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Standard_Molecule.pkml
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Standard_Molecule.pkml
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<?xml version="1.0" encoding="utf-8"?>
<MoleculeBuilder id="WILstbQoOEmwa9UkL0akxA" name="Standard_Molecule" icon="DRUG" mode="Logical" containerType="Other" isFloating="1" quantityType="Drug" isXenobiotic="1" dim="Amount" defaultStartFormula="syb14uRedUOaEzQFexfdeA" displayUnit="µmol" version="14">
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<ValueOrigin id="34" source="Publication" description="Toxicol In Vitro. 2008 Mar;22(2):457-67 https://doi.org/10.1016/j.tiv.2007.09.010" />
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<Parameter id="YMRdHb0sxkuvjovc2blmDg" name="base_For_logD_Factor" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" buildMode="Property" isDefault="1" value="0.001">
<ValueOrigin id="34" source="Publication" description="Toxicol In Vitro. 2008 Mar;22(2):457-67 https://doi.org/10.1016/j.tiv.2007.09.010" />
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<Parameter id="199eDMQusUSF4oFbCJFISA" name="base_For_P_cell_Factor" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" buildMode="Property" isDefault="1" value="0.001">
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</Parameter>
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<Parameter id="MJV3LZzl8kupHVPpYOIMCA" name="BP_ALBUMIN" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" buildMode="Property" isDefault="1" value="1">
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</Parameter>
<Parameter id="e8yTrb-hB0me4vVPqXxTmQ" name="BP_UNKNOWN" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" buildMode="Property" isDefault="1" value="2">
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</Parameter>
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<Parameter id="NDMa3OeKz0eR35Lw0_YMEw" name="Is diprotic base monoprotic acid" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" formula="6c651731-3e73-465c-802f-9bc951909352" buildMode="Property" isDefault="1">
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<Parameter id="IqySRM75XEOGRFqsZQV4xw" name="Is small molecule" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" buildMode="Property" isDefault="0" value="1">
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<Parameter id="zPqx07U7pUOo5ta3m8JV5A" name="Is strong base" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" formula="52d3a743-a3c9-40de-aae5-dd2ee51ec789" buildMode="Property" isDefault="1">
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</Parameter>
<Parameter id="R_W8N0fYX0eBnOx6KL_9Mw" name="Is triprotic acid" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" formula="46e1e8f2-4c53-4c3a-ac1a-893d54cf11e1" buildMode="Property" isDefault="1">
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</Parameter>
<Parameter id="aWotiFddn02217YkSokqNw" name="Molecular weight" icon="Parameter" persistable="0" isFixedValue="0" dim="Molecular weight" quantityType="Parameter" negativeValuesAllowed="1" buildMode="Property" isDefault="0" value="2.2521E-07" displayUnit="g/mol">
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</Parameter>
<Parameter id="AJVg1BoYxU2q-r27INvDQw" name="pKa value 0" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" buildMode="Property" isDefault="1" value="0">
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<Parameter id="6hbJnQOyckWJjmwn0ZGamA" name="pKa value 1" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" buildMode="Property" isDefault="1" value="0">
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<Parameter id="73lncDWD0ke0Hc8Lbm4CWw" name="pKa value 2" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" buildMode="Property" isDefault="1" value="0">
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</Parameter>
<Parameter id="Eo1yRcynyk6oklKynlqyBA" name="pKa_Acid_0" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" formula="884fccf6-42c1-4242-b402-506df2b02b36" buildMode="Property" isDefault="1">
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<Parameter id="KJ7-o2vPE0eZPO3cemRbAA" name="pKa_Acid_1" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" formula="e8540347-c81c-4730-8d88-82db4084913b" buildMode="Property" isDefault="1">
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</Parameter>
<Parameter id="RVPxdDk6cUigJk9VEuM1qA" name="pKa_Acids_Count" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" formula="e1731078-5424-4f95-813a-1bc86e822c20" buildMode="Property" isDefault="1">
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</Parameter>
<Parameter id="8oDtrsjZIUmfNzEo4t2xGQ" name="pKa_Base_0" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" formula="9871e6a8-7f84-4231-8978-15bbf153f896" buildMode="Property" isDefault="1">
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<Parameter id="WefYVPh5PUWm2DO23HX7SA" name="pKa_Base_1" icon="Parameter" persistable="0" isFixedValue="0" quantityType="Parameter" negativeValuesAllowed="1" formula="4cf7ca90-ea1c-43ed-8ab3-05caf303ddd8" buildMode="Property" isDefault="1">
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<Formula id="eed093a5-9362-4956-b094-ff22791af639" name="PARAM_IsMonoproticBaseDiproticAcid" formula="pKa_Acids_Count=2 & pKa_Bases_Count = 1 ? 1 : 0">
<Paths>
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<Path path="21" as="22" />
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</Formula>
<Formula id="090b8ab5-e878-4f02-8e28-b557ac7675e9" name="PARAM_IsMonoproticBaseMonoproticAcid" formula="pKa_Acids_Count=1 & pKa_Bases_Count = 1 ? 1 : 0">
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<Formula id="334d4e73-7c63-428a-aee9-218e4aea2ade" name="PARAM_IsNeutral" formula="CT_0 = 0 AND CT_1 = 0 AND CT_2 = 0">
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<Formula id="52395372-8cde-4026-93ef-e509ac42bb36" name="PARAM_IsTriproticBase" formula="pKa_Acids_Count=0 & pKa_Bases_Count = 3 ? 1 : 0">
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<Formula id="884fccf6-42c1-4242-b402-506df2b02b36" name="PARAM_pKa_Acid_0" formula="pKa_OneAcid_0+pKa_TwoAcids_0+pKa_ThreeAcids_0">
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<Path path="39" as="40" />
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</Formula>
<Formula id="e8540347-c81c-4730-8d88-82db4084913b" name="PARAM_pKa_Acid_1" formula="pKa_TwoAcids_1+pKa_ThreeAcids_1">
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<Path path="43" as="44" />
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<Formula id="ec8d3be1-8e76-4b05-9c33-717634d6f561" name="PARAM_pKa_Acid_2" formula="IsTriproticAcid ? Max (pKa_0; Max (pKa_1; pKa_2)) : 0">
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<Formula id="9871e6a8-7f84-4231-8978-15bbf153f896" name="PARAM_pKa_Base_0" formula="pKa_OneBase_0+pKa_TwoBases_0+pKa_ThreeBases_0">
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<Path path="54" as="55" />
<Path path="56" as="57" />
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</Formula>
<Formula id="4cf7ca90-ea1c-43ed-8ab3-05caf303ddd8" name="PARAM_pKa_Base_1" formula="pKa_TwoBases_1+pKa_ThreeBases_1">
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<Path path="60" as="61" />
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<Formula id="40bba938-475b-4b17-bb5e-8470534d86d7" name="PARAM_pKa_Base_2" formula="IsTriproticBase ? Max (pKa_0; Max (pKa_1; pKa_2)) : 0">
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<Formula id="fadaecf4-5388-4a0a-947c-f0d30434ef3a" name="PARAM_pKa_Bases_Count" formula="(CT0 = CT_BASE ? 1 : 0) + (CT1 = CT_BASE ? 1 : 0) + (CT2 = CT_BASE ? 1 : 0)">
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<Formula id="c8eb3e95-663c-4b99-a75f-cfeadbf42f8c" name="PARAM_pKa_OneAcid_0" formula="pKa_Acids_Count=1 ? (CT0=CT_ACID ? pKa_0 : (CT1=CT_ACID ? pKa_1 : pKa_2)) : 0">
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<Formula id="28203288-f1f8-4b47-95e7-5130b45ce9f1" name="PARAM_pKa_OneBase_0" formula="pKa_Bases_Count=1 ? (CT0=CT_BASE ? pKa_0 : (CT1=CT_BASE ? pKa_1 : pKa_2)) : 0">
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<Formula id="b483c025-9149-4058-9c50-741aef9fb37d" name="PARAM_pKa_pH_WS_sol_F1" formula="CT0 != CT_NEUTRAL ? 1/(1+10^(CT0*(pKa_0-pH))) : 1">
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<Formula id="f2b612d6-6fae-4b18-a901-28bfaeb97fb9" name="PARAM_pKa_pH_WS_sol_F2" formula="CT1 != CT_NEUTRAL ? 1/(1+10^(CT1*(pKa_1-pH))) : 1">
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<Formula id="23e6b7c1-82e6-4d8f-8e74-8453eca25efe" name="PARAM_pKa_pH_WS_sol_F3" formula="CT2 != CT_NEUTRAL ? 1/(1+10^(CT2*(pKa_2-pH))) : 1">
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<Formula id="fb3238da-2f0a-4eb0-bb8a-43d16b3cc694" name="PARAM_pKa_pH_WS_sol_K1" formula="F1*F2*F3">
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<Formula id="7414c718-e5b4-4b9f-afa3-039680ab689e" name="PARAM_pKa_pH_WS_sol_K2" formula="(1-F1)*F2*F3">
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<Path path="74" as="75" />
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<Formula id="031ae87f-4a02-44ac-97c7-457de80bfa6a" name="PARAM_pKa_pH_WS_sol_K3" formula="F1*(1-F2)*F3">
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<Formula id="4141149e-afd1-4e49-93c3-9dabaf63624e" name="PARAM_pKa_pH_WS_sol_K4" formula="F1*F2*(1-F3)">
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<Formula id="fe3b77bc-f237-443b-9604-cae5bd28f50d" name="PARAM_pKa_pH_WS_sol_K5" formula="(1-F1)*(1-F2)*F3">
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<Formula id="bf00b956-7cfd-4689-a350-624a1c258893" name="PARAM_pKa_pH_WS_sol_K8" formula="(1-F1)*(1-F2)*(1-F3)">
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<Path path="74" as="75" />
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<Formula id="603b3c17-e65a-43ed-94fd-83577f605b23" name="PARAM_pKa_ThreeAcids_0" formula="IsTriproticAcid ? Min (pKa_0; Min (pKa_1; pKa_2)) : 0">
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<Formula id="3e2c738e-86b4-4593-b7ac-cacc3ef5c7c8" name="PARAM_pKa_ThreeAcids_1" formula="IsTriproticAcid ? (pKa_0 <= pKa_Acid_0 ? min(pKa_1; pKa_2) : (pKa_0 >= pKa_Acid_2 ? max(pKa_1; pKa_2) : pKa_0)) : 0">
<Paths>
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<Formula id="ce725a70-a221-4561-bce1-120cdf108f13" name="PARAM_pKa_ThreeBases_0" formula="IsTriproticBase ? Min (pKa_0; Min (pKa_1; pKa_2)) : 0">
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<Formula id="c5e3ddee-6600-4644-8013-c69d8a5295a2" name="PARAM_pKa_ThreeBases_1" formula="IsTriproticBase ? (pKa_0 <= pKa_Base_0 ? min(pKa_1; pKa_2) : (pKa_0 >= pKa_Base_2 ? max(pKa_1; pKa_2) : pKa_0)) : 0">
<Paths>
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<Path path="80" as="81" />
<Path path="82" as="83" />
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</Formula>
<Formula id="c442fe85-8a34-4dac-a541-35948e508149" name="PARAM_pKa_TwoAcids_0" formula="pKa_Acids_Count=2 ? (CT0 != CT_ACID ? Min(pKa_1;pKa_2) : (CT1 != CT_ACID ? Min(pKa_0;pKa_2) : Min(pKa_0;pKa_1))) : 0">
<Paths>
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</Formula>
<Formula id="6e8966f9-732d-42a4-8a5d-9597c547e560" name="PARAM_pKa_TwoAcids_1" formula="pKa_Acids_Count=2 ? (CT0 != CT_ACID ? Max(pKa_1;pKa_2) : (CT1 != CT_ACID ? Max(pKa_0;pKa_2) : Max(pKa_0;pKa_1))) : 0">
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<Formula id="0a4c0a94-a43e-42cc-86f2-82064dbc5e73" name="PARAM_pKa_TwoBases_0" formula="pKa_Bases_Count=2 ? (CT0 != CT_BASE ? Min(pKa_1;pKa_2) : (CT1 != CT_BASE ? Min(pKa_0;pKa_2) : Min(pKa_0;pKa_1))) : 0">
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</Formula>
<Formula id="7b93dd33-29e2-4a59-ab22-31ab071ce247" name="PARAM_pKa_TwoBases_1" formula="pKa_Bases_Count=2 ? (CT0 != CT_BASE ? Max(pKa_1;pKa_2) : (CT1 != CT_BASE ? Max(pKa_0;pKa_2) : Max(pKa_0;pKa_1))) : 0">
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</Formula>
<Formula id="6299b0a9-492f-4652-a05c-96a630778d71" name="PARAM_Solubility_pKa_RefpH_Factor" formula="K1+K2/base^(CT0^2)+K3/base^(CT1^2)+K4/base^(CT2^2)+K5/base^max(CT0+CT1;-CT0-CT1)+K6/base^max(CT0+CT2;-CT0-CT2)+K7/base^max(CT1+CT2;-CT1-CT2)+K8/base^max(CT0+CT1+CT2;-CT0-CT1-CT2)">
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<Path path="100" as="101" />
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</Formula>
<SumFormula id="13c2aa83-44dd-4960-9425-5dc9edaf1bc3" name="PARAM_TotalDrugMass" dim="Amount" variable="P" formulaString="P_#i">
<Criteria>
<DescriptorConditions>
<MatchTagCondition tag="DrugMass" />
<MatchTagCondition tag="MOLECULE" />
</DescriptorConditions>
</Criteria>
</SumFormula>
<Formula id="ca1c45f3-838b-41e2-b0e4-0cf085a72ee5" name="PARAM_P" dim="Velocity" formula="IsSmallMolecule ? (MWEff *1E9 / 336) ^ (-6) * 10^LogMA / 5 * 1E-4 *1E-1: 0">
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</Formula>
<Formula id="f48081ad-0762-432b-8cc5-eca1cc799a1d" name="PARAM_KProt" formula="(0.81 + 0.11 * 10^LogMA) / 24.92 * 5.0">
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<Path path="5" as="6" dim="7" />
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</Formula>
<Formula id="96018e12-e756-4b0f-b95b-b6f1e1f15553" name="PARAM_Aqueous_diffusion_coefficient" dim="Diffusion coefficient" formula="60 * 10^(-4.113-0.4609*Log10(MW * 1E9)) *1E-2">
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</Formula>
<Formula id="443b6be4-e8d8-4336-a15a-74a50f1d6f9d" name="PARAM_Ae" dim="Length" formula="0,0333 * (MW * 1E9) ^ 0,4226 * 1E-8">
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</Formula>
<Formula id="67022844-9595-46d8-94f9-4f9f4d0a45d2" name="ConcFormula" dim="Concentration (molar)" formula="V>0 ? M/V : 0">
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</Formula>
<Formula id="RL-Ziy0HVkK-FYQSApm11g" name="Solubility_in_ELF_formula" dim="Concentration (mass)" formula="Solubility_at_reference_pH">
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<Path path="108" as="109" dim="110" />
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</Formula>
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<StringMap>
<Map s="..|Effective molecular weight" id="0" />
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<Map s="Molecular weight" id="2" />
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<Map s="Log Units" id="7" />
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<Map s="Cl" id="11" />
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<Map s="F" id="13" />
<Map s="..|I" id="14" />
<Map s="I" id="15" />
<Map s="..|Molecular weight" id="16" />
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<Map s="Chlor" id="18" />
<Map s="..|pKa_Acids_Count" id="19" />
<Map s="pKa_Acids_Count" id="20" />
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<Map s="pKa_Bases_Count" id="22" />
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<Map s="pKa_2" id="34" />
<Map s="..|pKa_OneAcid_0" id="35" />
<Map s="pKa_OneAcid_0" id="36" />
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<Map s="pKa_ThreeBases_0" id="55" />
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<Map s="pKa_TwoBases_0" id="57" />
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<Map s="pKa_TwoBases_1" id="61" />
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<Map s="IsTriproticBase" id="63" />
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<Map s="..|pKa_Acid_0" id="76" />
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<Map s="pKa_Acid_2" id="79" />
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<Map s="pKa_Base_0" id="81" />
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<Map s="pKa_Base_2" id="83" />
<Map s="..|Solubility gain per charge" id="84" />
<Map s="base" id="85" />
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<Map s="K2" id="89" />
<Map s="..|pKa_pH_WS_sol_K3" id="90" />
<Map s="K3" id="91" />
<Map s="..|pKa_pH_WS_sol_K4" id="92" />
<Map s="K4" id="93" />
<Map s="..|pKa_pH_WS_sol_K5" id="94" />
<Map s="K5" id="95" />
<Map s="..|pKa_pH_WS_sol_K6" id="96" />
<Map s="K6" id="97" />
<Map s="..|pKa_pH_WS_sol_K7" id="98" />
<Map s="K7" id="99" />
<Map s="..|pKa_pH_WS_sol_K8" id="100" />
<Map s="K8" id="101" />
<Map s=".." id="102" />
<Map s="M" id="103" />
<Map s="Amount" id="104" />
<Map s="..|..|Volume" id="105" />
<Map s="V" id="106" />
<Map s="Volume" id="107" />
<Map s="..|Solubility at reference pH" id="108" />
<Map s="Solubility_at_reference_pH" id="109" />
<Map s="Concentration (mass)" id="110" />
</StringMap>
</FormulaCache>
</MoleculeBuilder>