fixed typos

axsk · Sep 10, 2024 · 4ecdd1d · 4ecdd1d
1 parent c7f928d
commit 4ecdd1d
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/scripts/atefe.jl b/scripts/atefe.jl
@@ -4,7 +4,7 @@
     using CUDA
 end
 
-@time "loading" sim = OpenMMScript("data/atefe/mor.py", steps=10_000)
+@time "loading" sim = OpenMMSimulation(py="data/atefe/mor.py", steps=10_000)
 
 NFEATURES = 3000
 NX = 1_000

diff --git a/src/ISOKANN.jl b/src/ISOKANN.jl
@@ -53,6 +53,8 @@ import LinearAlgebra
 import MLUtils: numobs
 import Flux: cpu, gpu
 
+export OpenMM
+
 export pairnet
 #export PDB_ACEMD, PDB_1UAO, PDB_diala_water
 #export MollyLangevin, propagate, solve#, MollySDE

diff --git a/src/simulators/openmm.jl b/src/simulators/openmm.jl
@@ -108,7 +108,7 @@ end
 mmthreads(sim::OpenMMSimulation) = get(sim.constructor, :mmthreads, CUDA.has_cuda() ? "gpu" : 1)
 nthreads(sim::OpenMMSimulation) = get(sim.constructor, :nthreads, CUDA.has_cuda() ? 1 : Threads.nthreads())
 momenta(sim::OpenMMSimulation) = get(sim.constructor, :momenta, false)
-pdbfile(sim::OpenMMSimulation) = get(sim.constructor, :pdb, () -> createpdb(sim))
+pdbfile(sim::OpenMMSimulation) = get(() -> createpdb(sim), sim.constructor, :pdb)
 
 steps(sim) = sim.steps::Int
 friction(sim) = friction(sim.pysim)
@@ -133,7 +133,7 @@ function createpdb(sim)
     pysim = sim.pysim
     file = tempname() * ".pdb"
     pdb = py"app.PDBFile"
-    pdb.writeFile(pysim.topology, pysim.positions, file)  # TODO: fix this
+    pdb.writeFile(pysim.topology, PyReverseDims(reshape(getcoords(sim), 3, :)), file)  # TODO: fix this
     return file
 end