Skip to main content
Back to top
Ctrl
+
K
About
Showcase
User guide
Developer guide
API documentation
AI Assistants
Search
Ctrl
+
K
GitHub
Search
Ctrl
+
K
About
Showcase
User guide
Developer guide
API documentation
AI Assistants
GitHub
Section Navigation
Introduction
What’s MolSysMT?
Installation
Molecular systems
Description
Items and forms
Forms
Elements
Attributes
Demo Systems
Native forms
file:h5msm
Selection syntaxes
Tools
Viewers
Supported
Memory management
Quantities and units
Configuration options
MolSysMT Logging Setup — User Guide
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 chains
Get dihedral quartets
Get sequence alignment
Get sequence identity
Structure
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 geometric axis
Get radius of gyration
Get RMSD
Least RMSD align
Least RMSD fit
Move away
Principal component analysis
Rotate
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
Get volume from box
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 hydrophobicity
Get mass
Get polarity
Get SASA
Get surface area
Get transmembrane tendency
Get volume
Hydrogen bonds
Get acceptor atoms
Get donor atoms
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
Thirds
NGLView
Add arrows
Add contacts
Add cylinders
Add hbonds
Set color by value
Show as balls and sticks
Show as licorice
Show as surface
OpenMM
Custom External Forces
Reporters
Cookbook
Barnase-Barstar
Working with OpenMM
Working with NGLView
User guide
Cookbook
Working with OpenMM
%
load_ext
autoreload
%
autoreload
2
Working with OpenMM
#
To written soon.
