// Action_MultiVector::DoAction()
Action::RetType Action_MultiVector::DoAction(int frameNum, ActionFrame& frm) {
for (unsigned int nv = 0; nv < CrdIdx1_.size(); ++nv) {
Vec3 CXYZ( frm.Frm().CRD( CrdIdx1_[nv] ) );
Vec3 VXYZ( frm.Frm().CRD( CrdIdx2_[nv] ) );
VXYZ -= CXYZ;
data_[nv]->AddVxyz(VXYZ, CXYZ);
}
return Action::OK;
}
// Action_MultiVector::DoAction()
Action::RetType Action_MultiVector::DoAction(int frameNum, Frame* currentFrame,
Frame** frameAddress)
{
for (unsigned int nv = 0; nv < CrdIdx1_.size(); ++nv) {
Vec3 CXYZ( currentFrame->CRD( CrdIdx1_[nv] ) );
Vec3 VXYZ( currentFrame->CRD( CrdIdx2_[nv] ) );
VXYZ -= CXYZ;
data_[nv]->AddVxyz(VXYZ, CXYZ);
}
return Action::OK;
}
void Action_Vector::Dipole(Frame const& currentFrame) {
Vec3 VXYZ(0.0, 0.0, 0.0);
Vec3 CXYZ(0.0, 0.0, 0.0);
double total_mass = 0;
for (AtomMask::const_iterator atom = mask_.begin();
atom != mask_.end(); ++atom)
{
double mass = (*CurrentParm_)[*atom].Mass();
total_mass += mass;
Vec3 XYZ = currentFrame.XYZ( *atom );
CXYZ += ( XYZ * mass );
double charge = (*CurrentParm_)[*atom].Charge();
XYZ *= charge;
VXYZ += ( XYZ );
}
CXYZ /= total_mass;
Vec_->AddVxyz( VXYZ, CXYZ );
}
void sprintf_hb(char * o_str, int i, int j, struct vect nearest, float d, float ha, float daaa_ang, float haaa_ang)
{
char bndtyp[3], acctyp[4], dontyp[4], space=' ';
int ca_d, ri, rj, gap;
char buf1[20],buf2[20]; /* buffers for atomid routines */
float tmp;
/*we have a hydrogen bond!*/
bndtyp[0] = bndtyp[1] = '?';
acctyp[3] = dontyp[3] = bndtyp[2] = '\0';
if (atom[i].aacode == TOTNAA || atom[i].hetflg )
bndtyp[0] = 'H';
else
{
if (atom[i].aacode <STDAA)
{
bndtyp[0] = (atom[i].atmtyp <=3) ? 'M' : 'S';
}
else
{
bndtyp[0] = (atom[i].atmtyp <=3) ? 'm' : 's';
}
}
if (atom[j].aacode == TOTNAA || atom[j].hetflg )
bndtyp[1] = 'H';
else
{
if (atom[j].aacode <STDAA)
{
bndtyp[1] = (atom[j].atmtyp <=3) ? 'M' : 'S';
}
else
{
bndtyp[1] = (atom[j].atmtyp <=3) ? 'm' : 's';
}
}
ri = atom[i].caindex;
rj = atom[j].caindex;
gap=find_gap( ri, rj);
#if 0
if (atom[i].aacode==TOTNAA || (ri == -99) || !residue[ri].ca || atom[j].aacode==TOTNAA || (rj == -99) || !residue[rj].ca )
gap = -1;
else
{
gap = cagap(ri,rj);
}
#endif
if (atom[i].aacode==TOTNAA || (ri == -99) || !residue[ri].ca ||
atom[j].aacode==TOTNAA || (rj == -99) || !residue[rj].ca )
ca_d = -1.0;
else
{
ca_d = length_squared( to(*(residue[ri].ca),*(residue[rj].ca)) );
if (ca_d > SQR(CAWARN) && debug)
{
printf("WARNING: unusual CA-CA distance of %5.2f for",sqrt(ca_d));
printf("%s number ??\n", (nnbflg)?" interaction":" H-bond"/*,nhb*/);
printf(" between %s and %s\n", atomid(i,buf1),atomid(j,buf2));
}
}
#if 0
printf("%4s", brcode);
printf("%c", (atom[i].chnid == '-') ? space : atom[i].chnid);
printf("%4s/", brcode);
printf("%c", atom[i].chnid);
printf("%04d", atom[i].aanum);
if(OMLINSERT && atom[i].hetflg)
printf("h");
else
printf("%c", atom[i].inscode);
/* printf("%3s", dontyp); */
printf("%3s", atom[i].resnam);
printf("%4s", atom[i].atmnam);
printf("%c", atom[i].strucsum);
printf("%c", (atom[j].chnid == '-') ? space : atom[j].chnid);
printf("%4s/", brcode);
printf("%c", atom[j].chnid);
printf("%04d", atom[j].aanum);
if(OMLINSERT && atom[j].hetflg)
printf("h");
else
printf("%c", atom[j].inscode);
/* printf("%3s", acctyp); */
printf("%3s", atom[j].resnam);
printf("%4s", atom[j].atmnam);
printf("%c", atom[j].strucsum);
printf("%4.1f", sqrt(d));
printf(" %2s", bndtyp);
printf("%4d", gap);
printf("%4.1f", (ca_d <= 0.0) ? -1.0 : sqrt(ca_d));
printf("%6.1d", 180/3.1415927*angle(atom[i].p,nearest,atom[j].p) );
printf("%4.1d", d);
printf("%6d\n", nhb);
#endif
*o_str = 0 ;
/*This isn't neccessary if the longoutput format is used, but if the short
format is used, then the first output must (i) include a 'strlen' in case
it is part of a 'long format' output, and (ii) have some way of knowing
where to begin in case of a 'short format' output. */
if (longoutflg)
{
/* start to output the line, *.hhb format */
sprintf(o_str , "%4s", brcode);
sprintf(o_str+strlen(o_str), "%c", (atom[i].chnid == '-') ? space :
atom[i].chnid);
sprintf(o_str+strlen(o_str), "%4s/", brcode);
}
sprintf(o_str+strlen(o_str), "%c", atom[i].chnid);
sprintf(o_str+strlen(o_str), "%04d", atom[i].aanum);
if(OMLINSERT && atom[i].hetflg) /*v3.13*/
sprintf(o_str+strlen(o_str), "h");
else
sprintf(o_str+strlen(o_str), "%c", atom[i].inscode);
/* sprintf(o_str+strlen(o_str), "%3s", dontyp); */
/* Amendment. RAL 14 Jun 2012 --> */
// if (atom[i].aacode==Cys && atom[i].atmtyp == 5 & cssflg)
if (atom[i].aacode==Cys && atom[i].atmtyp == 5 && cssflg)
/* <-- Amendment. RAL 14 Jun 2012 */
{
if (atom[i].ssflg)
sprintf(o_str+strlen(o_str),"CSS");
else
sprintf(o_str+strlen(o_str),"CYH"); }
else
sprintf(o_str+strlen(o_str), "%3s", atom[i].resnam);
sprintf(o_str+strlen(o_str), "%4s", atom[i].atmnam);
if (longoutflg)
{
sprintf(o_str+strlen(o_str), "%c", atom[i].strucsum);
sprintf(o_str+strlen(o_str), "%c", (atom[j].chnid == '-') ? space :
atom[j].chnid);
sprintf(o_str+strlen(o_str), "%4s/", brcode);
}
else
sprintf(o_str+strlen(o_str), " ");
sprintf(o_str+strlen(o_str), "%c", atom[j].chnid);
sprintf(o_str+strlen(o_str), "%04d", atom[j].aanum);
if(OMLINSERT && atom[j].hetflg) /*v3.13 start*/
sprintf(o_str+strlen(o_str),"h");
else /*v3.13 end*/
sprintf(o_str+strlen(o_str), "%c", atom[j].inscode);
/* sprintf(o_str+strlen(o_str), "%3s", acctyp); */
if (atom[j].aacode==Cys && atom[j].atmtyp == 5 && cssflg)
{
if (atom[j].ssflg)
sprintf(o_str+strlen(o_str),"CSS");
else
sprintf(o_str+strlen(o_str),"CYH"); }
else
sprintf(o_str+strlen(o_str), "%3s", atom[j].resnam);
sprintf(o_str+strlen(o_str), "%4s", atom[j].atmnam);
if (longoutflg)
sprintf(o_str+strlen(o_str), "%c", atom[j].strucsum);
sprintf(o_str+strlen(o_str), "%5.2f", sqrt(d));
if (!longoutflg)
sprintf(o_str+strlen(o_str), " ");
sprintf(o_str+strlen(o_str), "%2s", bndtyp);
sprintf(o_str+strlen(o_str), "%4d", gap);
if (!longoutflg)
sprintf(o_str+strlen(o_str), " ");
sprintf(o_str+strlen(o_str), "%5.2f", (ca_d <= 0.0) ? -1.0 : sqrt(ca_d));
if (!longoutflg)
sprintf(o_str+strlen(o_str), " ");
if (atom[i].nh && h_atm[atom[i].h_ptr].typ)
{
/* if it has hydrogens and if they have been placed */
tmp = angle(atom[i].p,nearest,atom[j].p);
sprintf(o_str+strlen(o_str), "%5.1f", (180.0/3.1415927)* tmp );
if (!longoutflg)
sprintf(o_str+strlen(o_str), " ");
sprintf(o_str+strlen(o_str), "%5.2f", ha);
if (!longoutflg)
sprintf(o_str+strlen(o_str), " ");
if (haaa_ang>-50.0)
sprintf(o_str+strlen(o_str),"%5.1f", 180/3.1415927* (float) acos(haaa_ang) );
else
sprintf(o_str+strlen(o_str),"%5.1f", -1.0);
}
else
if (longoutflg)
sprintf(o_str+strlen(o_str), "%5.1f%5.2f%5.1f", -1.0, -1.0, -1.0);
else
sprintf(o_str+strlen(o_str), "%5.1f %5.2f %5.1f", -1.0, -1.0, -1.0);
if (daaa_ang>-50.0)
sprintf(o_str+strlen(o_str),"%6.1f", 180/3.1415927*acos(daaa_ang) );
else
sprintf(o_str+strlen(o_str),"%6.1f", -1.0);
if (debug)
{
sprintf(o_str+strlen(o_str), "D " );
sprintf(o_str+strlen(o_str), TF,VXYZ(atom[i].p) );
sprintf(o_str+strlen(o_str), " H " );
sprintf(o_str+strlen(o_str), TF,VXYZ(nearest) );
sprintf(o_str+strlen(o_str), " A " );
sprintf(o_str+strlen(o_str), TF, VXYZ(atom[j].p) );
}
/* sprintf(o_str+strlen(o_str), "%6d\n", nhb);
THIS IS DONE BY THE CALLING ROUTINE */
/* end of outputting the line, *.hhb format */
return;
}
int calc_hb(char o_str[256],int i, int j)
{
int l, /*ri, rj, gap,*/ h, near_h;
/*char bndtyp[3], acctyp[4], dontyp[4], space=' ';*/
float /*ca_d,*/ d, ha2,/*IM*/tmp_d, hd, ha, haaa_ang, daaa_ang;
struct vect nearest, tmp_point, aromatic_axis, aa[MAXCON] /* acceptor antecedants*/;
char buf1[20],buf2[20]; /* buffers for atomid routines */
/* void find_ss()*/
/* {*/
/* int i,j;*/
/* float d;*/
short aromatic_flg;
*o_str=0;
/* if(i==203 && j==210)
{
printf("Testing from %s",atomid(i,buf1));
printf(" to %s at start of calc_hb.\n",atomid(j,buf1));
debug=0;
}
else
debug=0;
*/
d = length_squared( to(atom[i].p, atom[j].p) );
if (debug==2)
printf("don-acc distance ^2 = %f\n",d);
if (d <= SQR(HBDIST))
/* these are nearby ! */; /*IM begins*/
else return(0);
if (debug) printf("Acceptable distance\n");
/* time to fill the acceptor array */
daaa_ang= -99.9; /* reset it . . . . */
aromatic_flg = ( atom[j].aacode < TOTNAA )?(accepts[atom[j].aacode][atom[j].atmtyp] < 0):0;
if (!aromatic_flg)
{
for(l=0;l<MAXCON;l++)
{
if (icon[j][l]>-1)
{
float daaa_tmp,aaa;
char buf1[20],buf2[20];
aa[l]=atom[icon[j][l] ].p;
daaa_tmp= dot_product(
to( aa[l], atom[j].p ), to( atom[i].p, atom[j].p ) ); /* = DA * A-AA * cos D-A-AA */
aaa=vector_length ( to(aa[l], atom[j].p) );
daaa_tmp/= aaa * sqrt( d); /* = cos D-A-AA */
/* d= DA^2 */
if (daaa_tmp>daaa_ang) daaa_ang=daaa_tmp; /* select lowest */
if (aaa<0.8 || aaa > 6.0)
printf("WARNING: %5.2fA between %s and %s ((D..)A-AA bond).\n", aaa,atomid(icon[j][l],buf1),atomid(j,buf2));
}
}
if (daaa_ang > cosMIN_DAAA && daaa_ang>-99.9)
if (!nnbflg)
return(0);
/*NB -99 was not originally used as a default whilst checking
because we were wrongly trying to find a lowest possible
value */
/* printf("lowest daaa_ang %6.1f\n",daaa_ang);*/
}
else /*aromatic_hbond*/
{
float daaa_tmp;
/*if( !strncmp("4DFR/A0030-TRP CE3",atomid(j,buf1),18))
debug=1;*/
if (debug){
printf("NOTE: %s is aromatic.\n",atomid(j,buf1));
printf(" connects to ");
for(l=0;l< atom[j].ncon;l++)
printf("%s ",atomid(icon[j][l],buf1));
printf("\n");
}
if ( accepts[atom[j].aacode][atom[j].atmtyp] != -1 )
printf("BUG: %s not registered as aromatic acceptor in \"aromatic_hbond\".\n",atomid(j,buf1));
if ( atom[j].ncon!=2 && atom[j].ncon!=3 )
printf("BUG: %s has connectivity %d but is registered as aromatic.\n",atomid(j,buf1),atom[j].ncon);
if ( atom[j].ncon==3 )
{
aromatic_axis = unit_vector(
vector_plus( perpendicular( atom[ icon[j][0] ].p, atom[j].p, atom[ icon[j][1] ].p),
vector_plus( perpendicular( atom[ icon[j][0] ].p, atom[j].p, atom[ icon[j][2] ].p),
perpendicular( atom[ icon[j][1] ].p, atom[j].p, atom[ icon[j][2] ].p) ) ) );
}
else
aromatic_axis = unit_vector(perpendicular( atom[ icon[j][0] ].p, atom[j].p, atom[ icon[j][1] ].p));
aa[0]= vector_plus( aromatic_axis, atom[j].p );
aa[1]= vector_plus( float_times_vect( -1.0, aromatic_axis), atom[j].p );
if (debug) printf("Perpendicular gives angles %5.3f and %5.3f with 1,2 / %d.\n",angle( atom[ icon[j][0] ].p, atom[j].p, aa[0] ), angle( atom[ icon[j][1] ].p, atom[j].p, aa[0] ) , atom[j].ncon);
for(l=0;l<2;l++)
{
daaa_tmp= dot_product( to( aa[l], atom[j].p), to( atom[i].p, atom[j].p ) ); /*=DA*A-AA*cosD-A-AA */
daaa_tmp /= sqrt(d); /* = cos D-A-AX */
if ( daaa_tmp > daaa_ang ) daaa_ang=daaa_tmp; /* select high values of cos D-A-AX ie low, better angles*/
if (debug) printf("Cosine of D-A-AX = %5.3f\n",daaa_tmp);
if (debug) {
printf("AX co-ods");
printf(TF,VXYZ( aa[l] ) );
printf("\n");
}
}
if (daaa_ang < cosMAX_DAAX)
{
if (debug)
printf("Rejected because DAAX too high.\n");
if (!nnbflg)
return(0);
}
}
#define nearer(vector) { tmp_d=length_squared( to( atom[j].p, vector ) ); if (ha2>tmp_d) { ha2=tmp_d; nearest=vector; near_h = h;} }
/* find the nearest possible H position on donor i */
ha2=100;
/* if (i==362) debug=1;
else debug=0;*/
if (debug && atom[i].hetflg) printf("H on %s %d ",atom[i].resnam, atom[i].aanum);
if (debug) printf("%d Hs positioned\n",atom[i].nh);
for(h=atom[i].h_ptr;h<atom[i].nh+atom[i].h_ptr;h++)
{
if (debug)
printf("Hydrogen %d - type %d\n",atom[i].h_ptr,h_atm[h].typ);
if (debug) printf("atom[i].nh %d, ].h_ptr %d, h %d\n",atom[i].nh,atom[i].h_ptr,h);
switch (h_atm[h].typ)
{
case 0:
if (debug) printf("Atom %d (%s%s %d) has H %d missing\n",i,atom[i].atmnam,atom[i].resnam, atom[i].aanum, h);
/* no H present, must be HETATM */
;/* used to be ha2=1, cannot decide why */
break;
case alternatives:
nearer( h_atm[h].a );
if (debug) printf("Checked alternative position: ha2 = %f\n",ha2);
case fixed:
nearer( h_atm[h].p );
if (debug) printf("Checked default position: ha2 = %f\n",ha2);
break;
case circle:
tmp_point= intersect(to(atom[i].p,h_atm[h].a),
h_atm[h].p, atom[i].p, atom[j].p );
tmp_point= onto_sphere(tmp_point, h_atm[h].a,
vector_length( to(h_atm[h].a, h_atm[h].p) ));
nearer(tmp_point);
tmp_point= vector_plus( tmp_point,
float_times_vect(2,to(tmp_point, h_atm[h].a)));
nearer(tmp_point);
break;
default:
printf("\nBUG: Unforseen htyp for atom %s in find_hb.\n", atomid(i,buf1));
printf("Please mail [email protected]\n");
}/* end of switch*/
}/* end of h loop */
if (ha2<100) /* ie if any Hydrogens have been found and
their positions taken. Or, to put it
another way, if it anything other than a hetatm
which is flagged in .nh as having hydrogens but
has no positons in h_atm[].typ. */
{
hd=vector_length( to(nearest, atom[i].p));
ha=vector_length( to(nearest, atom[j].p));
if (hd<0.9 || hd > 2.0)
{
printf("WARNING: %5.2fA between %s and %d (H).\n", hd, atomid(i,buf1),near_h-atom[i].h_ptr+1);
if (debug) printf("atom[i].nh %d, ].h_ptr %d, h %d\n",atom[i].nh,atom[i].h_ptr,h);
}
if (debug) printf("hd=%f, ha=%f\n",hd,ha);
if (!nnbflg)
{
if (ha>MAX_HA)
return(0);
if (debug)
printf("HA length OK\n");
if (dot_product( to(nearest, atom[i].p),
to(nearest, atom[j].p) ) >= hd*ha*cosMIN_DHA)
return(0);
}
haaa_ang=100.0; /* reset it . . . . */
if (!aromatic_flg)
{
for(l=0;l<MAXCON;l++)
{
if (icon[j][l]>-1)
{
float haaa_tmp,aaa;
aa[l]=atom[icon[j][l] ].p;
haaa_tmp= dot_product(
to(atom[j].p, aa[l] ), to( atom[j].p, nearest ) );
aaa= vector_length( to(aa[l],atom[j].p) );
haaa_tmp/= aaa *ha;
if (haaa_tmp<haaa_ang) haaa_ang=haaa_tmp; /* select lowest */
if (aaa<0.8 || aaa > 6.0)
printf("WARNING: %5.2fA between %s and %s ((H..)A-AA).\n", aaa,atomid(j,buf1),atomid(icon[j][l],buf2));
}
}
if ((haaa_ang > cosMIN_HAAA && haaa_ang<100.0) && !nnbflg)
return(0);
else
if (haaa_ang==100.0)
haaa_ang= -99.9;
/*NB -99 could not have been used as a default whilst checking
because we are trying to find a lowest possible value */
if (debug)
printf("Angle OK\n");
}
else
{
float haaa_tmp;
haaa_ang= -99; /*dealing with hAax, prefer small, ie big cosines*/
for(l=0;l<2;l++)
{
haaa_tmp=dot_product( to(atom[j].p,aa[l]),to(atom[j ].p,nearest));
haaa_tmp/= ha;
if (debug) printf("Cosine of H-A-AX = %5.3f\n",haaa_tmp);
if (haaa_tmp > haaa_ang) {
if (debug) printf("%5.3f > %5.3f.\n",haaa_tmp,haaa_ang);
haaa_ang=haaa_tmp; /* select the low ie more meaningful */
if (debug) printf("Lowest yet.\n");
}
}
if (haaa_ang < cosMAX_HAAX /* && haaa_ang<100.0 */ )
{
if (debug) {
printf("Rejected because of wide HAAX angle.\n");
printf("Cos haaa_ang = %5.3f, cosMAX_HAAX = %5.3f.\n", haaa_ang, cosMAX_HAAX);
}
if (!nnbflg)
return(0);
}
}
}/* end of 'if any Hs actually found' clause */
else
if (d>SQR(MAX_HA+1.0))
if (!nnbflg)
return(0); /* if the hydrogens are unfixed, knock
anything more than 1.0 Ang - the
normal DH distance - back. */
sprintf_hb(o_str,i,j,nearest,d,ha,daaa_ang,haaa_ang);
return(1);
}
