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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 "substr.h" |
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#include "field.h" |
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#include "atom_k.h" |
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#include "pot.h" |
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#include "energies.h" |
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#include "solv.h" |
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#include "fix.h" |
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EXTERN int ncol[]; |
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struct t_residues { |
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int nchain, ichainstart[10]; |
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int ngroup, iresnum[200], irestype[200], istartatom[200]; |
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} residues; |
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EXTERN struct t_minim_values { |
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int iprint, ndc, nconst; |
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float dielc; |
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} minim_values; |
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EXTERN struct t_units { |
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double bndunit, cbnd, qbnd; |
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double angunit, cang, qang, pang, sang, aaunit; |
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double stbnunit, ureyunit, torsunit, storunit, v14scale; |
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double aterm, bterm, cterm, dielec, chgscale; |
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} units; |
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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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EXTERN struct t_dmomv { |
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float xn,yn,zn,xp,yp,zp; |
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} dmomv; |
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EXTERN struct t_dipolemom { |
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double total, xdipole, ydipole, zdipole; |
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} dipolemom; |
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EXTERN struct t_vdw1 { |
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int nvdw; |
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float rad[MAXVDWCONST], eps[MAXVDWCONST]; |
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int lpd[MAXVDWCONST], ihtyp[MAXVDWCONST], ihdon[MAXVDWCONST]; |
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float alpha[MAXVDWCONST],n[MAXVDWCONST],a[MAXVDWCONST],g[MAXVDWCONST]; |
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char da[MAXVDWCONST][2]; |
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} vdw1; |
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EXTERN struct { |
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int mm3, mmff, amber, opls; |
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} AtomTypes[]; |
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EXTERN struct ElementType { char symbol[3]; |
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int atomnum; |
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float weight, covradius, vdwradius; |
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int s,p,d,f, type; |
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} Elements[]; |
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EXTERN struct t_centroid { |
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int ncentroid, numsel[10]; |
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int isel[10][10]; |
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double x[10], y[10], z[10]; |
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} centroid; |
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void InitialTransform(void); |
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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 generate_bonds(void); |
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void deleteatom(int); |
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void deletebond(int, int); |
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void set_atomtype(int,int,int,int,int,int); |
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void set_atomdata(int,int,int,int,int,int); |
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extern void matrotat(float (*)[4], int, float); |
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extern void matxform(float (*)[4], int); |
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void message_alert(char *, char *); |
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void charge_dipole(void); |
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int isangle(int,int); |
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int mm3_mmxtype(int); |
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int mmff_mmxtype(int); |
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// =============================================== |
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void set_atomdata(int ia, int mmxtype, int mm3type, int mmfftype,int ambertype,int oplstype) |
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{ |
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int type; |
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if (mmxtype > 0) |
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atom[ia].mmx_type = mmxtype; |
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if (mm3type > 0) |
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atom[ia].mm3_type = mm3type; |
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if (mmfftype > 0) |
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atom[ia].mmff_type = mmfftype; |
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if (ambertype > 0) |
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atom[ia].amber_type = ambertype; |
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if (oplstype > 0) |
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atom[ia].opls_type = oplstype; |
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if (field.type == MMX || field.type == MM2) |
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{ |
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type = mmxtype; |
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} else if (field.type == MM3) |
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{ |
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type = mm3type; |
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}else if (field.type == AMBER) |
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{ |
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type = ambertype; |
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} else if (field.type == MMFF94) |
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{ |
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type = mmfftype; |
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} else if (field.type == OPLSAA) |
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{ |
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type = oplstype; |
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} |
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if ( type < 300) |
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{ |
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atom[ia].tclass = atom_k.tclass[type]; |
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atom[ia].atomnum = atom_k.number[type]; |
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atom[ia].atomwt = atom_k.weight[type]; |
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strcpy(atom[ia].name, atom_k.symbol[type]); |
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} |
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if ( field.type == MMX && mmxtype == LPTYPE) |
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atom[ia].color = 1; |
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else if ( type < 300 && mmxtype != LPTYPE ) |
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atom[ia].color = ncol[atom[ia].atomnum-1]; |
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else |
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atom[ia].color = 7; |
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} |
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// =============================================== |
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void set_atomtype(int ia, int mmxtype, int mm3type, int mmfftype,int ambertype,int oplstype) |
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{ |
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if (mmxtype > 0) |
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atom[ia].mmx_type = mmxtype; |
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if (mm3type > 0) |
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atom[ia].mm3_type = mm3type; |
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if (mmfftype > 0) |
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atom[ia].mmff_type = mmfftype; |
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if (ambertype > 0) |
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atom[ia].amber_type = ambertype; |
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if (oplstype > 0) |
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atom[ia].opls_type = oplstype; |
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} |
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// ====================================================== |
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int make_atom(int type, float x, float y, float z,char *name) |
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{ |
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int i,iz; |
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int mmxtype, mm3type, mmfftype,ambertype,oplstype; |
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natom++; |
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if (natom >= MAXATOM - 10) |
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{ |
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natom--; |
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message_alert("Max atoms exceeded in makeatom","PCMODEL Error"); |
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return -1; |
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} |
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iz = strlen(name); |
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if (iz > 0) // got an atom name use it |
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{ |
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for (i=1; i <= atom_k.natomtype; i++) |
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{ |
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if (strcmp(name,atom_k.symbol[i]) == 0) // names match |
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{ |
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strcpy(atom[natom].name,name); |
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atom[natom].tclass = atom_k.tclass[i]; |
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atom[natom].atomwt = atom_k.weight[i]; |
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atom[natom].atomnum = atom_k.number[i]; |
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atom[natom].type = atom_k.type[i]; |
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if (type == 0) |
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{ |
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type = atom[natom].type; // this is an mmff type |
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mmxtype = mmff_mmxtype(type); |
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mm3type = 0; |
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mmfftype = type; |
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ambertype = 0; |
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oplstype = 0; |
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set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
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if (mmfftype == 0) return -1; |
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} else if (field.type == MMX || field.type == MM2) |
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{ |
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atom[natom].mmx_type = type; |
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mmxtype = type; |
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mm3type = AtomTypes[type-1].mm3; |
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mmfftype = AtomTypes[type-1].mmff; |
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ambertype = AtomTypes[type-1].amber; |
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oplstype = AtomTypes[type-1].opls; |
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set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
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} else if (field.type == MM3) |
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{ |
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atom[natom].mm3_type = type; |
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mmxtype = mm3_mmxtype(type); |
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mm3type = type; |
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mmfftype = AtomTypes[mmxtype-1].mmff; |
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ambertype = AtomTypes[mmxtype-1].amber; |
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oplstype = AtomTypes[mmxtype-1].opls; |
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set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
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} else if (field.type == MMFF94) |
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{ |
| 198 |
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atom[natom].mmff_type = type; |
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mmxtype = mmff_mmxtype(type); |
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mm3type = AtomTypes[mmxtype-1].mm3; |
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mmfftype = type; |
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ambertype = AtomTypes[mmxtype-1].amber; |
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oplstype = AtomTypes[mmxtype-1].opls; |
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set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
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} |
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atom[natom].color = ncol[atom[natom].atomnum-1]; |
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atom[natom].x = x; atom[natom].y = y; atom[natom].z = z; |
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atom[natom].vdw_radius = Elements[atom[natom].atomnum-1].covradius; |
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atom[natom].substr[0] = (1L << 0); |
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atom[natom].flags = 0; |
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substr.istract[0] = TRUE; |
| 213 |
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return natom; |
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} |
| 215 |
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} |
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for( i = 0; i < 103; i++ ) |
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{ |
| 218 |
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if( strcasecmp(Elements[i].symbol,name) == 0 ) |
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{ |
| 220 |
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strcpy(atom[natom].name,Elements[i].symbol); |
| 221 |
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atom[natom].atomwt = Elements[i].weight; |
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atom[natom].atomnum = Elements[i].atomnum; |
| 223 |
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atom[natom].type = Elements[i].type; // set generic type |
| 224 |
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atom[natom].tclass = Elements[i].type; // set generic type |
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atom[natom].mmx_type = Elements[i].type; // set generic type |
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if (type > 0) |
| 227 |
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{ |
| 228 |
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atom[natom].type = type; // overwrite type if type is passed in |
| 229 |
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if (field.type == MMX || field.type == MM2) |
| 230 |
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atom[natom].mmx_type = type; |
| 231 |
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else if (field.type == MM3) |
| 232 |
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atom[natom].mm3_type = type; |
| 233 |
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else if (field.type == MMFF94) |
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atom[natom].mmff_type = type; |
| 235 |
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else if (field.type == AMBER) |
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atom[natom].amber_type = type; |
| 237 |
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else if (field.type == OPLSAA) |
| 238 |
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atom[natom].opls_type = type; |
| 239 |
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} |
| 240 |
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if (type != 0) atom[natom].type = type; |
| 241 |
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atom[natom].color = ncol[atom[natom].atomnum-1]; |
| 242 |
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atom[natom].x = x; atom[natom].y = y; atom[natom].z = z; |
| 243 |
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atom[natom].vdw_radius = Elements[i].covradius; |
| 244 |
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atom[natom].substr[0] = (1L << 0); |
| 245 |
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substr.istract[0] = TRUE; |
| 246 |
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if (type > 299) |
| 247 |
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return -1; |
| 248 |
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else if (atom[natom].mmff_type == 0) |
| 249 |
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return -1; |
| 250 |
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else |
| 251 |
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return natom; |
| 252 |
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} |
| 253 |
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} |
| 254 |
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} else |
| 255 |
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{ |
| 256 |
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message_alert("Input atom does not have valid atomic symbol or atom type","Error"); |
| 257 |
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return -1; |
| 258 |
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} |
| 259 |
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return -1; |
| 260 |
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} |
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// ==================================================== |
| 262 |
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void make_bond(int ia1, int ia2, int bo) |
| 263 |
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{ |
| 264 |
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int loop,loop1; |
| 265 |
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| 266 |
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if (ia1 < 1 || ia1 > MAXATOM) return; |
| 267 |
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if (ia2 < 1 || ia2 > MAXATOM) return; |
| 268 |
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/* find if bond exists */ |
| 269 |
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for (loop = 0; loop < MAXIAT; loop++) |
| 270 |
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{ |
| 271 |
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if (atom[ia1].iat[loop] == ia2) |
| 272 |
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{ |
| 273 |
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if (bo == 1) |
| 274 |
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atom[ia1].bo[loop] += bo; |
| 275 |
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else |
| 276 |
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atom[ia1].bo[loop] = bo; |
| 277 |
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| 278 |
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for (loop1 = 0; loop1 < MAXIAT; loop1++) |
| 279 |
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{ |
| 280 |
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if (atom[ia2].iat[loop1] == ia1) |
| 281 |
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{ |
| 282 |
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if ( bo == 1) |
| 283 |
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{ |
| 284 |
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atom[ia2].bo[loop1] += bo; /* bond exists return */ |
| 285 |
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return; |
| 286 |
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} else |
| 287 |
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{ |
| 288 |
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atom[ia2].bo[loop1] = bo; /* bond exists return */ |
| 289 |
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return; |
| 290 |
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} |
| 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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/* bond does not exist create it */ |
| 296 |
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for (loop = 0; loop < MAXIAT; loop++) |
| 297 |
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{ |
| 298 |
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if (atom[ia1].iat[loop] == 0) |
| 299 |
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{ |
| 300 |
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atom[ia1].iat[loop] = ia2; |
| 301 |
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atom[ia1].bo[loop] = bo; |
| 302 |
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break; |
| 303 |
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} |
| 304 |
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} |
| 305 |
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for (loop = 0; loop < MAXIAT; loop++) |
| 306 |
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{ |
| 307 |
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if (atom[ia2].iat[loop] == 0) |
| 308 |
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{ |
| 309 |
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atom[ia2].iat[loop] = ia1; |
| 310 |
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atom[ia2].bo[loop] = bo; |
| 311 |
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break; |
| 312 |
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} |
| 313 |
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} |
| 314 |
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} |
| 315 |
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// =============================================== |
| 316 |
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void deleteatom(int i) |
| 317 |
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{ |
| 318 |
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int j,k, ibo; |
| 319 |
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atom[i].type = 0; |
| 320 |
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atom[i].x = 0.0F; |
| 321 |
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atom[i].y = 0.0F; |
| 322 |
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atom[i].z = 0.0F; |
| 323 |
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atom[i].flags = 0; |
| 324 |
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for (j=0; j < MAXSSCLASS; j++) |
| 325 |
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atom[i].substr[j] = 0; |
| 326 |
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for (j=0; j<MAXIAT; j++) |
| 327 |
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{ |
| 328 |
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if (atom[i].iat[j] != 0 ) |
| 329 |
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{ |
| 330 |
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if (atom[atom[i].iat[j]].atomnum == 1 || atom[atom[i].iat[j]].atomnum == 0 ) |
| 331 |
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{ |
| 332 |
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atom[atom[i].iat[j]].type = 0; |
| 333 |
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atom[atom[i].iat[j]].x = 0.0F; |
| 334 |
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atom[atom[i].iat[j]].y = 0.0F; |
| 335 |
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atom[atom[i].iat[j]].z = 0.0F; |
| 336 |
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atom[atom[i].iat[j]].flags = 0; |
| 337 |
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} |
| 338 |
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ibo = atom[i].bo[j]; |
| 339 |
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for (k=1; k <= ibo; k++) |
| 340 |
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deletebond(i,atom[i].iat[j]); |
| 341 |
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atom[i].iat[j] = 0; |
| 342 |
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} |
| 343 |
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} |
| 344 |
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natom--; |
| 345 |
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} |
| 346 |
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// ================================================== |
| 347 |
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void deletebond(int i, int j) |
| 348 |
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{ |
| 349 |
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int i1,j1; |
| 350 |
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for (i1=0; i1 < MAXIAT; i1++) |
| 351 |
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{ |
| 352 |
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if (atom[i].iat[i1] == j) |
| 353 |
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{ |
| 354 |
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if (atom[i].bo[i1] == 9) /* if deleting a coordinated bond - delete it completely */ |
| 355 |
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{ |
| 356 |
|
|
atom[i].bo[i1] = 0; |
| 357 |
|
|
atom[i].iat[i1] = 0; |
| 358 |
|
|
} |
| 359 |
|
|
atom[i].bo[i1] -= 1; |
| 360 |
|
|
if (atom[i].bo[i1] <= 0 ) |
| 361 |
|
|
atom[i].iat[i1] = 0; |
| 362 |
|
|
break; |
| 363 |
|
|
} |
| 364 |
|
|
} |
| 365 |
|
|
for (j1=0; j1 < MAXIAT; j1++) |
| 366 |
|
|
{ |
| 367 |
|
|
if (atom[j].iat[j1] == i) |
| 368 |
|
|
{ |
| 369 |
|
|
if (atom[j].bo[j1] == 9) /* if deleting a coordinated bond - delete it completely */ |
| 370 |
|
|
{ |
| 371 |
|
|
atom[j].bo[j1] = 0; |
| 372 |
|
|
atom[j].iat[j1] = 0; |
| 373 |
|
|
} |
| 374 |
|
|
atom[j].bo[j1] -= 1; |
| 375 |
|
|
if (atom[j].bo[j1] <= 0) |
| 376 |
|
|
atom[j].iat[j1] = 0; |
| 377 |
|
|
break; |
| 378 |
|
|
} |
| 379 |
|
|
} |
| 380 |
|
|
} |
| 381 |
|
|
/* --------------------------- */ |
| 382 |
|
|
void generate_bonds(void) |
| 383 |
|
|
{ |
| 384 |
|
|
int i,j; |
| 385 |
|
|
|
| 386 |
|
|
bonds.numbonds = 0; |
| 387 |
|
|
for (i= 0; i <= natom; i++) |
| 388 |
|
|
{ |
| 389 |
|
|
bonds.ia1[i] = 0; |
| 390 |
|
|
bonds.ia2[i] = 0; |
| 391 |
|
|
bonds.bondorder[i] = 0; |
| 392 |
|
|
} |
| 393 |
|
|
|
| 394 |
|
|
for (i = 1; i <= natom; i++) |
| 395 |
|
|
{ |
| 396 |
|
|
for (j = 0; j < MAXIAT; j++) |
| 397 |
|
|
{ |
| 398 |
|
|
if (atom[i].iat[j] > i && atom[i].iat[j] != 0) |
| 399 |
|
|
{ |
| 400 |
|
|
bonds.ia1[bonds.numbonds] = i; |
| 401 |
|
|
bonds.ia2[bonds.numbonds] = atom[i].iat[j]; |
| 402 |
|
|
bonds.bondorder[bonds.numbonds] = atom[i].bo[j]; |
| 403 |
|
|
bonds.numbonds++; |
| 404 |
|
|
} |
| 405 |
|
|
} |
| 406 |
|
|
} |
| 407 |
|
|
} |
