From 94eded67eaa697b9d9aec21dd56384d901377b5f Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 10 Feb 2022 20:19:36 +0100
Subject: [PATCH] Add kwargs to modelling.MinimizeModelEnergy
Add tolerance values that are passed to the according SD/LBFGS minimizers
---
modelling/pymod/_pipeline.py | 15 ++++++++++++---
1 file changed, 12 insertions(+), 3 deletions(-)
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index 8b79f214..db7fc2ad 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -256,7 +256,8 @@ def BuildSidechains(mhandle, merge_distance=4, fragment_db=None,
def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
max_iter_lbfgs=10, use_amber_ff=False,
- extra_force_fields=list()):
+ extra_force_fields=list(),
+ tolerance_sd=1.0, tolerance_lbfgs=1.0):
'''Minimize energy of final model using molecular mechanics.
Uses :mod:`ost.mol.mm` to perform energy minimization.
@@ -291,6 +292,14 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
:param max_iter_lbfgs: Max. number of iterations within LBFGS method
:type max_iter_lbfgs: :class:`int`
+ :param tolerance_sd: Tolerance parameter passed to ApplySD of
+ :class:`ost.mol.mm.Simulation` object.
+ :type tolerance_sd: :class:`float`
+
+ :param tolerance_lbfgs: Tolerance parameter passed to ApplyLBFGS of
+ :class:`ost.mol.mm.Simulation` object.
+ :type tolerance_lbfgs: :class:`float`
+
:param use_amber_ff: if True, use the AMBER force field instead of the def.
CHARMM one (see :meth:`BuildFromRawModel`).
:type use_amber_ff: :class:`bool`
@@ -335,8 +344,8 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
ost.LogInfo("Perform energy minimization "
"(iteration %d, energy: %g)" % (i+1, cur_energy))
try:
- sim.ApplySD(tolerance = 1.0, max_iterations = max_iter_sd)
- sim.ApplyLBFGS(tolerance = 1.0, max_iterations = max_iter_lbfgs)
+ sim.ApplySD(tolerance = tolerance_sd, max_iterations = max_iter_sd)
+ sim.ApplyLBFGS(tolerance = tolerance_lbfgs, max_iterations = max_iter_lbfgs)
sim.UpdatePositions()
except Exception as ex:
# ABORT ON FAIL
--
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