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7 files changed

+358
-133
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‎.github/workflows/CI.yaml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -53,7 +53,7 @@ jobs:
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shell: bash -l {0}
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run: |
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pytest -v --cov=blues --cov-report=xml --color=yes blues/tests/test_propane.py blues/tests/test_randomrotation.py blues/tests/test_randomrotation.py blues/tests/test_watertranslation.py
56+
pytest -v --cov=blues --cov-report=xml --color=yes blues/tests/test_propane.py blues/tests/test_randomrotation.py blues/tests/test_watertranslation.py
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- name: CodeCov
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uses: codecov/codecov-action@v4

‎blues/moves.py‎

Lines changed: 8 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -160,7 +160,8 @@ class RandomLigandRotationMove(Move):
160160
ParmEd Structure object of the relevant system to be moved.
161161
random_state : integer or numpy.RandomState, optional
162162
The generator used for random numbers. If an integer is given, it fixes the seed. Defaults to the global numpy random number generator.
163-
163+
ligand_indices : list of int, optional
164+
List of atom indices identifying the ligand to be rotated. If provided, overrides `resname` selection.
164165
Attributes
165166
----------
166167
structure : parmed.Structure
@@ -190,17 +191,21 @@ class RandomLigandRotationMove(Move):
190191
'LIG'
191192
"""
192193

193-
def __init__(self, structure, resname='LIG', random_state=None):
194+
def __init__(self, structure, resname='LIG', ligand_indices=None, random_state=None):
194195
self.structure = structure
195196
self.resname = resname
196197
self.random_state = random_state
197198
self.atom_indices = self.getAtomIndices(structure, self.resname)
198-
#atom_indices_1based = [i + 1 for i in self.atom_indices]
199+
self.ligand_indices = ligand_indices
199200
self.topology = structure[self.atom_indices].topology
200201
self.totalmass = 0
201202
self.masses = []
202203
self.center_of_mass = None
203204
self.positions = structure[self.atom_indices].positions
205+
if self.ligand_indices:
206+
self.topology = structure[self.ligand_indices].topology
207+
self.positions = structure[self.ligand_indices].positions
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204209
self._calculateProperties()
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206211
def getAtomIndices(self, structure, resname):

‎blues/tests/data/propane.pdb‎

Lines changed: 24 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,25 @@
1-
HETATM 1 C1 LIG 1 1.236 -0.188 0.286 1.00 0.00 C
2-
HETATM 2 C2 LIG 1 -0.010 -0.181 -0.595 1.00 0.00 C
3-
HETATM 3 C3 LIG 1 -1.228 0.327 0.171 1.00 0.00 C
4-
HETATM 4 H1 LIG 1 2.102 -0.562 -0.299 1.00 0.00 H
5-
HETATM 5 H2 LIG 1 1.085 -0.854 1.162 1.00 0.00 H
6-
HETATM 6 H3 LIG 1 1.463 0.840 0.640 1.00 0.00 H
7-
HETATM 7 H4 LIG 1 -0.209 -1.213 -0.958 1.00 0.00 H
8-
HETATM 8 H5 LIG 1 0.168 0.472 -1.477 1.00 0.00 H
9-
HETATM 9 H6 LIG 1 -2.116 0.320 -0.496 1.00 0.00 H
10-
HETATM 10 H7 LIG 1 -1.056 1.366 0.523 1.00 0.00 H
11-
HETATM 11 H8 LIG 1 -1.435 -0.327 1.044 1.00 0.00 H
1+
REMARK 1 PDBFIXER FROM: propane.pdb
2+
REMARK 1 CREATED WITH OPENMM 8.2, 2025-06-25
3+
HETATM 1 C1 LIG 1 1.236 -0.188 0.286 1.00 0.00 C
4+
HETATM 2 C2 LIG 1 -0.010 -0.181 -0.595 1.00 0.00 C
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HETATM 3 C3 LIG 1 -1.228 0.327 0.171 1.00 0.00 C
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HETATM 4 H1 LIG 1 2.102 -0.562 -0.299 1.00 0.00 H
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HETATM 5 H2 LIG 1 1.085 -0.854 1.162 1.00 0.00 H
8+
HETATM 6 H3 LIG 1 1.463 0.840 0.640 1.00 0.00 H
9+
HETATM 7 H4 LIG 1 -0.209 -1.213 -0.958 1.00 0.00 H
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HETATM 8 H5 LIG 1 0.168 0.472 -1.477 1.00 0.00 H
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HETATM 9 H6 LIG 1 -2.116 0.320 -0.496 1.00 0.00 H
12+
HETATM 10 H7 LIG 1 -1.056 1.366 0.523 1.00 0.00 H
13+
HETATM 11 H8 LIG 1 -1.435 -0.327 1.044 1.00 0.00 H
14+
CONECT 1 5 6 2 4
15+
CONECT 2 7 1 8 3
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CONECT 3 2 9 10 11
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CONECT 4 1
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CONECT 5 1
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CONECT 6 1
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CONECT 7 2
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CONECT 8 2
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CONECT 9 3
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CONECT 10 3
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CONECT 11 3
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END

‎blues/tests/data/toluene.inpcrd‎

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1+
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15 0.0000000e+00
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1.6505151 2.3553057 0.2462374 0.7973633 1.1386719 0.1192017
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0.4377441 0.6679687 -1.1435547 -0.3596191 -0.4704590 -1.2626953
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-0.7973633 -1.1386719 -0.1192627 -0.4377441 -0.6679687 1.1435547
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0.3596191 0.4704590 1.2626953 2.7125959 2.0887830 0.2582531
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1.4384768 2.8850422 1.1811140 1.4649291 3.0316851 -0.5937200
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0.7728785 1.1821948 -2.0403757 -0.6393896 -0.8371950 -2.2460353
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-1.4178188 -2.0250971 -0.2121662 -0.7776626 -1.1885103 2.0337892
10+
0.6345623 0.8301715 2.2507930
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50.0000000 50.0000000 50.0000000 90.0000000 90.0000000 90.0000000
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‎blues/tests/data/toluene.prmtop‎

Lines changed: 195 additions & 0 deletions
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%VERSION VERSION_STAMP = V0001.000 DATE = 09/03/25 09:34:25
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%FLAG TITLE
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%FORMAT(20a4)
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%FLAG ATOMIC_NUMBER
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1 1 1 1 1
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%FLAG MASS
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%FORMAT(5E16.8)
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1.20107800E+01 1.20107800E+01 1.00794700E+00 1.00794700E+00 1.00794700E+00
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1.00794700E+00 1.00794700E+00 1.00794700E+00 1.00794700E+00 1.00794700E+00
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%FLAG ATOM_TYPE_INDEX
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%FORMAT(10I8)
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1 2 2 2 2 2 2 3 3 3
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4 4 4 4 4
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%FLAG NUMBER_EXCLUDED_ATOMS
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%FORMAT(10I8)
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10 12 11 7 7 5 7 2 1 1
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1 1 1 1 1
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%FLAG NONBONDED_PARM_INDEX
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%FORMAT(10I8)
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1 2 4 7 2 3 5 8 4 5
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6 9 7 8 9 10
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%FLAG RESIDUE_LABEL
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%FORMAT(5E16.8)
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1.50959129E+00 1.09420646E+00 1.40070606E+00 1.08603611E+00
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3.26847485E+00 1.89899006E-01 1.74359686E+00
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%FLAG DIHEDRAL_PERIODICITY
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%FORMAT(5E16.8)
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2.00000000E+00 3.00000000E+00 2.00000000E+00
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%FLAG DIHEDRAL_PHASE
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%FORMAT(5E16.8)
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3.14159265E+00 0.00000000E+00 3.14159265E+00
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%FLAG SCEE_SCALE_FACTOR
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1.20000000E+00 1.20000000E+00 1.20000000E+00
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%FLAG SCNB_SCALE_FACTOR
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%FORMAT(5E16.8)
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2.00000000E+00 2.00000000E+00 2.00000000E+00
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%FLAG SOLTY
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0.00000000E+00
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9.66338652E+05 1.03176034E+06 1.09874263E+06 9.24328843E+04 1.00841583E+05
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2.15902147E+01 1.14557301E+02 1.13235010E+02 1.97803496E+01 1.81015245E+01
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0 21 2 0 24 2 0 27 2 6
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30 4 9 33 4 12 36 4 15 39
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4 18 42 4
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6 9 12 36 1 9 12 15 39 1
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15 12 9 33 1 21 0 3 18 2
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36 12 15 39 1 39 15 18 42 1
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6 30 -3 -9 3 18 3 -15 -42 3
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18 15 -42 -3 3 18 42 -3 -15 3
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0 3 6 9 1 0 3 18 15 1
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6 3 18 15 1 6 9 -12 15 1
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9 6 3 18 1 9 12 -15 18 1
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14 15 4 5 6 7 8 9 10 11
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%FLAG HBOND_BCOEF
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%FLAG HBCUT
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%FLAG AMBER_ATOM_TYPE
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%FORMAT(20a4)
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C1 C2 C3 C4 C5 C6 C7 H1 H2 H3 H4 H5 H6 H7 H8
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%FLAG TREE_CHAIN_CLASSIFICATION
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%FORMAT(20a4)
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BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
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%FLAG JOIN_ARRAY
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%FORMAT(10I8)
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0 0 0 0 0 0 0 0 0 0
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%FLAG IROTAT
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%FLAG ATOMS_PER_MOLECULE
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‎blues/tests/test_propane.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -68,7 +68,7 @@ def runPropaneTest(N, preferred_platform):
6868
structure = parmed.load_file(structure_pdb)
6969

7070
# Initialize Move Proposal Class
71-
rot_move = RandomLigandRotationMove(structure, 'LIG') # Propane ligand
71+
rot_move = RandomLigandRotationMove(structure, 'LIG', ligand_indices=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]) # Propane ligand
7272
mover = MoveEngine(rot_move)
7373

7474
# Load OpenMM System and Integrator

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