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  • About
  • Showcase
  • User Guide
  • Developer guide
  • API documentation
  • MolSys-AI
  • GitHub
  • About
  • Showcase
  • User Guide
  • Developer guide
  • API documentation
  • MolSys-AI
  • GitHub

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
  • Foundations
  • The Ecosystem

The Ecosystem#

3D molecular viewers, NGLView integration, MolSysViewer, and third-party package bridges.

  • Viewers and Visualization
  • MolSysViewer
  • Third-party Bridges

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Viewers
© 2026, Liliana M. Moreno Vargas, Diego Prada Gracia and contributors | UIBCDF Lab at the Federico Gómez Children’s Hospital of Mexico
MolSysMT is an open source project shared under an MIT license

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