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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
Wrapping Simulations
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
CHARMM builder
AMBER builder
MD Simulations
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.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.metricdatagenerator module
htmd.model module
htmd.modelhmm module
htmd.mutualinformation 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 moleculekit 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
Capabilities
Performance
Speed benchmarks
Release notes
3.5.0 (2021-09-27)
3.4.1 (2021-04-21)
3.4.0 (2021-03-30)
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
Requiments
Install with Conda
Tutorial
Molecular dynamics simulation of DHFR
Metadynamics simulation of alaninde dipeptide
Manual
Command line arguments
Input file options
Force field
Iteractions
Restraints
Metadynamics
Initial state
Minimization
Integrator
Thermostat
Barostat
Output
Licence
Licence types
Node-locked licence
Floating licence
Cloud licence
Licence server
Support
PlayMolecule-API
Installation
Miniconda installation
Create conda environment
Install playmolecule python api package
Tutorials
Contents
PlayMolecule API Tutorial
Interacting with the PlayMolecule server
App pipeline example on Adaptive Sampling
The Session class
The Job class
The DataCenter class
Dev Only: PlayMolecule Dev Tools
Version:
latest
Docs
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HTMD
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htmd package
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htmd.projections package
htmd.projections package
¶
Submodules
¶
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
Module contents
¶
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