diff --git a/README.md b/README.md index 26a60a0..127aab3 100644 --- a/README.md +++ b/README.md @@ -267,7 +267,72 @@ To view more examples of common ECNet tasks such as hyperparameter optimization ECNet databases are comma-separated value (CSV) formatted files that provide information such as the ID of each data point, an optional explicit sort type, various strings and groups to identify data points, target values and input parameters. Row 1 is used to identify which columns are used for ID, explicit sorting assignment, various strings and groups, and target and input data, and row 2 contains the names of these strings/groups/targets/inputs. Additional rows are data points. -The [databases](https://github.com/TJKessler/ECNet/tree/master/databases) directory contains databases for cetane number as well as a database template. +The [databases](https://github.com/TJKessler/ECNet/tree/master/databases) directory contains databases for cetane number, cloud point, pour point and yield sooting index, as well as a database template. + +You can create an ECNet-formatted database with molecule names or SMILES and (optionally) target values. The following programs must be installed for you to do so: +- [Open Babel](http://openbabel.org/wiki/Main_Page) software +- [Java JRE](https://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html) version 6 and above + +Supplied names or SMILES must exist in a text file, one entry per line: +``` +Acetaldehyde +Acetaldehyde dimethyl acetal +Acetic acid +Acetic anhydride +Acetol +Acetone +Acetonitrile +Acetonylacetone +``` + +If target values are supplied, they must also exist in a text file (of equal length to the supplied names or SMILES): +``` +70 +147 +244 +284 +295 +133 +180 +376 +``` + +The database can then be constructed with: +```python +from ecnet.tools import create_db + +create_db('names.txt', 'my_database.csv', targets='targets.txt') +``` + +If SMILES strings are supplied instead of names: +```python +from ecnet.tools import create_db + +create_db('smiles.txt', 'my_database.csv', targets='targets.txt', form='smiles') +``` + +Your database's DATAID column (essentially Bates numbers for each molecule) will increment starting at 0001: + +| DATAID | +|-------- | +| DATAID | +| 0001 | +| 0002 | +| 0003 | + +If a prefix is desired for these values, specify it with: +```python +from ecnet.tools import create_db + +create_db('names.txt', 'my_database.csv', targets='targets.txt', id_prefix='MOL') +``` + +| DATAID | +|----------- | +| DATAID | +| MOL0001 | +| MOL0002 | +| MOL0003 | # Contributing, Reporting Issues and Other Support: diff --git a/databases/README.md b/databases/README.md index ec6d7c8..95075e0 100644 --- a/databases/README.md +++ b/databases/README.md @@ -2,5 +2,9 @@ ### Here are brief descriptions of the databases: - **cn_model_v1.0_full.csv**: cetane number database containing 482 molecules from 11 compound groups, each with an experimental cetane number and over 1600 QSPR descriptors generated using [E-Dragon](http://www.vcclab.org/lab/edragon/) - - **cn_model_v1.0.csv**: cetane number database containing 482 molecules from 11 compound groups, each with an experimental cetane number and 15 QSPR descriptors chosen via the [limit_parameters](https://github.com/TJKessler/ECNet/blob/master/examples/limit_db_parameters.py) server method + - **cn_model_v1.0.csv**: cetane number database containing 482 molecules from 11 compound groups, each with an experimental cetane number and 15 QSPR descriptors chosen via the [limit_parameters](https://github.com/tjkessler/ECNet/blob/master/examples/limit_input_parameters.py) Server method + - **cp_model_v1.0_full.csv**: cloud point database containing 43 molecules, each with an experimental cloud point value and over 1800 QSPR descriptors generated using [PaDEL-Descriptor](http://www.yapcwsoft.com/dd/padeldescriptor/) + - **cp_model_v1.0.csv**: cloud point database containing 43 molecules, each with an experimental cloud point value and 15 QSPR descriptors chosen via the [limit_parameters](https://github.com/tjkessler/ECNet/blob/master/examples/limit_input_parameters.py) Server method + - **pp_model_v1.0_full.csv**: pour point database containing 41 molecules, each with an experimental pour point value and over 1800 QSPR descriptors generated using [PaDEL-Descriptor](http://www.yapcwsoft.com/dd/padeldescriptor/) + - **pp_model_v1.0.csv**: pour point database containing 41 molecules, each with an experimental pour point value and 15 QSPR descriptors chosen via the [limit_parameters](https://github.com/tjkessler/ECNet/blob/master/examples/limit_input_parameters.py) Server method - **db_template.csv**: ECNet-formatted database template diff --git a/databases/cp_model_v1.0.csv b/databases/cp_model_v1.0.csv new file mode 100644 index 0000000..bb1afb4 --- /dev/null +++ b/databases/cp_model_v1.0.csv @@ -0,0 +1,45 @@ +DATAID,ASSIGNMENT,STRING,STRING,TARGET,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT 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R,SpMax_Dt,SpDiam_Dt,SpAD_Dt,SpMAD_Dt,EE_Dt,VE1_Dt,VE2_Dt,VE3_Dt,VR1_Dt,VR2_Dt,VR3_Dt,ECCEN,nHBd,nwHBd,nHBa,nwHBa,nHBint2,nHBint3,nHBint4,nHBint5,nHBint6,nHBint7,nHBint8,nHBint9,nHBint10,nHsOH,nHdNH,nHsSH,nHsNH2,nHssNH,nHaaNH,nHsNH3p,nHssNH2p,nHsssNHp,nHtCH,nHdCH2,nHdsCH,nHaaCH,nHCHnX,nHCsats,nHCsatu,nHAvin,nHother,nHmisc,nsLi,nssBe,nssssBem,nsBH2,nssBH,nsssB,nssssBm,nsCH3,ndCH2,nssCH2,ntCH,ndsCH,naaCH,nsssCH,nddC,ntsC,ndssC,naasC,naaaC,nssssC,nsNH3p,nsNH2,nssNH2p,ndNH,nssNH,naaNH,ntN,nsssNHp,ndsN,naaN,nsssN,nddsN,naasN,nssssNp,nsOH,ndO,nssO,naaO,naOm,nsOm,nsF,nsSiH3,nssSiH2,nsssSiH,nssssSi,nsPH2,nssPH,nsssP,ndsssP,nddsP,nsssssP,nsSH,ndS,nssS,naaS,ndssS,nddssS,nssssssS,nSm,nsCl,nsGeH3,nssGeH2,nsssGeH,nssssGe,nsAsH2,nssAsH,nsssAs,ndsssAs,nddsAs,nsssssAs,nsSeH,ndSe,nssSe,naaSe,ndssSe,nssssssSe,nddssSe,nsBr,nsSnH3,nssSnH2,nsssSnH,nssssSn,nsI,nsPbH3,nssPbH2,nsssPbH,nssssPb,SHBd,SwHBd,SHBa,SwHBa,SHBint2,SHBint3,SHBint4,SHBint5,SHBint6,SHBint7,SHBint8,SHBint9,SHBint10,SHsOH,SHdNH,SHsSH,SHsNH2,SHssNH,SHaaNH,SHsNH3p,SHssNH2p,SHsssNHp,SHtCH,SHdCH2,SHdsCH,SHaaCH,SHCHnX,SHCsats,SHCsatu,SHAvin,SHother,SHmisc,SsLi,SssBe,SssssBem,SsBH2,SssBH,SsssB,SssssBm,SsCH3,SdCH2,SssCH2,StCH,SdsCH,SaaCH,SsssCH,SddC,StsC,SdssC,SaasC,SaaaC,SssssC,SsNH3p,SsNH2,SssNH2p,SdNH,SssNH,SaaNH,StN,SsssNHp,SdsN,SaaN,SsssN,SddsN,SaasN,SssssNp,SsOH,SdO,SssO,SaaO,SaOm,SsOm,SsF,SsSiH3,SssSiH2,SsssSiH,SssssSi,SsPH2,SssPH,SsssP,SdsssP,SddsP,SsssssP,SsSH,SdS,SssS,SaaS,SdssS,SddssS,SssssssS,SSm,SsCl,SsGeH3,SssGeH2,SsssGeH,SssssGe,SsAsH2,SssAsH,SsssAs,SdsssAs,SddsAs,SsssssAs,SsSeH,SdSe,SssSe,SaaSe,SdssSe,SssssssSe,SddssSe,SsBr,SsSnH3,SssSnH2,SsssSnH,SssssSn,SsI,SsPbH3,SssPbH2,SsssPbH,SssssPb,minHBd,minwHBd,minHBa,minwHBa,minHBint2,minHBint3,minHBint4,minHBint5,minHBint6,minHBint7,minHBint8,minHBint9,minHBint10,minHsOH,minHdNH,minHsSH,minHsNH2,minHssNH,minHaaNH,minHsNH3p,minHssNH2p,minHsssNHp,minHtCH,minHdCH2,minHdsCH,minHaaCH,minHCHnX,minHCsats,minHCsatu,minHAvin,minHother,minHmisc,minsLi,minssBe,minssssBem,minsBH2,minssBH,minsssB,minssssBm,minsCH3,mindCH2,minssCH2,mintCH,mindsCH,minaaCH,minsssCH,minddC,mintsC,mindssC,minaasC,minaaaC,minssssC,minsNH3p,minsNH2,minssNH2p,mindNH,minssNH,minaaNH,mintN,minsssNHp,mindsN,minaaN,minsssN,minddsN,minaasN,minssssNp,minsOH,mindO,minssO,minaaO,minaOm,minsOm,minsF,minsSiH3,minssSiH2,minsssSiH,minssssSi,minsPH2,minssPH,minsssP,mindsssP,minddsP,minsssssP,minsSH,mindS,minssS,minaaS,mindssS,minddssS,minssssssS,minSm,minsCl,minsGeH3,minssGeH2,minsssGeH,minssssGe,minsAsH2,minssAsH,minsssAs,mindsssAs,minddsAs,minsssssAs,minsSeH,mindSe,minssSe,minaaSe,mindssSe,minssssssSe,minddssSe,minsBr,minsSnH3,minssSnH2,minsssSnH,minssssSn,minsI,minsPbH3,minssPbH2,minsssPbH,minssssPb,maxHBd,maxwHBd,maxHBa,maxwHBa,maxHBint2,maxHBint3,maxHBint4,maxHBint5,maxHBint6,maxHBint7,maxHBint8,maxHBint9,maxHBint10,maxHsOH,maxHdNH,maxHsSH,maxHsNH2,maxHssNH,maxHaaNH,maxHsNH3p,maxHssNH2p,maxHsssNHp,maxHtCH,maxHdCH2,maxHdsCH,maxHaaCH,maxHCHnX,maxHCsats,maxHCsatu,maxHAvin,maxHother,maxHmisc,maxsLi,maxssBe,maxssssBem,maxsBH2,maxssBH,maxsssB,maxssssBm,maxsCH3,maxdCH2,maxssCH2,maxtCH,maxdsCH,maxaaCH,maxsssCH,maxddC,maxtsC,maxdssC,maxaasC,maxaaaC,maxssssC,maxsNH3p,maxsNH2,maxssNH2p,maxdNH,maxssNH,maxaaNH,maxtN,maxsssNHp,maxdsN,maxaaN,maxsssN,maxddsN,maxaasN,maxssssNp,maxsOH,maxdO,maxssO,maxaaO,maxaOm,maxsOm,maxsF,maxsSiH3,maxssSiH2,maxsssSiH,maxssssSi,maxsPH2,maxssPH,maxsssP,maxdsssP,maxddsP,maxsssssP,maxsSH,maxdS,maxssS,maxaaS,maxdssS,maxddssS,maxssssssS,maxSm,maxsCl,maxsGeH3,maxssGeH2,maxsssGeH,maxssssGe,maxsAsH2,maxssAsH,maxsssAs,maxdsssAs,maxddsAs,maxsssssAs,maxsSeH,maxdSe,maxssSe,maxaaSe,maxdssSe,maxssssssSe,maxddssSe,maxsBr,maxsSnH3,maxssSnH2,maxsssSnH,maxssssSn,maxsI,maxsPbH3,maxssPbH2,maxsssPbH,maxssssPb,sumI,meanI,hmax,gmax,hmin,gmin,LipoaffinityIndex,MAXDN,MAXDP,DELS,MAXDN2,MAXDP2,DELS2,ETA_Alpha,ETA_AlphaP,ETA_dAlpha_A,ETA_dAlpha_B,ETA_Epsilon_1,ETA_Epsilon_2,ETA_Epsilon_3,ETA_Epsilon_4,ETA_Epsilon_5,ETA_dEpsilon_A,ETA_dEpsilon_B,ETA_dEpsilon_C,ETA_dEpsilon_D,ETA_Psi_1,ETA_dPsi_A,ETA_dPsi_B,ETA_Shape_P,ETA_Shape_Y,ETA_Shape_X,ETA_Beta,ETA_BetaP,ETA_Beta_s,ETA_BetaP_s,ETA_Beta_ns,ETA_BetaP_ns,ETA_dBeta,ETA_dBetaP,ETA_Beta_ns_d,ETA_BetaP_ns_d,ETA_Eta,ETA_EtaP,ETA_Eta_R,ETA_Eta_F,ETA_EtaP_F,ETA_Eta_L,ETA_EtaP_L,ETA_Eta_R_L,ETA_Eta_F_L,ETA_EtaP_F_L,ETA_Eta_B,ETA_EtaP_B,ETA_Eta_B_RC,ETA_EtaP_B_RC,FMF,fragC,nHBAcc,nHBAcc2,nHBAcc3,nHBAcc_Lipinski,nHBDon,nHBDon_Lipinski,HybRatio,IC0,IC1,IC2,IC3,IC4,IC5,TIC0,TIC1,TIC2,TIC3,TIC4,TIC5,SIC0,SIC1,SIC2,SIC3,SIC4,SIC5,CIC0,CIC1,CIC2,CIC3,CIC4,CIC5,BIC0,BIC1,BIC2,BIC3,BIC4,BIC5,MIC0,MIC1,MIC2,MIC3,MIC4,MIC5,ZMIC0,ZMIC1,ZMIC2,ZMIC3,ZMIC4,ZMIC5,Kier1,Kier2,Kier3,nAtomLC,nAtomP,nAtomLAC,MLogP,McGowan_Volume,MDEC-11,MDEC-12,MDEC-13,MDEC-14,MDEC-22,MDEC-23,MDEC-24,MDEC-33,MDEC-34,MDEC-44,MDEO-11,MDEO-12,MDEO-22,MDEN-11,MDEN-12,MDEN-13,MDEN-22,MDEN-23,MDEN-33,MLFER_A,MLFER_BH,MLFER_BO,MLFER_S,MLFER_E,MLFER_L,MPC2,MPC3,MPC4,MPC5,MPC6,MPC7,MPC8,MPC9,MPC10,TPC,piPC1,piPC2,piPC3,piPC4,piPC5,piPC6,piPC7,piPC8,piPC9,piPC10,TpiPC,R_TpiPCTPC,PetitjeanNumber,nRing,n3Ring,n4Ring,n5Ring,n6Ring,n7Ring,n8Ring,n9Ring,n10Ring,n11Ring,n12Ring,nG12Ring,nFRing,nF4Ring,nF5Ring,nF6Ring,nF7Ring,nF8Ring,nF9Ring,nF10Ring,nF11Ring,nF12Ring,nFG12Ring,nTRing,nT4Ring,nT5Ring,nT6Ring,nT7Ring,nT8Ring,nT9Ring,nT10Ring,nT11Ring,nT12Ring,nTG12Ring,nHeteroRing,n3HeteroRing,n4HeteroRing,n5HeteroRing,n6HeteroRing,n7HeteroRing,n8HeteroRing,n9HeteroRing,n10HeteroRing,n11HeteroRing,n12HeteroRing,nG12HeteroRing,nFHeteroRing,nF4HeteroRing,nF5HeteroRing,nF6HeteroRing,nF7HeteroRing,nF8HeteroRing,nF9HeteroRing,nF10HeteroRing,nF11HeteroRing,nF12HeteroRing,nFG12HeteroRing,nTHeteroRing,nT4HeteroRing,nT5HeteroRing,nT6HeteroRing,nT7HeteroRing,nT8HeteroRing,nT9HeteroRing,nT10HeteroRing,nT11HeteroRing,nT12HeteroRing,nTG12HeteroRing,nRotB,RotBFrac,nRotBt,RotBtFrac,LipinskiFailures,topoRadius,topoDiameter,topoShape,GGI1,GGI2,GGI3,GGI4,GGI5,GGI6,GGI7,GGI8,GGI9,GGI10,JGI1,JGI2,JGI3,JGI4,JGI5,JGI6,JGI7,JGI8,JGI9,JGI10,JGT,SpMax_D,SpDiam_D,SpAD_D,SpMAD_D,EE_D,VE1_D,VE2_D,VE3_D,VR1_D,VR2_D,VR3_D,TopoPSA,VABC,VAdjMat,MWC2,MWC3,MWC4,MWC5,MWC6,MWC7,MWC8,MWC9,MWC10,TWC,SRW2,SRW3,SRW4,SRW5,SRW6,SRW7,SRW8,SRW9,SRW10,TSRW,MW,AMW,WTPT-1,WTPT-2,WTPT-3,WTPT-4,WTPT-5,WPATH,WPOL,XLogP,Zagreb,TDB1u,TDB2u,TDB3u,TDB4u,TDB5u,TDB6u,TDB7u,TDB8u,TDB9u,TDB10u,TDB1m,TDB2m,TDB3m,TDB4m,TDB5m,TDB6m,TDB7m,TDB8m,TDB9m,TDB10m,TDB1v,TDB2v,TDB3v,TDB4v,TDB5v,TDB6v,TDB7v,TDB8v,TDB9v,TDB10v,TDB1e,TDB2e,TDB3e,TDB4e,TDB5e,TDB6e,TDB7e,TDB8e,TDB9e,TDB10e,TDB1p,TDB2p,TDB3p,TDB4p,TDB5p,TDB6p,TDB7p,TDB8p,TDB9p,TDB10p,TDB1i,TDB2i,TDB3i,TDB4i,TDB5i,TDB6i,TDB7i,TDB8i,TDB9i,TDB10i,TDB1s,TDB2s,TDB3s,TDB4s,TDB5s,TDB6s,TDB7s,TDB8s,TDB9s,TDB10s,TDB1r,TDB2r,TDB3r,TDB4r,TDB5r,TDB6r,TDB7r,TDB8r,TDB9r,TDB10r,PPSA-1,PPSA-2,PPSA-3,PNSA-1,PNSA-2,PNSA-3,DPSA-1,DPSA-2,DPSA-3,FPSA-1,FPSA-2,FPSA-3,FNSA-1,FNSA-2,FNSA-3,WPSA-1,WPSA-2,WPSA-3,WNSA-1,WNSA-2,WNSA-3,RPCG,RNCG,RPCS,RNCS,THSA,TPSA,RHSA,RPSA,GRAV-1,GRAV-2,GRAV-3,GRAVH-1,GRAVH-2,GRAVH-3,GRAV-4,GRAV-5,GRAV-6,LOBMAX,LOBMIN,MOMI-X,MOMI-Y,MOMI-Z,MOMI-XY,MOMI-XZ,MOMI-YZ,MOMI-R,geomRadius,geomDiameter,geomShape,RDF10u,RDF15u,RDF20u,RDF25u,RDF30u,RDF35u,RDF40u,RDF45u,RDF50u,RDF55u,RDF60u,RDF65u,RDF70u,RDF75u,RDF80u,RDF85u,RDF90u,RDF95u,RDF100u,RDF105u,RDF110u,RDF115u,RDF120u,RDF125u,RDF130u,RDF135u,RDF140u,RDF145u,RDF150u,RDF155u,RDF10m,RDF15m,RDF20m,RDF25m,RDF30m,RDF35m,RDF40m,RDF45m,RDF50m,RDF55m,RDF60m,RDF65m,RDF70m,RDF75m,RDF80m,RDF85m,RDF90m,RDF95m,RDF100m,RDF105m,RDF110m,RDF115m,RDF120m,RDF125m,RDF130m,RDF135m,RDF140m,RDF145m,RDF150m,RDF155m,RDF10v,RDF15v,RDF20v,RDF25v,RDF30v,RDF35v,RDF40v,RDF45v,RDF50v,RDF55v,RDF60v,RDF65v,RDF70v,RDF75v,RDF80v,RDF85v,RDF90v,RDF95v,RDF100v,RDF105v,RDF110v,RDF115v,RDF120v,RDF125v,RDF130v,RDF135v,RDF140v,RDF145v,RDF150v,RDF155v,RDF10e,RDF15e,RDF20e,RDF25e,RDF30e,RDF35e,RDF40e,RDF45e,RDF50e,RDF55e,RDF60e,RDF65e,RDF70e,RDF75e,RDF80e,RDF85e,RDF90e,RDF95e,RDF100e,RDF105e,RDF110e,RDF115e,RDF120e,RDF125e,RDF130e,RDF135e,RDF140e,RDF145e,RDF150e,RDF155e,RDF10p,RDF15p,RDF20p,RDF25p,RDF30p,RDF35p,RDF40p,RDF45p,RDF50p,RDF55p,RDF60p,RDF65p,RDF70p,RDF75p,RDF80p,RDF85p,RDF90p,RDF95p,RDF100p,RDF105p,RDF110p,RDF115p,RDF120p,RDF125p,RDF130p,RDF135p,RDF140p,RDF145p,RDF150p,RDF155p,RDF10i,RDF15i,RDF20i,RDF25i,RDF30i,RDF35i,RDF40i,RDF45i,RDF50i,RDF55i,RDF60i,RDF65i,RDF70i,RDF75i,RDF80i,RDF85i,RDF90i,RDF95i,RDF100i,RDF105i,RDF110i,RDF115i,RDF120i,RDF125i,RDF130i,RDF135i,RDF140i,RDF145i,RDF150i,RDF155i,RDF10s,RDF15s,RDF20s,RDF25s,RDF30s,RDF35s,RDF40s,RDF45s,RDF50s,RDF55s,RDF60s,RDF65s,RDF70s,RDF75s,RDF80s,RDF85s,RDF90s,RDF95s,RDF100s,RDF105s,RDF110s,RDF115s,RDF120s,RDF125s,RDF130s,RDF135s,RDF140s,RDF145s,RDF150s,RDF155s,L1u,L2u,L3u,P1u,P2u,E1u,E2u,E3u,Tu,Au,Vu,Ku,Du,L1m,L2m,L3m,P1m,P2m,E1m,E2m,E3m,Tm,Am,Vm,Km,Dm,L1v,L2v,L3v,P1v,P2v,E1v,E2v,E3v,Tv,Av,Vv,Kv,Dv,L1e,L2e,L3e,P1e,P2e,E1e,E2e,E3e,Te,Ae,Ve,Ke,De,L1p,L2p,L3p,P1p,P2p,E1p,E2p,E3p,Tp,Ap,Vp,Kp,Dp,L1i,L2i,L3i,P1i,P2i,E1i,E2i,E3i,Ti,Ai,Vi,Ki,Di,L1s,L2s,L3s,P1s,P2s,E1s,E2s,E3s,Ts,As,Vs,Ks,Ds 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diff --git a/databases/pp_model_v1.0.csv b/databases/pp_model_v1.0.csv new file mode 100644 index 0000000..b8dec79 --- /dev/null +++ b/databases/pp_model_v1.0.csv @@ -0,0 +1,43 @@ +DATAID,ASSIGNMENT,STRING,STRING,TARGET,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT,INPUT +DATAID,ASSIGNMENT,Compound Name,SMILES,Target,MATS1c,minsssN,MIC0,C1SP3,P1u,P2u,AATS2p,maxwHBa,nF5Ring,MIC2,Km,maxaasC,maxHBint10,nHBint4,RHSA +UMLPP0001,L,Iso-propyle Alcohol + Oleic Acid,CCCCCCCCC=CCCCCCCCC(=O)OC(C)C,-21,-0.520768609,0,9.286541018,3,0.907172387,0.081264929,1.23748538,2.362838846,0,22.67139345,0.88631219,0,0,0,0.954618688 +UMLPP0002,V,Iso-butyl Alcohol + Oleic Acid,CCCCCCCCC=CCCCCCCCC(=O)OCC(C)C,-50,-0.488190337,0,9.203044452,4,0.97629813,0.015000922,1.246627005,2.365626212,0,23.22369051,0.982223991,0,0,0,0.94883256 +UMLPP0003,V,2-Ethylhexyl Alcohol + Oleic Acid,CCCCCCCCC=CCCCCCCCC(=O)OCC(CC)CCCC,-35,-0.462768039,0,8.921996436,4,0.851361906,0.135783242,1.252246684,2.3749036,0,22.48206279,0.800110302,0,0,0,0.955774557 +UMLPP0004,L,Iso-octyl Alcohol + Oleic Acid,CCCCCCCCC=CCCCCCCCC(=O)OCCCCCC(C)C,-29,-0.460162933,0,8.921996436,4,0.907659801,0.070959547,1.252246684,2.373673192,0,23.21358395,0.88230387,0,0,0,0.97376254 +UMLPP0005,L,Decyl Alcohol + Oleic Acid,CCCCCCCCC=CCCCCCCCC(=O)OCCCCCCCCCC,-3,-0.445281801,0,8.80639615,3,0.973146285,0.020468502,1.248134158,2.377274742,0,20.63799374,0.967568861,0,0,0,0.952576854 +UMLPP0006,V,Glycerol mono oleate Alcohol + Oleic Acid,CCCCCCCCC=CCCCCCCCC(=O)CCC(O)COC(=O)CCCCCCCC=CCCCCCCCC,0,-0.419191946,0,9.421515776,3,0.735645759,0.25638974,1.276988949,2.354874683,0,23.46152275,0.58034456,0,0,0,0.918166497 +UMLPP0007,V,2-Ethylhexyl Adipate,CCCCC(CC)COC(=O)CCCCC(=O)OCC(CC)CCCC,-68,-0.579711702,0,10.59910717,6,0.895546198,0.077973443,1.22459029,0,0,24.73009472,0.870423355,0,0,0,0.889231344 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Name,SMILES,Target,nAcid,ALogP,ALogp2,AMR,apol,naAromAtom,nAromBond,nAtom,nHeavyAtom,nH,nB,nC,nN,nO,nS,nP,nF,nCl,nBr,nI,nX,ATS0m,ATS1m,ATS2m,ATS3m,ATS4m,ATS5m,ATS6m,ATS7m,ATS8m,ATS0v,ATS1v,ATS2v,ATS3v,ATS4v,ATS5v,ATS6v,ATS7v,ATS8v,ATS0e,ATS1e,ATS2e,ATS3e,ATS4e,ATS5e,ATS6e,ATS7e,ATS8e,ATS0p,ATS1p,ATS2p,ATS3p,ATS4p,ATS5p,ATS6p,ATS7p,ATS8p,ATS0i,ATS1i,ATS2i,ATS3i,ATS4i,ATS5i,ATS6i,ATS7i,ATS8i,ATS0s,ATS1s,ATS2s,ATS3s,ATS4s,ATS5s,ATS6s,ATS7s,ATS8s,AATS0m,AATS1m,AATS2m,AATS3m,AATS4m,AATS5m,AATS6m,AATS7m,AATS8m,AATS0v,AATS1v,AATS2v,AATS3v,AATS4v,AATS5v,AATS6v,AATS7v,AATS8v,AATS0e,AATS1e,AATS2e,AATS3e,AATS4e,AATS5e,AATS6e,AATS7e,AATS8e,AATS0p,AATS1p,AATS2p,AATS3p,AATS4p,AATS5p,AATS6p,AATS7p,AATS8p,AATS0i,AATS1i,AATS2i,AATS3i,AATS4i,AATS5i,AATS6i,AATS7i,AATS8i,AATS0s,AATS1s,AATS2s,AATS3s,AATS4s,AATS5s,AATS6s,AATS7s,AATS8s,ATSC0c,ATSC1c,ATSC2c,ATSC3c,ATSC4c,ATSC5c,ATSC6c,ATSC7c,ATSC8c,ATSC0m,ATSC1m,ATSC2m,ATSC3m,ATSC4m,ATSC5m,ATSC6m,ATSC7m,ATSC8m,ATSC0v,ATSC1v,ATSC2v,ATSC3v,ATSC4v,ATSC5v,ATSC6v,ATSC7v,ATSC8v,ATSC0e,ATSC1e,ATSC2e,ATSC3e,ATSC4e,ATSC5e,ATSC6e,ATSC7e,ATSC8e,ATSC0p,ATSC1p,ATSC2p,ATSC3p,ATSC4p,ATSC5p,ATSC6p,ATSC7p,ATSC8p,ATSC0i,ATSC1i,ATSC2i,ATSC3i,ATSC4i,ATSC5i,ATSC6i,ATSC7i,ATSC8i,ATSC0s,ATSC1s,ATSC2s,ATSC3s,ATSC4s,ATSC5s,ATSC6s,ATSC7s,ATSC8s,AATSC0c,AATSC1c,AATSC2c,AATSC3c,AATSC4c,AATSC5c,AATSC6c,AATSC7c,AATSC8c,AATSC0m,AATSC1m,AATSC2m,AATSC3m,AATSC4m,AATSC5m,AATSC6m,AATSC7m,AATSC8m,AATSC0v,AATSC1v,AATSC2v,AATSC3v,AATSC4v,AATSC5v,AATSC6v,AATSC7v,AATSC8v,AATSC0e,AATSC1e,AATSC2e,AATSC3e,AATSC4e,AATSC5e,AATSC6e,AATSC7e,AATSC8e,AATSC0p,AATSC1p,AATSC2p,AATSC3p,AATSC4p,AATSC5p,AATSC6p,AATSC7p,AATSC8p,AATSC0i,AATSC1i,AATSC2i,AATSC3i,AATSC4i,AATSC5i,AATSC6i,AATSC7i,AATSC8i,AATSC0s,AATSC1s,AATSC2s,AATSC3s,AATSC4s,AATSC5s,AATSC6s,AATSC7s,AATSC8s,MATS1c,MATS2c,MATS3c,MATS4c,MATS5c,MATS6c,MATS7c,MATS8c,MATS1m,MATS2m,MATS3m,MATS4m,MATS5m,MATS6m,MATS7m,MATS8m,MATS1v,MATS2v,MATS3v,MATS4v,MATS5v,MATS6v,MATS7v,MATS8v,MATS1e,MATS2e,MATS3e,MATS4e,MATS5e,MATS6e,MATS7e,MATS8e,MATS1p,MATS2p,MATS3p,MATS4p,MATS5p,MATS6p,MATS7p,MATS8p,MATS1i,MATS2i,MATS3i,MATS4i,MATS5i,MATS6i,MATS7i,MATS8i,MATS1s,MATS2s,MATS3s,MATS4s,MATS5s,MATS6s,MATS7s,MATS8s,GATS1c,GATS2c,GATS3c,GATS4c,GATS5c,GATS6c,GATS7c,GATS8c,GATS1m,GATS2m,GATS3m,GATS4m,GATS5m,GATS6m,GATS7m,GATS8m,GATS1v,GATS2v,GATS3v,GATS4v,GATS5v,GATS6v,GATS7v,GATS8v,GATS1e,GATS2e,GATS3e,GATS4e,GATS5e,GATS6e,GATS7e,GATS8e,GATS1p,GATS2p,GATS3p,GATS4p,GATS5p,GATS6p,GATS7p,GATS8p,GATS1i,GATS2i,GATS3i,GATS4i,GATS5i,GATS6i,GATS7i,GATS8i,GATS1s,GATS2s,GATS3s,GATS4s,GATS5s,GATS6s,GATS7s,GATS8s,SpAbs_DzZ,SpMax_DzZ,SpDiam_DzZ,SpAD_DzZ,SpMAD_DzZ,EE_DzZ,SM1_DzZ,VE1_DzZ,VE2_DzZ,VE3_DzZ,VR1_DzZ,VR2_DzZ,VR3_DzZ,SpAbs_Dzm,SpMax_Dzm,SpDiam_Dzm,SpAD_Dzm,SpMAD_Dzm,EE_Dzm,SM1_Dzm,VE1_Dzm,VE2_Dzm,VE3_Dzm,VR1_Dzm,VR2_Dzm,VR3_Dzm,SpAbs_Dzv,SpMax_Dzv,SpDiam_Dzv,SpAD_Dzv,SpMAD_Dzv,EE_Dzv,SM1_Dzv,VE1_Dzv,VE2_Dzv,VE3_Dzv,VR1_Dzv,VR2_Dzv,VR3_Dzv,SpAbs_Dze,SpMax_Dze,SpDiam_Dze,SpAD_Dze,SpMAD_Dze,EE_Dze,SM1_Dze,VE1_Dze,VE2_Dze,VE3_Dze,VR1_Dze,VR2_Dze,VR3_Dze,SpAbs_Dzp,SpMax_Dzp,SpDiam_Dzp,SpAD_Dzp,SpMAD_Dzp,EE_Dzp,SM1_Dzp,VE1_Dzp,VE2_Dzp,VE3_Dzp,VR1_Dzp,VR2_Dzp,VR3_Dzp,SpAbs_Dzi,SpMax_Dzi,SpDiam_Dzi,SpAD_Dzi,SpMAD_Dzi,EE_Dzi,SM1_Dzi,VE1_Dzi,VE2_Dzi,VE3_Dzi,VR1_Dzi,VR2_Dzi,VR3_Dzi,SpAbs_Dzs,SpMax_Dzs,SpDiam_Dzs,SpAD_Dzs,SpMAD_Dzs,EE_Dzs,SM1_Dzs,VE1_Dzs,VE2_Dzs,VE3_Dzs,VR1_Dzs,VR2_Dzs,VR3_Dzs,nBase,BCUTw-1l,BCUTw-1h,BCUTc-1l,BCUTc-1h,BCUTp-1l,BCUTp-1h,nBonds,nBonds2,nBondsS,nBondsS2,nBondsS3,nBondsD,nBondsD2,nBondsT,nBondsQ,nBondsM,bpol,SpMax1_Bhm,SpMax2_Bhm,SpMax3_Bhm,SpMax4_Bhm,SpMax5_Bhm,SpMax6_Bhm,SpMax7_Bhm,SpMax8_Bhm,SpMin1_Bhm,SpMin2_Bhm,SpMin3_Bhm,SpMin4_Bhm,SpMin5_Bhm,SpMin6_Bhm,SpMin7_Bhm,SpMin8_Bhm,SpMax1_Bhv,SpMax2_Bhv,SpMax3_Bhv,SpMax4_Bhv,SpMax5_Bhv,SpMax6_Bhv,SpMax7_Bhv,SpMax8_Bhv,SpMin1_Bhv,SpMin2_Bhv,SpMin3_Bhv,SpMin4_Bhv,SpMin5_Bhv,SpMin6_Bhv,SpMin7_Bhv,SpMin8_Bhv,SpMax1_Bhe,SpMax2_Bhe,SpMax3_Bhe,SpMax4_Bhe,SpMax5_Bhe,SpMax6_Bhe,SpMax7_Bhe,SpMax8_Bhe,SpMin1_Bhe,SpMin2_Bhe,SpMin3_Bhe,SpMin4_Bhe,SpMin5_Bhe,SpMin6_Bhe,SpMin7_Bhe,SpMin8_Bhe,SpMax1_Bhp,SpMax2_Bhp,SpMax3_Bhp,SpMax4_Bhp,SpMax5_Bhp,SpMax6_Bhp,SpMax7_Bhp,SpMax8_Bhp,SpMin1_Bhp,SpMin2_Bhp,SpMin3_Bhp,SpMin4_Bhp,SpMin5_Bhp,SpMin6_Bhp,SpMin7_Bhp,SpMin8_Bhp,SpMax1_Bhi,SpMax2_Bhi,SpMax3_Bhi,SpMax4_Bhi,SpMax5_Bhi,SpMax6_Bhi,SpMax7_Bhi,SpMax8_Bhi,SpMin1_Bhi,SpMin2_Bhi,SpMin3_Bhi,SpMin4_Bhi,SpMin5_Bhi,SpMin6_Bhi,SpMin7_Bhi,SpMin8_Bhi,SpMax1_Bhs,SpMax2_Bhs,SpMax3_Bhs,SpMax4_Bhs,SpMax5_Bhs,SpMax6_Bhs,SpMax7_Bhs,SpMax8_Bhs,SpMin1_Bhs,SpMin2_Bhs,SpMin3_Bhs,SpMin4_Bhs,SpMin5_Bhs,SpMin6_Bhs,SpMin7_Bhs,SpMin8_Bhs,C1SP1,C2SP1,C1SP2,C2SP2,C3SP2,C1SP3,C2SP3,C3SP3,C4SP3,SCH-3,SCH-4,SCH-5,SCH-6,SCH-7,VCH-3,VCH-4,VCH-5,VCH-6,VCH-7,SC-3,SC-4,SC-5,SC-6,VC-3,VC-4,VC-5,VC-6,SPC-4,SPC-5,SPC-6,VPC-4,VPC-5,VPC-6,SP-0,SP-1,SP-2,SP-3,SP-4,SP-5,SP-6,SP-7,ASP-0,ASP-1,ASP-2,ASP-3,ASP-4,ASP-5,ASP-6,ASP-7,VP-0,VP-1,VP-2,VP-3,VP-4,VP-5,VP-6,VP-7,AVP-0,AVP-1,AVP-2,AVP-3,AVP-4,AVP-5,AVP-6,AVP-7,Sv,Sse,Spe,Sare,Sp,Si,Mv,Mse,Mpe,Mare,Mp,Mi,CrippenLogP,CrippenMR,SpMax_Dt,SpDiam_Dt,SpAD_Dt,SpMAD_Dt,EE_Dt,VE1_Dt,VE2_Dt,VE3_Dt,VR1_Dt,VR2_Dt,VR3_Dt,ECCEN,nHBd,nwHBd,nHBa,nwHBa,nHBint2,nHBint3,nHBint4,nHBint5,nHBint6,nHBint7,nHBint8,nHBint9,nHBint10,nHsOH,nHdNH,nHsSH,nHsNH2,nHssNH,nHaaNH,nHsNH3p,nHssNH2p,nHsssNHp,nHtCH,nHdCH2,nHdsCH,nHaaCH,nHCHnX,nHCsats,nHCsatu,nHAvin,nHother,nHmisc,nsLi,nssBe,nssssBem,nsBH2,nssBH,nsssB,nssssBm,nsCH3,ndCH2,nssCH2,ntCH,ndsCH,naaCH,nsssCH,nddC,ntsC,ndssC,naasC,naaaC,nssssC,nsNH3p,nsNH2,nssNH2p,ndNH,nssNH,naaNH,ntN,nsssNHp,ndsN,naaN,nsssN,nddsN,naasN,nssssNp,nsOH,ndO,nssO,naaO,naOm,nsOm,nsF,nsSiH3,nssSiH2,nsssSiH,nssssSi,nsPH2,nssPH,nsssP,ndsssP,nddsP,nsssssP,nsSH,ndS,nssS,naaS,ndssS,nddssS,nssssssS,nSm,nsCl,nsGeH3,nssGeH2,nsssGeH,nssssGe,nsAsH2,nssAsH,nsssAs,ndsssAs,nddsAs,nsssssAs,nsSeH,ndSe,nssSe,naaSe,ndssSe,nssssssSe,nddssSe,nsBr,nsSnH3,nssSnH2,nsssSnH,nssssSn,nsI,nsPbH3,nssPbH2,nsssPbH,nssssPb,SHBd,SwHBd,SHBa,SwHBa,SHBint2,SHBint3,SHBint4,SHBint5,SHBint6,SHBint7,SHBint8,SHBint9,SHBint10,SHsOH,SHdNH,SHsSH,SHsNH2,SHssNH,SHaaNH,SHsNH3p,SHssNH2p,SHsssNHp,SHtCH,SHdCH2,SHdsCH,SHaaCH,SHCHnX,SHCsats,SHCsatu,SHAvin,SHother,SHmisc,SsLi,SssBe,SssssBem,SsBH2,SssBH,SsssB,SssssBm,SsCH3,SdCH2,SssCH2,StCH,SdsCH,SaaCH,SsssCH,SddC,StsC,SdssC,SaasC,SaaaC,SssssC,SsNH3p,SsNH2,SssNH2p,SdNH,SssNH,SaaNH,StN,SsssNHp,SdsN,SaaN,SsssN,SddsN,SaasN,SssssNp,SsOH,SdO,SssO,SaaO,SaOm,SsOm,SsF,SsSiH3,SssSiH2,SsssSiH,SssssSi,SsPH2,SssPH,SsssP,SdsssP,SddsP,SsssssP,SsSH,SdS,SssS,SaaS,SdssS,SddssS,SssssssS,SSm,SsCl,SsGeH3,SssGeH2,SsssGeH,SssssGe,SsAsH2,SssAsH,SsssAs,SdsssAs,SddsAs,SsssssAs,SsSeH,SdSe,SssSe,SaaSe,SdssSe,SssssssSe,SddssSe,SsBr,SsSnH3,SssSnH2,SsssSnH,SssssSn,SsI,SsPbH3,SssPbH2,SsssPbH,SssssPb,minHBd,minwHBd,minHBa,minwHBa,minHBint2,minHBint3,minHBint4,minHBint5,minHBint6,minHBint7,minHBint8,minHBint9,minHBint10,minHsOH,minHdNH,minHsSH,minHsNH2,minHssNH,minHaaNH,minHsNH3p,minHssNH2p,minHsssNHp,minHtCH,minHdCH2,minHdsCH,minHaaCH,minHCHnX,minHCsats,minHCsatu,minHAvin,minHother,minHmisc,minsLi,minssBe,minssssBem,minsBH2,minssBH,minsssB,minssssBm,minsCH3,mindCH2,minssCH2,mintCH,mindsCH,minaaCH,minsssCH,minddC,mintsC,mindssC,minaasC,minaaaC,minssssC,minsNH3p,minsNH2,minssNH2p,mindNH,minssNH,minaaNH,mintN,minsssNHp,mindsN,minaaN,minsssN,minddsN,minaasN,minssssNp,minsOH,mindO,minssO,minaaO,minaOm,minsOm,minsF,minsSiH3,minssSiH2,minsssSiH,minssssSi,minsPH2,minssPH,minsssP,mindsssP,minddsP,minsssssP,minsSH,mindS,minssS,minaaS,mindssS,minddssS,minssssssS,minSm,minsCl,minsGeH3,minssGeH2,minsssGeH,minssssGe,minsAsH2,minssAsH,minsssAs,mindsssAs,minddsAs,minsssssAs,minsSeH,mindSe,minssSe,minaaSe,mindssSe,minssssssSe,minddssSe,minsBr,minsSnH3,minssSnH2,minsssSnH,minssssSn,minsI,minsPbH3,minssPbH2,minsssPbH,minssssPb,maxHBd,maxwHBd,maxHBa,maxwHBa,maxHBint2,maxHBint3,maxHBint4,maxHBint5,maxHBint6,maxHBint7,maxHBint8,maxHBint9,maxHBint10,maxHsOH,maxHdNH,maxHsSH,maxHsNH2,maxHssNH,maxHaaNH,maxHsNH3p,maxHssNH2p,maxHsssNHp,maxHtCH,maxHdCH2,maxHdsCH,maxHaaCH,maxHCHnX,maxHCsats,maxHCsatu,maxHAvin,maxHother,maxHmisc,maxsLi,maxssBe,maxssssBem,maxsBH2,maxssBH,maxsssB,maxssssBm,maxsCH3,maxdCH2,maxssCH2,maxtCH,maxdsCH,maxaaCH,maxsssCH,maxddC,maxtsC,maxdssC,maxaasC,maxaaaC,maxssssC,maxsNH3p,maxsNH2,maxssNH2p,maxdNH,maxssNH,maxaaNH,maxtN,maxsssNHp,maxdsN,maxaaN,maxsssN,maxddsN,maxaasN,maxssssNp,maxsOH,maxdO,maxssO,maxaaO,maxaOm,maxsOm,maxsF,maxsSiH3,maxssSiH2,maxsssSiH,maxssssSi,maxsPH2,maxssPH,maxsssP,maxdsssP,maxddsP,maxsssssP,maxsSH,maxdS,maxssS,maxaaS,maxdssS,maxddssS,maxssssssS,maxSm,maxsCl,maxsGeH3,maxssGeH2,maxsssGeH,maxssssGe,maxsAsH2,maxssAsH,maxsssAs,maxdsssAs,maxddsAs,maxsssssAs,maxsSeH,maxdSe,maxssSe,maxaaSe,maxdssSe,maxssssssSe,maxddssSe,maxsBr,maxsSnH3,maxssSnH2,maxsssSnH,maxssssSn,maxsI,maxsPbH3,maxssPbH2,maxsssPbH,maxssssPb,sumI,meanI,hmax,gmax,hmin,gmin,LipoaffinityIndex,MAXDN,MAXDP,DELS,MAXDN2,MAXDP2,DELS2,ETA_Alpha,ETA_AlphaP,ETA_dAlpha_A,ETA_dAlpha_B,ETA_Epsilon_1,ETA_Epsilon_2,ETA_Epsilon_3,ETA_Epsilon_4,ETA_Epsilon_5,ETA_dEpsilon_A,ETA_dEpsilon_B,ETA_dEpsilon_C,ETA_dEpsilon_D,ETA_Psi_1,ETA_dPsi_A,ETA_dPsi_B,ETA_Shape_P,ETA_Shape_Y,ETA_Shape_X,ETA_Beta,ETA_BetaP,ETA_Beta_s,ETA_BetaP_s,ETA_Beta_ns,ETA_BetaP_ns,ETA_dBeta,ETA_dBetaP,ETA_Beta_ns_d,ETA_BetaP_ns_d,ETA_Eta,ETA_EtaP,ETA_Eta_R,ETA_Eta_F,ETA_EtaP_F,ETA_Eta_L,ETA_EtaP_L,ETA_Eta_R_L,ETA_Eta_F_L,ETA_EtaP_F_L,ETA_Eta_B,ETA_EtaP_B,ETA_Eta_B_RC,ETA_EtaP_B_RC,FMF,fragC,nHBAcc,nHBAcc2,nHBAcc3,nHBAcc_Lipinski,nHBDon,nHBDon_Lipinski,HybRatio,IC0,IC1,IC2,IC3,IC4,IC5,TIC0,TIC1,TIC2,TIC3,TIC4,TIC5,SIC0,SIC1,SIC2,SIC3,SIC4,SIC5,CIC0,CIC1,CIC2,CIC3,CIC4,CIC5,BIC0,BIC1,BIC2,BIC3,BIC4,BIC5,MIC0,MIC1,MIC2,MIC3,MIC4,MIC5,ZMIC0,ZMIC1,ZMIC2,ZMIC3,ZMIC4,ZMIC5,Kier1,Kier2,Kier3,nAtomLC,nAtomP,nAtomLAC,MLogP,McGowan_Volume,MDEC-11,MDEC-12,MDEC-13,MDEC-14,MDEC-22,MDEC-23,MDEC-24,MDEC-33,MDEC-34,MDEC-44,MDEO-11,MDEO-12,MDEO-22,MDEN-11,MDEN-12,MDEN-13,MDEN-22,MDEN-23,MDEN-33,MLFER_A,MLFER_BH,MLFER_BO,MLFER_S,MLFER_E,MLFER_L,MPC2,MPC3,MPC4,MPC5,MPC6,MPC7,MPC8,MPC9,MPC10,TPC,piPC1,piPC2,piPC3,piPC4,piPC5,piPC6,piPC7,piPC8,piPC9,piPC10,TpiPC,R_TpiPCTPC,PetitjeanNumber,nRing,n3Ring,n4Ring,n5Ring,n6Ring,n7Ring,n8Ring,n9Ring,n10Ring,n11Ring,n12Ring,nG12Ring,nFRing,nF4Ring,nF5Ring,nF6Ring,nF7Ring,nF8Ring,nF9Ring,nF10Ring,nF11Ring,nF12Ring,nFG12Ring,nTRing,nT4Ring,nT5Ring,nT6Ring,nT7Ring,nT8Ring,nT9Ring,nT10Ring,nT11Ring,nT12Ring,nTG12Ring,nHeteroRing,n3HeteroRing,n4HeteroRing,n5HeteroRing,n6HeteroRing,n7HeteroRing,n8HeteroRing,n9HeteroRing,n10HeteroRing,n11HeteroRing,n12HeteroRing,nG12HeteroRing,nFHeteroRing,nF4HeteroRing,nF5HeteroRing,nF6HeteroRing,nF7HeteroRing,nF8HeteroRing,nF9HeteroRing,nF10HeteroRing,nF11HeteroRing,nF12HeteroRing,nFG12HeteroRing,nTHeteroRing,nT4HeteroRing,nT5HeteroRing,nT6HeteroRing,nT7HeteroRing,nT8HeteroRing,nT9HeteroRing,nT10HeteroRing,nT11HeteroRing,nT12HeteroRing,nTG12HeteroRing,nRotB,RotBFrac,nRotBt,RotBtFrac,LipinskiFailures,topoRadius,topoDiameter,topoShape,GGI1,GGI2,GGI3,GGI4,GGI5,GGI6,GGI7,GGI8,GGI9,GGI10,JGI1,JGI2,JGI3,JGI4,JGI5,JGI6,JGI7,JGI8,JGI9,JGI10,JGT,SpMax_D,SpDiam_D,SpAD_D,SpMAD_D,EE_D,VE1_D,VE2_D,VE3_D,VR1_D,VR2_D,VR3_D,TopoPSA,VABC,VAdjMat,MWC2,MWC3,MWC4,MWC5,MWC6,MWC7,MWC8,MWC9,MWC10,TWC,SRW2,SRW3,SRW4,SRW5,SRW6,SRW7,SRW8,SRW9,SRW10,TSRW,MW,AMW,WTPT-1,WTPT-2,WTPT-3,WTPT-4,WTPT-5,WPATH,WPOL,XLogP,Zagreb,TDB1u,TDB2u,TDB3u,TDB4u,TDB5u,TDB6u,TDB7u,TDB8u,TDB9u,TDB10u,TDB1m,TDB2m,TDB3m,TDB4m,TDB5m,TDB6m,TDB7m,TDB8m,TDB9m,TDB10m,TDB1v,TDB2v,TDB3v,TDB4v,TDB5v,TDB6v,TDB7v,TDB8v,TDB9v,TDB10v,TDB1e,TDB2e,TDB3e,TDB4e,TDB5e,TDB6e,TDB7e,TDB8e,TDB9e,TDB10e,TDB1p,TDB2p,TDB3p,TDB4p,TDB5p,TDB6p,TDB7p,TDB8p,TDB9p,TDB10p,TDB1i,TDB2i,TDB3i,TDB4i,TDB5i,TDB6i,TDB7i,TDB8i,TDB9i,TDB10i,TDB1s,TDB2s,TDB3s,TDB4s,TDB5s,TDB6s,TDB7s,TDB8s,TDB9s,TDB10s,TDB1r,TDB2r,TDB3r,TDB4r,TDB5r,TDB6r,TDB7r,TDB8r,TDB9r,TDB10r,PPSA-1,PPSA-2,PPSA-3,PNSA-1,PNSA-2,PNSA-3,DPSA-1,DPSA-2,DPSA-3,FPSA-1,FPSA-2,FPSA-3,FNSA-1,FNSA-2,FNSA-3,WPSA-1,WPSA-2,WPSA-3,WNSA-1,WNSA-2,WNSA-3,RPCG,RNCG,RPCS,RNCS,THSA,TPSA,RHSA,RPSA,GRAV-1,GRAV-2,GRAV-3,GRAVH-1,GRAVH-2,GRAVH-3,GRAV-4,GRAV-5,GRAV-6,LOBMAX,LOBMIN,MOMI-X,MOMI-Y,MOMI-Z,MOMI-XY,MOMI-XZ,MOMI-YZ,MOMI-R,geomRadius,geomDiameter,geomShape,RDF10u,RDF15u,RDF20u,RDF25u,RDF30u,RDF35u,RDF40u,RDF45u,RDF50u,RDF55u,RDF60u,RDF65u,RDF70u,RDF75u,RDF80u,RDF85u,RDF90u,RDF95u,RDF100u,RDF105u,RDF110u,RDF115u,RDF120u,RDF125u,RDF130u,RDF135u,RDF140u,RDF145u,RDF150u,RDF155u,RDF10m,RDF15m,RDF20m,RDF25m,RDF30m,RDF35m,RDF40m,RDF45m,RDF50m,RDF55m,RDF60m,RDF65m,RDF70m,RDF75m,RDF80m,RDF85m,RDF90m,RDF95m,RDF100m,RDF105m,RDF110m,RDF115m,RDF120m,RDF125m,RDF130m,RDF135m,RDF140m,RDF145m,RDF150m,RDF155m,RDF10v,RDF15v,RDF20v,RDF25v,RDF30v,RDF35v,RDF40v,RDF45v,RDF50v,RDF55v,RDF60v,RDF65v,RDF70v,RDF75v,RDF80v,RDF85v,RDF90v,RDF95v,RDF100v,RDF105v,RDF110v,RDF115v,RDF120v,RDF125v,RDF130v,RDF135v,RDF140v,RDF145v,RDF150v,RDF155v,RDF10e,RDF15e,RDF20e,RDF25e,RDF30e,RDF35e,RDF40e,RDF45e,RDF50e,RDF55e,RDF60e,RDF65e,RDF70e,RDF75e,RDF80e,RDF85e,RDF90e,RDF95e,RDF100e,RDF105e,RDF110e,RDF115e,RDF120e,RDF125e,RDF130e,RDF135e,RDF140e,RDF145e,RDF150e,RDF155e,RDF10p,RDF15p,RDF20p,RDF25p,RDF30p,RDF35p,RDF40p,RDF45p,RDF50p,RDF55p,RDF60p,RDF65p,RDF70p,RDF75p,RDF80p,RDF85p,RDF90p,RDF95p,RDF100p,RDF105p,RDF110p,RDF115p,RDF120p,RDF125p,RDF130p,RDF135p,RDF140p,RDF145p,RDF150p,RDF155p,RDF10i,RDF15i,RDF20i,RDF25i,RDF30i,RDF35i,RDF40i,RDF45i,RDF50i,RDF55i,RDF60i,RDF65i,RDF70i,RDF75i,RDF80i,RDF85i,RDF90i,RDF95i,RDF100i,RDF105i,RDF110i,RDF115i,RDF120i,RDF125i,RDF130i,RDF135i,RDF140i,RDF145i,RDF150i,RDF155i,RDF10s,RDF15s,RDF20s,RDF25s,RDF30s,RDF35s,RDF40s,RDF45s,RDF50s,RDF55s,RDF60s,RDF65s,RDF70s,RDF75s,RDF80s,RDF85s,RDF90s,RDF95s,RDF100s,RDF105s,RDF110s,RDF115s,RDF120s,RDF125s,RDF130s,RDF135s,RDF140s,RDF145s,RDF150s,RDF155s,L1u,L2u,L3u,P1u,P2u,E1u,E2u,E3u,Tu,Au,Vu,Ku,Du,L1m,L2m,L3m,P1m,P2m,E1m,E2m,E3m,Tm,Am,Vm,Km,Dm,L1v,L2v,L3v,P1v,P2v,E1v,E2v,E3v,Tv,Av,Vv,Kv,Dv,L1e,L2e,L3e,P1e,P2e,E1e,E2e,E3e,Te,Ae,Ve,Ke,De,L1p,L2p,L3p,P1p,P2p,E1p,E2p,E3p,Tp,Ap,Vp,Kp,Dp,L1i,L2i,L3i,P1i,P2i,E1i,E2i,E3i,Ti,Ai,Vi,Ki,Di,L1s,L2s,L3s,P1s,P2s,E1s,E2s,E3s,Ts,As,Vs,Ks,Ds +UMLPP0001,L,Iso-propyle Alcohol + Oleic 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+UMLPP0002,L,Iso-butyl Alcohol + Oleic 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+UMLPP0004,L,Iso-octyl Alcohol + Oleic 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+UMLPP0005,L,Decyl Alcohol + Oleic 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diff --git a/databases/ysi_model_v1.0.csv b/databases/ysi_model_v1.0.csv new file mode 100644 index 0000000..7572456 --- /dev/null +++ b/databases/ysi_model_v1.0.csv @@ -0,0 +1,423 @@ +"DATAID","ASSIGNMENT","STRING","STRING","TARGET","INPUT","INPUT","INPUT","INPUT","INPUT","INPUT","INPUT","INPUT","INPUT","INPUT","INPUT","INPUT","INPUT","INPUT","INPUT" +"DATAID","ASSIGNMENT","Compound Name","SMILES","Target","SpMax6_Bhs","R_TpiPCTPC","AATS3p","VP-0","SIC1","nsssSnH","MIC0","nN","nC","CIC2","R_TpiPCTPC","MLFER_L","maxsAsH2","WPOL","RNCG" +"UMLYSI0001","L","","C1=CC=C(C=C1)C2=CC=CC=C2C3=CC=CC=C3","1338.9","2.7466847270768713","7.394396551724138","1.623417584413223","10.082903768654765","0.2837128886399193","0.0","6.128871424445239","0","18","3.025398247285419","7.394396551724138","9.672","0.0","26.0","0.07107768971544853" 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diff --git a/ecnet/__init__.py b/ecnet/__init__.py index 95021aa..cdd7f16 100644 --- a/ecnet/__init__.py +++ b/ecnet/__init__.py @@ -3,4 +3,4 @@ import ecnet.error_utils import ecnet.model import ecnet.limit_parameters -__version__ = '2.0.1' +__version__ = '2.1.0' diff --git a/ecnet/data_utils.py b/ecnet/data_utils.py index 96c5b20..dd7cd37 100644 --- a/ecnet/data_utils.py +++ b/ecnet/data_utils.py @@ -2,8 +2,8 @@ # -*- coding: utf-8 -*- # # ecnet/data_utils.py -# v.2.0.1 -# Developed in 2018 by Travis Kessler +# v.2.1.0 +# Developed in 2019 by Travis Kessler # # Contains the "DataFrame" class, and functions for processing/importing/ # outputting data. High-level usage is handled by the "Server" class in diff --git a/ecnet/error_utils.py b/ecnet/error_utils.py index 0556351..6177ee4 100644 --- a/ecnet/error_utils.py +++ b/ecnet/error_utils.py @@ -2,8 +2,8 @@ # -*- coding: utf-8 -*- # # ecnet/error_utils.py -# v.2.0.1 -# Developed in 2018 by Travis Kessler +# v.2.1.0 +# Developed in 2019 by Travis Kessler # # Contains functions for error calculations # diff --git a/ecnet/fitness_functions.py b/ecnet/fitness_functions.py index 70f58e8..6e97b66 100644 --- a/ecnet/fitness_functions.py +++ b/ecnet/fitness_functions.py @@ -2,8 +2,8 @@ # -*- coding: utf-8 -*- # # ecnet/fitness_functions.py -# v.2.0.1 -# Developed in 2018 by Travis Kessler +# v.2.1.0 +# Developed in 2019 by Travis Kessler # # Contains fitness functions used for input dimensionality reduction, # hyperparameter tuning diff --git a/ecnet/limit_parameters.py b/ecnet/limit_parameters.py index f98b2e6..082f2d1 100644 --- a/ecnet/limit_parameters.py +++ b/ecnet/limit_parameters.py @@ -2,8 +2,8 @@ # -*- coding: utf-8 -*- # # ecnet/limit_parameters.py -# v.2.0.1 -# Developed in 2018 by Travis Kessler +# v.2.1.0 +# Developed in 2019 by Travis Kessler # # Contains the functions necessary for reducing the input dimensionality of a # database to the most influential input parameters, using either an iterative @@ -139,18 +139,18 @@ def limit_iterative_include(DataFrame, limit_num, vars, logger=None): logger.log( 'debug', 'Currently retained: {}'.format(retained_input_list), - call_loc={'call_loc': 'LIMIT'} + call_loc='LIMIT' ) logger.log( 'debug', 'Current RMSE: {}'.format(rmse_val), - call_loc={'call_loc': 'LIMIT'} + call_loc='LIMIT' ) logger.log( 'debug', 'Limited inputs: {}'.format(retained_input_list), - call_loc={'call_loc': 'LIMIT'} + call_loc='LIMIT' ) return retained_input_list @@ -208,7 +208,7 @@ def limit_genetic(DataFrame, limit_num, vars, population_size, num_generations, if logger is not None: logger.log('debug', 'Generation: 0 - Population fitness: {}'.format( sum(p.fitness_score for p in population.members) / len(population), - ), call_loc={'call_loc': 'LIMIT'}) + ), call_loc='LIMIT') for gen in range(num_generations): population.next_generation() @@ -221,7 +221,7 @@ def limit_genetic(DataFrame, limit_num, vars, population_size, num_generations, p.fitness_score for p in population.members ) / len(population) ), - call_loc={'call_loc': 'LIMIT'} + call_loc='LIMIT' ) min_idx = 0 @@ -239,12 +239,12 @@ def limit_genetic(DataFrame, limit_num, vars, population_size, num_generations, 'Best member fitness score: {}'.format( population.members[min_idx].fitness_score ), - call_loc={'call_loc': 'LIMIT'} + call_loc='LIMIT' ) logger.log( 'debug', 'Best member parameters: {}'.format(input_list), - call_loc={'call_loc': 'LIMIT'} + call_loc='LIMIT' ) return input_list diff --git a/ecnet/model.py b/ecnet/model.py index 69e537d..4c625f3 100644 --- a/ecnet/model.py +++ b/ecnet/model.py @@ -2,8 +2,8 @@ # -*- coding: utf-8 -*- # # ecnet/error_utils.py -# v.2.0.1 -# Developed in 2018 by Travis Kessler +# v.2.1.0 +# Developed in 2019 by Travis Kessler # # Contains functions necessary creating, training, saving, and reusing neural # network models diff --git a/ecnet/server.py b/ecnet/server.py index ae5ff90..e894078 100644 --- a/ecnet/server.py +++ b/ecnet/server.py @@ -2,8 +2,8 @@ # -*- coding: utf-8 -*- # # ecnet/server.py -# v.2.0.1 -# Developed in 2018 by Travis Kessler +# v.2.1.0 +# Developed in 2019 by Travis Kessler # # Contains the "Server" class, which handles ECNet project creation, neural # network model creation, data hand-off to models, and prediction error @@ -74,21 +74,21 @@ def __init__(self, config_filename='config.yml', project_file=None, self._logger.log( 'warn', 'Supplied configuration file not found', - call_loc={'call_loc': 'INIT'} + call_loc='INIT' ) self._logger.log( 'warn', 'Generating default configuration for {}'.format( config_filename ), - call_loc={'call_loc': 'INIT'} + call_loc='INIT' ) config_dict = { 'learning_rate': 0.1, - 'keep_prob': 0.0, + 'keep_prob': 1.0, 'hidden_layers': [ - [10, 'relu'], - [10, 'relu'] + [32, 'relu'], + [32, 'relu'] ], 'input_activation': 'relu', 'output_activation': 'linear', @@ -207,7 +207,7 @@ def create_project(self, project_name, num_builds=1, num_nodes=5, self._logger.log( 'info', 'Created project {}'.format(project_name), - call_loc={'call_loc': 'PROJECT'} + call_loc='PROJECT' ) def import_data(self, data_filename, sort_type='random', @@ -231,7 +231,7 @@ def import_data(self, data_filename, sort_type='random', self._logger.log( 'info', 'Imported data from {}'.format(data_filename), - call_loc={'call_loc': 'IMPORT'} + call_loc='IMPORT' ) def limit_input_parameters(self, limit_num, output_filename=None, @@ -267,13 +267,13 @@ def limit_input_parameters(self, limit_num, output_filename=None, self._logger.log('debug', 'Limiting input dimensionality to {}'.format( limit_num - ), call_loc={'call_loc': 'LIMIT'}) + ), call_loc='LIMIT') if use_genetic: self._logger.log( 'info', 'Limiting input dimensionality using a genetic algorithm', - call_loc={'call_loc': 'LIMIT'} + call_loc='LIMIT' ) params = ecnet.limit_parameters.limit_genetic( self.DataFrame, limit_num, self.vars, population_size, @@ -284,7 +284,7 @@ def limit_input_parameters(self, limit_num, output_filename=None, self._logger.log( 'info', 'Limiting input dimensionality using iterative inclusion', - call_loc={'call_loc': 'LIMIT'} + call_loc='LIMIT' ) params = ecnet.limit_parameters.limit_iterative_include( self.DataFrame, limit_num, self.vars, logger=self._logger @@ -296,7 +296,7 @@ def limit_input_parameters(self, limit_num, output_filename=None, self._logger.log( 'info', 'Saved limited database to {}'.format(output_filename), - call_loc={'call_loc': 'LIMIT'} + call_loc='LIMIT' ) return params @@ -361,7 +361,7 @@ def tune_hyperparameters(self, target_score=None, num_iterations=50, self._logger.log( 'info', 'Tuning neural network hyperparameters with an ABC', - call_loc={'call_loc': 'TUNE'} + call_loc='TUNE' ) abc.create_employers() @@ -385,17 +385,17 @@ def tune_hyperparameters(self, target_score=None, num_iterations=50, self._logger.log( 'debug', 'Tuned learning rate: {}'.format(new_hyperparameters[0]), - call_loc={'call_loc': 'TUNE'} + call_loc='TUNE' ) self._logger.log( 'debug', 'Tuned max validation epochs: {}'.format(new_hyperparameters[1]), - call_loc={'call_loc': 'TUNE'} + call_loc='TUNE' ) self._logger.log( 'debug', 'Tuned neuron keep probability: {}'.format(new_hyperparameters[2]), - call_loc={'call_loc': 'TUNE'} + call_loc='TUNE' ) for idx, layer in enumerate(self.vars['hidden_layers'], 3): self._logger.log( @@ -403,7 +403,7 @@ def tune_hyperparameters(self, target_score=None, num_iterations=50, 'Tuned number of neurons in hidden layer {}: {}'.format( idx - 2, new_hyperparameters[idx] ), - call_loc={'call_loc': 'TUNE'} + call_loc='TUNE' ) return new_hyperparameters @@ -428,7 +428,7 @@ def train_model(self, validate=False, shuffle=None, self._logger.log( 'info', 'Training single model', - call_loc={'call_loc': 'TRAIN'} + call_loc='TRAIN' ) ecnet.model.train_model( validate, @@ -444,7 +444,7 @@ def train_model(self, validate=False, shuffle=None, self.__num_builds, self.__num_nodes, self.__num_candidates ), - call_loc={'call_loc': 'TRAIN'} + call_loc='TRAIN' ) if self.__num_processes > 1: @@ -476,7 +476,7 @@ def train_model(self, validate=False, shuffle=None, 'Build {}, Node {}, candidate {}'.format( build + 1, node + 1, candidate + 1 ), - call_loc={'call_loc': 'TRAIN'} + call_loc='TRAIN' ) ecnet.model.train_model( validate, @@ -524,7 +524,7 @@ def select_best(self, dset=None, error_fn='mean_abs_error'): self._logger.log( 'info', 'Selecting best models from each node for each build', - call_loc={'call_loc': 'SELECTION'} + call_loc='SELECTION' ) x_vals = self.__determine_x_vals(dset) y_vals = self.__determine_y_vals(dset) @@ -580,13 +580,13 @@ def use_model(self, dset=None, output_filename=None): self._logger.log( 'info', 'Predicting values for all data', - call_loc={'call_loc': 'USE'} + call_loc='USE' ) else: self._logger.log( 'info', 'Predicting values for {} set'.format(dset), - call_loc={'call_loc': 'USE'} + call_loc='USE' ) results = self.__use(dset) if output_filename is not None: @@ -596,6 +596,11 @@ def use_model(self, dset=None, output_filename=None): self.DataFrame, output_filename ) + self._logger.log( + 'info', + 'Results saved to {}'.format(output_filename), + call_loc='USE' + ) return results def calc_error(self, *args, dset=None): @@ -618,13 +623,13 @@ def calc_error(self, *args, dset=None): self._logger.log( 'info', 'Calculating {} for all data'.format(arg), - call_loc={'call_loc': 'METRICS'} + call_loc='METRICS' ) else: self._logger.log( 'info', 'Calculating {} for {} set'.format(arg, dset), - call_loc={'call_loc': 'METRICS'} + call_loc='METRICS' ) error_dict = {} y_hat = self.__use(dset) @@ -640,7 +645,7 @@ def calc_error(self, *args, dset=None): self._logger.log( 'debug', '{} : {}'.format(arg, error_dict[arg]), - call_loc={'call_loc': 'METRICS'} + call_loc='METRICS' ) return error_dict @@ -699,7 +704,7 @@ def save_project(self, filename=None, clean_up=False): self._logger.log( 'info', 'Project saved to {}'.format(save_file), - call_loc={'call_loc': 'PROJECT'} + call_loc='PROJECT' ) def __open_project(self, project_name): @@ -758,7 +763,7 @@ def __open_project(self, project_name): self._logger.log( 'info', 'Opened project {}'.format(project_name), - call_loc={'call_loc': 'PROJECT'} + call_loc='PROJECT' ) def __determine_x_vals(self, dset): diff --git a/tools/PaDEL-Descriptor/Descriptors.xls b/ecnet/tools/PaDEL-Descriptor/Descriptors.xls similarity index 100% rename from tools/PaDEL-Descriptor/Descriptors.xls rename to ecnet/tools/PaDEL-Descriptor/Descriptors.xls diff --git a/tools/PaDEL-Descriptor/PaDEL-Descriptor.jar b/ecnet/tools/PaDEL-Descriptor/PaDEL-Descriptor.jar similarity index 100% rename from tools/PaDEL-Descriptor/PaDEL-Descriptor.jar rename to ecnet/tools/PaDEL-Descriptor/PaDEL-Descriptor.jar diff --git a/tools/PaDEL-Descriptor/descriptors.xml b/ecnet/tools/PaDEL-Descriptor/descriptors.xml similarity index 100% rename from tools/PaDEL-Descriptor/descriptors.xml rename to ecnet/tools/PaDEL-Descriptor/descriptors.xml diff --git a/tools/PaDEL-Descriptor/lib/ambit2-base-2.4.7-SNAPSHOT.jar b/ecnet/tools/PaDEL-Descriptor/lib/ambit2-base-2.4.7-SNAPSHOT.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/ambit2-base-2.4.7-SNAPSHOT.jar rename to ecnet/tools/PaDEL-Descriptor/lib/ambit2-base-2.4.7-SNAPSHOT.jar diff --git a/tools/PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT.jar b/ecnet/tools/PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT.jar rename to ecnet/tools/PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT.jar diff --git a/tools/PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT.jar b/ecnet/tools/PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT.jar rename to ecnet/tools/PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT.jar diff --git a/tools/PaDEL-Descriptor/lib/appframework-1.0.3.jar b/ecnet/tools/PaDEL-Descriptor/lib/appframework-1.0.3.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/appframework-1.0.3.jar rename to ecnet/tools/PaDEL-Descriptor/lib/appframework-1.0.3.jar diff --git a/tools/PaDEL-Descriptor/lib/cdk-1.4.15.jar b/ecnet/tools/PaDEL-Descriptor/lib/cdk-1.4.15.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/cdk-1.4.15.jar rename to ecnet/tools/PaDEL-Descriptor/lib/cdk-1.4.15.jar diff --git a/tools/PaDEL-Descriptor/lib/commons-cli-1.2.jar b/ecnet/tools/PaDEL-Descriptor/lib/commons-cli-1.2.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/commons-cli-1.2.jar rename to ecnet/tools/PaDEL-Descriptor/lib/commons-cli-1.2.jar diff --git a/tools/PaDEL-Descriptor/lib/guava-17.0.jar b/ecnet/tools/PaDEL-Descriptor/lib/guava-17.0.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/guava-17.0.jar rename to ecnet/tools/PaDEL-Descriptor/lib/guava-17.0.jar diff --git a/tools/PaDEL-Descriptor/lib/jama.jar b/ecnet/tools/PaDEL-Descriptor/lib/jama.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/jama.jar rename to ecnet/tools/PaDEL-Descriptor/lib/jama.jar diff --git a/tools/PaDEL-Descriptor/lib/jgrapht-0.6.0.jar b/ecnet/tools/PaDEL-Descriptor/lib/jgrapht-0.6.0.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/jgrapht-0.6.0.jar rename to ecnet/tools/PaDEL-Descriptor/lib/jgrapht-0.6.0.jar diff --git a/tools/PaDEL-Descriptor/lib/l2fprod-common-all.jar b/ecnet/tools/PaDEL-Descriptor/lib/l2fprod-common-all.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/l2fprod-common-all.jar rename to ecnet/tools/PaDEL-Descriptor/lib/l2fprod-common-all.jar diff --git a/tools/PaDEL-Descriptor/lib/libPaDEL-Descriptor.jar b/ecnet/tools/PaDEL-Descriptor/lib/libPaDEL-Descriptor.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/libPaDEL-Descriptor.jar rename to ecnet/tools/PaDEL-Descriptor/lib/libPaDEL-Descriptor.jar diff --git a/tools/PaDEL-Descriptor/lib/libPaDEL-Jobs.jar b/ecnet/tools/PaDEL-Descriptor/lib/libPaDEL-Jobs.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/libPaDEL-Jobs.jar rename to ecnet/tools/PaDEL-Descriptor/lib/libPaDEL-Jobs.jar diff --git a/tools/PaDEL-Descriptor/lib/libPaDEL.jar b/ecnet/tools/PaDEL-Descriptor/lib/libPaDEL.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/libPaDEL.jar rename to ecnet/tools/PaDEL-Descriptor/lib/libPaDEL.jar diff --git a/tools/PaDEL-Descriptor/lib/swing-worker-1.1.jar b/ecnet/tools/PaDEL-Descriptor/lib/swing-worker-1.1.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/swing-worker-1.1.jar rename to ecnet/tools/PaDEL-Descriptor/lib/swing-worker-1.1.jar diff --git a/tools/PaDEL-Descriptor/lib/vecmath1.2-1.14.jar b/ecnet/tools/PaDEL-Descriptor/lib/vecmath1.2-1.14.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/vecmath1.2-1.14.jar rename to ecnet/tools/PaDEL-Descriptor/lib/vecmath1.2-1.14.jar diff --git a/tools/PaDEL-Descriptor/lib/xom-1.1.jar b/ecnet/tools/PaDEL-Descriptor/lib/xom-1.1.jar similarity index 100% rename from tools/PaDEL-Descriptor/lib/xom-1.1.jar rename to ecnet/tools/PaDEL-Descriptor/lib/xom-1.1.jar diff --git a/tools/PaDEL-Descriptor/license/LICENSE.txt b/ecnet/tools/PaDEL-Descriptor/license/LICENSE.txt similarity index 100% rename from tools/PaDEL-Descriptor/license/LICENSE.txt rename to ecnet/tools/PaDEL-Descriptor/license/LICENSE.txt diff --git a/tools/PaDEL-Descriptor/license/README - CDK b/ecnet/tools/PaDEL-Descriptor/license/README - CDK similarity index 100% rename from tools/PaDEL-Descriptor/license/README - CDK rename to ecnet/tools/PaDEL-Descriptor/license/README - CDK diff --git a/tools/PaDEL-Descriptor/license/lgpl-2.1.txt b/ecnet/tools/PaDEL-Descriptor/license/lgpl-2.1.txt similarity index 100% rename from tools/PaDEL-Descriptor/license/lgpl-2.1.txt rename to ecnet/tools/PaDEL-Descriptor/license/lgpl-2.1.txt diff --git a/tools/PaDEL-Descriptor/license/lgpl.license b/ecnet/tools/PaDEL-Descriptor/license/lgpl.license similarity index 100% rename from tools/PaDEL-Descriptor/license/lgpl.license rename to ecnet/tools/PaDEL-Descriptor/license/lgpl.license diff --git a/ecnet/tools/__init__.py b/ecnet/tools/__init__.py new file mode 100644 index 0000000..d47794a --- /dev/null +++ b/ecnet/tools/__init__.py @@ -0,0 +1,2 @@ +from ecnet.tools.tools import create_db, get_smiles, smiles_to_mdl,\ + mdl_to_descriptors, predict_with_prj diff --git a/ecnet/tools/tools.py b/ecnet/tools/tools.py new file mode 100644 index 0000000..282b344 --- /dev/null +++ b/ecnet/tools/tools.py @@ -0,0 +1,276 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +# +# ecnet/tools/tools.py +# v.2.0.1 +# Developed in 2019 by Travis Kessler +# +# Contains various tools for database creation, MDL file creation, QSPR +# descriptor calculation +# + +# Stdlib imports +from copy import deepcopy +from csv import writer, QUOTE_ALL, DictReader +from os import devnull, remove +from os.path import abspath, dirname, isfile, join +from re import compile, IGNORECASE +from shutil import rmtree, which +from subprocess import call + +# ECNet imports +from ecnet import Server +from ecnet.data_utils import DataFrame + +# 3rd party imports +from pubchempy import get_compounds + +# Path to PaDEL is included in the package +_PADEL_PATH = join( + dirname(abspath(__file__)), + 'PaDEL-Descriptor', + 'PaDEL-Descriptor.jar' +) + + +def predict_with_prj(input_txt, results_file, prj_file, form='name', + temp_db='_new_mols.csv', clean_up=True): + '''Predicts values for supplied molecules using already-built ECNet project + + Args: + input_txt (str): path to file containing either molecule names or + SMILES (one entry per line) + results_file (str): path to resulting CSV results file + prj_file (str): path to already-built ECNet project + form (str): `name` or `smiles` for selecting input format + temp_db (str): path to temporary database generated by this function + clean_up (bool): if True, cleans up all files generated during + processing except for the input text files and output results + ''' + + sv = Server(project_file=prj_file, log_level='disable') + input_names = sv.DataFrame.input_names + create_db(input_txt, temp_db, form=form, clean_up=clean_up) + new_data = DataFrame(temp_db) + new_data.set_inputs(input_names) + new_data.save(temp_db) + sv.import_data(temp_db) + sv.use_model(output_filename=results_file) + if clean_up: + remove(temp_db) + rmtree(prj_file.replace('.prj', '')) + + +def create_db(input_txt, output_name, id_prefix='', targets=None, form='name', + smiles_file='mols.smi', mdl_file='mols.mdl', + desc_file='descriptors.csv', clean_up=True): + '''Create an ECNet-formatted database from either molecule names or SMILES + strings + + Args: + input_txt (str): path to file containing either molecule names or + SMILES (one entry per line) + output_name (str): path to desired database file once created + id_prefix (str): prefix for DATAID column entries, if supplied + targets (str): path to file containing target values (optional) + form (str): `name` or `smiles` for selecting input format + smiles_file (str): if input format is not SMILES, this is the name of + a temporary .smi file containing SMILES strings + mdl_file (str): name of MDL file generated by Open Babel + desc_file (str): name of descriptors file generated by PaDEL-Descriptor + clean_up (bool): if True, cleans up all files generated during + processing except for the input text files and output database + ''' + + input_data = _read_txt(input_txt) + if form == 'name': + input_names = deepcopy(input_data) + for i, d in enumerate(input_data): + input_data[i] = get_smiles(d) + with open(smiles_file, 'w') as smi_file: + for d in input_data: + smi_file.write(d + '\n') + elif form == 'smiles': + input_names = ['' for _ in range(len(input_data))] + smiles_file = input_txt + + else: + raise ValueError('Unknown `format` argument: {}'.format(form)) + + if targets is not None: + target_data = _read_txt(targets) + if len(target_data) != len(input_data): + raise IndexError( + 'Number of targets does not equal the number of supplied' + ' molecules: {}, {}'.format( + len(target_data), len(input_data) + ) + ) + else: + target_data = [0 for _ in range(len(input_data))] + + smiles_to_mdl(smiles_file, mdl_file) + desc = mdl_to_descriptors(mdl_file, desc_file) + desc_keys = list(desc[0].keys()) + try: + desc_keys.remove('Name') + except: + pass + + valid_keys = [] + for ds in desc_keys: + is_valid = True + for row in desc[1:]: + if row[ds] == '' or row[ds] is None: + row[ds] = 0 + if is_valid: + valid_keys.append(ds) + desc_keys = valid_keys + + rows = [] + type_row = ['DATAID', 'ASSIGNMENT', 'STRING', 'STRING', 'TARGET'] + type_row.extend(['INPUT' for _ in range(len(desc_keys))]) + title_row = ['DATAID', 'ASSIGNMENT', 'Compound Name', 'SMILES', 'Target'] + title_row.extend(desc_keys) + rows.append(type_row) + rows.append(title_row) + + for idx, name in enumerate(input_names): + mol_row = [ + '{}'.format(id_prefix) + '%04d' % (idx + 1), + 'L', + name, + input_data[idx], + target_data[idx] + ] + mol_row.extend([desc[idx][k] for k in desc_keys]) + rows.append(mol_row) + + with open(output_name, 'w', encoding='utf-8') as new_db: + wr = writer(new_db, quoting=QUOTE_ALL, lineterminator='\n') + for row in rows: + wr.writerow(row) + + if clean_up: + if form != 'smiles': + remove(smiles_file) + remove(mdl_file) + remove(desc_file) + + +def _read_txt(file): + '''Reads text file, returns contents + + Args: + file (str): path to file + + Returns: + list: each line in the text file is a list element + ''' + + with open(file, 'r') as txt_file: + return txt_file.read().split('\n') + + +def get_smiles(name): + '''Queries PubChemPy for SMILES string for supplied molecule + + Args: + name (str): name of the molecule + + Returns: + str or None: if molecule found, returns first idenitifying SMILES, + else None + ''' + + smiles = [m.isomeric_smiles for m in get_compounds(name, 'name')] + if len(smiles) == 0: + raise IndexError('PubChem entry not found for {}'.format(name)) + else: + return smiles[0] + + +def smiles_to_mdl(smiles_file, mdl_file): + '''Invoke Open Babel to generate an MDL file containing all supplied + molecules; requires Open Babel to be installed externally + + Args: + smiles_file (str): path to .smi file (text file) with SMILES strings + mdl_file (str): path to resulting MDL file + ''' + + if which('obabel') is None: + raise ReferenceError('Open Babel installation not found') + + is_mdl = compile(r'.*\.mdl$', IGNORECASE) + if is_mdl.match(mdl_file) is None: + raise ValueError('Output file must have an MDL extension: {}'.format( + mdl_file + )) + + dn = open(devnull, 'w') + for attempt in range(3): + try: + call([ + 'obabel', + '-i', + 'smi', + smiles_file, + '-o', + 'mdl', + '-O', + mdl_file, + '--gen3D' + ], stdout=dn, stderr=dn, timeout=3600) + break + except Exception as e: + if attempt == 2: + raise e + else: + continue + + +def mdl_to_descriptors(mdl_file, descriptors_csv): + '''Generates QSPR descriptors from supplied MDL file using + PaDEL-Descriptor + + Args: + mdl_file (str): path to source MDL file + descriptors_csv (str): path to resulting CSV file w/ descriptors + + Returns: + list: list of dicts, where each dict is a molecule populated with + descriptor names (keys) and values + ''' + + if which('java') is None: + raise ReferenceError( + 'Java JRE 6+ not found (required for PaDEL-Descriptor)' + ) + + dn = open(devnull, 'w') + for attempt in range(3): + try: + call([ + 'java', + '-jar', + _PADEL_PATH, + '-2d', + '-3d', + '-retainorder', + '-retain3d', + '-dir', + mdl_file, + '-file', + descriptors_csv + ], stdout=dn, stderr=dn, timeout=3600) + break + except Exception as e: + if attempt == 2: + raise e + else: + continue + + with open(descriptors_csv, 'r', encoding='utf-8') as desc_file: + reader = DictReader(desc_file) + return [row for row in reader] diff --git a/setup.py b/setup.py index 1e3321d..a8a7ec1 100644 --- a/setup.py +++ b/setup.py @@ -1,14 +1,32 @@ -from setuptools import setup +from setuptools import setup, find_packages setup( name='ecnet', - version='2.0.1', - description='UMass Lowell Energy and Combustion Research Laboratory Neural Network Software', + version='2.1.0', + description='UMass Lowell Energy and Combustion Research Laboratory Neural' + ' Network Software', url='http://github.com/tjkessler/ecnet', author='Travis Kessler, Hernan Gelaf-Romer, Sanskriti Sharma', - author_email='travis.j.kessler@gmail.com, Hernan_Gelafromer@student.uml.edu, Sanskriti_Sharma@student.uml.edu', + author_email='travis.j.kessler@gmail.com,' + ' Hernan_Gelafromer@student.uml.edu,' + ' Sanskriti_Sharma@student.uml.edu', license='MIT', - packages=['ecnet'], - install_requires=['pyyaml', 'ecabc', 'pygenetics', 'colorlogging', 'numpy', 'tensorflow'], + packages=find_packages(), + install_requires=[ + 'colorlogging', + 'ecabc', + 'numpy', + 'pubchempy', + 'pygenetics', + 'pyyaml', + 'tensorflow' + ], + package_data={ + 'ecnet': [ + 'tools/PaDEL-Descriptor/*', + 'tools/PaDEL-Descriptor/lib/*', + 'tools/PaDEL-Descriptor/license/*' + ] + }, zip_safe=False ) diff --git a/tests/cp_model_v1.5.prj b/tests/cp_model_v1.5.prj new file mode 100644 index 0000000..d829ebe Binary files /dev/null and b/tests/cp_model_v1.5.prj differ diff --git a/tests/mols_names.txt b/tests/mols_names.txt new file mode 100644 index 0000000..58ca59c --- /dev/null +++ b/tests/mols_names.txt @@ -0,0 +1,5 @@ +ethanol +octanal +hexanal +pentanal +butanal \ No newline at end of file diff --git a/tests/mols_smiles.txt b/tests/mols_smiles.txt new file mode 100644 index 0000000..58b0f0c --- /dev/null +++ b/tests/mols_smiles.txt @@ -0,0 +1,5 @@ +CCO +CCCCCCCC=O +CCCCCC=O +CCCCC=O +CCCC=O \ No newline at end of file diff --git a/tests/mols_targets.txt b/tests/mols_targets.txt new file mode 100644 index 0000000..e96533f --- /dev/null +++ b/tests/mols_targets.txt @@ -0,0 +1,5 @@ +11 +102.5 +75.2 +65.1 +41.1 \ No newline at end of file diff --git a/tests/test_create_db.py b/tests/test_create_db.py new file mode 100644 index 0000000..28bb2b2 --- /dev/null +++ b/tests/test_create_db.py @@ -0,0 +1,28 @@ +from ecnet.tools import create_db + + +def from_names(): + + print('Creating database from names...') + create_db( + 'mols_names.txt', + 'db_from_names.csv', + targets='mols_targets.txt' + ) + + +def from_smiles(): + + print('Creating database from SMILES...') + create_db( + 'mols_smiles.txt', + 'db_from_smiles.csv', + targets='mols_targets.txt', + form='smiles' + ) + + +if __name__ == '__main__': + + from_names() + from_smiles() diff --git a/tests/test_hyperparam_tuning.py b/tests/test_hyperparam_tuning.py index a57a4da..3d84d02 100644 --- a/tests/test_hyperparam_tuning.py +++ b/tests/test_hyperparam_tuning.py @@ -6,7 +6,7 @@ def tune(num_processes): sv = Server(log_level='debug', num_processes=num_processes) sv._logger.log('crit', 'TUNE HYPERPARAMS | processes: {}'.format( num_processes - ), call_loc={'call_loc': 'UNIT TESTING'}) + ), call_loc='UNIT TESTING') sv.import_data('cn_model_v1.0.csv') sv.tune_hyperparameters( num_employers=10, diff --git a/tests/test_input_limit.py b/tests/test_input_limit.py index 1004c62..a81f3f0 100644 --- a/tests/test_input_limit.py +++ b/tests/test_input_limit.py @@ -6,7 +6,7 @@ def limit_iterative(output_filename=None): sv = Server(log_level='debug') sv._logger.log('crit', 'LIMIT ITER | output file: {}'.format( output_filename - ), call_loc={'call_loc': 'UNIT TESTING'}) + ), call_loc='UNIT TESTING') sv.import_data('cn_model_v1.0.csv') sv.limit_input_parameters( 3, output_filename=output_filename @@ -20,7 +20,7 @@ def limit_genetic(num_processes, shuffle=False, output_filename=None): 'crit', 'LIMIT GEN | Processes: {} | shuffle: {} | output file: {}'.format( num_processes, shuffle, output_filename - ), call_loc={'call_loc': 'UNIT TESTING'} + ), call_loc='UNIT TESTING' ) sv.import_data('cn_model_v1.0.csv') sv.limit_input_parameters( diff --git a/tests/test_logging.py b/tests/test_logging.py index 9e5f12d..40fe474 100644 --- a/tests/test_logging.py +++ b/tests/test_logging.py @@ -9,7 +9,7 @@ def test_init(log_level, log_dir): 'LOGGING INIT | log_level: {} | log_dir: {}'.format( log_level, log_dir ), - call_loc={'call_loc': 'UNIT TESTING'} + call_loc='UNIT TESTING' ) sv._logger.log('debug', 'Debug') sv._logger.log('info', 'Info') @@ -26,7 +26,7 @@ def test_set(log_level, log_dir): 'LOGGING SET | log_level: {} | log_dir: {}'.format( log_level, log_dir ), - call_loc={'call_loc': 'UNIT TESTING'} + call_loc='UNIT TESTING' ) sv._logger.log('debug', 'Debug') sv._logger.log('info', 'Info') diff --git a/tests/test_predict_with_prj.py b/tests/test_predict_with_prj.py new file mode 100644 index 0000000..a60cc4d --- /dev/null +++ b/tests/test_predict_with_prj.py @@ -0,0 +1,16 @@ +from ecnet.tools import predict_with_prj + + +def predict(): + + predict_with_prj( + 'mols_smiles.txt', + '_test_results.csv', + 'cp_model_v1.5.prj', + form='smiles' + ) + + +if __name__ == '__main__': + + predict() diff --git a/tests/test_training.py b/tests/test_training.py index a2fbf7b..14e3081 100644 --- a/tests/test_training.py +++ b/tests/test_training.py @@ -6,7 +6,7 @@ def train(validate, dset=None): sv = Server(log_level='debug') sv._logger.log('crit', 'NO PROJECT | validate: {} | dset: {}'.format( validate, dset - ), call_loc={'call_loc': 'UNIT TESTING'}) + ), call_loc='UNIT TESTING') sv.import_data('cn_model_v1.0.csv') sv.train_model(validate=validate) sv.use_model() @@ -22,7 +22,7 @@ def train_project(validate, shuffle, num_processes, dset, 'PROJECT | validate: {} | shuffle: {} | processes: {} | dset: {} | file: {}' .format( validate, shuffle, num_processes, dset, output_filename - ), call_loc={'call_loc': 'UNIT TESTING'} + ), call_loc='UNIT TESTING' ) sv.import_data('cn_model_v1.0.csv') sv.create_project( diff --git a/tests/test_use_project.py b/tests/test_use_project.py index b131243..9f0b65d 100644 --- a/tests/test_use_project.py +++ b/tests/test_use_project.py @@ -7,7 +7,7 @@ def create_project(): sv._logger.log( 'crit', 'CREATING PROJECT', - call_loc={'call_loc': 'UNIT TESTING'} + call_loc='UNIT TESTING' ) sv.import_data('cn_model_v1.0.csv') sv.create_project( @@ -27,7 +27,7 @@ def use_project(): sv._logger.log( 'crit', 'USING PROJECT', - call_loc={'call_loc': 'UNIT TESTING'} + call_loc='UNIT TESTING' ) sv.use_model('train', output_filename='use_project_train.csv') sv.use_model('test', output_filename='use_project_test.csv') diff --git a/tools/README.md b/tools/README.md deleted file mode 100644 index 3b50f79..0000000 --- a/tools/README.md +++ /dev/null @@ -1,77 +0,0 @@ -# Creating an ECNet-formatted database from molecule names, target values - -### Prerequisites - -To create an ECNet-formatted database from molecule names and target values, you must have the following packages/programs installed: -- [PubChemPy](https://github.com/mcs07/PubChemPy) Python package -- [Open Babel](http://openbabel.org/wiki/Main_Page) software -- [Java JRE](https://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html) version 6 and above - -Additionally, a distributable version of [PaDEL-Descriptor](http://www.yapcwsoft.com/dd/padeldescriptor/) is required for QSPR descriptor generation (we have plans for adding a wrapper for Dragon software too!) - we have included a distributed version of PaDEL-Descriptor in this directory. - -All source files in this directory are required to create a database, and must exist next to each other in your current working directory: -- **create_ecnet_db.py** (aggregates SMILES, QSPR descriptors for database creation) -- **name_to_smiles.py** (uses PubChemPy to obtain SMILES strings for supplied molecule names) -- **smiles_to_qspr.py** (generates QSPR descriptors from SMILES strings using Open Babel and PaDEL-Descriptor) - -You also need a .txt file populated with molecule names, one per line: -``` -Acetaldehyde -Acetaldehyde dimethyl acetal -Acetic acid -Acetic anhydride -Acetol -Acetone -Acetonitrile -Acetonylacetone -``` - -And another .txt file populated with target (experimental) values (as an example, here are the molecules' boiling points in degrees Fahrenheit): -``` -70 -147 -244 -284 -295 -133 -180 -376 -``` -Target values are optional; if no target values are supplied, the resulting database will not have its TARGET column populated. The supplied targets file must be of equal length to the supplied molecules file. - -### Creating a database - -Run create_ecnet_db.py from the command line with: -```console -foo@bar:~$ python create_ecnet_db.py molecules.txt my_database.csv --experimental_vals targets.txt -``` -Where molecules.txt is the path to your molecules file, my_database.csv is the name of the database you are creating, and targets.txt are your target values. - -### Additional options - -create_ecnet_db.py assumes your version of PaDEL-Descriptor is adjacent to the script (located at .\PaDEL-Descriptor\PaDEL-Descriptor.jar). If your version of PaDEL-Descriptor is located elsewhere, you can supply the "--padel_path" argument: -```console -foo@bar:~$ python create_ecnet_db.py molecules.txt my_database.csv --experimental_vals targets.txt --padel_path \path\to\PaDEL-Descriptor.jar -``` - -Your database's DATAID column (essentially Bates numbers for each molecule) will increment starting at 0001: - -| DATAID | -|-------- | -| DATAID | -| 0001 | -| 0002 | -| 0003 | - -To include a prefix for your molecule ID's, supply the "--id_prefix" argument: - -```console -foo@bar:~$ python create_ecnet_db.py molecules.txt my_database.csv --experimental_vals targets.txt --id_prefix MOL -``` - -| DATAID | -|----------- | -| DATAID | -| MOL0001 | -| MOL0002 | -| MOL0003 | diff --git a/tools/create_ecnet_db.py b/tools/create_ecnet_db.py deleted file mode 100644 index eb04743..0000000 --- a/tools/create_ecnet_db.py +++ /dev/null @@ -1,155 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -# -# tools/create_database.py -# -# Creates ECNet-formatted database from molecule names -# - -from argparse import ArgumentParser -from sys import argv -from csv import writer, QUOTE_ALL -from os import remove - -import name_to_smiles -import smiles_to_qspr - - -def parse_args(): - - ap = ArgumentParser() - ap.add_argument( - 'input_file', - type=str, - help='Path to TXT file with molecule names' - ) - ap.add_argument( - 'output_file', - type=str, - help='Path to resulting CSV database' - ) - ap.add_argument( - '--experimental_vals', - type=str, - help='Path to TXT file containing experimental values', - default=None - ) - ap.add_argument( - '--id_prefix', - type=str, - help='Prefix for molecule ID in resulting CSV database' - ) - ap.add_argument( - '--smiles_file', - type=str, - help='Path to temporary .smiles file created when processing', - default='./mols.smiles' - ) - ap.add_argument( - '--padel_path', - type=str, - help='Path to PaDEL-Descriptor.jar' - ' (defaults to ..\PaDEL-Descriptor\PaDEL-Descriptor.jar)', - default=smiles_to_qspr._PADEL_PATH - ) - ap.add_argument( - '--model_file', - type=str, - help='Path to temporary .mdl file created when processing', - default='./mols.mdl' - ) - ap.add_argument( - '--descriptors_file', - type=str, - help='Path to temporary unformatted .csv descriptor file created when' - ' processing', - default='./descriptors.csv' - ) - ap.add_argument( - '--clean_up', - type=str, - help='If True, cleans up all temporary files created when processing', - default='True', - choices=['True', 'False'] - ) - return vars(ap.parse_args(argv[1:])) - - -def main(args): - - # Open names, experimental vals (if supplied) get SMILES strings (if found) - print('Reading molecule names from {}'.format(args['input_file'])) - names = name_to_smiles.get_names(args['input_file']) - if args['experimental_vals'] is not None: - print('Reading experimental values from {}'.format( - args['experimental_vals']) - ) - experimental_vals = name_to_smiles.get_names( - args['experimental_vals'] - ) - else: - experimental_vals = ['' for _ in range(len(names))] - smiles = name_to_smiles.get_smiles(names) - - # Aggregate names, SMILES, experimental values in tuples - to_process = [] - for idx, name in enumerate(names): - if smiles[idx] != '': - to_process.append((name, smiles[idx], experimental_vals[idx])) - - # Write temporary .smiles file, obtain QSPR descriptors - with open(args['smiles_file'], 'w') as smi_file: - for mol in to_process: - smi_file.write('{}\n'.format(mol[1])) - molecules = smiles_to_qspr.get_descriptors( - args['smiles_file'], - padel_path=args['padel_path'], - model_file=args['model_file'], - descriptors_file=args['descriptors_file'], - clean_up=args['clean_up'] - ) - if args['clean_up'] == 'True': - remove(args['smiles_file']) - - # Create ECNet-formatted database - print('Saving database: {}'.format(args['output_file'])) - fieldnames = sorted(list(molecules[0].keys())) - fieldnames.remove('SMILES') - valid_fieldnames = [] - for fn in fieldnames: - is_valid = True - for mol in molecules: - if mol[fn] == '' or mol[fn] is None: - is_valid = False - break - if is_valid: - valid_fieldnames.append(fn) - fieldnames = valid_fieldnames - rows = [] - type_row = ['DATAID', 'ASSIGNMENT', 'STRING', 'STRING', 'TARGET'] - type_row.extend(['INPUT' for _ in range(len(fieldnames))]) - title_row = ['DATAID', 'ASSIGNMENT', 'Compound Name', 'SMILES', 'Exp'] - title_row.extend(fieldnames) - rows.append(type_row) - rows.append(title_row) - for idx, mol in enumerate(to_process): - mol_row = [ - '{}'.format(args['id_prefix']) + '%04d' % (idx + 1), - 'L', - mol[0], - mol[1], - mol[2] - ] - for fn in fieldnames: - mol_row.append(molecules[idx][fn]) - rows.append(mol_row) - - with open(args['output_file'], 'w', encoding='utf-8') as output_file: - wr = writer(output_file, quoting=QUOTE_ALL, lineterminator='\n') - for row in rows: - wr.writerow(row) - - -if __name__ == '__main__': - - main(parse_args()) diff --git a/tools/name_to_smiles.py b/tools/name_to_smiles.py deleted file mode 100644 index 5d6f5e4..0000000 --- a/tools/name_to_smiles.py +++ /dev/null @@ -1,140 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -# -# tools/names_to_smiles.py -# -# Houses functions to obtain SMILES strings from molecule names -# - -from argparse import ArgumentParser -from csv import DictReader, DictWriter -from sys import argv -from pubchempy import get_compounds - - -def get_names(names_file): - '''Reads molecule names from supplied .txt file - - Args: - names_file (str): path to .txt file - - Returns: - list: list of names, strings - ''' - - with open(names_file, 'r') as txt_file: - return txt_file.read().split('\n') - - -def get_smiles(names): - '''Queries PubChem for SMILES strings for supplied names - - Args: - names (list): list of molecule names - - Returns: - list: list of corresponding SMILES strings - ''' - - smiles = [] - for name in names: - smi = [m.isomeric_smiles for m in get_compounds(name, 'name')] - if len(smi) == 0: - print('Warning: SMILES for {} not found'.format(name)) - smi = '' - else: - smi = smi[0] - smiles.append(smi) - return smiles - - -def save_file(names, smiles, output_filename, names_header='Compound Name', - smiles_header='SMILES'): - '''Saves names and SMILES to CSV file - - Args: - names (list): list of molecule names - smiles (list): list of SMILES strings (equal length to names) - output_filename (str): path to resulting file - names_header (str): names column header (defaults to 'Compound Name') - smiles_header (str): SMILES column header (defaults to 'SMILES') - ''' - - with open(output_filename, 'w', encoding='utf-8') as file: - writer = DictWriter( - file, - delimiter=',', - lineterminator='\n', - fieldnames=[names_header, smiles_header] - ) - writer.writeheader() - for idx, name in enumerate(names): - writer.writerow({ - names_header: name, - smiles_header: smiles[idx] - }) - - -def parse_args(): - '''Run from command line - - Returns: - dict: { - 'input_file', - 'output_file', - 'names_header', - 'smiles_header' - } - ''' - - ap = ArgumentParser() - ap.add_argument( - 'input_file', - type=str, - help='Path to TXT file with molecule names' - ) - ap.add_argument( - '--output_file', - type=str, - help='Name of the resulting file containing names, SMILES', - default=None - ) - ap.add_argument( - '--names_header', - type=str, - help='Header for molecule names column of output file', - default='Compound Name' - ) - ap.add_argument( - '--smiles_header', - type=str, - help='Header for SMILES column of output file', - default='SMILES' - ) - - return vars(ap.parse_args(argv[1:])) - - -def main(args): - '''Run from command line''' - - names = get_names(args['input_file']) - smiles = get_smiles(names) - if args['output_file'] is None: - args['output_file'] = args['input_file'].replace( - '.csv', - '_smiles.csv' - ) - save_file( - names, - smiles, - args['output_file'], - names_header=args['names_header'], - smiles_header=args['smiles_header'] - ) - - -if __name__ == '__main__': - '''Run from command line''' - - main(parse_args()) diff --git a/tools/smiles_to_qspr.py b/tools/smiles_to_qspr.py deleted file mode 100644 index 349209f..0000000 --- a/tools/smiles_to_qspr.py +++ /dev/null @@ -1,197 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -# -# tools/smiles_to_qspr.py -# -# Obtains QSPR descriptors for SMILES strings -# TODO: Add wrapper for Dragon software -# - -from os.path import abspath, dirname, isfile, join -from os import remove -from shutil import which -from argparse import ArgumentParser -from sys import argv -from subprocess import check_output -from csv import reader, DictWriter - -# Default path is ..\PaDEL-Descriptor\PaDEL-Descriptor.jar -_PADEL_PATH = join( - dirname(abspath(__file__)), - 'PaDEL-Descriptor', - 'PaDEL-Descriptor.jar' -) - -# Check installations -if which('obabel') is None: - - raise ReferenceError('Open Babel installation not found') - -if which('java') is None: - - raise ReferenceError('Java installation not found') - - -def get_descriptors(smiles_file, padel_path=_PADEL_PATH, - model_file='mols.mdl', descriptors_file='descriptors.csv', - clean_up=True): - '''Obtains descriptors for SMILES strings - - Args: - smiles_file (str): path to .smiles file, one string per line - padel_path (str): path to PaDEL-Descriptor - model_file (str): path to .mdl file generated by this function - descriptors_file (str): path to raw .csv file generated by this - function - clean_up (bool): if True, removes model_file and descriptors_file when - this function is complete - - Returns: - list: each element is a dictionary for each molecule, containing its - SMILES string and all descriptors generated - ''' - - if not isfile(padel_path): - - raise FileNotFoundError('PaDEL-Descriptor.jar not found at {}'.format( - padel_path - )) - - print('Invoking Open Babel to generate MDL file...') - check_output( - [ - 'obabel', - '-i', - 'smi', - smiles_file, - '-o', - 'mdl', - '-O', - model_file, - '--gen3D' - ] - ) - print('Invoking PaDEL-Descriptor to generate QSPR descriptors...') - check_output( - [ - 'java', - '-jar', - padel_path, - '-2d', - '-3d', - '-retainorder', - '-retain3d', - '-dir', - 'mols.mdl', - '-file', - descriptors_file - ] - ) - print('Descriptors Generated') - with open(smiles_file, 'r') as smi_file: - smiles_strings = smi_file.read().split('\n') - molecules = [] - with open(descriptors_file, 'r', encoding='utf-8') as csv_file: - rows = list(reader(csv_file)) - fieldnames = rows[0][1:] - for sidx, row in enumerate(rows[1:]): - mol_dict = {'SMILES': smiles_strings[sidx]} - for idx, cell in enumerate(row[1:]): - mol_dict[fieldnames[idx]] = cell - molecules.append(mol_dict) - if clean_up == 'True': - remove(model_file) - remove(descriptors_file) - return molecules - - -def save_file(molecules, output_file): - '''Save generated descriptors to specified file - - Args: - molecules (list): list of dicts, generated by get_descriptors - output_file (str): path to save file - ''' - - with open(output_file, 'w', encoding='utf-8') as csv_file: - fieldnames = sorted(list(molecules[0].keys())) - fieldnames.remove('SMILES') - csv_headers = ['SMILES'] - csv_headers.extend(fieldnames) - writer = DictWriter( - csv_file, - delimiter=',', - lineterminator='\n', - fieldnames=csv_headers - ) - writer.writeheader() - for mol in molecules: - writer.writerow(mol) - - -def parse_args(): - '''Run from command line - - Returns: - dict: { - 'smiles_file', - 'output_file', - 'padel_path', - 'model_file' - } - ''' - - ap = ArgumentParser() - ap.add_argument( - 'smiles_file', - type=str, - help='Path to .smiles file' - ) - ap.add_argument( - '--output_file', - type=str, - help='Path to output file', - default=None - ) - ap.add_argument( - '--padel_path', - type=str, - help='Path to PaDEL-Descriptor.jar' - ' (defaults to ..\PaDEL-Descriptor\PaDEL-Descriptor.jar)', - default=_PADEL_PATH - ) - ap.add_argument( - '--model_file', - type=str, - help='Path to temporary .mdl file', - default='./mols.mdl' - ) - ap.add_argument( - '--descriptors_file', - type=str, - help='Path to temporary descriptor .csv file', - default='./descriptors.csv' - ) - ap.add_argument( - '--clean_up', - type=str, - help='If True, cleans up temporary files', - default='True', - choices=['True', 'False'] - ) - return vars(ap.parse_args(argv[1:])) - - -def main(args): - '''Run from command line''' - - molecules = get_descriptors(args['smiles_file'], clean_up=args['clean_up']) - if args['output_file'] is None: - args['output_file'] = args['smiles_file'].replace('.smiles', '.csv') - save_file(molecules, args['output_file']) - - -if __name__ == '__main__': - '''Run from command line''' - - main(parse_args())