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Random placement linkers #15

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Mar 28, 2022
Merged

Random placement linkers #15

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11 changes: 9 additions & 2 deletions pycomplexes/pycomplexes/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -258,9 +258,12 @@ def __init__(self, node, name, randomize=False, box=None):

# guess connections for gaussian domains
guessed_connections = []
flag_linkers_plus_random_placement=False
for dom in self.domains:
n = dom.node
if dom.type == "gaussian":
if randomize:
flag_linkers_plus_random_placement=True
start_atom = u.select_atoms(n["start_connection"][1])
if start_atom.n_atoms != 1:
raise RuntimeError(
Expand All @@ -287,7 +290,11 @@ def __init__(self, node, name, randomize=False, box=None):
}
guessed_connections.append(con3)
dom._metadata['connection_id'] = len(guessed_connections) - 1

if flag_linkers_plus_random_placement:
print("WARNING: You used the randomized starting position in combination with Gaussian linker domains!")
print("The random placement does not respect the distance restraints, " +
"which are implied by the Gaussian linker domains")
print("We strongly recommend not to combine random initial placement with Gaussian Linker domains!")

# update connections
connections = node.get("connections", dict())
Expand Down Expand Up @@ -477,7 +484,7 @@ def parser(p):
p.add_argument("--debye_length", type=float, default=10)
p.add_argument("--dielectric_constant", type=float, default=80)
p.add_argument(
"--random", type=bool, help="random placement of the topologies in the box"
"--random", action="store_true", help="random placement of the topologies in the box"
)
p.add_argument(
"--list_forcefields",
Expand Down
13 changes: 2 additions & 11 deletions tutorials/Linker/chmp3_simulations.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
"outputs": [],
"source": [
"%%writefile chmp3.top\n",
"box: [100, 100, 100]\n",
"box: [200, 200, 200]\n",
"topology:\n",
" CHMP3:\n",
" coordinate-file: chmp3.pdb\n",
Expand Down Expand Up @@ -59,7 +59,7 @@
"metadata": {},
"outputs": [],
"source": [
"!pycomplexes convert chmp3.top chmp3.cplx --random=True"
"!pycomplexes convert chmp3.top chmp3.cplx"
]
},
{
Expand Down Expand Up @@ -126,15 +126,6 @@
"!pycomplexes visualize -cc config.yaml"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"pwd"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down