WIP: multipucker

pytraj/__init__.py

@@ -188,6 +188,7 @@
 from .all_actions import ti
 from .all_actions import lipidscd
 from .all_actions import xtalsymm
+from .all_actions import multipucker
 from .all_actions import hausdorff
 from .all_actions import permute_dihedrals
 

pytraj/all_actions.py

@@ -133,6 +133,7 @@
     'ti',
     'lipidscd',
     'xtalsymm',
+    'multipucker',
     'hausdorff',
     'permute_dihedrals',
 ]
@@ -3114,6 +3115,21 @@ def xtalsymm(traj, mask='', options='', ref=None, **kwargs):
     return traj
 
 
+@super_dispatch()
+def multipucker(traj, options='', dtype='dict', top=None, frame_indices=None):
+    '''
+
+    Parameters
+    ----------
+    traj : Trajectory-like
+    options : str, cpptraj's options
+        See `pytraj.info("multipucker")` for further information.
+    '''
+    command = options
+    c_dslist, _ = do_action(traj, command, c_action.Action_MultiPucker)
+    return get_data_from_dtype(c_dslist, dtype=dtype)
+
+
 def analyze_modes(mode_type,
                   eigenvectors,
                   eigenvalues,

pytraj/analysis/c_action/c_action.pxd

@@ -972,3 +972,14 @@ cdef extern from "Action_XtalSymm.h":
 
 cdef class Action_XtalSymm(Action):
     cdef _Action_XtalSymm* thisptr
+
+
+cdef extern from "Action_MultiPucker.h":
+    cdef cppclass _Action_MultiPucker "Action_MultiPucker" (_Action) nogil:
+        _Action_MultiPucker()
+        _DispatchObject * Alloc()
+        void Help()
+
+
+cdef class Action_MultiPucker(Action):
+    cdef _Action_MultiPucker* thisptr

pytraj/analysis/c_action/c_action.pyx

@@ -1280,6 +1280,7 @@ cdef class Action_Volume(Action):
     def help(self):
         self.thisptr.Help()
 
+
 cdef class Action_Watershell(Action):
     def __cinit__(self):
         self.baseptr = <_Action*> new _Action_Watershell()
@@ -1293,6 +1294,7 @@ cdef class Action_Watershell(Action):
     def help(self):
         self.thisptr.Help()
 
+
 cdef class Action_XtalSymm(Action):
     def __cinit__(self):
         self.baseptr = <_Action*> new _Action_XtalSymm()
@@ -1305,3 +1307,17 @@ cdef class Action_XtalSymm(Action):
 
     def help(self):
         self.thisptr.Help()
+
+
+cdef class Action_MultiPucker(Action):
+    def __cinit__(self):
+        self.baseptr = <_Action*> new _Action_MultiPucker()
+        self.thisptr = <_Action_MultiPucker*> self.baseptr
+        self.own_memory = True
+
+    def __dealloc__(self):
+        if self.baseptr is not NULL and self.own_memory:
+            del self.baseptr
+
+    def help(self):
+        self.thisptr.Help()

tests/test_analysis/test_multipucker.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python
+
+import unittest
+import pytraj as pt
+from utils import fn
+from pytraj.testing import aa_eq
+
+cm = '''
+multipucker
+'''
+
+def test_multipucker():
+    traj = pt.iterload(fn('Test_NAstruct/adh026.3.pdb'))
+    state = pt.load_cpptraj_state(cm, traj)
+    state.run()
+
+    print(state.data[1:])
+
+    data = pt.multipucker(traj)
+    print(data)

tests/test_analysis/test_pucker.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-from __future__ import print_function
 import unittest
 import pytraj as pt
 from utils import fn
@@ -16,24 +15,16 @@
 '''
 
 
-class TestPucker(unittest.TestCase):
-    '''TestPucker
-    '''
+def test_pucker():
+    traj = pt.iterload(fn('Test_NAstruct/adh026.3.pdb'))
+    state = pt.load_cpptraj_state(cm, traj)
+    state.run()
 
-    def test_pucker(self):
-        traj = pt.iterload(fn('Test_NAstruct/adh026.3.pdb'))
-        state = pt.load_cpptraj_state(cm, traj)
-        state.run()
+    data_altona = pt.pucker(traj, resrange=range(3))
+    data_cremer = pt.pucker(traj, resrange=range(3), method='cremer')
+    aa_eq(data_altona.values, state.data[1:4].values)
+    aa_eq(data_cremer.values, state.data[4:].values)
 
-        data_altona = pt.pucker(traj, resrange=range(3))
-        data_cremer = pt.pucker(traj, resrange=range(3), method='cremer')
-        aa_eq(data_altona.values, state.data[1:4].values)
-        aa_eq(data_cremer.values, state.data[4:].values)
-
-        # resrange=None
-        data_full_residues = pt.pucker(traj, resrange=None)
-        aa_eq(data_full_residues[:3].values, data_altona[:3].values)
-
-
-if __name__ == "__main__":
-    unittest.main()
+    # resrange=None
+    data_full_residues = pt.pucker(traj, resrange=None)
+    aa_eq(data_full_residues[:3].values, data_altona[:3].values)

tests/test_io/test_io.py

@@ -444,8 +444,8 @@ def add_velocity(traj):
             for frame in add_velocity(traj):
                 writer.write(frame)
         traj2 = pt.iterload(out_fn, top=traj.top)
-        assert traj2.metadata['has_velocity']
-        assert not traj2.metadata['has_force']
+        assert traj2.crdinfo['has_velocity']
+        assert not traj2.crdinfo['has_force']
         # make sure no segmentation fault
         # issues/1486
         assert traj2[:].n_frames == traj2.n_frames
@@ -469,8 +469,8 @@ def add_force(traj):
             for frame in add_force(traj):
                 writer.write(frame)
         traj2 = pt.iterload(out_fn, top=traj.top)
-        assert traj2.metadata['has_force']
-        assert not traj2.metadata['has_velocity']
+        assert traj2.crdinfo['has_force']
+        assert not traj2.crdinfo['has_velocity']
         # issues/1486
         assert traj2[:].n_frames == traj2.n_frames
 
@@ -498,24 +498,24 @@ def add_force_and_velocity(traj):
             for frame in add_force_and_velocity(traj):
                 writer.write(frame)
         traj2 = pt.iterload(out_fn, top=traj.top)
-        assert traj2.metadata['has_force']
-        assert traj2.metadata['has_velocity']
+        assert traj2.crdinfo['has_force']
+        assert traj2.crdinfo['has_velocity']
 
 
 def test_write_force_and_velocity():
     trajin = cpptraj_test_dir + '/Test_systemVF/systemVF.nc'
     tn = cpptraj_test_dir + '/Test_systemVF/systemVF.parm7'
     traj = pt.iterload(trajin, tn)
-    assert traj.metadata['has_force']
-    assert traj.metadata['has_velocity']
+    assert traj.crdinfo['has_force']
+    assert traj.crdinfo['has_velocity']
 
     with tempfolder():
         fn2 = 'test.nc'
-        traj.save(fn2, overwrite=True, crdinfo=traj.metadata)
+        traj.save(fn2, overwrite=True, crdinfo=traj.crdinfo)
 
         traj2 = pt.iterload(fn2, traj.top)
-        assert traj2.metadata['has_force']
-        assert traj2.metadata['has_velocity']
+        assert traj2.crdinfo['has_force']
+        assert traj2.crdinfo['has_velocity']
 
         forces_traj = np.array([frame.force.copy() for frame in traj])
         forces_traj2 = np.array([frame.force.copy() for frame in traj2])