| 1 |
tjod |
3 |
#define EXTERN extern |
| 2 |
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| 3 |
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#include "pcwin.h" |
| 4 |
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#include "pcmod.h" |
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| 6 |
gilbertke |
63 |
static int get_hybrid(int); |
| 7 |
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static int check_ring1(int); |
| 8 |
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int is_ring31(int); |
| 9 |
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int is_ring41(int); |
| 10 |
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int is_ring51(int); |
| 11 |
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int is_ring61(int); |
| 12 |
tjod |
3 |
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| 13 |
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void xlogp(float *result) |
| 14 |
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{ |
| 15 |
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int i,j,k,ia; |
| 16 |
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int iz,nh,nx,npi,nc,itype,dbond,nox,ndouble,nf; |
| 17 |
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int npi_c,npi_x; |
| 18 |
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int nhydrophobic, namino_acid, nhbond, n13FX, n13XX; |
| 19 |
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int atype[100]; |
| 20 |
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long int pi_mask; |
| 21 |
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float total; |
| 22 |
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// char astring[60]; |
| 23 |
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float datype[] = { |
| 24 |
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0.000, 0.484, 0.168,-0.181, 0.358, 0.009,-0.344,-0.439, 0.051,-0.138, |
| 25 |
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-0.417,-0.454,-0.378, 0.223,-0.598,-0.396,-0.699,-0.362, 0.395, 0.236, |
| 26 |
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-0.166, 1.726, 0.098,-0.108, 1.637, 1.774, 0.281, 0.142, 0.715, 0.302, |
| 27 |
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-0.064, 0.079, 0.200, 0.869, 0.316, 0.054, 0.347, 0.046,-0.399,-0.029, |
| 28 |
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-0.330, 0.397, 0.068, 0.327,-2.057, 0.218,-0.582,-0.449,-0.774, 0.040, |
| 29 |
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-0.381, 0.443,-0.117,-2.052,-1.716, 0.321,-0.921,-0.704, 0.119, 1.192, |
| 30 |
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0.434, 0.587, 0.668,-0.791,-0.212, 0.016, 0.752, 1.071, 0.964,-1.817, |
| 31 |
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-1.214,-0.778, 0.493, 1.010, 1.187, 1.489,-0.802,-0.256, 1.626, 0.077, |
| 32 |
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0.264, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, |
| 33 |
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0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 }; |
| 34 |
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| 35 |
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pi_mask = (1L << PI_MASK); |
| 36 |
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for (i=0;i < 100; i++) |
| 37 |
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atype[i] = 0; |
| 38 |
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// |
| 39 |
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// loop through atoms and classify |
| 40 |
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for (i=1; i <= natom; i++) |
| 41 |
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{ |
| 42 |
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if (atom[i].atomnum == 6) // carbon |
| 43 |
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{ |
| 44 |
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iz = get_hybrid(i); |
| 45 |
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nh = nx = npi = nc = 0; |
| 46 |
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for (j=0; j < MAXIAT; j++) |
| 47 |
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{ |
| 48 |
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if (atom[i].iat[j] != 0) |
| 49 |
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{ |
| 50 |
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if (atom[atom[i].iat[j]].atomnum == 1) nh++; |
| 51 |
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if (atom[atom[i].iat[j]].flags & pi_mask) npi++; |
| 52 |
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itype = atom[atom[i].iat[j]].atomnum; |
| 53 |
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if (itype == 6) nc++; |
| 54 |
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if (itype == 7 || itype == 8 || itype == 15 || itype == 16) nx++; |
| 55 |
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itype = atom[atom[i].iat[j]].mmx_type; |
| 56 |
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if (itype == 11 || itype == 12 || itype == 13 || itype == 14) nx++; |
| 57 |
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} |
| 58 |
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} |
| 59 |
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if (iz == 1) // sp3 |
| 60 |
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{ |
| 61 |
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if (nh == 3 && nc == 1 && npi == 0) |
| 62 |
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atype[1]++; |
| 63 |
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else if (nh == 3 && nc == 1 && npi > 0) |
| 64 |
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atype[2]++; |
| 65 |
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else if (nh == 3 && nx == 1) |
| 66 |
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atype[3]++; |
| 67 |
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else if (nh == 2 && nc == 2 && npi == 0) |
| 68 |
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atype[4]++; |
| 69 |
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else if (nh == 2 && nc == 2 && npi > 0) |
| 70 |
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atype[5]++; |
| 71 |
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else if (nh == 2 && nc == 1 && nx == 1) |
| 72 |
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atype[6]++; |
| 73 |
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else if (nh == 2 && nx == 2) |
| 74 |
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atype[7]++; |
| 75 |
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else if (nh == 1 && nc == 3 && npi == 0) |
| 76 |
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atype[8]++; |
| 77 |
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else if (nh == 1 && nc == 3 && npi > 0) |
| 78 |
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atype[9]++; |
| 79 |
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else if (nh == 1 && nc == 2 && nx == 1) |
| 80 |
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atype[10]++; |
| 81 |
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else if (nh == 1 && nc == 1 && nx == 2) |
| 82 |
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atype[11]++; |
| 83 |
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else if (nh == 1 && nx == 3) |
| 84 |
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atype[11]++; |
| 85 |
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else if (nh == 0 && nc == 4 && npi == 0) |
| 86 |
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atype[12]++; |
| 87 |
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else if (nh == 0 && nc == 4 && npi > 0) |
| 88 |
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atype[13]++; |
| 89 |
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else if (nh == 0 && nc == 3 && nx == 1) |
| 90 |
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atype[14]++; |
| 91 |
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else if (nh == 0 && nc == 2 && nx == 2) |
| 92 |
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atype[15]++; |
| 93 |
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else if (nh == 0 && nc == 1 && nx == 3) |
| 94 |
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atype[16]++; |
| 95 |
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else if (nh == 0 && nc == 0 && nx == 4) |
| 96 |
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atype[17]++; |
| 97 |
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} else if (iz == 2) // sp2 |
| 98 |
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{ |
| 99 |
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dbond = 0; |
| 100 |
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// find double bond atom |
| 101 |
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for (j=0; j < 4; j++) |
| 102 |
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{ |
| 103 |
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if (atom[i].iat[j] != 0 && atom[i].bo[j] == 2) |
| 104 |
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{ |
| 105 |
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dbond = atom[i].iat[j]; |
| 106 |
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break; |
| 107 |
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} |
| 108 |
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} |
| 109 |
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if (dbond == 0) goto L_10; // bad atoms |
| 110 |
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if (nh == 2 && nc == 1) |
| 111 |
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{ |
| 112 |
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atype[18]++; |
| 113 |
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goto L_10; |
| 114 |
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} |
| 115 |
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// if not a pi atom |
| 116 |
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if (!(atom[i].flags & pi_mask)) // non pi atoms |
| 117 |
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{ |
| 118 |
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if (atom[dbond].atomnum == 6) // c=c |
| 119 |
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{ |
| 120 |
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if (nh == 1 & nc == 2) |
| 121 |
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{ |
| 122 |
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atype[19]++; |
| 123 |
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goto L_10; |
| 124 |
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} else if (nh == 1 && nx == 1) |
| 125 |
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{ |
| 126 |
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atype[20]++; |
| 127 |
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goto L_10; |
| 128 |
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} else if (nh == 0 && nc == 3) |
| 129 |
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{ |
| 130 |
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atype[22]++; |
| 131 |
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goto L_10; |
| 132 |
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} else if (nh == 0 && nx >= 1) |
| 133 |
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{ |
| 134 |
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atype[23]++; |
| 135 |
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goto L_10; |
| 136 |
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} |
| 137 |
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}else // c=x |
| 138 |
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{ |
| 139 |
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if (nh == 1) |
| 140 |
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{ |
| 141 |
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atype[21]++; |
| 142 |
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goto L_10; |
| 143 |
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} else if (nc >= 1) |
| 144 |
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{ |
| 145 |
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atype[24]++; |
| 146 |
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goto L_10; |
| 147 |
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} else if (nx == 3) |
| 148 |
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{ |
| 149 |
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atype[25]++; |
| 150 |
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goto L_10; |
| 151 |
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} |
| 152 |
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} |
| 153 |
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} else // pi conjugated systems |
| 154 |
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{ |
| 155 |
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nh = nc = nx = npi = 0; |
| 156 |
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npi_c = 0; |
| 157 |
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npi_x = 0; |
| 158 |
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for (j = 0; j < 3; j++) |
| 159 |
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{ |
| 160 |
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if (atom[atom[i].iat[j]].atomnum == 1) |
| 161 |
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nh++; |
| 162 |
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if (atom[atom[i].iat[j]].atomnum == 6) |
| 163 |
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{ |
| 164 |
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nc++; |
| 165 |
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if (atom[atom[i].iat[j]].flags & pi_mask) |
| 166 |
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{ |
| 167 |
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npi++; |
| 168 |
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npi_c++; |
| 169 |
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} |
| 170 |
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} |
| 171 |
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if (atom[atom[i].iat[j]].atomnum >= 6) |
| 172 |
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{ |
| 173 |
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nx++; |
| 174 |
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if (atom[atom[i].iat[j]].flags & pi_mask) |
| 175 |
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{ |
| 176 |
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npi++; |
| 177 |
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npi_x++; |
| 178 |
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} |
| 179 |
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} |
| 180 |
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} |
| 181 |
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if (nh == 1 && nc == 2) |
| 182 |
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atype[26]++; |
| 183 |
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else if (nh == 1 && nc ==1 && nx == 1) |
| 184 |
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atype[27]++; |
| 185 |
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else if (nh == 1 && nx == 2) |
| 186 |
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atype[28]++; |
| 187 |
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else if (nc == 3 && npi == 2) |
| 188 |
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atype[29]++; |
| 189 |
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else if (nc == 2 && npi_x == 2 && nx == 1) |
| 190 |
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atype[30]++; |
| 191 |
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else if (nc == 2 && npi_x == 1 && nx == 1 && npi_x == 1) |
| 192 |
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atype[31]++; |
| 193 |
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else if (nc == 1 && nx == 2 && npi_x == 1 && npi_c == 1) |
| 194 |
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atype[32]++; |
| 195 |
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else if (nc == 1 && nx == 2 && npi_x == 2) |
| 196 |
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atype[33]++; |
| 197 |
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else if (npi == 3) |
| 198 |
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atype[34]++; |
| 199 |
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} |
| 200 |
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} else if (iz == 3) |
| 201 |
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{ |
| 202 |
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for (j=0; j < 4; j++) |
| 203 |
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{ |
| 204 |
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if (atom[i].iat[j] != 0 && atom[i].bo[j] == 3) |
| 205 |
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{ |
| 206 |
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if (atom[atom[i].iat[j]].atomnum == 7) |
| 207 |
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{ |
| 208 |
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atype[77]++; |
| 209 |
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goto L_10; |
| 210 |
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} |
| 211 |
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} |
| 212 |
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} |
| 213 |
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if (nh == 1) |
| 214 |
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atype[35]++; |
| 215 |
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else if (nc == 1) |
| 216 |
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atype[36]++; |
| 217 |
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} |
| 218 |
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} else if (atom[i].atomnum == 1) // hydrogen |
| 219 |
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{ |
| 220 |
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atype[37]++; |
| 221 |
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} else if (atom[i].atomnum == 8) // oxygen |
| 222 |
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{ |
| 223 |
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nh = npi = nx = nc = 0; |
| 224 |
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for (j=0; j < 4; j++) |
| 225 |
|
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{ |
| 226 |
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if (atom[atom[i].iat[j]].atomnum == 1) |
| 227 |
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nh++; |
| 228 |
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if (atom[atom[i].iat[j]].atomnum == 6) |
| 229 |
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{ |
| 230 |
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nc++; |
| 231 |
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if (atom[atom[i].iat[j]].flags & pi_mask) npi++; |
| 232 |
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} |
| 233 |
|
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if (atom[atom[i].iat[j]].atomnum > 6) |
| 234 |
|
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{ |
| 235 |
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nx++; |
| 236 |
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if (atom[atom[i].iat[j]].flags & pi_mask) npi++; |
| 237 |
|
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} |
| 238 |
|
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} |
| 239 |
|
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if (atom[i].mmx_type == 6) |
| 240 |
|
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{ |
| 241 |
|
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if (nh == 1 && nc == 1 && npi == 0) |
| 242 |
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atype[38]++; |
| 243 |
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else if (nh == 1 && nc == 1 && npi == 1) |
| 244 |
|
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atype[39]++; |
| 245 |
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else if (nh == 1 && nx == 1) |
| 246 |
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atype[40]++; |
| 247 |
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else if (nc == 2 && npi < 2) |
| 248 |
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atype[41]++; |
| 249 |
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else if ( (nc == 1 && nx == 1) || nx == 2) |
| 250 |
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atype[42]++; |
| 251 |
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else if (nc == 2 && npi == 2) |
| 252 |
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atype[43]++; |
| 253 |
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} else if (atom[i].mmx_type == 7) |
| 254 |
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{ |
| 255 |
|
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if (nc == 1) |
| 256 |
|
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atype[44]++; |
| 257 |
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else if (nx == 1) |
| 258 |
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atype[45]++; |
| 259 |
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} |
| 260 |
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} else if (atom[i].atomnum == 7) // nitrogen |
| 261 |
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{ |
| 262 |
|
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nh = nx = nc = npi = 0; |
| 263 |
|
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for (j=0; j < MAXIAT; j++) |
| 264 |
|
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{ |
| 265 |
|
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if (atom[i].iat[j] != 0) |
| 266 |
|
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{ |
| 267 |
|
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if (atom[atom[i].iat[j]].atomnum == 1) nh++; |
| 268 |
|
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if (atom[atom[i].iat[j]].atomnum == 6) nc++; |
| 269 |
|
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if (atom[atom[i].iat[j]].atomnum > 6) nx++; |
| 270 |
|
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if (atom[atom[i].iat[j]].flags & pi_mask) npi++; |
| 271 |
|
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} |
| 272 |
|
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} |
| 273 |
|
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if (atom[i].mmx_type == 8) |
| 274 |
|
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{ |
| 275 |
|
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if (nh == 2 && nc == 1 && npi == 0) atype[46]++; |
| 276 |
|
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else if (nh == 2 && nc == 1 && npi > 1) atype[47]++; |
| 277 |
|
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else if (nh == 2 && nx == 1) atype[48]++; |
| 278 |
|
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else if (nh == 1 && nc == 2) atype[49]++; |
| 279 |
|
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else if (nh == 1 && nc == 1 && nx == 1) atype[50]++; |
| 280 |
|
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else if (nh == 1 && nx == 2) atype[50]++; |
| 281 |
|
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else if (nh == 0 && nc == 3) atype[51]++; |
| 282 |
|
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else if (nh == 0 && nx >= 1) atype[52]++; |
| 283 |
|
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} else if (atom[i].mmx_type == 9) |
| 284 |
|
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{ |
| 285 |
|
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for (j=0; j < 4; j++) |
| 286 |
|
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{ |
| 287 |
|
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if (atom[i].iat[j] != 0 ) |
| 288 |
|
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{ |
| 289 |
|
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if (atom[i].bo[j] == 2) // imine type |
| 290 |
|
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{ |
| 291 |
|
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if (atom[atom[i].iat[j]].atomnum == 6) |
| 292 |
|
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{ |
| 293 |
|
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if (nx == 0) |
| 294 |
|
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atype[53]++; |
| 295 |
|
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else |
| 296 |
|
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atype[54]++; |
| 297 |
|
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goto L_10; |
| 298 |
|
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} else if (atom[atom[i].iat[j]].atomnum > 6) |
| 299 |
|
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{ |
| 300 |
|
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if (nc == 1) |
| 301 |
|
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atype[55]++; |
| 302 |
|
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else |
| 303 |
|
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atype[56]++; |
| 304 |
|
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goto L_10; |
| 305 |
|
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} |
| 306 |
|
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} |
| 307 |
|
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} |
| 308 |
|
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} |
| 309 |
|
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for (j=0; j < 4; j++) // amides |
| 310 |
|
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{ |
| 311 |
|
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if (atom[i].iat[j] != 0 && atom[atom[i].iat[j]].atomnum == 6) |
| 312 |
|
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{ |
| 313 |
|
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ia = atom[i].iat[j]; |
| 314 |
|
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for (k=0; k < 4; k++) |
| 315 |
|
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{ |
| 316 |
|
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if (atom[ia].iat[k] != 0 && atom[ia].bo[k] == 2) |
| 317 |
|
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{ |
| 318 |
|
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if (atom[atom[ia].iat[k]].atomnum == 8) // amide |
| 319 |
|
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{ |
| 320 |
|
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if (nh == 2 && nc == 1) atype[63]++; |
| 321 |
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else if (nh == 1) atype[64]++; |
| 322 |
|
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else atype[65]++; |
| 323 |
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goto L_10; |
| 324 |
|
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} |
| 325 |
|
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} |
| 326 |
|
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} |
| 327 |
|
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} |
| 328 |
|
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} |
| 329 |
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// picked up amides and imines - everything else must be aromatic |
| 330 |
|
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if (nh == 1 && nc == 2) atype[58]++; |
| 331 |
|
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else if (nh == 1 && nx >= 1) atype[59]++; |
| 332 |
|
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else if (nc == 3) atype[61]++; |
| 333 |
|
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goto L_10; |
| 334 |
|
|
} |
| 335 |
|
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} else if (atom[i].atomnum == 16) // sulfur |
| 336 |
|
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{ |
| 337 |
|
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nh = 0; |
| 338 |
|
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nox = 0; |
| 339 |
|
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ndouble = 0; |
| 340 |
|
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for (j=0; j < MAXIAT; j++) |
| 341 |
|
|
{ |
| 342 |
|
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if (atom[i].iat[j] != 0) |
| 343 |
|
|
{ |
| 344 |
|
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if (atom[atom[i].iat[j]].atomnum == 1) nh++; |
| 345 |
|
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if (atom[atom[i].iat[j]].atomnum == 8) nox++; |
| 346 |
|
|
if (atom[i].bo[j] == 2) ndouble++; |
| 347 |
|
|
} |
| 348 |
|
|
} |
| 349 |
|
|
if (nox == 2) |
| 350 |
|
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{ |
| 351 |
|
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atype[71]++; |
| 352 |
|
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goto L_10; |
| 353 |
|
|
} else if (nox == 1) |
| 354 |
|
|
{ |
| 355 |
|
|
atype[70]++; |
| 356 |
|
|
goto L_10; |
| 357 |
|
|
} |
| 358 |
|
|
if (nox == 0 && ndouble == 1) |
| 359 |
|
|
{ |
| 360 |
|
|
atype[69]++; |
| 361 |
|
|
goto L_10; |
| 362 |
|
|
} |
| 363 |
|
|
if (nh == 1) |
| 364 |
|
|
{ |
| 365 |
|
|
atype[66]++; |
| 366 |
|
|
goto L_10; |
| 367 |
|
|
} else |
| 368 |
|
|
{ |
| 369 |
|
|
if (check_ring1(i)) |
| 370 |
|
|
{ |
| 371 |
|
|
if ((atom[atom[i].iat[0]].flags & pi_mask) && (atom[atom[i].iat[1]].flags & pi_mask)) |
| 372 |
|
|
{ |
| 373 |
|
|
atype[68]++; |
| 374 |
|
|
goto L_10; |
| 375 |
|
|
} |
| 376 |
|
|
} else |
| 377 |
|
|
{ |
| 378 |
|
|
atype[67]++; |
| 379 |
|
|
goto L_10; |
| 380 |
|
|
} |
| 381 |
|
|
} |
| 382 |
|
|
} else if (atom[i].atomnum == 15) // phosphorus |
| 383 |
|
|
{ |
| 384 |
|
|
atype[76]++; |
| 385 |
|
|
} else if (atom[i].atomnum == 11) // fluorine |
| 386 |
|
|
{ |
| 387 |
|
|
atype[72]++; |
| 388 |
|
|
} else if (atom[i].atomnum == 17) // chlorine |
| 389 |
|
|
{ |
| 390 |
|
|
atype[73]++; |
| 391 |
|
|
} else if (atom[i].atomnum == 35) // bromine |
| 392 |
|
|
{ |
| 393 |
|
|
atype[74]++; |
| 394 |
|
|
} else if (atom[i].atomnum == 53) // iodine |
| 395 |
|
|
{ |
| 396 |
|
|
atype[75]++; |
| 397 |
|
|
} else if (atom[i].mmx_type == 20) |
| 398 |
|
|
{ |
| 399 |
|
|
atype[0]++; |
| 400 |
|
|
} else |
| 401 |
|
|
{ |
| 402 |
|
|
// sprintf(astring,"Atom %d type %d not supported\0",i,atom[i].type); |
| 403 |
|
|
// message_alert(astring,"Error in LogP"); |
| 404 |
|
|
} |
| 405 |
|
|
L_10: |
| 406 |
|
|
continue; |
| 407 |
|
|
} |
| 408 |
|
|
// done assigning types = compute logP |
| 409 |
|
|
total = 0.0; |
| 410 |
|
|
for (i=0; i < 100; i++) |
| 411 |
|
|
total += atype[i]*datype[i]; |
| 412 |
|
|
|
| 413 |
|
|
// now do correction factors |
| 414 |
|
|
nhydrophobic = namino_acid = nhbond = n13FX = n13XX = 0; |
| 415 |
|
|
|
| 416 |
|
|
nhydrophobic = atype[1] + atype[2] + atype[4] + atype[5] + atype[8] + atype[9] + atype[12] + atype[13] + atype[18] + |
| 417 |
|
|
atype[19] + atype[22]; |
| 418 |
|
|
|
| 419 |
|
|
// 1,3 halogens |
| 420 |
|
|
for (i=1; i <= natom; i++) |
| 421 |
|
|
{ |
| 422 |
|
|
nf = 0; |
| 423 |
|
|
nx = 0; |
| 424 |
|
|
if (atom[i].atomnum == 6) |
| 425 |
|
|
{ |
| 426 |
|
|
for (j=0; j < MAXIAT; j++) |
| 427 |
|
|
{ |
| 428 |
|
|
if (atom[atom[i].iat[j]].atomnum == 9) |
| 429 |
|
|
nf++; |
| 430 |
|
|
if (atom[atom[i].iat[j]].atomnum == 17) |
| 431 |
|
|
nx++; |
| 432 |
|
|
if (atom[atom[i].iat[j]].atomnum == 35) |
| 433 |
|
|
nx++; |
| 434 |
|
|
if (atom[atom[i].iat[j]].atomnum == 53) |
| 435 |
|
|
nx++; |
| 436 |
|
|
} |
| 437 |
|
|
if ((nf >= 1 && nx >= 1) || nf >= 2) |
| 438 |
|
|
n13FX++; |
| 439 |
|
|
if (nx >=2 && nf == 0) |
| 440 |
|
|
n13XX++; |
| 441 |
|
|
} |
| 442 |
|
|
} |
| 443 |
|
|
// amino acids |
| 444 |
|
|
// hydrogen bonds |
| 445 |
|
|
|
| 446 |
|
|
|
| 447 |
|
|
*result = total + nhydrophobic*0.19F + n13FX*0.08 + n13XX*(-0.26F); |
| 448 |
|
|
} |
| 449 |
gilbertke |
63 |
// ================== |
| 450 |
|
|
// ================================== |
| 451 |
|
|
int check_ring1(int ia) |
| 452 |
|
|
{ |
| 453 |
|
|
if (is_ring61(ia)) return TRUE; |
| 454 |
|
|
if (is_ring51(ia)) return TRUE; |
| 455 |
|
|
if (is_ring31(ia)) return TRUE; |
| 456 |
|
|
if (is_ring41(ia)) return TRUE; |
| 457 |
|
|
return FALSE; |
| 458 |
|
|
} |
| 459 |
|
|
/* =============================================== */ |
| 460 |
|
|
// get hybridization of atom - tetrahedral = 1, planar = 2, linear = 3 |
| 461 |
|
|
// |
| 462 |
|
|
int get_hybrid(int ia) |
| 463 |
|
|
{ |
| 464 |
|
|
int itype; |
| 465 |
|
|
|
| 466 |
|
|
itype = atom[ia].mmx_type; |
| 467 |
|
|
if (itype == 2 || itype == 3 || itype == 7 || itype == 9 || itype == 25 || |
| 468 |
|
|
itype == 26 || itype == 29 || itype == 30 || itype == 37 || itype == 38 || |
| 469 |
|
|
itype == 40 || itype == 57 ) |
| 470 |
|
|
return 2; |
| 471 |
|
|
else if (itype == 4 || itype == 10) |
| 472 |
|
|
return 3; |
| 473 |
|
|
else |
| 474 |
|
|
return 1; |
| 475 |
|
|
} |
