├── .gitignore ├── LICENSE ├── README.md ├── forcefields ├── atom.typ ├── combined.fld ├── os-dihydroxylation-alkene.fld ├── rh-hydrogenation-enamide.fld ├── ru-hydrogenation-ketone.fld └── sulfone.fld ├── ligands ├── diphos_pd │ ├── 1.mae │ ├── 10.mae │ ├── 100.mae │ ├── 101.mae │ ├── 102.mae │ ├── 103.mae │ ├── 104.mae │ ├── 105.mae │ ├── 106.mae │ ├── 107.mae │ ├── 108.mae │ ├── 109.mae │ ├── 11.mae │ ├── 110.mae │ ├── 111.mae │ ├── 112.mae │ ├── 113.mae │ ├── 114.mae │ ├── 115.mae │ ├── 12.mae │ ├── 13.mae │ ├── 14.mae │ ├── 15.mae │ ├── 16.mae │ ├── 17.mae │ ├── 18.mae │ ├── 19.mae │ ├── 2.mae │ ├── 20.mae │ ├── 21.mae │ ├── 22.mae │ ├── 23.mae │ ├── 24.mae │ ├── 25.mae │ ├── 26.mae │ ├── 27.mae │ ├── 28.mae │ ├── 29.mae │ ├── 3.mae │ ├── 30.mae │ ├── 31.mae │ ├── 32.mae │ ├── 33.mae │ ├── 34.mae │ ├── 35.mae │ ├── 36.mae │ ├── 37.mae │ ├── 38.mae │ ├── 39.mae │ ├── 4.mae │ ├── 40.mae │ ├── 41.mae │ ├── 42.mae │ ├── 43.mae │ ├── 44.mae │ ├── 45.mae │ ├── 46.mae │ ├── 47.mae │ ├── 48.mae │ ├── 49.mae │ ├── 5.mae │ ├── 50.mae │ ├── 51.mae │ ├── 52.mae │ ├── 53.mae │ ├── 54.mae │ ├── 55.mae │ ├── 56.mae │ ├── 57.mae │ ├── 58.mae │ ├── 59.mae │ ├── 6.mae │ ├── 60.mae │ ├── 61.mae │ ├── 62.mae │ ├── 63.mae │ ├── 64.mae │ ├── 65.mae │ ├── 66.mae │ ├── 67.mae │ ├── 68.mae │ ├── 69.mae │ ├── 7.mae │ ├── 70.mae │ ├── 71.mae │ ├── 72.mae │ ├── 73.mae │ ├── 74.mae │ ├── 75.mae │ ├── 76.mae │ ├── 77.mae │ ├── 78.mae │ ├── 79.mae │ ├── 8.mae │ ├── 80.mae │ ├── 81.mae │ ├── 82.mae │ ├── 83.mae │ ├── 84.mae │ ├── 85.mae │ ├── 86.mae │ ├── 87.mae │ ├── 88.mae │ ├── 89.mae │ ├── 9.mae │ ├── 90.mae │ ├── 91.mae │ ├── 92.mae │ ├── 93.mae │ ├── 94.mae │ ├── 95.mae │ ├── 96.mae │ ├── 97.mae │ ├── 98.mae │ ├── 99.mae │ └── list ├── diphosphines │ ├── binap-ether-r.mae │ ├── binap-ether-s.mae │ ├── binap-r.mae │ ├── binap-s.mae │ ├── bpe.mae │ ├── duphos.mae │ ├── lc.mae │ ├── ld.mae │ ├── le.mae │ ├── lf.mae │ ├── lg.mae │ ├── lh.mae │ ├── li.mae │ ├── lj.mae │ ├── lk.mae │ ├── ll.mae │ └── lm.mae ├── phox │ ├── norbornane.mae │ ├── phox1.mae │ ├── phox2.mae │ ├── phox3.mae │ ├── phox4.mae │ ├── phox5.mae │ └── phox6.mae └── pyrox │ ├── Heck-ligands.cdx │ ├── L1.mae │ ├── L10.mae │ ├── L11.mae │ ├── L12.mae │ ├── L13.mae │ ├── L14.mae │ ├── L15.mae │ ├── L16.mae │ ├── L17.mae │ ├── L18.mae │ ├── L19.mae │ ├── L2.mae │ ├── L20.mae │ ├── L21.mae │ ├── L22.mae │ ├── L23.mae │ ├── L24.mae │ ├── L25.mae │ ├── L26.mae │ ├── L27.mae │ ├── L28.mae │ ├── L29.mae │ ├── L3.mae │ ├── L30.mae │ ├── L31.mae │ ├── L32.mae │ ├── L33.mae │ ├── L34.mae │ ├── L35.mae │ ├── L36.mae │ ├── L37.mae │ ├── L38.mae │ ├── L39.mae │ ├── L4.mae │ ├── L40.mae │ ├── L41.mae │ ├── L42.mae │ ├── L43.mae │ ├── L44.mae │ ├── L45.mae │ ├── L46.mae │ ├── L5.mae │ ├── L6.mae │ ├── L7.mae │ ├── L8.mae │ └── L9.mae ├── q2mm ├── __init__.py ├── calculate.py ├── compare.py ├── constants.py ├── datatypes.py ├── filetypes.py ├── gradient.py ├── gui.py ├── loop.py ├── opt.py ├── parameters.py ├── setup_esp.py └── simplex.py ├── q2mm_example ├── amber │ ├── Ash.in │ ├── Ash.mol2 │ ├── frcmod │ └── loop.in ├── atom.typ ├── loop.in ├── meets1.log ├── meets1.mae ├── meets2.log ├── meets2.mae ├── mm3.fld └── qparam.txt ├── reactions ├── Pdheckrxn-asymNu.mae ├── Pdheckrxn-symNu.mae ├── readme ├── rh-hydrogenation-enamide.mae ├── ru-hydrogenation-ketone.com └── ru-hydrogenation-ketone.mae ├── requirements.txt ├── screen ├── README.md ├── merge.py ├── setup_com_from_mae.py ├── setup_com_from_mae_many.py ├── setup_mae_from_com.py └── setup_mae_from_com_many.py ├── screen_sample ├── NOTE.txt ├── atom.typ ├── example.sh ├── mm3.fld ├── step-0_mae-original │ ├── binap-b.com │ ├── binap-b.mae │ ├── binap.com │ ├── binap.mae │ ├── rh-hydrogenation-enamides.com │ ├── rh-hydrogenation-enamides.mae │ ├── s1.com │ └── s1.mae ├── step-1_mae-manual │ ├── binap-b.com │ ├── binap-b.mae │ ├── binap.com │ ├── binap.mae │ ├── rh-hydrogenation-enamides.com │ ├── rh-hydrogenation-enamides.mae │ ├── s1.com │ └── s1.mae ├── step-2_mae-automatic │ ├── binap-b.com │ ├── binap-b.mae │ ├── binap.com │ ├── binap.mae │ ├── rh-hydrogenation-enamides.com │ ├── rh-hydrogenation-enamides.mae │ ├── s1.com │ └── s1.mae ├── step-3_merge-output-in-one.mae ├── step-3_merge-output │ ├── atom.typ │ ├── mm3.fld │ ├── rh-hydrogenation-enamides_binap-b_s1_5r.mae │ ├── rh-hydrogenation-enamides_binap-b_s1_5s.mae │ ├── rh-hydrogenation-enamides_binap_s1_5r.mae │ └── rh-hydrogenation-enamides_binap_s1_5s.mae ├── step-4_conformational-search │ ├── atom.typ │ ├── job.sh │ ├── mm3.fld │ ├── rh-hydrogenation-enamides_binap-b_s1_5r.mae │ ├── rh-hydrogenation-enamides_binap-b_s1_5r_cs.com │ ├── rh-hydrogenation-enamides_binap-b_s1_5r_cs.mae │ ├── rh-hydrogenation-enamides_binap-b_s1_5r_cs.mmo │ ├── rh-hydrogenation-enamides_binap-b_s1_5s.mae │ ├── rh-hydrogenation-enamides_binap-b_s1_5s_cs.com │ ├── rh-hydrogenation-enamides_binap-b_s1_5s_cs.mae │ ├── rh-hydrogenation-enamides_binap-b_s1_5s_cs.mmo │ ├── rh-hydrogenation-enamides_binap-b_s1_5s_single.com │ ├── rh-hydrogenation-enamides_binap_s1_5r.mae │ ├── rh-hydrogenation-enamides_binap_s1_5r_cs.com │ ├── rh-hydrogenation-enamides_binap_s1_5r_cs.mae │ ├── rh-hydrogenation-enamides_binap_s1_5r_cs.mmo │ ├── rh-hydrogenation-enamides_binap_s1_5s.mae │ ├── rh-hydrogenation-enamides_binap_s1_5s_cs.com │ ├── rh-hydrogenation-enamides_binap_s1_5s_cs.mae │ └── rh-hydrogenation-enamides_binap_s1_5s_cs.mmo ├── step-5_redundant-conformer-elimination │ ├── atom.typ │ ├── job.sh │ ├── mm3.fld │ ├── rh-hydrogenation-enamides_binap-b_s1_5r_cs.inf │ ├── rh-hydrogenation-enamides_binap-b_s1_5r_cs.mae │ ├── rh-hydrogenation-enamides_binap-b_s1_5r_cs_re.com │ ├── rh-hydrogenation-enamides_binap-b_s1_5r_cs_re.mae │ ├── rh-hydrogenation-enamides_binap-b_s1_5s_cs.inf │ ├── rh-hydrogenation-enamides_binap-b_s1_5s_cs.mae │ ├── rh-hydrogenation-enamides_binap-b_s1_5s_cs_re.com │ ├── rh-hydrogenation-enamides_binap-b_s1_5s_cs_re.mae │ ├── rh-hydrogenation-enamides_binap_s1_5r_cs.inf │ ├── rh-hydrogenation-enamides_binap_s1_5r_cs.mae │ ├── rh-hydrogenation-enamides_binap_s1_5r_cs_re.com │ ├── rh-hydrogenation-enamides_binap_s1_5r_cs_re.mae │ ├── rh-hydrogenation-enamides_binap_s1_5s_cs.inf │ ├── rh-hydrogenation-enamides_binap_s1_5s_cs.mae │ ├── rh-hydrogenation-enamides_binap_s1_5s_cs_re.com │ └── rh-hydrogenation-enamides_binap_s1_5s_cs_re.mae └── step-6_data-analysis.csv ├── smiles_to_catvs └── scripts │ ├── finish.py │ ├── prepare.py │ ├── sdf_to_mae.py │ └── search.py ├── smiles_to_catvs_example ├── allyl6.mae ├── atom.typ ├── mm3.fld ├── run ├── smi │ └── strem_bisphosphines.smi └── template_diphos.mae ├── substrates ├── alkenes │ ├── a.mae │ ├── aa.mae │ ├── ab.mae │ ├── ac.mae │ ├── ad.mae │ ├── ae.mae │ ├── af.mae │ ├── ag.mae │ ├── ah.mae │ ├── ai.mae │ ├── aj.mae │ ├── ak.mae │ ├── al.mae │ ├── alkene-substrates.cdx │ ├── am.mae │ ├── an.mae │ ├── ao.mae │ ├── ap.mae │ ├── aq.mae │ ├── ar.mae │ ├── as.mae │ ├── at.mae │ ├── au.mae │ ├── av.mae │ ├── aw.mae │ ├── ax.mae │ ├── ay.mae │ ├── az.mae │ ├── b.mae │ ├── ba.mae │ ├── bb.mae │ ├── bc.mae │ ├── bd.mae │ ├── be.mae │ ├── bf.mae │ ├── bg.mae │ ├── bh.mae │ ├── bi.mae │ ├── bj.mae │ ├── bk.mae │ ├── bl.mae │ ├── bm.mae │ ├── bn.mae │ ├── bo.mae │ ├── bp.mae │ ├── bq.mae │ ├── br.mae │ ├── bs.mae │ ├── bt.mae │ ├── bu.mae │ ├── bv.mae │ ├── bw.mae │ ├── bx.mae │ ├── by.mae │ ├── bz.mae │ ├── c.mae │ ├── ca.mae │ ├── cb.mae │ ├── cc.mae │ ├── cd.mae │ ├── ce.mae │ ├── d.mae │ ├── e.mae │ ├── f.mae │ ├── g.mae │ ├── h.mae │ ├── i.mae │ ├── j.mae │ ├── k.mae │ ├── l.mae │ ├── m.mae │ ├── n.mae │ ├── o.mae │ ├── p.mae │ ├── q.mae │ ├── r.mae │ ├── s.mae │ ├── t.mae │ ├── u.mae │ ├── v.mae │ ├── w.mae │ ├── x.mae │ ├── y.mae │ └── z.mae ├── aryl_alkenyl │ ├── A.mae │ ├── AA.mae │ ├── AB.mae │ ├── AC.mae │ ├── AD.mae │ ├── AE.mae │ ├── AF.mae │ ├── AG.mae │ ├── AH.mae │ ├── AI.mae │ ├── AJ.mae │ ├── AK.mae │ ├── AL.mae │ ├── AM.mae │ ├── AN.mae │ ├── AO.mae │ ├── AP.mae │ ├── AQ.mae │ ├── AR.mae │ ├── AS.mae │ ├── AT.mae │ ├── AU.mae │ ├── AV.mae │ ├── AW.mae │ ├── AX.mae │ ├── AY.mae │ ├── AZ.mae │ ├── B.mae │ ├── BA.mae │ ├── BB.mae │ ├── BC.mae │ ├── BD.mae │ ├── BE.mae │ ├── BF.mae │ ├── BG.mae │ ├── BH.mae │ ├── BI.mae │ ├── BJ.mae │ ├── BK.mae │ ├── BL.mae │ ├── BM.mae │ ├── BN.mae │ ├── BO.mae │ ├── BP.mae │ ├── BQ.mae │ ├── BR.mae │ ├── BS.mae │ ├── BT.mae │ ├── BU.mae │ ├── BV.mae │ ├── BW.mae │ ├── BX.mae │ ├── BY.mae │ ├── BZ.mae │ ├── C.mae │ ├── CA.mae │ ├── CB.mae │ ├── CC.mae │ ├── CD.mae │ ├── CE.mae │ ├── CF.mae │ ├── CG.mae │ ├── CH.mae │ ├── CI.mae │ ├── CJ.mae │ ├── CK.mae │ ├── CL.mae │ ├── CM.mae │ ├── CN.mae │ ├── D.mae │ ├── E.mae │ ├── F.mae │ ├── G.mae │ ├── H.mae │ ├── I.mae │ ├── J.mae │ ├── K.mae │ ├── L.mae │ ├── M.mae │ ├── N.mae │ ├── O.mae │ ├── P.mae │ ├── Q.mae │ ├── R.mae │ ├── S.mae │ ├── T.mae │ ├── U.mae │ ├── V.mae │ ├── W.mae │ ├── X.mae │ ├── Y.mae │ ├── Z.mae │ └── aryl_alkenyl-substrates.cdx ├── enamide │ ├── enamide-ac-h.mae │ ├── enamide-ac-me.mae │ ├── enamide-phe-ac-h.mae │ ├── enamide-phe-ac-me.mae │ ├── enamide-phe-bn-h.mae │ ├── enamide-phz-ac-h.mae │ ├── enamide-phz-ac-me.mae │ ├── enamide-phz-bn-h.mae │ ├── enamide-phz-bn-me.mae │ └── enamide-phz-co2et-et.mae ├── enones │ ├── enone1.mae │ ├── enone10.mae │ ├── enone11.mae │ ├── enone12.mae │ ├── enone13.mae │ ├── enone14.mae │ ├── enone15.mae │ ├── enone16.mae │ ├── enone17.mae │ ├── enone18.mae │ ├── enone19.mae │ ├── enone2.mae │ ├── enone20.mae │ ├── enone21.mae │ ├── enone22.mae │ ├── enone23.mae │ ├── enone24.mae │ ├── enone25.mae │ ├── enone26.mae │ ├── enone27.mae │ ├── enone28.mae │ ├── enone29.mae │ ├── enone3.mae │ ├── enone30.mae │ ├── enone4.mae │ ├── enone5.mae │ ├── enone6.mae │ ├── enone7.mae │ ├── enone8.mae │ ├── enone9.mae │ └── enones.cdx └── ketone │ ├── acetophenone.com │ └── acetophenone.mae ├── substrates_old ├── NOTES.txt ├── s1.mae ├── s2.mae ├── s3.mae ├── 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