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Fix issues #215 and #216 #217

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merged 2 commits into from
Dec 8, 2023
Merged

Fix issues #215 and #216 #217

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3ca9d3f
Fix imports in metadynamics driver script. [closes #215]
lohedges Dec 6, 2023
407835f
Make sure force constant parameters have unique names. [closes #216]
lohedges Dec 6, 2023
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6 changes: 2 additions & 4 deletions python/BioSimSpace/Metadynamics/_aux/metadynamics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,10 +28,8 @@
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""

from ..._Utils import _try_import

mm = _try_import("openmm")
unit = _try_import("openmm.unit", "conda install -c conda-forge openmm")
import openmm as mm
from openmm import unit

from collections import namedtuple
from functools import reduce
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12 changes: 6 additions & 6 deletions python/BioSimSpace/Process/_openmm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -877,13 +877,13 @@ def _generate_config(self):

self.addToConfig("\n# Upper wall.")
self.addToConfig(
"upper_wall_rest = CustomCentroidBondForce(3, '(k/2)*max(distance(g1,g2)*cos(angle(g1,g2,g3)) - upper_wall, 0)^2')"
"upper_wall_rest = CustomCentroidBondForce(3, '(k1/2)*max(distance(g1,g2)*cos(angle(g1,g2,g3)) - upper_wall, 0)^2')"
)
self.addToConfig("upper_wall_rest.addGroup(lig)")
self.addToConfig("upper_wall_rest.addGroup(p1)")
self.addToConfig("upper_wall_rest.addGroup(p2)")
self.addToConfig("upper_wall_rest.addBond([0,1,2])")
self.addToConfig("upper_wall_rest.addGlobalParameter('k', k1)")
self.addToConfig("upper_wall_rest.addGlobalParameter('k1', k1)")
self.addToConfig(
"upper_wall_rest.addGlobalParameter('upper_wall', upper_wall)"
)
Expand All @@ -903,13 +903,13 @@ def _generate_config(self):
)

self.addToConfig(
"dist_restraint = CustomCentroidBondForce(3, '(k/2)*max(distance(g1,g2)*sin(angle(g1,g2,g3)) - (a/(1+exp(b*(distance(g1,g2)*cos(angle(g1,g2,g3))-c)))+d), 0)^2')"
"dist_restraint = CustomCentroidBondForce(3, '(k2/2)*max(distance(g1,g2)*sin(angle(g1,g2,g3)) - (a/(1+exp(b*(distance(g1,g2)*cos(angle(g1,g2,g3))-c)))+d), 0)^2')"
)
self.addToConfig("dist_restraint.addGroup(lig)")
self.addToConfig("dist_restraint.addGroup(p1)")
self.addToConfig("dist_restraint.addGroup(p2)")
self.addToConfig("dist_restraint.addBond([0,1,2])")
self.addToConfig("dist_restraint.addGlobalParameter('k', k2)")
self.addToConfig("dist_restraint.addGlobalParameter('k2', k2)")
self.addToConfig("dist_restraint.addGlobalParameter('a', wall_width)")
self.addToConfig("dist_restraint.addGlobalParameter('b', beta_cent)")
self.addToConfig("dist_restraint.addGlobalParameter('c', s_cent)")
Expand All @@ -919,13 +919,13 @@ def _generate_config(self):

self.addToConfig("\n# Lower wall.")
self.addToConfig(
"lower_wall_rest = CustomCentroidBondForce(3, '(k/2)*min(distance(g1,g2)*cos(angle(g1,g2,g3)) - lower_wall, 0)^2')"
"lower_wall_rest = CustomCentroidBondForce(3, '(k1/2)*min(distance(g1,g2)*cos(angle(g1,g2,g3)) - lower_wall, 0)^2')"
)
self.addToConfig("lower_wall_rest.addGroup(lig)")
self.addToConfig("lower_wall_rest.addGroup(p1)")
self.addToConfig("lower_wall_rest.addGroup(p2)")
self.addToConfig("lower_wall_rest.addBond([0,1,2])")
self.addToConfig("lower_wall_rest.addGlobalParameter('k', k1)")
self.addToConfig("lower_wall_rest.addGlobalParameter('k1', k1)")
self.addToConfig(
"lower_wall_rest.addGlobalParameter('lower_wall', lower_wall)"
)
Expand Down
6 changes: 2 additions & 4 deletions python/BioSimSpace/Sandpit/Exscientia/Metadynamics/_aux/metadynamics.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,10 +28,8 @@
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""

from ..._Utils import _try_import

mm = _try_import("openmm")
unit = _try_import("openmm.unit", "conda install -c conda-forge openmm")
import openmm as mm
from openmm import unit

from collections import namedtuple
from functools import reduce
Expand Down
12 changes: 6 additions & 6 deletions python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -878,13 +878,13 @@ def _generate_config(self):

self.addToConfig("\n# Upper wall.")
self.addToConfig(
"upper_wall_rest = CustomCentroidBondForce(3, '(k/2)*max(distance(g1,g2)*cos(angle(g1,g2,g3)) - upper_wall, 0)^2')"
"upper_wall_rest = CustomCentroidBondForce(3, '(k1/2)*max(distance(g1,g2)*cos(angle(g1,g2,g3)) - upper_wall, 0)^2')"
)
self.addToConfig("upper_wall_rest.addGroup(lig)")
self.addToConfig("upper_wall_rest.addGroup(p1)")
self.addToConfig("upper_wall_rest.addGroup(p2)")
self.addToConfig("upper_wall_rest.addBond([0,1,2])")
self.addToConfig("upper_wall_rest.addGlobalParameter('k', k1)")
self.addToConfig("upper_wall_rest.addGlobalParameter('k1', k1)")
self.addToConfig(
"upper_wall_rest.addGlobalParameter('upper_wall', upper_wall)"
)
Expand All @@ -904,13 +904,13 @@ def _generate_config(self):
)

self.addToConfig(
"dist_restraint = CustomCentroidBondForce(3, '(k/2)*max(distance(g1,g2)*sin(angle(g1,g2,g3)) - (a/(1+exp(b*(distance(g1,g2)*cos(angle(g1,g2,g3))-c)))+d), 0)^2')"
"dist_restraint = CustomCentroidBondForce(3, '(k2/2)*max(distance(g1,g2)*sin(angle(g1,g2,g3)) - (a/(1+exp(b*(distance(g1,g2)*cos(angle(g1,g2,g3))-c)))+d), 0)^2')"
)
self.addToConfig("dist_restraint.addGroup(lig)")
self.addToConfig("dist_restraint.addGroup(p1)")
self.addToConfig("dist_restraint.addGroup(p2)")
self.addToConfig("dist_restraint.addBond([0,1,2])")
self.addToConfig("dist_restraint.addGlobalParameter('k', k2)")
self.addToConfig("dist_restraint.addGlobalParameter('k2', k2)")
self.addToConfig("dist_restraint.addGlobalParameter('a', wall_width)")
self.addToConfig("dist_restraint.addGlobalParameter('b', beta_cent)")
self.addToConfig("dist_restraint.addGlobalParameter('c', s_cent)")
Expand All @@ -920,13 +920,13 @@ def _generate_config(self):

self.addToConfig("\n# Lower wall.")
self.addToConfig(
"lower_wall_rest = CustomCentroidBondForce(3, '(k/2)*min(distance(g1,g2)*cos(angle(g1,g2,g3)) - lower_wall, 0)^2')"
"lower_wall_rest = CustomCentroidBondForce(3, '(k1/2)*min(distance(g1,g2)*cos(angle(g1,g2,g3)) - lower_wall, 0)^2')"
)
self.addToConfig("lower_wall_rest.addGroup(lig)")
self.addToConfig("lower_wall_rest.addGroup(p1)")
self.addToConfig("lower_wall_rest.addGroup(p2)")
self.addToConfig("lower_wall_rest.addBond([0,1,2])")
self.addToConfig("lower_wall_rest.addGlobalParameter('k', k1)")
self.addToConfig("lower_wall_rest.addGlobalParameter('k1', k1)")
self.addToConfig(
"lower_wall_rest.addGlobalParameter('lower_wall', lower_wall)"
)
Expand Down
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