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Video Tutorials
Contents
HTMD
Installation
Tutorials
Introduction to HTMD
Python primer
Getting started with HTMD
HTMD Molecules
Visualization in HTMD
Building with HTMD
Protein preparation
Advanced building
System building protein-ligand
System building protein in Membrane
Simulations in HTMD
Molecular Dynamics in HTMD
Adaptive Sampling Explained
Adaptive Sampling Tutorial
Adaptive Bandit Tutorial
Analysis in HTMD
Getting Started with Projections
Ligand binding analysis
Protein folding analysis
CXCL12 conformational analysis
Advanced uses
System building Protein-Protein
Using docking to initialize positions
Equilibration protocol for the mu opioid GPCR
Tools
Maximal Substructural Alignment
Sequence Based Alignment
FFEvaluate
Membrane Builder
Changelog
1.12.0 (stable) - 2018/03/22
1.10.0 (stable) - 2017/10/25
1.8.0 (stable) - 2017/07/17
1.6.0 (stable) - 2017/03/01
Documentation
Molecule
Building
Solvating
Protein preparation
CHARMM builder
AMBER builder
MD Simulations
Applications
Adaptive sampling
State-of-the-art protocols for molecular simulations
Simulation List
Projections
MetricData - Storage for projected data
Metric - Helper class for combining Metrics for projection
MetricCoordinate - coordinates of an atom selection
MetricDistance - (Self-)distance-based metrics between atoms selections
MetricDihedral - Dihedral-based metrics
MetricRmsd - RMSD-based metric
MetricShell - occupancy of an atom selection (e.g. water) around another selection
MetricSecondaryStructure - secondary structure-based metric
MetricPlumed2 - access all Plumed2 metrics (CVs)
MetricSasa - Solvent accessible surface area
MetricTMscore - TMscore-based metric
MetricFluctuation - RMSF-based metric
Dimensionality Reduction
TICA - Time independent component analysis
KMeansTri - kmeans triangle inequality
GWPCA Principal Component Analysis
Clustering
KCenters clustering method
RegCluster regular sized clustering
Markov state models
Kinetics
API
Subpackages
htmd.adaptive package
htmd.apps package
htmd.builder package
htmd.clustering package
htmd.mdengine package
htmd.membranebuilder package
htmd.molecule package
htmd.projections package
htmd.protocols package
htmd.queues package
Submodules
htmd.config module
htmd.decorators module
htmd.dock module
htmd.home module
htmd.kinetics module
htmd.kineticshmm module
htmd.latest module
htmd.metricdata module
htmd.model module
htmd.modelhmm module
htmd.mutualinformation module
htmd.numbautil module
htmd.parallelprogress module
htmd.pathplanning module
htmd.session module
htmd.simlist module
htmd.ui module
htmd.units module
htmd.util module
htmd.version module
htmd.versionwarnings module
Module contents
Developer’s Guide
How to contribute
Introduction
How to Contribute Fixes
How to Contribute New Features
Contributor Agreement
List of Features Interesting for HTMD
Guidelines for developers
Coding Style Tips
Using modules inside HTMD
Using Docstrings and Doctests
Versioning
HTMD Versions Explained
How to release a new HTMD version?
Moleculekit
Installation
Downloading miniconda
Create a conda environment
Install with pip
Install with conda
The Molecule class
The SmallMol class
Molecule tools
Contents
Protein segmentation: Automatically detects and assigns segments in proteins
Protein preparation: Protonates proteins and optimizes hbond networks
Sequence-based structure alignment: Aligns two protein structures by their sequence alignment
Voxel Descriptors: Calculates 3D voxels channels containing features of a Molecule or SmallMol
Maximal substructure alignment: Aligns two small molecules by their maximal substructure
Projections
Contents
MetricCoordinate: xyz coordinate projection
MetricDihedral: dihedral angles projection
MetricDistance: atom distances/contacts projection
MetricFluctuation: atom position fluctuations
MetricPlumed2: support for Plumed2 projections
MetricRmsd: root mean square deviation of structures to a reference
MetricSasa: solvent accessible surface area projection
MetricSecondaryStructure: protein secondary structure projection
MetricShell: density of atoms in shells around other atoms
MetricSphericalCoordinate: spherical coordinates of two COMs
MetricTMscore: TMscore projection
Tutorials
Contents
Voxelization
ACEMD v3
Capabilities
Not available capabilities
Performance
Speed benchmarks
Release notes
3.3.0 (2020-06-23)
3.2.4 (2020-04-23)
3.2.3 (2019-11-12)
3.2.2 (2019-10-08)
3.2.1 (2019-09-20)
3.2.0 (2019-08-27)
3.1.2 (2019-06-04)
3.1.1 (2019-05-08)
3.1.0 (2019-04-18)
3.0.4 (2019-02-27)
3.0.3 (2019-02-25)
3.0.2 (2018-03-28)
3.0.1 (2017-12-18)
3.0.0 (2017-12-12)
Installation
Dependencies
Tutorial
Molecular dynamics simulation of DHFR
Metadynamics simulation of alaninde dipeptide
Migrating from the old
ACEMD
Manual
Command line arguments
Input file options
Force field
Iteractions
Restraints
Metadynamics
Initial state
Minimization
Integrator
Thermostat
Barostat
Output
Licence
Support
ACEMD v2 (deprecated)
ACEMD Manual
Introduction
Fundamental units
Force field parameters
Running ACEMD
Specifying an Input File
Command Help
Selecting a GPU
Running parallel ensembles
Simulation Configuration
Quick Configurations
NVT vs NPT ensemble
Input Files
Output Files
Standard output
Restarting
Advanced material
Tcl Scripting
Debug TCL scripts
PLUMED library
Plugin interface
Getting support
Citations
ACEMD Command Reference
Configuration
Input
Output
Forcefield
Charmm
Amber
Martini
Electrostatics
Barostat
Thermostat
Constraints
External Forces
Minimisation
Interactive
Extensions
TCL Extension
Analysis
Parameterize
Method
Tutorial
Prepare molecule
Get command-line options
Positional Arguments
Named Arguments
Set total charge
Choose force field
Atomic charges
List parameterizable dihedral angles
Choose QM code
Choose QM level
Control the execution of QM calculations
Reuse QM and re-parametrize
Find and validate parameters
Usage
Positional Arguments
Named Arguments
Version:
latest
Docs
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Index
Index
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B
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C
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D
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E
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F
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G
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I
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J
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K
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L
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M
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N
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O
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Q
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
_
__call__() (moleculekit.smallmol.tools.molvstautomer.TautomerEnumerator method)
(moleculekit.smallmol.tools.tautomers.TautomerCanonicalizer method)
__getitem__() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
A
abs2rel() (htmd.metricdata.MetricData method)
abs2sim() (htmd.metricdata.MetricData method)
Acemd (class in htmd.apps.acemd)
(class in htmd.mdengine.acemd.acemd)
Acemd2 (class in htmd.mdengine.acemd.acemd)
AdaptiveBandit (class in htmd.adaptive.adaptivebandit)
AdaptiveBase (class in htmd.adaptive.adaptive)
AdaptiveGoal (class in htmd.adaptive.adaptivegoal)
AdaptiveGoalEG (class in htmd.adaptive.adaptivegoaleg)
AdaptiveMD (class in htmd.adaptive.adaptiverun)
add() (moleculekit.molecule.Representations method)
add_fields() (playmolecule.jsonlogger.JsonFormatter method)
addConstraint() (htmd.protocols.equilibration_v1.Equilibration method)
(htmd.protocols.equilibration_v2.Equilibration method)
(htmd.protocols.production_v5.Production method)
(htmd.protocols.production_v6.Production method)
addHs() (moleculekit.smallmol.smallmol.SmallMol method)
addPoint() (htmd.pathplanning.Tree method)
aggregateTime() (htmd.metricdata.MetricData property)
align() (moleculekit.molecule.Molecule method)
(moleculekit.smallmol.smallmol.SmallMol method)
alignBySequence() (moleculekit.molecule.Molecule method)
altloc (moleculekit.molecule.Molecule attribute)
angles (moleculekit.molecule.Molecule attribute)
append() (htmd.metricdata.MetricData method)
(moleculekit.molecule.Molecule method)
(moleculekit.molecule.Representations method)
(moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)
(moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
appendAttribute() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
appendAttributeExtendRows() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
appendFrames() (moleculekit.molecule.Molecule method)
appendSmallLib() (moleculekit.smallmol.smallmollib.SmallMolLib method)
appendSmallMol() (moleculekit.smallmol.smallmollib.SmallMolLib method)
areLigandsDocked() (in module moleculekit.tools.moleculechecks)
areLigandsOptimized() (in module moleculekit.tools.moleculechecks)
args() (htmd.protocols.oldprotocolinterface.BinaryValidator method)
(htmd.protocols.oldprotocolinterface.BooleanValidator method)
(htmd.protocols.oldprotocolinterface.ClassValidator method)
(htmd.protocols.oldprotocolinterface.DictionaryValidator method)
(htmd.protocols.oldprotocolinterface.FileValidator method)
(htmd.protocols.oldprotocolinterface.FunctionValidator method)
(htmd.protocols.oldprotocolinterface.ListListValidator method)
(htmd.protocols.oldprotocolinterface.ListValidator method)
(htmd.protocols.oldprotocolinterface.ObjectValidator method)
(htmd.protocols.oldprotocolinterface.StringValidator method)
(htmd.protocols.oldprotocolinterface.TimestepValidator method)
assertSameAsReferenceDir() (in module htmd.util)
(in module moleculekit.util)
atominfo() (moleculekit.readers.Topology property)
AtomNotFoundException
AtomRestraint (class in htmd.mdengine.acemd.acemd)
atoms (moleculekit.smallmol.tools.tautomers.Fragment attribute)
atomselect() (moleculekit.molecule.Molecule method)
atomtype (moleculekit.molecule.Molecule attribute)
atomtypingValidityChecks() (in module moleculekit.tools.atomtyper)
attributePart() (moleculekit.pdbx.reader.PdbxContainers.CifName static method)
autoSegment() (in module moleculekit.tools.autosegment)
autoSegment2() (in module moleculekit.tools.autosegment)
B
basenameInputs() (in module playmolecule.devutils)
beta (moleculekit.molecule.Molecule attribute)
BinaryValidator (class in htmd.protocols.oldprotocolinterface)
BINCOORread() (in module moleculekit.readers)
BINCOORwrite() (in module moleculekit.writers)
BONDMAP (moleculekit.smallmol.tools.molvstautomer.TautomerTransform attribute)
bonds (moleculekit.molecule.Molecule attribute)
bondtype (moleculekit.molecule.Molecule attribute)
BooleanValidator (class in htmd.protocols.oldprotocolinterface)
bootstrap() (htmd.metricdata.MetricData method)
boundingBox() (in module moleculekit.util)
box (moleculekit.molecule.Molecule attribute)
boxangles (moleculekit.molecule.Molecule attribute)
build() (in module htmd.builder.amber)
(in module htmd.builder.charmm)
BuildError
buildMembrane() (in module htmd.membranebuilder.build_membrane)
C
calculate() (htmd.mutualinformation.MutualInformation method)
calculateUniqueBonds() (in module moleculekit.molecule)
cancel() (playmolecule.job.Job method)
cancelJob() (playmolecule.session.Session method)
canonicalize() (moleculekit.smallmol.tools.tautomers.TautomerCanonicalizer method)
categoryPart() (moleculekit.pdbx.reader.PdbxContainers.CifName static method)
center() (moleculekit.molecule.Molecule method)
centerFrames (htmd.clustering.kcenters.KCenter attribute)
(htmd.clustering.regular.RegCluster attribute)
Centers (htmd.metricdata.MetricData attribute)
chain (moleculekit.molecule.Molecule attribute)
charge (moleculekit.molecule.Molecule attribute)
CHARGEMAP (moleculekit.smallmol.tools.molvstautomer.TautomerTransform attribute)
checkTruncations() (in module moleculekit.writers)
chi1() (moleculekit.projections.metricdihedral.Dihedral static method)
chi2() (moleculekit.projections.metricdihedral.Dihedral static method)
chi3() (moleculekit.projections.metricdihedral.Dihedral static method)
chi4() (moleculekit.projections.metricdihedral.Dihedral static method)
chi5() (moleculekit.projections.metricdihedral.Dihedral static method)
CifName (class in moleculekit.pdbx.reader.PdbxContainers)
cktest() (htmd.model.Model method)
ClassValidator (class in htmd.protocols.oldprotocolinterface)
close() (moleculekit.vmdviewer.VMD method)
closestDistance() (in module moleculekit.tools.moleculechecks)
cluster() (htmd.metricdata.MetricData method)
(htmd.metricdata.Trajectory property)
(in module moleculekit.smallmol.tools.clustering)
cluster_centers (htmd.clustering.kcenters.KCenter attribute)
(htmd.clustering.regular.RegCluster attribute)
cluster_centers_() (htmd.clustering.regular.RegCluster property)
cluster_ofmicro() (htmd.model.Model property)
clusterSize() (htmd.clustering.regular.RegCluster property)
clusterSize_ (htmd.clustering.kcenters.KCenter attribute)
(htmd.clustering.regular.RegCluster attribute)
combine() (htmd.metricdata.MetricData method)
(in module htmd.builder.charmm)
compareGraphs() (in module moleculekit.tools.graphalignment)
compareVersions() (in module htmd.latest)
COMPLETED (playmolecule.job.JobStatus attribute)
completed() (moleculekit.vmdviewer.VMD method)
compute_paths() (moleculekit.smallmol.tools.tautomers.MolFragmenter method)
compute_score() (moleculekit.smallmol.tools.tautomers.TautomerCanonicalizer method)
config() (in module htmd.config)
(in module moleculekit.config)
conformationStationaryDistribution() (htmd.adaptive.adaptivebandit.AdaptiveBandit method)
connection (moleculekit.smallmol.tools.tautomers.Fragment attribute)
construct() (moleculekit.readers.MolFactory static method)
contactVecToMatrix() (in module moleculekit.projections.metricdistance)
ContainerBase (class in moleculekit.pdbx.reader.PdbxContainers)
convert() (in module htmd.units)
convertDisulfide() (in module htmd.builder.builder)
convertToString() (in module moleculekit.smallmol.util)
coords (moleculekit.molecule.Molecule attribute)
copy() (htmd.metricdata.MetricData method)
(htmd.metricdata.Trajectory method)
(htmd.model.Model method)
(htmd.simlist.Sim method)
(moleculekit.molecule.Molecule method)
(moleculekit.projections.projection.Projection method)
(moleculekit.smallmol.smallmol.SmallMol method)
(moleculekit.smallmol.smallmollib.SmallMolLib method)
(moleculekit.vmdviewer.VMD method)
count (moleculekit.vmdgraphics.VMDLabels attribute)
count_pucb() (htmd.adaptive.adaptivebandit.AdaptiveBandit method)
count_ucb() (htmd.adaptive.adaptivebandit.AdaptiveBandit method)
counter (moleculekit.vmdgraphics.VMDGraphicObject attribute)
CRDCARDread() (in module moleculekit.readers)
CRDread() (in module moleculekit.readers)
createCoreSetModel() (htmd.model.Model method)
createProductGraph() (in module moleculekit.tools.graphalignment)
createState() (htmd.model.Model method)
cross() (in module htmd.numbautil)
crystalinfo (moleculekit.molecule.Molecule attribute)
D
dat (htmd.metricdata.MetricData attribute)
dat() (htmd.metricdata.MetricData property)
data (moleculekit.tools.preparationdata.PreparationData attribute)
DataCategory (class in moleculekit.pdbx.reader.PdbxContainers)
DataCategoryBase (class in moleculekit.pdbx.reader.PdbxContainers)
DataContainer (class in moleculekit.pdbx.reader.PdbxContainers)
deconcatenate() (htmd.metricdata.MetricData method)
default() (playmolecule.jsonlogger.JsonEncoder method)
defaultAmberHome() (in module htmd.builder.amber)
defaultEquilRestraints() (htmd.protocols.equilibration_v3.Equilibration method)
defaultFf() (in module htmd.builder.amber)
defaultParam() (in module htmd.builder.amber)
(in module htmd.builder.charmm)
defaultStream() (in module htmd.builder.charmm)
defaultTopo() (in module htmd.builder.amber)
(in module htmd.builder.charmm)
DefinitionContainer (class in moleculekit.pdbx.reader.PdbxContainers)
delete() (moleculekit.vmdgraphics.VMDGraphicObject method)
(moleculekit.vmdgraphics.VMDIsosurface method)
(moleculekit.vmdgraphics.VMDLabels method)
deleteBonds() (moleculekit.molecule.Molecule method)
depict() (moleculekit.smallmol.smallmol.SmallMol method)
(moleculekit.smallmol.smallmollib.SmallMolLib method)
depict_tautomers() (moleculekit.smallmol.tools.tautomers.TautomerCanonicalizer method)
depictMultipleMols() (in module moleculekit.smallmol.util)
describe() (playmolecule.job.Job method)
(playmolecule.job.JobStatus method)
describeApp() (playmolecule.session.Session method)
describeNextReport() (htmd.membranebuilder.pdbreporter.PDBReporter method)
detectCisPeptideBonds() (in module htmd.builder.builder)
detectDisulfideBonds() (in module htmd.builder.builder)
DiceDistances() (in module moleculekit.smallmol.tools.clustering)
DictionaryValidator (class in htmd.protocols.oldprotocolinterface)
diffMolecules() (in module htmd.util)
Dihedral (class in moleculekit.projections.metricdihedral)
dihedralAngle() (in module moleculekit.dihedral)
dihedralAngleFrames() (in module moleculekit.dihedral)
dihedralAngleFull() (in module moleculekit.dihedral)
dihedrals (moleculekit.molecule.Molecule attribute)
dihedralsToIndexes() (moleculekit.projections.metricdihedral.Dihedral static method)
distance (htmd.clustering.kcenters.KCenter attribute)
distributeLipids() (in module htmd.membranebuilder.ljfluid)
DisulfideBridge (class in htmd.builder.builder)
dock() (in module htmd.dock)
(in module moleculekit.tools.docking)
docString() (htmd.protocols.oldprotocolinterface.Validator method)
dot() (in module htmd.numbautil)
dropDimensions() (htmd.metricdata.MetricData method)
dropFrames() (htmd.metricdata.MetricData method)
(htmd.metricdata.Trajectory method)
(moleculekit.molecule.Molecule method)
(moleculekit.smallmol.smallmol.SmallMol method)
dropTraj() (htmd.metricdata.MetricData method)
dumpIt() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
E
element (moleculekit.molecule.Molecule attribute)
elements_from_masses() (in module moleculekit.periodictable)
embed() (in module htmd.builder.builder)
empty() (moleculekit.molecule.Molecule method)
enable_json_logger() (in module playmolecule.jsonlogger)
ensurelist() (in module htmd.util)
(in module moleculekit.util)
(in module playmolecule.utils)
enumerate() (moleculekit.smallmol.tools.molvstautomer.TautomerEnumerator method)
epochSimIndexes() (in module htmd.adaptive.adaptive)
eqDistribution() (htmd.model.Model method)
(htmd.modelhmm.ModelHMM method)
equilibrateSystem() (in module htmd.membranebuilder.simulate_openmm)
Equilibration (class in htmd.protocols.equilibration_v1)
(class in htmd.protocols.equilibration_v2)
(class in htmd.protocols.equilibration_v3)
(class in htmd.protocols.pmemdequilibration)
ERROR (playmolecule.job.JobStatus attribute)
exists() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)
F
fileloc (moleculekit.molecule.Molecule attribute)
FileValidator (class in htmd.protocols.oldprotocolinterface)
filter() (moleculekit.molecule.Molecule method)
(moleculekit.smallmol.smallmol.SmallMol method)
filter_tautomers() (moleculekit.smallmol.tools.tautomers.TautomerCanonicalizer static method)
findHbonds() (moleculekit.tools.preparationdata.PreparationData method)
fit() (htmd.clustering.kcenters.KCenter method)
(htmd.clustering.regular.RegCluster method)
format() (playmolecule.jsonlogger.JsonFormatter method)
format_datetime_obj() (playmolecule.jsonlogger.JsonEncoder method)
FormatError
foundBondBetween() (moleculekit.smallmol.smallmol.SmallMol method)
Fragment (class in moleculekit.smallmol.tools.tautomers)
fragment() (moleculekit.smallmol.tools.tautomers.MolFragmenter method)
fragments (moleculekit.smallmol.tools.tautomers.MolFragmenter attribute)
Frame (class in htmd.simlist)
frame (htmd.simlist.Frame attribute)
(moleculekit.molecule.Molecule attribute)
frame() (moleculekit.molecule.Molecule property)
(moleculekit.smallmol.smallmol.SmallMol property)
fromMolecule() (moleculekit.molecule.UniqueAtomID static method)
(moleculekit.molecule.UniqueResidueID static method)
(moleculekit.readers.Topology method)
fstep (htmd.metricdata.MetricData attribute)
(moleculekit.molecule.Molecule attribute)
fstep() (moleculekit.molecule.Molecule property)
ftype (moleculekit.smallmol.tools.tautomers.Fragment attribute)
FunctionValidator (class in htmd.protocols.oldprotocolinterface)
G
g0eq (htmd.kinetics.Rates attribute)
generateConformers() (moleculekit.smallmol.smallmol.SmallMol method)
generateCrystalPacking() (in module moleculekit.tools.crystalpacking)
genTemplate() (in module moleculekit.projections.metricplumed2)
(moleculekit.projections.metricplumed2.PlumedCV method)
get() (moleculekit.molecule.Molecule method)
(moleculekit.pdbx.reader.PdbxContainers.DataCategoryBase method)
(moleculekit.smallmol.smallmol.SmallMol method)
get_conjugate() (moleculekit.smallmol.tools.tautomers.TautomerCanonicalizer method)
get_conjugate_length() (moleculekit.smallmol.tools.tautomers.MolFragmenter method)
get_connection() (moleculekit.smallmol.tools.tautomers.Fragment method)
get_depiction_atoms() (moleculekit.smallmol.tools.tautomers.MolFragmenter method)
get_fragment() (moleculekit.smallmol.tools.tautomers.MolFragmenter method)
get_graphs() (moleculekit.smallmol.tools.tautomers.MolFragmenter method)
get_longest_path() (moleculekit.smallmol.tools.tautomers.MolFragmenter method)
get_num_fragments() (moleculekit.smallmol.tools.tautomers.MolFragmenter method)
getAllNeighbours() (in module htmd.membranebuilder.ringpenetration)
getAtoms() (moleculekit.smallmol.smallmol.SmallMol method)
getAttributeCount() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getAttributeIndex() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getAttributeLengthMaximumList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getAttributeList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getAttributeListWithOrder() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getAttributeValueMaxLengthList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getCenter() (moleculekit.smallmol.smallmol.SmallMol method)
getCenters() (in module moleculekit.tools.voxeldescriptors)
getChannels() (in module moleculekit.tools.voxeldescriptors)
getChemblLigandByDrugName() (in module moleculekit.smallmol.util)
getChemblSimilarLigandsBySmile() (in module moleculekit.smallmol.util)
getChildren() (playmolecule.job.Job method)
getConfig() (playmolecule.job.Job method)
getCurrentAttribute() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getCurrentViewer() (in module moleculekit.vmdviewer)
getDestinationFile() (in module playmolecule.utils)
getDestinationFolder() (in module playmolecule.utils)
getDihedral() (moleculekit.molecule.Molecule method)
getEpochFromName() (in module htmd.adaptive.adaptive)
getEpochSimIdx() (in module htmd.adaptive.util)
getEpochTrajectoryDictionary() (in module htmd.adaptive.util)
getErrorInfo() (playmolecule.job.Job method)
getFeatures() (in module moleculekit.tools.atomtyper)
getFormatTypeList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getFormatTypeListX() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getFullRow() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getGlobal() (moleculekit.pdbx.reader.PdbxContainers.DataContainer method)
getIndex() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getItemNameList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getJob() (playmolecule.session.Session method)
getJobId() (in module playmolecule.devutils)
getJobsByGroup() (playmolecule.session.Session method)
getMapping() (htmd.projections.metric.Metric method)
(moleculekit.projections.metriccoordinate.MetricCoordinate method)
(moleculekit.projections.metricdihedral.MetricDihedral method)
(moleculekit.projections.metricdistance.MetricDistance method)
(moleculekit.projections.metricfluctuation.MetricFluctuation method)
(moleculekit.projections.metricplumed2.MetricPlumed2 method)
(moleculekit.projections.metricrmsd.MetricRmsd method)
(moleculekit.projections.metricsasa.MetricSasa method)
(moleculekit.projections.metricsecondarystructure.MetricSecondaryStructure method)
(moleculekit.projections.metricshell.MetricShell method)
(moleculekit.projections.metricsphericalcoordinate.MetricSphericalCoordinate method)
(moleculekit.projections.metrictmscore.MetricTMscore method)
(moleculekit.projections.projection.Projection method)
getMaximumCommonSubstructure() (in module moleculekit.smallmol.tools.clustering)
getMols() (moleculekit.smallmol.smallmollib.SmallMolLib method)
getName() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)
(moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getObj() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)
getObjNameList() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)
getParentSimIdxFrame() (in module htmd.adaptive.util)
getPDBQTAtomType() (in module moleculekit.tools.atomtyper)
getPDBQTAtomTypesAndCharges() (in module moleculekit.tools.atomtyper)
getPdbStrings() (in module htmd.util)
getProgress() (playmolecule.job.Job method)
getProperties() (in module moleculekit.tools.atomtyper)
getRates() (htmd.kinetics.Kinetics method)
(htmd.kineticshmm.KineticsHMM method)
getRCSBLigandByLigname() (in module moleculekit.smallmol.util)
getRewards() (htmd.adaptive.adaptivebandit.AdaptiveBandit method)
getRow() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getRowCount() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getRowIndex() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getRowList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getSequenceProfile() (in module moleculekit.tools.hhblitsprofile)
getServiceStatus() (playmolecule.session.Session method)
getStates() (htmd.model.Model method)
getStateStatistic() (in module htmd.model)
getStatus() (playmolecule.job.Job method)
getTerminiBuriedness() (moleculekit.tools.preparationdata.PreparationData method)
getTerminiHbonds() (moleculekit.tools.preparationdata.PreparationData method)
getType() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)
getURLs() (playmolecule.job.Job method)
getValue() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getValueFormatted() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getValueFormattedByIndex() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
getVMDpath() (in module moleculekit.vmdviewer)
getVoxelDescriptors() (in module moleculekit.tools.voxeldescriptors)
GJFread() (in module moleculekit.readers)
graphs (moleculekit.smallmol.tools.tautomers.Fragment attribute)
GROTOPread() (in module moleculekit.readers)
GroupRestraint (class in htmd.mdengine.acemd.acemd)
GROwrite() (in module moleculekit.writers)
guessAnglesAndDihedrals() (in module moleculekit.util)
guessbonds() (in module moleculekit.vmdparser)
GWPCA (class in htmd.projections.gwpca)
H
hasAttribute() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
header (moleculekit.tools.preparationdata.PreparationData attribute)
home() (in module htmd.home)
(in module moleculekit.home)
htmd
module
htmd.adaptive
module
htmd.adaptive.adaptive
module
htmd.adaptive.adaptivebandit
module
htmd.adaptive.adaptivegoal
module
htmd.adaptive.adaptivegoaleg
module
htmd.adaptive.adaptiverun
module
htmd.adaptive.util
module
htmd.apps
module
htmd.apps.acemd
module
htmd.apps.pmemd
module
htmd.builder
module
htmd.builder.amber
module
htmd.builder.builder
module
htmd.builder.charmm
module
htmd.builder.ionize
module
htmd.builder.loopmodeler
module
htmd.builder.preparation
module
htmd.builder.solvate
module
htmd.clustering
module
htmd.clustering.kcenters
module
htmd.clustering.regular
module
htmd.config
module
htmd.decorators
module
htmd.dock
module
htmd.home
module
htmd.kinetics
module
htmd.kineticshmm
module
htmd.latest
module
htmd.mdengine
module
htmd.mdengine.acemd
module
htmd.mdengine.acemd.acemd
module
htmd.membranebuilder
module
htmd.membranebuilder.build_membrane
module
htmd.membranebuilder.globalminimization
module
htmd.membranebuilder.ljfluid
module
htmd.membranebuilder.pdbreporter
module
htmd.membranebuilder.ringpenetration
module
htmd.membranebuilder.simulate_openmm
module
htmd.metricdata
module
htmd.model
module
htmd.modelhmm
module
htmd.molecule
module
htmd.molecule.molecule
module
htmd.molecule.util
module
htmd.mutualinformation
module
htmd.numbautil
module
htmd.parallelprogress
module
htmd.pathplanning
module
htmd.projections
module
htmd.projections.gwpca
module
htmd.projections.kmeanstri
module
htmd.projections.metric
module
htmd.projections.metriccoordinate
module
htmd.projections.metricdihedral
module
htmd.projections.metricdistance
module
htmd.projections.metricfluctuation
module
htmd.projections.metricplumed2
module
htmd.projections.metricrmsd
module
htmd.projections.metricsasa
module
htmd.projections.metricsecondarystructure
module
htmd.projections.metricshell
module
htmd.projections.metricsphericalcoordinate
module
htmd.projections.metrictmscore
module
htmd.projections.tica
module
htmd.protocols
module
htmd.protocols.equilibration_v1
module
htmd.protocols.equilibration_v2
module
htmd.protocols.equilibration_v3
module
htmd.protocols.oldprotocolinterface
module
htmd.protocols.pmemdequilibration
module
htmd.protocols.pmemdproduction
module
htmd.protocols.production_v1
module
htmd.protocols.production_v2
module
htmd.protocols.production_v3
module
htmd.protocols.production_v4
module
htmd.protocols.production_v5
module
htmd.protocols.production_v6
module
htmd.queues
module
htmd.queues.localqueue
module
htmd.queues.lsfqueue
module
htmd.queues.pbsqueue
module
htmd.queues.playqueue
module
htmd.queues.simqueue
module
htmd.queues.slurmqueue
module
htmd.session
module
htmd.simlist
module
htmd.ui
module
htmd.units
module
htmd.util
module
htmd.version
module
htmd.versionwarnings
module
htmdAmberHome() (in module htmd.builder.amber)
htmdCharmmHome() (in module htmd.builder.charmm)
htmdload() (in module htmd.session)
htmdsave() (in module htmd.session)
I
impropers (moleculekit.molecule.Molecule attribute)
inprogress() (htmd.queues.playqueue.PlayQueue method)
input (htmd.simlist.Sim attribute)
insert() (moleculekit.molecule.Molecule method)
insertion (moleculekit.molecule.Molecule attribute)
invokeAttributeMethod() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
invokeCategoryMethod() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
invokeDataBlockMethod() (moleculekit.pdbx.reader.PdbxContainers.DataContainer method)
ionize() (in module htmd.builder.ionize)
ionizePlace() (in module htmd.builder.ionize)
isAttribute() (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method)
isCategory() (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method)
isChiral() (moleculekit.smallmol.smallmol.SmallMol method)
isLigandDocked() (in module moleculekit.tools.moleculechecks)
isLigandOptimized() (in module moleculekit.tools.moleculechecks)
isProteinProtonated() (in module moleculekit.tools.moleculechecks)
J
Job (class in playmolecule.job)
JobBucketNotFoundError
JobConfigNotLoadedError
JobError
JobStatus (class in playmolecule.job)
JsonEncoder (class in playmolecule.jsonlogger)
JsonFormatter (class in playmolecule.jsonlogger)
jsonify_log_record() (playmolecule.jsonlogger.JsonFormatter method)
K
K (htmd.metricdata.MetricData attribute)
KCenter (class in htmd.clustering.kcenters)
kdeq (htmd.kinetics.Rates attribute)
Kinetics (class in htmd.kinetics)
KineticsHMM (class in htmd.kineticshmm)
KMeansTri (class in htmd.projections.kmeanstri)
koff (htmd.kinetics.Rates attribute)
kon (htmd.kinetics.Rates attribute)
L
labels_ (htmd.clustering.kcenters.KCenter attribute)
(htmd.clustering.regular.RegCluster attribute)
least_square_fit_plane() (in module htmd.membranebuilder.ringpenetration)
ligname() (moleculekit.smallmol.smallmol.SmallMol property)
list() (moleculekit.molecule.Representations method)
listApps() (playmolecule.session.Session method)
listFiles() (in module htmd.builder.amber)
(in module htmd.builder.charmm)
listJobs() (playmolecule.session.Session method)
listLipids() (in module htmd.membranebuilder.build_membrane)
ListListValidator (class in htmd.protocols.oldprotocolinterface)
ListValidator (class in htmd.protocols.oldprotocolinterface)
load() (htmd.apps.acemd.Acemd method)
(htmd.apps.pmemd.Pmemd method)
(htmd.metricdata.MetricData method)
(htmd.model.Model method)
loadConfig() (in module playmolecule.config)
loadMI() (htmd.mutualinformation.MutualInformation method)
loadMol() (moleculekit.vmdviewer.VMD method)
login() (playmolecule.session.Session method)
loopModeller() (in module htmd.builder.loopmodeler)
M
macro_ofcluster() (htmd.model.Model property)
macro_ofmicro() (htmd.model.Model property)
macroAccumulate() (in module htmd.model)
macronum() (htmd.model.Model property)
(htmd.modelhmm.ModelHMM property)
MAEread() (in module moleculekit.readers)
makeMolGraph() (in module moleculekit.tools.graphalignment)
manual() (in module moleculekit.projections.metricplumed2)
map (htmd.metricdata.MetricData attribute)
map() (htmd.metricdata.MetricData property)
markovModel() (htmd.model.Model method)
(htmd.modelhmm.ModelHMM method)
masses (moleculekit.molecule.Molecule attribute)
MAX_TAUTOMERS (in module moleculekit.smallmol.tools.molvstautomer)
maxConnectedLag() (htmd.model.Model method)
maxDistance() (in module moleculekit.util)
maximalSubstructureAlignment() (in module moleculekit.tools.graphalignment)
MDTRAJread() (in module moleculekit.readers)
MDTRAJTOPOread() (in module moleculekit.readers)
MDTRAJwrite() (in module moleculekit.writers)
memoized_property() (in module moleculekit.smallmol.tools.molvstautomer)
memory() (htmd.queues.playqueue.PlayQueue property)
merge_record_extra() (in module playmolecule.jsonlogger)
Metric (class in htmd.projections.metric)
MetricCoordinate (class in moleculekit.projections.metriccoordinate)
MetricData (class in htmd.metricdata)
MetricDihedral (class in moleculekit.projections.metricdihedral)
MetricDistance (class in moleculekit.projections.metricdistance)
MetricFluctuation (class in moleculekit.projections.metricfluctuation)
MetricPlumed2 (class in moleculekit.projections.metricplumed2)
MetricRmsd (class in moleculekit.projections.metricrmsd)
MetricSasa (class in moleculekit.projections.metricsasa)
MetricSecondaryStructure (class in moleculekit.projections.metricsecondarystructure)
MetricSelfDistance (class in moleculekit.projections.metricdistance)
MetricShell (class in moleculekit.projections.metricshell)
MetricSphericalCoordinate (class in moleculekit.projections.metricsphericalcoordinate)
MetricTMscore (class in moleculekit.projections.metrictmscore)
mfptGraph() (htmd.kinetics.Kinetics method)
mfptoff (htmd.kinetics.Rates attribute)
mfpton (htmd.kinetics.Rates attribute)
micro_ofcluster() (htmd.model.Model property)
micronum() (htmd.model.Model property)
minimalRotation() (in module htmd.builder.builder)
minimize() (in module htmd.membranebuilder.globalminimization)
missedLigands (moleculekit.tools.preparationdata.PreparationData attribute)
MissingAngleError
MissingAtomTypeError
MissingBondError
MissingParameterError
MissingTorsionError
MixedSegmentError
Model (class in htmd.model)
ModelHMM (class in htmd.modelhmm)
module
htmd
htmd.adaptive
htmd.adaptive.adaptive
htmd.adaptive.adaptivebandit
htmd.adaptive.adaptivegoal
htmd.adaptive.adaptivegoaleg
htmd.adaptive.adaptiverun
htmd.adaptive.util
htmd.apps
htmd.apps.acemd
htmd.apps.pmemd
htmd.builder
htmd.builder.amber
htmd.builder.builder
htmd.builder.charmm
htmd.builder.ionize
htmd.builder.loopmodeler
htmd.builder.preparation
htmd.builder.solvate
htmd.clustering
htmd.clustering.kcenters
htmd.clustering.regular
htmd.config
htmd.decorators
htmd.dock
htmd.home
htmd.kinetics
htmd.kineticshmm
htmd.latest
htmd.mdengine
htmd.mdengine.acemd
htmd.mdengine.acemd.acemd
htmd.membranebuilder
htmd.membranebuilder.build_membrane
htmd.membranebuilder.globalminimization
htmd.membranebuilder.ljfluid
htmd.membranebuilder.pdbreporter
htmd.membranebuilder.ringpenetration
htmd.membranebuilder.simulate_openmm
htmd.metricdata
htmd.model
htmd.modelhmm
htmd.molecule
htmd.molecule.molecule
htmd.molecule.util
htmd.mutualinformation
htmd.numbautil
htmd.parallelprogress
htmd.pathplanning
htmd.projections
htmd.projections.gwpca
htmd.projections.kmeanstri
htmd.projections.metric
htmd.projections.metriccoordinate
htmd.projections.metricdihedral
htmd.projections.metricdistance
htmd.projections.metricfluctuation
htmd.projections.metricplumed2
htmd.projections.metricrmsd
htmd.projections.metricsasa
htmd.projections.metricsecondarystructure
htmd.projections.metricshell
htmd.projections.metricsphericalcoordinate
htmd.projections.metrictmscore
htmd.projections.tica
htmd.protocols
htmd.protocols.equilibration_v1
htmd.protocols.equilibration_v2
htmd.protocols.equilibration_v3
htmd.protocols.oldprotocolinterface
htmd.protocols.pmemdequilibration
htmd.protocols.pmemdproduction
htmd.protocols.production_v1
htmd.protocols.production_v2
htmd.protocols.production_v3
htmd.protocols.production_v4
htmd.protocols.production_v5
htmd.protocols.production_v6
htmd.queues
htmd.queues.localqueue
htmd.queues.lsfqueue
htmd.queues.pbsqueue
htmd.queues.playqueue
htmd.queues.simqueue
htmd.queues.slurmqueue
htmd.session
htmd.simlist
htmd.ui
htmd.units
htmd.util
htmd.version
htmd.versionwarnings
moleculekit
moleculekit.align
moleculekit.config
moleculekit.dihedral
moleculekit.home
moleculekit.molecule
moleculekit.pdbx
moleculekit.pdbx.reader
moleculekit.pdbx.reader.PdbxContainers
moleculekit.pdbx.reader.PdbxParser
moleculekit.pdbx.reader.PdbxReader
moleculekit.pdbx.tests
moleculekit.pdbx.tests.PdbxReaderTests
moleculekit.pdbx.tests.PdbxReadWriteTests
moleculekit.pdbx.tests.PdbxWriterTests
moleculekit.pdbx.writer
moleculekit.pdbx.writer.PdbxWriter
moleculekit.periodictable
moleculekit.projections
moleculekit.projections.metriccoordinate
moleculekit.projections.metricdihedral
moleculekit.projections.metricdistance
moleculekit.projections.metricfluctuation
moleculekit.projections.metricplumed2
moleculekit.projections.metricrmsd
moleculekit.projections.metricsasa
moleculekit.projections.metricsecondarystructure
moleculekit.projections.metricshell
moleculekit.projections.metricsphericalcoordinate
moleculekit.projections.metrictmscore
moleculekit.projections.projection
moleculekit.projections.util
moleculekit.rcsb
moleculekit.rdkitintegration
moleculekit.readers
moleculekit.smallmol
moleculekit.smallmol.smallmol
moleculekit.smallmol.smallmollib
moleculekit.smallmol.test_smallmol
moleculekit.smallmol.test_smallmollib
moleculekit.smallmol.tools
moleculekit.smallmol.tools.clustering
moleculekit.smallmol.tools.molvstautomer
moleculekit.smallmol.tools.restrainedembed
moleculekit.smallmol.tools.tautomers
moleculekit.smallmol.tools.test_tools
moleculekit.smallmol.util
moleculekit.support
moleculekit.tools
moleculekit.tools.atomtyper
moleculekit.tools.autosegment
moleculekit.tools.crystalpacking
moleculekit.tools.docking
moleculekit.tools.graphalignment
moleculekit.tools.hhblitsprofile
moleculekit.tools.moleculechecks
moleculekit.tools.pka
moleculekit.tools.preparation
moleculekit.tools.preparationdata
moleculekit.tools.sequencestructuralalignment
moleculekit.tools.voxeldescriptors
moleculekit.util
moleculekit.version
moleculekit.vmdgraphics
moleculekit.vmdparser
moleculekit.vmdviewer
moleculekit.wrap
moleculekit.writers
playmolecule
playmolecule.config
playmolecule.devutils
playmolecule.job
playmolecule.jsonlogger
playmolecule.session
playmolecule.utils
mol (moleculekit.smallmol.tools.tautomers.MolFragmenter attribute)
MOL2read() (in module moleculekit.readers)
MOL2write() (in module moleculekit.writers)
mol_equal() (in module moleculekit.molecule)
Molecule (class in moleculekit.molecule)
moleculekit
module
moleculekit.align
module
moleculekit.config
module
moleculekit.dihedral
module
moleculekit.home
module
moleculekit.molecule
module
moleculekit.pdbx
module
moleculekit.pdbx.reader
module
moleculekit.pdbx.reader.PdbxContainers
module
moleculekit.pdbx.reader.PdbxParser
module
moleculekit.pdbx.reader.PdbxReader
module
moleculekit.pdbx.tests
module
moleculekit.pdbx.tests.PdbxReaderTests
module
moleculekit.pdbx.tests.PdbxReadWriteTests
module
moleculekit.pdbx.tests.PdbxWriterTests
module
moleculekit.pdbx.writer
module
moleculekit.pdbx.writer.PdbxWriter
module
moleculekit.periodictable
module
moleculekit.projections
module
moleculekit.projections.metriccoordinate
module
moleculekit.projections.metricdihedral
module
moleculekit.projections.metricdistance
module
moleculekit.projections.metricfluctuation
module
moleculekit.projections.metricplumed2
module
moleculekit.projections.metricrmsd
module
moleculekit.projections.metricsasa
module
moleculekit.projections.metricsecondarystructure
module
moleculekit.projections.metricshell
module
moleculekit.projections.metricsphericalcoordinate
module
moleculekit.projections.metrictmscore
module
moleculekit.projections.projection
module
moleculekit.projections.util
module
moleculekit.rcsb
module
moleculekit.rdkitintegration
module
moleculekit.readers
module
moleculekit.smallmol
module
moleculekit.smallmol.smallmol
module
moleculekit.smallmol.smallmollib
module
moleculekit.smallmol.test_smallmol
module
moleculekit.smallmol.test_smallmollib
module
moleculekit.smallmol.tools
module
moleculekit.smallmol.tools.clustering
module
moleculekit.smallmol.tools.molvstautomer
module
moleculekit.smallmol.tools.restrainedembed
module
moleculekit.smallmol.tools.tautomers
module
moleculekit.smallmol.tools.test_tools
module
moleculekit.smallmol.util
module
moleculekit.support
module
moleculekit.tools
module
moleculekit.tools.atomtyper
module
moleculekit.tools.autosegment
module
moleculekit.tools.crystalpacking
module
moleculekit.tools.docking
module
moleculekit.tools.graphalignment
module
moleculekit.tools.hhblitsprofile
module
moleculekit.tools.moleculechecks
module
moleculekit.tools.pka
module
moleculekit.tools.preparation
module
moleculekit.tools.preparationdata
module
moleculekit.tools.sequencestructuralalignment
module
moleculekit.tools.voxeldescriptors
module
moleculekit.util
module
moleculekit.version
module
moleculekit.vmdgraphics
module
moleculekit.vmdparser
module
moleculekit.vmdviewer
module
moleculekit.wrap
module
moleculekit.writers
module
MolFactory (class in moleculekit.readers)
molfile (htmd.simlist.Sim attribute)
MolFragmenter (class in moleculekit.smallmol.tools.tautomers)
molRMSD() (in module moleculekit.util)
molTMscore() (in module moleculekit.util)
moveBy() (moleculekit.molecule.Molecule method)
moveLipidToPos() (in module htmd.membranebuilder.ringpenetration)
mutateResidue() (moleculekit.molecule.Molecule method)
MutualInformation (class in htmd.mutualinformation)
N
N (htmd.metricdata.MetricData attribute)
name (moleculekit.molecule.Molecule attribute)
(moleculekit.smallmol.tools.tautomers.Fragment attribute)
natsorted() (in module moleculekit.util)
ncpu() (htmd.queues.playqueue.PlayQueue property)
ngpu() (htmd.queues.playqueue.PlayQueue property)
norm() (in module htmd.numbautil)
numAtoms (moleculekit.molecule.Molecule attribute)
numAtoms() (moleculekit.molecule.Molecule property)
(moleculekit.smallmol.smallmol.SmallMol property)
numDimensions() (htmd.metricdata.MetricData property)
(htmd.metricdata.Trajectory property)
numframes (htmd.simlist.Sim attribute)
numFrames (moleculekit.molecule.Molecule attribute)
numFrames() (htmd.metricdata.MetricData property)
(htmd.metricdata.Trajectory property)
(moleculekit.molecule.Molecule property)
(moleculekit.readers.Trajectory property)
(moleculekit.smallmol.smallmol.SmallMol property)
numMols (moleculekit.smallmol.smallmollib.SmallMolLib attribute)
numMols() (moleculekit.smallmol.smallmollib.SmallMolLib property)
numResidues (moleculekit.molecule.Molecule attribute)
numResidues() (moleculekit.molecule.Molecule property)
numTrajectories() (htmd.metricdata.MetricData property)
O
ObjectValidator (class in htmd.protocols.oldprotocolinterface)
occupancy (moleculekit.molecule.Molecule attribute)
omega() (moleculekit.projections.metricdihedral.Dihedral static method)
openbabelConvert() (in module moleculekit.smallmol.util)
opm() (in module moleculekit.util)
orientOnAxes() (in module moleculekit.util)
P
P() (htmd.model.Model property)
pack_double_buffer() (in module moleculekit.support)
pack_int_buffer() (in module moleculekit.support)
pack_string_buffer() (in module moleculekit.support)
pack_ulong_buffer() (in module moleculekit.support)
pairwise() (in module moleculekit.smallmol.tools.molvstautomer)
pairwiseRMSD() (in module htmd.numbautil)
parallel() (in module moleculekit.tools.atomtyper)
ParallelExecutor() (in module htmd.parallelprogress)
(in module moleculekit.smallmol.tools.clustering)
parallelfunc() (in module htmd.pathplanning)
parent (htmd.metricdata.MetricData attribute)
(htmd.simlist.Sim attribute)
parse() (playmolecule.jsonlogger.JsonFormatter method)
paths (moleculekit.smallmol.tools.tautomers.MolFragmenter attribute)
pdbGuessElementByName() (in module moleculekit.readers)
PDBQTread() (in module moleculekit.readers)
PDBQTwrite() (in module moleculekit.writers)
PDBread() (in module moleculekit.readers)
PDBReporter (class in htmd.membranebuilder.pdbreporter)
PDBwrite() (in module moleculekit.writers)
PdbxError
,
[1]
,
[2]
PDBXMMCIFread() (in module moleculekit.readers)
PdbxReader (class in moleculekit.pdbx.reader.PdbxParser)
(class in moleculekit.pdbx.reader.PdbxReader)
PDBxReporter (class in htmd.membranebuilder.pdbreporter)
PdbxWriter (class in moleculekit.pdbx.reader.PdbxParser)
(class in moleculekit.pdbx.writer.PdbxWriter)
phi() (moleculekit.projections.metricdihedral.Dihedral static method)
piece (htmd.simlist.Frame attribute)
playmolecule
module
playmolecule.config
module
playmolecule.devutils
module
playmolecule.job
module
playmolecule.jsonlogger
module
playmolecule.session
module
playmolecule.utils
module
PlayQueue (class in htmd.queues.playqueue)
plotClusters() (htmd.metricdata.MetricData method)
plotCounts() (htmd.metricdata.MetricData method)
plotFES() (htmd.model.Model method)
plotFluxPathways() (htmd.kinetics.Kinetics method)
plotRates() (htmd.kinetics.Kinetics method)
plotTimescales() (htmd.model.Model method)
(htmd.modelhmm.ModelHMM method)
plotTrajSizes() (htmd.metricdata.MetricData method)
PlumedCOM (class in moleculekit.projections.metricplumed2)
PlumedCV (class in moleculekit.projections.metricplumed2)
PlumedGenericGroup (class in moleculekit.projections.metricplumed2)
PlumedGroup (class in moleculekit.projections.metricplumed2)
PlumedMolinfo (class in moleculekit.projections.metricplumed2)
PlumedStatement (class in moleculekit.projections.metricplumed2)
PlumedVerbatim (class in moleculekit.projections.metricplumed2)
Pmemd (class in htmd.apps.pmemd)
pmtryexcept() (in module playmolecule.devutils)
pp_calcDistances() (in module moleculekit.projections.util)
pp_calcMinDistances() (in module moleculekit.projections.util)
PreparationData (class in moleculekit.tools.preparationdata)
prepareProteinForAtomtyping() (in module moleculekit.tools.atomtyper)
PREPIread() (in module moleculekit.readers)
prettyPrintResidue() (in module moleculekit.tools.preparationdata)
printIt() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)
(moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
(moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method)
PRMTOPread() (in module moleculekit.readers)
process_log_record() (playmolecule.jsonlogger.JsonFormatter method)
Production (class in htmd.protocols.pmemdproduction)
(class in htmd.protocols.production_v1)
(class in htmd.protocols.production_v2)
(class in htmd.protocols.production_v3)
(class in htmd.protocols.production_v4)
(class in htmd.protocols.production_v5)
(class in htmd.protocols.production_v6)
project() (htmd.projections.gwpca.GWPCA method)
(htmd.projections.kmeanstri.KMeansTri method)
(htmd.projections.metric.Metric method)
(htmd.projections.tica.TICA method)
(moleculekit.projections.metriccoordinate.MetricCoordinate method)
(moleculekit.projections.metricdihedral.MetricDihedral method)
(moleculekit.projections.metricdistance.MetricDistance method)
(moleculekit.projections.metricfluctuation.MetricFluctuation method)
(moleculekit.projections.metricplumed2.MetricPlumed2 method)
(moleculekit.projections.metricrmsd.MetricRmsd method)
(moleculekit.projections.metricsasa.MetricSasa method)
(moleculekit.projections.metricsecondarystructure.MetricSecondaryStructure method)
(moleculekit.projections.metricshell.MetricShell method)
(moleculekit.projections.metricsphericalcoordinate.MetricSphericalCoordinate method)
(moleculekit.projections.metrictmscore.MetricTMscore method)
(moleculekit.projections.projection.Projection method)
Projection (class in moleculekit.projections.projection)
projection() (htmd.metricdata.Trajectory property)
propkaContainer (moleculekit.tools.preparationdata.PreparationData attribute)
proteinDihedrals() (moleculekit.projections.metricdihedral.Dihedral static method)
proteinPrepare() (in module moleculekit.tools.preparation)
ProtocolInterface (class in htmd.protocols.oldprotocolinterface)
PSFread() (in module moleculekit.readers)
PSFwrite() (in module moleculekit.writers)
psi() (moleculekit.projections.metricdihedral.Dihedral static method)
Q
QUEUED (playmolecule.job.JobStatus attribute)
R
Rates (class in htmd.kinetics)
raytracing() (in module htmd.pathplanning)
rcsbFindLigands() (in module moleculekit.rcsb)
rcsbFindMutatedResidues() (in module moleculekit.rcsb)
read() (moleculekit.molecule.Molecule method)
(moleculekit.pdbx.reader.PdbxParser.PdbxReader method)
(moleculekit.pdbx.reader.PdbxReader.PdbxReader method)
readArguments() (playmolecule.job.Job method)
readConfig() (htmd.mdengine.acemd.acemd.Acemd method)
reconstructAdaptiveTraj() (in module htmd.adaptive.adaptive)
reconstructContactMap() (in module moleculekit.projections.metricdistance)
record (moleculekit.molecule.Molecule attribute)
ref (htmd.metricdata.MetricData attribute)
ref() (htmd.metricdata.MetricData property)
reference() (htmd.metricdata.Trajectory property)
RegCluster (class in htmd.clustering.regular)
register() (playmolecule.session.Session method)
rel2sim() (htmd.metricdata.MetricData method)
remove() (moleculekit.molecule.Molecule method)
(moleculekit.molecule.Representations method)
(moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)
removeAtomsInHull() (in module htmd.builder.builder)
removeHET() (in module htmd.builder.builder)
removeHs() (moleculekit.smallmol.smallmol.SmallMol method)
removeLipidsInProtein() (in module htmd.builder.builder)
removeMols() (moleculekit.smallmol.smallmollib.SmallMolLib method)
removeRow() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
rename() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)
renameAttribute() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
render() (moleculekit.vmdviewer.VMD method)
renumberResidues() (moleculekit.molecule.Molecule method)
reorderAtoms() (moleculekit.molecule.Molecule method)
rep() (moleculekit.vmdviewer.VMD method)
replace() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)
replaceSubstring() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
replaceValue() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
report() (htmd.membranebuilder.pdbreporter.PDBReporter method)
(htmd.membranebuilder.pdbreporter.PDBxReporter method)
reprepare() (moleculekit.tools.preparationdata.PreparationData method)
Representations (class in moleculekit.molecule)
reps (moleculekit.molecule.Molecule attribute)
resid (moleculekit.molecule.Molecule attribute)
ResidueInsertionError
resname (moleculekit.molecule.Molecule attribute)
resolveRingPenetrations() (in module htmd.membranebuilder.ringpenetration)
restrainedEmbed() (in module moleculekit.smallmol.tools.restrainedembed)
retrieve() (htmd.queues.playqueue.PlayQueue method)
(playmolecule.job.Job method)
retrieveJobs() (playmolecule.session.Session method)
rotateBy() (moleculekit.molecule.Molecule method)
rotateCoordinates() (in module moleculekit.tools.voxeldescriptors)
rotationMatrix() (in module moleculekit.util)
rrt() (in module htmd.pathplanning)
rrtstarsmart() (in module htmd.pathplanning)
RTFread() (in module moleculekit.readers)
run() (htmd.adaptive.adaptive.AdaptiveBase method)
RUNNING (playmolecule.job.JobStatus attribute)
S
sampleClusters() (htmd.metricdata.MetricData method)
sampleRegion() (htmd.metricdata.MetricData method)
sampleStates() (htmd.model.Model method)
save() (htmd.apps.acemd.Acemd method)
(htmd.apps.pmemd.Pmemd method)
(htmd.metricdata.MetricData method)
(htmd.model.Model method)
save_graphml() (htmd.mutualinformation.MutualInformation method)
saveMI() (htmd.mutualinformation.MutualInformation method)
SCORE_dict (moleculekit.smallmol.tools.tautomers.MolFragmenter attribute)
sdfReader() (in module moleculekit.smallmol.smallmollib)
SDFwrite() (in module moleculekit.writers)
search() (in module htmd.builder.charmm)
search_fragment_by_atom() (moleculekit.smallmol.tools.tautomers.MolFragmenter method)
segid (moleculekit.molecule.Molecule attribute)
selectAtom() (moleculekit.molecule.UniqueAtomID method)
selectAtoms() (moleculekit.molecule.UniqueResidueID method)
send() (moleculekit.vmdviewer.VMD method)
sequence() (moleculekit.molecule.Molecule method)
sequenceID() (in module moleculekit.util)
sequenceStructureAlignment() (in module moleculekit.tools.sequencestructuralalignment)
serial (moleculekit.molecule.Molecule attribute)
Session (class in playmolecule.session)
SessionError
set() (htmd.projections.metric.Metric method)
(moleculekit.molecule.Molecule method)
setAsCompleted() (in module playmolecule.devutils)
setAsError() (in module playmolecule.devutils)
setAsSleep() (in module playmolecule.devutils)
setAttributeNameList() (moleculekit.pdbx.reader.PdbxContainers.DataCategoryBase method)
setComplete() (playmolecule.job.Job method)
setDihedral() (moleculekit.molecule.Molecule method)
setError() (playmolecule.job.Job method)
setGlobal() (moleculekit.pdbx.reader.PdbxContainers.DataContainer method)
setJobStatus() (playmolecule.session.Session method)
setName() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)
(moleculekit.pdbx.reader.PdbxContainers.DataCategoryBase method)
setProgress() (playmolecule.job.Job method)
setRowList() (moleculekit.pdbx.reader.PdbxContainers.DataCategoryBase method)
setRowPartition() (moleculekit.pdbx.writer.PdbxWriter.PdbxWriter method)
setSleep() (playmolecule.job.Job method)
setStart() (playmolecule.job.Job method)
setType() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)
setup() (htmd.apps.acemd.Acemd method)
(htmd.apps.pmemd.Pmemd method)
setValue() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)
show() (htmd.apps.acemd.Acemd method)
(htmd.apps.pmemd.Pmemd method)
Sim (class in htmd.simlist)
sim (htmd.simlist.Frame attribute)
simfilter() (in module htmd.simlist)
simid (htmd.simlist.Sim attribute)
simlist (htmd.metricdata.MetricData attribute)
simlist() (htmd.metricdata.MetricData property)
(in module htmd.simlist)
simmerge() (in module htmd.simlist)
simpleSuite() (in module moleculekit.pdbx.tests.PdbxReaderTests)
(in module moleculekit.pdbx.tests.PdbxReadWriteTests)
SLEEPING (playmolecule.job.JobStatus attribute)
SmallMol (class in moleculekit.smallmol.smallmol)
SmallMolLib (class in moleculekit.smallmol.smallmollib)
SmallMolStack (in module moleculekit.smallmol.smallmollib)
smarts() (moleculekit.smallmol.tools.molvstautomer.TautomerScore property)
smiReader() (in module moleculekit.smallmol.smallmollib)
solvate() (in module htmd.builder.solvate)
split() (in module htmd.builder.charmm)
splitCols() (htmd.metricdata.MetricData method)
St (htmd.metricdata.MetricData attribute)
St() (htmd.metricdata.MetricData property)
StandardPDBChiralAtom() (in module moleculekit.rdkitintegration)
StandardPDBResidueChirality() (in module moleculekit.rdkitintegration)
startApp() (playmolecule.session.Session method)
stop() (htmd.queues.playqueue.PlayQueue method)
string_to_tempfile() (in module moleculekit.support)
StringValidator (class in htmd.protocols.oldprotocolinterface)
submit() (htmd.queues.playqueue.PlayQueue method)
(playmolecule.job.Job method)
suite() (in module moleculekit.pdbx.tests.PdbxWriterTests)
SyntaxError
,
[1]
T
TanimotoDistances() (in module moleculekit.smallmol.tools.clustering)
tarFolder() (in module playmolecule.devutils)
tautomer() (moleculekit.smallmol.tools.molvstautomer.TautomerTransform property)
TAUTOMER_SCORES (in module moleculekit.smallmol.tools.molvstautomer)
TAUTOMER_TRANSFORMS (in module moleculekit.smallmol.tools.molvstautomer)
TautomerCanonicalizer (class in moleculekit.smallmol.tools.tautomers)
TautomerEnumerator (class in moleculekit.smallmol.tools.molvstautomer)
TautomerScore (class in moleculekit.smallmol.tools.molvstautomer)
TautomerTransform (class in moleculekit.smallmol.tools.molvstautomer)
tempname() (in module htmd.util)
(in module moleculekit.util)
testDHFR() (in module htmd.util)
TICA (class in htmd.projections.tica)
tileMembrane() (in module htmd.builder.builder)
time (moleculekit.molecule.Molecule attribute)
TimestepValidator (class in htmd.protocols.oldprotocolinterface)
toDataFrame() (moleculekit.smallmol.smallmollib.SmallMolLib method)
toMolecule() (moleculekit.smallmol.smallmol.SmallMol method)
Topology (class in moleculekit.readers)
TopologyInconsistencyError
,
[1]
toRDKITmol() (in module moleculekit.rdkitintegration)
toSMARTS() (moleculekit.smallmol.smallmol.SmallMol method)
toSMILES() (moleculekit.smallmol.smallmol.SmallMol method)
tq() (moleculekit.vmdgraphics.VMDGraphicObject static method)
Trajectory (class in htmd.metricdata)
(class in moleculekit.readers)
trajectory (htmd.simlist.Sim attribute)
trajLengths() (htmd.metricdata.MetricData property)
Tree (class in htmd.pathplanning)
U
uniformRandomRotation() (in module moleculekit.util)
UniqueAtomID (class in moleculekit.molecule)
UniqueResidueID (class in moleculekit.molecule)
UnknownResidueError
unzipit() (in module playmolecule.devutils)
updatingMean() (in module htmd.adaptive.util)
uploadFolder() (in module playmolecule.devutils)
V
validate() (htmd.protocols.oldprotocolinterface.BinaryValidator method)
(htmd.protocols.oldprotocolinterface.BooleanValidator method)
(htmd.protocols.oldprotocolinterface.ClassValidator method)
(htmd.protocols.oldprotocolinterface.DictionaryValidator method)
(htmd.protocols.oldprotocolinterface.FileValidator method)
(htmd.protocols.oldprotocolinterface.FunctionValidator method)
(htmd.protocols.oldprotocolinterface.ListListValidator method)
(htmd.protocols.oldprotocolinterface.ListValidator method)
(htmd.protocols.oldprotocolinterface.ObjectValidator method)
(htmd.protocols.oldprotocolinterface.StringValidator method)
(htmd.protocols.oldprotocolinterface.TimestepValidator method)
(htmd.protocols.oldprotocolinterface.ValueValidator method)
VALIDATING (playmolecule.job.JobStatus attribute)
Validator (class in htmd.protocols.oldprotocolinterface)
ValueValidator (class in htmd.protocols.oldprotocolinterface)
version() (in module htmd.version)
(in module moleculekit.version)
view() (moleculekit.molecule.Molecule method)
(moleculekit.smallmol.smallmol.SmallMol method)
viewer() (in module moleculekit.vmdviewer)
viewname (moleculekit.molecule.Molecule attribute)
viewStates() (htmd.model.Model method)
(htmd.modelhmm.ModelHMM method)
viewVoxelFeatures() (in module moleculekit.tools.voxeldescriptors)
VMD (class in moleculekit.vmdviewer)
VMDBox (class in moleculekit.vmdgraphics)
VMDConvexHull (class in moleculekit.vmdgraphics)
VMDCylinder (class in moleculekit.vmdgraphics)
VMDGraphicObject (class in moleculekit.vmdgraphics)
VMDIsosurface (class in moleculekit.vmdgraphics)
VMDLabels (class in moleculekit.vmdgraphics)
vmdselection() (in module moleculekit.vmdparser)
VMDSphere (class in moleculekit.vmdgraphics)
VMDText (class in moleculekit.vmdgraphics)
W
wait() (playmolecule.job.Job method)
waitChildren() (playmolecule.job.Job method)
WAITING_APPROVAL (playmolecule.job.JobStatus attribute)
WAITING_DATA (playmolecule.job.JobStatus attribute)
warnIfTerminiSuspect() (moleculekit.tools.preparationdata.PreparationData method)
weightGraph() (htmd.mutualinformation.MutualInformation method)
wrap() (in module htmd.membranebuilder.ringpenetration)
(in module moleculekit.wrap)
(moleculekit.molecule.Molecule method)
wrapBondedDistance() (in module moleculekit.dihedral)
wrapDistance() (in module moleculekit.dihedral)
wrapping_dist_python() (in module htmd.membranebuilder.build_membrane)
write() (htmd.mdengine.acemd.acemd.Acemd method)
(htmd.protocols.equilibration_v1.Equilibration method)
(htmd.protocols.equilibration_v2.Equilibration method)
(htmd.protocols.equilibration_v3.Equilibration method)
(htmd.protocols.pmemdequilibration.Equilibration method)
(htmd.protocols.pmemdproduction.Production method)
(htmd.protocols.production_v1.Production method)
(htmd.protocols.production_v2.Production method)
(htmd.protocols.production_v3.Production method)
(htmd.protocols.production_v4.Production method)
(htmd.protocols.production_v5.Production method)
(htmd.protocols.production_v6.Production method)
(moleculekit.molecule.Molecule method)
(moleculekit.pdbx.reader.PdbxParser.PdbxWriter method)
(moleculekit.pdbx.writer.PdbxWriter.PdbxWriter method)
(moleculekit.smallmol.smallmol.SmallMol method)
writeArguments() (playmolecule.job.Job method)
writeConf() (htmd.apps.acemd.Acemd method)
(htmd.apps.pmemd.Pmemd method)
writeContainer() (moleculekit.pdbx.reader.PdbxParser.PdbxWriter method)
(moleculekit.pdbx.writer.PdbxWriter.PdbxWriter method)
writeInputsOptionsLog() (in module playmolecule.devutils)
writeSdf() (moleculekit.smallmol.smallmollib.SmallMolLib method)
writeSentinel() (in module playmolecule.devutils)
writeSmiles() (moleculekit.smallmol.smallmollib.SmallMolLib method)
writeVoxels() (in module moleculekit.util)
X
x() (moleculekit.molecule.Molecule property)
XSCread() (in module moleculekit.readers)
XSCwrite() (in module moleculekit.writers)
xtc_lib() (in module moleculekit.support)
XTCread() (in module moleculekit.readers)
XTCwrite() (in module moleculekit.writers)
XYZread() (in module moleculekit.readers)
XYZwrite() (in module moleculekit.writers)
Y
y() (moleculekit.molecule.Molecule property)
Z
z() (moleculekit.molecule.Molecule property)
zipdir() (in module playmolecule.devutils)
zipit() (in module playmolecule.devutils)