def test_add_dummy():
A = mw.Apparatus()
dummy = mw.Dummy(name="dummy")
A.add(dummy, mw.Vessel(), tube)
P = mw.Protocol(A)
with pytest.raises(ValueError):
P.add(dummy, active=1) # should be a bool!
def test_add_valve():
A = mw.Apparatus()
valve = mw.Valve(mapping={pump1: 1, pump2: 2})
bad_valve = mw.Valve()
A.add([pump1, pump2], [valve, bad_valve], tube)
P = mw.Protocol(A)
expected = [
dict(start=0, stop=None, component=valve, params={"setting": 1})
]
# directly pass the pump object
P.add(valve, setting=pump1)
assert P.procedures == expected
P.procedures = []
# using its name
P.add(valve, setting="pump1")
assert P.procedures == expected
P.procedures = []
# using its port number
P.add(valve, setting=1)
assert P.procedures == expected
with pytest.raises(ValueError):
P.add(valve, setting=3)
with pytest.raises(ValueError):
P.add(bad_valve, setting=3)
def test_describe():
C = mw.Apparatus()
C.add(mw.Vessel("water"), b, t)
assert (
C.describe() ==
"A vessel containing water was connected to Component Component_1 using PVC tubing (length 1 foot, ID 1 inch, OD 2 inch). "
)
import json
from datetime import timedelta
import pytest
import yaml
import mechwolf as mw
A = mw.Apparatus()
pump1 = mw.Pump(name="pump1")
pump2 = mw.Pump(name="pump2")
tube = mw.Tube(length="1 foot", ID="1 in", OD="2 in", material="PVC")
A.add(pump1, pump2, tube)
def test_create_protocol():
# test naming
assert mw.Protocol(A, name="testing").name == "testing"
assert mw.Protocol(A).name == "Protocol_0"
assert mw.Protocol(A).name == "Protocol_1"
def test_add():
P = mw.Protocol(A)
procedure = {
"component": pump1,
"params": {
"rate": "10 mL/min"
},
"start": 0,
def create_apparatus(
valve1: mw.Valve = mw.Valve(),
valve2: mw.Valve = mw.Valve(),
valve3: mw.Valve = mw.Valve(),
pump1: mw.Pump = mw.Pump(),
pump2: mw.Pump = mw.Pump(),
pump3: mw.Pump = mw.Pump(),
) -> mw.Apparatus:
aa_vessels = {
"ala": mw.Vessel(name="FmocAla"),
"arg": mw.Vessel(name="FmocArg_Pbf"),
"asn": mw.Vessel(name="FmocAsn_Trt"),
"asp": mw.Vessel(name="FmocAsp_tBu"),
"cys": mw.Vessel(name="FmocCys_Trt"),
"gln": mw.Vessel(name="FmocGln_Trt"),
"glu": mw.Vessel(name="FmocGlu_tBu"),
"gly": mw.Vessel(name="FmocGly"),
"his": mw.Vessel(name="FmocHis_Trt"),
"ile": mw.Vessel(name="FmocIle"),
"leu": mw.Vessel(name="FmocLeu"),
"lys": mw.Vessel(name="FmocLys_Boc"),
"met": mw.Vessel(name="FmocMet"),
"phe": mw.Vessel(name="FmocPhe"),
"pro": mw.Vessel(name="FmocPro"),
"ser": mw.Vessel(name="FmocSer_tBu"),
"thr": mw.Vessel(name="FmocThr_tBu"),
"trp": mw.Vessel(name="FmocTrp_Boc"),
"tyr": mw.Vessel(name="FmocTyr_tBu"),
"val": mw.Vessel(name="FmocVal"),
}
# other vessels
solvent = mw.Vessel("Solvent", name="solvent")
deprotection = mw.Vessel("20% Piperdine", name="deprotection")
coupling_agent = mw.Vessel("HATU", name="coupling_agent")
coupling_base = mw.Vessel("NMM", name="coupling_base")
output = mw.Vessel("waste", name="output")
valve1.mapping = {
aa_vessels["ala"]: 1,
aa_vessels["cys"]: 2,
aa_vessels["asp"]: 3,
aa_vessels["glu"]: 4,
aa_vessels["phe"]: 5,
aa_vessels["gly"]: 6,
aa_vessels["his"]: 7,
coupling_agent: 8,
coupling_base: 9,
solvent: 10,
}
valve2.mapping = {
aa_vessels["leu"]: 1,
aa_vessels["met"]: 2,
aa_vessels["asn"]: 3,
aa_vessels["pro"]: 4,
aa_vessels["gln"]: 5,
aa_vessels["arg"]: 6,
aa_vessels["ser"]: 7,
coupling_agent: 8,
coupling_base: 9,
solvent: 10,
}
valve3.mapping = {
aa_vessels["thr"]: 1,
aa_vessels["trp"]: 2,
aa_vessels["ile"]: 3,
aa_vessels["lys"]: 4,
aa_vessels["tyr"]: 5,
aa_vessels["val"]: 6,
deprotection: 7,
coupling_agent: 8,
coupling_base: 9,
solvent: 10,
}
# tubes and mixer
fat_short_tube = mw.Tube(length="1 foot", ID="1/16 in", OD="1/8 in", material="PFA")
thin_short_tube = mw.Tube(length="1 ft", ID="0.04 in", OD="1/16 in", material="PFA")
thin_rxn_tube = mw.Tube(length="50 ft", ID="0.04 in", OD="1/16 in", material="PFA")
mixer = mw.CrossMixer(name="Cross mixer")
# define apparatus
A = mw.Apparatus("Generic peptide synthesizer")
A.add(valve1.mapping, valve1, fat_short_tube)
A.add(valve1, pump1, fat_short_tube)
A.add(pump1, mixer, thin_short_tube)
A.add(valve2.mapping, valve2, fat_short_tube)
A.add(valve2, pump2, fat_short_tube)
A.add(pump2, mixer, thin_short_tube)
A.add(valve3.mapping, valve3, fat_short_tube)
A.add(valve3, pump3, fat_short_tube)
A.add(pump3, mixer, thin_short_tube)
A.add(mixer, output, thin_rxn_tube)
A._validate() # just an extra safety check (ya never know)
return A
def test_add_multiple():
# multiple components connected to same component in one line
B = mw.Apparatus()
B.add([a, b, c], d, t)
assert B.network == [(a, d, t), (b, d, t), (c, d, t)]