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System Settings
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Section Navigation
Foundations
The Entrance
What is MolSysMT?
Installation
Navigating the Documentation
Overview of Tools
Demo Systems
The Molecular System
The Molecular System
Items and Forms
Elements
Attributes
The Native World
Classes
MolSys
MolSysBuilder
MolSysDict
Topology
TopologyDict
Structures
StructuresDict
MolecularMechanics
MolecularMechanicsDict
ViewerJSON
Files
h5msm
File Handlers
PDBFileHandler
H5MSMFileHandler
GROFileHandler
CIFFileHandler
The Language
Selection Language and Syntax
Performance
Lazy Loading
Chunked Execution
The Rust Core
Parallel Execution
Internal Optimizations
Diagnostics & Profiling
Caching & Memoization
Benchmarks
GPU Acceleration
Governance
Quantities & Units
Argument Digestion
Public API & Lifecycle
Dependency Management
Configuration Options
Precision & Data Standards
SMonitor & Telemetry
Supported
Forms
Classes
Files
Strings
Physical-Chemical Data
Molecular Mechanics Data
Selection Syntaxes
Viewers
The Ecosystem
Viewers and Visualization
MolSysViewer
Third-party Bridges
Tools
Basic
Add
Append structures
Are multiple molecular systems
Compare
Concatenate structures
Contains
Convert
Copy
Extract
Get attributes
Get form
Get label
Get
Has attribute
Info
Is a molecular system
Is composed of
Iterator
Merge
Remove
Select
Set
View
Where is attribute
Build
Add bonds
Add missing bonds
Add missing heavy atoms
Add missing hydrogens
Add missing terminal cappings
Build peptide
Define new chain
Get disulfide bonds
Get missing bonds
Get missing heavy atoms
Get missing residues
Get missing terminals
Get non standard residues
Has hydrogens
Is solvated
Make bioassembly
Make water box
Mutate
Remove overlapping molecules
Solvate
Solve atoms with alternate locations
Topology
Get bondgraph
Get covalent blocks
Get covalent paths
Get dihedral quartets
Get sequence alignment
Get sequence identity
Structure
Aligning principal axes
Center
Flip
Get angles
Get center
Get contacts
Get dihedral angles
Get distances
Get least RMSD
Get maximum distances
Get minimum distances
Get neighbors
Getting principal axes
Getting the radius of gyration
Get RMSD
Getting root-mean-square fluctuations
Least RMSD align
Fitting by least RMSD
Move away
Computing principal components
Rotating coordinates
Set dihedral angles
Shift dihedral angles
Show contacts
Translate
Periodic boundary conditions
Get angles from vectors
Get boxfrom lengths and angles
Get lengths and angles from box
Get lengths from box
Get shape from box
Shape from angles
Angles from vectors
Getting volume from box lengths and angles
Has PBC
Unwrapping temporal trajectories
Wrapping to the minimum image
Wrapping to the primary periodic box
Physical and chemical properties
Get area buried
Get atomic radius
Get buried fraction
Get charge
Get degrees of freedom
Get hydrophobicity
Get mass
Get polarity
Get SASA
Get surface area
Get transmembrane tendency
Get volume
Hydrogen bonds
Get acceptor atoms
Get donor atoms
Get Buch hbonds
Get Luzard and Chandler hbonds
Molecular mechanics
Get forces
Potential energy minimization
Get non bonded potential energy
Get potential energy
Element
Atom
Get atom type from atom name
Molecule
Get bonded atom pairs
Get group type
Is group type
Component
Get component id
Get component index
Get component name
Get component type
Get number of components
Is component type
Molecule
Get molecule id
Get molecule index
Get molecule name
Get molecule type
Get number of molecules
Is component type
Entity
Get entity id
Get entity index
Get entity name
Get entity type
Get number of components
Chain
Get chain type
Form
Get attributes
Has attribute
Third Party
NGLView
Add arrows
Add contacts
Add cylinders
Add hbonds
Set color by value
Show as balls and sticks
Show as licorice
Show as surface
Show as balls and sticks
OpenMM
Custom External Forces
Reporters
Course
Common Core
Module 1: The Form-Agnostic Philosophy
Module 2: Molecular Attributes
Module 3: Molecular Elements
Module 4: Native Forms
Module 5: Combined Forms
Module 6: Visualizing Anything
Module 7: Selection Mechanism
Module 8: Extracting Molecular Attributes
Module 9: Physical Unit Safety
Module 10: Modifying Molecular Attributes
Module 11: Iterating Systems
Module 12: Building, Repairing and Auditing Systems
Module 13: Topological Analysis
Module 14: System Comparison and Validation
Module 15: Semantic Labeling
Module 16: Structural Operations
Module 17: Merging and Growing Systems
Module 18: Extracting and Removing Elements
Module 19: Structures and Trajectories
Module 20: The Specialized Domains
Path Alzheimer
Path A - Module 21: Surgical Extraction & Deletion
Path A - Module 22: Structural Auditing (Diagnostics)
Path A - Module 23: Structural Repair & Mutagenesis
Path A - Module 24: Peptide Synthesis
Path A - Module 25: Solvation & Ion Engineering
Path A - Module 26: Attribute Engineering (Patching)
Path A - Module 27: Conformational Engineering
Path A - Module 28: The MolSysBuilder API
Path A - Module 29: PDB Bioassemblies & AltLocs
Path A - Module 30: Geometrical Measurements
Path A - Module 31: Proximity & Neighborhoods
Path A - Module 32: Visualizing Interaction Matrices
Path A - Module 33: Ensemble Descriptors (Global Metrics)
Path A - Module 34: Comparison & Superposition
Path A - Module 35: Principal Components (PCA) & Axes
Path A - Module 36: Secondary Structure & Folds
Path A - Module 37: Hydrogen Bonds & Salt Bridges
Path A - Module 38: Advanced H-Bond Algorithms
Path A - Module 39: Physicochemical Properties
Path A - Module 40: PBC Geometry & Conventions
Path A - Module 41: Wrapping & Unwrapping
Path A - Module 42: Molecular Mechanics (Energies)
Path A - Module 43: Energy Minimization
Path A - Module 44: AMBER TLeap Integration
Path A - Module 45: OpenMM Integration
Path A - Module 46: Geometric Transformations (Space)
Path A - Module 47: Trajectory Management (Slicing)
Path A - Module 48: Scalability & Heavy Trajectories
Path A - Module 49: Performance Optimization
Path A - Module 50: Virtual Forms & Memory I/O
Path A - Module 51: Writing Your Own Form-Agnostic Functions
Path A - Module 52: Framework Reliability & SMonitor
Path A - Module 53: Capability Matrix & Config
Path A - Module 54: Final Project: From Sequence to Analysis
Path Enzyme
Path B - Module 21: Surgical Extraction & Deletion
Path B - Module 22: Structural Auditing (Diagnostics)
Path B - Module 23: Structural Repair & Mutagenesis
Path B - Module 24: Peptide Synthesis
Path B - Module 25: Solvation & Ion Engineering
Path B - Module 26: Attribute Engineering (Patching)
Path B - Module 27: Conformational Engineering
Path B - Module 28: The MolSysBuilder API
Path B - Module 29: PDB Bioassemblies & AltLocs
Path B - Module 30: Geometrical Measurements
Path B - Module 31: Proximity & Neighborhoods
Path B - Module 32: Visualizing Interaction Matrices
Path B - Module 33: Ensemble Descriptors (Global Metrics)
Path B - Module 34: Comparison & Superposition
Path B - Module 35: Principal Components (PCA) & Axes
Path B - Module 36: Secondary Structure & Folds
Path B - Module 37: Hydrogen Bonds & Salt Bridges
Path B - Module 38: Advanced H-Bond Algorithms
Path B - Module 39: Physicochemical Properties
Path B - Module 40: PBC Geometry & Conventions
Path B - Module 41: Wrapping & Unwrapping
Path B - Module 42: Molecular Mechanics (Energies)
Path B - Module 43: Energy Minimization
Path B - Module 44: AMBER TLeap Integration
Path B - Module 45: OpenMM Integration
Path B - Module 46: Geometric Transformations (Space)
Path B - Module 47: Trajectory Management (Slicing)
Path B - Module 48: Scalability & Heavy Trajectories
Path B - Module 49: Performance Optimization
Path B - Module 50: Virtual Forms & Memory I/O
Path B - Module 51: Writing Your Own Form-Agnostic Functions
Path B - Module 52: Framework Reliability & SMonitor
Path B - Module 53: Capability Matrix & Config
Path B - Module 54: Final Project: Rational Enzyme Engineering
Path Antiviral
Path C - Module 21: Surgical Extraction & Deletion
Path C - Module 22: Structural Auditing (Diagnostics)
Path C - Module 23: Structural Repair & Mutagenesis
Path C - Module 24: Peptide Synthesis
Path C - Module 25: Solvation & Ion Engineering
Path C - Module 26: Attribute Engineering (Patching)
Path C - Module 27: Conformational Engineering
Path C - Module 28: The MolSysBuilder API
Path C - Module 29: PDB Bioassemblies & AltLocs
Path C - Module 30: Geometrical Measurements
Path C - Module 31: Proximity & Neighborhoods
Path C - Module 32: Visualizing Interaction Matrices
Path C - Module 33: Ensemble Descriptors (Global Metrics)
Path C - Module 34: Comparison & Superposition
Path C - Module 35: Principal Components (PCA) & Axes
Path C - Module 36: Secondary Structure & Folds
Path C - Module 37: Hydrogen Bonds & Salt Bridges
Path C - Module 38: Advanced H-Bond Algorithms
Path C - Module 39: Physicochemical Properties
Path C - Module 40: PBC Geometry & Conventions
Path C - Module 41: Wrapping & Unwrapping
Path C - Module 42: Molecular Mechanics (Energies)
Path C - Module 43: Energy Minimization
Path C - Module 44: AMBER TLeap Integration
Path C - Module 45: OpenMM Integration
Path C - Module 46: Geometric Transformations (Space)
Path C - Module 47: Trajectory Management (Slicing)
Path C - Module 48: Scalability & Heavy Trajectories
Path C - Module 49: Performance Optimization
Path C - Module 50: Virtual Forms & Memory I/O
Path C - Module 51: Writing Your Own Form-Agnostic Functions
Path C - Module 52: Framework Reliability & SMonitor
Path C - Module 53: Capability Matrix & Config
Path C - Module 54: Final Project: Antiviral Drug Hunter
Path Biophysics
Path D - Module 21: Surgical Extraction & Deletion
Path D - Module 22: Structural Auditing (Diagnostics)
Path D - Module 23: Structural Repair & Mutagenesis
Path D - Module 24: Peptide Synthesis
Path D - Module 25: Solvation & Ion Engineering
Path D - Module 26: Attribute Engineering (Patching)
Path D - Module 27: Conformational Engineering
Path D - Module 28: The MolSysBuilder API
Path D - Module 29: PDB Bioassemblies & AltLocs
Path D - Module 30: Geometrical Measurements
Path D - Module 31: Proximity & Neighborhoods
Path D - Module 32: Visualizing Interaction Matrices
Path D - Module 33: Ensemble Descriptors (Global Metrics)
Path D - Module 34: Comparison & Superposition
Path D - Module 35: Principal Components (PCA) & Axes
Path D - Module 36: Secondary Structure & Folds
Path D - Module 37: Hydrogen Bonds & Salt Bridges
Path D - Module 38: Advanced H-Bond Algorithms
Path D - Module 39: Physicochemical Properties
Path D - Module 40: PBC Geometry & Conventions
Path D - Module 41: Wrapping & Unwrapping
Path D - Module 42: Molecular Mechanics (Energies)
Path D - Module 43: Energy Minimization
Path D - Module 44: AMBER TLeap Integration
Path D - Module 45: OpenMM Integration
Path D - Module 46: Geometric Transformations (Space)
Path D - Module 47: Trajectory Management (Slicing)
Path D - Module 48: Scalability & Heavy Trajectories
Path D - Module 49: Performance Optimization
Path D - Module 50: Virtual Forms & Memory I/O
Path D - Module 51: Writing Your Own Form-Agnostic Functions
Path D - Module 52: Framework Reliability & SMonitor
Path D - Module 53: Capability Matrix & Config
Path D - Module 54: Final Project: Computational Biophysics of Ion Permeation
Cookbook
Building Complex Dimers from Multiple PDBs
Working with NGLView
Working with OpenMM
MSMH5 file
From PDB to Solvated Box
Binding Pocket Isolation
Trajectory Performance Analysis
Structural Surgery: In-memory Mutagenesis
Form Teleportation: Seamless Conversions
User Guide
Cookbook
Working with OpenMM
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