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tjod |
3 |
#define EXTERN extern |
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#include "pcwin.h" |
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#include "pcmod.h" |
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#include "field.h" |
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#include "atom_k.h" |
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void deleteatom(int); |
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int make_atom(int, float, float, float,char *); |
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void make_bond(int, int, int); |
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void hadd(void); |
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void hdel(int); |
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void type(void); |
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void set_atomtypes(int); |
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void nhadd(void); |
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void hcoord(void); |
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void revec(void); |
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void xyplan(float *, float *, float *); |
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void xaxis(float *,float *,float *); |
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void getvec(void); |
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void reseq(void); |
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void generate_bonds(void); |
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void set_atomdata(int, int,int,int,int,int); |
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void message_alert(char *, char *); |
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EXTERN struct t_minim_control { |
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int type, method, field, added_const; |
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char added_path[256],added_name[256]; |
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} minim_control; |
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void hadd(void) |
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{ |
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type(); |
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if (field.type == MM3) |
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{ |
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nhadd(); |
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hcoord(); |
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hdel(1); |
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} else if (field.type == AMBER) |
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{ |
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nhadd(); |
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hcoord(); |
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hdel(1); |
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} else if (field.type == OPLSAA) |
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{ |
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nhadd(); |
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hcoord(); |
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hdel(1); |
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} else if (field.type == MMFF94) |
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{ |
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nhadd(); |
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hcoord(); |
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hdel(1); |
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} else |
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{ |
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set_atomtypes(MMX); |
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nhadd(); |
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hcoord(); |
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} |
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type(); |
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generate_bonds(); |
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} |
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void nhadd() |
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{ |
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int i, i1, ik, im, it, itads, j, jk, nhadds, newatom; |
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int jji, bo,ncount; |
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static int iadd[MAXVDW]={ 0,0,0,0,0,3,1,6,0,1, |
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0,0,0,0,3,6,3,0,0,0, |
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0,0,0,0,6,0,0,0,0,0, |
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0,0,0,3,0,0,6,1,1,0, |
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0,4,0,0,0,6,0,6,0,0, |
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3,3,3,0,6,0,0,0,0,0, |
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0,0,0,0,0,1,6,0,0,0, |
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0,0,0,0,0}; |
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/* this routine calculates the #'s of h to be added |
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* to carbon and packs it symbolically into iat(i,j) table |
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* as well as into the connection table via the appropriate |
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* manipulation instructions. hydrogen coordinates |
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* are not added by this routine. lp are also added to oxygen. */ |
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/* 0 to disregard : 1 and 4 for lp's only |
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* 2 and 5 for h's only and 3 and 6 for h and lp |
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* add 3 for trigonal atoms */ |
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ncount = natom; |
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for( i = 1 ; i <= ncount; i++ ) |
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{ |
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if( atom[i].mmx_type > 0 && (atom[i].mmx_type < 300) && atom[i].atomnum != 1 ) |
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{ |
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jji = 0; |
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bo = 0; |
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for (j=0; j < MAXIAT; j++) |
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{ |
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if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9) |
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{ |
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jji ++; |
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bo += atom[i].bo[j]; |
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} |
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} |
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nhadds = atom_def.ligands[atom[i].mmx_type] - jji; |
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if (atom[i].mmx_type >= 11 && atom[i].mmx_type <= 14) |
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nhadds = 0; |
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if (atom[i].mmx_type == 41 || atom[i].mmx_type == 46) |
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nhadds = atom_def.ligands[atom[i].mmx_type] - bo; |
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if (atom[i].mmx_type == 49 || atom[i].mmx_type == 50 || atom[i].mmx_type == 51) |
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nhadds = atom_def.ligands[atom[i].mmx_type] - bo; |
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| 110 |
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/* add atom and bond it to atom i */ |
| 111 |
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if( nhadds > 0 ) |
| 112 |
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{ |
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for( im = 1; im <= nhadds; im++ ) |
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{ |
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newatom = make_atom(5,0.F,0.F,0.F,"H"); |
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set_atomdata(newatom,5,5,5,34,29); |
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if (newatom == -1) |
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{ |
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message_alert("Error in nhadd newatom = -1","Error"); |
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hdel(0); |
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return; |
| 122 |
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} |
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make_bond(i,newatom,1); |
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} |
| 125 |
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} |
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} |
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} |
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/* *** check for lp's *** */ |
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if (field.type == MMX) |
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{ |
| 132 |
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ncount = natom; |
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for( i = 1 ; i <= ncount; i++ ) |
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{ |
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it = iadd[atom[i].mmx_type-1]; |
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if( it >= 1 ) |
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{ |
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itads = atom[i].mmx_type ; |
| 139 |
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if (it == 1 || it == 3 || it == 4 || it == 6 ) |
| 140 |
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{ |
| 141 |
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nhadds = 4; |
| 142 |
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for( i1 = 0; i1 < MAXIAT; i1++ ) |
| 143 |
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{ |
| 144 |
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if( atom[i].bo[i1] != 0 && atom[i].bo[i1] != 9 ) |
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nhadds = nhadds - atom[i].bo[i1]; |
| 146 |
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} |
| 147 |
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if( itads == 6 || itads == 15 || itads == 34 || itads == 42 || itads == 53 || itads == 48 ) |
| 148 |
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{ |
| 149 |
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for( ik = 0; ik < MAXIAT; ik++ ) |
| 150 |
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{ |
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if( atom[i].iat[ik] != 0 && atom[i].bo[ik] != 9 ) |
| 152 |
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{ |
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jk = atom[atom[i].iat[ik]].mmx_type; |
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if( jk == 2 || jk == 3 || jk == 4 || jk == 9 |
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|| jk == 10 || jk == 30 || jk == 37 || jk == 40 ) |
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{ |
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nhadds = nhadds - 1; |
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break; |
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} |
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} |
| 161 |
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} |
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} |
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| 164 |
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/* correction for sulfoxide */ |
| 165 |
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if( itads == 17 ) |
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nhadds = nhadds + 1; |
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if (itads == 66) |
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nhadds = 2; |
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if( nhadds > 0 ) |
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{ |
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for( i1 = 1; i1 <= nhadds; i1++ ) |
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{ |
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newatom = make_atom(20, 0.F,0.F,0.F,""); |
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set_atomdata(newatom,20,0,0,0,0); |
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make_bond(i,newatom,1); |
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} |
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} |
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} |
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} |
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} |
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} |
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return; |
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} |
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// ================================== |
| 187 |
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void hcoord() |
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{ |
| 189 |
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int i, i1, i3, i4, i5, i6, i7, i8, |
| 190 |
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i9, iadj[10], ii, ii1, ii2, ii3, iii, |
| 191 |
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ij, ijk[3], it, j, j1, j2, j3, j4, j5, j8, |
| 192 |
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j9, k1, k2, l1, na, nhadds, ni; |
| 193 |
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float adj, dis, xpnt, ypnt, zpnt; |
| 194 |
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| 195 |
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getvec(); |
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for( i = 1; i <= natom; i++ ) |
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{ |
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it = atom[i].mmx_type; |
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if( it < 300) |
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{ |
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for( j = 0; j < 10; j++ ) |
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iadj[j] = 0; |
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for( j = 0; j < 3; j++ ) |
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ijk[j] = 0; |
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nhadds = 0; |
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l1 = 0; |
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for( j = 0; j < MAXIAT; j++ ) |
| 210 |
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{ |
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if( atom[i].iat[j] != 0 && atom[i].bo[j] != 9 ) |
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{ |
| 213 |
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if( atom[atom[i].iat[j]].mmx_type == 5 || atom[atom[i].iat[j]].mmx_type == 20 ) |
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nhadds++ ; |
| 215 |
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else |
| 216 |
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{ |
| 217 |
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iadj[l1] = atom[i].iat[j]; |
| 218 |
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l1++; |
| 219 |
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} |
| 220 |
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} |
| 221 |
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} |
| 222 |
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if( nhadds != 0 ) |
| 223 |
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{ |
| 224 |
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/* **** calculate the coordinates of the center we |
| 225 |
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* are going to move to the x-axis */ |
| 226 |
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xpnt = atom[i].x; |
| 227 |
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ypnt = atom[i].y; |
| 228 |
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zpnt = atom[i].z; |
| 229 |
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for( ii = 1; ii <= (natom + 4); ii++ ) |
| 230 |
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{ |
| 231 |
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atom[ii].x = atom[ii].x - xpnt; |
| 232 |
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atom[ii].y = atom[ii].y - ypnt; |
| 233 |
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atom[ii].z = atom[ii].z - zpnt; |
| 234 |
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} |
| 235 |
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xpnt = 0.F; |
| 236 |
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ypnt = 0.F; |
| 237 |
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zpnt = 0.F; |
| 238 |
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adj = 0.F; |
| 239 |
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for( i1 = 0; i1 < 10; i1++ ) |
| 240 |
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{ |
| 241 |
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if( iadj[i1] != 0 ) |
| 242 |
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{ |
| 243 |
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na = iadj[i1]; |
| 244 |
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adj += 1.0001F ; |
| 245 |
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xpnt += atom[na].x; |
| 246 |
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ypnt += atom[na].y; |
| 247 |
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zpnt += atom[na].z; |
| 248 |
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} |
| 249 |
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} |
| 250 |
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if( adj > 0.01F ) |
| 251 |
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{ |
| 252 |
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xpnt /= adj; |
| 253 |
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ypnt /= adj; |
| 254 |
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zpnt /= adj; |
| 255 |
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xaxis( &xpnt, &ypnt, &zpnt ); |
| 256 |
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if( xpnt > 0.F ) |
| 257 |
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{ |
| 258 |
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for( i3 = 1; i3 <= (natom + 4); i3++ ) |
| 259 |
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atom[i3].x = -atom[i3].x; |
| 260 |
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} |
| 261 |
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/* **** after moving, check the # of h added to the carbon i */ |
| 262 |
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if( nhadds == 1 ) |
| 263 |
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{ |
| 264 |
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/* **** there is only 1 h added to the carbon i */ |
| 265 |
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for( i4 = 0; i4 < MAXIAT; i4++ ) |
| 266 |
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{ |
| 267 |
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if( atom[i].iat[i4] != 0 && atom[i].bo[i4] != 9 ) |
| 268 |
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{ |
| 269 |
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i5 = atom[i].iat[i4]; |
| 270 |
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if( atom[i5].mmx_type == 5 || atom[i5].mmx_type == 20 ) |
| 271 |
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{ |
| 272 |
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/* i5 is the atom to attach */ |
| 273 |
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if (adj < 2.0) // fix for OH in MMFF |
| 274 |
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{ |
| 275 |
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atom[i5].x = 0.70; |
| 276 |
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atom[i5].y = 0.70; |
| 277 |
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atom[i5].z = 0.00; |
| 278 |
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} else |
| 279 |
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{ |
| 280 |
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atom[i5].x = 1.10F; |
| 281 |
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if( atom[i5].mmx_type == 20 ) |
| 282 |
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atom[i5].x = 0.6F; |
| 283 |
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atom[i5].y = 0.00F; |
| 284 |
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atom[i5].z = 0.00F; |
| 285 |
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} |
| 286 |
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if( atom[i].atomnum == 16 ) |
| 287 |
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{ |
| 288 |
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atom[i5].x = 0.F; |
| 289 |
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atom[i5].y = 0.3796F; |
| 290 |
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atom[i5].z = 1.043F; |
| 291 |
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} |
| 292 |
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} |
| 293 |
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} |
| 294 |
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} |
| 295 |
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} |
| 296 |
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/* **** there are 2 h added to the carbon i */ |
| 297 |
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if( nhadds == 2 ) |
| 298 |
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{ |
| 299 |
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if( it == 2 || it == 3 || it == 29 || it == 30 || it == 9 || it == 41 || it == 46 |
| 300 |
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|| it == 48 || it == 7 || it == 37 || it == 39 |
| 301 |
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|| it == 42 || it == 38 || it == 40 || it == 44 || it == 66) |
| 302 |
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{ |
| 303 |
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for( i8 = 0; i8 < 10; i8++ ) |
| 304 |
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{ |
| 305 |
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if( iadj[i8] != 0 ) |
| 306 |
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{ |
| 307 |
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ii1 = iadj[i8]; |
| 308 |
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for( ii2 = 0; ii2 < MAXIAT; ii2++ ) |
| 309 |
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{ |
| 310 |
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ii3 = 0; |
| 311 |
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if( atom[ii1].iat[ii2] != 0 && atom[ii1].iat[ii2] != i && atom[ii1].bo[ii2] != 9 ) |
| 312 |
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{ |
| 313 |
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ii3 = atom[ii1].iat[ii2]; |
| 314 |
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xpnt = atom[ii3].x; |
| 315 |
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ypnt = atom[ii3].y; |
| 316 |
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zpnt = atom[ii3].z; |
| 317 |
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xyplan( &xpnt, &ypnt, &zpnt ); |
| 318 |
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ij = 0; |
| 319 |
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for( i9 = 0; i9 < MAXIAT; i9++ ) |
| 320 |
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{ |
| 321 |
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if( atom[i].iat[i9] != 0 && atom[i].bo[i9] != 9 ) |
| 322 |
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{ |
| 323 |
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iii = atom[i].iat[i9]; |
| 324 |
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if( atom[iii].mmx_type == 5 || atom[iii].mmx_type == 20 ) |
| 325 |
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{ |
| 326 |
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ijk[ij] = iii; |
| 327 |
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ij++; |
| 328 |
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if( ij == 2 ) |
| 329 |
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{ |
| 330 |
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/* *** =ch2 *** */ |
| 331 |
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atom[ijk[0]].x = 0.5582F; |
| 332 |
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atom[ijk[1]].x = 0.5582F; |
| 333 |
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atom[ijk[0]].y = 0.9478F; |
| 334 |
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atom[ijk[1]].y = -0.9478F; |
| 335 |
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atom[ijk[0]].z = 0.00F; |
| 336 |
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atom[ijk[1]].z = 0.00F; |
| 337 |
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if( it == 7 || it == 38 || it == 42 || it == 39 || it == 66) |
| 338 |
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{ |
| 339 |
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atom[ijk[0]].x = 0.30F; |
| 340 |
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atom[ijk[1]].x = 0.30F; |
| 341 |
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atom[ijk[0]].y = 0.52F; |
| 342 |
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atom[ijk[1]].y = -0.52F; |
| 343 |
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} |
| 344 |
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if( atom[i].mmx_type == 37 ) |
| 345 |
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{ |
| 346 |
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atom[ijk[1]].x = 0.35F; |
| 347 |
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atom[ijk[1]].y = -0.5F; |
| 348 |
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} |
| 349 |
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} |
| 350 |
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} |
| 351 |
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} |
| 352 |
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} |
| 353 |
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break; |
| 354 |
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} |
| 355 |
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if (ii3 == 0) // C=O with no lone pairs |
| 356 |
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{ |
| 357 |
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ij = 0; |
| 358 |
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for( i9 = 0; i9 < MAXIAT; i9++ ) |
| 359 |
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{ |
| 360 |
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if( atom[i].iat[i9] != 0 && atom[i].bo[i9] != 9 ) |
| 361 |
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{ |
| 362 |
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iii = atom[i].iat[i9]; |
| 363 |
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if( atom[iii].mmx_type == 5 || atom[iii].mmx_type == 20 ) |
| 364 |
|
|
{ |
| 365 |
|
|
ijk[ij] = iii; |
| 366 |
|
|
ij++; |
| 367 |
|
|
if( ij == 2 ) |
| 368 |
|
|
{ |
| 369 |
|
|
/* *** =ch2 *** */ |
| 370 |
|
|
atom[ijk[0]].x = 0.5582F; |
| 371 |
|
|
atom[ijk[1]].x = 0.5582F; |
| 372 |
|
|
atom[ijk[0]].y = 0.9478F; |
| 373 |
|
|
atom[ijk[1]].y = -0.9478F; |
| 374 |
|
|
atom[ijk[0]].z = 0.00F; |
| 375 |
|
|
atom[ijk[1]].z = 0.00F; |
| 376 |
|
|
if( it == 7 || it == 38 || it == 42 || it == 39 || it == 66) |
| 377 |
|
|
{ |
| 378 |
|
|
atom[ijk[0]].x = 0.30F; |
| 379 |
|
|
atom[ijk[1]].x = 0.30F; |
| 380 |
|
|
atom[ijk[0]].y = 0.52F; |
| 381 |
|
|
atom[ijk[1]].y = -0.52F; |
| 382 |
|
|
} |
| 383 |
|
|
if( atom[i].mmx_type == 37 ) |
| 384 |
|
|
{ |
| 385 |
|
|
atom[ijk[1]].x = 0.35F; |
| 386 |
|
|
atom[ijk[1]].y = -0.5F; |
| 387 |
|
|
} |
| 388 |
|
|
} |
| 389 |
|
|
} |
| 390 |
|
|
} |
| 391 |
|
|
} |
| 392 |
|
|
break; |
| 393 |
|
|
} |
| 394 |
|
|
} |
| 395 |
|
|
} |
| 396 |
|
|
} |
| 397 |
|
|
} else |
| 398 |
|
|
{ |
| 399 |
|
|
/* ** there are 2 atoms attached to carbon i, |
| 400 |
|
|
* one of which is "ni" and move these two atoms to xy-plane */ |
| 401 |
|
|
for( i6 = 0; i6 < 10; i6++ ) |
| 402 |
|
|
{ |
| 403 |
|
|
if( iadj[i6] != 0 ) |
| 404 |
|
|
{ |
| 405 |
|
|
ni = iadj[i6]; |
| 406 |
|
|
xpnt = atom[ni].x; |
| 407 |
|
|
ypnt = atom[ni].y; |
| 408 |
|
|
zpnt = atom[ni].z; |
| 409 |
|
|
xyplan( &xpnt, &ypnt, &zpnt ); |
| 410 |
|
|
} |
| 411 |
|
|
} |
| 412 |
|
|
ij = 0; |
| 413 |
|
|
for( i7 = 0; i7 < MAXIAT; i7++ ) |
| 414 |
|
|
{ |
| 415 |
|
|
if( atom[i].iat[i7] != 0 && atom[i].bo[i7] != 9 ) |
| 416 |
|
|
{ |
| 417 |
|
|
iii = atom[i].iat[i7]; |
| 418 |
|
|
if( atom[iii].mmx_type == 5 || atom[iii].mmx_type == 20 ) |
| 419 |
|
|
{ |
| 420 |
|
|
ijk[ij] = iii; |
| 421 |
|
|
ij++ ; |
| 422 |
|
|
if( ij == 2 ) |
| 423 |
|
|
{ |
| 424 |
|
|
/* *** -ch2- type 1 atom *** */ |
| 425 |
|
|
atom[ijk[0]].x = 0.6758F; |
| 426 |
|
|
atom[ijk[1]].x = 0.6758F; |
| 427 |
|
|
atom[ijk[0]].y = 0.00F; |
| 428 |
|
|
atom[ijk[1]].y = 0.00F; |
| 429 |
|
|
atom[ijk[0]].z = 0.8807F; |
| 430 |
|
|
atom[ijk[1]].z = -0.8807F; |
| 431 |
|
|
if( atom[i].mmx_type == 25 || atom[i].mmx_type == 46 || atom[i].mmx_type == 67) |
| 432 |
|
|
{ |
| 433 |
|
|
atom[ijk[0]].x = 0.3796F; |
| 434 |
|
|
atom[ijk[1]].x = 0.3796F; |
| 435 |
|
|
atom[ijk[0]].y = 1.043F; |
| 436 |
|
|
atom[ijk[1]].y = -0.5215F; |
| 437 |
|
|
atom[ijk[0]].z = 0.0000F; |
| 438 |
|
|
atom[ijk[1]].z = 0.9032F; |
| 439 |
|
|
} |
| 440 |
|
|
if( atom[i].mmx_type == 22 || atom[i].mmx_type == 30 ) |
| 441 |
|
|
{ |
| 442 |
|
|
/* *** -ch2- type 22 and 3o atoms *** */ |
| 443 |
|
|
atom[ijk[0]].x = 0.2F; |
| 444 |
|
|
atom[ijk[1]].x = 0.2F; |
| 445 |
|
|
atom[ijk[0]].y = 0.0F; |
| 446 |
|
|
atom[ijk[1]].y = 0.0F; |
| 447 |
|
|
atom[ijk[0]].z = 1.0F; |
| 448 |
|
|
atom[ijk[1]].z = -1.0F; |
| 449 |
|
|
} |
| 450 |
|
|
/* *** -o(lp)2- *** */ |
| 451 |
|
|
if (atom[i].mmx_type == 6 && (atom[iadj[0]].mmx_type == 3 || |
| 452 |
|
|
atom[iadj[0]].mmx_type == 2 || atom[iadj[0]].mmx_type == 30 || |
| 453 |
|
|
atom[iadj[0]].mmx_type == 37 || atom[iadj[0]].mmx_type == 40) ) |
| 454 |
|
|
{ |
| 455 |
|
|
atom[ijk[0]].x = 0.450F; |
| 456 |
|
|
atom[ijk[1]].x = 0.2488F; |
| 457 |
|
|
atom[ijk[0]].z = 0.0F; |
| 458 |
|
|
atom[ijk[1]].z = 0.0F; |
| 459 |
|
|
atom[ijk[0]].y = 0.9500F; |
| 460 |
|
|
atom[ijk[1]].y = -0.5460F; |
| 461 |
|
|
} |
| 462 |
|
|
else if( atom[i].mmx_type == 6 || atom[i].mmx_type == 15 || atom[i].mmx_type == |
| 463 |
|
|
42 || atom[i].mmx_type == 34 || atom[i].mmx_type == 35 || atom[i].mmx_type == 53 ) |
| 464 |
|
|
{ |
| 465 |
|
|
atom[ijk[0]].x = 0.2488F; |
| 466 |
|
|
atom[ijk[1]].x = 0.2488F; |
| 467 |
|
|
atom[ijk[0]].y = 0.0F; |
| 468 |
|
|
atom[ijk[1]].y = 0.0F; |
| 469 |
|
|
atom[ijk[0]].z = 0.5460F; |
| 470 |
|
|
atom[ijk[1]].z = -0.5460F; |
| 471 |
|
|
} |
| 472 |
|
|
} |
| 473 |
|
|
} |
| 474 |
|
|
} |
| 475 |
|
|
} |
| 476 |
|
|
} |
| 477 |
|
|
} |
| 478 |
|
|
/* end of nhadds = 2 |
| 479 |
|
|
* **** there are 3 h added to the carbon i *** */ |
| 480 |
|
|
if( nhadds == 3 ) |
| 481 |
|
|
{ |
| 482 |
|
|
for( j1 = 0; j1 < 10; j1++ ) |
| 483 |
|
|
{ |
| 484 |
|
|
if( iadj[j1] != 0 ) |
| 485 |
|
|
{ |
| 486 |
|
|
j2 = iadj[j1]; |
| 487 |
|
|
if( atom[j2].atomnum != 1 && atom[j2].mmx_type != 20 ) |
| 488 |
|
|
na = j2; |
| 489 |
|
|
if( atom[j2].mmx_type == 2 || atom[j2].mmx_type == 3 ) |
| 490 |
|
|
{ |
| 491 |
|
|
for( j3 = 0; j3 < MAXIAT; j3++ ) |
| 492 |
|
|
{ |
| 493 |
|
|
if( (atom[j2].iat[j3] != 0 && atom[j2].iat[j3] != i) && |
| 494 |
|
|
atom[j2].bo[j3] != 9 ) |
| 495 |
|
|
{ |
| 496 |
|
|
j4 = atom[j2].iat[j3]; |
| 497 |
|
|
if( atom[j4].mmx_type == 2 || (atom[j4].mmx_type == 7 && atom[j4].mmx_type == 38) ) |
| 498 |
|
|
{ |
| 499 |
|
|
xpnt = atom[j4].x; |
| 500 |
|
|
ypnt = atom[j4].y; |
| 501 |
|
|
zpnt = atom[j4].z; |
| 502 |
|
|
xyplan( &xpnt, &ypnt, &zpnt ); |
| 503 |
|
|
if( atom[j4].y < 0.F ) |
| 504 |
|
|
{ |
| 505 |
|
|
for( j5 = 1; j5 <= (natom + 4); j5++ ) |
| 506 |
|
|
atom[j5].y = -atom[j5].y; |
| 507 |
|
|
} |
| 508 |
|
|
} |
| 509 |
|
|
} |
| 510 |
|
|
} |
| 511 |
|
|
}else |
| 512 |
|
|
{ |
| 513 |
|
|
/* end of type 2 and type 3 adjacent* */ |
| 514 |
|
|
for( j8 = 0; j8 < MAXIAT; j8++ ) |
| 515 |
|
|
{ |
| 516 |
|
|
if( (atom[j2].iat[j8] != 0 && atom[j2].iat[j8] != i) |
| 517 |
|
|
&& atom[j2].bo[j8] != 9 ) |
| 518 |
|
|
{ |
| 519 |
|
|
j9 = atom[j2].iat[j8]; |
| 520 |
|
|
// if( atom[j9].mmx_type != 5 && atom[j9].mmx_type != 20 ) |
| 521 |
|
|
if(atom[j9].mmx_type != 20 ) |
| 522 |
|
|
{ |
| 523 |
|
|
xpnt = atom[j9].x; |
| 524 |
|
|
ypnt = atom[j9].y; |
| 525 |
|
|
zpnt = atom[j9].z; |
| 526 |
|
|
xyplan( &xpnt, &ypnt, &zpnt ); |
| 527 |
|
|
if( atom[j9].y > 0.F ) |
| 528 |
|
|
{ |
| 529 |
|
|
for( k1 = 1; k1 <= (natom + 4); k1++ ) |
| 530 |
|
|
atom[k1].y = -atom[k1].y; |
| 531 |
|
|
} |
| 532 |
|
|
} |
| 533 |
|
|
} |
| 534 |
|
|
} |
| 535 |
|
|
} |
| 536 |
|
|
/* do type 4 here */ |
| 537 |
|
|
ij = 0; |
| 538 |
|
|
for( k2 = 0; k2 < MAXIAT; k2++ ) |
| 539 |
|
|
{ |
| 540 |
|
|
if( !(atom[i].iat[k2] == 0 || atom[i].bo[k2] == 9) ) |
| 541 |
|
|
{ |
| 542 |
|
|
iii = atom[i].iat[k2]; |
| 543 |
|
|
if( !(atom[iii].mmx_type != 5 && atom[iii].mmx_type != 20) ) |
| 544 |
|
|
{ |
| 545 |
|
|
ijk[ij] = iii; |
| 546 |
|
|
ij++; |
| 547 |
|
|
if( ij == 3 ) |
| 548 |
|
|
{ |
| 549 |
|
|
dis = 0.F; |
| 550 |
|
|
/* *** -ch3 *** |
| 551 |
|
|
* *** add the hydrogens displaced along x enough |
| 552 |
|
|
* to give a normal length c-c bond *** */ |
| 553 |
|
|
atom[ijk[0]].x = 0.3796F + dis; |
| 554 |
|
|
atom[ijk[1]].x = 0.3796F + dis; |
| 555 |
|
|
atom[ijk[2]].x = 0.3796F + dis; |
| 556 |
|
|
atom[ijk[0]].y = 1.043F; |
| 557 |
|
|
atom[ijk[1]].y = -0.5215F; |
| 558 |
|
|
atom[ijk[2]].y = -0.5215F; |
| 559 |
|
|
atom[ijk[0]].z = 0.00F; |
| 560 |
|
|
atom[ijk[1]].z = 0.9032F; |
| 561 |
|
|
atom[ijk[2]].z = -0.9032F; |
| 562 |
|
|
} |
| 563 |
|
|
} |
| 564 |
|
|
} |
| 565 |
|
|
} |
| 566 |
|
|
} |
| 567 |
|
|
} |
| 568 |
|
|
} |
| 569 |
|
|
} |
| 570 |
|
|
} |
| 571 |
|
|
} |
| 572 |
|
|
} |
| 573 |
|
|
/* *** reorient the structure in starting orientation and |
| 574 |
|
|
* turn off atom markers *** */ |
| 575 |
|
|
revec(); |
| 576 |
|
|
return; |
| 577 |
|
|
} |
| 578 |
|
|
// ======================================================== |
| 579 |
|
|
void revec() |
| 580 |
|
|
{ |
| 581 |
|
|
int i; |
| 582 |
|
|
float xpnt, ypnt, zpnt; |
| 583 |
|
|
/* *** this routine used the unit vectors and origin saved |
| 584 |
|
|
* by 'subroutine getvec' to return the molecule to |
| 585 |
|
|
* its original orientation *** */ |
| 586 |
|
|
|
| 587 |
|
|
if( natom <= MAXATOM - 4 ) |
| 588 |
|
|
{ |
| 589 |
|
|
for( i = 1; i <= (natom + 4); i++ ) |
| 590 |
|
|
{ |
| 591 |
|
|
atom[i].x = atom[i].x - atom[natom + 4].x; |
| 592 |
|
|
atom[i].y = atom[i].y - atom[natom + 4].y; |
| 593 |
|
|
atom[i].z = atom[i].z - atom[natom + 4].z; |
| 594 |
|
|
} |
| 595 |
|
|
xpnt = atom[natom + 1].x; |
| 596 |
|
|
ypnt = atom[natom + 1].y; |
| 597 |
|
|
zpnt = atom[natom + 1].z; |
| 598 |
|
|
xaxis( &xpnt, &ypnt, &zpnt ); |
| 599 |
|
|
xpnt = atom[natom + 2].x; |
| 600 |
|
|
ypnt = atom[natom + 2].y; |
| 601 |
|
|
zpnt = atom[natom + 2].z; |
| 602 |
|
|
xyplan( &xpnt, &ypnt, &zpnt ); |
| 603 |
|
|
if( atom[natom + 1].x < 0. ) |
| 604 |
|
|
{ |
| 605 |
|
|
for( i = 1; i <= (natom + 4); i++ ) |
| 606 |
|
|
atom[i].x = -atom[i].x; |
| 607 |
|
|
} |
| 608 |
|
|
if( atom[natom + 2].y < 0. ) |
| 609 |
|
|
{ |
| 610 |
|
|
for( i = 1; i <= (natom + 4); i++ ) |
| 611 |
|
|
atom[i].y = -atom[i].y; |
| 612 |
|
|
} |
| 613 |
|
|
if( atom[natom + 3].z < 0. ) |
| 614 |
|
|
{ |
| 615 |
|
|
for( i = 1; i <= (natom + 4); i++ ) |
| 616 |
|
|
atom[i].z = -atom[i].z; |
| 617 |
|
|
} |
| 618 |
|
|
} |
| 619 |
|
|
return; |
| 620 |
|
|
} |
| 621 |
|
|
/* ------------------------ */ |
| 622 |
|
|
void xyplan(float *xr, float *yr, float *zr) |
| 623 |
|
|
{ |
| 624 |
|
|
int i; |
| 625 |
|
|
float cos3, denom, savex, sin3; |
| 626 |
|
|
|
| 627 |
|
|
/* this subroutine rotates the molecule to place atom (xr,yr,*zr) |
| 628 |
|
|
* in the x,y-plane. note0 y-coordinate will be +. */ |
| 629 |
|
|
|
| 630 |
|
|
denom = sqrt( *yr**yr + *zr**zr ); |
| 631 |
|
|
if( fabs( denom ) >= .00001F ) |
| 632 |
|
|
{ |
| 633 |
|
|
sin3 = *zr/denom; |
| 634 |
|
|
cos3 = *yr/denom; |
| 635 |
|
|
for( i = 1; i <= (natom + 4); i++ ) |
| 636 |
|
|
{ |
| 637 |
|
|
savex = atom[i].y; |
| 638 |
|
|
atom[i].y = atom[i].y*cos3 + atom[i].z*sin3; |
| 639 |
|
|
atom[i].z = atom[i].z*cos3 - savex*sin3; |
| 640 |
|
|
} |
| 641 |
|
|
savex = *yr; |
| 642 |
|
|
*yr = *yr*cos3 + *zr*sin3; |
| 643 |
|
|
*zr = *zr*cos3 - savex*sin3; |
| 644 |
|
|
} |
| 645 |
|
|
return; |
| 646 |
|
|
} |
| 647 |
|
|
/* ------------------------ */ |
| 648 |
|
|
void xaxis(float *xpnt,float *ypnt,float *zpnt) |
| 649 |
|
|
{ |
| 650 |
|
|
int i; |
| 651 |
|
|
float cos1, cos2, denom, save, sin1, sin2; |
| 652 |
|
|
|
| 653 |
|
|
/* this subroutine rotates the molecule about z-axis and then y-axis to |
| 654 |
|
|
* place point with coordinates (i*xpnt,iypnt,izpnt) along x-axis. */ |
| 655 |
|
|
|
| 656 |
|
|
denom = sqrt( *xpnt**xpnt + *ypnt**ypnt ); |
| 657 |
|
|
if( fabs( denom ) < .00001F ) |
| 658 |
|
|
{ |
| 659 |
|
|
sin1 = 0.F; |
| 660 |
|
|
cos1 = 1.F; |
| 661 |
|
|
}else |
| 662 |
|
|
{ |
| 663 |
|
|
sin1 = *ypnt/denom; |
| 664 |
|
|
cos1 = *xpnt/denom; |
| 665 |
|
|
for( i = 1; i <= (natom + 4); i++ ) |
| 666 |
|
|
{ |
| 667 |
|
|
save = atom[i].x; |
| 668 |
|
|
atom[i].x = atom[i].x*cos1 + atom[i].y*sin1; |
| 669 |
|
|
atom[i].y = atom[i].y*cos1 - save*sin1; |
| 670 |
|
|
} |
| 671 |
|
|
save = *xpnt; |
| 672 |
|
|
*xpnt = *xpnt*cos1 + *ypnt*sin1; |
| 673 |
|
|
*ypnt = *ypnt*cos1 - save*sin1; |
| 674 |
|
|
} |
| 675 |
|
|
denom = sqrt( *xpnt**xpnt + *zpnt**zpnt ); |
| 676 |
|
|
if( fabs( denom ) >= .00001F ) |
| 677 |
|
|
{ |
| 678 |
|
|
sin2 = *zpnt/denom; |
| 679 |
|
|
cos2 = *xpnt/denom; |
| 680 |
|
|
for( i = 1; i <= (natom + 4); i++ ) |
| 681 |
|
|
{ |
| 682 |
|
|
save = atom[i].x; |
| 683 |
|
|
atom[i].x = atom[i].x*cos2 + atom[i].z*sin2; |
| 684 |
|
|
atom[i].z = atom[i].z*cos2 - save*sin2; |
| 685 |
|
|
} |
| 686 |
|
|
save = *xpnt; |
| 687 |
|
|
*xpnt = *xpnt*cos2 + *zpnt*sin2; |
| 688 |
|
|
*zpnt = *zpnt*cos2 - save*sin2; |
| 689 |
|
|
} |
| 690 |
|
|
return; |
| 691 |
|
|
} |
| 692 |
|
|
/* ============================================== */ |
| 693 |
|
|
void getvec() |
| 694 |
|
|
{ |
| 695 |
|
|
|
| 696 |
|
|
/* *** this routine saves unit vectors and origin in the |
| 697 |
|
|
* n+1 - n+4 slots of x, y, and z *** */ |
| 698 |
|
|
|
| 699 |
|
|
if(natom > MAXATOM - 4 ) |
| 700 |
|
|
return; |
| 701 |
|
|
atom[natom + 1].x = 1.F; |
| 702 |
|
|
atom[natom + 1].y = 0.F; |
| 703 |
|
|
atom[natom + 1].z = 0.F; |
| 704 |
|
|
atom[natom + 2].x = 0.F; |
| 705 |
|
|
atom[natom + 2].y = 1.F; |
| 706 |
|
|
atom[natom + 2].z = 0.F; |
| 707 |
|
|
atom[natom + 3].x = 0.F; |
| 708 |
|
|
atom[natom + 3].y = 0.F; |
| 709 |
|
|
atom[natom + 3].z = 1.F; |
| 710 |
|
|
atom[natom + 4].x = 0.F; |
| 711 |
|
|
atom[natom + 4].y = 0.F; |
| 712 |
|
|
atom[natom + 4].z = 0.F; |
| 713 |
|
|
return; |
| 714 |
|
|
} |
| 715 |
|
|
/* ============================================== */ |
| 716 |
|
|
void hdel(int lptest) |
| 717 |
|
|
{ |
| 718 |
|
|
/* lptest = 0 to remove H and lone pair */ |
| 719 |
|
|
/* lptest = 1 to remove lone pairs only */ |
| 720 |
|
|
/* lptest = 2 to remove lp & reset various groups for amber */ |
| 721 |
|
|
int i, iatt, iatt1, iatyp, it, it1,ntemp; |
| 722 |
|
|
int j, jatom; |
| 723 |
|
|
/* *** delete hydrogens *** */ |
| 724 |
|
|
ntemp = natom; |
| 725 |
|
|
for( i = 1; i <= ntemp; i++ ) |
| 726 |
|
|
{ |
| 727 |
|
|
if( atom[i].mmx_type != 0 ) |
| 728 |
|
|
{ |
| 729 |
|
|
iatyp = atom[i].mmx_type; |
| 730 |
|
|
if( (lptest == 0 && (iatyp == 5 || iatyp == 20 )) || (lptest >= 1 && iatyp == 20) ) |
| 731 |
|
|
{ |
| 732 |
|
|
iatt = atom[i].iat[0]; |
| 733 |
|
|
iatt1 = atom[i].iat[1]; |
| 734 |
|
|
if( iatt != 0 || iatt1 != 0) |
| 735 |
|
|
{ |
| 736 |
|
|
it = atom[iatt].mmx_type; |
| 737 |
|
|
it1 = atom[iatt1].mmx_type; |
| 738 |
|
|
if (it >= 11 && it <= 14) // halogens |
| 739 |
|
|
goto L_10; |
| 740 |
|
|
if( (it < 300) && (it1 < 300)) // attached metals |
| 741 |
|
|
deleteatom(i); |
| 742 |
|
|
} |
| 743 |
|
|
} |
| 744 |
|
|
} |
| 745 |
|
|
L_10: |
| 746 |
|
|
continue; |
| 747 |
|
|
} |
| 748 |
|
|
reseq(); |
| 749 |
|
|
generate_bonds(); |
| 750 |
|
|
return; |
| 751 |
|
|
} |
| 752 |
|
|
/* -------------------------- */ |
| 753 |
|
|
void reseq() |
| 754 |
|
|
{ |
| 755 |
|
|
int i, ia, ib, iplus, ixx, j, jincr, k; |
| 756 |
|
|
|
| 757 |
|
|
/* ***this subroutine will repack the atom |
| 758 |
|
|
* ***connection table, making sure to fill in |
| 759 |
|
|
* **all "holes" caused by deleting atoms or bonds. |
| 760 |
|
|
* ***the necessary common blocks involve arrays |
| 761 |
|
|
* of the connection table (contb) */ |
| 762 |
|
|
|
| 763 |
|
|
for( i = 1; i < MAXATOM; i++ ) |
| 764 |
|
|
{ |
| 765 |
|
|
if( atom[i].type != 0 ) |
| 766 |
|
|
{ |
| 767 |
|
|
for( ia = 0; ia < (MAXIAT - 1); ia++ ) |
| 768 |
|
|
{ |
| 769 |
|
|
if( atom[i].iat[ia] == 0 ) |
| 770 |
|
|
{ |
| 771 |
|
|
/* *** for every zero entry in the array iat |
| 772 |
|
|
* for atom i, want to move down all remaining |
| 773 |
|
|
* entries of iat by one slot; after doing so |
| 774 |
|
|
* want to store that zero entry in the last |
| 775 |
|
|
* slot--iat *** */ |
| 776 |
|
|
for( ib = ia + 1; ib < MAXIAT; ib++ ) |
| 777 |
|
|
{ |
| 778 |
|
|
atom[i].iat[ib - 1] = atom[i].iat[ib]; |
| 779 |
|
|
atom[i].bo[ib - 1] = atom[i].bo[ib]; |
| 780 |
|
|
} |
| 781 |
|
|
atom[i].iat[MAXIAT - 1] = 0; |
| 782 |
|
|
} |
| 783 |
|
|
} |
| 784 |
|
|
} |
| 785 |
|
|
} |
| 786 |
|
|
|
| 787 |
|
|
/* *** now want to renumber atoms to leave |
| 788 |
|
|
* no "holes" caused by the deleted atoms *** */ |
| 789 |
|
|
jincr = 0; |
| 790 |
|
|
/* i points to first zero entry |
| 791 |
|
|
* kincr points to next real entry */ |
| 792 |
|
|
for( i = 1; i < (MAXATOM - 1); i++ ) |
| 793 |
|
|
{ |
| 794 |
|
|
iplus = 0; |
| 795 |
|
|
if( atom[i].type == 0 ) |
| 796 |
|
|
{ |
| 797 |
|
|
for( jincr = i; jincr < MAXATOM; jincr++ ) |
| 798 |
|
|
{ |
| 799 |
|
|
if( atom[jincr].type != 0 ) |
| 800 |
|
|
{ |
| 801 |
|
|
iplus = jincr; |
| 802 |
|
|
break; |
| 803 |
|
|
} |
| 804 |
|
|
} |
| 805 |
|
|
if (iplus == 0) |
| 806 |
|
|
break; |
| 807 |
|
|
for( j = 0; j < MAXIAT; j++ ) |
| 808 |
|
|
{ |
| 809 |
|
|
atom[i].iat[j] = atom[iplus].iat[j]; |
| 810 |
|
|
atom[i].bo[j] = atom[iplus].bo[j]; |
| 811 |
|
|
} |
| 812 |
|
|
|
| 813 |
|
|
atom[i].x = atom[iplus].x; |
| 814 |
|
|
atom[i].y = atom[iplus].y; |
| 815 |
|
|
atom[i].z = atom[iplus].z; |
| 816 |
|
|
atom[i].type = atom[iplus].type; |
| 817 |
|
|
atom[i].tclass = atom[iplus].tclass; |
| 818 |
|
|
atom[i].type = atom[iplus].type; |
| 819 |
|
|
atom[i].mmx_type = atom[iplus].mmx_type; |
| 820 |
|
|
atom[i].mm3_type = atom[iplus].mm3_type; |
| 821 |
|
|
atom[i].amber_type = atom[iplus].amber_type; |
| 822 |
|
|
atom[i].mmff_type = atom[iplus].mmff_type; |
| 823 |
|
|
atom[i].atomnum = atom[iplus].atomnum; |
| 824 |
|
|
atom[i].formal_charge = atom[iplus].formal_charge; |
| 825 |
|
|
atom[i].atomwt = atom[iplus].atomwt; |
| 826 |
|
|
atom[i].use = atom[iplus].use; |
| 827 |
|
|
strcpy(atom[i].name,atom[iplus].name); |
| 828 |
|
|
atom[i].charge = atom[iplus].charge; |
| 829 |
|
|
atom[i].flags = atom[iplus].flags; |
| 830 |
|
|
atom[i].radius = atom[iplus].radius; |
| 831 |
|
|
atom[i].energy = atom[iplus].energy; |
| 832 |
|
|
/* *** delete the atom whose statistics were just |
| 833 |
|
|
* stored in the i-th atom's connection table *** */ |
| 834 |
|
|
for( ixx = 0; ixx < MAXIAT; ixx++ ) |
| 835 |
|
|
{ |
| 836 |
|
|
atom[iplus].iat[ixx] = 0; |
| 837 |
|
|
atom[iplus].bo[ixx] = 0; |
| 838 |
|
|
} |
| 839 |
|
|
atom[iplus].x = 0.0F; |
| 840 |
|
|
atom[iplus].y = 0.0F; |
| 841 |
|
|
atom[iplus].z = 0.0F; |
| 842 |
|
|
atom[iplus].type = 0; |
| 843 |
|
|
atom[iplus].tclass = 0; |
| 844 |
|
|
atom[iplus].mmx_type = 0; |
| 845 |
|
|
atom[iplus].mm3_type = 0; |
| 846 |
|
|
atom[iplus].amber_type = 0; |
| 847 |
|
|
atom[iplus].mmff_type = 0; |
| 848 |
|
|
atom[iplus].atomnum = 0; |
| 849 |
|
|
atom[iplus].formal_charge = 0; |
| 850 |
|
|
atom[iplus].atomwt = 0.0F; |
| 851 |
|
|
atom[iplus].use = 0; |
| 852 |
|
|
atom[iplus].charge = 0.0F; |
| 853 |
|
|
atom[iplus].flags = 0; |
| 854 |
|
|
atom[iplus].radius = 0.0F; |
| 855 |
|
|
atom[iplus].energy = 0.0F; |
| 856 |
|
|
strcpy(atom[iplus].name,""); |
| 857 |
wdelano |
58 |
|
| 858 |
tjod |
3 |
for( j = 0; j < MAXIAT; j++ ) |
| 859 |
|
|
{ |
| 860 |
|
|
if( atom[i].iat[j] != 0 ) |
| 861 |
|
|
{ |
| 862 |
|
|
for( k = 0; k < MAXIAT; k++ ) |
| 863 |
|
|
{ |
| 864 |
|
|
if( atom[atom[i].iat[j]].iat[k] == iplus ) |
| 865 |
|
|
atom[atom[i].iat[j]].iat[k] = i; |
| 866 |
|
|
} |
| 867 |
|
|
} |
| 868 |
|
|
} |
| 869 |
|
|
} |
| 870 |
|
|
} |
| 871 |
|
|
/* ***now want to do the same resequencing for iat array */ |
| 872 |
|
|
|
| 873 |
|
|
/* recalc number of atoms */ |
| 874 |
|
|
natom = 0; |
| 875 |
|
|
for (i = 1; i < MAXATOM; i++) |
| 876 |
|
|
{ |
| 877 |
|
|
if (atom[i].type != 0) |
| 878 |
|
|
natom++; |
| 879 |
|
|
} |
| 880 |
|
|
return; |
| 881 |
|
|
} |
