Skip to content

GitLab

pd2af
pd2af
Commit 32147db1 authored by Denis Shirshov's avatar Denis Shirshov
Browse files
Options

9

parent a475596d
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 398 additions and 1507 deletions
code/test-xml.rkt
View file @ 32147db1
......@@ -22,4 +22,5 @@
(write-file "../html/generated/result.sbgn" af-xml)
))
(test-xml "../examples/metabolismregulation.org_refined/F020-pyrimidine-SBGNv02.sbgn")
; (test-xml "../examples/metabolismregulation.org_refined/F020-pyrimidine-SBGNv02.sbgn")
(test-xml "../examples/logical-combination.sbgn")
examples/logical-combination.sbgn 0 → 100644
View file @ 32147db1
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="process description">
<glyph compartmentOrder="-11.0" id="glyph1" class="compartment">
<label text="CompartmentA">
<bbox y="252.0" x="759.0" h="16.0" w="92.0"/>
</label>
<bbox y="190.0" x="605.0" h="140.0" w="400.0"/>
</glyph>
<glyph id="M1" class="simple chemical">
<label text="M1"/>
<bbox y="530.0" x="160.0" h="40.0" w="80.0"/>
</glyph>
<glyph id="M2" class="simple chemical">
<label text="M2"/>
<bbox y="530.0" x="360.0" h="40.0" w="80.0"/>
</glyph>
<glyph id="p1" class="process">
<bbox y="538.0" x="288.0" h="24.0" w="24.0"/>
<port y="550.0" x="283.0" id="p1.1"/>
<port y="550.0" x="317.0" id="p1.2"/>
</glyph>
<glyph id="A" class="macromolecule">
<label text="A"/>
<bbox y="75.0" x="190.0" h="40.0" w="80.0"/>
</glyph>
<glyph id="not-41" orientation="vertical" class="not">
<bbox y="227.0" x="327.0" h="25.0" w="25.0"/>
<port y="264.5" x="339.5" id="not-41.2"/>
<port y="214.5" x="339.5" id="not-41.1"/>
</glyph>
<glyph id="C" class="macromolecule">
<label text="C"/>
<bbox y="75.0" x="330.0" h="40.0" w="80.0"/>
</glyph>
<glyph id="B" class="macromolecule">
<label text="B"/>
<bbox y="80.0" x="455.0" h="40.0" w="80.0"/>
</glyph>
<glyph id="or-42" orientation="vertical" class="or">
<bbox y="165.0" x="427.0" h="25.0" w="25.0"/>
<port y="152.5" x="439.5" id="or-42.1"/>
</glyph>
<glyph compartmentRef="glyph1" id="glyph2" class="macromolecule">
<label text="D"/>
<bbox y="210.0" x="871.0" h="60.0" w="108.0"/>
</glyph>
<glyph id="or-37" orientation="vertical" class="or">
<bbox y="307.0" x="262.0" h="25.0" w="25.0"/>
<port y="344.5" x="274.5" id="or-37.2"/>
<port y="294.5" x="274.5" id="or-37.1"/>
</glyph>
<arc target="p1.1" source="M1" id="consumption-35" class="consumption">
<start y="550.0" x="240.0"/>
<end y="550.0" x="283.0"/>
</arc>
<arc target="M2" source="p1.2" id="production-36" class="production">
<start y="550.0" x="317.0"/>
<end y="550.0" x="360.0"/>
</arc>
<arc target="p1" source="or-37.2" id="catalysis-49" class="catalysis">
<start y="344.5" x="274.5"/>
<end y="538.0" x="298.67245"/>
</arc>
<arc target="or-37.1" source="A" id="logic-arc-46" class="logic arc">
<start y="115.0" x="234.46115"/>
<end y="294.5" x="274.5"/>
</arc>
<arc target="or-37.1" source="not-41.2" id="logic-arc-48" class="logic arc">
<start y="264.5" x="339.5"/>
<end y="294.5" x="274.5"/>
</arc>
<arc target="not-41.1" source="or-42" id="logic-arc-45" class="logic arc">
<start y="195.0" x="439.5"/>
<next y="202.5" x="439.5"/>
<end y="214.5" x="339.5"/>
</arc>
<arc target="or-42.1" source="C" id="logic-arc-43" class="logic arc">
<start y="115.0" x="394.17392"/>
<end y="152.5" x="439.5"/>
</arc>
<arc target="or-42.1" source="B" id="logic-arc-44" class="logic arc">
<start y="120.0" x="495.0"/>
<end y="152.5" x="439.5"/>
</arc>
<arc target="or-37.1" source="glyph2" id="arc1" class="logic arc">
<start y="244.52422" x="871.0"/>
<end y="294.5" x="274.5"/>
</arc>
</map>
</sbgn>
html/generated/result.sbgn
View file @ 32147db1
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="activity flow">
<glyph id="glyph_n2" class="biological activity">
<label text="ERK1/2" />
<bbox x="185.0" y="100.0" w="80.0" h="40.0" />
<glyph id="glyph1" class="compartment">
<label text="CompartmentA" />
<bbox x="605.0" y="190.0" w="400.0" h="140.0" />
</glyph>
<glyph id="glyph_n1" class="biological activity">
<label text="CAD" />
<bbox x="335.0" y="180.0" w="80.0" h="40.0" />
<glyph id="A" class="biological activity">
<label text="A" />
<bbox x="190.0" y="75.0" w="80.0" h="40.0" />
</glyph>
<glyph id="glyph_n4" class="biological activity">
<label text="glutamine" />
<bbox x="175.0" y="320.0" w="100.0" h="30.0" />
<glyph id="glyph_n4-uoi-22" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="205.0" y="315.0" w="40" h="10" />
</glyph>
<glyph id="glyph2" class="biological activity" compartmentRef="glyph1">
<label text="D" />
<bbox x="871.0" y="210.0" w="108.0" h="60.0" />
</glyph>
<glyph id="glyph_n8" class="biological activity">
<label text="glutamate" />
<bbox x="409.1602" y="370.0" w="100.0" h="30.0" />
<glyph id="glyph_n8-uoi-23" class="unit of information">
<glyph id="C" class="biological activity">
<label text="C" />
<bbox x="330.0" y="75.0" w="80.0" h="40.0" />
</glyph>
<glyph id="B" class="biological activity">
<label text="B" />
<bbox x="455.0" y="80.0" w="80.0" h="40.0" />
</glyph>
<glyph id="M1" class="biological activity">
<label text="M1" />
<bbox x="160.0" y="530.0" w="80.0" h="40.0" />
<glyph id="M1-uoi-24" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="439.1602" y="365.0" w="40" h="10" />
<bbox x="180.0" y="525.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="glyph_n10" class="biological activity">
<label text="carbamoyl-P" />
<bbox x="504.0" y="320.0" w="100.0" h="30.0" />
<glyph id="glyph_n10-uoi-24" class="unit of information">
<glyph id="M2" class="biological activity">
<label text="M2" />
<bbox x="360.0" y="530.0" w="80.0" h="40.0" />
<glyph id="M2-uoi-25" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="534.0" y="315.0" w="40" h="10" />
<bbox x="380.0" y="525.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="modulation-17" class="and">
<bbox x="390.0" y="301.0" w="25" h="25" />
<port id="modulation-17-in" x="385.0" y="313.5" />
<port id="modulation-17-out" x="420.0" y="313.5" />
<glyph id="and-11" class="and">
<bbox x="187.0" y="354.0" w="25" h="25" />
<port id="and-11-in" x="182.0" y="366.5" />
<port id="and-11-out" x="217.0" y="366.5" />
</glyph>
<glyph id="or-12" class="or">
<bbox x="376.0" y="208.0" w="25" h="25" />
<port id="or-12-in" x="388.5" y="203.0" />
<port id="or-12-out" x="388.5" y="238.0" />
</glyph>
<arc class="positive influence" id="modulation-16" source="glyph_n2" target="glyph_n1">
<start x="225.0" y="140.0" />
<end x="375.0" y="180.0" />
<glyph id="not-13" class="not">
<bbox x="187.0" y="262.0" w="25" h="25" />
<port id="not-13-in" x="199.5" y="257.0" />
<port id="not-13-out" x="199.5" y="292.0" />
</glyph>
<glyph id="or-14" class="or">
<bbox x="409.0" y="235.0" w="25" h="25" />
<port id="or-14-in" x="421.5" y="230.0" />
<port id="or-14-out" x="421.5" y="265.0" />
</glyph>
<arc class="positive influence" id="positive-influence-23" source="and-11-out" target="M2">
<start x="199.5" y="379.0" />
<end x="400.0" y="530.0" />
</arc>
<arc class="logic arc" id="logic-arc-21" source="M1" target="and-11-in">
<start x="200.0" y="530.0" />
<end x="182.0" y="366.5" />
</arc>
<arc class="logic arc" id="logic-arc-22" source="or-12" target="and-11-in">
<start x="388.5" y="238.0" />
<end x="182.0" y="366.5" />
</arc>
<arc class="logic arc" id="logic-arc-18" source="A" target="or-12-in">
<start x="230.0" y="115.0" />
<end x="388.5" y="203.0" />
</arc>
<arc class="logic arc" id="logic-arc-19" source="glyph2" target="or-12-in">
<start x="871.0" y="240.0" />
<end x="388.5" y="203.0" />
</arc>
<arc class="logic arc" id="logic-arc-18" source="glyph_n1" target="modulation-17-in">
<start x="375.0" y="220.0" />
<end x="385.0" y="313.5" />
<arc class="logic arc" id="logic-arc-20" source="not-13" target="or-12-in">
<start x="199.5" y="292.0" />
<end x="388.5" y="203.0" />
</arc>
<arc class="logic arc" id="logic-arc-19" source="glyph_n4" target="modulation-17-in">
<start x="275.0" y="335.0" />
<end x="385.0" y="313.5" />
<arc class="logic arc" id="logic-arc-17" source="or-14" target="not-13-in">
<start x="421.5" y="265.0" />
<end x="199.5" y="257.0" />
</arc>
<arc class="positive influence" id="positive-influence-20" source="modulation-17-out" target="glyph_n8">
<start x="402.5" y="326.0" />
<end x="459.1602" y="370.0" />
<arc class="logic arc" id="logic-arc-15" source="C" target="or-14-in">
<start x="370.0" y="115.0" />
<end x="421.5" y="230.0" />
</arc>
<arc class="positive influence" id="positive-influence-21" source="modulation-17-out" target="glyph_n10">
<start x="415.0" y="313.5" />
<end x="504.0" y="335.0" />
<arc class="logic arc" id="logic-arc-16" source="B" target="or-14-in">
<start x="495.0" y="120.0" />
<end x="421.5" y="230.0" />
</arc>
</map>
</sbgn>
\ No newline at end of file
html/specification.html
View file @ 32147db1
This diff is collapsed.
html/specification/_experiments/af.sbgn
View file @ 32147db1
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="activity flow">
<glyph id="A1" class="biological activity">
<label text="A-active1" />
<bbox x="160.0" y="230.0" w="80" h="40" />
<glyph id="M1" class="biological activity">
<label text="M1" />
<bbox x="160.0" y="530.0" w="80" h="40" />
<glyph id="M1-uoi-73" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="180.0" y="525.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="A2" class="biological activity">
<label text="A-active2" />
<bbox x="360.0" y="230.0" w="80" h="40" />
<glyph id="M2" class="biological activity">
<label text="M2" />
<bbox x="360.0" y="530.0" w="80" h="40" />
<glyph id="M2-uoi-74" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="380.0" y="525.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="A" class="biological activity">
<label text="A" />
<bbox x="260.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="B" class="biological activity">
<label text="B" />
<bbox x="460.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="C" class="biological activity">
<label text="C" />
<bbox x="260.0" y="130.0" w="80" h="40" />
<bbox x="360.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="D" class="biological activity">
<label text="D" />
<bbox x="560.0" y="230.0" w="80" h="40" />
</glyph>
<glyph id="and-57" class="and">
<bbox x="187.0" y="354.0" w="25" h="25" />
<port id="and-57-in" x="182.0" y="366.5" />
<port id="and-57-out" x="217.0" y="366.5" />
</glyph>
<glyph id="or-58" class="or">
<bbox x="162.0" y="162.0" w="25" h="25" />
<port id="or-58-in" x="174.5" y="157.0" />
<port id="or-58-out" x="174.5" y="192.0" />
</glyph>
<glyph id="and-59" class="and">
<bbox x="387.0" y="437.0" w="25" h="25" />
<port id="and-59-in" x="399.5" y="432.0" />
<port id="and-59-out" x="399.5" y="467.0" />
</glyph>
<glyph id="not-62" class="not">
<bbox x="187.0" y="262.0" w="25" h="25" />
<port id="not-62-in" x="199.5" y="257.0" />
<port id="not-62-out" x="199.5" y="292.0" />
</glyph>
<glyph id="or-63" class="or">
<bbox x="420.0" y="270.0" w="25" h="25" />
<port id="or-63-in" x="432.5" y="265.0" />
<port id="or-63-out" x="432.5" y="300.0" />
</glyph>
<arc class="positive influence" id="modulation-26" source="C" target="A1">
<start x="300.0" y="170.0" />
<end x="200.0" y="230.0" />
<arc class="positive influence" id="positive-influence-72" source="and-57-out" target="M2">
<start x="199.5" y="379.0" />
<end x="400.0" y="530.0" />
</arc>
<arc class="logic arc" id="logic-arc-70" source="M1" target="and-57-in">
<start x="200.0" y="530.0" />
<end x="182.0" y="366.5" />
</arc>
<arc class="logic arc" id="logic-arc-71" source="or-58" target="and-57-in">
<start x="174.5" y="192.0" />
<end x="182.0" y="366.5" />
</arc>
<arc class="logic arc" id="logic-arc-67" source="A" target="or-58-in">
<start x="260.0" y="150.0" />
<end x="174.5" y="157.0" />
</arc>
<arc class="logic arc" id="logic-arc-68" source="and-59" target="or-58-in">
<start x="399.5" y="467.0" />
<end x="174.5" y="157.0" />
</arc>
<arc class="logic arc" id="logic-arc-69" source="not-62" target="or-58-in">
<start x="199.5" y="292.0" />
<end x="174.5" y="157.0" />
</arc>
<arc class="logic arc" id="logic-arc-60" source="D" target="and-59-in">
<start x="600.0" y="270.0" />
<end x="399.5" y="432.0" />
</arc>
<arc class="logic arc" id="logic-arc-61" source="M1" target="and-59-in">
<start x="200.0" y="530.0" />
<end x="399.5" y="432.0" />
</arc>
<arc class="logic arc" id="logic-arc-66" source="or-63" target="not-62-in">
<start x="432.5" y="300.0" />
<end x="199.5" y="257.0" />
</arc>
<arc class="logic arc" id="logic-arc-64" source="C" target="or-63-in">
<start x="400.0" y="170.0" />
<end x="432.5" y="265.0" />
</arc>
<arc class="positive influence" id="modulation-27" source="C" target="A2">
<start x="300.0" y="170.0" />
<end x="400.0" y="230.0" />
<arc class="logic arc" id="logic-arc-65" source="B" target="or-63-in">
<start x="500.0" y="170.0" />
<end x="432.5" y="265.0" />
</arc>
</map>
</sbgn>
\ No newline at end of file
html/specification/_experiments/pd.sbgn
View file @ 32147db1
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="process description">
<glyph id="A1" class="macromolecule">
<label text="A" />
<bbox x="160.0" y="230.0" w="80" h="40" />
<glyph id="A1-state-variable-24" class="state variable">
<state value="active1" variable="" />
<bbox x="230.0" y="222.5" w="15" h="15" />
</glyph>
<glyph id="M1" class="simple chemical">
<label text="M1" />
<bbox x="160.0" y="530.0" w="80" h="40" />
</glyph>
<glyph id="M2" class="simple chemical">
<label text="M2" />
<bbox x="360.0" y="530.0" w="80" h="40" />
</glyph>
<glyph id="A2" class="macromolecule">
<glyph id="A" class="macromolecule">
<label text="A" />
<bbox x="360.0" y="230.0" w="80" h="40" />
<glyph id="A2-state-variable-25" class="state variable">
<state value="active2" variable="" />
<bbox x="430.0" y="222.5" w="15" h="15" />
</glyph>
<bbox x="260.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="C" class="macromolecule">
<label text="C" />
<bbox x="260.0" y="130.0" w="80" h="40" />
<bbox x="360.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="D" class="macromolecule">
<label text="D" />
<bbox x="560.0" y="230.0" w="80" h="40" />
</glyph>
<glyph id="p1" class="process">
<bbox x="288.0" y="538.0" w="24" h="24" />
<port id="p1-in" x="283.0" y="550.0" />
<port id="p1-out" x="317.0" y="550.0" />
</glyph>
<glyph id="B" class="macromolecule">
<label text="B" />
<bbox x="460.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="or-44" class="or">
<bbox x="137.0" y="162.0" w="25" h="25" />
<port id="or-44-in" x="149.5" y="157.0" />
<port id="or-44-out" x="149.5" y="192.0" />
</glyph>
<glyph id="and-45" class="and">
<bbox x="354.0" y="437.0" w="25" h="25" />
<port id="and-45-in" x="384.0" y="449.5" />
<port id="and-45-out" x="349.0" y="449.5" />
</glyph>
<glyph id="p" class="process">
<bbox x="288.0" y="238.0" w="24" h="24" />
<port id="p-in" x="283.0" y="250.0" />
<port id="p-out" x="317.0" y="250.0" />
<glyph id="not-48" class="not">
<bbox x="137.0" y="262.0" w="25" h="25" />
<port id="not-48-in" x="149.5" y="257.0" />
<port id="not-48-out" x="149.5" y="292.0" />
</glyph>
<arc class="production" id="production-21" source="p-in" target="A1">
<start x="317.0" y="250.0" />
<end x="240.0" y="250.0" />
<glyph id="or-49" class="or">
<bbox x="387.0" y="270.0" w="25" h="25" />
<port id="or-49-in" x="399.5" y="265.0" />
<port id="or-49-out" x="399.5" y="300.0" />
</glyph>
<arc class="consumption" id="consumption-42" source="M1" target="p1-in">
<start x="240.0" y="550.0" />
<end x="283.0" y="550.0" />
</arc>
<arc class="production" id="production-43" source="p1-out" target="M2">
<start x="317.0" y="550.0" />
<end x="360.0" y="550.0" />
</arc>
<arc class="catalysis" id="catalysis-56" source="or-44-out" target="p1">
<start x="149.5" y="187.0" />
<end x="300.0" y="538.0" />
</arc>
<arc class="logic arc" id="logic-arc-53" source="A" target="or-44-in">
<start x="260.0" y="150.0" />
<end x="149.5" y="157.0" />
</arc>
<arc class="logic arc" id="logic-arc-54" source="and-45" target="or-44-in">
<start x="349.0" y="449.5" />
<end x="149.5" y="157.0" />
</arc>
<arc class="logic arc" id="logic-arc-55" source="not-48" target="or-44-in">
<start x="149.5" y="292.0" />
<end x="149.5" y="157.0" />
</arc>
<arc class="logic arc" id="logic-arc-46" source="D" target="and-45-in">
<start x="600.0" y="270.0" />
<end x="384.0" y="449.5" />
</arc>
<arc class="logic arc" id="logic-arc-47" source="M1" target="and-45-in">
<start x="200.0" y="530.0" />
<end x="384.0" y="449.5" />
</arc>
<arc class="logic arc" id="logic-arc-52" source="or-49" target="not-48-in">
<start x="399.5" y="300.0" />
<end x="149.5" y="257.0" />
</arc>
<arc class="production" id="production-22" source="p-out" target="A2">
<start x="317.0" y="250.0" />
<end x="360.0" y="250.0" />
<arc class="logic arc" id="logic-arc-50" source="C" target="or-49-in">
<start x="400.0" y="170.0" />
<end x="399.5" y="265.0" />
</arc>
<arc class="catalysis" id="modulation-23" source="C" target="p">
<start x="300.0" y="170.0" />
<end x="300.0" y="238.0" />
<arc class="logic arc" id="logic-arc-51" source="B" target="or-49-in">
<start x="500.0" y="170.0" />
<end x="399.5" y="265.0" />
</arc>
</map>
</sbgn>
\ No newline at end of file
odysseus @ c64f4fa7
Subproject commit 0fb74ea180c3900a52cfbebf7ab4450cc024a308
Subproject commit c64f4fa791e232a0e11374c5f2625f93def21c94
odysseus_modules @ 7352ebb1
Subproject commit 52a525e8a58d89d9853b7853fdfcaf83dcc105b3
Subproject commit 7352ebb116f7957597e5ea4df7556de9d3badb11
tests/_experiments.pdafer
View file @ 32147db1
......@@ -2,48 +2,5 @@
(test-suite
(parameters name:_experiments)
(test-case
(parameters name:aiaimm-cat-aiiamm)
(sbgn-pd-context
(default:compartment
(A1 macromolecule name:A state:active1 q:1-2)
(B1 macromolecule name:B state:inactive1 q:1-3)
(C1 macromolecule name:C state:active1 q:1-4)
(D1 macromolecule name:D state:inactive1 q:1-5)
(M1 simple-chemical q:1-6)
(M2 simple-chemical q:1-7)
(ATP1 simple-chemical name:"ATP" q:1-8)
(NAD1 simple-chemical name:"NAD+" q:1-9)
(GTP1 simple-chemical name:"GTP" q:1-10)
(R macromolecule q:2-1)
(A2 macromolecule name:A state:active2 q:3-2)
(B2 macromolecule name:B state:inactive2 q:3-3)
(C2 macromolecule name:C state:inactive2 q:3-4)
(D2 macromolecule name:D state:active2 q:3-5)
(M3 simple-chemical q:3-6)
(M4 simple-chemical q:3-7)
(ADP1 simple-chemical name:"ADP" q:3-8)
(NADH1 simple-chemical name:"NADH" q:3-9)
(GDP1 simple-chemical name:"GDP" q:3-10)
((A1 B1 C1 D1 M1 M2 ATP1 NAD1 GTP1) (process p) (A2 B2 C2 D2 M3 M4 ADP1 NADH1 GDP1))
(R catalysis p)))
(sbgn-af-context
(default:compartment
(A1 biological-activity name:A-active1 q:1-2)
(C1 biological-activity name:C q:1-3)
(M1 biological-activity type:simple-chemical q:1-6)
(M2 biological-activity type:simple-chemical q:1-7)
(R biological-activity q:1-1)
(A2 biological-activity name:A-active2 q:3-1)
(D2 biological-activity name:D q:3-2)
(M3 biological-activity type:simple-chemical q:3-6)
(M4 biological-activity type:simple-chemical q:3-7)
((R M1 M2) positive-influence (A2 D2 M3 M4))
((R) negative-influence (A1 C1)))))
)
\ No newline at end of file
tests/elementary_regulation.pdafer
View file @ 32147db1
......@@ -106,7 +106,21 @@
(test-case-Cmm m-cat-m catalysis positive-influence)
(test-case-Cmm m-nsti-m necessary-stimulation necessary-stimulation)
(test-case-Cmm m-mod-m modulation unknown-influence)
(test-case-Cmm m-inh-m inhibition negative-influence) ; TODO: add NOT gate
(test-case
(parameters name:m-inh-m)
(sbgn-pd-context
(default:compartment
(C macromolecule q:2-1)
(A simple-chemical q:1-2)
(B simple-chemical q:3-2)
(A (process p) B)
(C inhibition p)))
(sbgn-af-context
(default:compartment
(C biological-activity q:2-1)
(A biological-activity type:simple-chemical q:1-2)
(B biological-activity type:simple-chemical q:3-2)
((C (not A)) negative-influence B))))
; multiple consumptions/production
(test-case
......@@ -171,4 +185,26 @@
(C biological-activity q:2-1)
(C positive-influence A1)
(C positive-influence A2))))
; logical gates
(test-case
(parameters name:logical_gates)
(sbgn-pd-context
(default:compartment
(M1 simple-chemical q:1-5)
(M2 simple-chemical q:3-5)
(A macromolecule q:2-1)
(C macromolecule q:3-1)
(D macromolecule q:5-2)
(M1 (process p1) M2)
((or A (and D M1) (not (or C (B macromolecule q:4-1)))) catalysis p1)))
(sbgn-af-context
(default:compartment
(M1 biological-activity type:simple-chemical q:1-5)
(M2 biological-activity type:simple-chemical q:3-5)
(A biological-activity q:2-1)
(B biological-activity q:4-1)
(C biological-activity q:3-1)
(D biological-activity q:5-2)
((M1 (or A (and D M1) (not (or C B)))) positive-influence M2))))
)
\ No newline at end of file
tests/test-results.tree
View file @ 32147db1
tests
elementary_regulation rule-number:1
i-sti-a rule-number:1 passed:<t>
i-cat-i rule-number:2 passed:<t>
i-nsti-i rule-number:3 passed:<t>
i-mod-i rule-number:4 passed:<t>
i-inh-i rule-number:5 passed:<t>
i-sti-a rule-number:6 passed:<t>
i-cat-a rule-number:7 passed:<t>
i-nsti-a rule-number:8 passed:<t>
i-mod-a rule-number:9 passed:<t>
i-inh-a rule-number:10 passed:<t>
a-sti-i rule-number:11 passed:<t>
a-cat-i rule-number:12 passed:<t>
a-nsti-i rule-number:13 passed:<t>
a-mod-i rule-number:14 passed:<t>
a-inh-i rule-number:15 passed:<t>