ProtoCaller
latest
Contents:
ProtoCaller
Documentation
Changelog
Examples
ProtoCaller
Docs
»
Index
Edit on GitHub
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
V
|
W
|
X
|
Y
|
Z
A
alignAndCreateMorph() (ProtoCaller.Ensemble.Perturbation.Perturbation method)
alignToEachOther() (ProtoCaller.Ensemble.Perturbation.Perturbation method)
alignToReference() (ProtoCaller.Ensemble.Perturbation.Perturbation method)
alignTwoMolecules() (in module ProtoCaller.Wrappers.rdkitwrapper)
altLoc (ProtoCaller.IO.PDB.Atom.Atom attribute)
amberWrapper() (in module ProtoCaller.Parametrise.amber)
AssignBondOrdersFromTemplate() (in module ProtoCaller.Wrappers.rdkitwrapper)
Atom (class in ProtoCaller.IO.PDB.Atom)
B
babelTransform() (in module ProtoCaller.Wrappers.babelwrapper)
barostat (ProtoCaller.Protocol.Protocol attribute)
bonded_lambdas (ProtoCaller.Protocol.Protocol attribute)
box_length_complex (ProtoCaller.Ensemble.Ensemble attribute)
box_length_morph (ProtoCaller.Ensemble.Ensemble attribute)
C
centre (ProtoCaller.Ensemble.Ensemble attribute)
centre() (in module ProtoCaller.Wrappers.biosimspacewrapper)
(in module ProtoCaller.Wrappers.parmedwrapper)
Chain (class in ProtoCaller.IO.PDB.Chain)
chainID (ProtoCaller.IO.PDB.Atom.Atom attribute)
(ProtoCaller.IO.PDB.Chain.Chain attribute)
(ProtoCaller.IO.PDB.Missing.MissingResidue attribute)
(ProtoCaller.IO.PDB.Residue.Residue attribute)
charge (ProtoCaller.IO.PDB.Atom.Atom attribute)
charmmguiTransform() (in module ProtoCaller.Wrappers.charmmguiwrapper)
checkFileExists() (in module ProtoCaller.Utils.fileio)
code (ProtoCaller.Utils.pdbconnect.PDBDownloader attribute)
code() (ProtoCaller.Ensemble.Protein.Protein property)
(ProtoCaller.Utils.pdbconnect.PDBDownloader property)
complex_template() (ProtoCaller.Ensemble.Protein.Protein property)
compressibility (ProtoCaller.Protocol.Protocol attribute)
ConditionalList (class in ProtoCaller.Utils.ConditionalList)
constraint (ProtoCaller.Protocol.Protocol attribute)
constraint_type (ProtoCaller.Protocol.Protocol attribute)
copydirname (ProtoCaller.Utils.fileio.Dir attribute)
coulomb_cutoff (ProtoCaller.Protocol.Protocol attribute)
coulomb_lambdas (ProtoCaller.Protocol.Protocol attribute)
coulomb_type (ProtoCaller.Protocol.Protocol attribute)
current_lambda (ProtoCaller.Protocol.Protocol attribute)
current_ref (ProtoCaller.Ensemble.Perturbation.Perturbation attribute)
D
Dir (class in ProtoCaller.Utils.fileio)
dirname (ProtoCaller.Utils.fileio.Dir attribute)
E
element (ProtoCaller.IO.PDB.Atom.Atom attribute)
engine (ProtoCaller.Ensemble.Ensemble attribute)
Ensemble (class in ProtoCaller.Ensemble)
F
fasta() (ProtoCaller.Ensemble.Protein.Protein property)
FASTA2PIR() (in module ProtoCaller.Wrappers.modellerwrapper)
filename() (ProtoCaller.IO.PDB.PDB property)
files (ProtoCaller.Simulation.RunGMX attribute)
filter() (ProtoCaller.Ensemble.Protein.Protein method)
(ProtoCaller.IO.PDB.PDB method)
fixCharge() (in module ProtoCaller.Wrappers.parmedwrapper)
free_energy (ProtoCaller.Protocol.Protocol attribute)
G
generateMBARData() (ProtoCaller.Simulation.RunGMX method)
get_morph() (ProtoCaller.Ensemble.Perturbation.Perturbation method)
get_parametrised_files1() (ProtoCaller.Ensemble.Perturbation.Perturbation method)
get_parametrised_files2() (ProtoCaller.Ensemble.Perturbation.Perturbation method)
getAlignmentScore() (in module ProtoCaller.Wrappers.rdkitwrapper)
getEZStereochemistry() (in module ProtoCaller.Wrappers.rdkitwrapper)
getFASTA() (ProtoCaller.Utils.pdbconnect.PDBDownloader method)
getFixedMCS() (in module ProtoCaller.Wrappers.rdkitwrapper)
getLigands() (ProtoCaller.Utils.pdbconnect.PDBDownloader method)
getMatchingAtomScore() (in module ProtoCaller.Wrappers.rdkitwrapper)
getMCSMap() (in module ProtoCaller.Wrappers.rdkitwrapper)
getPDB() (ProtoCaller.Utils.pdbconnect.PDBDownloader method)
I
iCode (ProtoCaller.IO.PDB.Atom.Atom attribute)
(ProtoCaller.IO.PDB.Missing.MissingResidue attribute)
(ProtoCaller.IO.PDB.Residue.Residue attribute)
ignore_warnings() (in module ProtoCaller.Utils.stdio)
initialdirnames (ProtoCaller.Utils.fileio.Dir attribute)
integrator (ProtoCaller.Protocol.Protocol attribute)
ion_conc (ProtoCaller.Ensemble.Ensemble attribute)
isAligned() (ProtoCaller.Ensemble.Perturbation.Perturbation property)
isAlignedTo() (ProtoCaller.Ensemble.Perturbation.Perturbation method)
L
lambda_dict (ProtoCaller.Simulation.RunGMX attribute)
lambda_size() (ProtoCaller.Simulation.RunGMX property)
Ligand (class in ProtoCaller.Ensemble.Ligand)
ligand1 (ProtoCaller.Ensemble.Perturbation.Perturbation attribute)
ligand2 (ProtoCaller.Ensemble.Perturbation.Perturbation attribute)
ligand_ff() (ProtoCaller.Parametrise.Params property)
ligand_ref() (ProtoCaller.Ensemble.Protein.Protein property)
ligandReader() (in module ProtoCaller.Wrappers.charmmguiwrapper)
ligands() (ProtoCaller.Ensemble.Protein.Protein property)
M
mass_lambdas (ProtoCaller.Protocol.Protocol attribute)
mbar_data (ProtoCaller.Simulation.RunGMX attribute)
minimise (ProtoCaller.Ensemble.Ligand.Ligand attribute)
minimiseAlignmentScore() (in module ProtoCaller.Wrappers.rdkitwrapper)
MissingAtoms (class in ProtoCaller.IO.PDB.Missing)
MissingResidue (class in ProtoCaller.IO.PDB.Missing)
modellerTransform() (in module ProtoCaller.Wrappers.modellerwrapper)
module
ProtoCaller.Ensemble
ProtoCaller.Ensemble.Ligand
ProtoCaller.Ensemble.Perturbation
ProtoCaller.Ensemble.PerturbationList
ProtoCaller.Ensemble.Protein
ProtoCaller.IO
ProtoCaller.IO.GROMACS
ProtoCaller.IO.PDB
ProtoCaller.IO.PDB.Atom
ProtoCaller.IO.PDB.Chain
ProtoCaller.IO.PDB.Missing
ProtoCaller.IO.PDB.Residue
ProtoCaller.Parametrise
ProtoCaller.Parametrise.amber
ProtoCaller.Protocol
ProtoCaller.Simulation
ProtoCaller.Solvate
ProtoCaller.Utils
ProtoCaller.Utils.ConditionalList
ProtoCaller.Utils.fileio
ProtoCaller.Utils.pdbconnect
ProtoCaller.Utils.runexternal
ProtoCaller.Utils.stdio
ProtoCaller.Wrappers
ProtoCaller.Wrappers.babelwrapper
ProtoCaller.Wrappers.biosimspacewrapper
ProtoCaller.Wrappers.charmmguiwrapper
ProtoCaller.Wrappers.modellerwrapper
ProtoCaller.Wrappers.parmedwrapper
ProtoCaller.Wrappers.pdb2pqrwrapper
ProtoCaller.Wrappers.pdbfixerwrapper
ProtoCaller.Wrappers.rdkitwrapper
molecule() (ProtoCaller.Ensemble.Ligand.Ligand property)
morph() (ProtoCaller.Ensemble.Perturbation.Perturbation property)
morphs (ProtoCaller.Ensemble.Ensemble attribute)
N
n_steps (ProtoCaller.Protocol.Protocol attribute)
name (ProtoCaller.Ensemble.Ligand.Ligand attribute)
(ProtoCaller.Ensemble.Protein.Protein attribute)
(ProtoCaller.IO.PDB.Atom.Atom attribute)
name() (ProtoCaller.Ensemble.Ligand.Ligand property)
(ProtoCaller.Ensemble.Perturbation.Perturbation property)
(ProtoCaller.Ensemble.Protein.Protein property)
neighbour_cutoff (ProtoCaller.Protocol.Protocol attribute)
neighbour_frequency (ProtoCaller.Protocol.Protocol attribute)
neutralise (ProtoCaller.Ensemble.Ensemble attribute)
numberOfAtoms() (ProtoCaller.IO.PDB.Chain.Chain property)
(ProtoCaller.IO.PDB.Residue.Residue property)
numberOfChains() (ProtoCaller.IO.PDB.PDB property)
numberOfResidues() (ProtoCaller.IO.PDB.Chain.Chain property)
(ProtoCaller.IO.PDB.PDB property)
O
occupancy (ProtoCaller.IO.PDB.Atom.Atom attribute)
openAsRdkit() (in module ProtoCaller.Wrappers.rdkitwrapper)
openFileAsRdkit() (in module ProtoCaller.Wrappers.rdkitwrapper)
openFilesAsParmed() (in module ProtoCaller.Wrappers.parmedwrapper)
overwrite (ProtoCaller.Utils.fileio.Dir attribute)
P
parametrise() (ProtoCaller.Ensemble.Ligand.Ligand method)
(ProtoCaller.Ensemble.Protein.Protein method)
parametriseAndLoadBSS() (in module ProtoCaller.Parametrise)
parametriseAndLoadPmd() (in module ProtoCaller.Parametrise)
parametrised() (ProtoCaller.Ensemble.Ligand.Ligand property)
parametrised_files() (ProtoCaller.Ensemble.Ligand.Ligand property)
parametrised_files1() (ProtoCaller.Ensemble.Perturbation.Perturbation property)
parametrised_files2() (ProtoCaller.Ensemble.Perturbation.Perturbation property)
parametriseFile() (in module ProtoCaller.Parametrise)
Params (class in ProtoCaller.Parametrise)
params (ProtoCaller.Ensemble.Ensemble attribute)
path (ProtoCaller.Utils.fileio.Dir attribute)
PDB (class in ProtoCaller.IO.PDB)
pdb() (ProtoCaller.Ensemble.Protein.Protein property)
pdb2pqrTransform() (in module ProtoCaller.Wrappers.pdb2pqrwrapper)
pdb_obj() (ProtoCaller.Ensemble.Protein.Protein property)
PDBDownloader (class in ProtoCaller.Utils.pdbconnect)
pdbfixerTransform() (in module ProtoCaller.Wrappers.pdbfixerwrapper)
PDBReader() (in module ProtoCaller.Wrappers.charmmguiwrapper)
periodic_boundary_conditions (ProtoCaller.Protocol.Protocol attribute)
Perturbation (class in ProtoCaller.Ensemble.Perturbation)
PerturbationList (class in ProtoCaller.Ensemble.PerturbationList)
pme_order (ProtoCaller.Protocol.Protocol attribute)
prepare() (ProtoCaller.Ensemble.Protein.Protein method)
prepareComplexes() (ProtoCaller.Ensemble.Ensemble method)
pres_frequency (ProtoCaller.Protocol.Protocol attribute)
pres_time_coupling (ProtoCaller.Protocol.Protocol attribute)
pressure (ProtoCaller.Protocol.Protocol attribute)
Protein (class in ProtoCaller.Ensemble.Protein)
protein (ProtoCaller.Ensemble.Ensemble attribute)
protein_ff() (ProtoCaller.Parametrise.Params property)
ProtoCaller.Ensemble
module
ProtoCaller.Ensemble.Ligand
module
ProtoCaller.Ensemble.Perturbation
module
ProtoCaller.Ensemble.PerturbationList
module
ProtoCaller.Ensemble.Protein
module
ProtoCaller.IO
module
ProtoCaller.IO.GROMACS
module
ProtoCaller.IO.PDB
module
ProtoCaller.IO.PDB.Atom
module
ProtoCaller.IO.PDB.Chain
module
ProtoCaller.IO.PDB.Missing
module
ProtoCaller.IO.PDB.Residue
module
ProtoCaller.Parametrise
module
ProtoCaller.Parametrise.amber
module
ProtoCaller.Protocol
module
ProtoCaller.Simulation
module
ProtoCaller.Solvate
module
ProtoCaller.Utils
module
ProtoCaller.Utils.ConditionalList
module
ProtoCaller.Utils.fileio
module
ProtoCaller.Utils.pdbconnect
module
ProtoCaller.Utils.runexternal
module
ProtoCaller.Utils.stdio
module
ProtoCaller.Wrappers
module
ProtoCaller.Wrappers.babelwrapper
module
ProtoCaller.Wrappers.biosimspacewrapper
module
ProtoCaller.Wrappers.charmmguiwrapper
module
ProtoCaller.Wrappers.modellerwrapper
module
ProtoCaller.Wrappers.parmedwrapper
module
ProtoCaller.Wrappers.pdb2pqrwrapper
module
ProtoCaller.Wrappers.pdbfixerwrapper
module
ProtoCaller.Wrappers.rdkitwrapper
module
Protocol (class in ProtoCaller.Protocol)
protocols (ProtoCaller.Simulation.RunGMX attribute)
protonate() (ProtoCaller.Ensemble.Ligand.Ligand method)
protonated() (ProtoCaller.Ensemble.Ligand.Ligand property)
protonated_filename() (ProtoCaller.Ensemble.Ligand.Ligand property)
purge_immediately (ProtoCaller.Utils.fileio.Dir attribute)
purgeAtoms() (ProtoCaller.IO.PDB.Chain.Chain method)
(ProtoCaller.IO.PDB.PDB method)
(ProtoCaller.IO.PDB.Residue.Residue method)
purgeEmpty() (ProtoCaller.IO.PDB.Chain.Chain method)
(ProtoCaller.IO.PDB.PDB method)
purgeResidues() (ProtoCaller.IO.PDB.Chain.Chain method)
(ProtoCaller.IO.PDB.PDB method)
R
random_velocities (ProtoCaller.Protocol.Protocol attribute)
random_velocities_seed (ProtoCaller.Protocol.Protocol attribute)
random_velocities_temperature (ProtoCaller.Protocol.Protocol attribute)
readPDB() (ProtoCaller.IO.PDB.PDB method)
reNumberAtoms() (ProtoCaller.IO.PDB.Chain.Chain method)
(ProtoCaller.IO.PDB.Residue.Residue method)
reNumberResidues() (ProtoCaller.IO.PDB.Chain.Chain method)
(ProtoCaller.IO.PDB.PDB method)
rescaleBondedDummies() (in module ProtoCaller.Wrappers.biosimspacewrapper)
rescaleSystemParams() (in module ProtoCaller.Wrappers.biosimspacewrapper)
Residue (class in ProtoCaller.IO.PDB.Residue)
resize() (in module ProtoCaller.Wrappers.biosimspacewrapper)
(in module ProtoCaller.Wrappers.parmedwrapper)
resName (ProtoCaller.IO.PDB.Atom.Atom attribute)
(ProtoCaller.IO.PDB.Missing.MissingResidue attribute)
(ProtoCaller.IO.PDB.Residue.Residue attribute)
resSeq (ProtoCaller.IO.PDB.Atom.Atom attribute)
(ProtoCaller.IO.PDB.Missing.MissingResidue attribute)
(ProtoCaller.IO.PDB.Residue.Residue attribute)
restraint_lambdas (ProtoCaller.Protocol.Protocol attribute)
runAntechamber() (in module ProtoCaller.Parametrise.amber)
runExternal() (in module ProtoCaller.Utils.runexternal)
RunGMX (class in ProtoCaller.Simulation)
runMBAR() (ProtoCaller.Simulation.RunGMX method)
runParmchk() (in module ProtoCaller.Parametrise.amber)
runSimulation() (ProtoCaller.Simulation.RunGMX method)
runTleap() (in module ProtoCaller.Parametrise.amber)
S
saveAsGromacs() (in module ProtoCaller.IO.GROMACS)
saveFilesFromParmed() (in module ProtoCaller.Wrappers.parmedwrapper)
saveFromRdkit() (in module ProtoCaller.Wrappers.rdkitwrapper)
saveSystems() (ProtoCaller.Ensemble.Ensemble method)
sequence() (ProtoCaller.IO.PDB.Chain.Chain property)
(ProtoCaller.IO.PDB.Missing.MissingResidue property)
(ProtoCaller.IO.PDB.PDB property)
(ProtoCaller.IO.PDB.Residue.Residue property)
serial (ProtoCaller.IO.PDB.Atom.Atom attribute)
shell (ProtoCaller.Ensemble.Ensemble attribute)
skip_energies (ProtoCaller.Protocol.Protocol attribute)
skip_forces (ProtoCaller.Protocol.Protocol attribute)
skip_positions (ProtoCaller.Protocol.Protocol attribute)
skip_velocities (ProtoCaller.Protocol.Protocol attribute)
softcore_alpha (ProtoCaller.Protocol.Protocol attribute)
softcore_coulomb (ProtoCaller.Protocol.Protocol attribute)
softcore_lambda_power (ProtoCaller.Protocol.Protocol attribute)
softcore_vdw (ProtoCaller.Protocol.Protocol attribute)
solvate() (in module ProtoCaller.Solvate)
sortResidueList() (ProtoCaller.IO.PDB.PDB static method)
stdout_stderr() (in module ProtoCaller.Utils.stdio)
stdout_stderr_cls (class in ProtoCaller.Utils.stdio)
string() (ProtoCaller.Ensemble.Ligand.Ligand property)
systems_prep (ProtoCaller.Ensemble.Ensemble attribute)
T
temp (ProtoCaller.Utils.fileio.Dir attribute)
temp_frequency (ProtoCaller.Protocol.Protocol attribute)
temp_groups (ProtoCaller.Protocol.Protocol attribute)
temp_time_coupling (ProtoCaller.Protocol.Protocol attribute)
temperature (ProtoCaller.Protocol.Protocol attribute)
temperature_lambdas (ProtoCaller.Protocol.Protocol attribute)
tempFactor (ProtoCaller.IO.PDB.Atom.Atom attribute)
thermostat (ProtoCaller.Protocol.Protocol attribute)
timestep (ProtoCaller.Protocol.Protocol attribute)
totalResidueList() (ProtoCaller.IO.PDB.PDB method)
translateMolecule() (in module ProtoCaller.Wrappers.rdkitwrapper)
type (ProtoCaller.IO.PDB.Atom.Atom attribute)
type() (ProtoCaller.IO.PDB.Chain.Chain property)
(ProtoCaller.IO.PDB.Missing.MissingResidue property)
(ProtoCaller.IO.PDB.PDB property)
V
vdw_corr (ProtoCaller.Protocol.Protocol attribute)
vdw_cutoff (ProtoCaller.Protocol.Protocol attribute)
vdw_lambdas (ProtoCaller.Protocol.Protocol attribute)
vdw_type (ProtoCaller.Protocol.Protocol attribute)
W
warnings_as_errors() (in module ProtoCaller.Utils.stdio)
water_ff() (ProtoCaller.Parametrise.Params property)
water_points() (ProtoCaller.Parametrise.Params property)
workdir (ProtoCaller.Ensemble.Ensemble attribute)
(ProtoCaller.Ensemble.Ligand.Ligand attribute)
(ProtoCaller.Ensemble.Protein.Protein attribute)
workdirname (ProtoCaller.Utils.fileio.Dir attribute)
write() (ProtoCaller.Protocol.Protocol method)
write_derivatives (ProtoCaller.Protocol.Protocol attribute)
writeHetatms() (ProtoCaller.IO.PDB.PDB method)
writePDB() (ProtoCaller.IO.PDB.PDB method)
X
x (ProtoCaller.IO.PDB.Atom.Atom attribute)
Y
y (ProtoCaller.IO.PDB.Atom.Atom attribute)
Z
z (ProtoCaller.IO.PDB.Atom.Atom attribute)
Read the Docs
v: latest
Versions
master
latest
stable
Downloads
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.