def __init__(self,
path: str = ".",
config_file: Optional[str] = None) -> None:
self.path = path
if config_file is not None:
SETTINGS.update_settings_with_file(
self.get_config_file(config_file))
self.tree = Tree(self.path, **SETTINGS["tree"])
def test_tree_create_node(basic_tree: Tree):
basic_tree.create_root_node()
node = basic_tree.create_node(0)
assert len(basic_tree.nodes) == 2
assert node.parent_id == 0
assert node.rmsd is None
assert node.depth == 1
assert len(basic_tree.nodes[0].children) == 1
assert os.path.exists(os.path.join(node.path, "top.prmtop"))
assert os.path.exists(os.path.join(node.path, "initial.rst7"))
assert os.path.exists(os.path.join(node.path, "ref.crd"))
def test_tree_create_root_node(basic_tree: Tree):
node = basic_tree.create_root_node()
assert node.rmsd == pytest.approx(17.29049097)
assert node.parent_id is None
assert node.depth == 0
assert os.path.exists(os.path.join(node.path, ".info.yml"))
assert len(basic_tree.nodes) == 1
class LigBinder:
def __init__(self,
path: str = ".",
config_file: Optional[str] = None) -> None:
self.path = path
if config_file is not None:
SETTINGS.update_settings_with_file(
self.get_config_file(config_file))
self.tree = Tree(self.path, **SETTINGS["tree"])
def get_config_file(self,
config_file: Optional[str] = None) -> Optional[str]:
local_default_config_file = os.path.join(self.path, "config.yml")
if config_file is not None and os.path.exists(config_file):
return config_file
elif os.path.exists(local_default_config_file):
return local_default_config_file
return None
def run(self):
self.log_initial_info()
metric_name = "nrmsd" if self.tree.use_normalized_rmsd else "rmsd"
self.setup_hmr()
if len(self.tree.nodes) == 0:
logger.info("No root node found. Instantiating...")
self.tree.create_root_node(**SETTINGS["data_files"])
while not self.tree.has_converged() and self.tree.can_grow():
node: Node = self.tree.create_node_from_candidate()
logger.info("New node chosen for expansion.")
logger.info(f"\tdepth: {node.depth}/{self.tree.max_depth}")
parent_node = self.tree.nodes[node.parent_id]
parent_metric = self.tree.get_metric(parent_node)
logger.info(f"\t{metric_name}: {parent_metric:.3f}")
engine = AmberMDEngine(node.path, **SETTINGS["md"])
engine.run()
node.calc_node_rmsd()
node_metric = self.tree.get_metric(node)
if node_metric < parent_metric:
logger.info(
f"Node {node.node_id} improved {metric_name} by {parent_metric - node_metric:.3f}!"
f" current {metric_name}: {node_metric:.3f}")
logger.info("Exploration finished.")
Reporter(self.tree).compile_results()
def setup_hmr(self):
if not SETTINGS["md"]["use_hmr"]:
return
top_file = SETTINGS["data_files"]["top_file"]
logger.info(f"Applying HMR on topology file {top_file}")
parm = AmberParm(top_file)
HMassRepartition(parm).execute()
parm.write_parm(top_file)
logger.info("HMR applied")
def log_initial_info(self):
logger.info(f"Running ligbinder v{VERSION}")
logger.info(f"Current directory: {os.path.abspath(os.getcwd())}")
logger.info("Full settings for this run:")
logger.info(SETTINGS.data)
def test_tree_load_nodes(basic_tree):
basic_tree.create_root_node()
basic_tree.create_node(0)
basic_tree.create_node(0)
tree = Tree(basic_tree.path)
assert len(tree.nodes) == len(basic_tree.nodes)
assert len(tree.nodes[0].children) == len(basic_tree.nodes[0].children)
for id in tree.nodes:
assert tree.nodes[id].depth == basic_tree.nodes[id].depth
assert tree.nodes[id].parent_id == basic_tree.nodes[id].parent_id
def test_tree_expandability(use_normalized_rmsd, basic_tree: Tree):
basic_tree.use_normalized_rmsd = use_normalized_rmsd
basic_tree.max_children = 2
basic_tree.max_depth = 1
basic_tree.create_root_node()
node = basic_tree.create_node(0)
node.rmsd = basic_tree.nodes[0].rmsd + 1
node.nrmsd = basic_tree.nodes[0].nrmsd + 1
basic_tree.max_nodes = 1
assert basic_tree.can_grow() is False
basic_tree.max_nodes = 500
assert basic_tree.can_grow()
node = basic_tree.create_node_from_candidate()
node.rmsd = basic_tree.nodes[0].rmsd + 1
node.nrmsd = basic_tree.nodes[0].nrmsd + 1
assert basic_tree.can_grow() is False
def test_tree_has_converged(use_normalized_rmsd, basic_tree: Tree):
basic_tree.use_normalized_rmsd = use_normalized_rmsd
basic_tree.create_root_node()
assert basic_tree.has_converged() is False
basic_tree.nodes[0].nrmsd = basic_tree.nodes[0].rmsd = 0.2
assert basic_tree.has_converged() is True
def basic_tree(tmpdir):
copy_input_files_to_tmpdir(tmpdir)
tree = Tree(tmpdir)
return tree
def test_node_weight(basic_tree: Tree):
root_node = basic_tree.create_root_node()
assert basic_tree.get_node_weight(root_node) == 1
node = basic_tree.create_node(0)
assert basic_tree.get_node_weight(root_node) == 1
assert basic_tree.get_node_weight(node) == 1
basic_tree.create_node(0)
last_node = basic_tree.create_node(0)
assert basic_tree.get_node_weight(root_node) == 3
assert basic_tree.get_node_weight(node) == 1
basic_tree.create_node(last_node.node_id)
basic_tree.create_node(last_node.node_id)
assert basic_tree.get_node_weight(root_node) == 4
assert basic_tree.get_node_weight(node) == 1
assert basic_tree.get_node_weight(last_node) == 2
def test_node_expandability(basic_tree: Tree, use_normalized_rmsd):
basic_tree.use_normalized_rmsd = use_normalized_rmsd
basic_tree.create_root_node()
parent_node = basic_tree.nodes[0]
parent_metric = basic_tree.get_metric(parent_node)
# deactivate relative improvement check
basic_tree.min_relative_improvement = 1
node = basic_tree.create_node(0)
node_metric = parent_metric - 0.5 * basic_tree.min_absolute_improvement
node.nrmsd = node.rmsd = node_metric
assert basic_tree.is_expandable(node) is False
node_metric = parent_metric - 1.5 * basic_tree.min_absolute_improvement
node.nrmsd = node.rmsd = node_metric
assert basic_tree.is_expandable(node) is True
# deactivate absolute improvement check and reactivate relative
basic_tree.min_absolute_improvement = parent_metric
basic_tree.min_relative_improvement = 0.1
node_metric = parent_metric * (1 -
0.5 * basic_tree.min_relative_improvement)
node.nrmsd = node.rmsd = node_metric
assert basic_tree.is_expandable(node) is False
node_metric = parent_metric * (1 -
1.5 * basic_tree.min_relative_improvement)
node.nrmsd = node.rmsd = node_metric
assert basic_tree.is_expandable(node) is True