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/*
* MacroModel atom typing
*
* (c) Schrodinger, Inc.
*/
#include "MmodTyping.h"
#include "AtomInfo.h"
/**
* Get the MacroModel atom type.
*
* Pre-condition: ObjectMoleculeVerifyChemistry
*/
int getMacroModelAtomType(const AtomInfoType * ai) {
// generic ions
switch (ai->formalCharge) {
case -2:
switch (ai->protons) {
case cAN_S: return 114; // Sm Sulfide anion, S2-
case cAN_O: return 115; // Om Oxide anion, O2-
}
break;
case -1:
switch (ai->protons) {
case cAN_C: return 10; // CM Carbanion (C-)
case cAN_O: return 18; // OM O- (alkoxide, carboxylate)
case cAN_H: return 45; // H5 H- (Anion)
case cAN_S: return 51; // SM S- (thiolate anion)
case cAN_Cl: return 102; // Cm Cl-
case cAN_F: return 104; // Fm F-
case cAN_Br: return 105; // Bm Br-
case cAN_I: return 106; // Im I-
}
break;
case 0:
switch (ai->protons) {
case cAN_Li: return 93; // L0 Lithium neutral
case cAN_Mg: return 94; // M0 Magnesium neutral
}
break;
case 1:
switch (ai->protons) {
case cAN_C: return 11; // CP Carbocation (C+)
case cAN_H: return 44; // H4 H+ (Cation)
case cAN_Li: return 65; // Li Li+
case cAN_Na: return 66; // Na Na+
case cAN_K: return 67; // K0 K+
case cAN_Rb: return 68; // Rb Rb+
case cAN_Cs: return 69; // Cs Cs+
case cAN_Cu: return 85; // c1 Cu+
case cAN_S: return 100; // SP S+
}
break;
case 2:
switch (ai->protons) {
case cAN_Ca: return 70; // Ca Ca+2
case cAN_Ba: return 71; // Ba Ba+2
case cAN_Mg: return 72; // Mg Mg+2
case cAN_Fe: return 79; // f2 Fe+2
case cAN_Co: return 81; // o2 Co+2
case cAN_Ni: return 83; // n2 Ni+2
case cAN_Cu: return 86; // c2 Cu+2
case cAN_Zn: return 87; // Zn Zn+2
}
break;
case 3:
switch (ai->protons) {
case cAN_Fe: return 80; // f3 Fe+3
case cAN_Co: return 82; // o3 Co+3
case cAN_Ni: return 84; // n3 Ni+3
}
break;
}
// others
switch (ai->protons) {
case cAN_C:
switch (ai->geom) {
case cAtomInfoLinear: return 1; // C1 Carbon - sp
case cAtomInfoPlanar: return 2; // C2 Carbon - sp2
case cAtomInfoTetrahedral: return 3; // C3 Carbon - sp3
}
return 14; // C0 Any Carbon
case cAN_O:
if ((ai->flags & cAtomFlag_solvent) && !ai->bonded) {
return 19; // OW United atom H2O - Water
}
switch (ai->geom) {
case cAtomInfoPlanar: return 15; // O2 Oxygen - double bond
case cAtomInfoTetrahedral: return 16; // O3 Oxygen - single bond
}
return 23; // O0 Any oxygen;
case cAN_N:
switch (ai->geom) {
case cAtomInfoLinear:
return 24; // N1 Nitrogen - sp
case cAtomInfoPlanar:
switch (ai->formalCharge) {
case -1: return 38; // NM N- - sp2
case 1: return 31; // N4 N+ - sp2
}
return 25; // N2 Nitrogen - sp2
case cAtomInfoTetrahedral:
switch (ai->formalCharge) {
case -1: return 39; // NP N- - sp2
case 1: return 32; // N5 N+ - sp2
}
return 26; // N3 Nitrogen - sp3
}
return 40; // N0 Any Nitrogen
case cAN_H:
return 48; // H0 Any Hydrogen
case cAN_S:
switch (ai->geom) {
case cAtomInfoPlanar: return 101; // S2 Sulfur - sp2
}
return 52; // S0 Any Sulfur
case cAN_P:
if (ai->geom == cAtomInfoTetrahedral) {
switch (ai->valence) {
case 3: return 53; // P3 Phosphorus, trivalent
case 4: return 107; // P5 Phosphorus, pentavalent tetrahedral
}
}
return 108; // P0 Any phosphorus
case cAN_B:
switch (ai->geom) {
case cAtomInfoPlanar: return 54; // B2 Boron - sp2
case cAtomInfoTetrahedral: return 55; // B3 Boron - sp3
}
return 103; // B0 Any boron
case cAN_F:
return 56; // F0 Fluorine
case cAN_Cl:
return 57; // Cl Chlorine
case cAN_Br:
return 58; // Br Bromine
case cAN_I:
return 59; // I0 Iodine
case cAN_Si:
return 60; // Si Silicon
case cAN_Mn:
switch (ai->formalCharge) {
case 2: return 73; // M2 Mn+2
case 3: return 74; // M3 Mn+3
case 4: return 75; // M4 Mn+4
case 5: return 76; // M5 Mn+5
case 6: return 77; // M6 Mn+6
case 7: return 78; // M7 Mn+7
}
break;
case cAN_Se:
return 112; // Se Selenium
case 0:
if (strcmp(ai->elem, "LP") == 0)
return 63; // Lp Lone electron pair
return 61; // Du Dummy atom
}
return 64; // 00 Any Atom
}
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