Add multipucker action
hainm opened this issue · comments
Please see the pucker function here:
Lines 2244 to 2294 in 6d62181
| @register_pmap | |
| def pucker(traj=None, | |
| pucker_mask=("C1'", "C2'", "C3'", "C4'", "O4'"), | |
| resrange=None, | |
| top=None, | |
| dtype='dataset', | |
| range360=False, | |
| method='altona', | |
| use_com=True, | |
| amplitude=False, | |
| offset=None): | |
| """compute pucker | |
| Parameters | |
| ---------- | |
| traj : Trajectory-like | |
| pucker_mask : str | |
| resrange : None or array of int | |
| top : Topology, optional | |
| dtype : str, return type | |
| range360: bool, use 360 or 180 scale | |
| method : {'altona', 'cremer'}, default 'altona' | |
| use_com : bool | |
| amplitude : bool, default False | |
| offset : None or float | |
| Returns | |
| ------- | |
| Dataset | |
| """ | |
| top_ = get_topology(traj, top) | |
| if resrange is None: | |
| resrange = range(top_.n_residues) | |
| _range360 = "range360" if range360 else "" | |
| geom = "geom" if not use_com else "" | |
| amp = "amplitude" if amplitude else "" | |
| offset_ = "offset " + str(offset) if offset else "" | |
| c_dslist = CpptrajDatasetList() | |
| for res in resrange: | |
| command = " ".join((":" + str(res + 1) + '@' + x for x in pucker_mask)) | |
| name = "pucker_res" + str(res + 1) | |
| command = " ".join((name, command, _range360, method, geom, amp, | |
| offset_)) | |
| act = c_action.Action_Pucker() | |
| act(command, traj, top=top_, dslist=c_dslist) | |
| return get_data_from_dtype(c_dslist, dtype) |
You could do similar to multipucker