Lazy merge

bin/martinize2

@@ -316,12 +316,14 @@ def entry():
         default=False,
         help="Write separate topologies for identical chains",
     )
-    file_group.add_argument(
+    chain_merging = file_group.add_argument(
         "-merge",
         dest="merge_chains",
-        type=lambda x: x.split(","),
+        type=str,
         action="append",
-        help="Merge chains: e.g. -merge A,B,C (+)",
+        help="Merge chains: either a comma separated list of chains to merge e.g. -merge A,B,C (+), or -merge all\n"
+             "if instead all chains in the input file should be merged.\n"
+             "Can be given multiple times for different groups of chains to merge.",
     )
     file_group.add_argument(
         "-resid",
@@ -974,8 +976,19 @@ def entry():
         itp_paths = []
         # Merge chains if required.
         if args.merge_chains:
-            for chain_set in args.merge_chains:
-                vermouth.MergeChains(chain_set).run_system(system)
+            #if "all" is not in the list of chains to be merged
+            if "all" not in args.merge_chains:
+                input_chain_sets = [i.split(",") for i in args.merge_chains]
+                for chain_set in input_chain_sets:
+                    vermouth.MergeChains(chains=chain_set, all_chains=False).run_system(system)
+            #if "all" is in the list and is the only argument
+            elif "all" in args.merge_chains and len(args.merge_chains) == 1:
+                vermouth.MergeChains(chains=[], all_chains=True).run_system(system)
+            #otherwise there are multiple arguments and we need to raise an ArgumentError
+            else:
+                raise argparse.ArgumentError(chain_merging,
+                                             message=("Multiple conflicting merging arguments given. "
+                                                      "Either specify -merge all or -merge A,B,C (+)."))
         vermouth.NameMolType(deduplicate=not args.keep_duplicate_itp).run_system(system)
         defines = ()
 

vermouth/processors/merge_chains.py

@@ -20,9 +20,11 @@
 
 from ..molecule import Molecule
 from ..processors.processor import Processor
+from ..log_helpers import StyleAdapter, get_logger
+LOGGER = StyleAdapter(get_logger(__name__))
 
 
-def merge_chains(system, chains):
+def merge_chains(system, chains, all_chains):
     """
     Merge molecules with the given chains as a single molecule.
 
@@ -42,15 +44,29 @@ def merge_chains(system, chains):
         The system to modify.
     chains: list[str]
         A container of chain identifier.
+    all_chains: bool
+        If True, all chains will be merged.
     """
-    chains = set(chains)
+    if not all_chains and len(chains) > 0:
+        _chains = set(chains)
+    elif all_chains and len(chains) == 0:
+        _chains = set()
+        for molecule in system.molecules:
+            # Molecules can contain multiple chains
+            _chains.update(node.get('chain') for node in molecule.nodes.values())
+    else:
+        raise ValueError("Can specify specific chains or all chains, but not both")
+
+    if any(not c for c in _chains):
+        LOGGER.warning('One or more of your chains does not have a chain identifier in input file.')
+
     merged = Molecule()
     merged._force_field = system.force_field
     has_merged = False
     new_molecules = []
     for molecule in system.molecules:
         molecule_chains = set(node.get('chain') for node in molecule.nodes.values())
-        if molecule_chains.issubset(chains):
+        if molecule_chains.issubset(_chains):
             if not has_merged:
                 merged.nrexcl = molecule.nrexcl
                 new_molecules.append(merged)
@@ -65,8 +81,9 @@ def merge_chains(system, chains):
 class MergeChains(Processor):
     name = 'MergeChains'
 
-    def __init__(self, chains):
-        self.chains = chains
+    def __init__(self, chains=None, all_chains=False):
+        self.chains = chains or []
+        self.all_chains = all_chains
 
     def run_system(self, system):
-        merge_chains(system, self.chains)
+        merge_chains(system, self.chains, self.all_chains)

vermouth/tests/test_merge_chains.py

@@ -0,0 +1,123 @@
+# Copyright 2018 University of Groningen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+Contains unittests for vermouth.processors.merge_chains.
+"""
+
+import networkx as nx
+import pytest
+from vermouth.system import System
+from vermouth.molecule import Molecule
+from vermouth.forcefield import ForceField
+from vermouth.processors.merge_chains import (
+    MergeChains
+)
+from vermouth.tests.datafiles import (
+    FF_UNIVERSAL_TEST,
+)
+
+@pytest.mark.parametrize('node_data, edge_data, merger, expected', [
+    (
+            [
+                {'chain': 'A', 'resname': 'ALA', 'resid': 1},
+                {'chain': 'A', 'resname': 'ALA', 'resid': 2},
+                {'chain': 'A', 'resname': 'ALA', 'resid': 3},
+                {'chain': 'B', 'resname': 'ALA', 'resid': 1},
+                {'chain': 'B', 'resname': 'ALA', 'resid': 2},
+                {'chain': 'B', 'resname': 'ALA', 'resid': 3}
+            ],
+            [(0, 1), (1, 2), (3, 4), (4, 5)],
+            {"chains": ["A", "B"], "all_chains": False},
+            False
+    ),
+    (
+            [
+                {'chain': 'A', 'resname': 'ALA', 'resid': 1},
+                {'chain': 'A', 'resname': 'ALA', 'resid': 2},
+                {'chain': 'A', 'resname': 'ALA', 'resid': 3},
+                {'chain': 'B', 'resname': 'ALA', 'resid': 1},
+                {'chain': 'B', 'resname': 'ALA', 'resid': 2},
+                {'chain': 'B', 'resname': 'ALA', 'resid': 3}
+            ],
+            [(0, 1), (1, 2), (3, 4), (4, 5)],
+            {"chains": [], "all_chains": True},
+            False
+    ),
+    (
+            [
+                {'chain': 'A', 'resname': 'ALA', 'resid': 1},
+                {'chain': 'A', 'resname': 'ALA', 'resid': 2},
+                {'chain': 'A', 'resname': 'ALA', 'resid': 3},
+                {'chain': None, 'resname': 'ALA', 'resid': 1},
+                {'chain': None, 'resname': 'ALA', 'resid': 2},
+                {'chain': None, 'resname': 'ALA', 'resid': 3}
+            ],
+            [(0, 1), (1, 2), (3, 4), (4, 5)],
+            {"chains": [], "all_chains": True},
+            True
+    ),
+
+])
+def test_merge(caplog, node_data, edge_data, merger, expected):
+    """
+    Tests that the merging works as expected.
+    """
+    system = System(force_field=ForceField(FF_UNIVERSAL_TEST))
+    mol = Molecule(force_field=system.force_field)
+    mol.add_nodes_from(enumerate(node_data))
+    mol.add_edges_from(edge_data)
+
+    mols = nx.connected_components(mol)
+    for nodes in mols:
+        system.add_molecule(mol.subgraph(nodes))
+
+    processor = MergeChains(**merger)
+    caplog.clear()
+    processor.run_system(system)
+
+    if expected:
+        assert any(rec.levelname == 'WARNING' for rec in caplog.records)
+    else:
+        assert caplog.records == []
+
+def test_too_many_args():
+    """
+    Tests that error is raised when too many arguments are given.
+    """
+    node_data = [
+                {'chain': 'A', 'resname': 'ALA', 'resid': 1},
+                {'chain': 'A', 'resname': 'ALA', 'resid': 2},
+                {'chain': 'A', 'resname': 'ALA', 'resid': 3},
+                {'chain': 'B', 'resname': 'ALA', 'resid': 1},
+                {'chain': 'B', 'resname': 'ALA', 'resid': 2},
+                {'chain': 'B', 'resname': 'ALA', 'resid': 3}
+                ]
+    edge_data = [(0, 1), (1, 2), (3, 4), (4, 5)]
+
+    system = System(force_field=ForceField(FF_UNIVERSAL_TEST))
+    mol = Molecule(force_field=system.force_field)
+    mol.add_nodes_from(enumerate(node_data))
+    mol.add_edges_from(edge_data)
+
+    mols = nx.connected_components(mol)
+    for nodes in mols:
+        system.add_molecule(mol.subgraph(nodes))
+
+    merger = {"chains": ["A", "B"], "all_chains": True}
+
+    processor = MergeChains(**merger)
+
+    with pytest.raises(ValueError):
+        processor.run_system(system)
+