raise warning if geometry is out of bounds

polyply/src/build_file_parser.py

@@ -53,8 +53,9 @@ def _molecule(self, line, lineno=0):
         self.current_molidxs = np.arange(float(tokens[1]), float(tokens[2]), 1., dtype=int)
         for idx in self.current_molidxs:
             if idx not in self.topology.mol_idx_by_name[tokens[0]]:
-                LOGGER.warning("parsing build file: could not find molecule with name {name} and index {index}.",
-                              **{"index": idx, "name": tokens[0]})
+                msg = ("parsing build file: could not find molecule with "
+                       "name {name} and index {index}.")
+                LOGGER.warning(msg, **{"index": idx, "name": tokens[0]})
 
     @SectionLineParser.section_parser('molecule', 'cylinder', geom_type="cylinder")
     @SectionLineParser.section_parser('molecule', 'sphere', geom_type="sphere")
@@ -231,18 +232,17 @@ def _tag_nodes(molecule, keyword, option, molname=""):
                                                 [option['parameters']]
             # broadcast warning if we find the resid but it doesn't match the resname
             elif molecule.nodes[node]["resid"] in resids and not\
-                 molecule.nodes[node]["resname"] == resname:
-                 msg = "parsing build file: could not find resid {resid} with resname {resname} in molecule {molname}."
-                 LOGGER.warning(msg, **{"resid": molecule.nodes[node]["resid"], "resname": resname,
-                                          "molname": molname})
+                molecule.nodes[node]["resname"] == resname:
+                msg = "parsing build file: could not find resid {resid} with resname {resname} in molecule {molname}."
+                LOGGER.warning(msg, **{"resid": molecule.nodes[node]["resid"], "resname": resname,
+                                       "molname": molname})
 
             # broadcast warning if we find the resname but it doesn't match the resid
             elif molecule.nodes[node]["resname"] == resname and not\
-                 molecule.nodes[node]["resid"]:
-                 msg = "parsing build file: could not find residue {resname} with resid {resid} in molecule {molname}."
-                 LOGGER.warning(msg, **{"resid": molecule.nodes[node]["resid"], "resname": resname,
-                                        "molname": molname})
-
+                molecule.nodes[node]["resid"]:
+                msg = "parsing build file: could not find residue {resname} with resid {resid} in molecule {molname}."
+                LOGGER.warning(msg, **{"resid": molecule.nodes[node]["resid"], "resname": resname,
+                                       "molname": molname})
     @staticmethod
     def _base_parser_geometry(tokens, _type):
         geometry_def = {}
@@ -258,8 +258,44 @@ def _base_parser_geometry(tokens, _type):
 
         parameters.append(_type)
         geometry_def["parameters"] = parameters
+
+        _check_geometry_def(geometry_def, _type)
         return geometry_def
 
+def _check_geometry_def(geom_def, geom_type):
+    """
+    Raise a warning if the point of reference
+    for the geometry type is too close to the
+    origin.
+
+    Parameters
+    ----------
+    geom_def: dict
+        dict with entries: resname, start, stop, point, parameters
+    geom_type: str
+        one of sphere, cylinder, rectangle
+    """
+    msg = ("Geometry restriction {geom_def} extends beyond definite "
+           "positive coordiantes relative to the center point "
+           "{x:.3f} {y:.3f} {z:.3f}. Be aware polyply only builds "
+           "in positive coordinate space.")
+
+    point = geom_def['parameters'][1]
+    if geom_type == "sphere":
+        radius = geom_def['parameters'][2]
+        if any( i < j for i, j in zip([radius, radius, radius], point)):
+            LOGGER.warning(msg, geom_def=geom_def, x=point[0], y=point[1], z=point[2])
+
+    if geom_type == "rectangle":
+        a, b, c = geom_def['parameters'][2:5]
+        if any( i < j for i, j in zip([a, b, c], point)):
+            LOGGER.warning(msg, geom_def=geom_def, x=point[0], y=point[1], z=point[2])
+
+    if geom_type == "cylinder":
+        z, r = geom_def['parameters'][2:4]
+        if z < point[2] or r < np.linalg.norm(point[:2]):
+            LOGGER.warning(msg, geom_def=geom_def, x=point[0], y=point[1], z=point[2])
+
 def read_build_file(lines, molecules, topology):
     """
     Parses `lines` of itp format and adds the

polyply/tests/test_build_file_parser.py

@@ -14,6 +14,7 @@
 """
 Test that build files are properly read.
 """
+import logging
 import textwrap
 import pytest
 import numpy as np
@@ -51,6 +52,29 @@ def test_base_parser_geometry(tokens, _type, expected):
             for result_param, expected_param in zip(result[key][2:], expected[key][2:]):
                 assert result_param == expected_param
 
+@pytest.mark.parametrize('tokens, _type', (
+   # for cylinder z is not covered
+   (["PEO", "63", "154", "in", "8", "8", "6", "6", "7"],
+    "cylinder",),
+   # for cylinder z is not covered
+   (["PEO", "63", "154", "in", "2", "2", "8", "6", "7"],
+    "cylinder",),
+   # for recangle one of the sides is out
+   (["PEO", "0", "10", "out", "11", "0", "13", "1", "2", "3"],
+    "rectangle",),
+   # for sphere radius is to large/small
+   (["PEO", "0", "10", "in", "0", "12", "13", "5"],
+    "sphere",),
+   ))
+def test_base_parser_geometry_warning(caplog, tokens, _type):
+    with caplog.at_level(logging.WARNING):
+        result = polyply.src.build_file_parser.BuildDirector._base_parser_geometry(tokens, _type)
+        for record in caplog.records:
+            assert record.levelname == "WARNING"
+            break
+        else:
+            assert False
+
 @pytest.fixture
 def test_molecule():
     # dummy vermouth force-field