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  • Developer Guide
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  • 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
      • Third-Party Bridges
    • The Ecosystem
      • MolSysSuite
  • 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 missing bonds
      • Add missing heavy atoms
      • Add missing hydrogens
      • Add missing terminal cappings
      • Build peptide
      • Editable
      • Get disulfide bonds
      • Get missing bonds
      • Get missing heavy atoms
      • Get missing residues
      • Get missing terminal cappings
      • 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
      • Align 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
      • Get principal axes
      • Get radius of gyration
      • Get RMSD
      • Get RMSF
      • Get secondary structure
      • Least RMSD align
      • Least RMSD fit
      • Move away
      • Principal Component Analysis
      • Rotate
      • Set dihedral angles
      • Shift dihedral angles
      • Translate
    • Periodic boundary conditions
      • Get angles from box
      • Get box from lengths and angles
      • Get box with shape
      • Get lengths and angles from box
      • Get lengths from box
      • Get shape from angles
      • Get shape from box
      • Get volume from box
      • Get volume from lengths and angles
      • Has PBC
      • Unwrap
      • Wrap to MIC
      • Wrap to PBC
    • Physical and chemical properties
      • Get area buried
      • Get atomic radius
      • Get buried fraction
      • Get charge
      • Get electronegativity
      • 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 hydrogen bonds
      • Get Luzar-Chandler hydrogen bonds
    • Molecular mechanics
      • Get degrees of freedom
      • Get engine forcefield
      • Get forces
      • Get non-bonded potential energy
      • Get potential energy
      • Potential energy minimization
    • Element
      • Is element
      • Is composed of
      • Atom
        • Get atom type from atom name
      • Group
        • Get group type
        • Get group type from group name
        • Get bonded atom pairs
        • Is group type
        • Amino Acid
        • Ion
        • Water
        • Terminal Capping
        • Small Molecule
        • Nucleotide
        • Lipid
        • Saccharide
      • Component
        • Get component id
        • Get component index
        • Get component name
        • Get component type
        • Get n components
        • Is component type
      • Molecule
        • Get molecule id
        • Get molecule index
        • Get molecule name
        • Get molecule type
        • Get n molecules
        • Is molecule type
      • Entity
        • Get entity id
        • Get entity index
        • Get entity name
        • Get entity type
        • Get n entities
      • Chain
        • Get chain id
        • Get chain index
        • Get chain name
        • Get chain type
    • Form
      • Class Forms
        • MolSysMT
        • OpenMM
        • MDTraj
        • MDAnalysis
        • ParmEd
        • PyTraj
        • Biopython
        • OpenFF
        • RDKit
        • Viewers
        • Others
      • File Forms
        • bcif
        • bcif.gz
        • cif
        • cif.gz
        • crd
        • dcd
        • fasta
        • gro
        • h5
        • h5msm
        • inpcrd
        • mdcrd
        • mol2
        • molsys_yaml
        • pdb
        • pir
        • prmtop
        • psf
        • smi
        • structures_yaml
        • top
        • topology_yaml
        • trjpk
        • xtc
        • xyz
        • xyznpy
      • String Forms
        • alphafold_id
        • amino_acids_1
        • amino_acids_3
        • pdb_id
        • pdb_text
        • smiles
        • uniprot_id
      • Get attributes
      • Has attribute
      • Is item
      • Is file
      • Is string
      • Close
    • Third Party
      • NGLView
        • Add arrows
        • Add contacts
        • Add cylinders
        • Add hydrogen bonds
        • Clear
        • Load HTML in Jupyter Notebook
        • Set color
        • Set color by value
        • Show as balls and sticks
        • Show as cartoon
        • Show as licorice
        • Show as surface
        • Show GUI
        • Standardize view
        • Write HTML
      • OpenMM
        • Custom External Forces
        • Platforms
        • Reporters
      • tLEaP
        • tLEaP
  • 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
    • Working with NGLView
    • Working with OpenMM
    • Big Data Trajectories
    • From PDB to Solvated Box
    • Binding Pocket Isolation
    • Trajectory Analysis
    • In Silico Mutagenesis
    • Form Conversions
  • User Guide
  • The Four Paths of the MolSysMT’s Master
  • Common Core

Common Core#

The Common Core (Modules 01-20) equips every Master with the foundational language and tools of MolSysMT. All paths share this common training ground using the T4 Lysozyme (PDB 181L) and related demonstration systems.

  • 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

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The Four Paths of the MolSysMT’s Master

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Module 1: The Form-Agnostic Philosophy

© 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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