Table of Contents

1. Front

2. First Steps

Building simple Molecules

3. Component and Composite Iterators

Looping over Components in a Composite

Looping over Bonds of an Atom

Looping over Neighbors of an Atom

Looping over Residues of an Protein

4. Predicates

Predicate Functions

Looping over Atoms or Bonds with a Predicate

User defined Predicates

Composition of Predicates in NTSChem

5. Periodic Table of Elements

Element Member Functions

6. Molecular File Formats

Molecular File Formats

7. Ring Processing

Cycle Membership

Number of Ring Bonds to an Atom

8. Connected Components Processing

Identifying Connected Components

9. Atom and Bond Typing

Reading and Writing Files with Atom Types and Bond Orders

Build Bonds Processing

Processes Atom and Bond Types

10. Pattern Matching

Using SMILES

Using SMARTS

Using Predicates for Query Molecules

Maximum Common Substructure Search (MCS Search)

11. Coordinates

Setting and Getting Coordinates

12. Structural Analysis

Root Mean Square Deviation (RMSD)