Open Force Field for PELE
1.4.3
Installation
Release History
Generate PELE parameter files
Examples
Topology representations
Forcefield methods
Template handlers
Solvent models
Open Force Field for PELE
»
Index
Index
_
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A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
M
|
N
|
O
|
P
|
R
|
S
|
T
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U
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V
|
W
|
Z
_
__init__() (peleffy.forcefield.calculators.Am1bccCalculator method)
(peleffy.forcefield.calculators.DummyChargeCalculator method)
(peleffy.forcefield.calculators.GasteigerCalculator method)
(peleffy.forcefield.calculators.OPLSChargeCalculator method)
(peleffy.forcefield.OpenFFOPLS2005ForceField method)
(peleffy.forcefield.OpenForceField method)
(peleffy.forcefield.OPLS2005ForceField method)
(peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
(peleffy.forcefield.selectors.ChargeCalculatorSelector method)
(peleffy.forcefield.selectors.ForceFieldSelector method)
(peleffy.solvent.OBC1 method)
(peleffy.solvent.OBC2 method)
(peleffy.solvent.OPLSOBC method)
(peleffy.template.Impact method)
(peleffy.template.impact.WritableAngle method)
(peleffy.template.impact.WritableAtom method)
(peleffy.template.impact.WritableBond method)
(peleffy.template.impact.WritableImproper method)
(peleffy.template.impact.WritableProper method)
(peleffy.template.impact.WritableWrapper method)
(peleffy.topology.Angle method)
(peleffy.topology.Atom method)
(peleffy.topology.Bond method)
(peleffy.topology.Dihedral method)
(peleffy.topology.elements.DummyAtom method)
(peleffy.topology.elements.OFFDihedral method)
(peleffy.topology.elements.OFFImproper method)
(peleffy.topology.elements.OFFProper method)
(peleffy.topology.Improper method)
(peleffy.topology.Molecule method)
(peleffy.topology.Proper method)
(peleffy.topology.rotamer.MolecularGraph method)
(peleffy.topology.rotamer.Rotamer method)
(peleffy.topology.rotamer.RotamerLibrary method)
(peleffy.topology.Topology method)
(peleffy.topology.ZMatrix method)
A
add_angle() (peleffy.topology.Topology method)
add_atom() (peleffy.topology.Topology method)
add_bond() (peleffy.topology.Topology method)
add_edge() (peleffy.topology.rotamer.MolecularGraph method)
add_edges_from() (peleffy.topology.rotamer.MolecularGraph method)
add_improper() (peleffy.topology.Topology method)
add_node() (peleffy.topology.rotamer.MolecularGraph method)
add_nodes_from() (peleffy.topology.rotamer.MolecularGraph method)
add_OFF_improper() (peleffy.topology.Topology method)
add_OFF_proper() (peleffy.topology.Topology method)
add_parameters() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
add_proper() (peleffy.topology.Topology method)
add_weighted_edges_from() (peleffy.topology.rotamer.MolecularGraph method)
adjacency() (peleffy.topology.rotamer.MolecularGraph method)
all() (peleffy.topology.ZMatrix method)
Am1bccCalculator (class in peleffy.forcefield.calculators)
Angle (class in peleffy.topology)
any() (peleffy.topology.ZMatrix method)
apply_lambda() (peleffy.template.impact.WritableAngle method)
(peleffy.template.impact.WritableAtom method)
(peleffy.template.impact.WritableBond method)
(peleffy.template.impact.WritableImproper method)
(peleffy.template.impact.WritableProper method)
(peleffy.topology.Angle method)
(peleffy.topology.Atom method)
(peleffy.topology.Bond method)
(peleffy.topology.Dihedral method)
(peleffy.topology.elements.DummyAtom method)
(peleffy.topology.elements.OFFDihedral method)
(peleffy.topology.elements.OFFImproper method)
(peleffy.topology.elements.OFFProper method)
(peleffy.topology.Improper method)
(peleffy.topology.Proper method)
argmax() (peleffy.topology.ZMatrix method)
argmin() (peleffy.topology.ZMatrix method)
argpartition() (peleffy.topology.ZMatrix method)
argsort() (peleffy.topology.ZMatrix method)
assign_partial_charges() (peleffy.forcefield.calculators.Am1bccCalculator method)
(peleffy.forcefield.calculators.DummyChargeCalculator method)
(peleffy.forcefield.calculators.GasteigerCalculator method)
(peleffy.forcefield.calculators.OPLSChargeCalculator method)
astype() (peleffy.topology.ZMatrix method)
Atom (class in peleffy.topology)
B
BaseParameterWrapper (class in peleffy.forcefield.parameters)
Bond (class in peleffy.topology)
byteswap() (peleffy.topology.ZMatrix method)
C
ChargeCalculatorSelector (class in peleffy.forcefield.selectors)
choose() (peleffy.topology.ZMatrix method)
clear() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
(peleffy.topology.rotamer.MolecularGraph method)
clear_edges() (peleffy.topology.rotamer.MolecularGraph method)
clip() (peleffy.topology.ZMatrix method)
compress() (peleffy.topology.ZMatrix method)
conj() (peleffy.topology.ZMatrix method)
conjugate() (peleffy.topology.ZMatrix method)
copy() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
(peleffy.topology.rotamer.MolecularGraph method)
(peleffy.topology.ZMatrix method)
cumprod() (peleffy.topology.ZMatrix method)
cumsum() (peleffy.topology.ZMatrix method)
D
diagonal() (peleffy.topology.ZMatrix method)
Dihedral (class in peleffy.topology)
dot() (peleffy.topology.ZMatrix method)
dummy_to_writable() (peleffy.template.impact.WritableAngle static method)
(peleffy.template.impact.WritableAtom static method)
(peleffy.template.impact.WritableBond static method)
(peleffy.template.impact.WritableImproper static method)
(peleffy.template.impact.WritableProper static method)
(peleffy.template.impact.WritableWrapper static method)
DummyAtom (class in peleffy.topology.elements)
DummyChargeCalculator (class in peleffy.forcefield.calculators)
dump() (peleffy.topology.ZMatrix method)
dumps() (peleffy.topology.ZMatrix method)
E
edge_subgraph() (peleffy.topology.rotamer.MolecularGraph method)
exclude_from_14_list() (peleffy.template.impact.WritableProper method)
(peleffy.topology.Proper method)
F
fill() (peleffy.topology.ZMatrix method)
flatten() (peleffy.topology.ZMatrix method)
ForceFieldSelector (class in peleffy.forcefield.selectors)
from_ffld_output() (peleffy.forcefield.parameters.OPLS2005ParameterWrapper static method)
from_file() (peleffy.template.Impact class method)
from_impact_template() (peleffy.forcefield.parameters.BaseParameterWrapper static method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper static method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper static method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper static method)
from_json() (peleffy.forcefield.parameters.BaseParameterWrapper static method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper static method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper static method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper static method)
from_label_molecules() (peleffy.forcefield.parameters.OpenForceFieldParameterWrapper static method)
from_openff() (peleffy.topology.Molecule static method)
from_rdkit() (peleffy.topology.Molecule static method)
fromkeys() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
G
GasteigerCalculator (class in peleffy.forcefield.calculators)
get() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
get_by_name() (peleffy.forcefield.selectors.ChargeCalculatorSelector method)
(peleffy.forcefield.selectors.ForceFieldSelector method)
get_conformer() (peleffy.topology.Molecule method)
get_edge_data() (peleffy.topology.rotamer.MolecularGraph method)
get_list() (peleffy.forcefield.selectors.ChargeCalculatorSelector method)
(peleffy.forcefield.selectors.ForceFieldSelector method)
get_parents() (peleffy.topology.rotamer.MolecularGraph method)
get_partial_charges() (peleffy.forcefield.calculators.Am1bccCalculator method)
(peleffy.forcefield.calculators.DummyChargeCalculator method)
(peleffy.forcefield.calculators.GasteigerCalculator method)
(peleffy.forcefield.calculators.OPLSChargeCalculator method)
get_pdb_atom_names() (peleffy.topology.Molecule method)
get_rotamers() (peleffy.topology.rotamer.MolecularGraph method)
getfield() (peleffy.topology.ZMatrix method)
H
has_edge() (peleffy.topology.rotamer.MolecularGraph method)
has_node() (peleffy.topology.rotamer.MolecularGraph method)
I
Impact (class in peleffy.template)
Improper (class in peleffy.topology)
in_angstrom() (peleffy.template.impact.WritableAngle static method)
(peleffy.template.impact.WritableAtom static method)
(peleffy.template.impact.WritableBond static method)
(peleffy.template.impact.WritableImproper static method)
(peleffy.template.impact.WritableProper static method)
(peleffy.template.impact.WritableWrapper static method)
in_deg() (peleffy.template.impact.WritableAngle static method)
(peleffy.template.impact.WritableAtom static method)
(peleffy.template.impact.WritableBond static method)
(peleffy.template.impact.WritableImproper static method)
(peleffy.template.impact.WritableProper static method)
(peleffy.template.impact.WritableWrapper static method)
in_elementarycharge() (peleffy.template.impact.WritableAngle static method)
(peleffy.template.impact.WritableAtom static method)
(peleffy.template.impact.WritableBond static method)
(peleffy.template.impact.WritableImproper static method)
(peleffy.template.impact.WritableProper static method)
(peleffy.template.impact.WritableWrapper static method)
in_kcal_angstrom2mol() (peleffy.template.impact.WritableAngle static method)
(peleffy.template.impact.WritableAtom static method)
(peleffy.template.impact.WritableBond static method)
(peleffy.template.impact.WritableImproper static method)
(peleffy.template.impact.WritableProper static method)
(peleffy.template.impact.WritableWrapper static method)
in_kcal_rad2mol() (peleffy.template.impact.WritableAngle static method)
(peleffy.template.impact.WritableAtom static method)
(peleffy.template.impact.WritableBond static method)
(peleffy.template.impact.WritableImproper static method)
(peleffy.template.impact.WritableProper static method)
(peleffy.template.impact.WritableWrapper static method)
in_kcalmol() (peleffy.template.impact.WritableAngle static method)
(peleffy.template.impact.WritableAtom static method)
(peleffy.template.impact.WritableBond static method)
(peleffy.template.impact.WritableImproper static method)
(peleffy.template.impact.WritableProper static method)
(peleffy.template.impact.WritableWrapper static method)
include_in_14_list() (peleffy.template.impact.WritableProper method)
(peleffy.topology.Proper method)
is_directed() (peleffy.topology.rotamer.MolecularGraph method)
is_empty() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
is_multigraph() (peleffy.topology.rotamer.MolecularGraph method)
item() (peleffy.topology.ZMatrix method)
items() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
itemset() (peleffy.topology.ZMatrix method)
K
keys() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
M
max() (peleffy.topology.ZMatrix method)
mean() (peleffy.topology.ZMatrix method)
min() (peleffy.topology.ZMatrix method)
MolecularGraph (class in peleffy.topology.rotamer)
Molecule (class in peleffy.topology)
N
nbunch_iter() (peleffy.topology.rotamer.MolecularGraph method)
neighbors() (peleffy.topology.rotamer.MolecularGraph method)
newbyteorder() (peleffy.topology.ZMatrix method)
none_to_dummy() (peleffy.template.impact.WritableAngle static method)
(peleffy.template.impact.WritableAtom static method)
(peleffy.template.impact.WritableBond static method)
(peleffy.template.impact.WritableImproper static method)
(peleffy.template.impact.WritableProper static method)
(peleffy.template.impact.WritableWrapper static method)
none_to_zero() (peleffy.template.impact.WritableAngle static method)
(peleffy.template.impact.WritableAtom static method)
(peleffy.template.impact.WritableBond static method)
(peleffy.template.impact.WritableImproper static method)
(peleffy.template.impact.WritableProper static method)
(peleffy.template.impact.WritableWrapper static method)
nonzero() (peleffy.topology.ZMatrix method)
number_of_edges() (peleffy.topology.rotamer.MolecularGraph method)
number_of_nodes() (peleffy.topology.rotamer.MolecularGraph method)
O
OBC1 (class in peleffy.solvent)
OBC2 (class in peleffy.solvent)
OFFDihedral (class in peleffy.topology.elements)
OFFImproper (class in peleffy.topology.elements)
OFFProper (class in peleffy.topology.elements)
OpenFFOPLS2005ForceField (class in peleffy.forcefield)
OpenFFOPLS2005ParameterWrapper (class in peleffy.forcefield.parameters)
OpenForceField (class in peleffy.forcefield)
OpenForceFieldParameterWrapper (class in peleffy.forcefield.parameters)
OPLS2005ForceField (class in peleffy.forcefield)
OPLS2005ParameterWrapper (class in peleffy.forcefield.parameters)
OPLSChargeCalculator (class in peleffy.forcefield.calculators)
OPLSOBC (class in peleffy.solvent)
order() (peleffy.topology.rotamer.MolecularGraph method)
P
parameterize() (peleffy.forcefield.OpenFFOPLS2005ForceField method)
(peleffy.forcefield.OpenForceField method)
(peleffy.forcefield.OPLS2005ForceField method)
partition() (peleffy.topology.ZMatrix method)
plot() (peleffy.template.impact.WritableImproper method)
(peleffy.template.impact.WritableProper method)
(peleffy.topology.Dihedral method)
(peleffy.topology.elements.OFFDihedral method)
(peleffy.topology.elements.OFFImproper method)
(peleffy.topology.elements.OFFProper method)
(peleffy.topology.Improper method)
(peleffy.topology.Proper method)
pop() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
popitem() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
prod() (peleffy.topology.ZMatrix method)
Proper (class in peleffy.topology)
ptp() (peleffy.topology.ZMatrix method)
put() (peleffy.topology.ZMatrix method)
R
ravel() (peleffy.topology.ZMatrix method)
remove_edge() (peleffy.topology.rotamer.MolecularGraph method)
remove_edges_from() (peleffy.topology.rotamer.MolecularGraph method)
remove_node() (peleffy.topology.rotamer.MolecularGraph method)
remove_nodes_from() (peleffy.topology.rotamer.MolecularGraph method)
repeat() (peleffy.topology.ZMatrix method)
reshape() (peleffy.topology.ZMatrix method)
resize() (peleffy.topology.ZMatrix method)
Rotamer (class in peleffy.topology.rotamer)
RotamerLibrary (class in peleffy.topology.rotamer)
round() (peleffy.topology.ZMatrix method)
S
searchsorted() (peleffy.topology.ZMatrix method)
set_angle_parameters() (peleffy.forcefield.OpenFFOPLS2005ForceField method)
set_as_branch() (peleffy.template.impact.WritableAtom method)
(peleffy.topology.Atom method)
(peleffy.topology.elements.DummyAtom method)
set_as_core() (peleffy.template.impact.WritableAtom method)
(peleffy.topology.Atom method)
(peleffy.topology.elements.DummyAtom method)
set_atom1_idx() (peleffy.template.impact.WritableAngle method)
(peleffy.template.impact.WritableBond method)
(peleffy.template.impact.WritableImproper method)
(peleffy.template.impact.WritableProper method)
(peleffy.topology.Angle method)
(peleffy.topology.Bond method)
(peleffy.topology.Dihedral method)
(peleffy.topology.Improper method)
(peleffy.topology.Proper method)
set_atom2_idx() (peleffy.template.impact.WritableAngle method)
(peleffy.template.impact.WritableBond method)
(peleffy.template.impact.WritableImproper method)
(peleffy.template.impact.WritableProper method)
(peleffy.topology.Angle method)
(peleffy.topology.Bond method)
(peleffy.topology.Dihedral method)
(peleffy.topology.Improper method)
(peleffy.topology.Proper method)
set_atom3_idx() (peleffy.template.impact.WritableAngle method)
(peleffy.template.impact.WritableImproper method)
(peleffy.template.impact.WritableProper method)
(peleffy.topology.Angle method)
(peleffy.topology.Dihedral method)
(peleffy.topology.Improper method)
(peleffy.topology.Proper method)
set_atom4_idx() (peleffy.template.impact.WritableImproper method)
(peleffy.template.impact.WritableProper method)
(peleffy.topology.Dihedral method)
(peleffy.topology.Improper method)
(peleffy.topology.Proper method)
set_bond_parameters() (peleffy.forcefield.OpenFFOPLS2005ForceField method)
set_born_radius() (peleffy.template.impact.WritableAtom method)
(peleffy.topology.Atom method)
(peleffy.topology.elements.DummyAtom method)
set_charge() (peleffy.template.impact.WritableAtom method)
(peleffy.topology.Atom method)
(peleffy.topology.elements.DummyAtom method)
set_conformer() (peleffy.topology.Molecule method)
set_coords() (peleffy.template.impact.WritableAtom method)
(peleffy.topology.Atom method)
(peleffy.topology.elements.DummyAtom method)
set_dihedral_parameters() (peleffy.forcefield.OpenFFOPLS2005ForceField method)
set_epsilon() (peleffy.template.impact.WritableAtom method)
(peleffy.topology.Atom method)
(peleffy.topology.elements.DummyAtom method)
set_index() (peleffy.template.impact.WritableAngle method)
(peleffy.template.impact.WritableAtom method)
(peleffy.template.impact.WritableBond method)
(peleffy.template.impact.WritableImproper method)
(peleffy.template.impact.WritableProper method)
(peleffy.topology.Angle method)
(peleffy.topology.Atom method)
(peleffy.topology.Bond method)
(peleffy.topology.Dihedral method)
(peleffy.topology.elements.DummyAtom method)
(peleffy.topology.Improper method)
(peleffy.topology.Proper method)
set_name() (peleffy.topology.Molecule method)
set_nonbonding_parameters() (peleffy.forcefield.OpenFFOPLS2005ForceField method)
set_nonpolar_alpha() (peleffy.template.impact.WritableAtom method)
(peleffy.topology.Atom method)
(peleffy.topology.elements.DummyAtom method)
set_nonpolar_gamma() (peleffy.template.impact.WritableAtom method)
(peleffy.topology.Atom method)
(peleffy.topology.elements.DummyAtom method)
set_OPLS_type() (peleffy.template.impact.WritableAtom method)
(peleffy.topology.Atom method)
(peleffy.topology.elements.DummyAtom method)
set_parent() (peleffy.template.impact.WritableAtom method)
(peleffy.topology.Atom method)
(peleffy.topology.elements.DummyAtom method)
set_PDB_name() (peleffy.template.impact.WritableAtom method)
(peleffy.topology.Atom method)
(peleffy.topology.elements.DummyAtom method)
set_SASA_radius() (peleffy.template.impact.WritableAtom method)
(peleffy.topology.Atom method)
(peleffy.topology.elements.DummyAtom method)
set_sigma() (peleffy.template.impact.WritableAtom method)
(peleffy.topology.Atom method)
(peleffy.topology.elements.DummyAtom method)
set_tag() (peleffy.topology.Molecule method)
setdefault() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
setfield() (peleffy.topology.ZMatrix method)
setflags() (peleffy.topology.ZMatrix method)
size() (peleffy.topology.rotamer.MolecularGraph method)
sort() (peleffy.topology.ZMatrix method)
squeeze() (peleffy.topology.ZMatrix method)
std() (peleffy.topology.ZMatrix method)
subgraph() (peleffy.topology.rotamer.MolecularGraph method)
sum() (peleffy.topology.ZMatrix method)
swapaxes() (peleffy.topology.ZMatrix method)
T
take() (peleffy.topology.ZMatrix method)
to_dict() (peleffy.solvent.OBC1 method)
(peleffy.solvent.OBC2 method)
to_directed() (peleffy.topology.rotamer.MolecularGraph method)
to_directed_class() (peleffy.topology.rotamer.MolecularGraph method)
to_file() (peleffy.solvent.OBC1 method)
(peleffy.solvent.OBC2 method)
(peleffy.solvent.OPLSOBC method)
(peleffy.template.Impact method)
(peleffy.topology.rotamer.RotamerLibrary method)
to_json() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
to_pdb_file() (peleffy.topology.Molecule method)
to_PELE() (peleffy.topology.elements.OFFDihedral method)
(peleffy.topology.elements.OFFImproper method)
(peleffy.topology.elements.OFFProper method)
to_string() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
to_undirected() (peleffy.topology.rotamer.MolecularGraph method)
to_undirected_class() (peleffy.topology.rotamer.MolecularGraph method)
tobytes() (peleffy.topology.ZMatrix method)
tofile() (peleffy.topology.ZMatrix method)
tolist() (peleffy.topology.ZMatrix method)
Topology (class in peleffy.topology)
tostring() (peleffy.topology.ZMatrix method)
trace() (peleffy.topology.ZMatrix method)
transpose() (peleffy.topology.ZMatrix method)
U
update() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
(peleffy.topology.rotamer.MolecularGraph method)
V
values() (peleffy.forcefield.parameters.BaseParameterWrapper method)
(peleffy.forcefield.parameters.OpenFFOPLS2005ParameterWrapper method)
(peleffy.forcefield.parameters.OpenForceFieldParameterWrapper method)
(peleffy.forcefield.parameters.OPLS2005ParameterWrapper method)
var() (peleffy.topology.ZMatrix method)
view() (peleffy.topology.ZMatrix method)
W
WritableAngle (class in peleffy.template.impact)
WritableAtom (class in peleffy.template.impact)
WritableBond (class in peleffy.template.impact)
WritableImproper (class in peleffy.template.impact)
WritableProper (class in peleffy.template.impact)
WritableWrapper (class in peleffy.template.impact)
Z
ZMatrix (class in peleffy.topology)