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JacksonBurns / mordred-community

Community-Maintained Version of mordred
https://jacksonburns.github.io/mordred-community/
BSD 3-Clause "New" or "Revised" License
49 stars 3 forks source link

Overflow eeror #5

Closed dkchalmers closed 1 year ago

dkchalmers commented 1 year ago

Hi,

Thanks for your efforts in making mordred work.

I am getting this error from some (not all) compounds.

mordred/lib64/python3.11/site-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce return ufunc.reduce(obj, axis, dtype, out, **passkwargs)

minimal reproduction code

python3.11 -m mordred err.smi

err.smi is attached as err.smi.txt.

environment

OS/distribution

NAME="openSUSE Leap" VERSION="15.5"

conda or pip

pip

python version

Python 3.11.4

library version

python -m pip list Package Version

mordredcommunity 2.0.2 networkx 3.1 numpy 1.25.2 packaging 23.1 Pillow 10.0.0 pip 23.2.1 rdkit 2023.3.2 setuptools 68.0.0 six 1.16.0 wheel 0.41.0

rdkit 2023.03.2

err.smi.txt

JacksonBurns commented 1 year ago

Thanks for the report @dkchalmers! I am able to reproduce this error on my machine as well.

Here was my output, for future reference:

output ```bash (mordredc) jackson@jackson-Precision-7540:~/Downloads$ python -m mordred err.smi name,ABC,ABCGG,nAcid,nBase,SpAbs_A,SpMax_A,SpDiam_A,SpAD_A,SpMAD_A,LogEE_A,VE1_A,VE2_A,VE3_A,VR1_A,VR2_A,VR3_A,nAromAtom,nAromBond,nAtom,nHeavyAtom,nSpiro,nBridgehead,nHetero,nH,nB,nC,nN,nO,nS,nP,nF,nCl,nBr,nI,nX,ATS0dv,ATS1dv,ATS2dv,ATS3dv,ATS4dv,ATS5dv,ATS6dv,ATS7dv,ATS8dv,ATS0d,ATS1d,ATS2d,ATS3d,ATS4d,ATS5d,ATS6d,ATS7d,ATS8d,ATS0s,ATS1s,ATS2s,ATS3s,ATS4s,ATS5s,ATS6s,ATS7s,ATS8s,ATS0Z,ATS1Z,ATS2Z,ATS3Z,ATS4Z,ATS5Z,ATS6Z,ATS7Z,ATS8Z,ATS0m,ATS1m,ATS2m,ATS3m,ATS4m,ATS5m,ATS6m,ATS7m,ATS8m,ATS0v,ATS1v,ATS2v,ATS3v,ATS4v,ATS5v,ATS6v,ATS7v,ATS8v,ATS0se,ATS1se,ATS2se,ATS3se,ATS4se,ATS5se,ATS6se,ATS7se,ATS8se,ATS0pe,ATS1pe,ATS2pe,ATS3pe,ATS4pe,ATS5pe,ATS6pe,ATS7pe,ATS8pe,ATS0are,ATS1are,ATS2are,ATS3are,ATS4are,ATS5are,ATS6are,ATS7are,ATS8are,ATS0p,ATS1p,ATS2p,ATS3p,ATS4p,ATS5p,ATS6p,ATS7p,ATS8p,ATS0i,ATS1i,ATS2i,ATS3i,ATS4i,ATS5i,ATS6i,ATS7i,ATS8i,AATS0dv,AATS1dv,AATS2dv,AATS3dv,AATS4dv,AATS5dv,AATS6dv,AATS7dv,AATS8dv,AATS0d,AATS1d,AATS2d,AATS3d,AATS4d,AATS5d,AATS6d,AATS7d,AATS8d,AATS0s,AATS1s,AATS2s,AATS3s,AATS4s,AATS5s,AATS6s,AATS7s,AATS8s,AATS0Z,AATS1Z,AATS2Z,AATS3Z,AATS4Z,AATS5Z,AATS6Z,AATS7Z,AATS8Z,AATS0m,AATS1m,AATS2m,AATS3m,AATS4m,AATS5m,AATS6m,AATS7m,AATS8m,AATS0v,AATS1v,AATS2v,AATS3v,AATS4v,AATS5v,AATS6v,AATS7v,AATS8v,AATS0se,AATS1se,AATS2se,AATS3se,AATS4se,AATS5se,AATS6se,AATS7se,AATS8se,AATS0pe,AATS1pe,AATS2pe,AATS3pe,AATS4pe,AATS5pe,AATS6pe,AATS7pe,AATS8pe,AATS0are,AATS1are,AATS2are,AATS3are,AATS4are,AATS5are,AATS6are,AATS7are,AATS8are,AATS0p,AATS1p,AATS2p,AATS3p,AATS4p,AATS5p,AATS6p,AATS7p,AATS8p,AATS0i,AATS1i,AATS2i,AATS3i,AATS4i,AATS5i,AATS6i,AATS7i,AATS8i,ATSC0c,ATSC1c,ATSC2c,ATSC3c,ATSC4c,ATSC5c,ATSC6c,ATSC7c,ATSC8c,ATSC0dv,ATSC1dv,ATSC2dv,ATSC3dv,ATSC4dv,ATSC5dv,ATSC6dv,ATSC7dv,ATSC8dv,ATSC0d,ATSC1d,ATSC2d,ATSC3d,ATSC4d,ATSC5d,ATSC6d,ATSC7d,ATSC8d,ATSC0s,ATSC1s,ATSC2s,ATSC3s,ATSC4s,ATSC5s,ATSC6s,ATSC7s,ATSC8s,ATSC0Z,ATSC1Z,ATSC2Z,ATSC3Z,ATSC4Z,ATSC5Z,ATSC6Z,ATSC7Z,ATSC8Z,ATSC0m,ATSC1m,ATSC2m,ATSC3m,ATSC4m,ATSC5m,ATSC6m,ATSC7m,ATSC8m,ATSC0v,ATSC1v,ATSC2v,ATSC3v,ATSC4v,ATSC5v,ATSC6v,ATSC7v,ATSC8v,ATSC0se,ATSC1se,ATSC2se,ATSC3se,ATSC4se,ATSC5se,ATSC6se,ATSC7se,ATSC8se,ATSC0pe,ATSC1pe,ATSC2pe,ATSC3pe,ATSC4pe,ATSC5pe,ATSC6pe,ATSC7pe,ATSC8pe,ATSC0are,ATSC1are,ATSC2are,ATSC3are,ATSC4are,ATSC5are,ATSC6are,ATSC7are,ATSC8are,ATSC0p,ATSC1p,ATSC2p,ATSC3p,ATSC4p,ATSC5p,ATSC6p,ATSC7p,ATSC8p,ATSC0i,ATSC1i,ATSC2i,ATSC3i,ATSC4i,ATSC5i,ATSC6i,ATSC7i,ATSC8i,AATSC0c,AATSC1c,AATSC2c,AATSC3c,AATSC4c,AATSC5c,AATSC6c,AATSC7c,AATSC8c,AATSC0dv,AATSC1dv,AATSC2dv,AATSC3dv,AATSC4dv,AATSC5dv,AATSC6dv,AATSC7dv,AATSC8dv,AATSC0d,AATSC1d,AATSC2d,AATSC3d,AATSC4d,AATSC5d,AATSC6d,AATSC7d,AATSC8d,AATSC0s,AATSC1s,AATSC2s,AATSC3s,AATSC4s,AATSC5s,AATSC6s,AATSC7s,AATSC8s,AATSC0Z,AATSC1Z,AATSC2Z,AATSC3Z,AATSC4Z,AATSC5Z,AATSC6Z,AATSC7Z,AATSC8Z,AATSC0m,AATSC1m,AATSC2m,AATSC3m,AATSC4m,AATSC5m,AATSC6m,AATSC7m,AATSC8m,AATSC0v,AATSC1v,AATSC2v,AATSC3v,AATSC4v,AATSC5v,AATSC6v,AATSC7v,AATSC8v,AATSC0se,AATSC1se,AATSC2se,AATSC3se,AATSC4se,AATSC5se,AATSC6se,AATSC7se,AATSC8se,AATSC0pe,AATSC1pe,AATSC2pe,AATSC3pe,AATSC4pe,AATSC5pe,AATSC6pe,AATSC7pe,AATSC8pe,AATSC0are,AATSC1are,AATSC2are,AATSC3are,AATSC4are,AATSC5are,AATSC6are,AATSC7are,AATSC8are,AATSC0p,AATSC1p,AATSC2p,AATSC3p,AATSC4p,AATSC5p,AATSC6p,AATSC7p,AATSC8p,AATSC0i,AATSC1i,AATSC2i,AATSC3i,AATSC4i,AATSC5i,AATSC6i,AATSC7i,AATSC8i,MATS1c,MATS2c,MATS3c,MATS4c,MATS5c,MATS6c,MATS7c,MATS8c,MATS1dv,MATS2dv,MATS3dv,MATS4dv,MATS5dv,MATS6dv,MATS7dv,MATS8dv,MATS1d,MATS2d,MATS3d,MATS4d,MATS5d,MATS6d,MATS7d,MATS8d,MATS1s,MATS2s,MATS3s,MATS4s,MATS5s,MATS6s,MATS7s,MATS8s,MATS1Z,MATS2Z,MATS3Z,MATS4Z,MATS5Z,MATS6Z,MATS7Z,MATS8Z,MATS1m,MATS2m,MATS3m,MATS4m,MATS5m,MATS6m,MATS7m,MATS8m,MATS1v,MATS2v,MATS3v,MATS4v,MATS5v,MATS6v,MATS7v,MATS8v,MATS1se,MATS2se,MATS3se,MATS4se,MATS5se,MATS6se,MATS7se,MATS8se,MATS1pe,MATS2pe,MATS3pe,MATS4pe,MATS5pe,MATS6pe,MATS7pe,MATS8pe,MATS1are,MATS2are,MATS3are,MATS4are,MATS5are,MATS6are,MATS7are,MATS8are,MATS1p,MATS2p,MATS3p,MATS4p,MATS5p,MATS6p,MATS7p,MATS8p,MATS1i,MATS2i,MATS3i,MATS4i,MATS5i,MATS6i,MATS7i,MATS8i,GATS1c,GATS2c,GATS3c,GATS4c,GATS5c,GATS6c,GATS7c,GATS8c,GATS1dv,GATS2dv,GATS3dv,GATS4dv,GATS5dv,GATS6dv,GATS7dv,GATS8dv,GATS1d,GATS2d,GATS3d,GATS4d,GATS5d,GATS6d,GATS7d,GATS8d,GATS1s,GATS2s,GATS3s,GATS4s,GATS5s,GATS6s,GATS7s,GATS8s,GATS1Z,GATS2Z,GATS3Z,GATS4Z,GATS5Z,GATS6Z,GATS7Z,GATS8Z,GATS1m,GATS2m,GATS3m,GATS4m,GATS5m,GATS6m,GATS7m,GATS8m,GATS1v,GATS2v,GATS3v,GATS4v,GATS5v,GATS6v,GATS7v,GATS8v,GATS1se,GATS2se,GATS3se,GATS4se,GATS5se,GATS6se,GATS7se,GATS8se,GATS1pe,GATS2pe,GATS3pe,GATS4pe,GATS5pe,GATS6pe,GATS7pe,GATS8pe,GATS1are,GATS2are,GATS3are,GATS4are,GATS5are,GATS6are,GATS7are,GATS8are,GATS1p,GATS2p,GATS3p,GATS4p,GATS5p,GATS6p,GATS7p,GATS8p,GATS1i,GATS2i,GATS3i,GATS4i,GATS5i,GATS6i,GATS7i,GATS8i,BCUTc-1h,BCUTc-1l,BCUTdv-1h,BCUTdv-1l,BCUTd-1h,BCUTd-1l,BCUTs-1h,BCUTs-1l,BCUTZ-1h,BCUTZ-1l,BCUTm-1h,BCUTm-1l,BCUTv-1h,BCUTv-1l,BCUTse-1h,BCUTse-1l,BCUTpe-1h,BCUTpe-1l,BCUTare-1h,BCUTare-1l,BCUTp-1h,BCUTp-1l,BCUTi-1h,BCUTi-1l,BalabanJ,SpAbs_DzZ,SpMax_DzZ,SpDiam_DzZ,SpAD_DzZ,SpMAD_DzZ,LogEE_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,LogEE_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,LogEE_Dzv,SM1_Dzv,VE1_Dzv,VE2_Dzv,VE3_Dzv,VR1_Dzv,VR2_Dzv,VR3_Dzv,SpAbs_Dzse,SpMax_Dzse,SpDiam_Dzse,SpAD_Dzse,SpMAD_Dzse,LogEE_Dzse,SM1_Dzse,VE1_Dzse,VE2_Dzse,VE3_Dzse,VR1_Dzse,VR2_Dzse,VR3_Dzse,SpAbs_Dzpe,SpMax_Dzpe,SpDiam_Dzpe,SpAD_Dzpe,SpMAD_Dzpe,LogEE_Dzpe,SM1_Dzpe,VE1_Dzpe,VE2_Dzpe,VE3_Dzpe,VR1_Dzpe,VR2_Dzpe,VR3_Dzpe,SpAbs_Dzare,SpMax_Dzare,SpDiam_Dzare,SpAD_Dzare,SpMAD_Dzare,LogEE_Dzare,SM1_Dzare,VE1_Dzare,VE2_Dzare,VE3_Dzare,VR1_Dzare,VR2_Dzare,VR3_Dzare,SpAbs_Dzp,SpMax_Dzp,SpDiam_Dzp,SpAD_Dzp,SpMAD_Dzp,LogEE_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,LogEE_Dzi,SM1_Dzi,VE1_Dzi,VE2_Dzi,VE3_Dzi,VR1_Dzi,VR2_Dzi,VR3_Dzi,BertzCT,nBonds,nBondsO,nBondsS,nBondsD,nBondsT,nBondsA,nBondsM,nBondsKS,nBondsKD,RNCG,RPCG,C1SP1,C2SP1,C1SP2,C2SP2,C3SP2,C1SP3,C2SP3,C3SP3,C4SP3,HybRatio,FCSP3,Xch-3d,Xch-4d,Xch-5d,Xch-6d,Xch-7d,Xch-3dv,Xch-4dv,Xch-5dv,Xch-6dv,Xch-7dv,Xc-3d,Xc-4d,Xc-5d,Xc-6d,Xc-3dv,Xc-4dv,Xc-5dv,Xc-6dv,Xpc-4d,Xpc-5d,Xpc-6d,Xpc-4dv,Xpc-5dv,Xpc-6dv,Xp-0d,Xp-1d,Xp-2d,Xp-3d,Xp-4d,Xp-5d,Xp-6d,Xp-7d,AXp-0d,AXp-1d,AXp-2d,AXp-3d,AXp-4d,AXp-5d,AXp-6d,AXp-7d,Xp-0dv,Xp-1dv,Xp-2dv,Xp-3dv,Xp-4dv,Xp-5dv,Xp-6dv,Xp-7dv,AXp-0dv,AXp-1dv,AXp-2dv,AXp-3dv,AXp-4dv,AXp-5dv,AXp-6dv,AXp-7dv,SZ,Sm,Sv,Sse,Spe,Sare,Sp,Si,MZ,Mm,Mv,Mse,Mpe,Mare,Mp,Mi,SpAbs_Dt,SpMax_Dt,SpDiam_Dt,SpAD_Dt,SpMAD_Dt,LogEE_Dt,SM1_Dt,VE1_Dt,VE2_Dt,VE3_Dt,VR1_Dt,VR2_Dt,VR3_Dt,DetourIndex,SpAbs_D,SpMax_D,SpDiam_D,SpAD_D,SpMAD_D,LogEE_D,VE1_D,VE2_D,VE3_D,VR1_D,VR2_D,VR3_D,NsLi,NssBe,NssssBe,NssBH,NsssB,NssssB,NsCH3,NdCH2,NssCH2,NtCH,NdsCH,NaaCH,NsssCH,NddC,NtsC,NdssC,NaasC,NaaaC,NssssC,NsNH3,NsNH2,NssNH2,NdNH,NssNH,NaaNH,NtN,NsssNH,NdsN,NaaN,NsssN,NddsN,NaasN,NssssN,NsOH,NdO,NssO,NaaO,NsF,NsSiH3,NssSiH2,NsssSiH,NssssSi,NsPH2,NssPH,NsssP,NdsssP,NsssssP,NsSH,NdS,NssS,NaaS,NdssS,NddssS,NsCl,NsGeH3,NssGeH2,NsssGeH,NssssGe,NsAsH2,NssAsH,NsssAs,NsssdAs,NsssssAs,NsSeH,NdSe,NssSe,NaaSe,NdssSe,NddssSe,NsBr,NsSnH3,NssSnH2,NsssSnH,NssssSn,NsI,NsPbH3,NssPbH2,NsssPbH,NssssPb,SsLi,SssBe,SssssBe,SssBH,SsssB,SssssB,SsCH3,SdCH2,SssCH2,StCH,SdsCH,SaaCH,SsssCH,SddC,StsC,SdssC,SaasC,SaaaC,SssssC,SsNH3,SsNH2,SssNH2,SdNH,SssNH,SaaNH,StN,SsssNH,SdsN,SaaN,SsssN,SddsN,SaasN,SssssN,SsOH,SdO,SssO,SaaO,SsF,SsSiH3,SssSiH2,SsssSiH,SssssSi,SsPH2,SssPH,SsssP,SdsssP,SsssssP,SsSH,SdS,SssS,SaaS,SdssS,SddssS,SsCl,SsGeH3,SssGeH2,SsssGeH,SssssGe,SsAsH2,SssAsH,SsssAs,SsssdAs,SsssssAs,SsSeH,SdSe,SssSe,SaaSe,SdssSe,SddssSe,SsBr,SsSnH3,SssSnH2,SsssSnH,SssssSn,SsI,SsPbH3,SssPbH2,SsssPbH,SssssPb,MAXsLi,MAXssBe,MAXssssBe,MAXssBH,MAXsssB,MAXssssB,MAXsCH3,MAXdCH2,MAXssCH2,MAXtCH,MAXdsCH,MAXaaCH,MAXsssCH,MAXddC,MAXtsC,MAXdssC,MAXaasC,MAXaaaC,MAXssssC,MAXsNH3,MAXsNH2,MAXssNH2,MAXdNH,MAXssNH,MAXaaNH,MAXtN,MAXsssNH,MAXdsN,MAXaaN,MAXsssN,MAXddsN,MAXaasN,MAXssssN,MAXsOH,MAXdO,MAXssO,MAXaaO,MAXsF,MAXsSiH3,MAXssSiH2,MAXsssSiH,MAXssssSi,MAXsPH2,MAXssPH,MAXsssP,MAXdsssP,MAXsssssP,MAXsSH,MAXdS,MAXssS,MAXaaS,MAXdssS,MAXddssS,MAXsCl,MAXsGeH3,MAXssGeH2,MAXsssGeH,MAXssssGe,MAXsAsH2,MAXssAsH,MAXsssAs,MAXsssdAs,MAXsssssAs,MAXsSeH,MAXdSe,MAXssSe,MAXaaSe,MAXdssSe,MAXddssSe,MAXsBr,MAXsSnH3,MAXssSnH2,MAXsssSnH,MAXssssSn,MAXsI,MAXsPbH3,MAXssPbH2,MAXsssPbH,MAXssssPb,MINsLi,MINssBe,MINssssBe,MINssBH,MINsssB,MINssssB,MINsCH3,MINdCH2,MINssCH2,MINtCH,MINdsCH,MINaaCH,MINsssCH,MINddC,MINtsC,MINdssC,MINaasC,MINaaaC,MINssssC,MINsNH3,MINsNH2,MINssNH2,MINdNH,MINssNH,MINaaNH,MINtN,MINsssNH,MINdsN,MINaaN,MINsssN,MINddsN,MINaasN,MINssssN,MINsOH,MINdO,MINssO,MINaaO,MINsF,MINsSiH3,MINssSiH2,MINsssSiH,MINssssSi,MINsPH2,MINssPH,MINsssP,MINdsssP,MINsssssP,MINsSH,MINdS,MINssS,MINaaS,MINdssS,MINddssS,MINsCl,MINsGeH3,MINssGeH2,MINsssGeH,MINssssGe,MINsAsH2,MINssAsH,MINsssAs,MINsssdAs,MINsssssAs,MINsSeH,MINdSe,MINssSe,MINaaSe,MINdssSe,MINddssSe,MINsBr,MINsSnH3,MINssSnH2,MINsssSnH,MINssssSn,MINsI,MINsPbH3,MINssPbH2,MINsssPbH,MINssssPb,ECIndex,ETA_alpha,AETA_alpha,ETA_shape_p,ETA_shape_y,ETA_shape_x,ETA_beta,AETA_beta,ETA_beta_s,AETA_beta_s,ETA_beta_ns,AETA_beta_ns,ETA_beta_ns_d,AETA_beta_ns_d,ETA_eta,AETA_eta,ETA_eta_L,AETA_eta_L,ETA_eta_R,AETA_eta_R,ETA_eta_RL,AETA_eta_RL,ETA_eta_F,AETA_eta_F,ETA_eta_FL,AETA_eta_FL,ETA_eta_B,AETA_eta_B,ETA_eta_BR,AETA_eta_BR,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_dBeta,AETA_dBeta,ETA_psi_1,ETA_dPsi_A,ETA_dPsi_B,fragCpx,fMF,nHBAcc,nHBDon,IC0,IC1,IC2,IC3,IC4,IC5,TIC0,TIC1,TIC2,TIC3,TIC4,TIC5,SIC0,SIC1,SIC2,SIC3,SIC4,SIC5,BIC0,BIC1,BIC2,BIC3,BIC4,BIC5,CIC0,CIC1,CIC2,CIC3,CIC4,CIC5,MIC0,MIC1,MIC2,MIC3,MIC4,MIC5,ZMIC0,ZMIC1,ZMIC2,ZMIC3,ZMIC4,ZMIC5,Kier1,Kier2,Kier3,Lipinski,GhoseFilter,FilterItLogS,VMcGowan,LabuteASA,PEOE_VSA1,PEOE_VSA2,PEOE_VSA3,PEOE_VSA4,PEOE_VSA5,PEOE_VSA6,PEOE_VSA7,PEOE_VSA8,PEOE_VS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/home/jackson/mambaforge/envs/mordredc/lib/python3.11/site-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce return ufunc.reduce(obj, axis, dtype, out, **passkwargs) 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```

I will start looking at a patch now - I think we just need to prevent that warning from being written to standard out and disrupting the output. The values that affected by the overflow error are still being treated correctly (i.e. they are just missing, as mordred intends).

JacksonBurns commented 1 year ago

@dkchalmers I think I got it fixed, could you try this out and make sure it works for you? You can install the changes I have made over on that branch using this command: pip install git+https://github.com/JacksonBurns/mordred-community.git@develop. Thanks again for the thorough report!

dkchalmers commented 1 year ago

That looks to do the trick!

Thanks very much.

Cheers

David