Sub-Loop Inverse Kinematics Monte Carlo

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Here is a quick tutorial of SLIKMC package. Some example code can be found at LoopTK_SLIKMC/slikmc/main.cc.

Example 1. Set up SLIKMC for sampling

Example 2. Define custom energy functions

Example 1. Given one protein chain 1B8C, how to sample possible conformations of a subloop from residue with index 0 to residue with index 10?

1. Create an instance of PProtein for protein 1B8C by providing the PDB file.

PProtein* chain = PDBIO::readFromFile("1B8C.pdb");

2. Create an instance of class SLIKMCSampler with chain as parameter:

SLIKMCSampler sampler(chain);

3. Set up the sampler. Several settings, such as using B-factors as prior, enable side-chain sampling, enable logging output conformation files, etc., can be defined according to user's preference.

By default, these settings are all disabled. To enable these settings, user can call functions like:

Enable collision checking. The sampler will check the steric-clash of the conformation with itself and rest of the chain.

sampler.enableCollisionChecking();

Enable using B-factors as prior. User can provide a protein file with desired distribution of atom positions. By default, the distributions of atom positions are defined according to chain p.

sampler.enableBFactors();

Enable recording the generated conformations. User can provide the number of skipped samples. By default, skip length equals to 1. All the generated files will be put in the pdbfiles_out folder with name slikmc_i.pdb which i is a index starting from 0.

sampler.enableLog(10);

Display settings. Once finishing the settings, the user can call function display() to print the current setting status of the sampler.

sampler.display();

4. Call the sampler User can call function sample() to sample conformations of the chain/subchain for 60 seconds.

sampler.sample( 60.0, 0, 10);

Example 2. How to define a custom energy function and incorporate into sampling?

1. Define a custom energy class by inheriting the interface class Prior

class SamplePrior:public Prior { ... }

2. Override the function evaluate. Note: the density value MUST be returned in logarithm.

double SamplePrior::evaluate( PChain* chain){

   //The following is a toy example: the probability of the distance d between two C-alpha atoms is proportional to exp(-d). Use your custom code to replace it.

   Vector3 p1 = chain->getResidue(3)->getAtomPosition( PID::C_ALPHA);

   Vector3 p2 = chain->getResidue(6)->getAtomPosition( PID::C_ALPHA);

   return -p1.distance(p2);

}

3. Enable the setting of using custom energy function for a SLIKMCSampler instance sampler.

sampler.enableCustomPriors();

4. Add the custom prior into the sampler. There is no limitation for the number of custom priors.

SamplePrior prior;

sampler.addCustomPrior( prior);