Example Workflows

A collection of tutorials to help understand the main features of QMzyme.

• Getting Started
  • Classes used in this example
  • Initialize Model
• QM-only Calculation
  • Objective
  • Classes used in this example
  • Required Files
  • Initialize Model and Define Regions
  • Designate Coordinate Constraints
  • Build the QM Method and Assign to Region
  • Truncate Model
  • Write QM Input File
• QM/QM2 Calculation
  • Objective
  • Classes used in this example
  • Required Files
  • Initialize Model and Define Regions
  • Build the QM Methods and Assign to Regions
  • Truncate Model
  • Write QM Input File
• QM/xTB Calculation
  • Objective
  • Classes used in this example
  • Required Files
  • Initialize Model and Define Regions
  • Build the QM Method and Assign to Region
  • Initialize the xTB method and Assign to Region
  • Truncate Model
  • Write QM Input File for ORCA
• Ligand Parameterization
  • Objective
  • Classes used in this example
  • Required Files
  • Initialize Model
  • Add Ligand Charge
  • Designate Ligand Region
  • Build the QM Method and Assign to Region
  • Write Calculation Input File
  • References Cited
• Working with Trajectories
  • Objective
  • Classes used in this example:
  • Required Files
  • Initialize Model and Define Regions
  • QM-only: Loop over frames to generate QMzymeModels
  • QM/xTB: Loop over frames to generate QMzymeModels
• QMzyme Serialization
  • Objective
  • Classes used in this example
  • Required Files
  • Define the QM and QM2 regions
  • Serialize QMzymeModel object
  • Upload serialized QMzymeModel object
  • Build the QM Methods and Assign to Regions
  • Truncate Model
  • Write QM Input File
• Molecule Replacement Using QMzyme
  • Objective
  • Classes used in this example
  • Required Files
  • Initialize Model and Define Regions
  • Acquire Replacement Region
  • Aligning the Substrate to the Bound Ligand
  • Replace the Currently Bound Ligand with the Aligned Substrate
  • Write QM Input File
  • References Cited
• Verifying Optimized Structures
  • Objective
  • Classes used in this example
  • Required Files
  • Preparing QM Input File for Optimization
  • Loading Pickled QMzymeModel
  • Aligning C-alpha Atoms of Original and Optimized Structuresd
  • Identifying Potential Clasing Residues
  • Visualizing Clashing Residues
  • References Cited

Cookbook

A collection of "recipes" to perform specific tasks in QMzyme.

• Inspecting Model Architecture
  • Objective
  • Classes used in this example
  • Required Files
  • Using Print Statements
  • Using region.summarize with Pandas Dataframe
  • Using print_overview()
• Manipulating QMzymeRegion
  • Objective
  • Classes used in this example
  • Required Files
  • Combining Two Regions
  • Subtracting Two Regions
• Pymol Visualization
  • Objective
  • Classes used in this example
  • Required Files
  • Visualizing the Full Model
  • Visualizing the QMzyme-prepared structure
  • Visualizing the .pkl file
  • References Cited
• Using Various SelectionScheme Classes
  • Objective
  • Classes used in this example
  • Required Files
  • Manual Region Selection
  • Distance Cutoff
  • ChargeShiftAnalysis
  • References Cited