CodeLibrary

Code Library

Welcome to the Code Library. Here you can find useful code snippets for the direct use in your programs. If you want to post code yourself, great! Just read [#HowtoPost how to post] and paste your code!

Programming in C++

If you do not use the CMake buildsystem to make your own written BALL code, here you find an exemplary makefile:

• A simple BALL Makefile
• Disable BALL Warnings and Errors

Input / Output

• Opening and writing any molecular file format known by BALL (C++ , Python)
• Load a PDBFile into a Protein (C++ , Python)
• Load a ligand file into a System (C++ , Python)
• Write a system into a PDBFile (C++ , Python)
• Load a DCDFile into a Protein (C++)
• Write a protein into a DCDFile (C++))
• Convert molecular files between different formats (C++, Python)

Iterate over atoms, bonds, residues, chains, molecules, ...

• Iterate over all Chains in a System (C++ , Python)
• Iterate over all Residues of a System (C++ , Python)
• Iterate over Atoms specified by SMARTS expression(s) (C++ , Python)
• Iterate over all Proteins of a System (C++ , Python)
• Iterate over all Chains of a Protein (C++ , Python)
• Iterate over all Residues of a Chain (C++ , Python)
• Iterate over all Atoms of a Residue (C++ , Python)
• Iterate over all Atoms of a Molecule (C++ , Python)
• Iterate over all Bonds of an Atom (C++ , Python)
• Iterate over all Atoms in an AtomContainer (C++ , Python)
• Iterate over all Atom pairs in an AtomContainer
• Iterate over all Bonds in an AtomContainer

Handling Molecules

• Create a simple Molecule (C++ , Python)

• Determining the element type of an Atom

• Create a peptide from its amino acid sequence (C++ , Python)

• Copy a Molecule

• Determining the Protein's amino acid sequence in one/three-letter-code (C++ , Python)

• Get the one letter code amino acid sequence out of a .pdb file

• Identify atoms during a complex algorithm

• Get a single chain out of a system

• Get backbone atoms of a protein(C++ , Python)

• Map two Molecules([wiki:CodeLibrary/Mapping2Proteins])

• Remove water in a System(C++ , Python)

• Computing angles in BALL (C++ , Python)

• Translate an entire Molecule

• Locate atoms in a spatial proximity (HashGrid) (C++ , Python) {{{ #!comment

• Compute bond orders of a ligand(C++ , Python) }}}

• Compute Hydrogen bonds of a molecule

• Compute Secondary Structures of a molecule

• Aromatize a molecule's bonds

• Check whether a bond is aromatic without actually setting aromaticity

• Change the rotamer of a residue

• Add caps to a peptide

• Mutate amino acids of a protein or peptide

• Translate a functional group

• Compute the Surface (Solvent Accessible Surface - SAS) areas of atoms (C++ , Python)

• Assign radii (C++ , Python)

• Add missing hydrogens to a protein

• Add missing hydrogens to a ligand (C++ , Python)

• Energetically minimize a protein's conformation

• Compute Amber Energy of a system

• Map two structures onto each other and calculate their RMSD (C++ , Python)

• Physical constants in BALL (C++ , Python)

• Store user defined properties of atoms (C++ , Python)

• Create temporary files (C++ , Python)

New version (1.4.0)

• Assign chemical shifts from an NMRStar file
• Aromatize a Molecule's bonds
• Convert atom names between naming schemata
• Convert hydrogens from PDB to BMRB naming scheme
• Compute Hydrogen bonds of a Molecule (C++ , Python)
• Kekulize a Molecule's bond orders

Version (1.4.1)

• Compute bond orders of a ligand (C++ , Python)

Upcomming version (1.4.2)

Scripting with python

An introduction to our python interface can be found here.

via BALLView

• Visualize the results of your python script in BALLView
• Identify neighboring residues in BALLView given a selection
• Minimize the RMSD of two systems
• Remove Water
• Add missing hydrogens to a system and optimize their positions
• Create simple geometric objects in BALLView
• Setup an explicit solvent molecular dynamics (MD) simulation

via pure BALL python

All function and type definitions needed to use the BALL API are included in your code by the following line:

#!python
import BALL

or

#!python
from BALL import *

How to Post

If you have code snippets, that should be useful for others, post them here.

*Please make sure that your code compiles prior to posting! *

You can get syntax highlighting by enclosing your code in ticks ` in markdown followed by the language (either cpp or python)

For further information on how to post, just look at some examples found on this page.