changed xtc.Trajectory class to use utilize own xdrlib and keep old s…

…cripts working

.gitignore

@@ -2,3 +2,4 @@
 *~
 build.sh
 .localhistory
+build

pmx/__init__.py

@@ -37,7 +37,7 @@
 functionality. Take a look at the example scripts.
 
 """
-__version__ = '1.0.0'
+__version__ = '1.1.0dev'
 
 PMX_VERSION = __version__
 

pmx/xdrfile.py

@@ -27,20 +27,17 @@
 #  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 #  DEALINGS IN THE SOFTWARE.
 # 
+#  Adapted by Daniel Seeliger for use in the pmx package (Aug 2015)
+#
 
 from ctypes import *
 import os.path
 
 mTrr,mNumPy=1,2
-try:
-    from numpy import *
-    from numpy.ctypeslib import ndpointer
-    auto_mode=mNumPy                 
-except:
-    auto_mode=0
+auto_mode=0
 
 
-class frame:
+class Frame:
     #variables
     #x: rvec*natoms / numpy array if installed
     #box DIM*DIM
@@ -51,6 +48,7 @@ class frame:
 
     def __init__(self,n,mode):
         #create vector for x
+		self.natoms = n
         if mode&mNumPy:
             self.x=empty((n,3),dtype=float32)
             self.box = empty((3,3),float32)
@@ -59,7 +57,48 @@ def __init__(self,n,mode):
             self.box = (c_float*3*3)()
 
 
-class xdrfile:
+    def update_box( self, box ):
+        for i in range(3):
+            for k in range(3):
+                box[i][k] = self.box[i][k]
+
+    def update_atoms( self, atom_sel ):
+        for i, atom in enumerate(atom_sel.atoms):
+            if atom_sel.unity == 'A':
+                atom.x[0] = self.x[i][0]*10
+                atom.x[1] = self.x[i][1]*10
+                atom.x[2] = self.x[i][2]*10
+            else:
+                atom.x[0] = self.x[i][0]
+                atom.x[1] = self.x[i][1]
+                atom.x[2] = self.x[i][2]
+
+    def update( self, atom_sel ):
+        self.update_atoms(atom_sel )
+        self.update_box( atom_sel.box )
+
+
+    def get_natoms(self):
+        return self.natoms
+    def get_time(self):
+        return self.time
+    def get_step(self):
+        return self.step
+    def get_prec(self):
+        return self.prec
+	def get_box(self):
+		return self.box
+
+
+    def __str__(self):
+
+        s = '< xdrlib.Frame: natoms = %d | step = %d | time = %8.2f >' % (self.get_natoms(), self.get_step(), self.get_time())
+        return s
+
+
+
+
+class XDRFile:
     exdrOK, exdrHEADER, exdrSTRING, exdrDOUBLE, exdrINT, exdrFLOAT, exdrUINT, exdr3DX, exdrCLOSE, exdrMAGIC, exdrNOMEM, exdrENDOFFILE, exdrNR = range(13)
 
     #
@@ -118,7 +157,7 @@ def __init__(self,fn,mode="Auto",ft="Auto"):
 
 
     def __iter__(self):
-        f = frame(self.natoms,self.mode)
+        f = Frame(self.natoms,self.mode)
         #temporary c_type variables (frame variables are python type)
         step = c_int()
         time = c_float()

pmx/xtc.py

@@ -28,125 +28,21 @@
 # CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 # ----------------------------------------------------------------------
 
-import sys, os
+import sys, os, xdrfile
 
-from ctypes import cdll, c_int, c_float, c_double
-from ctypes import c_char_p,POINTER,c_int,byref
 
-c_real = c_float
-rvec=c_real*3
-matrix=c_real*3*3
+class Trajectory(xdrfile.XDRFile):
+    """ changed Trajectory class to use new XDRFile class and keep old scripts working"""
 
+    def __init__(self, filename, **kwargs):
+        xdrfile.XDRFile.__init__(self, filename, **kwargs)
 
-class Trajectory:
-
-    def __init__(self, filename):
-        self.filename = filename
-        self.libgmx_path = self.__check_gmxlib()
-        self.libgmx = cdll.LoadLibrary(self.libgmx_path)
-        self.fp = None
-        self.natoms = c_int()
-        self.step = c_int()
-        self.time = c_real()
-        self.prec = c_real()
-        self.bOK = c_int()
-        self.box =  matrix()
-        self.x = POINTER(rvec)()
-        self.__have_first_frame = False
-        self.open_xtc(filename)
-        self.read_first_xtc()
-
-    def __check_gmxlib(self):
-        p = os.environ.get('GMX_DLL')
-        if not p:
-            print >> sys.stderr, "pmx_Error_> Path to Gromacs shared libraries is not set (GMX_DLL)"
-            print >> sys.stderr, "pmx_Error_> Cannot load \"libgmx.so\""
-            sys.exit(1)
-        return os.path.join(p,'libgmx.so')
-
-
-    def open_xtc(self, filename):
-	self.libgmx.open_xtc.restype = POINTER(c_char_p)
-        self.fp = self.libgmx.open_xtc(filename, "r")
-
-    def close_xtc(self):
-        self.libgmx.close_xtc(self.fp)
-
-    def read_first_xtc(self):
-
-        ret = self.libgmx.read_first_xtc(self.fp,byref(self.natoms),byref(self.step),byref(self.time),self.box,byref(self.x),byref(self.prec),byref(self.bOK))
-        if not ret:
-            print >> sys.stderr, "pmx_Error_> in Trajectory.read_first_xtc()"
-            sys.exit(1)
-        self.__have_first_frame = True
-
-    def read_next_xtc(self):
-        if not self.__have_first_frame:
-            print >> sys.stderr, "pmx_Error_> First frame not read"
-            sys.exit(1)
-        ret = self.libgmx.read_next_xtc(self.fp,self.natoms,byref(self.step),byref(self.time),self.box,self.x,byref(self.prec),byref(self.bOK))
-        return ret
-
-    def update_box( self, box ):
-        for i in range(3):
-            for k in range(3):
-                box[i][k] = self.box[i][k]
-
-    def update_atoms( self, atom_sel ):
-        assert len(atom_sel.atoms) == self.natoms.value
-        for i, atom in enumerate(atom_sel.atoms):
-            if atom_sel.unity == 'A':
-                atom.x[0] = self.x[i][0]*10
-                atom.x[1] = self.x[i][1]*10
-                atom.x[2] = self.x[i][2]*10
-            else:
-                atom.x[0] = self.x[i][0]
-                atom.x[1] = self.x[i][1]
-                atom.x[2] = self.x[i][2]
-
-    def update( self, atom_sel ):
-        self.update_atoms(atom_sel )
-        self.update_box( atom_sel.box )
-
-    def get_box(self):
-        return [
-            [self.box[0][0], self.box[0][1], self.box[0][1]],
-            [self.box[1][0], self.box[1][1], self.box[1][1]],
-            [self.box[2][0], self.box[2][1], self.box[2][1]],
-            ]
 
     def get_natoms(self):
-        return self.natoms.value
-    def get_time(self):
-        return self.time.value
-    def get_step(self):
-        return self.step.value
-    def get_prec(self):
-        return self.prec.value
-    def get_x(self, unity='nm'):
-        x = []
-        for i in range(self.get_natoms):
-            if unity == 'A':
-                x.append( [self.x[i][0]*10, self.x[i][1]*10, self.x[i][2]*10 ])
-            else:                
-                x.append( [self.x[i][0], self.x[i][1], self.x[i][2] ])
-        return x
-
-    def __str__(self):
+        return self.natoms
 
-        s = '< Trajectory: %s | natoms = %d | step = %d | time = %8.2f >' % (self.filename, self.get_natoms(), self.get_step(), self.get_time())
-        return s
-
 
-    def __iter__(self):
-        return self
 
-    def next(self):
 
-        ok = self.read_next_xtc()
-        if not ok:
-            raise StopIteration
-        return self
-
 
 

setup.py

@@ -42,9 +42,17 @@ def run(self):
 
 pmx = Extension('pmx/_pmx',
                    libraries = ['m'],
-                   include_dirs = ['src'],
-                   sources = ['src/Geometry.c','src/wrap_Geometry.c',
-                              'src/init.c', 'src/Energy.c']
+                   include_dirs = ['src/pmx'],
+                   sources = ['src/pmx/Geometry.c','src/pmx/wrap_Geometry.c',
+                              'src/pmx/init.c', 'src/pmx/Energy.c']
+
+                 )
+
+xdrio = Extension('pmx/_xdrio',
+                   libraries = ['m'],
+                   include_dirs = ['src/xdr'],
+                   sources = ['src/xdr/xdrfile.c','src/xdr/xdrfile_trr.c',
+                              'src/xdr/xdrfile_xtc.c']
 
                  )
 
@@ -58,11 +66,11 @@ def run(self):
 
 
 setup (name = 'pmx',
-       version = '1.0.0',
+       version = '1.1.0dev',
        description = 'Python Toolbox structure file editing and writing simulation setup/analysis tools',
        author = 'Daniel Seeliger',
        author_email = 'seeliger.biosoft@gmail.de',
-       url = 'http://code.google.com/p/pmx/',
+       url = 'https://github.com/dseeliger/pmx/',
        long_description = '''Tools to play with structure files, topologies, index files, xtc files, etc....''',
        packages = ['pmx'],
        data_files = [('pmx/data',['data/bbdep.pkl']),
@@ -73,7 +81,7 @@ def run(self):
                      ('pmx/data',['data/ffamber99sbnb.itp']),
                      ('pmx/data',['data/blosum62_new.mat'])
                      ],
-       ext_modules = [pmx],
+       ext_modules = [pmx,xdrio],
        cmdclass = {'install_data': install_data_files
                    },