Merge f47e09c into 558466c

pytraj/__init__.py

@@ -187,6 +187,7 @@
 from .all_actions import xcorr
 from .all_actions import ti
 from .all_actions import lipidscd
+from .all_actions import xtalsymm
 
 from .analysis.matrix import dist as distance_matrix
 from .analysis import matrix

pytraj/all_actions.py

@@ -133,6 +133,7 @@
     'rotdif',
     'ti',
     'lipidscd',
+    'xtalsymm',
 ]
 
 
@@ -3064,6 +3065,50 @@ def lipidscd(traj, mask='', options='', dtype='dict'):
     return get_data_from_dtype(c_dslist, dtype=dtype)
 
 
+@super_dispatch()
+def xtalsymm(traj, mask='', options='', ref=None, **kwargs):
+    '''
+    
+    Parameters
+    ----------
+    traj : Mutable `pytraj.Trajectory`
+    mask : str, default '' (all)
+    options : str, extra cpptraj's options
+        See `pytraj.info("xtalsymm")` for further information.
+        NOTE: Should not provide 'mask' or 'reference' in `options`, use the keyword arguments.
+    ref : Frame | Trajectory
+        Reference frame
+    kwargs : dummy key words arguments for `super_dispatch`
+
+    Examples
+    --------
+        >>> pytraj.xtalsymm(traj, mask=':1-16', ref=ref, options="group P22(1)2(1) na 2 nb 1 nc 1") # doctest: +SKIP
+    '''
+    top = traj.top
+    command = ' '.join((mask, options))
+
+    c_dslist = CpptrajDatasetList()
+
+    if ref is not None:
+        c_dslist.add('reference', name='xtalsymm_ref')
+        c_dslist[0].top = top
+        c_dslist[0].add_frame(ref)
+        command = ' '.join((command, 'reference'))
+
+    act = c_action.Action_XtalSymm()
+    act.read_input(command, top=top, dslist=c_dslist)
+    act.setup(top)
+
+    for frame in traj:
+        act.compute(frame)
+    act.post_process()
+
+    # remove ref
+    c_dslist._pop(0)
+
+    return traj
+
+
 def analyze_modes(mode_type,
                   eigenvectors,
                   eigenvalues,

pytraj/analysis/c_action/c_action.pxd

@@ -959,3 +959,13 @@ cdef extern from "Action_Watershell.h":
 cdef class Action_Watershell(Action):
     cdef _Action_Watershell* thisptr
 
+
+cdef extern from "Action_XtalSymm.h":
+    cdef cppclass _Action_XtalSymm "Action_XtalSymm" (_Action) nogil:
+        _Action_XtalSymm()
+        _DispatchObject * Alloc()
+        void Help()
+
+
+cdef class Action_XtalSymm(Action):
+    cdef _Action_XtalSymm* thisptr

pytraj/analysis/c_action/c_action.pyx

@@ -1292,3 +1292,16 @@ 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()
+        self.thisptr = <_Action_XtalSymm*> 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_xtalsymm.py

@@ -0,0 +1,25 @@
+import os
+import pytraj as pt
+from pytraj.testing import cpptraj_test_dir, aa_eq
+
+
+def test_xtalsymm(tmpdir):
+    with tmpdir.as_cwd():
+        x6dky_parm = os.path.join(cpptraj_test_dir, 'x6dky.parm7')
+        x6dky_tname = os.path.join(cpptraj_test_dir, 'mdXtal.nc')
+        x6dky_refname = os.path.join(cpptraj_test_dir, 'mdXtal.inpcrd')
+        state = pt.load_cpptraj_state(
+        """
+        parm {parm}
+        trajin {trajin}
+        reference {reference}
+        xtalsymm :1-16 reference group P22(1)2(1) na 2 nb 1 nc 1
+        trajout mdAsuOnly.pdb
+        """.format(parm=x6dky_parm, trajin=x6dky_tname, reference=x6dky_refname))
+        state.run()
+
+        traj = pt.load(x6dky_tname, x6dky_parm)
+        ref = pt.load(x6dky_refname, traj.top)
+        pt.xtalsymm(traj, mask=':1-16', ref=ref, options="group P22(1)2(1) na 2 nb 1 nc 1")
+        c_traj = pt.load('mdAsuOnly.pdb')
+        aa_eq(traj.xyz, c_traj.xyz, decimal=2)