The coordinates will not be, but the point that you have calculate. Residue.add((name=' H ', coord=np.array(), bfactor=0., occupancy=1., altloc=' ', fullname=' H ', serial_number=last_serial+1,element='H')) last_serial = list(structure.get_residues()).child_rial_number + 1 #Stopping chemdoodle from auto adding hydrogens serial number#One the serial number is a PDB thing, which is sequential for the model. #Stopping chemdoodle from auto adding hydrogens how to#on the attributes of an existing atom will reveal how to do it. In the case of residue.add(atom), creating the instance is slightly problematic as there's no typehinting or :type xxx: declarations in the docstring. The end of the above rabbit hole may just add a child Entity-inheriting class instance to this list, but it also do other things that is worth keeping an eye out. In the specific case of PDB module, everything inherits Entity, which has the attribute child_list, which is what the iterators ( _iter_ is the topmost) read without making a copy. Until you find a nice constructor that declares nicely an atom instance or whatever you ever fancy searching for -that is the great thing of open source code. So parser.get_structure "magically" makes a structure, eh? This means it can add stuff! As mentioned print_code(parser.get_structure) will reveal its secrets, or within it call some self._private_fun(), which can be inspected ( self = parser) all the way down the rabbit hole. Structure : = parser.get_structure("tryp-cage", "") in the standard library module inspect is the function inspect.getsource(function), which for a notebook is messy due to newlines so needs to be print_code = lambda fun: print(inspect.getsource(fun)) and print_code(fun).type(object) or object._class_ gives you what the class is, but object._class_._mro_ tells you what it inherits.dir(object) shows all the public and magic attributes and methods -note a class will not show the instance methods. In a Jupyter Notebook or IPython shell (don't), you can do: But I thought I'd give a few pointers in how one can understand how to do something with a given Python module -teach a man to fish kind of thing.
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