atomset Package

atomset Module

class AdaptivePELE.atomset.atomset.Atom

Bases: object

Create an atom from a pdb line

Parameters

atomContent (basestring) – Line of the pdb from which the atom will be created

atomSerial

equivalentResname()

getAtomCoords()

Get the coordinates of the atom

Returns

numpy.Array – Array with the coordinate of the atom

id

isHeavyAtom()

Check if Atom is a heavy atom

Returns

bool – True if Atom is heavy atom, false otherwise

isHeteroAtom()

Check if Atom is an hetero atom

Returns

bool – True if Atom is an hetero atom, false otherwise

isProtein()

Check if Atom is a protein atom

Returns

bool – True if Atom is a protein atom, false otherwise

mass

name

printAtom()

Print Atom information

protein

resChain

resname

resnum

set_properties()

squaredDistance()

Calculate the squared distance between two atoms

Parameters

atom2 (Atom) – Second Atom to whom the distance will be calculated

Returns

float – The distance between the atoms

type

x

y

z

class AdaptivePELE.atomset.atomset.PDB

Bases: object

Object that will contain the information of a PDB file. Has to call the initialise method to load the file

ATOM_LINE_TEMPLATE = '%s%s %s %s %s%s%s   %.3f%.3f%.3f%.2f%.2f          %s   '

CMAtoms = {'ALA': 'empty', 'ARG': 'NE', 'ASN': 'empty', 'ASP': 'OD1', 'CYS': 'empty', 'GLN': 'empty', 'GLU': 'OE1', 'GLY': 'empty', 'HID': 'CE1', 'HIE': 'CE1', 'HIP': 'CE1', 'HIS': 'CE1', 'ILE': 'empty', 'LEU': 'empty', 'LYS': 'NZ', 'MET': 'empty', 'PHE': 'CZ', 'PRO': 'empty', 'SER': 'empty', 'THR': 'empty', 'TRP': 'CH2', 'TYR': 'OH', 'VAL': 'empty'}

atomList

atoms

centroid

com

computeTotalMass()

Calculate the total mass of the PDB

countContacts()

Count the number of alpha carbons that are in contact with the protein (i.e. less than contactThresholdDistance Amstrogms away)

Parameters

• ligandResname (basestring) – Residue name of the ligand in the PDB

• contactThresholdDistance (int) – Maximum distance at which two atoms are considered in contanct (in Angstroms)

Returns

int – The number of alpha carbons in contact with the ligand

extractCOM()

Calculate the PDB’s center of mass

Returns

list – List with the center of mass coordinates

extractCentroid()

Calculate the PDB centroid

Returns

List – List with the centroid coordinates

getAtom()

Get an Atom in the PDB by its id

Parameters

atomId (basestring) – Id of the Atom (in the format “atomserial:atomName:resname”)

Returns

int – Number of atoms in the PDB

Raises

KeyError if the id is not in the PDB

getCOM()

Get the PDB’s center of mass

Returns

list – List with the center of mass coordinates

getCentroid()

Get the PDB’s centroid

Returns

list – List with the centroid coordinates

getNumberOfAtoms()

Get the number of Atoms in the PDB

Returns

int – Number of atoms in the PDB

get_pdb_string()

initialise()

Wrapper function

isfromPDBFile()

ispdb

join_PDB_lines()

pdb

printAtoms()

Print Atom information for all the atoms in the PDB

totalMass

updateCoords()

writePDB()

Write the pdb contents of the file from wich the PDB object was created

Parameters

path (basestring) – Path of the file where to write the pdb

AdaptivePELE.atomset.atomset.computeCOMDifference()

Compute the difference between the center of mass of two PDB

Parameters

• PDB1 (PDB) – First PDB with which the RMSD will be calculated

• PDB2 (PDB) – First PDB with which the RMSD will be calculated

Returns

float – The distance between the centers of mass between two PDB

AdaptivePELE.atomset.atomset.computeCOMSquaredDifference()

Compute the squared difference between the center of mass of two PDB

Parameters

• PDB1 (PDB) – First PDB with which the RMSD will be calculated

• PDB2 (PDB) – First PDB with which the RMSD will be calculated

Returns

float – The squared distance between the centers of mass between two PDB

AdaptivePELE.atomset.atomset.computeSquaredCentroidDifference()

Compute the centroid squared difference between two PDBs

Parameters

• PDB1 (PDB) – First PDB

• PDB2 (PDB) – Second PDB

Returns

float – The squared centroid distance between two PDB

AdaptivePELE.atomset.atomset.readPDB()

Helper function, parses a string with PDB content or the path of a pdb file into a string

Parameters

pdbfile (basestring) – A string with PDB content or the path of a pdb file

Returns

basestring – A string with PDB content

class AdaptivePELE.atomset.RMSDCalculator.RMSDCalculator

Bases: object

Parameters

symmetries (list) – List of dictionaries with gropus of symmetric atoms atomId:symmetricalAtomId corresponding with the symmetrical atoms

computeNonSymmAtoms()

computeRMSD()

Compute the RMSD between two PDB

Parameters

• PDB1 (PDB) – First PDB with which the RMSD will be calculated

• PDB2 (PDB) – First PDB with which the RMSD will be calculated

Returns

float – The squared RMSD between two PDB

computeRMSD2()

Compute the squared RMSD between two PDB

Parameters

• PDB1 (PDB) – First PDB with which the RMSD will be calculated

• PDB2 (PDB) – First PDB with which the RMSD will be calculated

Returns

float – The squared RMSD between two PDB

nonSymmetricalAtomsSet

symmetries

class AdaptivePELE.atomset.SymmetryContactMapEvaluator.SymmetryContactMapEvaluator

Bases: object

Parameters

symmetries (list) – List of dictionaries with gropus of symmetric atoms atomId:symmetricalAtomId corresponding with the symmetrical atoms

buildContactMap()

Create the contact map of the protein and ligand. The contact map is a boolean matrix that has as many rows as the number of ligand heavy atoms and as many columns as the number of alpha carbons. The value is one if the ligand atom and the alpha carbons are less than contactThresholdDistance Amstrongs away

Parameters

• PDBobj (PDB) – PDB object that contains the conformation’s info

• ligandResname (basestring) – Residue name of the ligand in the PDB

• ligandResnum (int) – Integer containing the residue number of the ligand in the pdb

• ligandResChain (basestring) – String containing the chain name of the ligand in the pdb

• contactThresholdDistance (int) – Maximum distance at which two atoms are considered in contanct (in Angstroms)

Returns

numpy.Array – The contact map of the ligand and the protein

Returns

int – The number of alpha carbons in contact with the ligand

buildContactMapWithRowMap()

Create a map that relates symmetric atoms in the ligand to row indices in the contactMap matrix and the contact map of the protein and ligand. The contact map is a boolean matrix that has as many rows as the number of ligand heavy atoms and as many columns as the number of alpha carbons. The value is one if the ligand atom and the alpha carbons are less than contactThresholdDistance Amstrongs away

Parameters

• PDBobj (PDB) – PDB object that contains the conformation’s info

• ligandResname (basestring) – Residue name of the ligand in the PDB

• ligandResnum (int) – Integer containing the residue number of the ligand in the pdb

• ligandResChain (basestring) – String containing the chain name of the ligand in the pdb

• contactThresholdDistance (int) – Maximum distance at which two atoms are considered in contanct (in Angstroms)

Returns

numpy.Array – The contact map of the ligand and the protein

Returns

int – The number of alpha carbons in contact with the ligand

buildOptimalPermutationContactMap()

Build a permutated version of the contactMap which maximizes the similarity between the two contactMaps :param contactMap: contactMap of the conformation to compare :type contactMap: numpy.Array :param clusterContactMap: cluster contactMap to which we are comparing :type cluster: numpy.Array :returns: numpy.Array – The permutated contact map

createContactMap()

Create the contact map of the protein and ligand. The contact map is a boolean matrix that has as many rows as the number of ligand heavy atoms and as many columns as the number of alpha carbons. The value is one if the ligand atom and the alpha carbons are less than contactThresholdDistance Amstrongs away

Parameters

• ligandResname (basestring) – Residue name of the ligand in the PDB

• ligandResnum (int) – Integer containing the residue number of the ligand in the pdb

• ligandResChain (basestring) – String containing the chain name of the ligand in the pdb

• contactThresholdDistance (int) – Maximum distance at which two atoms are considered in contanct (in Angstroms)

Returns

numpy.Array – The contact map of the ligand and the protein

Returns

int – The number of alpha carbons in contact with the ligand

evaluateCorrelation()

evaluateDifferenceDistance()

evaluateJaccard()

ligandList

proteinList

symToRowMap

symmetricAtoms

symmetries

AdaptivePELE.atomset.SymmetryContactMapEvaluator.calculateCorrelationContactMaps()

Calculate the correlation of two contactMaps