Issue 1395 gro resid truncate

package/CHANGELOG

@@ -13,13 +13,14 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-mm/dd/yy
+mm/dd/17
 
-  * 0.16.2
+  * 0.16.2 richardjgowers
 
 Enhancements
 
 Fixes
+  * fixed GROWriter truncating long resids from the wrong end (Issue #1395)
 
 Changes
 

package/MDAnalysis/coordinates/CRD.py

@@ -251,9 +251,9 @@ def write(self, selection, frame=None):
                     current_resid += 1
 
                 # Truncate numbers
-                serial = int(str(i + 1)[-serial_len:])
-                resid = int(str(resid)[-resid_len:])
-                current_resid = int(str(current_resid)[-totres_len:])
+                serial = util.ltruncate_int(i + 1, serial_len)
+                resid = util.ltruncate_int(resid, resid_len)
+                current_resid = util.ltruncate_int(current_resid, totres_len)
 
                 crd.write(at_fmt.format(
                     serial=serial, totRes=current_resid, resname=resname,

package/MDAnalysis/coordinates/GRO.py

@@ -377,8 +377,8 @@ def write(self, obj):
             # all attributes could be infinite cycles!
             for atom_index, resid, resname, name in zip(
                     range(ag_or_ts.n_atoms), resids, resnames, names):
-                truncated_atom_index = int(str(atom_index + 1)[-5:])
-                truncated_resid = int(str(resid)[:5])
+                truncated_atom_index = util.ltruncate_int(atom_index + 1, 5)
+                truncated_resid = util.ltruncate_int(resid, 5)
                 if has_velocities:
                     output_gro.write(self.fmt['xyz_v'].format(
                         resid=truncated_resid,

package/MDAnalysis/coordinates/PDB.py

@@ -902,12 +902,12 @@ def get_attr(attrname, default):
 
         for i, atom in enumerate(atoms):
             vals = {}
-            vals['serial'] = int(str(i + 1)[-5:])  # check for overflow here?
+            vals['serial'] = util.ltruncate_int(i + 1, 5)  # check for overflow here?
             vals['name'] = self._deduce_PDB_atom_name(atomnames[i], resnames[i])
             vals['altLoc'] = altlocs[i][:1]
             vals['resName'] = resnames[i][:4]
             vals['chainID'] = segids[i][:1]
-            vals['resSeq'] = int(str(resids[i])[-4:])
+            vals['resSeq'] = util.ltruncate_int(resids[i], 4)
             vals['iCode'] = icodes[i][:1]
             vals['pos'] = pos[i]  # don't take off atom so conversion works
             vals['occupancy'] = occupancies[i]

package/MDAnalysis/coordinates/PDBQT.py

@@ -320,12 +320,12 @@ def write(self, selection, frame=None):
                     attrs['resids'], attrs['icodes'], attrs['occupancies'],
                     attrs['tempfactors'], attrs['charges'], attrs['types']),
                          start=1):
-            serial = int(str(serial)[-5:])  # check for overflow here?
+            serial = util.ltruncate_int(serial, 5)  # check for overflow here?
+            resid = util.ltruncate_int(resid, 4)
             name = name[:4]
             if len(name) < 4:
                 name = " " + name  # customary to start in column 14
             chainid = chainid.strip()[-1:]  # take the last character
-            resid = int(str(resid)[-4:])  # check for overflow here?
 
             self.pdb.write(self.fmt['ATOM'].format(
                 serial=serial,

package/MDAnalysis/lib/util.py

@@ -1574,3 +1574,28 @@ def __eq__(self, other):
         except AssertionError:
             return False
         return True
+
+
+def ltruncate_int(value, ndigits):
+    """Truncate an integer, retaining least significant digits
+
+    Parameters
+    ----------
+    value : int
+      value to truncate
+    ndigits : int
+      number of digits to keep
+
+    Returns
+    -------
+    truncated : int
+      only the `ndigits` least significant digits from `value`
+
+    Examples
+    --------
+    >>> ltruncate_int(123, 2)
+    23
+    >>> ltruncate_int(1234, 5)
+    1234
+    """
+    return int(str(value)[-ndigits:])

testsuite/MDAnalysisTests/coordinates/test_gro.py

@@ -20,22 +20,33 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 from __future__ import absolute_import
-from unittest import TestCase
 
 import MDAnalysis as mda
 import numpy as np
 from MDAnalysis.coordinates.GRO import GROReader, GROWriter
-from MDAnalysisTests import make_Universe
-from MDAnalysisTests.coordinates.base import BaseReference, BaseReaderTest, BaseWriterTest, BaseTimestepTest
+from MDAnalysisTests import make_Universe, tempdir
+from MDAnalysisTests.coordinates.base import (
+    BaseReference, BaseReaderTest, BaseWriterTest, BaseTimestepTest,
+)
 from MDAnalysisTests.coordinates.reference import RefAdK
-from MDAnalysisTests.datafiles import COORDINATES_GRO, COORDINATES_GRO_INCOMPLETE_VELOCITY, COORDINATES_GRO_BZ2, GRO, \
-    GRO_large
+from MDAnalysisTests.datafiles import (
+    COORDINATES_GRO,
+    COORDINATES_GRO_INCOMPLETE_VELOCITY,
+    COORDINATES_GRO_BZ2,
+    GRO,
+    GRO_large,
+)
 from nose.plugins.attrib import attr
-from numpy.testing import (assert_almost_equal, )
-from numpy.testing import assert_array_almost_equal, dec, assert_equal, assert_raises
-
-
-class TestGROReaderOld(TestCase, RefAdK):
+from numpy.testing import (
+    assert_,
+    assert_almost_equal,
+    assert_array_almost_equal,
+    dec,
+    assert_equal,
+    assert_raises
+)
+
+class TestGROReaderOld(RefAdK):
     def setUp(self):
         self.universe = mda.Universe(GRO)
         self.ts = self.universe.trajectory.ts
@@ -88,7 +99,7 @@ def test_unitcell(self):
             err_msg="unit cell dimensions (rhombic dodecahedron)")
 
 
-class TestGROReaderNoConversionOld(TestCase, RefAdK):
+class TestGROReaderNoConversionOld(RefAdK):
     def setUp(self):
         self.universe = mda.Universe(GRO, convert_units=False)
         self.ts = self.universe.trajectory.ts
@@ -407,6 +418,18 @@ def test_writer_large_residue_count(self):
                          err_msg="Writing GRO file with > 99 999 "
                                  "resids does not truncate properly.")
 
+@tempdir.run_in_tempdir()
+def test_growriter_resid_truncation():
+    u = make_Universe(extras=['resids'], trajectory=True)
+    u.residues[0].resid = 123456789
+    u.atoms.write('out.gro')
+
+    with open('out.gro', 'r') as grofile:
+        grofile.readline()
+        grofile.readline()
+        line = grofile.readline()
+    # larger digits should get truncated
+    assert_(line.startswith('56789UNK'))
 
 class TestGROTimestep(BaseTimestepTest):
     Timestep = mda.coordinates.GRO.Timestep

testsuite/MDAnalysisTests/lib/test_util.py

@@ -968,3 +968,19 @@ def test_iter(self):
             seen.append(val)
         for val in ['this', 'that', 'other']:
             assert_(val in seen)
+
+
+class TestTruncateInteger(object):
+    @staticmethod
+    def _check_vals(a, b):
+        assert_(util.ltruncate_int(*a) == b)
+
+    def test_ltruncate_int(self):
+        for vals, exp in (
+                ((1234, 1), 4),
+                ((1234, 2), 34),
+                ((1234, 3), 234),
+                ((1234, 4), 1234),
+                ((1234, 5), 1234),
+        ):
+            yield self._check_vals, vals, exp