GaudiMM
latest
User guide
How to install
Quick usage
Input files
Output files
FAQ & Known issues
For beginners
GaudiMM basics (start here!)
Tutorial: Your first GaudiMM calculation
Tutorial: Visualizing your first results
For developers
Developers guide
API documentation
GaudiMM
Docs
»
Index
Edit on GitHub
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Z
_
__CACHE (gaudi.base.BaseIndividual attribute)
__CACHE_OBJ (gaudi.base.BaseIndividual attribute)
_CATALOG (gaudi.genes.molecule.Molecule attribute)
_chimera2prody (gaudi.genes.normalmodes.NormalModes attribute)
_original_coords (gaudi.genes.normalmodes.NormalModes attribute)
_traj (gaudi.genes.trajectory.Trajectory attribute)
A
acceptor (gaudi.genes.molecule.Compound attribute)
add_dummy_atom() (gaudi.genes.molecule.Compound method)
add_hydrogens() (gaudi.genes.molecule.Compound method)
add_hydrogens_to_isolated_rotamer() (gaudi.genes.mutamers.Mutamers static method)
affine_cpd() (in module gaudi._cpdrift)
affine_xform() (in module gaudi._cpdrift)
alg3() (in module gaudi.genes.normalmodes)
all_chis() (gaudi.genes.rotamers.Rotamers static method)
allele (gaudi.genes.molecule.Molecule attribute)
(gaudi.genes.mutamers.Mutamers attribute)
(gaudi.genes.normalmodes.NormalModes attribute)
(gaudi.genes.rotamers.Rotamers attribute)
(gaudi.genes.search.Search attribute)
(gaudi.genes.torsion.Torsion attribute)
(gaudi.genes.trajectory.Trajectory attribute)
anchor (gaudi.genes.torsion.Torsion attribute)
Angle (class in gaudi.objectives.angle)
append() (gaudi.genes.molecule.Compound method)
apply_pdbfix() (gaudi.genes.molecule.Compound method)
args (gaudi.parse.Settings.similarity attribute)
AssertList() (in module gaudi.parse)
atom (gaudi.parse.MoleculeAtom attribute)
atoms() (gaudi.objectives.distance.Distance method)
atoms_between() (in module gaudi.box)
atoms_by_serial() (in module gaudi.box)
AtomsNotFound
attach() (gaudi.genes.molecule.Compound method)
AxesOfInertia (class in gaudi.objectives.inertia)
axis_angle (gaudi._cpdrift.Quaternion attribute)
B
BaseIndividual (class in gaudi.base)
BONDS_ROTS (gaudi.genes.torsion.Torsion attribute)
build() (gaudi.genes.molecule.Molecule method)
built_atoms (gaudi.genes.molecule.Compound attribute)
C
calculate_alignment() (in module gaudi.objectives.inertia)
calculate_axes_of_inertia() (in module gaudi.objectives.inertia)
calculate_energy() (gaudi.objectives.energy.Energy method)
(in module gaudi.objectives.energy)
calculate_inertial_matrix() (in module gaudi.objectives.inertia)
calculate_prody_normal_modes() (gaudi.genes.normalmodes.NormalModes method)
center (gaudi.genes.search.Search attribute)
center() (in module gaudi.genes.search)
(in module gaudi.genes.torsion)
centroid() (in module gaudi.objectives.inertia)
check_every (gaudi.parse.Settings.output attribute)
chimera_molecule_to_openmm_positions() (gaudi.objectives.energy.Energy static method)
chimera_molecule_to_openmm_topology() (gaudi.objectives.energy.Energy static method)
chimeracoords2numpy() (in module gaudi.genes.normalmodes)
choice() (gaudi.genes.mutamers.Mutamers method)
chunker() (in module gaudi.genes.normalmodes)
clean() (gaudi.objectives.dsx.DSX method)
(gaudi.objectives.gold.Gold method)
(gaudi.objectives.ligscore.LigScore method)
(gaudi.objectives.nwchem.NWChem method)
(gaudi.objectives.vina.Vina method)
clear_cache() (gaudi.base.BaseIndividual method)
(gaudi.base.Environment method)
(gaudi.genes.GeneProvider class method)
(gaudi.genes.molecule.Molecule class method)
(gaudi.genes.torsion.Torsion method)
(gaudi.objectives.ObjectiveProvider class method)
coherent_point_drift() (in module gaudi._cpdrift)
common_steps() (in module gaudi._cpdrift)
Compound (class in gaudi.genes.molecule)
compound (gaudi.genes.molecule.Molecule attribute)
compress (gaudi.parse.Settings.output attribute)
conjugate() (gaudi._cpdrift.Quaternion method)
Contacts (class in gaudi.objectives.contacts)
convert_chimera_molecule_to_prody() (in module gaudi.genes.normalmodes)
convexhull_volume() (in module gaudi.objectives.volume)
Coordinates() (in module gaudi.parse)
Coordination (class in gaudi.objectives.coordination)
coordination_sphere() (gaudi.objectives.coordination.Coordination method)
create_single_individual() (in module gaudi.box)
cx_eta (gaudi.parse.Settings.ga attribute)
cx_pb (gaudi.parse.Settings.ga attribute)
D
deep_update() (in module gaudi.parse)
default_values (gaudi.parse.Settings attribute)
Degrees() (in module gaudi.parse)
destroy() (gaudi.genes.molecule.Compound method)
display() (gaudi.objectives.hbonds.Hbonds method)
Distance (class in gaudi.objectives.distance)
distance() (in module gaudi.genes.search)
(in module gaudi.genes.torsion)
do_cprofile() (in module gaudi.box)
donor (gaudi.genes.molecule.Compound attribute)
draw_interactions() (in module gaudi.box)
DSX (class in gaudi.objectives.dsx)
dump_population() (in module gaudi.algorithms)
E
ea_mu_plus_lambda() (in module gaudi.algorithms)
echo_banner() (in module gaudi.cli.gaudi_cli)
enable() (in module gaudi.genes.molecule)
(in module gaudi.genes.mutamers)
(in module gaudi.genes.normalmodes)
(in module gaudi.genes.rotamers)
(in module gaudi.genes.search)
(in module gaudi.genes.torsion)
(in module gaudi.genes.trajectory)
(in module gaudi.objectives.angle)
(in module gaudi.objectives.contacts)
(in module gaudi.objectives.coordination)
(in module gaudi.objectives.distance)
(in module gaudi.objectives.dsx)
(in module gaudi.objectives.energy)
(in module gaudi.objectives.gold)
(in module gaudi.objectives.hbonds)
(in module gaudi.objectives.inertia)
(in module gaudi.objectives.ligscore)
(in module gaudi.objectives.nwchem)
(in module gaudi.objectives.solvation)
(in module gaudi.objectives.vina)
(in module gaudi.objectives.volume)
enable_logging() (in module gaudi.cli.gaudi_run)
Energy (class in gaudi.objectives.energy)
Environment (class in gaudi.base)
evaluate() (gaudi.base.BaseIndividual method)
(gaudi.base.Environment method)
(gaudi.objectives.ObjectiveProvider method)
(gaudi.objectives.angle.Angle method)
(gaudi.objectives.coordination.Coordination method)
(gaudi.objectives.dsx.DSX method)
(gaudi.objectives.energy.Energy method)
(gaudi.objectives.gold.Gold method)
(gaudi.objectives.hbonds.Hbonds method)
(gaudi.objectives.inertia.AxesOfInertia method)
(gaudi.objectives.ligscore.LigScore method)
(gaudi.objectives.nwchem.NWChem method)
(gaudi.objectives.vina.Vina method)
evaluate_area() (gaudi.objectives.solvation.Solvation method)
evaluate_center_of_mass() (gaudi.objectives.distance.Distance method)
evaluate_clashes() (gaudi.objectives.contacts.Contacts method)
evaluate_convexhull() (gaudi.objectives.volume.Volume method)
evaluate_distances() (gaudi.objectives.distance.Distance method)
evaluate_hydrophobic() (gaudi.objectives.contacts.Contacts method)
evaluate_volume() (gaudi.objectives.solvation.Solvation method)
(gaudi.objectives.volume.Volume method)
ExpandUserPathExists() (in module gaudi.parse)
express() (gaudi.base.BaseIndividual method)
(gaudi.genes.GeneProvider method)
(gaudi.genes.molecule.Molecule method)
(gaudi.genes.mutamers.Mutamers method)
(gaudi.genes.normalmodes.NormalModes method)
(gaudi.genes.rotamers.Rotamers method)
(gaudi.genes.search.Search method)
(gaudi.genes.torsion.Torsion method)
(gaudi.genes.trajectory.Trajectory method)
expressed() (in module gaudi.base)
F
files_in() (in module gaudi.box)
find_atom() (gaudi.genes.molecule.Molecule method)
find_atoms() (gaudi.genes.molecule.Molecule method)
find_interactions() (gaudi.objectives.contacts.Contacts method)
find_molecule() (gaudi.base.MolecularIndividual method)
find_nearest() (in module gaudi.box)
find_residue() (gaudi.genes.molecule.Molecule method)
find_residues() (gaudi.genes.molecule.Molecule method)
Fitness (class in gaudi.base)
frange (class in gaudi._cpdrift)
fromAxisAngle() (gaudi._cpdrift.Quaternion class method)
G
ga (gaudi.parse.Settings attribute)
gaudi (module)
gaudi._cpdrift (module)
gaudi.algorithms (module)
gaudi.base (module)
gaudi.box (module)
gaudi.cli (module)
gaudi.cli.gaudi_cli (module)
gaudi.cli.gaudi_run (module)
gaudi.exceptions (module)
gaudi.genes (module)
gaudi.genes.molecule (module)
gaudi.genes.mutamers (module)
gaudi.genes.normalmodes (module)
gaudi.genes.rotamers (module)
gaudi.genes.search (module)
gaudi.genes.torsion (module)
gaudi.genes.trajectory (module)
gaudi.objectives (module)
gaudi.objectives.angle (module)
gaudi.objectives.contacts (module)
gaudi.objectives.coordination (module)
gaudi.objectives.distance (module)
gaudi.objectives.dsx (module)
gaudi.objectives.energy (module)
gaudi.objectives.gold (module)
gaudi.objectives.hbonds (module)
gaudi.objectives.inertia (module)
gaudi.objectives.ligscore (module)
gaudi.objectives.nwchem (module)
gaudi.objectives.solvation (module)
gaudi.objectives.vina (module)
gaudi.objectives.volume (module)
gaudi.parallel (module)
gaudi.parse (module)
gaudi.plugin (module)
gaudi.similarity (module)
gaussian_modes() (in module gaudi.genes.normalmodes)
GeneProvider (class in gaudi.genes)
generations (gaudi.parse.Settings.ga attribute)
genes (gaudi.parse.Settings attribute)
get() (gaudi.genes.molecule.Molecule method)
get_molecule_by_name() (gaudi.objectives.dsx.DSX method)
(gaudi.objectives.gold.Gold method)
(gaudi.objectives.ligscore.LigScore method)
(gaudi.objectives.nwchem.NWChem method)
get_rotamers() (gaudi.genes.mutamers.Mutamers method)
get_xyz() (gaudi.objectives.nwchem.NWChem method)
Gold (class in gaudi.objectives.gold)
grid_sas_surface() (in module gaudi.objectives.solvation)
group_by_mass() (in module gaudi.genes.normalmodes)
group_by_residues() (in module gaudi.genes.normalmodes)
H
Hbonds (class in gaudi.objectives.hbonds)
highest_atom_indices() (in module gaudi.box)
history (gaudi.parse.Settings.output attribute)
I
ideal_bond_deviation() (in module gaudi.objectives.coordination)
ideal_bonded_positions() (in module gaudi.objectives.coordination)
import_plugins() (in module gaudi.plugin)
Importable() (in module gaudi.parse)
incremental_existing_path() (in module gaudi.box)
J
join() (gaudi.genes.molecule.Compound method)
K
kwargs (gaudi.parse.Settings.similarity attribute)
L
lambda_ (gaudi.parse.Settings.ga attribute)
last() (in module gaudi._cpdrift)
launch() (in module gaudi.cli.gaudi_run)
LigScore (class in gaudi.objectives.ligscore)
load_chimera() (in module gaudi.cli.gaudi_cli)
load_frame() (gaudi.genes.trajectory.Trajectory method)
load_plugins() (in module gaudi.plugin)
M
main() (in module gaudi.cli.gaudi_run)
MakeDir() (in module gaudi.parse)
mate() (gaudi.base.BaseIndividual method)
(gaudi.genes.GeneProvider method)
(gaudi.genes.molecule.Molecule method)
(gaudi.genes.mutamers.Mutamers method)
(gaudi.genes.normalmodes.NormalModes method)
(gaudi.genes.rotamers.Rotamers method)
(gaudi.genes.search.Search method)
(gaudi.genes.torsion.Torsion method)
(gaudi.genes.trajectory.Trajectory method)
matrix() (gaudi._cpdrift.Quaternion method)
module (gaudi.parse.Settings.similarity attribute)
mol (gaudi.genes.molecule.Compound attribute)
MolecularIndividual (class in gaudi.base)
Molecule (class in gaudi.genes.molecule)
molecule (gaudi.genes.normalmodes.NormalModes attribute)
(gaudi.genes.search.Search attribute)
(gaudi.genes.torsion.Torsion attribute)
(gaudi.genes.trajectory.Trajectory attribute)
(gaudi.parse.MoleculeAtom attribute)
(gaudi.parse.MoleculeResidue attribute)
Molecule_name() (in module gaudi.parse)
MoleculeAtom (class in gaudi.parse)
MoleculeResidue (class in gaudi.parse)
molecules() (gaudi.objectives.contacts.Contacts method)
(gaudi.objectives.coordination.Coordination method)
(gaudi.objectives.energy.Energy method)
(gaudi.objectives.hbonds.Hbonds method)
(gaudi.objectives.solvation.Solvation method)
MoleculesNotFound
mu (gaudi.parse.Settings.ga attribute)
mut_eta (gaudi.parse.Settings.ga attribute)
mut_indpb (gaudi.parse.Settings.ga attribute)
mut_pb (gaudi.parse.Settings.ga attribute)
Mutamers (class in gaudi.genes.mutamers)
mutate() (gaudi.base.BaseIndividual method)
(gaudi.genes.GeneProvider method)
(gaudi.genes.molecule.Molecule method)
(gaudi.genes.mutamers.Mutamers method)
(gaudi.genes.normalmodes.NormalModes method)
(gaudi.genes.rotamers.Rotamers method)
(gaudi.genes.search.Search method)
(gaudi.genes.torsion.Torsion method)
(gaudi.genes.trajectory.Trajectory method)
N
name (gaudi.parse.Settings.output attribute)
name_objectives (gaudi.parse.Settings attribute)
Named_spec() (in module gaudi.parse)
nearest_atom() (in module gaudi.genes.search)
(in module gaudi.genes.torsion)
nonrotatable (gaudi.genes.molecule.Compound attribute)
norm() (gaudi._cpdrift.Quaternion method)
NORMAL_MODE_SAMPLES (gaudi.genes.normalmodes.NormalModes attribute)
NORMAL_MODES (gaudi.genes.normalmodes.NormalModes attribute)
,
[1]
NORMAL_MODES_SAMPLES (gaudi.genes.normalmodes.NormalModes attribute)
NormalModes (class in gaudi.genes.normalmodes)
NWChem (class in gaudi.objectives.nwchem)
O
ObjectiveProvider (class in gaudi.objectives)
objectives (gaudi.parse.Settings attribute)
open_models_and_close() (in module gaudi.box)
origin (gaudi.genes.molecule.Compound attribute)
(gaudi.genes.search.Search attribute)
,
[1]
origin() (gaudi.objectives.gold.Gold method)
output (gaudi.parse.Settings attribute)
P
pairwise_sqdist() (in module gaudi._cpdrift)
pareto (gaudi.parse.Settings.output attribute)
parse_attr() (gaudi.genes.molecule.Compound method)
parse_origin() (in module gaudi.genes.search)
parse_output() (gaudi.objectives.dsx.DSX method)
(gaudi.objectives.gold.Gold method)
(gaudi.objectives.ligscore.LigScore method)
(gaudi.objectives.nwchem.NWChem method)
(gaudi.objectives.vina.Vina method)
parse_rawstring() (in module gaudi.parse)
patch_residue() (gaudi.genes.rotamers.Rotamers static method)
path (gaudi.parse.Settings.output attribute)
place() (gaudi.genes.molecule.Compound method)
place_for_bonding() (gaudi.genes.molecule.Compound method)
plot() (in module gaudi._cpdrift)
PluginMount (class in gaudi.plugin)
plugins (gaudi.genes.GeneProvider attribute)
(gaudi.objectives.ObjectiveProvider attribute)
population (gaudi.parse.Settings.ga attribute)
post_express() (gaudi.base.BaseIndividual method)
(gaudi.base.MolecularIndividual method)
post_unexpress() (gaudi.base.BaseIndividual method)
pre_express() (gaudi.base.BaseIndividual method)
pre_unexpress() (gaudi.base.BaseIndividual method)
precision (gaudi.parse.Settings.output attribute)
prepare_command() (gaudi.objectives.dsx.DSX method)
(gaudi.objectives.gold.Gold method)
(gaudi.objectives.ligscore.LigScore method)
prepare_ligand() (gaudi.objectives.vina.Vina method)
prepare_ligands() (gaudi.objectives.dsx.DSX method)
(gaudi.objectives.gold.Gold method)
(gaudi.objectives.ligscore.LigScore method)
prepare_nwfile() (gaudi.objectives.nwchem.NWChem method)
prepare_proteins() (gaudi.objectives.dsx.DSX method)
(gaudi.objectives.gold.Gold method)
(gaudi.objectives.ligscore.LigScore method)
prepare_receptor() (gaudi.objectives.vina.Vina method)
prepend() (gaudi.genes.molecule.Compound method)
probe() (gaudi.objectives.coordination.Coordination method)
probes() (gaudi.objectives.angle.Angle method)
(gaudi.objectives.contacts.Contacts method)
(gaudi.objectives.hbonds.Hbonds method)
prody_modes() (in module gaudi.genes.normalmodes)
prompt_on_exception (gaudi.parse.Settings.output attribute)
pseudobond_to_bond() (in module gaudi.box)
Q
Quaternion (class in gaudi._cpdrift)
R
rand_xform() (in module gaudi.genes.search)
random_angle() (gaudi.genes.torsion.Torsion method)
random_frame_number() (gaudi.genes.trajectory.Trajectory method)
random_transform() (gaudi.genes.search.Search method)
random_translation() (in module gaudi.genes.search)
read_gaussian_normal_modes() (gaudi.genes.normalmodes.NormalModes method)
read_prody_normal_modes() (gaudi.genes.normalmodes.NormalModes method)
reciprocal() (gaudi._cpdrift.Quaternion method)
reference() (gaudi.objectives.inertia.AxesOfInertia method)
RelPathToInputFile() (in module gaudi.parse)
residue (gaudi.parse.MoleculeResidue attribute)
residues() (gaudi.objectives.coordination.Coordination method)
ResiduesNotFound
ResidueThreeLetterCode() (in module gaudi.parse)
retrieve_rotamers() (gaudi.genes.rotamers.Rotamers method)
rigid_cpd() (in module gaudi._cpdrift)
rigid_xform() (in module gaudi._cpdrift)
RMSD() (in module gaudi._cpdrift)
rmsd() (in module gaudi.box)
(in module gaudi.similarity)
Rotamers (class in gaudi.genes.rotamers)
rotatable_bonds (gaudi.genes.molecule.Compound attribute)
(gaudi.genes.torsion.Torsion attribute)
rotate() (in module gaudi.genes.search)
rotation_matrix() (in module gaudi._cpdrift)
run_parallel() (in module gaudi.parallel)
S
schema (gaudi.parse.Settings attribute)
Search (class in gaudi.genes.search)
seed (gaudi.genes.molecule.Compound attribute)
sequential_bonds() (in module gaudi.box)
set_vdw_radii() (gaudi.genes.molecule.Compound method)
Settings (class in gaudi.parse)
silent_stdout() (in module gaudi.box)
similar() (gaudi.base.BaseIndividual method)
similarity (gaudi.parse.Settings attribute)
simulation (gaudi.objectives.energy.Energy attribute)
Solvation (class in gaudi.objectives.solvation)
spaced_rotations() (in module gaudi._cpdrift)
std() (in module gaudi._cpdrift)
stdout_to_file() (in module gaudi.box)
SUPPORTED_FILETYPES (gaudi.genes.molecule.Molecule attribute)
suppress_ksdssp() (in module gaudi.box)
surface() (gaudi.objectives.solvation.Solvation method)
T
target() (gaudi.objectives.volume.Volume method)
targets() (gaudi.objectives.inertia.AxesOfInertia method)
(gaudi.objectives.solvation.Solvation method)
test_import() (in module gaudi.cli.gaudi_cli)
timeit() (in module gaudi.cli.gaudi_cli)
tmpfile (gaudi.objectives.vina.Vina attribute)
to_zero (gaudi.genes.search.Search attribute)
TooManyAtoms
TooManyResidues
topology (gaudi.genes.trajectory.Trajectory attribute)
Torsion (class in gaudi.genes.torsion)
Trajectory (class in gaudi.genes.trajectory)
translate() (in module gaudi.genes.search)
U
unbuffer_stdout() (in module gaudi.cli.gaudi_run)
unexpress() (gaudi.base.BaseIndividual method)
(gaudi.genes.GeneProvider method)
(gaudi.genes.molecule.Molecule method)
(gaudi.genes.mutamers.Mutamers method)
(gaudi.genes.normalmodes.NormalModes method)
(gaudi.genes.rotamers.Rotamers method)
(gaudi.genes.search.Search method)
(gaudi.genes.torsion.Torsion method)
(gaudi.genes.trajectory.Trajectory method)
unit() (gaudi._cpdrift.Quaternion method)
update_attr() (gaudi.genes.molecule.Compound method)
update_rotamer() (gaudi.genes.rotamers.Rotamers static method)
update_rotamer_coords() (gaudi.genes.mutamers.Mutamers static method)
V
validate() (gaudi.genes.GeneProvider class method)
(gaudi.objectives.ObjectiveProvider class method)
(gaudi.parse.Settings method)
(in module gaudi.parse)
vector (gaudi._cpdrift.Quaternion attribute)
verbose (gaudi.parse.Settings.output attribute)
Vina (class in gaudi.objectives.vina)
Volume (class in gaudi.objectives.volume)
W
weights (gaudi.parse.Settings attribute)
with_validation() (gaudi.genes.GeneProvider class method)
(gaudi.objectives.ObjectiveProvider class method)
write() (gaudi.base.BaseIndividual method)
(gaudi.genes.GeneProvider method)
(gaudi.genes.molecule.Molecule method)
write_individuals() (in module gaudi.box)
wvalues (gaudi.base.Fitness attribute)
X
xyz() (gaudi.base.MolecularIndividual method)
(gaudi.genes.molecule.Molecule method)
Z
zone_atoms() (gaudi.objectives.solvation.Solvation method)
Read the Docs
v: latest
Versions
latest
stable
Downloads
pdf
html
epub
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.