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Merged
lohedges merged 1 commit into from
Jun 15, 2026
+91 −73
Merged

Fix issue #519 #520

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70 changes: 3 additions & 67 deletions nodes/playground/prepareFEP.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -118,49 +118,7 @@
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"node.addInput(\"input1\", BSS.Gateway.FileSet(help=\"A topology and coordinates file\"))\n",
"node.addInput(\"input2\", BSS.Gateway.FileSet(help=\"A topology and coordinates file\"))\n",
"node.addInput(\n",
" \"prematch\",\n",
" BSS.Gateway.String(\n",
" help=\"list of atom indices that are matched between input2 and input1. Syntax is of the format 1-3,4-8,9-11... Ignored if a mapping is provided\",\n",
" default=\"\",\n",
" ),\n",
")\n",
"node.addInput(\n",
" \"mapping\",\n",
" BSS.Gateway.File(\n",
" help=\"csv file that contains atom indices in input1 mapped ot atom indices in input2\",\n",
" optional=True,\n",
" ),\n",
")\n",
"node.addInput(\n",
" \"timeout\",\n",
" BSS.Gateway.Time(\n",
" help=\"The timeout for the maximum common substructure search\",\n",
" default=10 * BSS.Units.Time.second,\n",
" ),\n",
")\n",
"node.addInput(\n",
" \"allow_ring_breaking\",\n",
" BSS.Gateway.Boolean(\n",
" help=\"Whether to allow opening/closing of rings during merge\", default=False\n",
" ),\n",
")\n",
"node.addInput(\n",
" \"allow_ring_size_change\",\n",
" BSS.Gateway.Boolean(\n",
" help=\"Whether to allow ring size changes during merge\", default=False\n",
" ),\n",
")\n",
"node.addInput(\n",
" \"output\",\n",
" BSS.Gateway.String(\n",
" help=\"The root name for the files describing the perturbation input1->input2.\"\n",
" ),\n",
")"
]
"source": "node.addInput(\"input1\", BSS.Gateway.FileSet(help=\"A topology and coordinates file\"))\nnode.addInput(\"input2\", BSS.Gateway.FileSet(help=\"A topology and coordinates file\"))\nnode.addInput(\n \"prematch\",\n BSS.Gateway.String(\n help=\"list of atom indices that are matched between input2 and input1. Syntax is of the format 1-3,4-8,9-11... Ignored if a mapping is provided\",\n default=\"\",\n ),\n)\nnode.addInput(\n \"mapping\",\n BSS.Gateway.File(\n help=\"csv file that contains atom indices in input1 mapped ot atom indices in input2\",\n optional=True,\n ),\n)\nnode.addInput(\n \"timeout\",\n BSS.Gateway.Time(\n help=\"The timeout for the maximum common substructure search\",\n default=10 * BSS.Units.Time.second,\n ),\n)\nnode.addInput(\n \"allow_ring_breaking\",\n BSS.Gateway.Boolean(\n help=\"Whether to allow opening/closing of rings during merge\", default=False\n ),\n)\nnode.addInput(\n \"allow_ring_size_change\",\n BSS.Gateway.Boolean(\n help=\"Whether to allow ring size changes during merge\", default=False\n ),\n)\nnode.addInput(\n \"max_path\",\n BSS.Gateway.Integer(\n help=\"Maximum path length used when searching for rings. Increase for very large macrocycles.\",\n default=50,\n minimum=1,\n ),\n)\nnode.addInput(\n \"max_ring_size\",\n BSS.Gateway.Integer(\n help=\"Maximum ring size considered when checking for ring size changes.\",\n default=24,\n minimum=1,\n ),\n)\nnode.addInput(\n \"output\",\n BSS.Gateway.String(\n help=\"The root name for the files describing the perturbation input1->input2.\"\n ),\n)"
},
{
"cell_type": "code",
Expand Down Expand Up @@ -279,29 +237,7 @@
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Align lig2 to lig1 based on the best mapping (inverted). The molecule is aligned based\n",
"# on a root mean squared displacement fit to find the optimal translation vector\n",
"# (as opposed to merely taking the difference of centroids).\n",
"lig2 = BSS.Align.rmsdAlign(lig2, lig1, inverted_mapping)\n",
"\n",
"# Merge the two ligands based on the mapping.\n",
"merged = BSS.Align.merge(\n",
" lig1,\n",
" lig2,\n",
" mapping,\n",
" allow_ring_breaking=node.getInput(\"allow_ring_breaking\"),\n",
" allow_ring_size_change=node.getInput(\"allow_ring_size_change\"),\n",
")\n",
"\n",
"# Create a composite system\n",
"system1.removeMolecules(lig1)\n",
"system1.addMolecules(merged)\n",
"\n",
"# Make sure the box vectors are in reduced form.\n",
"system1.reduceBoxVectors()\n",
"system1.rotateBoxVectors()"
]
"source": "# Align lig2 to lig1 based on the best mapping (inverted). The molecule is aligned based\n# on a root mean squared displacement fit to find the optimal translation vector\n# (as opposed to merely taking the difference of centroids).\nlig2 = BSS.Align.rmsdAlign(lig2, lig1, inverted_mapping)\n\n# Merge the two ligands based on the mapping.\nmerged = BSS.Align.merge(\n lig1,\n lig2,\n mapping,\n allow_ring_breaking=node.getInput(\"allow_ring_breaking\"),\n allow_ring_size_change=node.getInput(\"allow_ring_size_change\"),\n max_path=node.getInput(\"max_path\"),\n max_ring_size=node.getInput(\"max_ring_size\"),\n)\n\n# Create a composite system\nsystem1.removeMolecules(lig1)\nsystem1.addMolecules(merged)\n\n# Make sure the box vectors are in reduced form.\nsystem1.reduceBoxVectors()\nsystem1.rotateBoxVectors()"
},
{
"cell_type": "code",
Expand Down Expand Up @@ -421,4 +357,4 @@
},
"nbformat": 4,
"nbformat_minor": 4
}
}
18 changes: 18 additions & 0 deletions nodes/playground/prepareFEP.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,22 @@ def loadMapping(mapping_file):
help="Whether to allow ring size changes during merge", default=False
),
)
node.addInput(
"max_path",
BSS.Gateway.Integer(
help="Maximum path length used when searching for rings. Increase for very large macrocycles.",
default=50,
minimum=1,
),
)
node.addInput(
"max_ring_size",
BSS.Gateway.Integer(
help="Maximum ring size considered when checking for ring size changes.",
default=24,
minimum=1,
),
)
node.addInput(
"output",
BSS.Gateway.String(
Expand Down Expand Up @@ -235,6 +251,8 @@ def loadMapping(mapping_file):
mapping,
allow_ring_breaking=node.getInput("allow_ring_breaking"),
allow_ring_size_change=node.getInput("allow_ring_size_change"),
max_path=node.getInput("max_path"),
max_ring_size=node.getInput("max_ring_size"),
)

# Create a composite system
Expand Down
38 changes: 35 additions & 3 deletions src/BioSimSpace/Align/_merge.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,8 @@ def merge(
fix_perturbable_zero_sigmas=True,
force=False,
roi=None,
max_path=50,
max_ring_size=24,
property_map0={},
property_map1={},
**kwargs,
Expand Down Expand Up @@ -75,6 +77,16 @@ def merge(
The region of interest to merge.
Consists of a list of ROI residue indices.

max_path : int
Maximum path length used when searching for rings. The default of
50 covers typical macrocycles. Increase if larger rings need to be
detected.

max_ring_size : int
Maximum ring size considered when checking for ring size changes.
The default of 24 covers most drug-like macrocycles. Rings larger
than this threshold are not subject to ring-size-change detection.

property_map0 : dict
A dictionary that maps "properties" in this molecule to their
user defined values. This allows the user to refer to properties
Expand Down Expand Up @@ -136,6 +148,12 @@ def merge(
if not isinstance(force, bool):
raise TypeError("'force' must be of type 'bool'")

if not isinstance(max_path, int) or max_path < 1:
raise TypeError("'max_path' must be a positive integer")

if not isinstance(max_ring_size, int) or max_ring_size < 1:
raise TypeError("'max_ring_size' must be a positive integer")

if not isinstance(mapping, dict):
raise TypeError("'mapping' must be of type 'dict'.")
else:
Expand Down Expand Up @@ -1202,7 +1220,14 @@ def merge(

# Combined ring check — calls find_paths once per connectivity.
is_ring_broken, is_ring_size_change = _check_ring(
c0, conn1, idx, idy, idx_map, idy_map
c0,
conn1,
idx,
idy,
idx_map,
idy_map,
max_path=max_path,
max_ring_size=max_ring_size,
)

# A ring was broken and it is not allowed.
Expand Down Expand Up @@ -1268,7 +1293,14 @@ def merge(

# Combined ring check — calls find_paths once per connectivity.
is_ring_broken, is_ring_size_change = _check_ring(
c1, conn0, idx, idy, idx_map, idy_map
c1,
conn0,
idx,
idy,
idx_map,
idy_map,
max_path=max_path,
max_ring_size=max_ring_size,
)

# A ring was broken and it is not allowed.
Expand Down Expand Up @@ -1494,7 +1526,7 @@ def merge(
return mol


def _check_ring(conn0, conn1, idx0, idy0, idx1, idy1, max_path=50, max_ring_size=12):
def _check_ring(conn0, conn1, idx0, idy0, idx1, idy1, max_path=50, max_ring_size=24):
"""
Internal function to test whether a perturbation opens/closes a ring or
changes its size for a given pair of atoms.
Expand Down
38 changes: 35 additions & 3 deletions src/BioSimSpace/Sandpit/Exscientia/Align/_merge.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,8 @@ def merge(
allow_ring_size_change=False,
force=False,
roi=None,
max_path=50,
max_ring_size=24,
property_map0={},
property_map1={},
**kwargs,
Expand Down Expand Up @@ -70,6 +72,16 @@ def merge(
roi : list
The region of interest to merge. Consist of two lists of atom indices.

max_path : int
Maximum path length used when searching for rings. The default of
50 covers typical macrocycles. Increase if larger rings need to be
detected.

max_ring_size : int
Maximum ring size considered when checking for ring size changes.
The default of 24 covers most drug-like macrocycles. Rings larger
than this threshold are not subject to ring-size-change detection.

property_map0 : dict
A dictionary that maps "properties" in this molecule to their
user defined values. This allows the user to refer to properties
Expand Down Expand Up @@ -127,6 +139,12 @@ def merge(
if not isinstance(force, bool):
raise TypeError("'force' must be of type 'bool'")

if not isinstance(max_path, int) or max_path < 1:
raise TypeError("'max_path' must be a positive integer")

if not isinstance(max_ring_size, int) or max_ring_size < 1:
raise TypeError("'max_ring_size' must be a positive integer")

if not isinstance(mapping, dict):
raise TypeError("'mapping' must be of type 'dict'.")
else:
Expand Down Expand Up @@ -1194,7 +1212,14 @@ def merge(

# Combined ring check — calls find_paths once per connectivity.
is_ring_broken, is_ring_size_change = _check_ring(
c0, conn, idx, idy, idx_map, idy_map
c0,
conn,
idx,
idy,
idx_map,
idy_map,
max_path=max_path,
max_ring_size=max_ring_size,
)

# A ring was broken and it is not allowed.
Expand Down Expand Up @@ -1260,7 +1285,14 @@ def merge(

# Combined ring check — calls find_paths once per connectivity.
is_ring_broken, is_ring_size_change = _check_ring(
c1, conn, idx, idy, idx_map, idy_map
c1,
conn,
idx,
idy,
idx_map,
idy_map,
max_path=max_path,
max_ring_size=max_ring_size,
)

# A ring was broken and it is not allowed.
Expand Down Expand Up @@ -1360,7 +1392,7 @@ def merge(
return mol


def _check_ring(conn0, conn1, idx0, idy0, idx1, idy1, max_path=50, max_ring_size=12):
def _check_ring(conn0, conn1, idx0, idy0, idx1, idy1, max_path=50, max_ring_size=24):
"""
Internal function to test whether a perturbation opens/closes a ring or
changes its size for a given pair of atoms.
Expand Down
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