More topology handling.

pygmx/topology.pxd

@@ -1,4 +1,6 @@
 
+from libc.stdio cimport FILE
+
 from utility cimport *
 from math cimport *
 from mdtypes cimport *
@@ -60,11 +62,32 @@ cdef extern from "gromacs/topology/block.h":
         pass
 
 cdef extern from "gromacs/topology/idef.h":
-  ctypedef struct t_ilist:
+    ctypedef struct t_ilist:
-    pass
+        pass
 
-  ctypedef struct gmx_ffparams_t:
+    cdef enum t_ft_enum:
-    pass
+        F_LJ
+
+    ctypedef union t_iparams:
+        pass
+
+    ctypedef int t_functype
+
+    ctypedef struct gmx_cmap_t:
+        pass
+
+    ctypedef struct gmx_ffparams_t:
+        int         ntypes;
+        int         atnr;
+        t_functype *functype;
+        t_iparams  *iparams;
+        double      reppow;    # The repulsion power for VdW: C12*r^-reppow   */
+        real        fudgeQQ;   # The scaling factor for Coulomb 1-4: f*q1*q2  */
+        gmx_cmap_t  cmap_grid; # The dihedral correction maps                 */
+
+
+    void pr_ffparams(FILE *fp, int indent, const char *title,
+                     const gmx_ffparams_t *ffparams, gmx_bool bShowNumbers)
 
 cdef extern from "gromacs/topology/topology.h":
     ctypedef struct gmx_moltype_t:

pygmx/tpxio.pyx

@@ -102,6 +102,17 @@ cdef open_tpx(const char* filename, t_inputrec *ir, matrix box, int *natoms, gmx
     stdio.setbuf(stdio.stderr, NULL)
     return return_code
 
+
+cdef read_ffparams(gmx_ffparams_t *ffparams, gmx_bool bShowNumbers):
+    cdef char buffer[stdio.BUFSIZ]
+    stdio.setbuf(stdio.stdout, buffer)
+    pr_ffparams(stdio.stdout, 0, '', ffparams, bShowNumbers)
+    stdio.fflush(stdio.stderr)
+    stdio.fseek(stdio.stderr, 0, stdio.SEEK_END)
+    stdio.setbuf(stdio.stderr, NULL)
+    return buffer
+
+
 cdef class TPXReader:
     cdef:
         t_tpxheader header
@@ -202,12 +213,15 @@ cdef class TPXReader:
     @property
     def nstxout_compressed(self):
         return self.input_record.nstxout_compressed
-        
+
     @property
     def nstenergy(self):
         return self.input_record.nstenergy
 
 
+    def read_ff(self):
+        return read_ffparams(&self.topology.ffparams, True)
+
     def __cinit__(self, filename):
         filename = cstr(filename)
 

setup.py

@@ -22,11 +22,11 @@ if 'gromacs' in os.environ.get('LD_LIBRARY_PATH', ''):
         if 'gromacs' in p:
             library_dirs.append(p)
             lib = p
-    gmx_root = lib.split('lib')[0]
+            gmx_root = lib.split('lib')[0]
-    include = os.path.join(gmx_root, 'include')
+            include = os.path.join(gmx_root, 'include')
-    if os.path.exists(include):
+            if os.path.exists(include):
-        include_dirs.append(include)
+                include_dirs.append(include)
-        check_header_version(include)
+                check_header_version(include)
 
 extensions = [
     Extension(