paramagpy.fit.gridsearch_fit_atom_restrain_distance

paramagpy.fit.gridsearch_fit_atom_restrain_distance(densityMapA, densityMapB, distUpper, distLower, number)[source]

Given two RMSD density maps, this function will compare all points pairwise and return only those within the bounds of a given distance cutoff and within a certain number of points that are that are sorted by RMSD value. This might be useful if two density maps for separate atoms in a molecule are known to be constrained w.r.t. one another and you would like to use that restraint to further restrict the space of PCS RMSD points. The calculation first sorts the RMSD points and takes the bottom <number> of points and then compares each point pariwise to fulfill the distance condition. It then returns those points from both maps. Unfortunately there is no correlation data available between these two maps.

Parameters

  • densityMapA (paramagpy.fit.DensityMap) – a density map of PCS RMSD values.

  • densityMapB (paramagpy.fit.DensityMap) – a second density map of PCS RMSD values.

  • distUpper (float) – The upper limit for distance. Any pairwise distances larger than this value will be rejected from the final space of points

  • distLower (float) – The lower distance limit for distance Any pairwise distance smaller than this value will be rejectet from the final space of points

  • number (int) – The total number of positions to be considered for the pairwise distance comparison. This calculation first sorts points by RMSD and takes <number> of points with minimum RMSD and uses these for the pairwise distance calculation. Note that the total number of points returned could be significnalty more than this value after the pairwise comparison

Returns

tuple – two lists of [x,y,z] coordinates are returned associated with the inputs <densityMapA> and <densityMapB>. The returned coordinates are taken from the original grids and represent points that have another associated point in the other grid which is within the distance bounds and contained with an RMSD low enough to be within the lowest <number> of points

Return type

np.ndarray of position coordinates