ofxMol

Data structures and functions to draw biological macromolecules.

Introduction

This addon is based on ESBTL, a Protein Data Bank (PDB) parser and data structure for the structural and geometric analysis of biological macromolecules.

Usage

ofApp.h

#pragma once

#include "ofMain.h"
#include "ofxMol.h"

class ofApp : public ofBaseApp
{

public:
    void setup();
    void draw();
    void update();
    
protected:
    OfxMol::System system;
    ofMesh mesh;
};

ofApp.cpp

#include "ofApp.h"

//--------------------------------------------------------------
void ofApp::setup()
{
    ofBackground(0);
    
    // setup system
    system.setup(ofFile("ice.pdb").path());
    mesh = system.getModel(0).atomsMesh(0.5f);
}

//--------------------------------------------------------------
void ofApp::update()
{
    ofSetWindowTitle(ofToString(ofGetFrameRate(), 0));
}

//--------------------------------------------------------------
void ofApp::draw()
{
    ofEnableDepthTest();
    ofPushMatrix();
    ofTranslate(ofGetWidth()/2.0, ofGetHeight()/2.0);
    ofScale(40.0, 40.0);
    ofRotate(ofGetElapsedTimef()*1.5,0,1,1);
    
    // draw atoms
    ofSetColor(255);
    mesh.draw();
    ofPopMatrix();

    ofDisableDepthTest();
    
    // log info
    ofSetColor(255);
    ofDrawBitmapString(system.getModel(0).log(),10,20);
}

void ofApp::update()
{
    for (int i = 0; i < model.number_of_atoms(); i++)
    {
        OfxMol::Atom atom = model.getAtom(i);
    }
}

License

Copyright (C) 2015 Davide Rambaldi

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see http://www.gnu.org/licenses/.

Installation

1. Install and link boost

   This addon DO NOT include boost, because probably you have it installed in your system somewhere.

   My suggestion to install boost on Mac is homebrew:

   brew install boost

   After installation you should link the includes directory where boost is installed:

   For homebrew the directory is /usr/local/include.

   In XCode:

   Build Settings --> Header Search Path --> add: /usr/local/include.

2. Install addon

   Clone the addon repository in your openFrameworks/addons/ folder.

3. Run Examples

   Open example-simple and change, if necessary, the boost header search path (see point 1).

Dependencies

• boost

Compatibility

Open Frameworks Version > 0.8.4

Known issues

Chain and Residues not implemented yet

Version history

Version 0.1 (14 September 2015):

Basic version with mesh generation and some examples

Notes on Molecules

ESBTL architecture

A system provides access to the hierarchical data structure.

It may contain one or several models.

Each model is made of chains.

Chains are then made of residues, and residues are made of atoms.

ofxMol architecture

There is a single system (OfxMol::System) that stores models (OfxMol::Models) and water_models.

The system is created using the function OfxMol::System::setup(ofFile file, SetupMode mode).

After setup the OfxMol::System contains a std::vector of OfxMol::Model named models and a std::vector of OfxMol::Model named water_models.

Possible SetupMode are:

Mode	Atoms	Occupancy	Notes
SIMPLE	All atoms in one system	Accept all occupancy policies	Use this mode for simple molecules
ADVANCED	2 systems the first one contains all heavy atoms that do not belong to a water molecule. the second one contains all containing heavy atoms of water molecules. Hydrogen atoms are discarded. Use water_models_begin and water_models_end to iterate over water models in second system	Accept all occupancy policies	Use this mode for proteins and other big molecules
CHAIN	TODO	TODO	TODO

Each OfxMol::Model contains:

• a vector of OfxMol::Atoms
• a vector of OfxMol::Coarse_Atoms

COARSE ATOMS

In molecular dynamics, coarse graining consists of replacing an atomistic description of a biological molecule with a lower-resolution coarse-grained model that averages or smooths away fine details.

BAR domain homodimer. The two monomers are shown in green and purple. The all-atom structure is shown on the left, and an example of a coarse-graining structure is shown on the right. Both all-atom and SBCG structures are shown from the top and from the side.

See also: Coarse-graining in wikipedia

GET PDB FILES

• http://www.rcsb.org/
• http://www.drugbank.ca/
• http://www.nyu.edu/pages/mathmol/library/drugs/

FIX PDB FILES

Install pymol to open and resave the molecule with Save Molecule in a new PDB files. This usually fix the PDB problems.