diff --git a/multi-ego-basic.ff/aminoacids.rtp b/multi-ego-basic.ff/aminoacids.rtp index 220febd8..a7abfe92 100644 --- a/multi-ego-basic.ff/aminoacids.rtp +++ b/multi-ego-basic.ff/aminoacids.rtp @@ -499,7 +499,7 @@ H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 - CG C 0.000 0 + CG CR 0.000 0 ND1 NR 0.000 0 CD2 CH 0.000 0 CE1 CH 0.000 0 @@ -728,7 +728,7 @@ CA CAH 0.000 0 CB CH2 0.000 0 CG CH2 0.000 0 - SD S 0.000 0 + SD SM 0.000 0 CE CH3 0.000 0 C C 0.000 0 O O 0.000 0 @@ -778,7 +778,7 @@ H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 - CG CH 0.000 0 + CG CR 0.000 0 CD1 CH 0.000 0 CD2 CH 0.000 0 CE1 CH 0.000 0 @@ -991,11 +991,11 @@ H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 - CG CH 0.000 0 + CG CR 0.000 0 CD1 CH 0.000 0 - CD2 CH 0.000 0 + CD2 CR 0.000 0 NE1 NR 0.000 0 - CE2 CH 0.000 0 + CE2 CR 0.000 0 CE3 CH 0.000 0 CZ2 CH 0.000 0 CZ3 CH 0.000 0 @@ -1083,7 +1083,7 @@ H H 0.000 0 CA CAH 0.000 0 CB CH2 0.000 0 - CG CH 0.000 0 + CG CR 0.000 0 CD1 CH 0.000 0 CD2 CH 0.000 0 CE1 CH 0.000 0 diff --git a/multi-ego-basic.ff/atomtypes.atp b/multi-ego-basic.ff/atomtypes.atp index 351e77f4..faaaac83 100644 --- a/multi-ego-basic.ff/atomtypes.atp +++ b/multi-ego-basic.ff/atomtypes.atp @@ -12,6 +12,7 @@ C 11.01100 ; bare carbon CZ 11.01100 ; bare carbon CH 13.01900 ; aromatic CH + CR 12.01100 ; aromatic C CAH 12.01100 ; aliphatic or sugar CH-group CH1 13.01900 ; aliphatic or sugar CH-group CH1t 13.01900 ; aliphatic or sugar CH-group @@ -20,6 +21,7 @@ CH3 15.03500 ; aliphatic CH3-group CH2r 14.02700 ; CH2-group in a ring S 32.06000 ; sulfur + SM 32.06000 ; sulfur MET SH 32.06000 ; sulfur H 4.03200 ; backbone Hydrogen ; LIPIDS diff --git a/multi-ego-basic.ff/ffnonbonded.itp b/multi-ego-basic.ff/ffnonbonded.itp index 31f66cfc..b38bd63b 100644 --- a/multi-ego-basic.ff/ffnonbonded.itp +++ b/multi-ego-basic.ff/ffnonbonded.itp @@ -10,6 +10,7 @@ NZ 7 0.000 0.000 A 0.0000000000 8.752940e-07 NE 7 0.000 0.000 A 0.0000000000 8.752940e-07 C 6 0.000 0.000 A 0.0000000000 2.598570e-06 + CR 6 0.000 0.000 A 0.0000000000 2.598570e-06 CZ 6 0.000 0.000 A 0.0000000000 2.598570e-06 CH 6 0.000 0.000 A 0.0000000000 2.598570e-06 H 1 0.000 0.000 A 0.0000000000 3.239247e-09 @@ -21,6 +22,7 @@ CH3 6 0.000 0.000 A 0.0000000000 8.595562e-06 CH2r 6 0.000 0.000 A 0.0000000000 1.193966e-05 S 16 0.000 0.000 A 0.0000000000 2.724050e-06 + SM 16 0.000 0.000 A 0.0000000000 2.724050e-06 SH 16 0.000 0.000 A 0.0000000000 2.724050e-06 CH3p 6 0.000 0.000 A 0.0000000000 8.736473e-06 P 15 0.000 0.000 A 0.0000000000 3.893600e-06 diff --git a/src/multiego/Minimum_CUTOFF_Manual_modif.csv b/src/multiego/Minimum_CUTOFF_Manual_modif.csv index 6bb53227..9f45ea57 100644 --- a/src/multiego/Minimum_CUTOFF_Manual_modif.csv +++ b/src/multiego/Minimum_CUTOFF_Manual_modif.csv @@ -9,6 +9,7 @@ O NR 1.2594349761073345e-07 6.296055527893412e-07 # >6 4.78449438233876e- O NZ 9.05167362258012e-08 4.799376617607296e-07 # >6 0.0 9.05167362258012e-08 O NE 1.2594349761073345e-07 4.799376617607296e-07 # >6 0.0 1.2594349761073345e-07 O C 1.5619221473243766e-07 2.5445798665780286e-06 # 4-5 1.5619221473243766e-07 1.8933619871479337e-06 +O CR 8.454178454694858e-07 2.5445798665780286e-06 # 4-5 8.454178454694858e-07 1.7356754565546296e-06 O CZ 9.271725969950735e-07 8.269390364517911e-07 # >6 0.0 9.271725969950735e-07 O CH 7.013840414318058e-07 8.269390364517911e-07 # 4-5 7.013840414318058e-07 1.0161170406288952e-06 O CH1 1.4558184529108867e-06 4.153527511548878e-06 # >6 1.59011205135462e-06 1.4558184529108867e-06 @@ -19,6 +20,7 @@ O CAH2 6.381454827742098e-07 2.015648815722931e-06 # >6 1.4922176228398963 O CH3 5.27066068361103e-07 1.503991708701826e-06 # 4-5 5.27066068361103e-07 1.1128214538294811e-06 O CH2r 9.271725969950735e-07 1.7725675979630829e-06 # >6 1.2178965067259558e-06 9.271725969950735e-07 O S 9.271725969950735e-07 8.466821298334225e-07 # 4-5 9.271725969950735e-07 1.8933619871479337e-06 +O SM 9.271725969950735e-07 8.466821298334225e-07 # 4-5 9.271725969950735e-07 1.8933619871479337e-06 O SH 8.454178454694858e-07 8.466821298334225e-07 # >6 1.0161170406288952e-06 8.454178454694858e-07 O H 4.826394797699592e-10 1.5516445117711974e-08 # >6 1.003911895429072e-08 4.826394797699592e-10 OM OM 1.2178965067259558e-06 2.5e-6 # Manual 2.1419726874683542e-07 1.2178965067259558e-06 @@ -30,6 +32,7 @@ OM NR 5.742618275042624e-08 5.096590509207162e-07 # >6 7.225302986991769e OM NZ 7.225302986991769e-08 3.885044725390518e-07 # >6 0.0 7.225302986991769e-08 OM NE 7.225302986991769e-08 3.885044725390518e-07 # >6 0.0 7.225302986991769e-08 OM C 1.4558184529108867e-06 2.0598105497110153e-06 # Manual 1.736919907132888e-07 1.4558184529108867e-06 +OM CR 1.4558184529108867e-06 2.0598105497110153e-06 # >6 1.7356754565546296e-06 1.4558184529108867e-06 OM CZ 8.454178454694858e-07 6.693984235369761e-07 # >6 0.0 8.454178454694858e-07 OM CH 7.703205086354507e-07 6.693984235369761e-07 # Manual 1.2594349761073345e-07 7.703205086354507e-07 OM CH1 2.897745766558051e-06 3.3622366895124407e-06 # Manual 9.271725969950735e-07 2.897745766558051e-06 @@ -40,6 +43,7 @@ OM CAH2 7.703205086354507e-07 1.6316464457144573e-06 # >6 1.4922176228398963 OM CH3 1.2178965067259558e-06 1.2174654169641174e-06 # Manual 4.543781405690857e-08 1.2178965067259558e-06 OM CH2r 9.271725969950735e-07 1.4348747651101918e-06 # >6 1.4558184529108867e-06 9.271725969950735e-07 OM S 1.59011205135462e-06 6.853802492857207e-07 # >6 1.59011205135462e-06 1.59011205135462e-06 +OM SM 1.59011205135462e-06 6.853802492857207e-07 # >6 1.59011205135462e-06 1.59011205135462e-06 OM SH 7.703205086354507e-07 6.853802492857207e-07 # Manual 8.091373121174105e-08 7.703205086354507e-07 OM H 4.0559363711814284e-10 1.2560398581812419e-08 # >6 2.4222480021401187e-09 4.0559363711814284e-10 OA OA 5.1110687858211906e-08 5.0183595334817e-07 # >6 0.0 5.1110687858211906e-08 @@ -50,6 +54,7 @@ OA NR 7.225302986991769e-08 8.694393736065237e-07 # >6 0.0 OA NZ 1.2594349761073345e-07 6.627589260653239e-07 # >6 0.0 1.2594349761073345e-07 OA NE 1.736919907132888e-07 6.627589260653239e-07 # >6 0.0 1.736919907132888e-07 OA C 1.1128214538294811e-06 3.513879309812254e-06 # >6 1.59011205135462e-06 1.1128214538294811e-06 +OA CR 1.8933619871479337e-06 3.513879309812254e-06 # >6 4.737322988859966e-06 1.8933619871479337e-06 OA CZ 1.1128214538294811e-06 1.1419425300144831e-06 # >6 0.0 1.1128214538294811e-06 OA CH 1.0161170406288952e-06 1.1419425300144831e-06 # >6 1.0303119972742315e-05 1.0161170406288952e-06 OA CH1 3.149574184402289e-06 5.735718724048164e-06 # >6 0.0 3.149574184402289e-06 @@ -60,6 +65,7 @@ OA CAH2 7.703205086354507e-07 2.7834640847572668e-06 # >6 1.110557678004124e OA CH3 1.2178965067259558e-06 2.076902916961151e-06 # >6 0.0 1.2178965067259558e-06 OA CH2r 1.2178965067259558e-06 2.4477866423199905e-06 # Manual 6.381454827742098e-07 1.2178965067259558e-06 OA S 1.2178965067259558e-06 1.1692063028111693e-06 # >6 0.0 1.2178965067259558e-06 +OA SM 1.2178965067259558e-06 1.1692063028111693e-06 # >6 0.0 1.2178965067259558e-06 OA SH 5.801734210627211e-07 1.1692063028111693e-06 # >6 0.0 5.801734210627211e-07 OA H 8.014267939679831e-10 2.1427079643716717e-08 # >6 1.927540226755784e-08 8.014267939679831e-10 N N 1.2884910181278791e-05 8.75284823952248e-07 # >6 0.0 1.2884910181278791e-05 @@ -69,6 +75,7 @@ N NR 5.27066068361103e-07 1.1482411765953813e-06 # 4-5 5.27066068361103e- N NZ 1.8933619871479337e-06 8.75284823952248e-07 # >6 0.0 1.8933619871479337e-06 N NE 1.59011205135462e-06 8.75284823952248e-07 # 4-5 1.59011205135462e-06 3.421320847663108e-06 N C 4.339756224213911e-07 4.640669649427428e-06 # 4-5 4.339756224213911e-07 3.149574184402289e-06 +N CR 1.2178965067259558e-06 4.640669649427428e-06 # 4-5 1.2178965067259558e-06 4.37074965270138e-06 N CZ 4.737322988859966e-06 1.508127506152659e-06 # >6 0.0 4.737322988859966e-06 N CH 2.897745766558051e-06 1.508127506152659e-06 # Manual 7.013840414318058e-07 2.897745766558051e-06 N CH1 2.897745766558051e-06 7.574982932969631e-06 # 4-5 2.897745766558051e-06 3.473598766179243e-05 @@ -79,6 +86,7 @@ N CAH2 8.20374377950018e-06 3.6760332838792072e-06 # >6 1.1964957655417957 N CH3 4.737322988859966e-06 2.742900219889418e-06 # Manual 9.271725969950735e-07 4.737322988859966e-06 N CH2r 6.503393009784176e-06 3.2327146659727425e-06 # Manual 8.454178454694858e-07 6.503393009784176e-06 N S 2.064082678151929e-06 1.544133911550011e-06 # >6 2.248809725327641e-06 2.064082678151929e-06 +N SM 2.064082678151929e-06 1.544133911550011e-06 # >6 2.248809725327641e-06 2.064082678151929e-06 N SH 1.0161170406288952e-06 1.544133911550011e-06 # 4-5 1.0161170406288952e-06 1.2178965067259558e-06 N H 7.654462535149269e-09 2.8298068718749842e-08 # 4-5 7.654462535149269e-09 4.339756224213911e-07 NT NT 7.013840414318058e-07 2.5961659689014112e-06 # >6 0.0 7.013840414318058e-07 @@ -87,6 +95,7 @@ NT NR 5.801734210627211e-07 1.9775371185017886e-06 # >6 0.0 NT NZ 5.27066068361103e-07 1.5074430911449656e-06 # >6 0.0 5.27066068361103e-07 NT NE 1.1128214538294811e-06 1.5074430911449656e-06 # >6 0.0 1.1128214538294811e-06 NT C 1.8933619871479337e-06 7.992307429401009e-06 # 4-5 1.8933619871479337e-06 2.064082678151929e-06 +NT CR 1.7356754565546296e-06 7.992307429401009e-06 # >6 1.8933619871479337e-06 1.7356754565546296e-06 NT CZ 1.7356754565546296e-06 2.5973446899834983e-06 # >6 0.0 1.7356754565546296e-06 NT CH 1.3319957855440268e-06 2.5973446899834983e-06 # >6 0.0 1.3319957855440268e-06 NT CH1 7.030422589392208e-06 1.3045874183315057e-05 # >6 9.244222827735503e-05 7.030422589392208e-06 @@ -97,6 +106,7 @@ NT CAH2 2.064082678151929e-06 6.330980299168271e-06 # >6 1.3869290966783295 NT CH3 1.8933619871479337e-06 4.723909147084545e-06 # >6 2.1373642831810142e-05 1.8933619871479337e-06 NT CH2r 2.248809725327641e-06 5.567483012968901e-06 # Manual 3.9332116172143173e-07 2.248809725327641e-06 NT S 1.3319957855440268e-06 2.6593560553903825e-06 # >6 0.0 1.3319957855440268e-06 +NT SM 1.3319957855440268e-06 2.6593560553903825e-06 # >6 0.0 1.3319957855440268e-06 NT SH 1.0161170406288952e-06 2.6593560553903825e-06 # >6 0.0 1.0161170406288952e-06 NT H 3.778004187152545e-09 4.873582520282809e-08 # >6 8.091373121174105e-08 3.778004187152545e-09 NL NL 2.897745766558051e-06 2.5e-5 # >6 0.0 2.897745766558051e-06 @@ -104,6 +114,7 @@ NL NR 2.631995597129722e-07 1.1482411765953813e-06 # >6 3.5618550662813837 NL NZ 2.897745766558051e-06 2.5e-5 # >6 0.0 2.897745766558051e-06 NL NE 9.271725969950735e-07 8.75284823952248e-07 # Manual 7.225302986991769e-08 9.271725969950735e-07 NL C 1.3319957855440268e-06 4.640669649427428e-06 # >6 1.59011205135462e-06 1.3319957855440268e-06 +NL CR 2.448580108078591e-06 4.640669649427428e-06 # >6 2.6644993987597274e-06 2.448580108078591e-06 NL CZ 2.448580108078591e-06 1.508127506152659e-06 # >6 0.0 2.448580108078591e-06 NL CH 2.064082678151929e-06 1.508127506152659e-06 # Manual 6.381454827742098e-07 2.064082678151929e-06 NL CH1 1.4922176228398963e-05 7.574982932969631e-06 # >6 7.175626843968198e-05 1.4922176228398963e-05 @@ -114,12 +125,14 @@ NL CAH2 4.030347871778446e-06 3.6760332838792072e-06 # >6 1.2884910181278791 NL CH3 2.897745766558051e-06 2.742900219889418e-06 # Manual 1.3319957855440268e-06 2.897745766558051e-06 NL CH2r 3.7144078137182355e-06 3.2327146659727425e-06 # Manual 2.9137432184408464e-07 3.7144078137182355e-06 NL S 1.1128214538294811e-06 1.544133911550011e-06 # Manual 8.454178454694858e-07 1.1128214538294811e-06 +NL SM 1.1128214538294811e-06 1.544133911550011e-06 # Manual 8.454178454694858e-07 1.1128214538294811e-06 NL SH 1.1292692029579082e-07 1.544133911550011e-06 # >6 0.0 1.1292692029579082e-07 NL H 4.365694982352848e-09 2.8298068718749842e-08 # 4-5 4.365694982352848e-09 8.772792870868534e-09 NR NR 2.9137432184408464e-07 1.5063185874465423e-06 # >6 0.0 2.9137432184408464e-07 NR NZ 5.801734210627211e-07 1.1482411765953813e-06 # >6 0.0 5.801734210627211e-07 NR NE 1.0161170406288952e-06 1.1482411765953813e-06 # >6 0.0 1.0161170406288952e-06 NR C 2.064082678151929e-06 6.087856012844263e-06 # Manual 8.454178454694858e-07 2.064082678151929e-06 +NR CR 2.064082678151929e-06 6.087856012844263e-06 # >6 2.248809725327641e-06 2.064082678151929e-06 NR CZ 1.4558184529108867e-06 1.9784349673759017e-06 # >6 0.0 1.4558184529108867e-06 NR CH 1.59011205135462e-06 1.9784349673759017e-06 # >6 8.855373008130008e-06 1.59011205135462e-06 NR CH1 7.030422589392208e-06 9.937230804903689e-06 # >6 0.0 7.030422589392208e-06 @@ -130,11 +143,13 @@ NR CAH2 1.8933619871479337e-06 4.822399140917269e-06 # >6 0.0 NR CH3 2.064082678151929e-06 3.598269831239962e-06 # >6 0.0 2.064082678151929e-06 NR CH2r 2.064082678151929e-06 4.2408322297796346e-06 # >6 0.0 2.064082678151929e-06 NR S 1.8933619871479337e-06 2.0256699201216162e-06 # >6 0.0 1.8933619871479337e-06 +NR SM 1.8933619871479337e-06 2.0256699201216162e-06 # >6 0.0 1.8933619871479337e-06 NR SH 1.1128214538294811e-06 2.0256699201216162e-06 # >6 0.0 1.1128214538294811e-06 NR H 1.1109248026469242e-09 3.7122782015431085e-08 # >6 1.003911895429072e-08 1.1109248026469242e-09 NZ NZ 6.381454827742098e-07 8.75284823952248e-07 # >6 0.0 6.381454827742098e-07 NZ NE 9.271725969950735e-07 8.75284823952248e-07 # >6 0.0 9.271725969950735e-07 NZ C 1.4558184529108867e-06 4.640669649427428e-06 # >6 0.0 1.4558184529108867e-06 +NZ CR 1.4558184529108867e-06 4.640669649427428e-06 # >6 1.7356754565546296e-06 1.4558184529108867e-06 NZ CZ 1.3319957855440268e-06 1.508127506152659e-06 # >6 0.0 1.3319957855440268e-06 NZ CH 1.4558184529108867e-06 1.508127506152659e-06 # >6 0.0 1.4558184529108867e-06 NZ CH1 7.596342311330096e-06 7.574982932969631e-06 # >6 0.0 7.596342311330096e-06 @@ -145,10 +160,12 @@ NZ CAH2 1.8933619871479337e-06 3.6760332838792072e-06 # >6 0.0 NZ CH3 1.7356754565546296e-06 2.742900219889418e-06 # >6 0.0 1.7356754565546296e-06 NZ CH2r 2.064082678151929e-06 3.2327146659727425e-06 # >6 0.0 2.064082678151929e-06 NZ S 1.3319957855440268e-06 1.544133911550011e-06 # >6 0.0 1.3319957855440268e-06 +NZ SM 1.3319957855440268e-06 1.544133911550011e-06 # >6 0.0 1.3319957855440268e-06 NZ SH 1.0161170406288952e-06 1.544133911550011e-06 # >6 0.0 1.0161170406288952e-06 NZ H 5.1110687858211906e-08 2.8298068718749842e-08 # >6 0.0 5.1110687858211906e-08 NE NE 1.59011205135462e-06 8.75284823952248e-07 # >6 0.0 1.59011205135462e-06 NE C 1.59011205135462e-06 4.640669649427428e-06 # >6 7.596342311330096e-06 1.59011205135462e-06 +NE CR 2.248809725327641e-06 4.640669649427428e-06 # >6 2.248809725327641e-06 2.248809725327641e-06 NE CZ 1.7356754565546296e-06 1.508127506152659e-06 # >6 0.0 1.7356754565546296e-06 NE CH 1.8933619871479337e-06 1.508127506152659e-06 # >6 0.0 1.8933619871479337e-06 NE CH1 1.110557678004124e-05 7.574982932969631e-06 # >6 0.0 1.110557678004124e-05 @@ -159,9 +176,11 @@ NE CAH2 3.149574184402289e-06 3.6760332838792072e-06 # >6 0.0 NE CH3 2.448580108078591e-06 2.742900219889418e-06 # >6 0.0 2.448580108078591e-06 NE CH2r 3.421320847663108e-06 3.2327146659727425e-06 # >6 0.0 3.421320847663108e-06 NE S 2.064082678151929e-06 1.544133911550011e-06 # >6 0.0 2.064082678151929e-06 +NE SM 2.064082678151929e-06 1.544133911550011e-06 # >6 0.0 2.064082678151929e-06 NE SH 1.3319957855440268e-06 1.544133911550011e-06 # >6 0.0 1.3319957855440268e-06 NE H 2.4782805153887164e-08 2.8298068718749842e-08 # >6 0.0 2.4782805153887164e-08 C C 2.4604350727657302e-05 2.4604350727657302e-05 # Manual 2.448580108078591e-06 2.4604350727657302e-05 +C CR 2.064082678151929e-06 2.4604350727657302e-05 # 4-5 2.064082678151929e-06 8.20374377950018e-06 C CZ 6.503393009784176e-06 7.995936127016803e-06 # >6 0.0 6.503393009784176e-06 C CH 4.37074965270138e-06 7.995936127016803e-06 # Manual 1.0161170406288952e-06 4.37074965270138e-06 C CH1 5.556363657234973e-06 4.0161776406945595e-05 # 4-5 5.556363657234973e-06 1.9908604884064596e-05 @@ -172,8 +191,23 @@ C CAH2 7.596342311330096e-06 1.948994844187309e-05 # >6 2.2936907742668513 C CH3 6.012808612204707e-06 1.4542573404132365e-05 # Manual 2.064082678151929e-06 6.012808612204707e-06 C CH2r 1.7356754565546296e-06 1.713951896012432e-05 # 4-5 1.7356754565546296e-06 6.012808612204707e-06 C S 4.030347871778446e-06 8.186838366082229e-06 # >6 4.37074965270138e-06 4.030347871778446e-06 +C SM 4.030347871778446e-06 8.186838366082229e-06 # >6 4.37074965270138e-06 4.030347871778446e-06 C SH 4.737322988859966e-06 8.186838366082229e-06 # Manual 2.897745766558051e-06 4.737322988859966e-06 C H 1.0115434594394737e-07 1.5003343488528082e-07 # Manual 3.578500073173326e-08 1.0115434594394737e-07 +CR CR 3.149574184402289e-06 2.4604350727657302e-05 # >6 4.737322988859966e-06 3.149574184402289e-06 +CR CZ 2.448580108078591e-06 7.995936127016803e-06 # >6 2.6644993987597274e-06 2.448580108078591e-06 +CR CH 2.6644993987597274e-06 7.995936127016803e-06 # >6 3.421320847663108e-06 2.6644993987597274e-06 +CR CH1 1.853615051555947e-05 4.0161776406945595e-05 # >6 2.1373642831810142e-05 1.853615051555947e-05 +CR CH1t 1.3869290966783295e-05 4.0161776406945595e-05 # >6 1.6047872836151582e-05 1.3869290966783295e-05 +CR CAH 1.4922176228398963e-05 4.0161776406945595e-05 # >6 2.1373642831810142e-05 1.4922176228398963e-05 +CR CH2 4.737322988859966e-06 1.948994844187309e-05 # >6 5.131884534481803e-06 4.737322988859966e-06 +CR CAH2 3.149574184402289e-06 1.948994844187309e-05 # >6 4.737322988859966e-06 3.149574184402289e-06 +CR CH3 3.7144078137182355e-06 1.4542573404132365e-05 # >6 4.030347871778446e-06 3.7144078137182355e-06 +CR CH2r 3.421320847663108e-06 1.713951896012432e-05 # >6 3.421320847663108e-06 3.421320847663108e-06 +CR S 0.0 0.0 # >6 0.0 0.0 +CR SM 4.37074965270138e-06 8.186838366082229e-06 # >6 5.131884534481803e-06 4.37074965270138e-06 +CR SH 3.7144078137182355e-06 8.186838366082229e-06 # >6 4.030347871778446e-06 3.7144078137182355e-06 +CR H 8.091373121174105e-08 1.5003343488528082e-07 # >6 9.05167362258012e-08 8.091373121174105e-08 CZ CZ 1.8933619871479337e-06 2.598523946232985e-06 # >6 0.0 1.8933619871479337e-06 CZ CH 2.064082678151929e-06 2.598523946232985e-06 # >6 0.0 2.064082678151929e-06 CZ CH1 1.1964957655417957e-05 1.3051797320401952e-05 # >6 0.0 1.1964957655417957e-05 @@ -184,6 +218,7 @@ CZ CAH2 3.7144078137182355e-06 6.333854714763538e-06 # >6 0.0 CZ CH3 2.448580108078591e-06 4.726053914163474e-06 # >6 0.0 2.448580108078591e-06 CZ CH2r 3.421320847663108e-06 5.570010782641626e-06 # >6 0.0 3.421320847663108e-06 CZ S 2.448580108078591e-06 2.6605634662742835e-06 # >6 0.0 2.448580108078591e-06 +CZ SM 2.448580108078591e-06 2.6605634662742835e-06 # >6 0.0 2.448580108078591e-06 CZ SH 2.448580108078591e-06 2.6605634662742835e-06 # >6 0.0 2.448580108078591e-06 CZ H 6.444980961093803e-08 4.8757952426321354e-08 # >6 0.0 6.444980961093803e-08 CH CH 2.6644993987597274e-06 2.598523946232985e-06 # >6 1.2884910181278791e-05 2.6644993987597274e-06 @@ -195,6 +230,7 @@ CH CAH2 2.6644993987597274e-06 6.333854714763538e-06 # >6 2.4604350727657302 CH CH3 3.149574184402289e-06 4.726053914163474e-06 # >6 0.0 3.149574184402289e-06 CH CH2r 2.064082678151929e-06 5.570010782641626e-06 # 4-5 2.064082678151929e-06 3.421320847663108e-06 CH S 3.421320847663108e-06 2.6605634662742835e-06 # >6 0.0 3.421320847663108e-06 +CH SM 3.421320847663108e-06 2.6605634662742835e-06 # >6 0.0 3.421320847663108e-06 CH SH 2.448580108078591e-06 2.6605634662742835e-06 # >6 0.0 2.448580108078591e-06 CH H 7.225302986991769e-08 4.8757952426321354e-08 # >6 1.0115434594394737e-07 7.225302986991769e-08 CH1 CH1 6.309156472163408e-05 6.555622223139519e-05 # >6 0.00021557010233386615 6.309156472163408e-05 @@ -205,6 +241,7 @@ CH1 CAH2 2.1373642831810142e-05 3.181351786802196e-05 # >6 3.473598766179243e CH1 CH3 1.4922176228398963e-05 2.3737898549049355e-05 # >6 0.0001916987884126441 1.4922176228398963e-05 CH1 CH2r 2.2936907742668513e-05 2.797690277700976e-05 # Manual 2.448580108078591e-06 2.2936907742668513e-05 CH1 S 1.1964957655417957e-05 1.3363407780104616e-05 # >6 0.0 1.1964957655417957e-05 +CH1 SM 1.1964957655417957e-05 1.3363407780104616e-05 # >6 0.0 1.1964957655417957e-05 CH1 SH 8.20374377950018e-06 1.3363407780104616e-05 # >6 0.0 8.20374377950018e-06 CH1 H 1.736919907132888e-07 2.44900153315381e-07 # 4-5 1.736919907132888e-07 1.0161170406288952e-06 CH1t CH1t 2.6382245451254078e-05 6.555622223139519e-05 # >6 0.00015106392932930527 2.6382245451254078e-05 @@ -214,6 +251,7 @@ CH1t CAH2 1.2884910181278791e-05 3.181351786802196e-05 # >6 2.6382245451254078 CH1t CH3 1.110557678004124e-05 2.3737898549049355e-05 # >6 0.00015106392932930527 1.110557678004124e-05 CH1t CH2r 1.4922176228398963e-05 2.797690277700976e-05 # Manual 1.3319957855440268e-06 1.4922176228398963e-05 CH1t S 7.596342311330096e-06 1.3363407780104616e-05 # >6 0.0 7.596342311330096e-06 +CH1t SM 7.596342311330096e-06 1.3363407780104616e-05 # >6 0.0 7.596342311330096e-06 CH1t SH 5.131884534481803e-06 1.3363407780104616e-05 # >6 0.0 5.131884534481803e-06 CH1t H 1.1292692029579082e-07 2.44900153315381e-07 # 4-5 1.1292692029579082e-07 1.9297259151556835e-07 CAH CAH 8.68129884517691e-05 6.555622223139519e-05 # >6 0.0 8.68129884517691e-05 @@ -222,6 +260,7 @@ CAH CAH2 3.0296190868820765e-05 3.181351786802196e-05 # >6 0.0 CAH CH3 1.4922176228398963e-05 2.3737898549049355e-05 # >6 2.2936907742668513e-05 1.4922176228398963e-05 CAH CH2r 1.853615051555947e-05 2.797690277700976e-05 # >6 2.2936907742668513e-05 1.853615051555947e-05 CAH S 6.503393009784176e-06 1.3363407780104616e-05 # >6 0.0 6.503393009784176e-06 +CAH SM 6.503393009784176e-06 1.3363407780104616e-05 # >6 0.0 6.503393009784176e-06 CAH SH 7.030422589392208e-06 1.3363407780104616e-05 # >6 3.0296190868820765e-05 7.030422589392208e-06 CAH H 1.3319957855440268e-06 2.44900153315381e-07 # >6 4.030347871778446e-06 1.3319957855440268e-06 CH2 CH2 1.110557678004124e-05 1.5438655320413708e-05 # >6 0.0001113988439841668 1.110557678004124e-05 @@ -229,26 +268,34 @@ CH2 CAH2 8.20374377950018e-06 1.5438655320413708e-05 # >6 2.827720357903463e CH2 CH3 5.556363657234973e-06 1.151967019963228e-05 # >6 0.00013386004153335797 5.556363657234973e-06 CH2 CH2r 7.596342311330096e-06 1.3576799670467695e-05 # Manual 1.7356754565546296e-06 7.596342311330096e-06 CH2 S 4.030347871778446e-06 6.485074913093783e-06 # >6 0.0 4.030347871778446e-06 +CH2 SM 4.030347871778446e-06 6.485074913093783e-06 # >6 0.0 4.030347871778446e-06 CH2 SH 3.421320847663108e-06 6.485074913093783e-06 # >6 0.0 3.421320847663108e-06 CH2 H 1.1292692029579082e-07 1.1884661956083523e-07 # 4-5 1.1292692029579082e-07 2.9137432184408464e-07 CAH2 CAH2 7.030422589392208e-06 1.5438655320413708e-05 # >6 0.0 7.030422589392208e-06 CAH2 CH3 4.030347871778446e-06 1.151967019963228e-05 # >6 2.4604350727657302e-05 4.030347871778446e-06 CAH2 CH2r 6.012808612204707e-06 1.3576799670467695e-05 # >6 1.9908604884064596e-05 6.012808612204707e-06 CAH2 S 2.897745766558051e-06 6.485074913093783e-06 # >6 0.0 2.897745766558051e-06 +CAH2 SM 2.897745766558051e-06 6.485074913093783e-06 # >6 0.0 2.897745766558051e-06 CAH2 SH 2.448580108078591e-06 6.485074913093783e-06 # >6 2.827720357903463e-05 2.448580108078591e-06 CAH2 H 7.703205086354507e-07 1.1884661956083523e-07 # >6 1.0161170406288952e-06 7.703205086354507e-07 CH3 CH3 3.7144078137182355e-06 8.5954896170802e-06 # >6 0.00017027339638628222 3.7144078137182355e-06 CH3 CH2r 4.737322988859966e-06 1.0130432432380583e-05 # Manual 1.7356754565546296e-06 4.737322988859966e-06 CH3 S 3.7144078137182355e-06 4.8388880163656295e-06 # >6 0.0 3.7144078137182355e-06 +CH3 SM 3.7144078137182355e-06 4.8388880163656295e-06 # >6 0.0 3.7144078137182355e-06 CH3 SH 3.149574184402289e-06 4.8388880163656295e-06 # >6 0.0 3.149574184402289e-06 CH3 H 1.0115434594394737e-07 8.86783099478706e-08 # 4-5 1.0115434594394737e-07 3.2228956345557457e-07 CH2r CH2r 6.012808612204707e-06 1.1939478242530793e-05 # Manual 1.7356754565546296e-06 6.012808612204707e-06 CH2r S 3.7144078137182355e-06 5.702994277398676e-06 # >6 0.0 3.7144078137182355e-06 +CH2r SM 3.7144078137182355e-06 5.702994277398676e-06 # >6 0.0 3.7144078137182355e-06 CH2r SH 2.248809725327641e-06 5.702994277398676e-06 # 4-5 2.248809725327641e-06 3.421320847663108e-06 CH2r H 1.9297259151556835e-07 1.045140727480474e-07 # 4-5 1.9297259151556835e-07 5.801734210627211e-07 S S 3.7144078137182355e-06 2.7240841741462863e-06 # >6 0.0 3.7144078137182355e-06 S SH 2.448580108078591e-06 2.7240841741462863e-06 # >6 0.0 2.448580108078591e-06 +S SM 2.448580108078591e-06 2.7240841741462863e-06 # >6 0.0 2.448580108078591e-06 S H 1.3088002451771873e-08 4.992204405268893e-08 # 4-5 1.3088002451771873e-08 1.696526259956281e-08 +SM SM 3.7144078137182355e-06 2.7240841741462863e-06 # >6 0.0 3.7144078137182355e-06 +SM SH 2.448580108078591e-06 2.7240841741462863e-06 # >6 0.0 2.448580108078591e-06 +SM H 1.3088002451771873e-08 4.992204405268893e-08 # 4-5 1.3088002451771873e-08 1.696526259956281e-08 SH SH 1.59011205135462e-06 2.7240841741462863e-06 # >6 0.0 1.59011205135462e-06 SH H 1.1471036561996625e-08 4.992204405268893e-08 # >6 1.1292692029579082e-07 1.1471036561996625e-08 H H 8.772792870868534e-09 9.148801296419777e-10 # 4-5 8.772792870868534e-09 4.543781405690857e-08 diff --git a/src/multiego/atdhisto.pkl b/src/multiego/atdhisto.pkl index ee4c8957..ea62958c 100644 Binary files a/src/multiego/atdhisto.pkl and b/src/multiego/atdhisto.pkl differ diff --git a/src/multiego/interaction_matrix.py b/src/multiego/interaction_matrix.py index b6fa2153..69e7a451 100644 --- a/src/multiego/interaction_matrix.py +++ b/src/multiego/interaction_matrix.py @@ -21,10 +21,11 @@ def find_class(self, module, name): class InteractionMatrix: - def __init__(self, pkl_file, emax=0.16, pth=None, show=False): + def __init__(self, pkl_file, emax=0.16, c12_rep_df=None, pth=None, show=False): self.atmat = self.read_pickle_file(pkl_file) self.emax = emax self.pth = pth + self.c12_rep_df = c12_rep_df self.define_p_threshold() self.nonlocal_matrix() self.plot_energy_matrix(show=show) @@ -44,7 +45,7 @@ def regall(self, ps, preference, emax, pth): emax: maximum energy value pth: threshold probability to split attractive and repulsive interactions """ - e = - emax/np.log(1e-4) * np.log(ps/(np.maximum(1e-4, preference*pth))) + e = - emax/np.log(1e-4) * np.log((ps + 1e-10)/(np.maximum(1e-4, preference*pth))) e /= np.max(e) e = np.where(e==-np.inf, -2, e) e = np.where(e > 0.0, 0.07 + e* (emax-0.07), e) @@ -59,8 +60,8 @@ def plot_energy_matrix(self, out_path = None, show = False): # TODO read them by gromos to avoid hardcoding them here bkbnd_atoms = ["C", "O", "N", "CAH", "CAH2", "H"] attype_ordering_charged = [ "OM", "NL", "NZ"] - attype_ordering_polar = [ "NE", "NR", "NT", "OA", "CZ", "S", "SH", "CH2r", "CH1t"] - attype_ordering_apolar = ["CH1","CH", "CH2", "CH3"] + attype_ordering_polar = [ "NE", "NR", "NT", "OA", "CZ", "S", "SM", "SH", "CH2r", "CH1t"] + attype_ordering_apolar = ["CH1","CR", "CH", "CH2", "CH3"] @@ -157,14 +158,17 @@ def read_pickle_file(self, filename): tot_reps = [] sum_probs = [] for key in data.keys(): - probs.append(data[key].p_repeats) + # probs.append(data[key].p_repeats_n2) + probs.append(data[key].p_density) + # probs.append(data[key].p_mindist_repeats_allpdbs) dists.append(data[key].exp_aver) cutoffs.append(data[key].cutoff) bins.append(data[key].xbins) kde.append(data[key].kde) tot_reps.append(data[key].tot_repeats) sum_probs.append(np.sum(data[key].sum_probs)) - atmat["probability"] = np.array(probs)#/np.array(cutoffs)**2 + atmat["probability"] = np.array(probs) + # atmat["probability"] = np.where(np.array(cutoffs) > 0 ,np.array(probs)/np.array(cutoffs)**2, np.array(probs)) # atmat["p_water"] =np.zeros(len(probs)) atmat["exp_aver"] = np.array(dists) atmat["attype1"] = atmat["atom_pair"].str.split("_").str[0] @@ -174,6 +178,10 @@ def read_pickle_file(self, filename): atmat["kde"] = kde atmat["tot_repeats"] = tot_reps atmat["sum_probs"] = sum_probs + # atmat["probability"] = atmat["sum_probs"]/atmat["tot_repeats"]**(0.5*1.8) if np.sum(atmat["sum_probs"]) > 0 else 0 + # fill nan values in probability with 0 + atmat["probability"] = atmat["probability"].fillna(0) + # where O-H set distance to 0.195 # atmat.loc[atmat["atom_pair"]=="O_H", "exp_aver"] = 0.195 # atmat.loc[atmat["atom_pair"]=="O_N", "exp_aver"] = 0.29 @@ -193,8 +201,8 @@ def define_p_threshold(self): print("Neither atpairref nor pth provided, or both provided. Optimizing pth to best fit KL_SCALE.") # find the minimum pth such that the following atom-pairs have energy < 0 # OM_OM, O_O, NL_NL, O_OM - pth = 0.001 # Initialize with a default value - dp = 0.001 + pth = 0.01 # Initialize with a default value + dp = 0.01 while True: self.atmat["energy"] = np.array(self.regall(self.atmat["probability"].to_numpy(), 1, self.emax, pth)) if (self.atmat.loc[self.atmat["atom_pair"]=="NL_NL", "energy"].values[0] < 0): @@ -209,7 +217,7 @@ def define_p_threshold(self): pth_max = pth while True: self.atmat["energy"] = np.array(self.regall(self.atmat["probability"].to_numpy(), 1, self.emax, pth_max)) - if self.atmat.loc[self.atmat["atom_pair"]=="OM_NZ", "energy"].values[0] < 0: + if self.atmat.loc[self.atmat["atom_pair"]=="CH_CH", "energy"].values[0] < 0: break pth_max += dp pth_max -= dp @@ -244,18 +252,19 @@ def define_special_nonlocal_dict(self): "atomtypes": ([atom_pair.split("_")[0]], [atom_pair.split("_")[1]]), "interaction": "rep", "sigma": None, - "epsilon": None, + "epsilon": float(self.c12_rep_df.loc[((self.c12_rep_df["atp1"]==atp1) & (self.c12_rep_df["atp2"]==atp2)) | ((self.c12_rep_df["atp1"]==atp2) & (self.c12_rep_df["atp2"]==atp1)), "c12"].values[0]), }) return special_nonlocal_dict def nonlocal_matrix(self): self.atmat["energy"] = np.array(self.regall(self.atmat["probability"].to_numpy(), 1, self.emax, self.pth)) - self.atmat.loc[self.atmat["atom_pair"]=="O_H", "energy"] = 0.45 - self.atmat.loc[self.atmat["atom_pair"]=="O_N", "energy"] = 0.45 - self.atmat.loc[self.atmat["atom_pair"]=="O_C", "energy"] = 0.45 - self.atmat.loc[self.atmat["atom_pair"]=="O_O", "energy"] = 0.09 - self.atmat.loc[self.atmat["atom_pair"]=="N_N", "energy"] = 0.09 - + self.atmat.loc[self.atmat["atom_pair"]=="O_H", "energy"] = 0.9 + self.atmat.loc[self.atmat["atom_pair"]=="O_N", "energy"] = 0.9 + self.atmat.loc[self.atmat["atom_pair"]=="O_C", "energy"] = 0.9 + self.atmat.loc[self.atmat["atom_pair"]=="O_O", "energy"] = 0.08 + self.atmat.loc[self.atmat["atom_pair"]=="N_N", "energy"] = 0.08 + self.atmat.loc[self.atmat["atom_pair"]=="C_C", "energy"] = 0.08 + self.special_nonlocal_dict = self.define_special_nonlocal_dict() diff --git a/src/multiego/type_definitions.py b/src/multiego/type_definitions.py index ca5873a6..dc7b0ac1 100644 --- a/src/multiego/type_definitions.py +++ b/src/multiego/type_definitions.py @@ -54,6 +54,7 @@ "NZ", "NE", "C", + "CR", "CZ", "CH", "CH1", @@ -64,6 +65,7 @@ "CH3", "CH2r", "S", + "SM", "SH", "CH3p", "P", @@ -72,7 +74,7 @@ "H", "C0", ], - "at.num": [8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 6, 15, 8, 6, 1, 20], + "at.num": [8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 6, 15, 8, 6, 1, 20], "rc_c12": [ 2.5 * 0.262134**12, # "O", 2.631580e-07 2.5 * 0.253061**12, # "OM", 1.724403e-07 @@ -84,6 +86,7 @@ 2.5 * 0.289746**12, # "NZ", 8.752940e-07 2.5 * 0.289746**12, # "NE", 8.752940e-07 2.5 * 0.317248**12, # "C", 2.598570e-06 + 2.5 * 0.317248**12, # "CR", 2.598570e-06 2.5 * 0.317248**12, # "CZ", 2.598570e-06 2.5 * 0.317248**12, # "CH", 2.598570e-06 2.5 * 0.415167**12, # "CH1", 6.555574e-05 @@ -94,6 +97,7 @@ 2.5 * 0.350505**12, # "CH3", 8.595562e-06 2.5 * 0.360236**12, # "CH2r",1.193966e-05 2.5 * 0.318498**12, # "S", 2.724050e-06 + 2.5 * 0.318498**12, # "SM", 2.724050e-06 2.5 * 0.318498**12, # "SH", 2.724050e-06 2.5 * 0.350981**12, # "CH3p",8.736473e-06 2.5 * 0.328121**12, # "P", 3.893600e-06 @@ -114,6 +118,7 @@ 4.0 * 0.31365**12 * eps_NZ, # "NZ", sig=0.31365 4.0 * 0.31365**12 * eps_NE, # "NE", sig=0.31365 4.0 * 0.35812**12 * eps_C, # "C", sig=0.35812 + 4.0 * 0.35812**12 * eps_C, # "CR", sig=0.35812 4.0 * 0.35812**12 * eps_CZ, # "CZ", sig=0.35812 4.0 * 0.35812**12 * eps_CH, # "CH", sig=0.35812 4.0 * 0.44592**12 * eps_CH1, # "CH1", sig=0.50192 @@ -124,6 +129,7 @@ 4.0 * 0.37479**12 * eps_CH3, # "CH3", sig=0.37479 4.0 * 0.39547**12 * eps_CH2r, # "CH2r", sig=0.39547 4.0 * 0.33077**12 * eps_S, # "S", sig=0.33077 + 4.0 * 0.33077**12 * eps_S, # "S", sig=0.33077 4.0 * 0.33077**12 * eps_SH, # "SH", sig=0.33077 4.0 * 0.37479**12 * eps_CH3p, # "CH3p", sig=0.37479 4.0 * 0.33856**12 * eps_P, # "P", sig=0.33856 @@ -143,6 +149,7 @@ 4.0 * 0.31365**6 * eps_NZ, # "NZ", 4.0 * 0.31365**6 * eps_NE, # "NE", 4.0 * 0.35812**6 * eps_C, # "C", + 4.0 * 0.35812**6 * eps_C, # "C", 4.0 * 0.35812**6 * eps_CZ, # "CZ", 4.0 * 0.35812**6 * eps_CH, # "CH" 4.0 * 0.44592**6 * eps_CH1, # "CH1" @@ -153,6 +160,7 @@ 4.0 * 0.37479**6 * eps_CH3, # "CH3" 4.0 * 0.39547**6 * eps_CH2r, # "CH2r" 4.0 * 0.33077**6 * eps_S, # "S", + 4.0 * 0.33077**6 * eps_S, # "S", 4.0 * 0.33077**6 * eps_SH, # "SH", 4.0 * 0.37479**6 * eps_CH3p, # "CH3p" 4.0 * 0.33856**6 * eps_P, # "P", @@ -332,12 +340,31 @@ # from .atdhist_matrix import special_nonlocal as special_non_local from .interaction_matrix import InteractionMatrix -EMAX = 0.15 #maximum epsilon value for the colorbar in the interaction matrix plot -P_TH = 0.006#None#1.0#0.3 # 0.005 # if P_TH is None it will be chosen in the InteractionMatrix class to have NL-NL repulsive -SHOW = False +_this_dir = os.path.dirname(os.path.abspath(__file__)) +_csv_path = os.path.join(_this_dir, "Minimum_CUTOFF_Manual_modif.csv") +# _csv_path = os.path.join(_this_dir, "Merged_c12_sigma.csv") + +# Fallback: older layout had the CSV in src/multiego relative to project root +if not os.path.exists(_csv_path): + _csv_path = os.path.join(_this_dir, "..", "src", "multiego", "Minimum_CUTOFF_Manual_modif.csv") +try: + _c12_df = pd.read_csv(_csv_path, sep="\s+") + +except Exception: + # If file not found or parsing fails, expose an empty list so other code + # can import the module without crashing. + raise RuntimeError( + f"Failed to load Minimum_CUTOFF_Manual_modif.csv from {_csv_path}. " + "Please ensure the file exists and is formatted correctly." + ) + + +EMAX = 0.14 #maximum epsilon value for the colorbar in the interaction matrix plot +P_TH = 1.0#0.009#0.008#0.12 # if P_TH is None it will be chosen in the InteractionMatrix class to have NL-NL repulsive +SHOW = False # if SHOW is True the interaction matrix will be plotted and saved in the current directory # PKL = "atdhisto_density.pkl" PKL = "atdhisto.pkl" -matrix = InteractionMatrix(pkl_file=PKL, emax = EMAX, pth=P_TH, show=SHOW) +matrix = InteractionMatrix(pkl_file=PKL, emax = EMAX, c12_rep_df = _c12_df, pth=P_TH, show=SHOW) special_non_local = matrix.special_nonlocal_dict # print(len(special_non_local_A), len(special_non_local)) # print(special_non_local_A[0]) @@ -402,26 +429,9 @@ # NTHBOND_C12_OVERRIDES available automatically when the module is imported # import pandas as pd -_this_dir = os.path.dirname(os.path.abspath(__file__)) -_csv_path = os.path.join(_this_dir, "Minimum_CUTOFF_Manual_modif.csv") -# _csv_path = os.path.join(_this_dir, "Merged_c12_sigma.csv") - -# Fallback: older layout had the CSV in src/multiego relative to project root -if not os.path.exists(_csv_path): - _csv_path = os.path.join(_this_dir, "..", "src", "multiego", "Minimum_CUTOFF_Manual_modif.csv") - -try: - _c12_df = pd.read_csv(_csv_path, sep="\s+") - NTHBOND_C12_OVERRIDES = [ - ({str(row["atp1"]).strip()}, {str(row["atp2"]).strip()}, float(row["c12"])) for _, row in _c12_df.iterrows() - ] -except Exception: - # If file not found or parsing fails, expose an empty list so other code - # can import the module without crashing. - raise RuntimeError( - f"Failed to load Minimum_CUTOFF_Manual_modif.csv from {_csv_path}. " - "Please ensure the file exists and is formatted correctly." - ) +NTHBOND_C12_OVERRIDES = [ + ({str(row["atp1"]).strip()}, {str(row["atp2"]).strip()}, float(row["c12"])) for _, row in _c12_df.iterrows() +] # NTHBOND_C12_OVERRIDES = [ # ({"O", "OM"}, {"O", "OM"}, mg_OO_c12_rep), # ({"OM"}, {"OM"}, mg_OMOM_c12_rep),