pytraj
2.0.0
Site
Overview
Installation
Tutorials
Analysis
Cookbook
Supported file formats
Topology
Trajectory
Atom mask selection
Parallel calculation
Developer guide for pytraj
Misc
API reference
What’s new?
Frequently Asked Questions
Page
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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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)
analyze_modes() (in module pytraj)
(in module pytraj.all_actions)
angle() (in module pytraj)
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.trajectory_iterator.TrajectoryIterator method)
(pytraj.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_map() (in module pytraj)
(in module pytraj.all_actions)
atomic_number (pytraj.Atom attribute)
(pytraj.topology.topology.SimplifiedAtom attribute)
atomiccorr() (in module pytraj)
(in module pytraj.all_actions)
AtomMask (class in pytraj)
(class in pytraj.core.c_core)
atoms (pytraj.Topology attribute)
(pytraj.topology.topology.SimplifiedResidue 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)
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_multidihedral() (in module pytraj)
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_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)
(pytraj.Frame method)
(pytraj.trajectory.frame.Frame method)
center_of_mass() (in module pytraj)
(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)
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)
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)
dict_to_ndarray() (in module pytraj.utils.tools)
dihcovar() (in module pytraj.analysis.matrix)
,
[1]
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)
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]
dssp() (in module pytraj)
(in module pytraj.analysis.dssp_analysis)
dssp_allatoms() (in module pytraj.analysis.dssp_analysis)
dssp_allresidues() (in module pytraj.analysis.dssp_analysis)
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)
,
[1]
(in module pytraj.all_actions)
(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)
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)
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)
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)
indices (pytraj.AtomMask attribute)
(pytraj.core.c_core.AtomMask attribute)
invert_mask() (pytraj.AtomMask method)
(pytraj.core.c_core.AtomMask method)
ired_vector_and_matrix() (in module pytraj)
(in module pytraj.analysis.nmr)
,
[1]
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.analysis.nmr)
,
[1]
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)
last_atom_index (pytraj.Residue attribute)
lie() (in module pytraj)
(in module pytraj.all_actions)
(in module pytraj.analysis.energy_analysis)
,
[1]
load() (in module pytraj)
(in module pytraj.io)
(pytraj.Trajectory method)
(pytraj.datasets.c_datasets.DatasetCoordsCRD 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)
minimage() (in module pytraj.analysis.vector)
,
[1]
Molecule (class in pytraj)
molnum (pytraj.Atom attribute)
(pytraj.topology.topology.SimplifiedAtom attribute)
mols (pytraj.Topology attribute)
(pytraj.topology.topology.Topology attribute)
molsurf() (in module pytraj)
moving_average() (in module pytraj.utils.tools)
multidihedral() (in module pytraj)
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)
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)
(in module pytraj.analysis.nmr)
,
[1]
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
pairwise_rmsd() (in module pytraj)
,
[1]
(in module pytraj.all_actions)
(in module pytraj.analysis.rmsd)
ParmFile (class in pytraj.topology.topology)
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.dssp_analysis (module)
pytraj.analysis.energy_analysis (module)
,
[1]
pytraj.analysis.hbond_analysis (module)
,
[1]
pytraj.analysis.matrix (module)
,
[1]
pytraj.analysis.nmr (module)
,
[1]
pytraj.analysis.rmsd (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)
randomize_ions() (in module pytraj)
,
[1]
(in module pytraj.all_actions)
read() (pytraj.topology.topology.ParmFile method)
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)
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)
residues (pytraj.Topology 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)
rmsd() (in module pytraj)
,
[1]
,
[2]
(in module pytraj.all_actions)
(in module pytraj.analysis.rmsd)
(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)
(in module pytraj.analysis.rmsd)
(pytraj.Frame method)
(pytraj.trajectory.frame.Frame method)
rmsd_perres() (in module pytraj)
,
[1]
,
[2]
(in module pytraj.all_actions)
,
[1]
(in module pytraj.analysis.rmsd)
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)
(in module pytraj.analysis.rmsd)
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_element() (pytraj.datasets.c_datasets.DatasetMatrixDouble method)
set_first() (pytraj.Molecule 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_reference() (pytraj.Topology method)
(pytraj.topology.topology.Topology 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)
swap_atoms (pytraj.Frame attribute)
(pytraj.trajectory.frame.Frame attribute)
symmrmsd() (in module pytraj)
(in module pytraj.all_actions)
(in module pytraj.analysis.rmsd)
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.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)
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.analysis.vector)
,
[1]
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)
wavelet() (in module pytraj)
(in module pytraj.all_actions)
write() (pytraj.topology.topology.ParmFile method)
(pytraj.TrajectoryWriter method)
write_parm() (in module pytraj)
(in module pytraj.io)
write_traj() (in module pytraj)
,
[1]
(in module pytraj.io)
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)