PyCGTOOL
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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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L
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M
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P
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R
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W
_
__call__() (pycgtool.__main__.BooleanAction method)
__contains__() (pycgtool.bondset.BondSet method)
(pycgtool.mapping.Mapping method)
__exit__() (pycgtool.parsers.CFG method)
(pycgtool.parsers.cfg.CFG method)
__getitem__() (pycgtool.bondset.BondSet method)
(pycgtool.mapping.BeadMap method)
(pycgtool.mapping.Mapping method)
__iter__() (pycgtool.bondset.Bond method)
(pycgtool.bondset.BondSet method)
(pycgtool.mapping.BeadMap method)
(pycgtool.mapping.Mapping method)
__len__() (pycgtool.bondset.BondSet method)
(pycgtool.mapping.BeadMap method)
(pycgtool.mapping.Mapping method)
__repr__() (pycgtool.bondset.Bond method)
(pycgtool.mapping.BeadMap method)
_cg_frame_setup() (pycgtool.mapping.Mapping method)
_create_angles() (pycgtool.bondset.BondSet static method)
_get_default_func_forms() (pycgtool.bondset.BondSet method)
_get_lines_for_bond_dump() (pycgtool.bondset.BondSet static method)
_guess_atom_masses() (pycgtool.mapping.Mapping method)
_itp_section_into_mol_map() (pycgtool.mapping.Mapping static method)
_load_itp() (pycgtool.mapping.Mapping method)
_load_trajectory() (pycgtool.frame.Frame method)
_mol_map_from_section() (pycgtool.mapping.Mapping static method)
_populate_atom_numbers() (pycgtool.bondset.BondSet method)
_read_file() (pycgtool.parsers.CFG method)
(pycgtool.parsers.cfg.CFG method)
(pycgtool.parsers.ITP method)
(pycgtool.parsers.itp.ITP method)
_read_line() (pycgtool.parsers.CFG method)
(pycgtool.parsers.cfg.CFG method)
_rename_atoms() (pycgtool.mapping.Mapping method)
_set_bead_weights() (pycgtool.mapping.Mapping method)
_slice_trajectory() (pycgtool.frame.Frame method)
A
add_atom() (pycgtool.frame.Frame method)
add_residue() (pycgtool.frame.Frame method)
any_starts_with() (in module pycgtool.util)
apply() (pycgtool.bondset.BondSet method)
(pycgtool.mapping.Mapping method)
apply_mapping() (pycgtool.__main__.PyCGTOOL method)
ArgumentValidationError
atom() (pycgtool.frame.Frame method)
atoms() (pycgtool.frame.Frame property)
B
backup_file() (in module pycgtool.util)
BeadMap (class in pycgtool.mapping)
boltzmann_invert() (pycgtool.bondset.Bond method)
(pycgtool.bondset.BondSet method)
Bond (class in pycgtool.bondset)
bond_section() (pycgtool.forcefield.ForceField static method)
BondSet (class in pycgtool.bondset)
BooleanAction (class in pycgtool.__main__)
build_trajectory() (pycgtool.frame.Frame method)
C
calc_coords_weight() (in module pycgtool.mapping)
CFG (class in pycgtool.parsers)
(class in pycgtool.parsers.cfg)
circular_mean() (in module pycgtool.util)
circular_variance() (in module pycgtool.util)
cmp_file_whitespace_float() (in module pycgtool.util)
cmp_whitespace_float() (in module pycgtool.util)
compare_trajectories() (in module pycgtool.util)
copy_files() (in module pycgtool.forcefield)
CosHarmonic (class in pycgtool.functionalforms)
D
dir_up() (in module pycgtool.util)
dump_values() (pycgtool.bondset.BondSet method)
DuplicateSectionError
E
EmptyIterableError
eqm() (pycgtool.functionalforms.FunctionalForm method)
extend_graph_chain() (in module pycgtool.util)
F
fconst() (pycgtool.functionalforms.CosHarmonic method)
(pycgtool.functionalforms.FunctionalForm method)
(pycgtool.functionalforms.Harmonic method)
(pycgtool.functionalforms.MartiniDefaultAngle method)
(pycgtool.functionalforms.MartiniDefaultDihedral method)
(pycgtool.functionalforms.MartiniDefaultLength method)
file_write_lines() (in module pycgtool.util)
ForceField (class in pycgtool.forcefield)
Frame (class in pycgtool.frame)
FunctionalForm (class in pycgtool.functionalforms)
G
get_bond_angles() (pycgtool.bondset.BondSet method)
get_bond_dihedrals() (pycgtool.bondset.BondSet method)
get_bond_length_constraints() (pycgtool.bondset.BondSet method)
get_bond_lengths() (pycgtool.bondset.BondSet method)
get_bonds() (pycgtool.bondset.BondSet method)
get_functional_forms() (in module pycgtool.functionalforms)
get_output_filepath() (pycgtool.__main__.PyCGTOOL method)
get_virtual_beads() (pycgtool.bondset.BondSet method)
gromacs_type_id_by_natoms() (pycgtool.functionalforms.FunctionalForm class method)
gromacs_type_ids (pycgtool.functionalforms.CosHarmonic attribute)
(pycgtool.functionalforms.Harmonic attribute)
(pycgtool.functionalforms.MartiniDefaultAngle attribute)
(pycgtool.functionalforms.MartiniDefaultDihedral attribute)
(pycgtool.functionalforms.MartiniDefaultLength attribute)
gromacs_type_ids() (pycgtool.functionalforms.FunctionalForm method)
guess_atom_masses() (pycgtool.mapping.BeadMap method)
(pycgtool.mapping.VirtualMap method)
H
Harmonic (class in pycgtool.functionalforms)
I
items() (pycgtool.mapping.Mapping method)
ITP (class in pycgtool.parsers)
(class in pycgtool.parsers.itp)
itp_text() (pycgtool.bondset.BondSet method)
L
load_optional_topology() (in module pycgtool.util)
load_traj() (in module pycgtool.frame)
logger (in module pycgtool.__main__)
(in module pycgtool.bondset)
(in module pycgtool.frame)
(in module pycgtool.mapping)
(in module pycgtool.parsers.itp)
(in module pycgtool.util)
M
main() (in module pycgtool.__main__)
Mapping (class in pycgtool.mapping)
MartiniDefaultAngle (class in pycgtool.functionalforms)
MartiniDefaultDihedral (class in pycgtool.functionalforms)
MartiniDefaultLength (class in pycgtool.functionalforms)
measure_bonds() (pycgtool.__main__.PyCGTOOL method)
module
pycgtool
pycgtool.__main__
pycgtool.bondset
pycgtool.forcefield
pycgtool.frame
pycgtool.functionalforms
pycgtool.mapping
pycgtool.parsers
pycgtool.parsers.cfg
pycgtool.parsers.itp
pycgtool.util
N
n_frames() (pycgtool.frame.Frame property)
natoms() (pycgtool.frame.Frame property)
needs_terminal_entries() (pycgtool.forcefield.ForceField static method)
NonMatchingSystemError
NoSectionError
number_or_string() (in module pycgtool.util)
P
parse_arguments() (in module pycgtool.__main__)
PathLike (in module pycgtool.__main__)
(in module pycgtool.bondset)
(in module pycgtool.forcefield)
(in module pycgtool.frame)
(in module pycgtool.mapping)
(in module pycgtool.parsers.cfg)
(in module pycgtool.util)
pycgtool
module
PyCGTOOL (class in pycgtool.__main__)
pycgtool.__main__
module
pycgtool.bondset
module
pycgtool.forcefield
module
pycgtool.frame
module
pycgtool.functionalforms
module
pycgtool.mapping
module
pycgtool.parsers
module
pycgtool.parsers.cfg
module
pycgtool.parsers.itp
module
pycgtool.util
module
R
residue() (pycgtool.frame.Frame method)
residues() (pycgtool.frame.Frame property)
S
save() (pycgtool.frame.Frame method)
sliding() (in module pycgtool.util)
T
train_backmapper() (pycgtool.__main__.PyCGTOOL method)
transpose_and_sample() (in module pycgtool.util)
U
UnsupportedFormatException
V
validate_arguments() (in module pycgtool.__main__)
VirtualMap (class in pycgtool.mapping)
W
write() (pycgtool.forcefield.ForceField method)
write_itp() (pycgtool.bondset.BondSet method)
write_r2b() (pycgtool.forcefield.ForceField static method)
write_rtp() (pycgtool.forcefield.ForceField static method)
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