Moved gromacs module from mdevaluate to pygmx

pygmx/gromacs/__init__.py

@@ -0,0 +1,64 @@
+import numpy as np
+from numpy import genfromtxt
+import itertools
+import re
+
+from .reader import XTCReader, TRRReader
+from .xtcindex import index_xtcfile
+
+def atoms_from_grofile(file):
+    """ Deprecated. Use Atoms.from_grofile"""
+    t = genfromtxt(file, skip_header=2, delimiter=(10, 5), dtype='U8', autostrip=True, skip_footer=1)
+    return t
+
+
+def _atoms_from_grofile(file):
+    t = genfromtxt(file, skip_header=2, delimiter=(5, 5, 5), dtype='U8', autostrip=True, skip_footer=1)
+    return t
+
+
+group_re = re.compile('\[ ([-+\w]+) \]')
+
+
+def load_indices(indexfile):
+    indices = {}
+    index_array = None
+    with open(indexfile) as idx_file:
+        for line in idx_file:
+            m = group_re.search(line)
+            if m is not None:
+                group_name = m.group(1)
+                index_array = indices.get(group_name, [])
+                indices[group_name] = index_array
+            else:
+                elements = line.strip().split('\t')
+                elements = [x.split(' ') for x in elements]
+                elements = itertools.chain(*elements)  # make a flat iterator
+                elements = [x for x in elements if x != '']
+                index_array += [int(x) - 1 for x in elements]
+    return indices
+
+
+def load_index(indexfile, index_names):
+    """
+    Load an indexfile, returns tuple of indices for index_names
+    """
+    index_arrays = [[] for _ in index_names]
+    index_array = []  # This array will contain all indices before the first index_group. Should be empty
+
+    with open(indexfile) as idx_file:
+        for line in idx_file:
+            if line.startswith("["):
+                for i, index in enumerate(index_names):
+                    if line.startswith("[ " + index + " ]"):
+                        index_array = index_arrays[i]
+                        break
+                    index_array = None
+            else:
+                elements = line.strip().split('\t')
+                elements = [x.split(' ') for x in elements]
+
+                elements = itertools.chain(*elements)  # make a flat iterator
+                elements = [x for x in elements if x != '']
+                index_array += [int(x) - 1 for x in elements]
+    return index_arrays