static PyObject *center(PyObject *self, PyObject *args) {
int molid, frame;
PyObject *selected;
PyObject *weightobj = NULL;
AtomSel *sel;
// parse arguments
if (!PyArg_ParseTuple(args, (char *)"iiO!|O",
&molid, &frame, &PyTuple_Type, &selected, &weightobj))
return NULL;
VMDApp *app = get_vmdapp();
// get selection
if (!(sel = sel_from_py(molid, frame, selected, app)))
return NULL;
// get weight
float *weight = parse_weight(sel, weightobj);
if (!weight) return NULL;
float cen[3];
// compute center
int ret_val = measure_center(sel, sel->coordinates(app->moleculeList),
weight, cen);
delete [] weight;
delete sel;
if (ret_val < 0) {
PyErr_SetString(PyExc_ValueError, measure_error(ret_val));
return NULL;
}
// return as (x, y, z)
PyObject *cenobj = PyTuple_New(3);
for (int i=0; i<3; i++)
PyTuple_SET_ITEM(cenobj, i, PyFloat_FromDouble(cen[i]));
return cenobj;
}
static PyObject *py_rmsd(PyObject *self, PyObject *args) {
int mol1, frame1, mol2, frame2;
PyObject *selected1, *selected2, *weightobj = NULL;
if (!PyArg_ParseTuple(args, (char *)"iiO!iiO!O:atomselection.rmsd",
&mol1, &frame1, &PyTuple_Type, &selected1,
&mol2, &frame2, &PyTuple_Type, &selected2,
&weightobj))
return NULL;
VMDApp *app = get_vmdapp();
AtomSel *sel1 = sel_from_py(mol1, frame1, selected1, app);
AtomSel *sel2 = sel_from_py(mol2, frame2, selected2, app);
if (!sel1 || !sel2) {
delete sel1;
delete sel2;
return NULL;
}
const Timestep *ts1 =app->moleculeList->mol_from_id(mol1)->get_frame(frame1);
const Timestep *ts2 =app->moleculeList->mol_from_id(mol2)->get_frame(frame2);
if (!ts1 || !ts2) {
PyErr_SetString(PyExc_ValueError, "No coordinates in selection");
delete sel1;
delete sel2;
return NULL;
}
float *weight = parse_weight(sel1, weightobj);
if (!weight) {
delete sel1;
delete sel2;
return NULL;
}
float rmsd;
int rc = measure_rmsd(sel1, sel2, sel1->selected, ts1->pos, ts2->pos,
weight, &rmsd);
delete sel1;
delete sel2;
delete [] weight;
if (rc < 0) {
PyErr_SetString(PyExc_ValueError, measure_error(rc));
return NULL;
}
return PyFloat_FromDouble(rmsd);
}
static PyObject *py_align(PyObject *self, PyObject *args) {
int selmol, selframe, refmol, refframe, movemol, moveframe;
PyObject *selobj, *refobj, *moveobj, *weightobj = NULL;
if (!PyArg_ParseTuple(args, (char *)"iiO!iiO!iiO!O:atomselection.align",
&selmol, &selframe, &PyTuple_Type, &selobj,
&refmol, &refframe, &PyTuple_Type, &refobj,
&movemol, &moveframe, &PyTuple_Type, &moveobj,
&weightobj))
return NULL;
// check if movemol is -1. If so, use the sel molecule and timestep instead
if (movemol == -1) {
movemol = selmol;
moveobj = NULL;
}
VMDApp *app = get_vmdapp();
AtomSel *sel=NULL, *ref=NULL, *move=NULL;
if (!(sel = sel_from_py(selmol, selframe, selobj, app)) ||
!(ref = sel_from_py(refmol, refframe, refobj, app)) ||
!(move = sel_from_py(movemol, moveframe, moveobj, app))) {
delete sel;
delete ref;
delete move;
return NULL;
}
const float *selts, *refts;
float *movets;
if (!(selts = sel->coordinates(app->moleculeList)) ||
!(refts = ref->coordinates(app->moleculeList)) ||
!(movets = move->coordinates(app->moleculeList))) {
delete sel;
delete ref;
delete move;
PyErr_SetString(PyExc_ValueError, "No coordinates in selection");
return NULL;
}
float *weight = parse_weight(sel, weightobj);
if (!weight) {
delete sel;
delete ref;
delete move;
return NULL;
}
// Find the matrix that aligns sel with ref. Apply the transformation to
// the atoms in move.
// XXX need to add support for the "order" parameter as in Tcl.
Matrix4 mat;
int rc = measure_fit(sel, ref, selts, refts, weight, NULL, &mat);
delete [] weight;
delete sel;
delete ref;
if (rc < 0) {
delete move;
PyErr_SetString(PyExc_ValueError, (char *)measure_error(rc));
return NULL;
}
for (int i=0; i<move->num_atoms; i++) {
if (move->on[i]) {
float *pos = movets+3*i;
mat.multpoint3d(pos, pos);
}
}
Molecule *mol = app->moleculeList->mol_from_id(move->molid());
mol->force_recalc(DrawMolItem::MOL_REGEN);
delete move;
Py_INCREF(Py_None);
return Py_None;
}
void ProcessWayTags(TagList *tags,int64_t way_id,int mode)
{
Way way={0};
int oneway=0,area=0;
int roundabout=0,lanes=0;
char *name=NULL,*ref=NULL,*refname=NULL;
way_t id;
int i;
/* Convert id */
id=(way_t)way_id;
logassert((int64_t)id==way_id,"Way ID too large (change way_t to 64-bits?)"); /* check way id can be stored in way_t data type. */
/* Delete */
if(mode==MODE_DELETE || mode==MODE_MODIFY)
{
way.type=WAY_DELETED;
AppendWayList(ways,id,&way,way_nodes,way_nnodes,"");
}
if(mode==MODE_DELETE)
return;
/* Sanity check */
if(way_nnodes==0)
{
logerror("Way %"Pway_t" has no nodes.\n",logerror_way(id));
return;
}
if(way_nnodes==1)
{
logerror_node(way_nodes[0]); /* Extra logerror information since way isn't stored */
logerror("Way %"Pway_t" has only one node.\n",logerror_way(id));
return;
}
/* Parse the tags - just look for highway */
for(i=0;i<tags->ntags;i++)
{
char *k=tags->k[i];
char *v=tags->v[i];
if(!strcmp(k,"highway"))
{
way.type=HighwayType(v);
if(way.type==Highway_None)
logerror("Way %"Pway_t" has an unrecognised highway type '%s' (after tagging rules); ignoring it.\n",logerror_way(id),v);
break;
}
}
/* Don't continue if this is not a highway (bypass error logging) */
if(way.type==Highway_None)
return;
/* Parse the tags - look for the others */
for(i=0;i<tags->ntags;i++)
{
int recognised=0;
char *k=tags->k[i];
char *v=tags->v[i];
switch(*k)
{
case 'a':
if(!strcmp(k,"area"))
{
if(ISTRUE(v))
area=1;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'area' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
break;
case 'b':
if(!strcmp(k,"bicycle"))
{
if(ISTRUE(v))
way.allow|=Transports_Bicycle;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'bicycle' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
if(!strcmp(k,"bicycleroute"))
{
if(ISTRUE(v))
way.props|=Properties_BicycleRoute;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'bicycleroute' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
if(!strcmp(k,"bridge"))
{
if(ISTRUE(v))
way.props|=Properties_Bridge;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'bridge' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
break;
case 'c':
if(!strcmp(k,"cycleway"))
{
if(!strcmp(v,"opposite_lane"))
way.props|=Properties_DoubleSens;
recognised=1; break;
}
break;
case 'f':
if(!strcmp(k,"foot"))
{
if(ISTRUE(v))
way.allow|=Transports_Foot;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'foot' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
if(!strcmp(k,"footroute"))
{
if(ISTRUE(v))
way.props|=Properties_FootRoute;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'footroute' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
break;
case 'g':
if(!strcmp(k,"goods"))
{
if(ISTRUE(v))
way.allow|=Transports_Goods;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'goods' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
break;
case 'h':
if(!strcmp(k,"highway"))
{recognised=1; break;}
if(!strcmp(k,"horse"))
{
if(ISTRUE(v))
way.allow|=Transports_Horse;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'horse' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
if(!strcmp(k,"hgv"))
{
if(ISTRUE(v))
way.allow|=Transports_HGV;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'hgv' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
break;
case 'i':
if(!strcmp(k,"incline"))
{
/* logerror("Way %"Pway_t" has an 'incline' = '%s' \n",logerror_way(id),v); */
way.incline=pourcent_to_incline(parse_incline(id,k,v));
recognised=1; break;
}
break;
case 'l':
if(!strcmp(k,"lanes"))
{
int en=0;
float lanesf;
if(sscanf(v,"%f%n",&lanesf,&en)==1 && en && !v[en])
lanes=(int)lanesf;
else
logerror("Way %"Pway_t" has an unrecognised tag 'lanes' = '%s' (after tagging rules); ignoring it.\n",logerror_way(id),v);
recognised=1; break;
}
break;
case 'm':
if(!strncmp(k,"max",3))
{
if(!strcmp(k+3,"speed"))
{
way.speed=kph_to_speed(parse_speed(id,k,v));
recognised=1; break;
}
if(!strcmp(k+3,"weight"))
{
way.weight=tonnes_to_weight(parse_weight(id,k,v));
recognised=1; break;
}
if(!strcmp(k+3,"height"))
{
way.height=metres_to_height(parse_length(id,k,v));
recognised=1; break;
}
if(!strcmp(k+3,"width"))
{
way.width=metres_to_height(parse_length(id,k,v));
recognised=1; break;
}
if(!strcmp(k+3,"length"))
{
way.length=metres_to_height(parse_length(id,k,v));
recognised=1; break;
}
}
if(!strcmp(k,"moped"))
{
if(ISTRUE(v))
way.allow|=Transports_Moped;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'moped' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
if(!strcmp(k,"motorcycle"))
{
if(ISTRUE(v))
way.allow|=Transports_Motorcycle;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'motorcycle' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
if(!strcmp(k,"motorcar"))
{
if(ISTRUE(v))
way.allow|=Transports_Motorcar;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'motorcar' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
if(!strcmp(k,"multilane"))
{
if(ISTRUE(v))
way.props|=Properties_Multilane;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'multilane' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
break;
case 'n':
if(!strcmp(k,"name"))
{
name=v;
recognised=1; break;
}
break;
case 'o':
if(!strcmp(k,"oneway"))
{
if(ISTRUE(v))
oneway=1;
else if(!strcmp(v,"-1"))
oneway=-1;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'oneway' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
break;
case 'p':
if(!strcmp(k,"paved"))
{
if(ISTRUE(v))
way.props|=Properties_Paved;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'paved' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
if(!strcmp(k,"psv"))
{
if(ISTRUE(v))
way.allow|=Transports_PSV;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'psv' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
break;
case 'r':
if(!strcmp(k,"ref"))
{
ref=v;
recognised=1; break;
}
if(!strcmp(k,"roundabout"))
{
if(ISTRUE(v))
roundabout=1;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'roundabout' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
break;
case 't':
if(!strcmp(k,"tunnel"))
{
if(ISTRUE(v))
way.props|=Properties_Tunnel;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'tunnel' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
break;
case 'w':
if(!strcmp(k,"wheelchair"))
{
if(ISTRUE(v))
way.allow|=Transports_Wheelchair;
else if(!ISFALSE(v))
logerror("Way %"Pway_t" has an unrecognised tag 'wheelchair' = '%s' (after tagging rules); using 'no'.\n",logerror_way(id),v);
recognised=1; break;
}
break;
default:
break;
}
if(!recognised)
logerror("Way %"Pway_t" has an unrecognised tag '%s' = '%s' (after tagging rules); ignoring it.\n",logerror_way(id),k,v);
}
/* Create the way */
if(area && oneway)
{
logerror("Way %"Pway_t" is an area and oneway; ignoring area tagging.\n",logerror_way(id));
area=0;
}
if(!way.allow)
return;
if(oneway)
{
way.type|=Highway_OneWay;
if(oneway==-1)
for(i=0;i<way_nnodes/2;i++)
{
node_t temp;
temp=way_nodes[i];
way_nodes[i]=way_nodes[way_nnodes-i-1];
way_nodes[way_nnodes-i-1]=temp;
}
}
if(roundabout)
way.type|=Highway_Roundabout;
if(area)
{
way.type|=Highway_Area;
if(way_nodes[0]!=way_nodes[way_nnodes-1])
logerror("Way %"Pway_t" is an area but not closed.\n",logerror_way(id));
}
if(lanes)
{
if(oneway || (lanes/2)>1)
way.props|=Properties_Multilane;
if(oneway && lanes==1)
way.props&=~Properties_Multilane;
}
if(ref && name)
{
refname=(char*)malloc(strlen(ref)+strlen(name)+4);
sprintf(refname,"%s (%s)",name,ref);
}
else if(ref && !name)
refname=ref;
else if(!ref && name)
refname=name;
else /* if(!ref && !name) */
refname="";
AppendWayList(ways,id,&way,way_nodes,way_nnodes,refname);
if(ref && name)
free(refname);
}