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libSRMCollider

This is a C++ library which is used by the SRMCollider software which also contains Python bindings as the main way to interact with the package.

To configure, and build run

cmake .
make

All tests are in ./test and in order to run them use

make && make test

All Python extension modules are in ./py and will not be built with cmake. Please use the setup.py script to build those extension modules.

Functionality

The C++ library consists of 5 components, a combinatorics module, a range tree module, a common library, a module for computation of eUIS (extended UIS) and a file for integrated runs which pushes most computation down to C++ to gain speed.

SRMCollider Library

General purpose library functions and data structures are in src/srmcolliderLib.h using namespace SRMCollider::Common. These include for example fragment ion mass calculations. The implementations are in the corresponding .cpp file.

Combinatorics

The combinatorics library is found in the file src/combinatorics.h using the namespace SRMCollider::Combinatorics which computes combinations of drawing M elements from a set of N elements (e.g. M transitions out of a total of N). This is for example useful when computing all combinations of non UIS transitions, see function get_non_uis.

Rangetree

The rangetree library is found in src/rangetree.h. It is able to build a tree and query a tree. There are two trees:

  • SRMCollider::SimpleRangetree which is a 2D tree on RT, Q1 and for each entry a struct with parent_id and q1_charge is stored
  • SRMCollider::ExtendedRangetree which is a 2D tree on RT, Q1 and for each entry a struct with sequence, peptide_key, transition_group_id, q1_charge and isotopic modification is stored. The additional information is needed for example in integratedrun.cpp

The implementations are in the corresponding .cpp file.

Extended UIS

Extended UIS can be calculated using src/calculate_eUIS.h, see function calculate_eUIS for example. The input for the module is a list of RT values for each transition to be tested. The implementations are in the corresponding .cpp file.

Integrated run

The functions necessary for an integrated, mostly C++ run are described in src/integratedrun.h and use the namespae SRMCollider::IntegratedRun to combine the rangetree query and the computation of the non UIS transitions into a single function, wrap_all_bitwise or min_needed. The implementations are in the corresponding .cpp file.

Python bindings

In the ./py folder, you can find bindings for four of the above modules plus a shared python integration library at py/py_srmcolliderLib.h. The common library contains some SRMCollider::Common functions as well as SRMCollider::pyToC which can convert from C++ to Python data structures and back. The individual bindings are

  • py/py_combinations.cpp
  • py/py_getNonUis.cpp
  • py/py_integratedrun.cpp
  • py/py_rangetree.cpp

Each of these can be compile to an independent Python module using the setup.py installation script provided with SRMCollider.