SimplifiedResidue method)
(pytraj.topology.topology.SimplifiedTopology method)
covar() (in module pytraj.analysis.matrix), [1]
CpptrajState (class in pytraj)
(class in pytraj.core.c_core)
crank() (in module pytraj)

D

data (pytraj.ActionList attribute)
(pytraj.CpptrajState attribute)
(pytraj.analysis.hbond_analysis.DatasetHBond attribute), [1]
(pytraj.core.c_core.CpptrajState attribute)
(pytraj.datasets.c_datasets.Dataset attribute)
(pytraj.datasets.c_datasets.Dataset1D attribute)
(pytraj.datasets.c_datasets.Dataset2D attribute)
(pytraj.datasets.c_datasets.Dataset3D attribute)
(pytraj.datasets.c_datasets.DatasetCoords attribute)
(pytraj.datasets.c_datasets.DatasetCoordsCRD attribute)
(pytraj.datasets.c_datasets.DatasetCoordsRef attribute)
(pytraj.datasets.c_datasets.DatasetDouble attribute)
(pytraj.datasets.c_datasets.DatasetFloat attribute)
(pytraj.datasets.c_datasets.DatasetGridDouble attribute)
(pytraj.datasets.c_datasets.DatasetGridFloat attribute)
(pytraj.datasets.c_datasets.DatasetInteger attribute)
(pytraj.datasets.c_datasets.DatasetMatrix3x3 attribute)
(pytraj.datasets.c_datasets.DatasetMatrixDouble attribute)
(pytraj.datasets.c_datasets.DatasetMatrixFloat attribute)
(pytraj.datasets.c_datasets.DatasetMesh attribute)
(pytraj.datasets.c_datasets.DatasetModes attribute)
(pytraj.datasets.c_datasets.DatasetString attribute)
(pytraj.datasets.c_datasets.DatasetTopology attribute)
(pytraj.datasets.c_datasets.DatasetVector attribute)
datafilelist (pytraj.core.c_core.CpptrajState attribute)
(pytraj.CpptrajState attribute)
Dataset (class in pytraj.datasets.c_datasets)
Dataset1D (class in pytraj.datasets.c_datasets)
Dataset2D (class in pytraj.datasets.c_datasets)
Dataset3D (class in pytraj.datasets.c_datasets)
DatasetCoords (class in pytraj.datasets.c_datasets)
DatasetCoordsCRD (class in pytraj.datasets.c_datasets)
DatasetCoordsRef (class in pytraj.datasets.c_datasets)
DatasetDouble (class in pytraj.datasets.c_datasets)
DatasetFloat (class in pytraj.datasets.c_datasets)
DatasetGridDouble (class in pytraj.datasets.c_datasets)
DatasetGridFloat (class in pytraj.datasets.c_datasets)
DatasetHBond (class in pytraj.analysis.hbond_analysis), [1]
DatasetInteger (class in pytraj.datasets.c_datasets)
DatasetMatrix3x3 (class in pytraj.datasets.c_datasets)
DatasetMatrixDouble (class in pytraj.datasets.c_datasets)
DatasetMatrixFloat (class in pytraj.datasets.c_datasets)
DatasetMesh (class in pytraj.datasets.c_datasets)
DatasetModes (class in pytraj.datasets.c_datasets)
DatasetRemLog (class in pytraj.datasets.c_datasets)
DatasetString (class in pytraj.datasets.c_datasets)
DatasetTopology (class in pytraj.datasets.c_datasets)
DatasetVector (class in pytraj.datasets.c_datasets)
dbscan() (in module pytraj.cluster)
density() (in module pytraj), [1]
(in module pytraj.all_actions)
diagonalize() (in module pytraj.analysis.matrix), [1]
dict_to_ndarray() (in module pytraj.utils.tools)
diffusion() (in module pytraj)
(in module pytraj.all_actions)
dihcovar() (in module pytraj.analysis.matrix), [1]
dihedral() (in module pytraj)
(in module pytraj.all_actions)
dihedral_indices (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
dihedrals (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
dipole() (in module pytraj.analysis.vector), [1]
dir_() (in module pytraj.utils.tools)
dispatch() (in module pytraj)
(pytraj.core.c_core.Command method)
dist() (in module pytraj.analysis.matrix), [1]
distance() (in module pytraj), [1]
(in module pytraj.all_actions)
distance_rmsd() (in module pytraj)
(in module pytraj.all_actions)
distcovar() (in module pytraj.analysis.matrix), [1]
donor_acceptor (pytraj.analysis.hbond_analysis.DatasetHBond attribute), [1]
dpeaks() (in module pytraj.cluster)
dssp() (in module pytraj)
dtype (pytraj.datasets.c_datasets.Dataset attribute)
(pytraj.datasets.c_datasets.Dataset1D attribute)
(pytraj.datasets.c_datasets.Dataset2D attribute)
(pytraj.datasets.c_datasets.Dataset3D attribute)
(pytraj.datasets.c_datasets.DatasetCoords attribute)
(pytraj.datasets.c_datasets.DatasetCoordsCRD attribute)
(pytraj.datasets.c_datasets.DatasetCoordsRef attribute)
(pytraj.datasets.c_datasets.DatasetDouble attribute)
(pytraj.datasets.c_datasets.DatasetFloat attribute)
(pytraj.datasets.c_datasets.DatasetGridDouble attribute)
(pytraj.datasets.c_datasets.DatasetGridFloat attribute)
(pytraj.datasets.c_datasets.DatasetInteger attribute)
(pytraj.datasets.c_datasets.DatasetMatrix3x3 attribute)
(pytraj.datasets.c_datasets.DatasetMatrixDouble attribute)
(pytraj.datasets.c_datasets.DatasetMatrixFloat attribute)
(pytraj.datasets.c_datasets.DatasetMesh attribute)
(pytraj.datasets.c_datasets.DatasetModes attribute)
(pytraj.datasets.c_datasets.DatasetString attribute)
(pytraj.datasets.c_datasets.DatasetTopology attribute)
(pytraj.datasets.c_datasets.DatasetVector attribute)

E

eigenvalues (pytraj.datasets.c_datasets.DatasetModes attribute)
eigenvectors (pytraj.datasets.c_datasets.DatasetModes attribute)
eigval_to_freq() (pytraj.datasets.c_datasets.DatasetModes method)
element (pytraj.Atom attribute)
(pytraj.topology.topology.SimplifiedAtom attribute)
element() (pytraj.datasets.c_datasets.DatasetMatrixDouble method)
end_atom (pytraj.Molecule attribute)
esander() (in module pytraj)
(in module pytraj.analysis.energy_analysis), [1]
estimate_size() (in module pytraj.utils.tools)

F

filelist (pytraj.trajectory.trajectory_iterator.TrajectoryIterator attribute)
(pytraj.TrajectoryIterator attribute)
FileName (class in pytraj.core.c_core)
filename (pytraj.Topology attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.topology.topology.Topology attribute)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator attribute)
filename() (pytraj.topology.topology.ParmFile method)
first (pytraj.Residue attribute)
(pytraj.topology.topology.SimplifiedResidue attribute)
first_atom_index (pytraj.Residue attribute)
flatten() (in module pytraj.utils.tools)
force (pytraj.Frame attribute)
(pytraj.trajectory.frame.Frame attribute)
Frame (class in pytraj)
(class in pytraj.trajectory.frame)
FrameIterator (class in pytraj.trajectory.frameiter)
from_array_like() (pytraj.datasets.c_datasets.Dataset1D method)
(pytraj.datasets.c_datasets.DatasetDouble method)
(pytraj.datasets.c_datasets.DatasetFloat method)
(pytraj.datasets.c_datasets.DatasetInteger method)
(pytraj.datasets.c_datasets.DatasetMesh method)
(pytraj.datasets.c_datasets.DatasetString method)
from_dict() (pytraj.Topology method)
(pytraj.topology.topology.Topology method)
from_iterable() (pytraj.Trajectory class method)
(pytraj.trajectory.trajectory.Trajectory class method)
fullname (pytraj.core.c_core.FileName attribute)

G

gb_radius (pytraj.Atom attribute)
get_amber_mask() (pytraj.analysis.hbond_analysis.DatasetHBond method), [1]
get_average_frame() (in module pytraj)
(in module pytraj.all_actions)
get_element() (pytraj.datasets.c_datasets.Dataset2D method)
(pytraj.datasets.c_datasets.DatasetMatrixDouble method)
(pytraj.datasets.c_datasets.DatasetMatrixFloat method)
get_formats() (pytraj.TrajectoryWriter method)
get_frame() (pytraj.datasets.c_datasets.DatasetCoords method)
(pytraj.datasets.c_datasets.DatasetCoordsCRD method)
(pytraj.datasets.c_datasets.DatasetCoordsRef method)
get_full_matrix() (pytraj.datasets.c_datasets.Dataset2D method)
(pytraj.datasets.c_datasets.DatasetMatrixDouble method)
(pytraj.datasets.c_datasets.DatasetMatrixFloat method)
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)
(in module pytraj.all_actions)
gist() (in module pytraj)
(in module pytraj.all_actions)
grep_key() (in module pytraj.utils.tools)
grid() (in module pytraj)
(in module pytraj.all_actions)
groupby() (in module pytraj.utils.tools)

H

has_box() (pytraj.Frame method)
(pytraj.Topology method)
(pytraj.topology.topology.Topology method)
(pytraj.trajectory.frame.Frame method)
has_force() (pytraj.Frame method)
(pytraj.trajectory.frame.Frame method)
has_key() (pytraj.core.c_core.ArgList method)
has_velocity() (pytraj.Frame method)
(pytraj.trajectory.frame.Frame method)
hbond() (in module pytraj.analysis.hbond_analysis), [1]
help() (pytraj.TrajectoryWriter method)
hieragglo() (in module pytraj.cluster)

I

idea() (in module pytraj.analysis.matrix), [1]
image() (in module pytraj)
(in module pytraj.all_actions)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
index (pytraj.Atom attribute)
(pytraj.Residue attribute)
(pytraj.topology.topology.SimplifiedAtom attribute)
(pytraj.topology.topology.SimplifiedResidue attribute)
index() (pytraj.topology.topology.SimplifiedTopology method)
indices (pytraj.AtomMask attribute)
(pytraj.core.c_core.AtomMask attribute)
indices_bonded_to() (pytraj.Topology method)
(pytraj.topology.topology.Topology method)
invert_mask() (pytraj.AtomMask method)
(pytraj.core.c_core.AtomMask method)
ired_vector_and_matrix() (in module pytraj.analysis.nmr)
is_() (pytraj.Frame method)
(pytraj.trajectory.frame.Frame method)
is_bonded_to() (pytraj.Atom method)
is_empty() (pytraj.AtomMask method)
(pytraj.Topology method)
(pytraj.core.c_core.ArgList method)
(pytraj.core.c_core.AtomMask method)
(pytraj.topology.topology.Topology method)
is_setup (pytraj.ActionList attribute)
is_solvent() (pytraj.Molecule method)
(pytraj.Residue method)
iterchunk() (in module pytraj)
(in module pytraj.trajectory.frameiter)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
iterframe() (in module pytraj)
(in module pytraj.trajectory.frameiter)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.trajectory.Trajectory method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
iteritems() (in module pytraj.utils.tools)
iterload() (in module pytraj)
(in module pytraj.io)
iterload_remd() (in module pytraj)
(in module pytraj.io)

J

jcoupling() (in module pytraj), [1]
(in module pytraj.all_actions)
join() (pytraj.Topology method)
(pytraj.topology.topology.Topology method)

K

key (pytraj.datasets.c_datasets.Dataset attribute)
(pytraj.datasets.c_datasets.Dataset1D attribute)
(pytraj.datasets.c_datasets.Dataset2D attribute)
(pytraj.datasets.c_datasets.Dataset3D attribute)
(pytraj.datasets.c_datasets.DatasetCoords attribute)
(pytraj.datasets.c_datasets.DatasetCoordsCRD attribute)
(pytraj.datasets.c_datasets.DatasetCoordsRef attribute)
(pytraj.datasets.c_datasets.DatasetDouble attribute)
(pytraj.datasets.c_datasets.DatasetFloat attribute)
(pytraj.datasets.c_datasets.DatasetGridDouble attribute)
(pytraj.datasets.c_datasets.DatasetGridFloat attribute)
(pytraj.datasets.c_datasets.DatasetInteger attribute)
(pytraj.datasets.c_datasets.DatasetMatrix3x3 attribute)
(pytraj.datasets.c_datasets.DatasetMatrixDouble attribute)
(pytraj.datasets.c_datasets.DatasetMatrixFloat attribute)
(pytraj.datasets.c_datasets.DatasetMesh attribute)
(pytraj.datasets.c_datasets.DatasetModes attribute)
(pytraj.datasets.c_datasets.DatasetString attribute)
(pytraj.datasets.c_datasets.DatasetTopology attribute)
(pytraj.datasets.c_datasets.DatasetVector attribute)
keys() (pytraj.ActionDict method)
(pytraj.AnalysisDict method)
kind (pytraj.datasets.c_datasets.Dataset2D attribute)
(pytraj.datasets.c_datasets.DatasetMatrixDouble attribute)
(pytraj.datasets.c_datasets.DatasetMatrixFloat attribute)
kmeans() (in module pytraj.cluster), [1]

L

last (pytraj.Residue attribute)
(pytraj.topology.topology.SimplifiedResidue attribute)
last_atom_index (pytraj.Residue attribute)
load() (in module pytraj)
(in module pytraj.io)
(pytraj.Topology method)
(pytraj.Trajectory method)
(pytraj.datasets.c_datasets.DatasetCoordsCRD method)
(pytraj.topology.topology.Topology method)
(pytraj.trajectory.trajectory.Trajectory method)
load_antechamber() (in module pytraj)
(in module pytraj.io)
load_cpptraj_file() (in module pytraj)
(in module pytraj.io)
load_leap() (in module pytraj)
(in module pytraj.io)
load_parmed() (in module pytraj)
(in module pytraj.io)
load_pdb_rcsb() (in module pytraj)
(in module pytraj.io)
load_remd() (in module pytraj)
(in module pytraj.io)
load_sample_data() (in module pytraj)
(in module pytraj.io)
load_topology() (in module pytraj)
(in module pytraj.io)
lowestcurve() (in module pytraj)
(in module pytraj.all_actions)

M

make_fake_topology() (in module pytraj.utils.tools)
make_structure() (in module pytraj)
(in module pytraj.all_actions)
mask_expression() (pytraj.AtomMask method)
(pytraj.core.c_core.AtomMask method)
mask_string (pytraj.AtomMask attribute)
(pytraj.core.c_core.AtomMask attribute)
mass (pytraj.Atom attribute)
(pytraj.Frame attribute)
(pytraj.Topology attribute)
(pytraj.datasets.c_datasets.DatasetMatrixDouble attribute)
(pytraj.topology.topology.SimplifiedAtom attribute)
(pytraj.topology.topology.Topology attribute)
(pytraj.trajectory.frame.Frame attribute)
match() (pytraj.core.c_core.NameType method)
mean_and_error() (in module pytraj.utils.tools)
mean_structure() (in module pytraj)
(in module pytraj.all_actions)
merge_coordinates() (in module pytraj.utils.tools)
merge_frame_from_trajs() (in module pytraj.utils.tools)
merge_frames() (in module pytraj.utils.tools)
merge_trajs() (in module pytraj.utils.tools)
metadata (pytraj.trajectory.trajectory_iterator.TrajectoryIterator attribute)
(pytraj.TrajectoryIterator attribute)
mindist() (in module pytraj), [1]
(in module pytraj.all_actions)
minimage() (in module pytraj.analysis.vector), [1]
Molecule (class in pytraj)
moleculelist (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
molnum (pytraj.Atom attribute)
(pytraj.topology.topology.SimplifiedAtom attribute)
mols (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
molsurf() (in module pytraj), [1]
(in module pytraj.all_actions)
moving_average() (in module pytraj.utils.tools)
multidihedral() (in module pytraj), [1]
(in module pytraj.all_actions)
multivector() (in module pytraj)
(in module pytraj.all_actions)
mwcovar() (in module pytraj.analysis.matrix), [1]

N

n_args (pytraj.core.c_core.ArgList attribute)
n_atoms (pytraj.AtomMask attribute)
(pytraj.Frame attribute)
(pytraj.Molecule attribute)
(pytraj.Residue attribute)
(pytraj.Topology attribute)
(pytraj.Trajectory attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.core.c_core.AtomMask attribute)
(pytraj.datasets.c_datasets.DatasetCoords attribute)
(pytraj.datasets.c_datasets.DatasetCoordsCRD attribute)
(pytraj.datasets.c_datasets.DatasetCoordsRef attribute)
(pytraj.topology.topology.Topology attribute)
(pytraj.trajectory.frame.Frame attribute)
(pytraj.trajectory.frameiter.FrameIterator attribute)
(pytraj.trajectory.trajectory.Trajectory attribute)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator attribute)
n_bonds (pytraj.Atom attribute)
n_cols (pytraj.datasets.c_datasets.Dataset2D attribute)
(pytraj.datasets.c_datasets.DatasetMatrixDouble attribute)
(pytraj.datasets.c_datasets.DatasetMatrixFloat attribute)
n_frames (pytraj.ActionList attribute)
(pytraj.Frame attribute)
(pytraj.Trajectory attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.datasets.c_datasets.DatasetCoords attribute)
(pytraj.datasets.c_datasets.DatasetCoordsCRD attribute)
(pytraj.datasets.c_datasets.DatasetCoordsRef attribute)
(pytraj.trajectory.frame.Frame attribute)
(pytraj.trajectory.frameiter.FrameIterator attribute)
(pytraj.trajectory.trajectory.Trajectory attribute)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator attribute)
n_grams() (in module pytraj.utils.tools)
n_modes (pytraj.datasets.c_datasets.DatasetModes attribute)
n_mols (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
n_residues (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
n_rows (pytraj.datasets.c_datasets.Dataset2D attribute)
(pytraj.datasets.c_datasets.DatasetMatrixDouble attribute)
(pytraj.datasets.c_datasets.DatasetMatrixFloat attribute)
n_selected (pytraj.AtomMask attribute)
(pytraj.core.c_core.AtomMask attribute)
n_snapshots (pytraj.datasets.c_datasets.DatasetMatrixDouble attribute)
n_solvents (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
name (pytraj.Atom attribute)
(pytraj.Residue attribute)
(pytraj.datasets.c_datasets.Dataset attribute)
(pytraj.datasets.c_datasets.Dataset1D attribute)
(pytraj.datasets.c_datasets.Dataset2D attribute)
(pytraj.datasets.c_datasets.Dataset3D attribute)
(pytraj.datasets.c_datasets.DatasetCoords attribute)
(pytraj.datasets.c_datasets.DatasetCoordsCRD attribute)
(pytraj.datasets.c_datasets.DatasetCoordsRef attribute)
(pytraj.datasets.c_datasets.DatasetDouble attribute)
(pytraj.datasets.c_datasets.DatasetFloat attribute)
(pytraj.datasets.c_datasets.DatasetGridDouble attribute)
(pytraj.datasets.c_datasets.DatasetGridFloat attribute)
(pytraj.datasets.c_datasets.DatasetInteger attribute)
(pytraj.datasets.c_datasets.DatasetMatrix3x3 attribute)
(pytraj.datasets.c_datasets.DatasetMatrixDouble attribute)
(pytraj.datasets.c_datasets.DatasetMatrixFloat attribute)
(pytraj.datasets.c_datasets.DatasetMesh attribute)
(pytraj.datasets.c_datasets.DatasetModes attribute)
(pytraj.datasets.c_datasets.DatasetString attribute)
(pytraj.datasets.c_datasets.DatasetTopology attribute)
(pytraj.datasets.c_datasets.DatasetVector attribute)
(pytraj.topology.topology.SimplifiedAtom attribute)
(pytraj.topology.topology.SimplifiedResidue attribute)
NameType (class in pytraj.core.c_core)
nastruct() (in module pytraj), [1]
native_contacts() (in module pytraj)
(in module pytraj.all_actions)
NH_order_parameters() (in module pytraj.analysis.nmr)
ntype() (pytraj.Residue method)
nx (pytraj.datasets.c_datasets.DatasetGridDouble attribute)
(pytraj.datasets.c_datasets.DatasetGridFloat attribute)
ny (pytraj.datasets.c_datasets.DatasetGridDouble attribute)
(pytraj.datasets.c_datasets.DatasetGridFloat attribute)
nz (pytraj.datasets.c_datasets.DatasetGridDouble attribute)
(pytraj.datasets.c_datasets.DatasetGridFloat attribute)

O

open() (pytraj.TrajectoryWriter method)
original_resid (pytraj.Residue attribute)

P

pairdist() (in module pytraj)
(in module pytraj.all_actions)
pairwise_distance() (in module pytraj)
(in module pytraj.all_actions)
pairwise_rmsd() (in module pytraj), [1]
(in module pytraj.all_actions)
ParmFile (class in pytraj.topology.topology)
pca() (in module pytraj)
(in module pytraj.all_actions)
pmap() (in module pytraj.parallel.multiprocess)
pmap_mpi() (in module pytraj.parallel.mpi)
post_process() (pytraj.ActionList method)
principal() (in module pytraj.analysis.vector), [1]
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
principal_axes() (in module pytraj), [1]
(in module pytraj.all_actions)
projection() (in module pytraj)
(in module pytraj.all_actions)
pucker() (in module pytraj)
(in module pytraj.all_actions)
pytraj (module)
pytraj.all_actions (module)
pytraj.analysis.dihedral_analysis (module)
pytraj.analysis.energy_analysis (module), [1]
pytraj.analysis.hbond_analysis (module), [1]
pytraj.analysis.matrix (module), [1]
pytraj.analysis.nmr (module)
pytraj.analysis.vector (module), [1]
pytraj.cluster (module)
pytraj.core.c_core (module)
pytraj.datasets.c_datasets (module)
pytraj.io (module)
pytraj.parallel.mpi (module)
pytraj.parallel.multiprocess (module)
pytraj.topology.topology (module)
pytraj.trajectory.frame (module)
pytraj.trajectory.frameiter (module)
pytraj.trajectory.trajectory (module)
pytraj.trajectory.trajectory_iterator (module)
pytraj.utils.tools (module)

R

radgyr() (in module pytraj), [1]
(in module pytraj.all_actions)
randomize_ions() (in module pytraj), [1]
(in module pytraj.all_actions)
rdf() (in module pytraj)
(in module pytraj.all_actions)
read_gaussian_output() (in module pytraj.utils.tools)
read_pickle() (in module pytraj)
(in module pytraj.io)
read_to_array() (in module pytraj.utils.tools)
readinfo() (in module pytraj.cluster)
readparm() (pytraj.topology.topology.ParmFile method)
replace_asterisk() (pytraj.core.c_core.NameType method)
ReplicaFrame (class in pytraj.datasets.c_datasets)
replicate_cell() (in module pytraj), [1]
(in module pytraj.all_actions)
resid (pytraj.Atom attribute)
(pytraj.topology.topology.SimplifiedAtom attribute)
Residue (class in pytraj)
residue() (pytraj.Topology method)
(pytraj.topology.topology.Topology method)
residue_names (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
residuelist (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
residues (pytraj.Topology attribute)
(pytraj.topology.topology.SimplifiedTopology attribute)
(pytraj.topology.topology.Topology attribute)
resize() (pytraj.datasets.c_datasets.DatasetDouble method)
(pytraj.datasets.c_datasets.DatasetFloat method)
(pytraj.datasets.c_datasets.DatasetGridDouble method)
(pytraj.datasets.c_datasets.DatasetGridFloat method)
(pytraj.datasets.c_datasets.DatasetInteger method)
(pytraj.datasets.c_datasets.DatasetString method)
(pytraj.datasets.c_datasets.DatasetVector method)
resname (pytraj.Atom attribute)
(pytraj.topology.topology.SimplifiedAtom attribute)
reverse() (pytraj.Trajectory method)
(pytraj.trajectory.trajectory.Trajectory method)
rmsd() (in module pytraj), [1], [2]
(in module pytraj.all_actions)
(in module pytraj.utils.tools)
(pytraj.Frame method)
(pytraj.trajectory.frame.Frame method)
rmsd_1darray() (in module pytraj.utils.tools)
rmsd_nofit() (in module pytraj)
(in module pytraj.all_actions)
(pytraj.Frame method)
(pytraj.trajectory.frame.Frame method)
rmsd_perres() (in module pytraj), [1]
(in module pytraj.all_actions)
rmsfit() (pytraj.Frame method)
(pytraj.Trajectory method)
(pytraj.trajectory.frame.Frame method)
(pytraj.trajectory.trajectory.Trajectory method)
rotate() (in module pytraj), [1]
(in module pytraj.all_actions)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.trajectory.Trajectory method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
rotate_dihedral() (in module pytraj)
rotation_matrix() (in module pytraj)
(in module pytraj.all_actions)
run() (pytraj.core.c_core.CpptrajState method)
(pytraj.CpptrajState method)

S

save() (in module pytraj)
(in module pytraj.io)
(pytraj.Topology method)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.topology.topology.Topology method)
(pytraj.trajectory.frameiter.FrameIterator method)
(pytraj.trajectory.trajectory.Trajectory method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
scalar_type (pytraj.datasets.c_datasets.Dataset attribute)
(pytraj.datasets.c_datasets.Dataset1D attribute)
(pytraj.datasets.c_datasets.Dataset2D attribute)
(pytraj.datasets.c_datasets.Dataset3D attribute)
(pytraj.datasets.c_datasets.DatasetCoords attribute)
(pytraj.datasets.c_datasets.DatasetCoordsCRD attribute)
(pytraj.datasets.c_datasets.DatasetCoordsRef attribute)
(pytraj.datasets.c_datasets.DatasetDouble attribute)
(pytraj.datasets.c_datasets.DatasetFloat attribute)
(pytraj.datasets.c_datasets.DatasetGridDouble attribute)
(pytraj.datasets.c_datasets.DatasetGridFloat attribute)
(pytraj.datasets.c_datasets.DatasetInteger attribute)
(pytraj.datasets.c_datasets.DatasetMatrix3x3 attribute)
(pytraj.datasets.c_datasets.DatasetMatrixDouble attribute)
(pytraj.datasets.c_datasets.DatasetMatrixFloat attribute)
(pytraj.datasets.c_datasets.DatasetMesh attribute)
(pytraj.datasets.c_datasets.DatasetModes attribute)
(pytraj.datasets.c_datasets.DatasetString attribute)
(pytraj.datasets.c_datasets.DatasetTopology attribute)
(pytraj.datasets.c_datasets.DatasetVector attribute)
scale() (in module pytraj), [1]
(in module pytraj.all_actions)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.trajectory.Trajectory method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
search_hbonds() (in module pytraj)
search_neighbors() (in module pytraj), [1]
(in module pytraj.all_actions)
select() (in module pytraj)
(pytraj.Topology method)
(pytraj.topology.topology.Topology method)
select_atoms() (in module pytraj)
(in module pytraj.io)
selected_indices() (pytraj.AtomMask method)
(pytraj.core.c_core.AtomMask method)
set_cpptraj_verbose() (in module pytraj)
set_dihedral() (in module pytraj)
(in module pytraj.all_actions)
set_distance_mask_reference() (pytraj.Topology method)
(pytraj.topology.topology.Topology method)
set_element() (pytraj.datasets.c_datasets.DatasetMatrixDouble method)
set_first() (pytraj.Molecule method)
set_integer_mask() (pytraj.Topology method)
(pytraj.topology.topology.Topology method)
set_last() (pytraj.Molecule method)
set_last_atom() (pytraj.Residue method)
set_mass() (pytraj.Frame method)
(pytraj.trajectory.frame.Frame method)
set_mol() (pytraj.Atom method)
set_no_solvent() (pytraj.Molecule method)
set_nobox() (pytraj.Frame method)
(pytraj.Topology method)
(pytraj.topology.topology.Topology method)
(pytraj.trajectory.frame.Frame method)
set_solvent() (pytraj.Molecule method)
(pytraj.Topology method)
(pytraj.topology.topology.Topology method)
setup() (pytraj.ActionList method)
shape (pytraj.datasets.c_datasets.Dataset1D attribute)
(pytraj.Frame attribute)
(pytraj.Trajectory attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.datasets.c_datasets.DatasetDouble attribute)
(pytraj.datasets.c_datasets.DatasetFloat attribute)
(pytraj.datasets.c_datasets.DatasetGridDouble attribute)
(pytraj.datasets.c_datasets.DatasetGridFloat attribute)
(pytraj.datasets.c_datasets.DatasetInteger attribute)
(pytraj.datasets.c_datasets.DatasetMesh attribute)
(pytraj.datasets.c_datasets.DatasetString attribute)
(pytraj.datasets.c_datasets.DatasetVector attribute)
(pytraj.trajectory.frame.Frame attribute)
(pytraj.trajectory.trajectory.Trajectory attribute)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator attribute)
show_versions() (in module pytraj)
SimplifiedAtom (class in pytraj.topology.topology)
SimplifiedResidue (class in pytraj.topology.topology)
SimplifiedTopology (class in pytraj.topology.topology)
simplify() (pytraj.Topology method)
(pytraj.topology.topology.Topology method)
size (pytraj.datasets.c_datasets.Dataset attribute)
(pytraj.Frame attribute)
(pytraj.datasets.c_datasets.Dataset1D attribute)
(pytraj.datasets.c_datasets.Dataset2D attribute)
(pytraj.datasets.c_datasets.Dataset3D attribute)
(pytraj.datasets.c_datasets.DatasetCoords attribute)
(pytraj.datasets.c_datasets.DatasetCoordsCRD attribute)
(pytraj.datasets.c_datasets.DatasetCoordsRef attribute)
(pytraj.datasets.c_datasets.DatasetDouble attribute)
(pytraj.datasets.c_datasets.DatasetFloat attribute)
(pytraj.datasets.c_datasets.DatasetGridDouble attribute)
(pytraj.datasets.c_datasets.DatasetGridFloat attribute)
(pytraj.datasets.c_datasets.DatasetInteger attribute)
(pytraj.datasets.c_datasets.DatasetMatrix3x3 attribute)
(pytraj.datasets.c_datasets.DatasetMatrixDouble attribute)
(pytraj.datasets.c_datasets.DatasetMatrixFloat attribute)
(pytraj.datasets.c_datasets.DatasetMesh attribute)
(pytraj.datasets.c_datasets.DatasetModes attribute)
(pytraj.datasets.c_datasets.DatasetString attribute)
(pytraj.datasets.c_datasets.DatasetTopology attribute)
(pytraj.datasets.c_datasets.DatasetVector attribute)
(pytraj.trajectory.frame.Frame attribute)
split() (in module pytraj.utils.tools)
split_and_write_traj() (in module pytraj.utils.tools)
split_traj_by_residues() (in module pytraj.utils.tools)
start_new_mol() (pytraj.Topology method)
(pytraj.topology.topology.Topology method)
store_mass() (pytraj.datasets.c_datasets.DatasetMatrixDouble method)
strip() (in module pytraj)
(in module pytraj.all_actions)
(pytraj.Frame method)
(pytraj.Topology method)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.topology.topology.Topology method)
(pytraj.trajectory.frame.Frame method)
(pytraj.trajectory.trajectory.Trajectory method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
summary() (pytraj.Topology method)
(pytraj.topology.topology.Topology method)
superpose() (in module pytraj), [1]
(in module pytraj.all_actions)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.trajectory.Trajectory method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
surf() (in module pytraj)
(in module pytraj.all_actions)
swap_atoms (pytraj.Frame attribute)
(pytraj.trajectory.frame.Frame attribute)

T

temperature (pytraj.Frame attribute)
(pytraj.trajectory.frame.Frame attribute)
temperatures (pytraj.trajectory.trajectory_iterator.TrajectoryIterator attribute)
(pytraj.TrajectoryIterator attribute)
time (pytraj.Frame attribute)
(pytraj.trajectory.frame.Frame attribute)
timecorr() (in module pytraj), [1]
(in module pytraj.all_actions)
to_buffer() (pytraj.core.c_core.NameType method)
to_dataframe() (pytraj.datasets.c_datasets.Dataset2D method)
(pytraj.Topology method)
(pytraj.datasets.c_datasets.DatasetCoords method)
(pytraj.datasets.c_datasets.DatasetCoordsCRD method)
(pytraj.datasets.c_datasets.DatasetCoordsRef method)
(pytraj.datasets.c_datasets.DatasetMatrixDouble method)
(pytraj.datasets.c_datasets.DatasetMatrixFloat method)
(pytraj.datasets.c_datasets.DatasetVector method)
(pytraj.topology.topology.Topology method)
to_dict() (pytraj.analysis.hbond_analysis.DatasetHBond method), [1]
(pytraj.Topology method)
(pytraj.datasets.c_datasets.Dataset method)
(pytraj.datasets.c_datasets.Dataset1D method)
(pytraj.datasets.c_datasets.Dataset2D method)
(pytraj.datasets.c_datasets.Dataset3D method)
(pytraj.datasets.c_datasets.DatasetCoords method)
(pytraj.datasets.c_datasets.DatasetCoordsCRD method)
(pytraj.datasets.c_datasets.DatasetCoordsRef method)
(pytraj.datasets.c_datasets.DatasetDouble method)
(pytraj.datasets.c_datasets.DatasetFloat method)
(pytraj.datasets.c_datasets.DatasetGridDouble method)
(pytraj.datasets.c_datasets.DatasetGridFloat method)
(pytraj.datasets.c_datasets.DatasetInteger method)
(pytraj.datasets.c_datasets.DatasetMatrix3x3 method)
(pytraj.datasets.c_datasets.DatasetMatrixDouble method)
(pytraj.datasets.c_datasets.DatasetMatrixFloat method)
(pytraj.datasets.c_datasets.DatasetMesh method)
(pytraj.datasets.c_datasets.DatasetModes method)
(pytraj.datasets.c_datasets.DatasetString method)
(pytraj.datasets.c_datasets.DatasetTopology method)
(pytraj.datasets.c_datasets.DatasetVector method)
(pytraj.topology.topology.Topology method)
to_half_matrix() (pytraj.datasets.c_datasets.DatasetMatrixDouble method)
(pytraj.datasets.c_datasets.DatasetMatrixFloat method)
to_ndarray() (pytraj.datasets.c_datasets.Dataset method)
(pytraj.Frame method)
(pytraj.datasets.c_datasets.Dataset1D method)
(pytraj.datasets.c_datasets.Dataset2D method)
(pytraj.datasets.c_datasets.Dataset3D method)
(pytraj.datasets.c_datasets.DatasetCoords method)
(pytraj.datasets.c_datasets.DatasetCoordsCRD method)
(pytraj.datasets.c_datasets.DatasetCoordsRef method)
(pytraj.datasets.c_datasets.DatasetDouble method)
(pytraj.datasets.c_datasets.DatasetFloat method)
(pytraj.datasets.c_datasets.DatasetGridDouble method)
(pytraj.datasets.c_datasets.DatasetGridFloat method)
(pytraj.datasets.c_datasets.DatasetInteger method)
(pytraj.datasets.c_datasets.DatasetMatrix3x3 method)
(pytraj.datasets.c_datasets.DatasetMatrixDouble method)
(pytraj.datasets.c_datasets.DatasetMatrixFloat method)
(pytraj.datasets.c_datasets.DatasetMesh method)
(pytraj.datasets.c_datasets.DatasetModes method)
(pytraj.datasets.c_datasets.DatasetString method)
(pytraj.datasets.c_datasets.DatasetTopology method)
(pytraj.datasets.c_datasets.DatasetVector method)
(pytraj.trajectory.frame.Frame method)
to_parmed() (pytraj.Topology method)
(pytraj.topology.topology.Topology method)
to_pickle() (in module pytraj)
(in module pytraj.io)
tolist() (pytraj.datasets.c_datasets.Dataset method)
(pytraj.datasets.c_datasets.Dataset1D method)
(pytraj.datasets.c_datasets.Dataset2D method)
(pytraj.datasets.c_datasets.Dataset3D method)
(pytraj.datasets.c_datasets.DatasetCoords method)
(pytraj.datasets.c_datasets.DatasetCoordsCRD method)
(pytraj.datasets.c_datasets.DatasetCoordsRef method)
(pytraj.datasets.c_datasets.DatasetDouble method)
(pytraj.datasets.c_datasets.DatasetFloat method)
(pytraj.datasets.c_datasets.DatasetGridDouble method)
(pytraj.datasets.c_datasets.DatasetGridFloat method)
(pytraj.datasets.c_datasets.DatasetInteger method)
(pytraj.datasets.c_datasets.DatasetMatrix3x3 method)
(pytraj.datasets.c_datasets.DatasetMatrixDouble method)
(pytraj.datasets.c_datasets.DatasetMatrixFloat method)
(pytraj.datasets.c_datasets.DatasetMesh method)
(pytraj.datasets.c_datasets.DatasetModes method)
(pytraj.datasets.c_datasets.DatasetString method)
(pytraj.datasets.c_datasets.DatasetTopology method)
(pytraj.datasets.c_datasets.DatasetVector method)
top (pytraj.datasets.c_datasets.DatasetCoords attribute)
(pytraj.Frame attribute)
(pytraj.Trajectory attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.datasets.c_datasets.DatasetCoordsCRD attribute)
(pytraj.datasets.c_datasets.DatasetCoordsRef attribute)
(pytraj.trajectory.frame.Frame attribute)
(pytraj.trajectory.trajectory.Trajectory attribute)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator attribute)
Topology (class in pytraj)
(class in pytraj.topology.topology)
topology (pytraj.Trajectory attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.trajectory.trajectory.Trajectory attribute)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator attribute)
total_solute_hbonds() (pytraj.analysis.hbond_analysis.DatasetHBond method), [1]
Trajectory (class in pytraj)
(class in pytraj.trajectory.trajectory)
TrajectoryIterator (class in pytraj)
(class in pytraj.trajectory.trajectory_iterator)
TrajectoryWriter (class in pytraj)
transform() (in module pytraj), [1]
(in module pytraj.all_actions)
(pytraj.Trajectory method)
(pytraj.trajectory.trajectory.Trajectory method)
translate() (in module pytraj), [1]
(in module pytraj.all_actions)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.trajectory.Trajectory method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
truncated_name (pytraj.core.c_core.NameType attribute)
type (pytraj.Atom attribute)
(pytraj.topology.topology.SimplifiedAtom attribute)

U

ucellx() (in module pytraj.analysis.vector), [1]
ucelly() (in module pytraj.analysis.vector), [1]
ucellz() (in module pytraj.analysis.vector), [1]
unitcells (pytraj.Trajectory attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.trajectory.trajectory.Trajectory attribute)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator attribute)

V

values (pytraj.analysis.hbond_analysis.DatasetHBond attribute), [1]
(pytraj.datasets.c_datasets.Dataset attribute)
(pytraj.datasets.c_datasets.Dataset1D attribute)
(pytraj.datasets.c_datasets.Dataset2D attribute)
(pytraj.datasets.c_datasets.Dataset3D attribute)
(pytraj.datasets.c_datasets.DatasetCoords attribute)
(pytraj.datasets.c_datasets.DatasetCoordsCRD attribute)
(pytraj.datasets.c_datasets.DatasetCoordsRef attribute)
(pytraj.datasets.c_datasets.DatasetDouble attribute)
(pytraj.datasets.c_datasets.DatasetFloat attribute)
(pytraj.datasets.c_datasets.DatasetGridDouble attribute)
(pytraj.datasets.c_datasets.DatasetGridFloat attribute)
(pytraj.datasets.c_datasets.DatasetInteger attribute)
(pytraj.datasets.c_datasets.DatasetMatrix3x3 attribute)
(pytraj.datasets.c_datasets.DatasetMatrixDouble attribute)
(pytraj.datasets.c_datasets.DatasetMatrixFloat attribute)
(pytraj.datasets.c_datasets.DatasetMesh attribute)
(pytraj.datasets.c_datasets.DatasetModes attribute)
(pytraj.datasets.c_datasets.DatasetString attribute)
(pytraj.datasets.c_datasets.DatasetTopology attribute)
(pytraj.datasets.c_datasets.DatasetVector attribute)
vect() (pytraj.datasets.c_datasets.DatasetMatrixDouble method)
vector() (in module pytraj.all_actions)
vector_mask() (in module pytraj.analysis.vector), [1]
vector_size (pytraj.datasets.c_datasets.DatasetModes attribute)
velocity (pytraj.Frame attribute)
(pytraj.trajectory.frame.Frame attribute)
velocityautocorr() (in module pytraj)
(in module pytraj.all_actions)
view() (pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.trajectory.Trajectory method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
visualize() (pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.trajectory.Trajectory method)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator method)
volmap() (in module pytraj)
(in module pytraj.all_actions)
volume() (in module pytraj), [1]
(in module pytraj.all_actions)

W

watershell() (in module pytraj), [1]
(in module pytraj.all_actions)
wavelet() (in module pytraj)
(in module pytraj.all_actions)
write() (pytraj.TrajectoryWriter method)
write_parm() (in module pytraj)
(in module pytraj.io)
write_traj() (in module pytraj), [1]
(in module pytraj.io)
writeparm() (pytraj.topology.topology.ParmFile method)

X

xcorr() (in module pytraj), [1]
(in module pytraj.all_actions)
xyz (pytraj.datasets.c_datasets.DatasetCoords attribute)
(pytraj.Frame attribute)
(pytraj.Trajectory attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.datasets.c_datasets.DatasetCoordsCRD attribute)
(pytraj.datasets.c_datasets.DatasetCoordsRef attribute)
(pytraj.trajectory.frame.Frame attribute)
(pytraj.trajectory.trajectory.Trajectory attribute)
(pytraj.trajectory.trajectory_iterator.TrajectoryIterator attribute)