Check if files in refdir are present in the directory given as second argument AND their content matches.
Raise an exception if not.
Check that name, resname, resid, insertion codes match between two molecules.
Coordinates are not checked.
diff – a list of differences, as human-readable strings (empty if structures are equal).
Examples
>>> m=Molecule("3PTB")
>>> m2=m.copy()
>>> m2.set("resname","HIE","resid 91")
>>> diffMolecules(m,m2,sel="name CA")
['CA HIS 91 vs CA HIE 91 ']
Convert np.ndarray and scalars to lists.
Lists and tuples are left as is. If a second argument is given, the type check is performed on the first argument, and the second argument is converted.
Return the PDB corresponding to molecule and selection, as a list of strings.
Examples
>>> m = Molecule("3PTB")
>>> getPdbStrings(m, "resname BEN")
['HETATM 1 C1 BEN A 1 -1.853 14.311 16.658 1.00 19.86 1 C ',
'HETATM 2 C2 BEN A 1 -2.107 15.653 16.758 1.00 19.86 1 C ',
'HETATM 3 C3 BEN A 1 -1.774 16.341 17.932 1.00 19.86 1 C ',
'HETATM 4 C4 BEN A 1 -1.175 15.662 19.005 1.00 19.86 1 C ',
'HETATM 5 C5 BEN A 1 -0.914 14.295 18.885 1.00 19.86 1 C ',
'HETATM 6 C6 BEN A 1 -1.257 13.634 17.708 1.00 19.86 1 C ',
'HETATM 7 C BEN A 1 -2.193 13.627 15.496 1.00 19.86 1 C ',
'HETATM 8 N1 BEN A 1 -2.797 14.235 14.491 1.00 19.86 1 N ',
'HETATM 9 N2 BEN A 1 -1.762 12.391 15.309 1.00 19.86 1 N ']