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First run at a WIP Martini implementation #13

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Merged
merged 16 commits into from
Nov 23, 2023
Merged

First run at a WIP Martini implementation #13

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925f267
Add Martini 3 itp.
andrewtarzia Nov 21, 2023
2b187fc
Add Martini terms.
andrewtarzia Nov 21, 2023
119040b
Contain martini_openmm.
andrewtarzia Nov 21, 2023
b73a532
Refactor and add Martini system.
andrewtarzia Nov 21, 2023
78039f4
Handle Martini terms.
andrewtarzia Nov 21, 2023
e1cf0da
Handle missing import.
andrewtarzia Nov 23, 2023
3a67825
Bug fix.
andrewtarzia Nov 23, 2023
d464434
Add remove entry option.
andrewtarzia Nov 23, 2023
9e747fa
Minor.
andrewtarzia Nov 23, 2023
e2e66c5
Mypy, change forcefield name.
andrewtarzia Nov 23, 2023
2783343
Handle bead type name.
andrewtarzia Nov 23, 2023
b4e0576
File ending.
andrewtarzia Nov 23, 2023
451f579
Init.
andrewtarzia Nov 23, 2023
91d3672
Init.
andrewtarzia Nov 23, 2023
55ea3ed
Rename class to either element or type when appropriate.
andrewtarzia Nov 23, 2023
3f48bd5
Fix.
andrewtarzia Nov 23, 2023
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29 changes: 13 additions & 16 deletions first_paper_example/analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,7 @@ def analyse_cage(
g_measure = GeomMeasure(
target_torsions=(
TargetTorsion(
search_string=("b", "a", "c", "a", "b"),
search_string=("b1", "a1", "c1", "a1", "b1"),
search_estring=("Pb", "Ba", "Ag", "Ba", "Pb"),
measured_atom_ids=[0, 1, 3, 4],
phi0=openmm.unit.Quantity(
Expand All @@ -146,9 +146,6 @@ def analyse_cage(
molecule=conformer.molecule,
absolute=True,
)
dihedral_data = {
str("_".join(i)): dihedral_data[i] for i in dihedral_data
}
min_b2b_distance = g_measure.calculate_minb2b(conformer.molecule)
radius_gyration = g_measure.calculate_radius_gyration(
molecule=conformer.molecule,
Expand Down Expand Up @@ -177,36 +174,36 @@ def analyse_cage(
c3r0 = None
clr0 = None
for bt in ff_targets["bonds"]:
cp = (bt.class1, bt.class2)
cp = (bt.type1, bt.type2)
if "6P8" in name:
if ("b", "n") in (cp, tuple(reversed(cp))):
if ("b1", "n1") in (cp, tuple(reversed(cp))):
c3r0 = bt.bond_r.value_in_unit(openmm.unit.angstrom)
if ("b", "m") in (cp, tuple(reversed(cp))):
if ("b1", "m1") in (cp, tuple(reversed(cp))):
clr0 = bt.bond_r.value_in_unit(openmm.unit.angstrom)
else:
if ("a", "c") in (cp, tuple(reversed(cp))):
if ("a1", "c1") in (cp, tuple(reversed(cp))):
c2r0 = bt.bond_r.value_in_unit(openmm.unit.angstrom)
if ("b", "n") in (cp, tuple(reversed(cp))):
if ("b1", "n1") in (cp, tuple(reversed(cp))):
clr0 = bt.bond_r.value_in_unit(openmm.unit.angstrom)
elif ("b", "m") in (cp, tuple(reversed(cp))):
elif ("b1", "m1") in (cp, tuple(reversed(cp))):
clr0 = bt.bond_r.value_in_unit(openmm.unit.angstrom)

c2angle = None
c3angle = None
clangle = None
for at in ff_targets["angles"]:
cp = (at.class1, at.class2, at.class3)
cp = (at.type1, at.type2, at.type3)
if "6P8" in name:
if ("b", "n", "b") in (cp, tuple(reversed(cp))):
if ("b1", "n1", "b1") in (cp, tuple(reversed(cp))):
c3angle = at.angle.value_in_unit(openmm.unit.degrees)
if ("b", "m", "b") in (cp, tuple(reversed(cp))):
if ("b1", "m1", "b1") in (cp, tuple(reversed(cp))):
clangle = at.angle.value_in_unit(openmm.unit.degrees)
else:
if ("b", "a", "c") in (cp, tuple(reversed(cp))):
if ("b1", "a1", "c1") in (cp, tuple(reversed(cp))):
c2angle = at.angle.value_in_unit(openmm.unit.degrees)
if ("b", "n", "b") in (cp, tuple(reversed(cp))):
if ("b1", "n1", "b1") in (cp, tuple(reversed(cp))):
clangle = at.angle.value_in_unit(openmm.unit.degrees)
elif ("b", "m", "b") in (cp, tuple(reversed(cp))):
elif ("b1", "m1", "b1") in (cp, tuple(reversed(cp))):
clangle = at.angle.value_in_unit(openmm.unit.degrees)

force_field_dict = {
Expand Down
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