def test_actionlist(self): '''test_actionlist ''' dslist = DatasetList() actlist = ActionList() traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top") mask_list = ['@CB @CA', '@CA @H'] for mask in mask_list: actlist.add(CA.Action_Vector(), mask, traj.top, dslist=dslist) actlist.compute(traj) dslist2 = pt.calc_vector(traj, mask_list) dslist4 = va.vector_mask(traj, mask_list) dslist3_0 = pt.calc_vector(traj, mask_list[0]) dslist3_1 = pt.calc_vector(traj, mask_list[1]) aa_eq(dslist3_0, dslist2[0]) aa_eq(dslist3_1, dslist2[1]) aa_eq(dslist3_0, dslist4[0]) aa_eq(dslist3_1, dslist4[1]) aa_eq(dslist3_0, dslist[0].values) aa_eq(dslist3_1, dslist[1].values)
def test_constructor_from_command_list_Trajectory(self): '''mutable Trajectory''' # use `load` method rather `iterload` traj = pt.load(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7")) # make sure no space-sensitivity # make the code (commands) ugly is my intention. commands = [ 'autoimage ', 'autoimage', 'rmsd @CA', 'distance :3 :7', 'distance :3 :7', 'vector :2 :3', ' distance :3 :7', 'rms @C,N,O', ] dslist = CpptrajDatasetList() actlist = ActionList(commands, traj.top, dslist=dslist) for frame in traj: actlist.compute(frame) aa_eq(pt.rmsd(traj, mask='@CA'), dslist[0]) aa_eq(pt.distance(traj, ':3 :7'), dslist[1]) aa_eq(pt.distance(traj, ':3 :7'), dslist[2]) # do not need to perform rmsfit again. aa_eq(pt.vector.vector_mask(traj, ':2 :3'), dslist[3].values) aa_eq(pt.distance(traj, ':3 :7'), dslist[4]) aa_eq(pt.rmsd(traj, mask='@C,N,O'), dslist[5])
def test_constructor_from_command_list_Trajectory(self): '''mutable Trajectory''' # use `load` method rather `iterload` traj = pt.load("data/tz2.ortho.nc", "data/tz2.ortho.parm7") # make sure no space-sensitivity # make the code (commands) ugly is my intention. commands = [ 'autoimage ', 'autoimage', 'rmsd @CA', 'distance :3 :7', 'distance :3 :7', 'vector :2 :3', ' distance :3 :7', 'rms @C,N,O', ] dslist = CpptrajDatasetList() actlist = ActionList(commands, traj.top, dslist=dslist) for frame in traj: actlist.compute(frame) aa_eq(pt.rmsd(traj, mask='@CA'), dslist[0]) aa_eq(pt.distance(traj, ':3 :7'), dslist[1]) aa_eq(pt.distance(traj, ':3 :7'), dslist[2]) # do not need to perform rmsfit again. aa_eq(pt.vector.vector_mask(traj, ':2 :3'), dslist[3].values) aa_eq(pt.distance(traj, ':3 :7'), dslist[4]) aa_eq(pt.rmsd(traj, mask='@C,N,O'), dslist[5])
def test_actionlist(self): '''test_actionlist ''' dslist = DatasetList() actlist = ActionList() traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top") mask_list = ['@CB @CA', '@CA @H'] for mask in mask_list: actlist.add(CA.Action_Vector(), mask, traj.top, dslist=dslist) actlist.compute(traj) dslist2 = pt.calc_vector(traj, mask_list) dslist4 = va.vector_mask(traj, mask_list) dslist3_0 = pt.calc_vector(traj, mask_list[0]) dslist3_1 = pt.calc_vector(traj, mask_list[1]) aa_eq(dslist3_0, dslist2[0]) aa_eq(dslist3_1, dslist2[1]) aa_eq(dslist3_0, dslist4[0]) aa_eq(dslist3_1, dslist4[1]) aa_eq(dslist3_0, dslist[0].values) aa_eq(dslist3_1, dslist[1].values)
def test_run_0(self): # load traj farray = pt.load(filename="./data/tz2.truncoct.nc", top="./data/tz2.truncoct.parm7")[:2] fold = farray.copy() act = allactions.Action_Image() ptrajin = """ center :2-11 image center familiar com :6 """ # create 'strip' action stripact = allactions.Action_Strip() # creat datasetlist to hold distance data dsetlist = CpptrajDatasetList() dflist = DataFileList() # creat ActionList to hold actions alist = ActionList() top = farray.top # add two actions: Action_Strip and Action_Distance alist.add(allactions.Action_Center(), ArgList(":2-11"), top=top) alist.add(allactions.Action_Image(), ArgList("center familiar com :6"), top=top) # do checking alist.check_topology(top) farray2 = Trajectory() frame0 = Frame() # testing how fast to do the actions # loop all frames # use iterator to make faster loop # don't use "for i in range(farray.n_frames)" for frame in farray: # perform actions for each frame # we make a copy since we want to keep orginal Frame frame0 = frame.copy() alist.compute(frame0) # we need to keep the modified frame in farray2 farray2.append(frame0) # make sure that Action_Strip does its job in stripping assert farray2.n_frames == farray.n_frames fsaved = pt.iterload(cpptraj_test_dir + "/Test_Image/image4.crd.save", "data/tz2.truncoct.parm7") assert fsaved.n_frames == 2
def test_run_0(self): # load traj farray = pt.load(filename="./data/tz2.truncoct.nc", top="./data/tz2.truncoct.parm7")[:2] fold = farray.copy() act = allactions.Action_Image() ptrajin = """ center :2-11 image center familiar com :6 """ # create 'strip' action stripact = allactions.Action_Strip() # creat datasetlist to hold distance data dsetlist = CpptrajDatasetList() dflist = DataFileList() # creat ActionList to hold actions alist = ActionList() top = farray.top # add two actions: Action_Strip and Action_Distance alist.add(allactions.Action_Center(), ArgList(":2-11"), top=top) alist.add(allactions.Action_Image(), ArgList("center familiar com :6"), top=top) # do checking alist.check_topology(top) farray2 = Trajectory() frame0 = Frame() # testing how fast to do the actions # loop all frames # use iterator to make faster loop # don't use "for i in range(farray.n_frames)" for frame in farray: # perform actions for each frame # we make a copy since we want to keep orginal Frame frame0 = frame.copy() alist.compute(frame0) # we need to keep the modified frame in farray2 farray2.append(frame0) # make sure that Action_Strip does its job in stripping assert farray2.n_frames == farray.n_frames fsaved = pt.iterload(cpptraj_test_dir + "/Test_Image/image4.crd.save", "data/tz2.truncoct.parm7") assert fsaved.n_frames == 2
def test_run_5(self): traj = pt.iterload(tc5b_trajin, tc5b_top) mask_list = ('@CB @CA', '@CA @H') dslist = CpptrajDatasetList() actlist = ActionList() for mask in mask_list: actlist.add(CA.Action_Distance(), mask, traj.top, dslist=dslist) actlist.compute(traj) dslist2 = pt.calc_distance(traj, mask_list) aa_eq(dslist.values, dslist2)
def test_rmsd_actlist(input_traj): from pytraj.analysis.c_action.c_action import Action_Rmsd from pytraj import ActionList from pytraj.datasets import DatasetList alist = ActionList() dslist = DatasetList() act = Action_Rmsd() alist.add(act, 'first @CA', top=input_traj.top, dslist=dslist) for frame in input_traj: alist.compute(frame) return (dslist.values)
def test_run_2(self): # load traj traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top") dslist = CpptrajDatasetList() dflist = DataFileList() # creat ActionList to hold actions alist = ActionList() alist.add(adict['distance'], ":2@CA :10@CA out ./output/_dist.out", traj.top, dslist, dflist) alist.compute([traj.iterchunk()]) print('dslist', dslist[0].size) assert len(dslist) == 1 assert dslist[0].size == traj.n_frames
def test_run_2(self): # load traj traj = pt.iterload(tc5b_trajin, tc5b_top) dslist = CpptrajDatasetList() dflist = DataFileList() # creat ActionList to hold actions alist = ActionList() alist.add(adict['distance'], ":2@CA :10@CA out _dist.out", traj.top, dslist, dflist) with tempfolder(): alist.compute([traj.iterchunk()]) assert len(dslist) == 1 assert dslist[0].size == traj.n_frames
def test_run_2(self): # load traj traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top") dslist = CpptrajDatasetList() dflist = DataFileList() # creat ActionList to hold actions alist = ActionList() alist.add(adict['distance'], ":2@CA :10@CA out ./output/_dist.out", traj.top, dslist, dflist) alist.compute([traj.iterchunk()]) print('dslist', dslist[0].size) assert len(dslist) == 1 assert dslist[0].size == traj.n_frames
def test_run_5(self): traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top") mask_list = ('@CB @CA', '@CA @H') dslist = CpptrajDatasetList() actlist = ActionList() for mask in mask_list: actlist.add(CA.Action_Distance(), mask, traj.top, dslist=dslist) actlist.compute(traj) dslist2 = pt.calc_distance(traj, mask_list) aa_eq(dslist.values, dslist2)
def test_rmsd_actlist(input_traj): from pytraj.c_action.c_action import Action_Rmsd from pytraj import ActionList from pytraj.datasets import DatasetList alist = ActionList() dslist = DatasetList() act = Action_Rmsd() alist.add(act, 'first @CA', top=input_traj.top, dslist=dslist) for frame in input_traj: alist.compute(frame) return (dslist.values)
def test_constructor_from_command_list_TrajectoryIterator_no_DatasetList( self): traj = pt.iterload(tc5b_trajin, tc5b_top) commands = [ 'rmsd @CA', 'distance :3 :7', 'distance :3 :7', 'vector :2 :3' ] actlist = ActionList(commands, top=traj.top) for frame in traj: actlist.compute(frame) aa_eq(pt.rmsd(traj, mask='@CA'), actlist.data[0]) aa_eq(pt.distance(traj, ':3 :7'), actlist.data[1]) aa_eq(pt.distance(traj, ':3 :7'), actlist.data[2]) aa_eq(pt.vector.vector_mask(traj(rmsfit=(0, '@CA')), ':2 :3'), actlist.data[3].values)
def test_run_3(self): dslist = CpptrajDatasetList() actlist = ActionList() traj = pt.iterload(tc5b_trajin, tc5b_top) mask_list = ['@CB @CA @N', '@CA @H @N'] for mask in mask_list: actlist.add(CA.Action_Angle(), mask, traj.top, dslist=dslist) actlist.compute(traj) pt.calc_angle(traj, mask_list) dslist3_0 = pt.calc_angle(traj, mask_list[0]) dslist3_1 = pt.calc_angle(traj, mask_list[1]) aa_eq(dslist3_0, dslist[0].to_ndarray()) aa_eq(dslist3_1, dslist[1].to_ndarray()) aa_eq(dslist3_0, dslist[0].to_ndarray()) aa_eq(dslist3_1, dslist[1].to_ndarray())
def test_modify_frame(self): traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7") dslist = CpptrajDatasetList() dslist.add_new('topology', name='mytop') # add a new topology dslist[0].data = pt.strip(traj.top, ':WAT') commands = ['autoimage', 'strip :WAT', 'createcrd mycrd', ] actlist = ActionList(commands, top=traj.top, dslist=dslist) for frame in traj: actlist.compute(frame) aa_eq(dslist['mycrd'].xyz, pt.get_coordinates(traj, mask='!:WAT', autoimage=True))
def test_run_4(self): dslist = CpptrajDatasetList() actlist = ActionList() traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top") mask_list = ['@CB @CA @N @H', '@CA @H @N @H='] for mask in mask_list: actlist.add(CA.Action_Dihedral(), mask, traj.top, dslist=dslist) actlist.compute(traj) dslist2 = pt.calc_dihedral(traj, mask_list) dslist3_0 = pt.calc_dihedral(traj, mask_list[0]) dslist3_1 = pt.calc_dihedral(traj, mask_list[1]) aa_eq(dslist3_0, dslist2[0]) aa_eq(dslist3_1, dslist2[1]) aa_eq(dslist3_0, dslist[0].to_ndarray()) aa_eq(dslist3_1, dslist[1].to_ndarray())
def test_modify_frame(self): traj = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7")) dslist = CpptrajDatasetList() dslist.add('topology', name='mytop') # add a new topology dslist[0].data = pt.strip(traj.top, ':WAT') commands = [ 'autoimage', 'strip :WAT', 'createcrd mycrd', ] actlist = ActionList(commands, top=traj.top, dslist=dslist) for frame in traj: actlist.compute(frame) aa_eq(dslist['mycrd'].xyz, pt.get_coordinates(traj, mask='!:WAT', autoimage=True))
def test_constructor_from_command_list_TrajectoryIterator_no_DatasetList( self): traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top") commands = ['rmsd @CA', 'distance :3 :7', 'distance :3 :7', 'vector :2 :3'] actlist = ActionList(commands, top=traj.top) for frame in traj: actlist.compute(frame) aa_eq(pt.rmsd(traj, mask='@CA'), actlist.data[0]) aa_eq(pt.distance(traj, ':3 :7'), actlist.data[1]) aa_eq(pt.distance(traj, ':3 :7'), actlist.data[2]) aa_eq( pt.vector.vector_mask( traj(rmsfit=(0, '@CA')), ':2 :3'), actlist.data[3].values)
def test_constructor_from_command_list_TrajectoryIterator(self): traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top") commands = [ 'rmsd @CA', 'distance :3 :7', 'distance :3 :7', 'vector :2 :3' ] dslist = CpptrajDatasetList() actlist = ActionList(commands, traj.top, dslist=dslist) d0 = dslist.add('ref_frame', 'my_ref') d0.add_frame(traj[3]) for frame in traj: actlist.compute(frame) aa_eq(pt.rmsd(traj, mask='@CA'), dslist[0]) aa_eq(pt.distance(traj, ':3 :7'), dslist[1]) aa_eq(pt.distance(traj, ':3 :7'), dslist[2]) aa_eq(pt.vector.vector_mask(traj(rmsfit=(0, '@CA')), ':2 :3'), dslist[3].values)
def test_run_4(self): dslist = CpptrajDatasetList() actlist = ActionList() traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top") mask_list = ['@CB @CA @N @H', '@CA @H @N @H='] for mask in mask_list: actlist.add(CA.Action_Dihedral(), mask, traj.top, dslist=dslist) actlist.compute(traj) dslist2 = pt.calc_dihedral(traj, mask_list) dslist3_0 = pt.calc_dihedral(traj, mask_list[0]) dslist3_1 = pt.calc_dihedral(traj, mask_list[1]) aa_eq(dslist3_0, dslist2[0]) aa_eq(dslist3_1, dslist2[1]) aa_eq(dslist3_0, dslist[0].to_ndarray()) aa_eq(dslist3_1, dslist[1].to_ndarray())
def test_constructor_from_command_list_TrajectoryIterator(self): traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top") commands = ['rmsd @CA', 'distance :3 :7', 'distance :3 :7', 'vector :2 :3'] dslist = CpptrajDatasetList() actlist = ActionList(commands, traj.top, dslist=dslist) d0 = dslist.add('ref_frame', 'my_ref') d0.add_frame(traj[3]) for frame in traj: actlist.compute(frame) aa_eq(pt.rmsd(traj, mask='@CA'), dslist[0]) aa_eq(pt.distance(traj, ':3 :7'), dslist[1]) aa_eq(pt.distance(traj, ':3 :7'), dslist[2]) aa_eq( pt.vector.vector_mask( traj(rmsfit=(0, '@CA')), ':2 :3'), dslist[3].values)