Add simple xyz reader (#423)

* Add simple xyz reader

* Remove old code

* Small pep8 fix

* Add io test

* Allow python2 compatability

* Various fixes

* Rework test with topology

* Clean up test

* Add a test for the case of an incorrect number of atoms

* Attempt to handle the case of an incorrect number of atoms

* Handle and test two cases of incorrect n_atoms

* Switch to raising MBuildError

* Add xyz to manifest

MANIFEST.in

@@ -1 +1 @@
-global-include *.pdb *.mol2 *.smi *.xml
+global-include *.pdb *.mol2 *.smi *.xml *.xyz

mbuild/compound.py

@@ -22,6 +22,7 @@
 from mbuild.bond_graph import BondGraph
 from mbuild.box import Box
 from mbuild.exceptions import MBuildError
+from mbuild.formats.xyz import read_xyz
 from mbuild.formats.hoomdxml import write_hoomdxml
 from mbuild.formats.lammpsdata import write_lammpsdata
 from mbuild.formats.gsdwriter import write_gsd
@@ -78,6 +79,12 @@ def load(filename, relative_to_module=None, compound=None, coords_only=False,
     if compound is None:
         compound = Compound()
 
+    # Handle the case of a xyz file, which must use an internal reader
+    extension = os.path.splitext(filename)[-1]
+    if extension == '.xyz' and not 'top' in kwargs:
+        compound = read_xyz(filename)
+        return compound
+
     if use_parmed:
         warn("use_parmed set to True.  Bonds may be inferred from inter-particle "
              "distances and standard residue templates!")

mbuild/formats/xyz.py

@@ -0,0 +1,62 @@
+import numpy as np
+
+import mbuild as mb
+from mbuild.exceptions import MBuildError
+
+__all__ = ['read_xyz']
+
+
+def read_xyz(filename):
+    """Read an XYZ file. The expected format is as follows:
+    The first line contains the number of atoms in the file The second line
+    contains a comment, which is not read.  Remaining lines, one for each
+    atom in the file, include an elemental symbol followed by X, Y, and Z
+    coordinates in Angstroms. Columns are expected tbe separated by
+    whitespace. See https://openbabel.org/wiki/XYZ_(format).
+
+    Parameters
+    ----------
+    filename : str
+        Path of the input file
+
+    Returns
+    -------
+    compound : mb.Compound
+
+    Notes
+    -----
+    The XYZ file format neglects many important details, notably as bonds,
+    residues, and box information.
+
+    There are some other flavors of the XYZ file format and not all are
+    guaranteed to be compatible with this reader. For example, the TINKER
+    XYZ format is not expected to be properly read.
+    """
+
+    compound = mb.Compound()
+
+    with open(filename, 'r') as xyz_file:
+        n_atoms = int(xyz_file.readline())
+        xyz_file.readline()
+        coords = np.zeros(shape=(n_atoms, 3), dtype=np.float64)
+        for row, _ in enumerate(coords):
+            line = xyz_file.readline().split()
+            if not line:
+                msg = ('Incorrect number of lines in input file. Based on the '
+                       'number in the first line of the file, {} rows of atoms '
+                       'were expected, but at least one fewer was found.')
+                raise MBuildError(msg.format(n_atoms))
+            coords[row] = line[1:4]
+            coords[row] *= 0.1
+            particle = mb.Compound(pos=coords[row], name=line[0])
+            compound.add(particle)
+
+        # Verify we have read the last line by ensuring the next line in blank
+        line = xyz_file.readline().split()
+        if line:
+            msg = ('Incorrect number of lines in input file. Based on the '
+                   'number in the first line of the file, {} rows of atoms '
+                   'were expected, but at least one more was found.')
+            raise MBuildError(msg.format(n_atoms))
+
+    return compound

mbuild/tests/test_xyz.py

@@ -0,0 +1,30 @@
+import numpy as np
+import pytest
+
+import mbuild as mb
+from mbuild.utils.io import get_fn
+from mbuild.tests.base_test import BaseTest
+from mbuild.exceptions import MBuildError
+
+
+class TestXYZ(BaseTest):
+    def test_load_no_top(self, ethane):
+        ethane.save(filename='ethane.xyz')
+        ethane_in = mb.load('ethane.xyz')
+        assert len(ethane_in.children) == 8
+        assert ethane_in.n_bonds == 0
+        assert set([child.name for child in ethane_in.children]) == {'C', 'H'}
+
+    def test_load_with_top(self, ethane):
+        ethane.save(filename='ethane.xyz')
+        ethane.save(filename='ethane.mol2')
+        ethane_in = mb.load('ethane.xyz', top='ethane.mol2')
+        assert len(ethane_in.children) == 8
+        assert ethane_in.n_bonds == 7
+        assert set([child.name for child in ethane_in.children]) == {'C', 'H'}
+
+    def test_wrong_n_atoms(self):
+        with pytest.raises(MBuildError):
+            mb.load(get_fn('too_few_atoms.xyz'))
+        with pytest.raises(MBuildError):
+            mb.load(get_fn('too_many_atoms.xyz'))

mbuild/utils/reference/too_few_atoms.xyz

@@ -0,0 +1,10 @@
+10
+Created with MDTraj 1.8.0, 2018-05-09
+C    0.000   -1.400   -0.000
+H   -1.070   -1.400    0.000
+H    0.357   -2.169    0.653
+H    0.357   -1.581   -0.993
+C    0.000    0.000    0.000
+H    1.070    0.000    0.000
+H   -0.357    0.769    0.653
+H   -0.357    0.181   -0.993

mbuild/utils/reference/too_many_atoms.xyz

@@ -0,0 +1,10 @@
+6
+Created with MDTraj 1.8.0, 2018-05-09
+C    0.000   -1.400   -0.000
+H   -1.070   -1.400    0.000
+H    0.357   -2.169    0.653
+H    0.357   -1.581   -0.993
+C    0.000    0.000    0.000
+H    1.070    0.000    0.000
+H   -0.357    0.769    0.653
+H   -0.357    0.181   -0.993