Merge pull request #555 from Lp0lp/Go

Cleanup to Go implementation

bin/martinize2

@@ -1029,7 +1029,7 @@ def entry():
         # if the go model hasn't been used we need to create virtual
         # sites for the biasing
         if not args.go:
-            vermouth.rcsu.go_vs_includes.VirtualSideCreator().run_system(system)
+            vermouth.rcsu.go_vs_includes.VirtualSiteCreator().run_system(system)
             itp_paths = ["virtual_sites_atomtypes.itp", "virtual_sites_nonbond_params.itp"]
         # now we add a bias by defining specific virtual-site water interactions
         vermouth.processors.ComputeWaterBias(args.water_bias,

vermouth/rcsu/go_pipeline.py

@@ -17,7 +17,7 @@
 import inspect
 import vermouth
 from ..processors.processor import Processor
-from .go_vs_includes import VirtualSideCreator
+from .go_vs_includes import VirtualSiteCreator
 from .go_structure_bias import ComputeStructuralGoBias
 from ..processors import SetMoleculeMeta
 
@@ -38,8 +38,6 @@ def prepare_run(self, system, moltype):
         # with the proper Go-model for multimers
         vermouth.MergeAllMolecules().run_system(system)
         molecule = system.molecules[0]
-#        res_graph = vermouth.graph_utils.make_residue_graph(molecule)
-#        molecule.res_graph = res_graph
         molecule.meta['moltype'] = moltype
 
     def run_system(self, system, **kwargs):
@@ -52,5 +50,5 @@ def run_system(self, system, **kwargs):
         return system
 
 GoPipeline = GoProcessorPipline([SetMoleculeMeta,
-                                 VirtualSideCreator,
+                                 VirtualSiteCreator,
                                  ComputeStructuralGoBias])

vermouth/rcsu/go_structure_bias.py

@@ -94,7 +94,7 @@ def __init__(self,
         self.res_graph = None
         self.system = None
         self.__chain_id_to_resnode = {}
-        self.magic_number = 1.12246204830
+        self.magic_number = 2**(1/6)
 
     # do not overwrite when subclassing
     def _chain_id_to_resnode(self, chain, resid):

vermouth/rcsu/go_vs_includes.py

@@ -24,7 +24,7 @@
 LOGGER = StyleAdapter(get_logger(__name__))
 
 
-class VirtualSideCreator(Processor):
+class VirtualSiteCreator(Processor):
     """
     Create virtual-sites for the Martini Go model implementation. 
     This processor also updates the gmx

vermouth/tests/gmx/test_topology.py

@@ -87,7 +87,7 @@ def test_atomtypes(tmp_path, dummy_molecule, atomtypes, expected, C6C12):
     DeferredFileWriter().write()
 
     with open(str(outpath)) as infile:
-        for line, ref_line in zip(infile.readlines(), expected):
+        for line, ref_line in zip(infile, expected):
             assert line == ref_line
 
 
@@ -147,7 +147,7 @@ def test_nonbond_params(tmp_path, nbparams, expected, C6C12):
     DeferredFileWriter().write()
 
     with open(str(outpath)) as infile:
-        for line, ref_line in zip(infile.readlines(), expected):
+        for line, ref_line in zip(infile, expected):
             assert line == ref_line
 
 def test_toplevel_topology(tmp_path, dummy_molecule):
@@ -199,7 +199,7 @@ def test_toplevel_topology(tmp_path, dummy_molecule):
 """
     ref_lines = textwrap.dedent(reference).splitlines()
     with open(str(outpath)) as infile:
-        for line, ref_line in zip(infile.readlines(), ref_lines):
+        for line, ref_line in zip(infile, ref_lines):
             print('l', line.strip())
             print('lr', ref_line.strip())
             assert line.strip() == ref_line

vermouth/tests/helper_functions.py

@@ -17,8 +17,13 @@
 """
 import operator
 import os
+import pytest
+import numpy as np
+import networkx as nx
 import networkx.algorithms.isomorphism as iso
-
+import vermouth
+from vermouth.system import System
+from vermouth.forcefield import ForceField
 
 def make_into_set(iter_of_dict):
     """
@@ -78,4 +83,123 @@ def find_in_path(names=('martinize2', 'martinize2.py')):
         for name in names:
             fullpath = os.path.join(folder, name)
             if os.path.isfile(fullpath):
-                return fullpath
+                return fullpath
+
+def create_sys_all_attrs(molecule, moltype, secstruc, defaults, attrs):
+    """
+    Generate a test system from a molecule
+    with all attributes set and blocks in
+    force-field.
+
+    Parameters
+    ----------
+    molecule: :class:vermouth.Molecule
+    moltype: str
+        sets meta['moltype']
+    secstruc: dict[int, str]
+        secondary structure attributes
+        as resid str pairs
+    defaults: dict
+        dict of attribute default value
+    attrs: dict
+        dict of attribute name and dict
+        of node value pairs
+
+    Returns
+    -------
+    :class:vermouth.System
+    """
+    # set mol meta
+    molecule.meta['moltype'] = moltype
+    # assign default node attributes
+    for attr, value in defaults.items():
+        nx.set_node_attributes(molecule, value, attr)
+
+    # assign node attributes
+    for attr, values in attrs.items():
+        nx.set_node_attributes(molecule, values, attr)
+
+    # assign resids
+    resids = nx.get_node_attributes(molecule, "resid")
+    nx.set_node_attributes(molecule, resids, "_old_resid")
+
+    # make the proper force-field
+    ff = ForceField("test")
+    ff.variables['water_type'] = "W"
+    ff.variables['regular'] = 0.47
+    ff.variables['small'] = 0.41
+    ff.variables['tiny'] = 0.38
+
+    res_graph = vermouth.graph_utils.make_residue_graph(molecule)
+    for node in res_graph.nodes:
+        mol_nodes = res_graph.nodes[node]['graph'].nodes
+        block = vermouth.molecule.Block()
+        resname = res_graph.nodes[node]['resname']
+        resid = res_graph.nodes[node]['resid']
+        # assign secondary structure
+        for mol_node in mol_nodes:
+            molecule.nodes[mol_node]['cgsecstruct'] = secstruc[resid]
+            block.add_node(molecule.nodes[mol_node]['atomname'],
+                           atype=molecule.nodes[mol_node]['atype'])
+
+        ff.blocks[resname] = block
+
+
+    # create the system
+    molecule._force_field = ff
+    system = System()
+    system.molecules.append(molecule)
+    return system
+
+@pytest.fixture
+def test_molecule(scope='function'):
+    """
+    Molecule with the following connectivity and atom-naming:
+
+    SC2:   2           8
+           |           |
+    SC1:   1   4       7
+           |   |       |
+    BB:    0 - 3 - 5 - 6
+           -------------
+    resid: 1   2   3   4  column wise
+    """
+
+    force_field = vermouth.forcefield.ForceField("test")
+    molecule = vermouth.molecule.Molecule(force_field=force_field)
+    molecule.meta['test'] = True
+    # The node keys should not be in a sorted order as it would mask any issue
+    # due to the keys being accidentally sorted.
+    molecule.add_node(2, atomname='SC2',
+                      position=np.array([0., 1.0, 0.0]), resid=1)
+    molecule.add_node(0, atomname='BB',
+                      position=np.array([0., 0., 0.]), resid=1)
+    molecule.add_node(1, atomname='SC1',
+                      position=np.array([0., 0.5, 0.0]), resid=1)
+
+    molecule.add_node(3, atomname='BB', position=np.array(
+        [0.5, 0.0, 0.0]), resid=2)
+    molecule.add_node(4, atomname='SC1', position=np.array(
+        [0.5, 0.5, 0.0]), resid=2)
+
+    molecule.add_node(5, atomname='BB', position=np.array(
+        [1.0, 0.0, 0.0]), resid=3)
+
+    molecule.add_node(6, atomname='BB', position=np.array(
+        [1.5, 0.0, 0.0]), resid=4)
+    molecule.add_node(7, atomname='SC1', position=np.array(
+        [1.5, 0.5, 0.0]), resid=4)
+    molecule.add_node(8, atomname='SC2', position=np.array(
+        [1.5, 1.0, 0.0]), resid=4)
+
+    molecule.add_edge(0, 1)
+    molecule.add_edge(0, 2)
+    molecule.add_edge(0, 3)
+    molecule.add_edge(3, 4)
+    molecule.add_edge(3, 5)
+    molecule.add_edge(5, 6)
+    molecule.add_edge(6, 7)
+    molecule.add_edge(7, 8)
+
+    return molecule
+

vermouth/tests/rcsu/test_go_structure_bias.py

@@ -5,7 +5,7 @@
 import numpy as np
 import networkx as nx
 import vermouth
-from vermouth.rcsu.go_vs_includes import VirtualSideCreator
+from vermouth.rcsu.go_vs_includes import VirtualSiteCreator
 from vermouth.tests.test_water_bias import create_sys_all_attrs
 from vermouth.tests.test_apply_rubber_band import test_molecule
 from vermouth.rcsu.go_structure_bias import ComputeStructuralGoBias
@@ -124,7 +124,7 @@ def test_contact_selector(test_molecule,
                                          "atype": atypes})
 
     # generate the virtual sites
-    VirtualSideCreator().run_system(system)
+    VirtualSiteCreator().run_system(system)
     # initialize the Go processor
     go_processor = ComputeStructuralGoBias(contact_map=cmap,
                                            cutoff_short=cshort,

vermouth/tests/rcsu/test_go_utils.py

@@ -43,7 +43,7 @@ def test_get_bead_size(atype, size):
         # two regions false
         ([(101, 120), (180, 210)], 15, False),
     ))
-def test_get_bead_size(regions, resid, result):
+def test_in_region(regions, resid, result):
     assert result == _in_resid_region(resid, regions)
 
 

vermouth/tests/test_apply_rubber_band.py

@@ -26,6 +26,7 @@
                                                    make_same_region_criterion,
                                                    are_connected,
                                                    build_connectivity_matrix)
+from vermouth.tests.helper_functions import test_molecule
 
 # pylint: disable=redefined-outer-name
 
@@ -260,58 +261,6 @@ def test_make_same_region_criterion(regions, left, right, nodes, edges, chain, r
     same_region = make_same_region_criterion(regions)
     assert same_region(graph=graph, left=left, right=right) == outcome
 
-@pytest.fixture
-def test_molecule(scope='function'):
-    """
-    Molecule with the following connectivity and atom-naming:
-
-    SC2:   2           8
-           |           |
-    SC1:   1   4       7
-           |   |       |
-    BB:    0 - 3 - 5 - 6
-           -------------
-    resid: 1   2   3   4  column wise
-    """
-
-    force_field = vermouth.forcefield.ForceField("test")
-    molecule = vermouth.molecule.Molecule(force_field=force_field)
-    molecule.meta['test'] = True
-    # The node keys should not be in a sorted order as it would mask any issue
-    # due to the keys being accidentally sorted.
-    molecule.add_node(2, atomname='SC2',
-                      position=np.array([0., 1.0, 0.0]), resid=1)
-    molecule.add_node(0, atomname='BB',
-                      position=np.array([0., 0., 0.]), resid=1)
-    molecule.add_node(1, atomname='SC1',
-                      position=np.array([0., 0.5, 0.0]), resid=1)
-
-    molecule.add_node(3, atomname='BB', position=np.array(
-        [0.5, 0.0, 0.0]), resid=2)
-    molecule.add_node(4, atomname='SC1', position=np.array(
-        [0.5, 0.5, 0.0]), resid=2)
-
-    molecule.add_node(5, atomname='BB', position=np.array(
-        [1.0, 0.0, 0.0]), resid=3)
-
-    molecule.add_node(6, atomname='BB', position=np.array(
-        [1.5, 0.0, 0.0]), resid=4)
-    molecule.add_node(7, atomname='SC1', position=np.array(
-        [1.5, 0.5, 0.0]), resid=4)
-    molecule.add_node(8, atomname='SC2', position=np.array(
-        [1.5, 1.0, 0.0]), resid=4)
-
-    molecule.add_edge(0, 1)
-    molecule.add_edge(0, 2)
-    molecule.add_edge(0, 3)
-    molecule.add_edge(3, 4)
-    molecule.add_edge(3, 5)
-    molecule.add_edge(5, 6)
-    molecule.add_edge(6, 7)
-    molecule.add_edge(7, 8)
-
-    return molecule
-
 
 @pytest.mark.parametrize('chain_attribute, atom_names, res_min_dist, outcome',
                          (({0: 'A', 1: 'A', 2: 'A',