Complex Formation Functions

This document explains the functions in eSBMTools that were used in this example.

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→ 3 modules from eSBMTools were imported into buildComplex.py:

            -GoModel.py
            -GroFile.py
            -TopFile.py

→ The function

    createGoModel(path_to_current_directory, pdbCode, pdbFileName='',
                    moleculeType='NA', chainIDlist=[],
        xmlFileName='nucleicAcids.xml', groFileName='start.gro',
        topFileName='start.top', topologyPath='')

takes a .pdb file as input and turns it into a fully functional .top file and .gro file as used for Go
Models. There is no return value but a .top file is created during the process.

This is a function of GoModel.py

→ The function

    parseGroFile(path_to_current_directory, fileName='start.gro')

is used to read a .gro file as input and output a list of file header, atoms section and box
information. The returned data from the function is then stored in the data structures description,
atoms and box as seen in buildComplex.py

The next function used is:

    writeGroFile(path_to_current_directory, groFileName, description,
        atoms, box=none, translate=[0.0,0.0,0.0],
        rotate=[0.0,0.0,0.0])

This function then takes the list of atoms as returned by parseGroFile and returns a .gro file.

The next functions are:

    mergeGroFiles(path1, fileName1, path2, filename2, pathOUT,
                fileNameOut)

and   mergeTopFiles(path1, fileName1, path2, filename2, pathOUT,
                fileNameOut)

These functions, as the names suggest, takes 2 .gro files and 2 .top files and merge them.

These functions belong to GroFile.py and TopFile.py

→ After this, the contact interfaces of the proteins are adjusted for a single protein and finally the
function

    addPairsToTop(path_to_current_directory, topFileNameComplex, path,
        topFileNameComplexContacts, atomContacts)

writes the pairs listed in atomContacts to the top of the file.

This function is a part of TopFile.py

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Cheers!