Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
_
__init__() (chimerax.isolde.atomic.ChiralCenter method)
(chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ChiralMgr method)
(chimerax.isolde.atomic.ProperDihedral method)
(chimerax.isolde.atomic.ProperDihedralMgr method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Rama method)
(chimerax.isolde.atomic.RamaMgr method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamer method)
(chimerax.isolde.atomic.Rotamers method)
(chimerax.isolde.atomic.RotaMgr method)
(chimerax.isolde.interpolation.RegularGridInterpolator method)
(chimerax.isolde.isolde.Isolde method)
(chimerax.isolde.manipulations.Peptide_Bond_Flipper method)
(chimerax.isolde.manipulations.ProteinRegisterShifter method)
(chimerax.isolde.openmm.custom_forces.AdaptiveDistanceRestraintForce method)
(chimerax.isolde.openmm.custom_forces.AmberCMAPForce method)
(chimerax.isolde.openmm.custom_forces.CubicInterpMapForce method)
(chimerax.isolde.openmm.custom_forces.CubicInterpMapForce_Old method)
(chimerax.isolde.openmm.custom_forces.FlatBottomTorsionRestraintForce method)
(chimerax.isolde.openmm.custom_forces.GBSAForce method)
(chimerax.isolde.openmm.custom_forces.LinearInterpMapForce method)
(chimerax.isolde.openmm.custom_forces.TopOutBondForce method)
(chimerax.isolde.openmm.custom_forces.TopOutRestraintForce method)
(chimerax.isolde.openmm.custom_forces.TopOutTorsionForce method)
(chimerax.isolde.openmm.OpenmmThreadHandler method)
(chimerax.isolde.openmm.SimConstruct method)
(chimerax.isolde.openmm.SimHandler method)
(chimerax.isolde.openmm.SimManager method)
(chimerax.isolde.openmm.SimParams method)
(chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDihedralRestraints method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints method)
(chimerax.isolde.restraints.ChiralRestraint method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraints method)
(chimerax.isolde.restraints.DistanceRestraint method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFAtom method)
(chimerax.isolde.restraints.MDFFAtoms method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraint method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.PositionRestraints method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraints method)
(chimerax.isolde.restraints.RestraintChangeTracker method)
(chimerax.isolde.restraints.RotamerRestraint method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraints method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
(chimerax.isolde.validation.RamaAnnotator method)
(chimerax.isolde.validation.RotamerAnnotator method)
A
accept_multishadow (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
accept_shadow (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
AdaptiveDihedralRestraint (class in chimerax.isolde.restraints)
AdaptiveDihedralRestraintMgr (class in chimerax.isolde.restraints)
AdaptiveDihedralRestraints (class in chimerax.isolde.restraints)
AdaptiveDistanceRestraint (class in chimerax.isolde.restraints)
AdaptiveDistanceRestraintForce (class in chimerax.isolde.openmm.custom_forces)
AdaptiveDistanceRestraintMgr (class in chimerax.isolde.restraints)
AdaptiveDistanceRestraints (class in chimerax.isolde.restraints)
add() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
add_adaptive_dihedral_restraint() (chimerax.isolde.openmm.SimHandler method)
add_adaptive_dihedral_restraints() (chimerax.isolde.openmm.SimHandler method)
add_adaptive_distance_restraint() (chimerax.isolde.openmm.SimHandler method)
add_adaptive_distance_restraints() (chimerax.isolde.openmm.SimHandler method)
add_all_defined_restraints_for_residues() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
add_amber_cmap_torsions() (chimerax.isolde.openmm.SimHandler method)
add_bonds() (chimerax.isolde.openmm.custom_forces.AdaptiveDistanceRestraintForce method)
(chimerax.isolde.openmm.custom_forces.TopOutBondForce method)
add_checkpoint_block() (chimerax.isolde.isolde.Isolde method)
add_chiral_def() (chimerax.isolde.atomic.ChiralMgr method)
add_dihedral_def() (chimerax.isolde.atomic.ProperDihedralMgr method)
add_dihedral_restraint() (chimerax.isolde.openmm.SimHandler method)
add_dihedral_restraints() (chimerax.isolde.openmm.SimHandler method)
add_distance_restraint() (chimerax.isolde.openmm.SimHandler method)
add_distance_restraints() (chimerax.isolde.openmm.SimHandler method)
add_drawing() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
add_mdff_atom() (chimerax.isolde.openmm.SimHandler method)
add_mdff_atoms() (chimerax.isolde.openmm.SimHandler method)
(chimerax.isolde.restraints.MDFFMgr method)
add_particles() (chimerax.isolde.openmm.custom_forces.TopOutRestraintForce method)
add_position_restraint() (chimerax.isolde.openmm.SimHandler method)
add_position_restraints() (chimerax.isolde.openmm.SimHandler method)
add_restraint() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
add_restraint_by_residue_and_name() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
add_restraints() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
add_restraints_by_atoms() (chimerax.isolde.restraints.ChiralRestraintMgr method)
add_restraints_by_residues_and_name() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
add_ss_restraints() (chimerax.isolde.restraints.DistanceRestraintMgr method)
add_torsions() (chimerax.isolde.openmm.custom_forces.AmberCMAPForce method)
(chimerax.isolde.openmm.custom_forces.FlatBottomTorsionRestraintForce method)
(chimerax.isolde.openmm.custom_forces.TopOutTorsionForce method)
add_tuggable() (chimerax.isolde.openmm.SimHandler method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
add_tuggables() (chimerax.isolde.openmm.SimHandler method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
addTorsion() (chimerax.isolde.openmm.custom_forces.AmberCMAPForce method)
all_atoms (chimerax.isolde.openmm.SimConstruct property)
all_drawings() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
ALL_EDGES_DISPLAY_MASK (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
all_models() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
all_residues (chimerax.isolde.openmm.SimConstruct property)
all_restraints (chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
allow_clipping (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
allow_depth_cue (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
allow_hydrogens (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
alpha (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
alphas (chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
AmberCMAPForce (class in chimerax.isolde.openmm.custom_forces)
ambient_texture (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
ambient_texture_transform (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
angle (chimerax.isolde.atomic.ChiralCenter property)
(chimerax.isolde.atomic.ProperDihedral property)
angle_range_to_kappa() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr static method)
angles (chimerax.isolde.atomic.ChiralCenters property)
(chimerax.isolde.atomic.ProperDihedrals property)
(chimerax.isolde.atomic.Rama property)
(chimerax.isolde.atomic.Ramas property)
(chimerax.isolde.atomic.Rotamer property)
annotation_color (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.ProperDihedralRestraint property)
annotation_colors (chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
(chimerax.isolde.restraints.ProperDihedralRestraints property)
any_part_highlighted() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
applied_force (chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
applied_forces (chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
applied_moment (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
applied_moments (chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
atom (chimerax.isolde.restraints.MDFFAtom property)
(chimerax.isolde.restraints.PositionRestraint property)
atom_restraints() (chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
atoms (chimerax.isolde.atomic.ChiralCenter property)
(chimerax.isolde.atomic.ChiralCenters property)
(chimerax.isolde.atomic.ProperDihedral property)
(chimerax.isolde.atomic.ProperDihedrals property)
(chimerax.isolde.atomic.Rama property)
(chimerax.isolde.atomic.Ramas property)
(chimerax.isolde.atomic.Rotamer property)
(chimerax.isolde.atomic.Rotamers property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
(chimerax.isolde.restraints.DistanceRestraint property)
(chimerax.isolde.restraints.MDFFAtoms property)
(chimerax.isolde.restraints.PositionRestraints property)
atoms_restraints() (chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
atomspec (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
axial_bond (chimerax.isolde.atomic.ProperDihedral property)
axial_bonds (chimerax.isolde.atomic.ProperDihedrals property)
axis_lengths (chimerax.isolde.interpolation.RegularGridInterpolator property)
B
bin_scores() (chimerax.isolde.atomic.RamaMgr method)
bounds() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
bounds_intercept_copies() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
C
c (chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
ca_atom (chimerax.isolde.atomic.Rama property)
ca_atoms (chimerax.isolde.atomic.Ramas property)
ca_cb_bond (chimerax.isolde.atomic.Rotamer property)
ca_cb_bonds (chimerax.isolde.atomic.Rotamers property)
ca_radius (chimerax.isolde.validation.RamaAnnotator property)
can_checkpoint (chimerax.isolde.isolde.Isolde property)
case (chimerax.isolde.atomic.Rama property)
cases (chimerax.isolde.atomic.Ramas property)
casts_shadows (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
center (chimerax.isolde.atomic.ChiralCenter property)
(chimerax.isolde.atomic.ProperDihedral property)
(chimerax.isolde.atomic.Rama property)
(chimerax.isolde.atomic.Rotamer property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
(chimerax.isolde.restraints.ChiralRestraint property)
(chimerax.isolde.restraints.DistanceRestraint property)
centers (chimerax.isolde.atomic.ChiralCenters property)
(chimerax.isolde.atomic.ProperDihedrals property)
(chimerax.isolde.atomic.Ramas property)
(chimerax.isolde.atomic.Rotamers property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
(chimerax.isolde.restraints.ChiralRestraints property)
change_selected_model() (chimerax.isolde.isolde.Isolde method)
checkpoint() (chimerax.isolde.isolde.Isolde method)
(chimerax.isolde.openmm.SimManager method)
chi_dihedrals (chimerax.isolde.atomic.Rotamer property)
chi_restraints (chimerax.isolde.restraints.RotamerRestraint property)
child_drawings() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
child_models() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
chimerax.isolde.atomic
module
chimerax.isolde.ctypes
module
chimerax.isolde.delayed_reaction
module
chimerax.isolde.interpolation
module
chimerax.isolde.isolde
module
chimerax.isolde.manipulations
module
chimerax.isolde.openmm
module
chimerax.isolde.openmm.custom_forces
module
chimerax.isolde.param_mgr
module
chimerax.isolde.restraints
module
chimerax.isolde.session_extensions
module
chimerax.isolde.validation
module
chimerax.isolde.view
module
chiral_atom (chimerax.isolde.atomic.ChiralCenter property)
chiral_atoms (chimerax.isolde.atomic.ChiralCenters property)
ChiralCenter (class in chimerax.isolde.atomic)
ChiralCenters (class in chimerax.isolde.atomic)
ChiralMgr (class in chimerax.isolde.atomic)
ChiralRestraint (class in chimerax.isolde.restraints)
ChiralRestraintMgr (class in chimerax.isolde.restraints)
ChiralRestraints (class in chimerax.isolde.restraints)
cis() (chimerax.isolde.atomic.RamaMgr method)
clear_highlight() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
clear_sim_indices() (chimerax.isolde.restraints.AdaptiveDistanceRestraints method)
(chimerax.isolde.restraints.MDFFAtoms method)
(chimerax.isolde.restraints.PositionRestraints method)
color (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
color_cas_by_rama_score() (chimerax.isolde.atomic.RamaMgr method)
color_scale (chimerax.isolde.atomic.RamaMgr property)
(chimerax.isolde.atomic.RotaMgr property)
(chimerax.isolde.validation.RamaAnnotator property)
(chimerax.isolde.validation.RotamerAnnotator property)
colormap (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
colormap_range (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
colors (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
commit_preview() (chimerax.isolde.restraints.RotamerRestraintMgr method)
commit_sim() (chimerax.isolde.isolde.Isolde method)
context_reinit_needed() (chimerax.isolde.openmm.SimHandler method)
coords (chimerax.isolde.openmm.OpenmmThreadHandler property)
copy() (chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamers method)
coupling_constant (chimerax.isolde.restraints.MDFFAtom property)
coupling_constants (chimerax.isolde.restraints.MDFFAtoms property)
cpp_del_model() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
cpp_pointer (chimerax.isolde.atomic.ChiralCenter property)
(chimerax.isolde.atomic.ProperDihedral property)
(chimerax.isolde.atomic.Rama property)
(chimerax.isolde.atomic.RamaMgr property)
(chimerax.isolde.atomic.Rotamer property)
(chimerax.isolde.atomic.RotaMgr property)
(chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraint property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraint property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFAtom property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraint property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RestraintChangeTracker property)
(chimerax.isolde.restraints.RotamerRestraint property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
create_all_dihedrals() (chimerax.isolde.atomic.ProperDihedralMgr method)
cs (chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
CubicInterpMapForce (class in chimerax.isolde.openmm.custom_forces)
CubicInterpMapForce_Old (class in chimerax.isolde.openmm.custom_forces)
custom_x3d() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
cutoff (chimerax.isolde.restraints.ChiralRestraint property)
(chimerax.isolde.restraints.ProperDihedralRestraint property)
cutoffs (chimerax.isolde.atomic.RamaMgr property)
(chimerax.isolde.atomic.RotaMgr property)
(chimerax.isolde.restraints.ChiralRestraints property)
(chimerax.isolde.restraints.ProperDihedralRestraints property)
D
define_forcefield() (chimerax.isolde.openmm.SimHandler method)
delayed_reaction() (in module chimerax.isolde.delayed_reaction)
delete() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
(chimerax.isolde.validation.RamaAnnotator method)
(chimerax.isolde.validation.RotamerAnnotator method)
delete_chirals() (chimerax.isolde.atomic.ChiralMgr method)
delete_dihedrals() (chimerax.isolde.atomic.ProperDihedralMgr method)
deleted (chimerax.isolde.atomic.ChiralCenter property)
(chimerax.isolde.atomic.ProperDihedral property)
(chimerax.isolde.atomic.Rama property)
(chimerax.isolde.atomic.RamaMgr property)
(chimerax.isolde.atomic.Rotamer property)
(chimerax.isolde.atomic.RotaMgr property)
(chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraint property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraint property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFAtom property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraint property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RestraintChangeTracker property)
(chimerax.isolde.restraints.RotamerRestraint property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
deviation (chimerax.isolde.atomic.ChiralCenter property)
deviations (chimerax.isolde.atomic.ChiralCenters property)
dihedral (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.ChiralRestraint property)
(chimerax.isolde.restraints.ProperDihedralRestraint property)
dihedral_manager (chimerax.isolde.atomic.RamaMgr property)
dihedrals (chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
(chimerax.isolde.restraints.ChiralRestraints property)
(chimerax.isolde.restraints.ProperDihedralRestraints property)
dim (chimerax.isolde.interpolation.RegularGridInterpolator property)
disable_mutually_exclusive_restraints() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
discard_sim() (chimerax.isolde.isolde.Isolde method)
display (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraint property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
(chimerax.isolde.validation.RamaAnnotator property)
(chimerax.isolde.validation.RotamerAnnotator property)
display_positions (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
display_style (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
display_threshold (chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
displays (chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
(chimerax.isolde.restraints.ProperDihedralRestraints property)
distance (chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
(chimerax.isolde.restraints.DistanceRestraint property)
DistanceRestraint (class in chimerax.isolde.restraints)
DistanceRestraintMgr (class in chimerax.isolde.restraints)
DistanceRestraints (class in chimerax.isolde.restraints)
distances (chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
Dot (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
draw() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
draw_self() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
drawing_lineage (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
E
edge_mask (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
effective_spring_constant (chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
effective_spring_constants (chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
empty_drawing() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
enabled (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
(chimerax.isolde.restraints.ChiralRestraint property)
(chimerax.isolde.restraints.DistanceRestraint property)
(chimerax.isolde.restraints.MDFFAtom property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraint property)
(chimerax.isolde.restraints.ProperDihedralRestraint property)
(chimerax.isolde.restraints.RotamerRestraint property)
enableds (chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
(chimerax.isolde.restraints.ChiralRestraints property)
(chimerax.isolde.restraints.MDFFAtoms property)
(chimerax.isolde.restraints.PositionRestraints property)
(chimerax.isolde.restraints.ProperDihedralRestraints property)
(chimerax.isolde.restraints.RotamerRestraints property)
equilibrate() (chimerax.isolde.isolde.Isolde method)
expand_mobile_selection() (chimerax.isolde.openmm.SimManager method)
expected_angle (chimerax.isolde.atomic.ChiralCenter property)
expected_angles (chimerax.isolde.atomic.ChiralCenters property)
F
filter() (chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamers method)
first_intercept() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
first_intercept_children() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
fixed_atoms (chimerax.isolde.openmm.SimConstruct property)
FlatBottomTorsionRestraintForce (class in chimerax.isolde.openmm.custom_forces)
flip_peptide_bond() (chimerax.isolde.isolde.Isolde method)
flip_peptide_omega() (chimerax.isolde.isolde.Isolde method)
focus_on_coord() (in module chimerax.isolde.view)
focus_on_selection() (in module chimerax.isolde.view)
force_update_needed() (chimerax.isolde.openmm.SimHandler method)
G
GBSAForce (class in chimerax.isolde.openmm.custom_forces)
geometry_bounds() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
get_adaptive_dihedral_restraint_mgr() (in module chimerax.isolde.session_extensions)
get_adaptive_distance_restraint_mgr() (in module chimerax.isolde.session_extensions)
get_all_adaptive_distance_restraint_mgrs() (in module chimerax.isolde.session_extensions)
get_all_dihedrals() (chimerax.isolde.atomic.ProperDihedralMgr method)
get_all_restraints_for_residues() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
get_chiral() (chimerax.isolde.atomic.ChiralMgr method)
get_chiral_restraint_mgr() (in module chimerax.isolde.session_extensions)
get_chirals() (chimerax.isolde.atomic.ChiralMgr method)
get_colormap() (chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
get_dihedral() (chimerax.isolde.atomic.ProperDihedralMgr method)
get_dihedrals() (chimerax.isolde.atomic.ProperDihedralMgr method)
get_distance_restraint_mgr() (in module chimerax.isolde.session_extensions)
get_mdff_atoms() (chimerax.isolde.restraints.MDFFMgr method)
get_mdff_mgr() (in module chimerax.isolde.session_extensions)
get_position_restraint_mgr() (in module chimerax.isolde.session_extensions)
get_proper_dihedral_restraint_mgr() (in module chimerax.isolde.session_extensions)
get_rama_annotator() (in module chimerax.isolde.session_extensions)
get_ramas() (chimerax.isolde.atomic.RamaMgr method)
get_restraint() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
get_restraint_by_residue_and_name() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
get_restraints() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
get_restraints_by_atoms() (chimerax.isolde.restraints.ChiralRestraintMgr method)
get_restraints_by_residues_and_name() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
get_rota_annotator() (in module chimerax.isolde.session_extensions)
get_rotamer() (chimerax.isolde.atomic.RotaMgr method)
get_rotamer_restraint_mgr() (in module chimerax.isolde.session_extensions)
get_rotamers() (chimerax.isolde.atomic.RotaMgr method)
get_selected() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
get_ss_restraints() (chimerax.isolde.restraints.DistanceRestraintMgr method)
get_target() (chimerax.isolde.atomic.Rotamer method)
get_tuggable_atoms_mgr() (in module chimerax.isolde.session_extensions)
get_tuggables() (chimerax.isolde.restraints.TuggableAtomsMgr method)
global_k (chimerax.isolde.restraints.MDFFMgr property)
grid (chimerax.isolde.interpolation.RegularGridInterpolator property)
guess_global_k() (chimerax.isolde.restraints.MDFFMgr method)
H
has_formatted_metadata() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
hash() (chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamers method)
hide_favored (chimerax.isolde.validation.RamaAnnotator property)
(chimerax.isolde.validation.RotamerAnnotator property)
HIGHLIGHT_DRAW_PASS (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
highlighted (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
highlighted_displayed_triangles_mask (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
highlighted_positions (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
highlighted_triangles_mask (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
I
id_string (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
ignored_residues (chimerax.isolde.isolde.Isolde property)
INCLUDE_MAPS (chimerax.isolde.atomic.ChiralCenter attribute)
(chimerax.isolde.atomic.ChiralCenters attribute)
(chimerax.isolde.atomic.ProperDihedral attribute)
(chimerax.isolde.atomic.ProperDihedrals attribute)
(chimerax.isolde.atomic.Ramas attribute)
(chimerax.isolde.atomic.Rotamers attribute)
(chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
index() (chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamers method)
indices() (chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamers method)
inherit_graphics_exemptions (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
initialize_adaptive_dihedral_restraints_force() (chimerax.isolde.openmm.SimHandler method)
initialize_adaptive_distance_restraints_force() (chimerax.isolde.openmm.SimHandler method)
initialize_dihedral_restraints_force() (chimerax.isolde.openmm.SimHandler method)
initialize_distance_restraints_force() (chimerax.isolde.openmm.SimHandler method)
initialize_implicit_solvent() (chimerax.isolde.openmm.SimHandler method)
initialize_mdff_force() (chimerax.isolde.openmm.SimHandler method)
initialize_mdff_forces() (chimerax.isolde.openmm.SimHandler method)
initialize_position_restraints_force() (chimerax.isolde.openmm.SimHandler method)
initialize_restraint_forces() (chimerax.isolde.openmm.SimHandler method)
initialize_tugging_force() (chimerax.isolde.openmm.SimHandler method)
instances() (chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamers method)
interpolate() (chimerax.isolde.interpolation.RegularGridInterpolator method)
interpolator_axes() (chimerax.isolde.atomic.RamaMgr method)
interpolator_axis_lengths() (chimerax.isolde.atomic.RamaMgr method)
interpolator_dim() (chimerax.isolde.atomic.RamaMgr method)
interpolator_limits() (chimerax.isolde.atomic.RamaMgr method)
interpolator_values() (chimerax.isolde.atomic.RamaMgr method)
intersect() (chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamers method)
intersects() (chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamers method)
intersects_each() (chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamers method)
intra_restraints() (chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
Isolde (class in chimerax.isolde.isolde)
IsoldeParams (class in chimerax.isolde.isolde)
K
kappa (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
kappas (chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
L
LAST_DRAW_PASS (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
LinearInterpMapForce (class in chimerax.isolde.openmm.custom_forces)
load_model_and_data() (chimerax.isolde.isolde.Isolde method)
M
mask() (chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamers method)
max (chimerax.isolde.interpolation.RegularGridInterpolator property)
max_force (chimerax.isolde.openmm.custom_forces.TopOutBondForce property)
(chimerax.isolde.openmm.custom_forces.TopOutRestraintForce property)
MDFFAtom (class in chimerax.isolde.restraints)
MDFFAtoms (class in chimerax.isolde.restraints)
MDFFMgr (class in chimerax.isolde.restraints)
merge() (chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamers method)
Mesh (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
mgr (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
(chimerax.isolde.restraints.ChiralRestraint property)
(chimerax.isolde.restraints.DistanceRestraint property)
(chimerax.isolde.restraints.MDFFAtom property)
(chimerax.isolde.restraints.PositionRestraint property)
(chimerax.isolde.restraints.ProperDihedralRestraint property)
(chimerax.isolde.restraints.RotamerRestraint property)
min (chimerax.isolde.interpolation.RegularGridInterpolator property)
minimize (chimerax.isolde.openmm.SimHandler property)
minimize() (chimerax.isolde.isolde.Isolde method)
(chimerax.isolde.openmm.OpenmmThreadHandler method)
mobile_atoms (chimerax.isolde.openmm.SimConstruct property)
mobile_heavy_atoms (chimerax.isolde.openmm.SimConstruct property)
mobile_residues (chimerax.isolde.openmm.SimConstruct property)
model_color (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
module
chimerax.isolde.atomic
chimerax.isolde.ctypes
chimerax.isolde.delayed_reaction
chimerax.isolde.interpolation
chimerax.isolde.isolde
chimerax.isolde.manipulations
chimerax.isolde.openmm
chimerax.isolde.openmm.custom_forces
chimerax.isolde.param_mgr
chimerax.isolde.restraints
chimerax.isolde.session_extensions
chimerax.isolde.validation
chimerax.isolde.view
moving_atoms() (chimerax.isolde.atomic.Rotamer method)
multitexture (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
multitexture_reverse_order (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
N
name (chimerax.isolde.atomic.ProperDihedral property)
(chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
nearest_target (chimerax.isolde.atomic.Rotamer property)
new_drawing() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
next_preview() (chimerax.isolde.restraints.RotamerRestraintMgr method)
non_favored() (chimerax.isolde.atomic.RamaMgr method)
non_favored_rotamers() (chimerax.isolde.atomic.RotaMgr method)
normals (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
num_chi_dihedrals (chimerax.isolde.atomic.Rotamer property)
num_mapped_dihedrals (chimerax.isolde.atomic.ProperDihedralMgr property)
num_restraints (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
num_targets (chimerax.isolde.atomic.Rotamer property)
num_tuggables (chimerax.isolde.restraints.TuggableAtomsMgr property)
number_of_positions() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
number_of_triangles() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
O
offset (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.ChiralRestraint property)
(chimerax.isolde.restraints.ProperDihedralRestraint property)
offsets (chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
(chimerax.isolde.restraints.ChiralRestraints property)
(chimerax.isolde.restraints.ProperDihedralRestraints property)
omega_dihedral (chimerax.isolde.atomic.Rama property)
omega_dihedrals (chimerax.isolde.atomic.Ramas property)
on_top (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
OPAQUE_DRAW_PASS (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
opaque_texture (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
OpenmmThreadHandler (class in chimerax.isolde.openmm)
outliers() (chimerax.isolde.atomic.RamaMgr method)
(chimerax.isolde.atomic.RotaMgr method)
P
Param_Mgr (class in chimerax.isolde.param_mgr)
params (chimerax.isolde.isolde.Isolde attribute)
pause (chimerax.isolde.openmm.SimHandler property)
pause() (chimerax.isolde.isolde.Isolde method)
pause_sim_toggle() (chimerax.isolde.isolde.Isolde method)
Peptide_Bond_Flipper (class in chimerax.isolde.manipulations)
phi_dihedral (chimerax.isolde.atomic.Rama property)
phi_dihedrals (chimerax.isolde.atomic.Ramas property)
phipsi (chimerax.isolde.atomic.Rama property)
phipsis (chimerax.isolde.atomic.Ramas property)
pickable (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
(chimerax.isolde.validation.RamaAnnotator attribute)
(chimerax.isolde.validation.RotamerAnnotator attribute)
planes_pick() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
position (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
PositionRestraint (class in chimerax.isolde.restraints)
PositionRestraintMgr (class in chimerax.isolde.restraints)
PositionRestraints (class in chimerax.isolde.restraints)
positions (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
prev_preview() (chimerax.isolde.restraints.RotamerRestraintMgr method)
ProperDihedral (class in chimerax.isolde.atomic)
ProperDihedralMgr (class in chimerax.isolde.atomic)
ProperDihedralRestraint (class in chimerax.isolde.restraints)
ProperDihedralRestraintMgr (class in chimerax.isolde.restraints)
ProperDihedralRestraints (class in chimerax.isolde.restraints)
ProperDihedrals (class in chimerax.isolde.atomic)
ProteinRegisterShifter (class in chimerax.isolde.manipulations)
psi_dihedral (chimerax.isolde.atomic.Rama property)
psi_dihedrals (chimerax.isolde.atomic.Ramas property)
push_coords_to_sim() (chimerax.isolde.openmm.SimHandler method)
R
Rama (class in chimerax.isolde.atomic)
rama_cases() (chimerax.isolde.atomic.RamaMgr method)
rama_colors() (chimerax.isolde.atomic.RamaMgr method)
RamaAnnotator (class in chimerax.isolde.validation)
RamaMgr (class in chimerax.isolde.atomic)
RamaMgr.RamaBin (class in chimerax.isolde.atomic)
RamaMgr.RamaCase (class in chimerax.isolde.atomic)
Ramas (class in chimerax.isolde.atomic)
redraw_needed() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
RegularGridInterpolator (class in chimerax.isolde.interpolation)
reinitialize_velocities() (chimerax.isolde.openmm.OpenmmThreadHandler method)
release_all() (chimerax.isolde.manipulations.ProteinRegisterShifter method)
release_fixed_atoms() (chimerax.isolde.openmm.SimHandler method)
release_restraint() (chimerax.isolde.openmm.custom_forces.TopOutRestraintForce method)
remove_all_drawings() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
remove_checkpoint_block() (chimerax.isolde.isolde.Isolde method)
remove_drawing() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
remove_drawings() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
reset_sim_params() (chimerax.isolde.isolde.Isolde method)
residue (chimerax.isolde.atomic.ChiralCenter property)
(chimerax.isolde.atomic.ProperDihedral property)
(chimerax.isolde.atomic.Rama property)
(chimerax.isolde.atomic.Rotamer property)
(chimerax.isolde.restraints.RotamerRestraint property)
residues (chimerax.isolde.atomic.ChiralCenters property)
(chimerax.isolde.atomic.ProperDihedrals property)
(chimerax.isolde.atomic.Ramas property)
(chimerax.isolde.atomic.Rotamers property)
(chimerax.isolde.restraints.RotamerRestraints property)
residues_have_dihedral() (chimerax.isolde.atomic.ProperDihedralMgr method)
restore_checkpoint() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
restore_geometry() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
restore_snapshot() (chimerax.isolde.atomic.ChiralCenter static method)
(chimerax.isolde.atomic.ChiralCenters static method)
(chimerax.isolde.atomic.ProperDihedral static method)
(chimerax.isolde.atomic.ProperDihedrals static method)
(chimerax.isolde.atomic.Rama static method)
(chimerax.isolde.atomic.Ramas static method)
(chimerax.isolde.atomic.Rotamer static method)
(chimerax.isolde.atomic.Rotamers static method)
(chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr static method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint static method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr static method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints static method)
(chimerax.isolde.restraints.ChiralRestraint static method)
(chimerax.isolde.restraints.ChiralRestraintMgr static method)
(chimerax.isolde.restraints.ChiralRestraints static method)
(chimerax.isolde.restraints.DistanceRestraint static method)
(chimerax.isolde.restraints.DistanceRestraintMgr static method)
(chimerax.isolde.restraints.MDFFAtom static method)
(chimerax.isolde.restraints.MDFFAtoms static method)
(chimerax.isolde.restraints.MDFFMgr static method)
(chimerax.isolde.restraints.PositionRestraint static method)
(chimerax.isolde.restraints.PositionRestraintMgr static method)
(chimerax.isolde.restraints.PositionRestraints static method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr static method)
(chimerax.isolde.restraints.RotamerRestraint static method)
(chimerax.isolde.restraints.RotamerRestraintMgr static method)
(chimerax.isolde.restraints.RotamerRestraints static method)
(chimerax.isolde.restraints.TuggableAtomsMgr static method)
(chimerax.isolde.validation.RamaAnnotator static method)
(chimerax.isolde.validation.RotamerAnnotator static method)
restrain_atom_distances_to_template() (chimerax.isolde.restraints method)
restrain_ca_distances_to_template() (chimerax.isolde.restraints method)
restrain_secondary_structure() (chimerax.isolde.restraints method)
restrain_small_ligands() (chimerax.isolde.restraints method)
restrain_torsions_to_template() (chimerax.isolde.restraints method)
RestraintChangeTracker (class in chimerax.isolde.restraints)
restrict_to_sel() (chimerax.isolde.restraints.ChiralRestraints method)
restrict_to_selected_residues() (chimerax.isolde.validation.RamaAnnotator method)
(chimerax.isolde.validation.RotamerAnnotator method)
resume() (chimerax.isolde.isolde.Isolde method)
revert_to_checkpoint() (chimerax.isolde.isolde.Isolde method)
(chimerax.isolde.openmm.SimManager method)
rotamer (chimerax.isolde.restraints.RotamerRestraint property)
Rotamer (class in chimerax.isolde.atomic)
RotamerAnnotator (class in chimerax.isolde.validation)
RotamerRestraint (class in chimerax.isolde.restraints)
RotamerRestraintMgr (class in chimerax.isolde.restraints)
RotamerRestraints (class in chimerax.isolde.restraints)
rotamers (chimerax.isolde.restraints.RotamerRestraints property)
Rotamers (class in chimerax.isolde.atomic)
RotaMgr (class in chimerax.isolde.atomic)
RotaMgr.RotaBin (class in chimerax.isolde.atomic)
S
satisfied (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
(chimerax.isolde.restraints.ChiralRestraint property)
(chimerax.isolde.restraints.DistanceRestraint property)
(chimerax.isolde.restraints.ProperDihedralRestraint property)
satisfied_limit (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
(chimerax.isolde.restraints.ChiralRestraint property)
(chimerax.isolde.restraints.DistanceRestraint property)
(chimerax.isolde.restraints.ProperDihedralRestraint property)
satisfied_limits (chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
(chimerax.isolde.restraints.ChiralRestraints property)
(chimerax.isolde.restraints.ProperDihedralRestraints property)
satisfieds (chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
(chimerax.isolde.restraints.ChiralRestraints property)
(chimerax.isolde.restraints.ProperDihedralRestraints property)
save_checkpoint() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
save_geometry() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
SCENE (chimerax.isolde.atomic.ChiralCenter attribute)
(chimerax.isolde.atomic.ChiralCenters attribute)
(chimerax.isolde.atomic.ProperDihedral attribute)
(chimerax.isolde.atomic.ProperDihedrals attribute)
(chimerax.isolde.atomic.Ramas attribute)
(chimerax.isolde.atomic.Rotamers attribute)
(chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
scene_position (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
score (chimerax.isolde.atomic.Rama property)
(chimerax.isolde.atomic.Rotamer property)
scores (chimerax.isolde.atomic.Ramas property)
(chimerax.isolde.atomic.Rotamers property)
selected (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
selected_atoms (chimerax.isolde.isolde.Isolde property)
selected_model (chimerax.isolde.isolde.Isolde property)
selected_model_has_maps (chimerax.isolde.isolde.Isolde property)
selected_model_has_mdff_enabled (chimerax.isolde.isolde.Isolde property)
SESSION (chimerax.isolde.atomic.ChiralCenter attribute)
(chimerax.isolde.atomic.ChiralCenters attribute)
(chimerax.isolde.atomic.ProperDihedral attribute)
(chimerax.isolde.atomic.ProperDihedrals attribute)
(chimerax.isolde.atomic.Ramas attribute)
(chimerax.isolde.atomic.Rotamers attribute)
(chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
set_arrow_color() (chimerax.isolde.restraints.TuggableAtomsMgr method)
set_bond_color() (chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
set_color_scale() (chimerax.isolde.atomic.RamaMgr method)
(chimerax.isolde.atomic.RotaMgr method)
(chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
set_colormap() (chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
set_default_colors() (chimerax.isolde.atomic.RamaMgr method)
(chimerax.isolde.atomic.RotaMgr method)
(chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
set_default_cutoffs() (chimerax.isolde.atomic.RamaMgr method)
(chimerax.isolde.atomic.RotaMgr method)
set_fixed_atoms() (chimerax.isolde.openmm.SimHandler method)
set_geometry() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
set_mdff_global_k() (chimerax.isolde.openmm.SimHandler method)
set_mdff_scale_factor() (chimerax.isolde.openmm.SimHandler method)
set_pin_color() (chimerax.isolde.restraints.PositionRestraintMgr method)
set_spring_constant() (chimerax.isolde.restraints.RotamerRestraint method)
(chimerax.isolde.restraints.RotamerRestraints method)
set_target_color() (chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
set_targets() (chimerax.isolde.restraints.RotamerRestraintMgr method)
set_transparency() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
shape_changed (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
shift_register() (chimerax.isolde.manipulations.ProteinRegisterShifter method)
show_master_help_in_browser() (chimerax.isolde.isolde.Isolde method)
show_metadata() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
showing_transparent() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
sim_handler (chimerax.isolde.isolde.Isolde property)
sim_index (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
(chimerax.isolde.restraints.ChiralRestraint property)
(chimerax.isolde.restraints.DistanceRestraint property)
(chimerax.isolde.restraints.MDFFAtom property)
(chimerax.isolde.restraints.PositionRestraint property)
(chimerax.isolde.restraints.ProperDihedralRestraint property)
sim_indices (chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
(chimerax.isolde.restraints.ChiralRestraints property)
(chimerax.isolde.restraints.MDFFAtoms property)
(chimerax.isolde.restraints.PositionRestraints property)
(chimerax.isolde.restraints.ProperDihedralRestraints property)
sim_manager (chimerax.isolde.isolde.Isolde property)
sim_paused (chimerax.isolde.isolde.Isolde property)
sim_running (chimerax.isolde.openmm.SimHandler property)
(chimerax.isolde.openmm.SimManager property)
SimConstruct (class in chimerax.isolde.openmm)
SimHandler (class in chimerax.isolde.openmm)
SimManager (class in chimerax.isolde.openmm)
SimParams (class in chimerax.isolde.openmm)
simulation_mode (chimerax.isolde.isolde.Isolde property)
simulation_running (chimerax.isolde.isolde.Isolde property)
skip_bounds (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
smoothing (chimerax.isolde.isolde.Isolde property)
(chimerax.isolde.openmm.OpenmmThreadHandler property)
(chimerax.isolde.openmm.SimHandler property)
smoothing_alpha (chimerax.isolde.isolde.Isolde property)
(chimerax.isolde.openmm.SimHandler property)
Solid (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
spring_constant (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.ChiralRestraint property)
(chimerax.isolde.restraints.DistanceRestraint property)
(chimerax.isolde.restraints.PositionRestraint property)
(chimerax.isolde.restraints.ProperDihedralRestraint property)
spring_constants (chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
(chimerax.isolde.restraints.ChiralRestraints property)
(chimerax.isolde.restraints.PositionRestraints property)
(chimerax.isolde.restraints.ProperDihedralRestraints property)
start_sim() (chimerax.isolde.isolde.Isolde method)
(chimerax.isolde.openmm.SimHandler method)
(chimerax.isolde.openmm.SimManager method)
step() (chimerax.isolde.openmm.OpenmmThreadHandler method)
stop() (chimerax.isolde.openmm.SimHandler method)
stop_sim() (chimerax.isolde.openmm.SimManager method)
stop_tugging() (chimerax.isolde.isolde.Isolde method)
subtract() (chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamers method)
T
take_snapshot() (chimerax.isolde.atomic.ChiralCenter method)
(chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ProperDihedral method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Rama method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamer method)
(chimerax.isolde.atomic.Rotamers method)
(chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints method)
(chimerax.isolde.restraints.ChiralRestraint method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraints method)
(chimerax.isolde.restraints.DistanceRestraint method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFAtom method)
(chimerax.isolde.restraints.MDFFAtoms method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraint method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.PositionRestraints method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraint method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraints method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
(chimerax.isolde.validation.RamaAnnotator method)
(chimerax.isolde.validation.RotamerAnnotator method)
target (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
(chimerax.isolde.restraints.ChiralRestraint property)
(chimerax.isolde.restraints.DistanceRestraint property)
(chimerax.isolde.restraints.PositionRestraint property)
(chimerax.isolde.restraints.ProperDihedralRestraint property)
target_index (chimerax.isolde.restraints.RotamerRestraint property)
(chimerax.isolde.restraints.RotamerRestraints property)
target_vector (chimerax.isolde.restraints.PositionRestraint property)
target_vectors (chimerax.isolde.restraints.PositionRestraints property)
targets (chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
(chimerax.isolde.restraints.ChiralRestraints property)
(chimerax.isolde.restraints.PositionRestraints property)
(chimerax.isolde.restraints.ProperDihedralRestraints property)
temperature (chimerax.isolde.openmm.SimHandler property)
texture (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
texture_coordinates (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
thread_handler (chimerax.isolde.openmm.SimHandler property)
toggle_pause() (chimerax.isolde.openmm.SimHandler method)
(chimerax.isolde.openmm.SimManager method)
tolerance (chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
tolerances (chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
TopOutBondForce (class in chimerax.isolde.openmm.custom_forces)
TopOutRestraintForce (class in chimerax.isolde.openmm.custom_forces)
TopOutTorsionForce (class in chimerax.isolde.openmm.custom_forces)
track_whole_model (chimerax.isolde.validation.RamaAnnotator property)
(chimerax.isolde.validation.RotamerAnnotator property)
TRANSPARENT_DEPTH_DRAW_PASS (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
TRANSPARENT_DRAW_PASS (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
triangle_mask (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
triangles (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
triggers (chimerax.isolde.openmm.SimHandler property)
tug_atom_to() (chimerax.isolde.isolde.Isolde method)
TuggableAtomsMgr (class in chimerax.isolde.restraints)
twisted() (chimerax.isolde.atomic.RamaMgr method)
U
unique() (chimerax.isolde.atomic.ChiralCenters method)
(chimerax.isolde.atomic.ProperDihedrals method)
(chimerax.isolde.atomic.Ramas method)
(chimerax.isolde.atomic.Rotamers method)
unsatisfied (chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
(chimerax.isolde.restraints.ChiralRestraint property)
(chimerax.isolde.restraints.DistanceRestraint property)
(chimerax.isolde.restraints.ProperDihedralRestraint property)
unsatisfieds (chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
(chimerax.isolde.restraints.ChiralRestraints property)
(chimerax.isolde.restraints.ProperDihedralRestraints property)
update_adaptive_dihedral_restraint() (chimerax.isolde.openmm.SimHandler method)
update_adaptive_dihedral_restraints() (chimerax.isolde.openmm.SimHandler method)
update_adaptive_distance_restraint() (chimerax.isolde.openmm.SimHandler method)
update_adaptive_distance_restraints() (chimerax.isolde.openmm.SimHandler method)
update_dihedral_restraint() (chimerax.isolde.openmm.SimHandler method)
update_dihedral_restraints() (chimerax.isolde.openmm.SimHandler method)
update_distance_restraint() (chimerax.isolde.openmm.SimHandler method)
update_distance_restraints() (chimerax.isolde.openmm.SimHandler method)
update_graphics() (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr method)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr method)
(chimerax.isolde.restraints.ChiralRestraintMgr method)
(chimerax.isolde.restraints.DistanceRestraintMgr method)
(chimerax.isolde.restraints.MDFFMgr method)
(chimerax.isolde.restraints.PositionRestraintMgr method)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr method)
(chimerax.isolde.restraints.RotamerRestraintMgr method)
(chimerax.isolde.restraints.TuggableAtomsMgr method)
update_mdff_atom() (chimerax.isolde.openmm.SimHandler method)
update_mdff_atoms() (chimerax.isolde.openmm.SimHandler method)
update_position_restraint() (chimerax.isolde.openmm.SimHandler method)
update_position_restraints() (chimerax.isolde.openmm.SimHandler method)
update_target() (chimerax.isolde.openmm.custom_forces.AdaptiveDistanceRestraintForce method)
(chimerax.isolde.openmm.custom_forces.FlatBottomTorsionRestraintForce method)
(chimerax.isolde.openmm.custom_forces.TopOutBondForce method)
(chimerax.isolde.openmm.custom_forces.TopOutRestraintForce method)
(chimerax.isolde.openmm.custom_forces.TopOutTorsionForce method)
update_targets() (chimerax.isolde.openmm.custom_forces.AdaptiveDistanceRestraintForce method)
(chimerax.isolde.openmm.custom_forces.FlatBottomTorsionRestraintForce method)
(chimerax.isolde.openmm.custom_forces.TopOutBondForce method)
(chimerax.isolde.openmm.custom_forces.TopOutRestraintForce method)
(chimerax.isolde.openmm.custom_forces.TopOutTorsionForce method)
update_tuggable() (chimerax.isolde.openmm.SimHandler method)
update_tuggables() (chimerax.isolde.openmm.SimHandler method)
use_lighting (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
V
valid (chimerax.isolde.atomic.Rama property)
validate() (chimerax.isolde.atomic.RamaMgr method)
validate_residues() (chimerax.isolde.atomic.RotaMgr method)
validate_rotamers() (chimerax.isolde.atomic.RotaMgr method)
validate_scale_and_color_rotamers() (chimerax.isolde.atomic.RotaMgr method)
valids (chimerax.isolde.atomic.Ramas property)
values (chimerax.isolde.interpolation.RegularGridInterpolator property)
vertex_colors (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
vertices (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.ChiralRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.MDFFMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
(chimerax.isolde.restraints.RotamerRestraintMgr property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
visible (chimerax.isolde.atomic.Rama property)
(chimerax.isolde.atomic.Rotamer property)
(chimerax.isolde.restraints.AdaptiveDihedralRestraint property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraint property)
(chimerax.isolde.restraints.DistanceRestraint property)
(chimerax.isolde.restraints.PositionRestraint property)
(chimerax.isolde.restraints.ProperDihedralRestraint property)
visible_ignoring_ribbon (chimerax.isolde.atomic.Rama property)
visible_restraints (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr property)
(chimerax.isolde.restraints.DistanceRestraintMgr property)
(chimerax.isolde.restraints.PositionRestraintMgr property)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr property)
visibles (chimerax.isolde.atomic.Ramas property)
(chimerax.isolde.atomic.Rotamers property)
(chimerax.isolde.restraints.AdaptiveDihedralRestraints property)
(chimerax.isolde.restraints.AdaptiveDistanceRestraints property)
(chimerax.isolde.restraints.PositionRestraints property)
(chimerax.isolde.restraints.ProperDihedralRestraints property)
(chimerax.isolde.restraints.TuggableAtomsMgr property)
visibles_ignoring_ribbon (chimerax.isolde.atomic.Ramas property)
volume (chimerax.isolde.restraints.MDFFMgr property)
W
was_deleted (chimerax.isolde.restraints.AdaptiveDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.AdaptiveDistanceRestraintMgr attribute)
(chimerax.isolde.restraints.ChiralRestraintMgr attribute)
(chimerax.isolde.restraints.DistanceRestraintMgr attribute)
(chimerax.isolde.restraints.MDFFMgr attribute)
(chimerax.isolde.restraints.PositionRestraintMgr attribute)
(chimerax.isolde.restraints.ProperDihedralRestraintMgr attribute)
(chimerax.isolde.restraints.RotamerRestraintMgr attribute)
(chimerax.isolde.restraints.TuggableAtomsMgr attribute)
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