schrodinger.trajectory.protliginteractionfinder module

Developed by Dmitry Lupyan

This class looks at protein-ligand geometric interaction

class schrodinger.trajectory.protliginteractionfinder.ProtLigInteractionFinder(protein_sel, ligand_sel, *args, **kwargs)

Bases: schrodinger.trajectory.analysistool.AnalysisTool

A tool to find between two selections.

convert_index_to_asl(index_list)

doFrameInit(frame)

initialize parameters on the first frame

findLigFrag(atm_index)

find_centroid(atomlist)

Computes the centroid of a group of atoms

Parameters:atomlist (list) – list of atom objects Return type:Centroid Returns:Centroid object for the atoms

getAllBonds()

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.

getClosestHydrophobicDist(res, frag)

getDictionaries()

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

getFrameResults()

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.

getLigandChargedAtoms(st)

getLigandUniquePDBName(st)

If all s_m_pdb_atom_name in the ligand are unique, then return true else return false

getProteinChargedAtoms(st)

getResCa(atom_index)

getResults()

get_distance(box, atom1, atom2)

Return the distance of the two atoms in the periodic box :param box: bondary box dimesions :type box: BondaryCondition :param atom1: index of atom1 :type atom1: int :param atom2: index of atom2 :type atom2: int

labelLigAtm(atm_idx, frag='')

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

labelProtAtm(atm_idx)

labelProtRes(atm_idx)

processFrame(frame)

processHbFrame(frame)

processHydrophobic(frame)

processMetalFrame(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

processPiFrame(frame)

processSbFrame(frame)

processWatersFrame(frame)

updatePositions(st, frame)

updateProteinNearResidues(frame)

schrodinger.trajectory.protliginteractionfinder.getLigandFragments(ligand_st)

fragments the ligand in several fragments using the murcko rules. returns the list of mappings