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by sowjanya — last modified 2009-01-22 12:05

The MolKit package provides classes to read molecules in a number of file formats (PDB, Mol2 ...) and build a tree-like hierarchical structure reproducing the molecule's internal structure. For instance, a protein molecule is represented using the following four levels: protien,  chain,  residue,  atom

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The number of levels can be modified. For instance, we have added a level between chains and residues to represent the secondary structure of the protein. All nodes in that tree-structure can be extended dynamically, i.e. to add a property like a radius to an instance of an atom called "A", one simply assigns the value to a member data of the atom: A.radius = 1.7. This structure allowing to extend dynamically any node and perform all kinds of selections has proven the be very powerful and provides a high-level interface to the molecule.
The following code instantiates a Protein object and builds its representation from a PDB file. Several selection and manipulation illustrate some of the basic capabilities of these classes:

>>> from MolKit.protein import Protein
>>> from MolKit.pdbParser import PdbParser
>>> ### create a parser object with a filename
>>> parser = PdbParser('1crn.pdb')
>>> ### the method parse of the parser read parse the file and returns a ProteinSet
>>> proteins = parser.parse()
>>> proteins
ProteinSet instance holding 1 Protein
>>> protein = proteins[0]
>>> ### You can also use the Read function of the MolKit packages to parse a
>>> ### file. That will choose the parser corresponding to the file format
>>> ### as long as one has been implemented. PdbParser, PdbqParser, Mol2Parser,
>>> ### PQRParser and PdbqsParser already exist.
>>> from MolKit import Read
>>> proteins = Read('1crn.pdb')
>>> ### Once the protein is loaded we can operate on that structure
>>> ### TreeNodeSets behave like Python arrays
>>> residues8Trhough15 = protein.chains[0].residues[8:16]
>>> allAtoms = protein.chains.residues.atoms
>>> print residues8Trhough15
ResidueSet instance holding 8 Residue
>>> ### select all atoms with their name in list bbnames:
>>> bbnames = ['N', 'CA', 'C', 'O']
>>> backBone = allAtoms.get(lambda x, names=bbnames: in names)
>>> ### perform boolean operations over set:
>>> sideChains = allAtoms - backBone
>>> ### add new members on the fly to any object or set of objects:
>>> ### here we add a member called "bb" to all atoms and set it to 1
>>> ### for backbone atoms and 0 for side chain atoms
>>> = 0
>>> = 1
>>> ### build bonds using atomic distances
>>> protein.buildBondsByDistance()

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