From 4ecdd1d07103cfea44fb569bbc1505071a9371e3 Mon Sep 17 00:00:00 2001
From: Sikorski <sikorski@zib.de>
Date: Tue, 10 Sep 2024 13:45:20 +0200
Subject: [PATCH] fixed typos

---
 scripts/atefe.jl         | 2 +-
 src/ISOKANN.jl           | 2 ++
 src/simulators/openmm.jl | 4 ++--
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/scripts/atefe.jl b/scripts/atefe.jl
index 406ea3d..c041a81 100644
--- 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
index f4043b5..688f276 100644
--- 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
index 58bc86b..3b6fc18 100644
--- 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