1. Zajęcia dydaktyczne
    1. Bioinformatyka
    2. Modelowanie Molekularne
    3. Struktura Polimerów i Biopolimerów
    4. Wstęp do Programowania w Naukach Przyrodniczych
    5. Wspomaganie Komputerowe Pracowni Chemicznej
    6. Laboratorium Chemii i Biologii Strukturalnej
  2. Courses in English
    1. Bioinformatics
    2. Molecular Modelling
GLU56 of 1NXB deposit has planar geometry of alpha-carbon (witch contradicts basic chemical knowledge)
ex_SelectPlanarCAGeometry

Tests whether alpha-carbons actually have tetrahedral geometry as they should.

B-factors of 2GB1 PDB deposit
ex_bf_by_residue

Reads a PDB file and per-residue statistics of B-factors

Energy over time in Ising model
ex_REMC_Ising

The program runs a Replica Exchange Monte Carlo simulation of a simple 2D Ising system (spin glass).

Planar angles in a toluen molecule
ex_Molecule

Demonstrates how to create a Molecule object based on PdbAtom data type (as nodes of the graph)

Keywords:
molecule
Planar angles in a toluen molecule
ex_Molecule_Vec3

Demonstrates how to create a Molecule object based on Vec3 data type (Vec3 are nodes of the graph)

Keywords:
molecule
Map of backbone hydrogen bonds for 2GB1 protein
ap_BackboneHBondMap

Calculates a map of backbone hydrogen bonds.

2GB1 model structure superimposed on the native, crmsd = 4.93952
ap_Crmsd

Calculates crmsd value on C-alpha coordinates. The program prints just the crmsd value.

Keywords:
PDB input crmsd
25 conformations of the same ligand randomly placed on the surface of a protein
ap_LigandTossingMover

To test LigandTossingMover mover, tosses a ligand on a proteins surface

Keywords:
docking mover
1K6M and 1BIF structures aligned according to HOMSTRAD database
ap_aligned_pdb

Reads an alignment between two proteins (PIR format) and the two structures and writes PDB for the aligned parts

Distribution of Chi1 angles of THR side chains approximated with a mixture of three von Mises distribution
ap_chi1_rotamers_estimation

Reads a file with 1D data and estimates a mixture of VonMissesDistribution based on these observations.

Distribution of Chi1 angles of THR side chains approximated with a mixture of three von Mises distribution
ap_fit_VonMises_mixture

Reads a file with 1D data and estimates a mixture of VonMissesDistribution based on these observations.

Contacts found between 5EDW protein and its ligand TTP
ap_ligand_contacts

Finds contacts between a ligand molecule and a protein.

Statistics of random sequence alignment between 1BC6 and SFL95851.1
ap_shuffled_sequence_alignment

Calculate global sequence alignment scores with one sequence randomly shuffled and estimates alignment p-value

Example tree node
ex_BinaryTreeNode

Simple demo for BinaryTreeNode class

Proline residue selected from 1OFZ deposit
ex_SelectChainResidueAtom

Extracts a fragment of a PDB file.

Example correlation of chi angles between two homologus structures
ex_chi_correlation

Calculates correlation between Chi dihedral angles measured in two different protein structures.

Chi1-Chi2 statistics for ILE residue
ex_evaluate_chi

Calculates all side chain Chi dihedral angles for the input protein structure

Mixture of von Mises functions plotted
ex_plot_VonMises_mixture

Example which evaluates a mixture of Von Mises distribution so it can be plotted nicely

Keywords:
statistics
BLOSUM62 matrix plotted
ex_NcbiSimilarityMatrixFactory

Test for loading substitution matrices available in BioShell

Alpha helix rotated a few times by a fixed angle
ap_orient_pdb

Shows how to rotate a piece of protein structure

Phi,Psi values plotted for every residue of 2KWI PDB deposit; radius of a circle denotes standard deviation calculated from the NMR ensemble
ex_evaluate_phi_psi

Calculates Phi,Psi angles (Ramachandran map) for the input protein structure

hexabin representation of Ramachandran map (histogram made from non-redundant subset of PDB)
ap_Hexbins

Reads a file with 2D observations (two columns) and makes hexbin histogram.

Example von Mises distribution
ex_VonMisesDistribution

Example which estimates parameters of von Mises distribution and tabulates its values

Keywords:
statistics
no_alt_img
ap_AAHydrophobicity

Reads a PDB file and substitutes b-factor column with hydrophobicity values according to Kyte-Doolittle scale

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_AlignmentPValuesProtocol

Uses AlignmentPValuesProtocol protocol to calculate all pairwise p-values for a given set of sequences

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_LocalStructureMatch

Finds contiguous structural segments that are similar between two structures

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_MSAColumnConservation

Reads a MSA in ClustalW format and evaluates sequence conservation for every column

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_NWAligner

Calculate all pairwise sequence alignments between sequences read from two FASTA files : query and database

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_OnlineStatistics

Reads a file with real values and calculates simple statistics: min, mean, stdev, max.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_PairwiseCrmsd

Calculates crmsd value for a set of protein structures (at least two)

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_PairwiseSequenceIdentityProtocol

Uses AlignmentPValuesProtocol protocol to calculate all pairwise p-values for a given set of sequences

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_ProteinArchitecture

Calculates a map of backbone hydrogen bonds.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_QuickSequenceIdentity

Estimates pairwise sequence similarity for a set of sequences given in a FASTA format

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_SWAligner

Calculate all pairwise sequence alignments between sequences read from two FASTA files : query and database

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_SequenceProfile

Reads a MSA in ClustalW format and prints a sequence profile

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_SequenceWeightingProtocol

Shows how to use SequenceWeightingProtocol class

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_build_crystal

ap_create_crystal reads a given PDB file and prints all atoms in a unit cell.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_docking_crmsd

ap_docking_crmsd calculates crmsd between two ligand positions after docking to a receptor.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_download_pdb

Simple app downloads a pdb file from RCSB website

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_dssp

DSSP implementation

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_dssp_to_ss2

Reads a DSSP file and prints the secondary structure of each chain in SS2 format.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_filter_fasta

This program reads a file with sequences in FASTA format and sorts them by length.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_find_in_fasta

ap_find_in_fasta reads a sequence database in FASTA format and looks for sequences by given IDs

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_ligand_trajectory

Finds contacts between a ligand molecule and a multimodel-protein.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_local_backbone_geometry

Reads a protein structure in PDB format and describes geometry local

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_pdb_to_fasta_ss

Reads a PDB file and writes protein sequence(s) in FASTA format.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_pdb_to_pir

Reads a PDB file and writes protein sequence(s) in PIR format

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_pir_to_fasta

Reads a file with sequences in PIR format and converts them to FASTA.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_rescore_alignment

Estimates pairwise sequence similarity for a set of sequences given in a FASTA format

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_scorefile_columns

Reads a score-file or a silent file (produced by Rosetta) and extracts requested columns of scores

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_stacking_interactions

Finds stacking interactions in a given PDB file.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ap_superipose_pdb_by_ligand

Superimposes protein structures by matching ligand molecules.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_Array2DSymmetric

Simple test for Array2DSymmetric class.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_AtomSelector

Demonstrates how to use atom selectors

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_AtomicElement

Example showing how to use AtomicElement class

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_BioShellVersion

Test for BioShellVersion class prints the BioShell version info

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_BitSet

Test for BitSet class

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_BivariateNormal

Estimates parameters of a two-dimensional Gaussian distribution

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_BoundedPriorityQueue

Simple demo for BoundedPriorityQueue class

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_CGRotamersEnergy

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_CGRotamersMovers

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_CGRotamersPairwise

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_Cart

Shows how to use CART classification model

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_CartesianToSpherical

Calculates spherical coordinates using BioShell and 'by hand' to check of it works

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_ChiAnglesDefinition

Shows how to look up information on Chi angle definitions

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_Cif

ex_Cif tests reading CIF files

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_Combinations

A simple example shows how to generate Combination

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_DMD

A test to check if DMD sampler works correctly

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_DMD_Ar

Simple DMD simulation of argon gas.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_DsspData

Reads a DSSP file and prints the sequence and the secondary structure of each chain in FASTA format.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_DynamicSystem

Shows how to set up a DynamicSystem class object

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_HierarchicalClustering

Example showing how to use hierarchical clustering method.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_Interpolate1D

Reads a file with two columns of data and calculates interpolated values

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_InterpolatePeriodic1D

Simple test for interpolation of a periodic 1D function

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_InterpolatePeriodic2D

Simple test for interpolation of a periodic 2D function

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_Ising2D

Simple but fully functional Ising simulating program.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_JsonNode

Demo for handling JSON data

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_KDE_1D

Reads one column of observations and calculates Kernel Density Estimator (KDE) for the data

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_LBFGS

Example shows how to use BFGS function minimizer

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_MC_Ar

Isothermal Monte Carlo simulation of argon gas.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_MMAtomTyping

Assigns MM atom typing for every atom of the given protein according to the given force field parametrisation file

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_MMBondEnergy

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_MMEnergy

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_MMNonBonded

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_MeanFieldDistributions

Prints values for a given Mean Field potential so it can be plotted nicely.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_Monomer

Example demonstrates functionality of core::chemical::Monomer data type.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_NormalDistribution

Demo for NormalDistribution class.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_OptionParser

Shows how to use BioShell command line parser in your own program

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_P2QuantileEstimation

Reads a file with real values and calculates simple statistics: min, mean, stdev, max.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_PairwiseAlignment

Simple example showing how to retrieve arbitrary data according to a sequence alignment object

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_PairwiseSequenceAlignment

Calculates the optimal global sequence alignment between two protein sequences.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_Pca3

Orients 3D points along the axes using PCA algorithm

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_Pdb

Reads a PDB file and creates a Structure object.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_PdbLineFilter

Simple cleanup for a PDB file.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_REMC_Ar

Isothermal Monte Carlo simulation of argon gas.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_ReduceSequenceAlphabet

ex_ReduceSequenceAlphabet lists all reduced amino acid alphabets registered in BioShell library

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_Remark290

ex_Remark290 demo shows how to access symmetry operators stored in a PDB file header.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_Residue

Reads a PDB file and checks if all amino acid residues have complete backbone

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_SelectResidueRange

Shows how to select a structural fragment based on residue IDs

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_SemiglobalAligner

Calculate a pairwise sequence alignment between two sequences with identity scoring method.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_Seqres

Reads a PDB file and extracts its SEQRES sequence(s)

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_Sequence

Reads a PDB file and prints a fragment of its sequence.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_SequenceAlignmentWidget

Prints values for a given Mean Field potential so it can be plotted nicely

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_SimulatedAnnealing

A simple example shows how to use Monte Carlo simulated annealing.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_Structure

Reads a PDB file and prints a list of all atoms grouped by residues they belong to.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_SwingChainFragment

Tests SwingChainFragment mover

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_ThreadPool

Simple test for a ThreadPool class

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_ThreeDTree

A simple example shows how to use BioShell kd-tree routines.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_TraxObserver

Converts PDB to binary trajectory and vice versa

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_TreeNode

Simple demo for TreeNode class

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_UnionFind

A simple example shows how to use UnionFind algorithm.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_WebServer

Simple test for WebServer class

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_XML

Simple for XML I/O utils.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_alignment_io

Read alignment in Edinburgh format or calculate a new one from given sequences; write Edinburgh.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_basic_algebra

ex_basic_algebra illustrates how to calculate eigenvalues and eigenvectors for a 3x3 matrix

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_benchmark_quick_seq_identity

Compares computational efficiency of three methods that estimate sequence identity without computing actual alignment.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_cabs_representation

Reads an all-atom structure from a PDB file and produces a structure in CABS representation.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_cabs_rotamers

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_cabsbb_representation

Converts all-atom protein structure to CABS-bb representation

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_chi2_independence_test

Chi-square test for independence.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_count_residues_by_type

Reads a MSA in ClustalW format and prints by-residue counts

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_define_rotamer

Prints rotamer type (M-P-T code) for each amino acid residue in the input PDB structure

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_expectation_maximization

Example showing how to use expectation-maximization method

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_find_side_group

A simple example shows how to select a chemical group of a molecule using find_side_group() method.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_greedy_clustering

Example showing how to use greedy clustering method.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_intersect_sorted

Shows how to find an intersection of two sorted vectors of data

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_k_tuples

Writes a set of 4-tuples that can be created for a protein sequence.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_local_BBQ_coordinates

Reads a PDB file and prints local coordinates for side chain atoms

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_local_coordinates_three_atoms

Reads a PDB file and prints local coordinates for sidechain atoms

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_monomer_io

The program converts a monomer structure from CIF format to internal formats used by BioShell.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_peptide_hydrogen

Reconstructs peptide hydrogen atoms using two methods and compares the error between them.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_protein_peptide_interface

Finds contacts atomic contacts between a receptor and a peptide

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_random_vector_on_sphere

Simple test shows that random_vector_on_sphere() really produces a unifirm distribution

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_read_properties_file

Simple test reads .properties file and prints these settings on the screen

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_selection_protocols

Shows how to use selection protocols

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_seq_io

Example reads SEQ file and prints the data stored there in FASTA format

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_set_dihedral

Sets a particular values for Phi, Psi and Omega angles at a certain residue in a protein.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_shared_pointers

A very basic example showing how to use shared pointers (from standard C++ 11 library) when programming in BioShell.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_simpson_integration

Example for numerical integration with Simpson method

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_split_fasta

Reads a file with sequences in FASTA format and writes each sequence to a separate FASTA file.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_structure_iterators

Shows how to iterate through structural components (residues, atoms, etc)

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_test_gzip

Simple test to gzip and un-gzip a string data

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_uniquify

Tests uniquify() method which removes redundant objects from a container.

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ex_web_client

Simple test for web_client methods

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ww_evaluate_chi

Calculates Chi angles for the input protein structure

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ww_evaluate_contact_map

Calculates Phi,Psi angles (Ramachandran map) for the input protein structure

Keywords:
no_keywords
Category:
no_categories
no_alt_img
ww_evaluate_phi_psi

Calculates Phi,Psi angles (Ramachandran map) for the input protein structure

Keywords:
no_keywords
Category:
no_categories