Package schrodinger :: Package trajectory :: Module protliginteractionfinder :: Class ProtLigInteractionFinder

Class ProtLigInteractionFinder

               object --+    
                        |    
analysistool.AnalysisTool --+
                            |
                           ProtLigInteractionFinder

A tool to find between two selections.

Instance Methods

[hide private]

__init__(self, protein_sel, ligand_sel, tol=0.01, *args, **kwargs)
Initialize frame slicing information.

isOrthogonal(self, box, tol)

getResCa(self, atom_index)

getClosestHydrophobicDist(self, res, frag)

getProteinChargedAtoms(self, st)

getLigandChargedAtoms(self, st)

Centroid

find_centroid(self, atomlist)
Computes the centroid of a group of atoms

convert_index_to_asl(self, index_list)

findLigFrag(self, atm_index)

labelProtAtm(self, atm_idx)

labelProtRes(self, atm_idx)

labelLigAtm(self, atm_idx, frag='')

labelLigFrag(self, atm_idx=-1, frag='')

doFrameInit(self, frame)
initialize parameters on the first frame

updatePositions(self, st, frame)

updateProteinNearResidues(self, frame)

processFrame(self, frame)
Collect data for the provided frame.

processWatersFrame(self, frame)

get_distance(self, box, atom1, atom2)
Return the distance of the two atoms in the periodic box

processMetalFrame(self, frame)
This function is searches for ions or metals that either interact with protein and a ligand or just a ligand.

processHydrophobic(self, frame)

processPiFrame(self, frame)

processSbFrame(self, frame)

processHbFrame(self, frame)

getDictionaries(self)
This function returns a dictionary of dictionaries of various system atoms, so the labels can be mapped back to the structure atoms.

getFrameResults(self)
For each frame, return a list of (acceptor, donor) integer tuples, each value being a 1-based atom index into the overall simulation structure.

getResults(self)
Return results for all values and frames as a numpy array with the first index across analyses.

getAllBonds(self)
Return a set of all hydrogen bonds found by the analysis.

getLigandUniquePDBName(self, st)
If all s_m_pdb_atom_name in the ligand are unique, then return true else return false

Inherited from analysistool.AnalysisTool: getDataLabels, getLabel, plot, plot2D, postProcess, setSlice, shouldProcessFrame

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, protein_sel, ligand_sel, tol=0.01, *args, **kwargs)
(Constructor)

Initialize frame slicing information.

The behavior of 'start', 'stop', 'step' is the same as the python built-in range function. That is, 'start' is included in the values to be processed, but 'stop' is not. Only the largest value satisfying 'start' and 'step' that is less than 'stop' will be processed.

Parameters:

protein_sel (AtomSelection instance) - The atom selection one
ligand_sel (AtomSelection instance) - The atom selection two.

Overrides: object.__init__

find_centroid(self, atomlist)

Computes the centroid of a group of atoms

Parameters:

atomlist (list) - list of atom objects

Returns: Centroid

Centroid object for the atoms

doFrameInit(self, frame)

initialize parameters on the first frame

Overrides: analysistool.AnalysisTool.doFrameInit

processFrame(self, frame)

Collect data for the provided frame.

Overrides: analysistool.AnalysisTool.processFrame: (inherited documentation)

get_distance(self, box, atom1, atom2)

Return the distance of the two atoms in the periodic box

Parameters:

box (BondaryCondition) - bondary box dimesions
atom1 (int) - index of atom1
atom2 (int) - index of atom2

processMetalFrame(self, frame)

This function is searches for ions or metals that either interact with protein and a ligand or just a ligand. 1) find ions/metals near ligand 2) find protein atoms near ions

getFrameResults(self)

For each frame, return a list of (acceptor, donor) integer tuples, each value being a 1-based atom index into the overall simulation structure.

Note that the returned value here is not a numpy array as each frame may have a different number of hydrogen bonds.

Overrides: analysistool.AnalysisTool.getFrameResults

getResults(self)

Return results for all values and frames as a numpy array with the first index across analyses.

So, if r = analysis.getResults(), and the analysis instance calculates three values for each frame, then r[0] will be the first value across all frames.

Overrides: analysistool.AnalysisTool.getResults: (inherited documentation)

getAllBonds(self)

Return a set of all hydrogen bonds found by the analysis. Results are in the same form as getFrameResults() - a pair of (acceptor, donor) integers.

Class ProtLigInteractionFinder

__init__(self, protein_sel, ligand_sel, tol=0.01, *args, **kwargs) (Constructor)

find_centroid(self, atomlist)

doFrameInit(self, frame)

processFrame(self, frame)

get_distance(self, box, atom1, atom2)

processMetalFrame(self, frame)

getFrameResults(self)

getResults(self)

getAllBonds(self)

init(self, protein_sel, ligand_sel, tol=0.01, *args, **kwargs)
(Constructor)