IMP::display::Geometries RestraintGeometry::get_components() const {
IMP_CHECK_OBJECT(r_);
base::Pointer<kernel::Restraint> rd = r_->create_current_decomposition();
if (!rd) return IMP::display::Geometries();
kernel::RestraintSet *rs = dynamic_cast<kernel::RestraintSet *>(rd.get());
rd->set_was_used(true);
IMP::display::Geometries ret;
if (!rs) {
kernel::ParticlesTemp ps = IMP::get_input_particles(r_->get_inputs());
r_->set_was_used(true);
for (unsigned int i = 0; i < ps.size(); ++i) {
if (!get_has_coordinates(ps[i])) continue;
for (unsigned int j = 0; j < i; ++j) {
if (!get_has_coordinates(ps[j])) continue;
ret.push_back(new SegmentGeometry(algebra::Segment3D(
get_coordinates(ps[i]), get_coordinates(ps[j]))));
}
}
} else {
for (unsigned int i = 0; i < rs->get_number_of_restraints(); ++i) {
kernel::Restraint *rc = rs->get_restraint(i);
rc->set_was_used(true);
ret.push_back(new RestraintGeometry(rc, m_));
}
}
return ret;
}
void Shmenu_window::draw_hexagon()
{
get_coordinates();
shapes.push_back(new Regular_polygon(Point(x,y),6,100));
attach(shapes[shapes.size()-1]);
redraw();
}
void Shmenu_window::draw_circle()
{
get_coordinates();
shapes.push_back(new Circle(Point(x,y),100));
attach(shapes[shapes.size()-1]);
redraw();
}
static PyObject *mmeval_elecenergy(PyObject *self, PyObject *args)
{
// Get the AmberSystem
PyObject *mol;
if(!PyArg_ParseTuple(args, "O", &mol))
return NULL;
int charge_size = 0;
float *charge = get_block_as_float_array(mol, "CHARGE", &charge_size);
if(charge == NULL)
{
fprintf(stderr, "Error: Couldn't find CHARGE block.\n");
return NULL;
}
// Extract coordinate arrays
float *x, *y, *z;
int num_atoms = get_coordinates(mol, &x, &y, &z);
float Eelec = calc_elec_energy(charge, x, y, z, num_atoms);
free(x);
free(y);
free(z);
return Py_BuildValue("f", Eelec);
}
IMPCORE_BEGIN_NAMESPACE
void XYZ::show(std::ostream &out) const
{
out << "(" <<algebra::commas_io(get_coordinates())<<")";
}
static void get_volume_onoff_coordinates(int &x1, int &y1, int &x2, int &y2){
get_coordinates(x1,y1,x2,y2);
x1 = x2-button_width-1;
//y1 = 0;
y2 = y1 + button_width-3;
}
static void
create_marker (EogImage *image,
EogMapPlugin *plugin)
{
gdouble lon, lat;
if (!image)
return;
if (!eog_image_has_data (image, EOG_IMAGE_DATA_EXIF) &&
!eog_image_load (image, EOG_IMAGE_DATA_EXIF, NULL, NULL))
return;
if (get_coordinates (image, &lat, &lon)) {
ChamplainLabel *marker;
marker = CHAMPLAIN_LABEL (champlain_label_new ());
champlain_label_set_draw_background (CHAMPLAIN_LABEL (marker), FALSE);
update_marker_image (marker, GTK_ICON_SIZE_MENU);
g_object_set_data_full (G_OBJECT (image), "marker", marker, (GDestroyNotify) clutter_actor_destroy);
g_object_set_data (G_OBJECT (marker), "image", image);
champlain_location_set_location (CHAMPLAIN_LOCATION (marker),
lat,
lon);
champlain_marker_layer_add_marker (plugin->layer, CHAMPLAIN_MARKER (marker));
g_signal_connect (marker,
"button-release-event",
G_CALLBACK (change_image),
plugin);
}
}
void Mvshape_window::next()
{
if (shapes.size()==0) error("No shapes available");
get_coordinates();
int dx = x - shapes[shapes.size()-1].point(0).x;
int dy = y - shapes[shapes.size()-1].point(0).y;
shapes[shapes.size()-1].move(dx,dy);
redraw();
}
std::string Breakpoint::to_string() {
std::stringstream ss;
if (positions.support.size() > 1) {
ss << "\t\tTREE: ";
ss << TRANS_type(this->get_SVtype());
ss << " ";
ss << get_coordinates().start.min_pos;
ss << ":";
ss << get_coordinates().stop.max_pos;
ss << " ";
ss << this->length;
ss << " ";
ss << positions.support.size();
ss << " ";
ss << get_strand(2);
}
return ss.str();
}
DeltaDistributionFunction::DeltaDistributionFunction(
const Particles& particles, double max_distance, double bin_size)
: Distribution<algebra::Vector3D>(bin_size) {
get_coordinates(particles, coordinates_);
get_form_factors(particles, get_default_form_factor_table(), form_factors_,
HEAVY_ATOMS);
// compute max distance if not given
max_distance_ = max_distance;
if (max_distance_ <= 0.0) max_distance_ = compute_max_distance(particles);
}
static void get_name_coordinates(int &x1, int &y1, int &x2, int &y2){
get_coordinates(x1,y1,x2,y2);
//get_slider2_coordinates(x1,y1,x2,y2);
x1 += 2;
x2 = x2-button_width-3;
y1 = y2-name_height;
// y1+=slider_height;
// y2+=name_height;
}
std::string Breakpoint::to_string(RefVector ref) {
std::stringstream ss;
ss << "(";
ss << get_chr(get_coordinates().start.min_pos, ref);
ss << ":";
ss << calc_pos(get_coordinates().start.min_pos, ref);
ss << "-";
ss << get_chr(get_coordinates().stop.max_pos, ref);
ss << ":";
ss << calc_pos(get_coordinates().stop.max_pos, ref);
ss << " ";
ss << positions.support.size();
ss << " ";
ss << this->sv_debug;
ss << " ";
ss << this->get_strand(2);
ss << "\n";
int num = 0;
for (std::map<std::string, read_str>::iterator i = positions.support.begin(); i != positions.support.end() && num < Parameter::Instance()->report_n_reads; i++) {
ss << "\t";
ss << (*i).first;
ss << " ";
ss << (*i).second.type;
if ((*i).second.strand.first) {
ss << "+";
} else {
ss << "-";
}
if ((*i).second.strand.second) {
ss << "+";
} else {
ss << "-";
}
num++;
ss << "\n";
}
ss << " ";
return ss.str();
}
void ResidueRotamer::set_coordinates(unsigned index,
IMP::atom::Residue &rd) const {
IMP_USAGE_CHECK(index < size_, "no rotamer at given index");
IMP_USAGE_CHECK(rd.get_residue_type() == residue_type_, "wrong residue type");
IMP::atom::Hierarchies mhs = IMP::atom::get_by_type(rd, IMP::atom::ATOM_TYPE);
for (size_t i = 0; i != mhs.size(); ++i) {
IMP::atom::Atom at = mhs[i].get_as_atom();
IMP::atom::AtomType at_t = at.get_atom_type();
if (get_atom_exists(at_t)) {
const IMP::algebra::Vector3D &coords = get_coordinates(index, at_t);
IMP::core::XYZ(at).set_coordinates(coords);
}
}
}
void HierarchyLoadXYZs::setup_particle(
RMF::NodeConstHandle n, Model *m, ParticleIndex p,
const ParticleIndexes &rigid_bodies) {
if (!ip_factory_.get_is(n)) return;
if (!core::XYZ::get_is_setup(m, p)) core::XYZ::setup_particle(m, p);
/* If there is a rigid body parent set up, add this particle as a child
(unless it's an old-style rigid body, in which case this has been
done already) */
if (!rigid_bodies.empty()
&& !(rigid_bodies.size()==1 && rigid_bodies.back() == p)
&& !n.get_has_value(rb_index_key_)) {
core::RigidBody rb(m, rigid_bodies.back());
/* For nested rigid bodies, this XYZ particle is *also* the rigid body.
So don't make ourselves our own child - add to the parent rigid body
instead. */
if (rigid_bodies.back() == p) {
IMP_INTERNAL_CHECK(rigid_bodies.size() >= 2,
"Nested rigid body " << m->get_particle_name(p)
<< " but could not find parent rigid body");
rb = core::RigidBody(m, rigid_bodies[rigid_bodies.size() - 2]);
}
rb.add_member(p);
if (reference_frame_factory_.get_is(n)
&& !reference_frame_factory_.get_is_static(n)) {
IMP_LOG_VERBOSE("Member particle " << m->get_particle_name(p)
<< " is not static and is also a rigid body"
<< std::endl);
rb.set_is_rigid_member(p, false);
} else if (!ip_factory_.get_is_static(n)) {
IMP_LOG_VERBOSE("Member particle " << m->get_particle_name(p)
<< " is not static" << std::endl);
rb.set_is_rigid_member(p, false);
} else {
IMP_LOG_VERBOSE("Member particle " << m->get_particle_name(p)
<< " is static" << std::endl);
rb.set_is_rigid_member(p, true);
core::RigidBodyMember(m, p)
.set_internal_coordinates(get_coordinates(n, ip_factory_));
}
}
link_particle(n, m, p, rigid_bodies);
}
/** \param[in] acc If true (not nullptr), partial first derivatives should be
calculated.
\return score associated with this restraint for the given state of
the model.
*/
double RadiusOfGyrationRestraint::unprotected_evaluate(
DerivativeAccumulator *acc) const
{
IMP_LOG_TERSE( "SAXS RadiusOfGyrationRestraint::evaluate score\n");
//get centroid
algebra::Vector3D centroid(0.0, 0.0, 0.0);
std::vector<algebra::Vector3D> coordinates(particles_.size());
get_coordinates(particles_, coordinates);
for (unsigned int i = 0; i < particles_.size(); i++) {
centroid += coordinates[i];
}
centroid /= particles_.size();
double radg = 0;
for (unsigned int i = 0; i < particles_.size(); i++) {
radg += get_squared_distance(coordinates[i], centroid);
}
radg /= particles_.size();
radg = sqrt(radg);
double score = (radg - exp_rg_)/exp_rg_; //TODO: improve
bool calc_deriv = acc? true: false;
if(!calc_deriv) return score;
IMP_LOG_TERSE( "SAXS RadiusOfGyrationRestraint::compute derivatives\n");
const FloatKeys keys = IMP::core::XYZ::get_xyz_keys();
double factor = 1.0/(particles_.size()*radg);
for (unsigned int i = 0; i < particles_.size(); i++) {
IMP::algebra::Vector3D derivative = (coordinates[i]-centroid)*factor;
for (int j = 0; j < 3; j++) {
particles_[i]->add_to_derivative(keys[j],derivative[j],*acc);
}
}
IMP_LOG_TERSE( "SAXS RadiusOfGyrationRestraint::done derivatives, score "
<< score << "\n");
return score;
}
BootloaderHandleMessageResponse handle_message(const void *message, void *response) {
switch(tfp_get_fid_from_message(message)) {
case FID_GET_COORDINATES:
return get_coordinates(message, response);
case FID_GET_STATUS:
return get_status(message, response);
case FID_GET_ALTITUDE:
return get_altitude(message, response);
case FID_GET_MOTION:
return get_motion(message, response);
case FID_GET_DATE_TIME:
return get_date_time(message, response);
case FID_RESTART:
return restart(message);
case FID_SET_COORDINATES_CALLBACK_PERIOD:
return set_coordinates_callback_period(message);
case FID_GET_COORDINATES_CALLBACK_PERIOD:
return get_coordinates_callback_period(message, response);
case FID_SET_STATUS_CALLBACK_PERIOD:
return set_status_callback_period(message);
case FID_GET_STATUS_CALLBACK_PERIOD:
return get_status_callback_period(message, response);
case FID_SET_ALTITUDE_CALLBACK_PERIOD:
return set_altitude_callback_period(message);
case FID_GET_ALTITUDE_CALLBACK_PERIOD:
return get_altitude_callback_period(message, response);
case FID_SET_MOTION_CALLBACK_PERIOD:
return set_motion_callback_period(message);
case FID_GET_MOTION_CALLBACK_PERIOD:
return get_motion_callback_period(message, response);
case FID_SET_DATE_TIME_CALLBACK_PERIOD:
return set_date_time_callback_period(message);
case FID_GET_DATE_TIME_CALLBACK_PERIOD:
return get_date_time_callback_period(message, response);
default:
return HANDLE_MESSAGE_RESPONSE_NOT_SUPPORTED;
}
}
/**
* Calculates the bond energy of an AmberSystem.
*/
static PyObject *mmeval_bondenergy(PyObject *self, PyObject *args)
{
// Get the AmberSystem
PyObject *mol;
if(!PyArg_ParseTuple(args, "O", &mol))
return NULL;
int bond_l0_size = 0, bond_k_size = 0;
float *bond_l0 = get_block_as_float_array(mol, "BOND_EQUIL_VALUE", &bond_l0_size);
float *bond_k = get_block_as_float_array(mol, "BOND_FORCE_CONSTANT", &bond_k_size);
if(bond_l0_size != bond_k_size)
{
fprintf(stderr, "Error: Size of BOND_EQUIL_VALUE and BOND_FORCE_CONSTANT blocks is not the same.\n");
return NULL;
}
// Extract coordinate arrays
float *x, *y, *z;
int num_atoms = get_coordinates(mol, &x, &y, &z);
int bond_list_size = 0;
int *bond_list = get_block_as_int_array(mol, "BONDS_INC_HYDROGEN", &bond_list_size);
float Ebond_h = calc_bond_energy(bond_list, bond_l0, bond_k, x, y, z, num_atoms,
bond_list_size, bond_l0_size);
free(bond_list);
bond_list = get_block_as_int_array(mol, "BONDS_WITHOUT_HYDROGEN", &bond_list_size);
float Ebond_nonh = calc_bond_energy(bond_list, bond_l0, bond_k, x, y, z, num_atoms,
bond_list_size, bond_l0_size);
free(bond_list);
free(x);
free(y);
free(z);
return Py_BuildValue("f", Ebond_h + Ebond_nonh);
}
static void get_effects_onoff_coordinates(int &x1, int &y1, int &x2, int &y2){
get_coordinates(x1,y1,x2,y2);
x1 = x2-button_width-1;
y1 = y2-button_width+2;
}
void process_commands() {
unsigned long codenum; //throw away variable
if (code_seen('N')) {
gcode_N = code_value_long();
if (gcode_N != gcode_LastN+1 && (strstr(cmdbuffer, "M110") == NULL) ) {
gcode_LastN=0;
pc.printf("ok");
//if(gcode_N != gcode_LastN+1 && !code_seen("M110") ) { //Hmm, compile size is different between using this vs the line above even though it should be the same thing. Keeping old method.
//pc.printf("Serial Error: Line Number is not Last Line Number+1, Last Line:");
//pc.printf("%d\n",gcode_LastN);
//FlushSerialRequestResend();
return;
}
if (code_seen('*')) {
int checksum = 0;
int count=0;
while (cmdbuffer[count] != '*') checksum = checksum^cmdbuffer[count++];
if ( (int)code_value() != checksum) {
//pc.printf("Error: checksum mismatch, Last Line:");
//pc.printf("%d\n",gcode_LastN);
//FlushSerialRequestResend();
return;
}
//if no errors, continue parsing
} else {
//pc.printf("Error: No Checksum with line number, Last Line:");
//pc.printf("%d\n",gcode_LastN);
//FlushSerialRequestResend();
return;
}
gcode_LastN = gcode_N;
//if no errors, continue parsing
} else { // if we don't receive 'N' but still see '*'
if (code_seen('*')) {
//pc.printf("Error: No Line Number with checksum, Last Line:");
//pc.printf("%d\n",gcode_LastN);
return;
}
}
//continues parsing only if we don't receive any 'N' or '*' or no errors if we do. :)
if (code_seen('G')) {
switch ((int)code_value()) {
case 0: // G0 -> G1
case 1: // G1
reset_timers();//avoid timer overflow after 30 seconds
get_coordinates(); // For X Y Z E F
x_steps_to_take = abs(destination_x - current_x)*x_steps_per_unit;
y_steps_to_take = abs(destination_y - current_y)*y_steps_per_unit;
z_steps_to_take = abs(destination_z - current_z)*z_steps_per_unit;
e_steps_to_take = abs(destination_e - current_e)*e_steps_per_unit;
//printf(" x_steps_to_take:%d\n", x_steps_to_take);
time_for_move = max(X_TIME_FOR_MOVE,Y_TIME_FOR_MOVE);
time_for_move = max(time_for_move,Z_TIME_FOR_MOVE);
time_for_move = max(time_for_move,E_TIME_FOR_MOVE);
if (x_steps_to_take) x_interval = time_for_move/x_steps_to_take;
if (y_steps_to_take) y_interval = time_for_move/y_steps_to_take;
if (z_steps_to_take) z_interval = time_for_move/z_steps_to_take;
if (e_steps_to_take) e_interval = time_for_move/e_steps_to_take;
x_steps_remaining = x_steps_to_take;
y_steps_remaining = y_steps_to_take;
z_steps_remaining = z_steps_to_take;
e_steps_remaining = e_steps_to_take;
if (DEBUGGING) {
pc.printf("destination_x: %f\n",destination_x);
pc.printf("current_x: %f\n",current_x);
pc.printf("x_steps_to_take: %d\n",x_steps_to_take);
pc.printf("X_TIME_FOR_MOVE: %f\n",X_TIME_FOR_MOVE);
pc.printf("x_interval: %f\n\n",x_interval);
pc.printf("destination_y: %f\n",destination_y);
pc.printf("current_y: %f\n",current_y);
pc.printf("y_steps_to_take: %d\n",y_steps_to_take);
pc.printf("Y_TIME_FOR_MOVE: %f\n",Y_TIME_FOR_MOVE);
pc.printf("y_interval: %f\n\n",y_interval);
pc.printf("destination_z: %f\n",destination_z);
pc.printf("current_z: %f\n",current_z);
pc.printf("z_steps_to_take: %d\n",z_steps_to_take);
pc.printf("Z_TIME_FOR_MOVE: %f\n",Z_TIME_FOR_MOVE);
pc.printf("z_interval: %f\n\n",z_interval);
pc.printf("destination_e: %f\n",destination_e);
pc.printf("current_e: %f\n",current_e);
pc.printf("e_steps_to_take: %d\n",e_steps_to_take);
pc.printf("E_TIME_FOR_MOVE: %f\n",E_TIME_FOR_MOVE);
pc.printf("e_interval: %f\n\n",e_interval);
}
linear_move(); // make the move
ClearToSend();
return;
case 4: // G4 dwell
codenum = 0;
if (code_seen('P')) codenum = code_value(); // milliseconds to wait
if (code_seen('S')) codenum = code_value()*1000; // seconds to wait
previous_millis_heater = millis(); // keep track of when we started waiting
while ((millis() - previous_millis_heater) < codenum ) manage_heater(); //manage heater until time is up
break;
case 90: // G90
relative_mode = false;
break;
case 91: // G91
relative_mode = true;
break;
case 92: // G92
if (code_seen('X')) current_x = code_value();
if (code_seen('Y')) current_y = code_value();
if (code_seen('Z')) current_z = code_value();
if (code_seen('E')) current_e = code_value();
break;
case 93: // G93
pc.printf("previous_micros:%d\n", previous_micros);
pc.printf("previous_micros_x:%d\n", previous_micros_x);
pc.printf("previous_micros_y:%d\n", previous_micros_y);
pc.printf("previous_micros_z:%d\n", previous_micros_z);
break;
}
}
if (code_seen('M')) {
switch ( (int)code_value() ) {
case 104: // M104 - set hot-end temp
if (code_seen('S'))
{
target_raw = temp2analog(code_value());
//pc.printf("target_raw: %d\n ", target_raw);
}
break;
case 140: // M140 - set heated-printbed temp
if (code_seen('S'))
{
target_raw1 = temp2analog(code_value());
//pc.printf("target_raw1: %d\n ", target_raw);
}
break;
case 105: // M105
pc.printf("ok T:");
if (TEMP_0_PIN != NC) {
pc.printf("%f\n", analog2temp( (p_temp0.read_u16()) ));
} else {
pc.printf("0.0\n");
}
if (!code_seen('N')) return; // If M105 is sent from generated gcode, then it needs a response.
break;
case 109: // M109 - Wait for heater to reach target.
if (code_seen('S')) target_raw = temp2analog(code_value());
previous_millis_heater = millis();
while (current_raw < target_raw) {
if ( (millis()-previous_millis_heater) > 1000 ) { //Print Temp Reading every 1 second while heating up.
pc.printf("ok T:");
if (TEMP_0_PIN != NC) {
pc.printf("%f\n", analog2temp(p_temp0.read_u16()));
} else {
pc.printf("0.0\n");
}
previous_millis_heater = millis();
}
manage_heater();
}
break;
case 106: //M106 Fan On
p_fan = 1;
break;
case 107: //M107 Fan Off
p_fan = 0;
break;
case 80: // M81 - ATX Power On
//if(PS_ON_PIN > -1) pinMode(PS_ON_PIN,OUTPUT); //GND
break;
case 81: // M81 - ATX Power Off
//if(PS_ON_PIN > -1) pinMode(PS_ON_PIN,INPUT); //Floating
break;
case 82:
relative_mode_e = false;
break;
case 83:
relative_mode_e = true;
break;
case 84:
disable_x();
disable_y();
disable_z();
disable_e();
break;
case 85: // M85
code_seen('S');
max_inactive_time = code_value()*1000;
break;
case 86: // M86 If Endstop is Not Activated then Abort Print
if (code_seen('X')) {
if (X_MIN_PIN != NC) {
if ( p_X_min == ENDSTOPS_INVERTING ) {
kill(3);
}
}
}
if (code_seen('Y')) {
if (Y_MIN_PIN != NC) {
if ( p_Y_min == ENDSTOPS_INVERTING ) {
kill(4);
}
}
}
break;
case 92: // M92
if (code_seen('X')) x_steps_per_unit = code_value();
if (code_seen('Y')) y_steps_per_unit = code_value();
if (code_seen('Z')) z_steps_per_unit = code_value();
if (code_seen('E')) e_steps_per_unit = code_value();
break;
}
}
ClearToSend();
}
/**
\brief Execute the command stored in com.
*/
void process_command(GCode *com)
{
unsigned long codenum; //throw away variable
#ifdef INCLUDE_DEBUG_COMMUNICATION
if(DEBUG_COMMUNICATION) {
if(GCODE_HAS_G(com) || (GCODE_HAS_M(com) && com->M!=111)) {
gcode_command_finished(); // free command cache
previous_millis_cmd = millis();
return;
}
}
#endif
if(GCODE_HAS_G(com))
{
switch(com->G)
{
case 0: // G0 -> G1
case 1: // G1
if(get_coordinates(com)) // For X Y Z E F
queue_move(ALWAYS_CHECK_ENDSTOPS);
break;
case 4: // G4 dwell
codenum = 0;
if(GCODE_HAS_P(com)) codenum = com->P; // milliseconds to wait
if(GCODE_HAS_S(com)) codenum = (long)com->S * 1000; // seconds to wait
codenum += millis(); // keep track of when we started waiting
while(millis() < codenum ) {
gcode_read_serial();
manage_temperatures(false);
}
break;
case 20: // Units to inches
unit_inches = 1;
break;
case 21: // Units to mm
unit_inches = 0;
break;
case 28: {//G28 Home all Axis one at a time
wait_until_end_of_move();
float saved_feedrate = printer_state.feedrate;
for(byte i=0; i < 4; i++) {
printer_state.destinationSteps[i] = printer_state.currentPositionSteps[i];
}
byte home_all_axis = !(GCODE_HAS_X(com) || GCODE_HAS_Y(com) || GCODE_HAS_Z(com));
if(home_all_axis || GCODE_HAS_X(com)) {
if ((X_MIN_PIN > -1 && X_HOME_DIR==-1) || (X_MAX_PIN > -1 && X_HOME_DIR==1)) {
printer_state.destinationSteps[0] = 1.5 * printer_state.xMaxSteps * X_HOME_DIR;
printer_state.currentPositionSteps[0] = -printer_state.destinationSteps[0];
printer_state.feedrate = homing_feedrate[0];
queue_move(true);
wait_until_end_of_move();
printer_state.currentPositionSteps[0] = 0;
printer_state.destinationSteps[0] = axis_steps_per_unit[0]*-5 * X_HOME_DIR;
queue_move(true);
wait_until_end_of_move();
printer_state.destinationSteps[0] = axis_steps_per_unit[0]*10 * X_HOME_DIR;
queue_move(true);
wait_until_end_of_move();
printer_state.currentPositionSteps[0] = (X_HOME_DIR == -1) ? 0 : printer_state.xMaxSteps;
printer_state.destinationSteps[0] = printer_state.currentPositionSteps[0];
}
}
if(home_all_axis || GCODE_HAS_Y(com)) {
if ((Y_MIN_PIN > -1 && Y_HOME_DIR==-1) || (Y_MAX_PIN > -1 && Y_HOME_DIR==1)) {
printer_state.currentPositionSteps[1] = 0;
printer_state.destinationSteps[1] = 1.5 * printer_state.yMaxSteps * Y_HOME_DIR;
printer_state.currentPositionSteps[1] = -printer_state.destinationSteps[1];
printer_state.feedrate = homing_feedrate[1];
queue_move(true);
wait_until_end_of_move();
printer_state.currentPositionSteps[1] = 0;
printer_state.destinationSteps[1] = axis_steps_per_unit[1]*-5 * Y_HOME_DIR;
queue_move(true);
wait_until_end_of_move();
printer_state.destinationSteps[1] = axis_steps_per_unit[1]*10 * Y_HOME_DIR;
queue_move(true);
wait_until_end_of_move();
printer_state.currentPositionSteps[1] = (Y_HOME_DIR == -1) ? 0 : printer_state.yMaxSteps;
printer_state.destinationSteps[1] = printer_state.currentPositionSteps[1];
}
}
if(home_all_axis || GCODE_HAS_Z(com)) {
if ((Z_MIN_PIN > -1 && Z_HOME_DIR==-1) || (Z_MAX_PIN > -1 && Z_HOME_DIR==1)) {
printer_state.currentPositionSteps[2] = 0;
printer_state.destinationSteps[2] = 1.5 * printer_state.zMaxSteps * Z_HOME_DIR;
printer_state.currentPositionSteps[2] = -printer_state.destinationSteps[2];
printer_state.feedrate = homing_feedrate[2];
queue_move(true);
wait_until_end_of_move();
printer_state.currentPositionSteps[2] = 0;
printer_state.destinationSteps[2] = axis_steps_per_unit[2]*-2 * Z_HOME_DIR;
queue_move(true);
wait_until_end_of_move();
printer_state.destinationSteps[2] = axis_steps_per_unit[2]*10 * Z_HOME_DIR;
queue_move(true);
wait_until_end_of_move();
printer_state.currentPositionSteps[2] = (Z_HOME_DIR == -1) ? 0 : printer_state.zMaxSteps;
printer_state.destinationSteps[2] = printer_state.currentPositionSteps[2];
}
}
printer_state.feedrate = saved_feedrate;
}
break;
case 90: // G90
relative_mode = false;
break;
case 91: // G91
relative_mode = true;
break;
case 92: // G92
if(GCODE_HAS_X(com)) printer_state.currentPositionSteps[0] = com->X*axis_steps_per_unit[0]*(unit_inches?25.4:1.0)-printer_state.offsetX;
if(GCODE_HAS_Y(com)) printer_state.currentPositionSteps[1] = com->Y*axis_steps_per_unit[1]*(unit_inches?25.4:1.0)-printer_state.offsetY;
if(GCODE_HAS_Z(com)) printer_state.currentPositionSteps[2] = com->Z*axis_steps_per_unit[2]*(unit_inches?25.4:1.0);
if(GCODE_HAS_E(com)) {
printer_state.currentPositionSteps[3] = com->E*axis_steps_per_unit[3]*(unit_inches?25.4:1.0);
}
break;
}
previous_millis_cmd = millis();
}
else if(GCODE_HAS_M(com)) { // Process M Code
switch( com->M ) {
#ifdef SDSUPPORT
case 20: // M20 - list SD card
out.println_P(PSTR("Begin file list"));
root.ls();
out.println_P(PSTR("End file list"));
break;
case 21: // M21 - init SD card
sdmode = false;
initsd();
break;
case 22: //M22 - release SD card
sdmode = false;
sdactive = false;
break;
case 23: //M23 - Select file
if(sdactive) {
sdmode = false;
file.close();
if (file.open(&root, com->text, O_READ)) {
out.print_P(PSTR("File opened:"));
out.print(com->text);
out.print_P(PSTR(" Size:"));
out.println(file.fileSize());
sdpos = 0;
filesize = file.fileSize();
out.println_P(PSTR("File selected"));
}
else {
out.println_P(PSTR("file.open failed"));
}
}
break;
case 24: //M24 - Start SD print
if(sdactive) {
sdmode = true;
}
break;
case 25: //M25 - Pause SD print
if(sdmode) {
sdmode = false;
}
break;
case 26: //M26 - Set SD index
if(sdactive && GCODE_HAS_S(com)) {
sdpos = com->S;
file.seekSet(sdpos);
}
break;
case 27: //M27 - Get SD status
if(sdactive) {
out.print_P(PSTR("SD printing byte "));
out.print(sdpos);
out.print("/");
out.println(filesize);
} else {
out.println_P(PSTR("Not SD printing"));
}
break;
case 28: //M28 - Start SD write
if(sdactive) {
char* npos = 0;
file.close();
sdmode = false;
if (!file.open(&root,com->text, O_CREAT | O_APPEND | O_WRITE | O_TRUNC)) {
out.print_P(PSTR("open failed, File: "));
out.print(com->text);
out.print_P(PSTR("."));
} else {
savetosd = true;
out.print_P(PSTR("Writing to file: "));
out.println(com->text);
}
}
break;
case 29: //M29 - Stop SD write
//processed in write to file routine above
//savetosd = false;
break;
case 30: // M30 filename - Delete file
if(sdactive) {
sdmode = false;
file.close();
if(SdFile::remove(&root, com->text)) {
out.println_P(PSTR("File deleted"));
} else {
out.println_P(PSTR("Deletion failed"));
}
}
break;
#endif
case 104: // M104
if(DEBUG_DRYRUN) break;
wait_until_end_of_move();
if (GCODE_HAS_S(com)) extruder_set_temperature(com->S);
break;
case 140: // M140 set bed temp
if(DEBUG_DRYRUN) break;
if (GCODE_HAS_S(com)) heated_bed_set_temperature(com->S);
break;
case 105: // M105 get temperature. Always returns the current temperature, doesn't wait until move stopped
print_temperatures();
break;
case 109: // M109 - Wait for extruder heater to reach target.
{
if(DEBUG_DRYRUN) break;
wait_until_end_of_move();
if (GCODE_HAS_S(com)) extruder_set_temperature(com->S);
if(current_extruder->currentTemperatureC >= current_extruder->targetTemperature) break;
codenum = millis();
long waituntil = 0;
while(waituntil==0 || (waituntil!=0 && waituntil>millis())) {
if( (millis() - codenum) > 1000 ) { //Print Temp Reading every 1 second while heating up.
print_temperatures();
codenum = millis();
}
manage_temperatures(false);
gcode_read_serial();
if(waituntil==0 && current_extruder->currentTemperatureC >= current_extruder->targetTemperatureC)
waituntil = millis()+1000*(long)current_extruder->watchPeriod; // now wait for temp. to stabalize
}
}
break;
case 190: // M190 - Wait bed for heater to reach target.
if(DEBUG_DRYRUN) break;
wait_until_end_of_move();
#if HEATED_BED_SENSOR_TYPE!=0
if (GCODE_HAS_S(com)) heated_bed_set_temperature(com->S);
codenum = millis();
while(current_bed_raw < target_bed_raw) {
if( (millis()-codenum) > 1000 ) { //Print Temp Reading every 1 second while heating up.
print_temperatures();
codenum = millis();
}
manage_temperatures(false);
}
#endif
break;
case 106: //M106 Fan On
wait_until_end_of_move();
if (GCODE_HAS_S(com)) {
digitalWrite(FAN_PIN, HIGH);
analogWrite(FAN_PIN, constrain(com->S,0,255) );
}
else
digitalWrite(FAN_PIN, HIGH);
break;
case 107: //M107 Fan Off
wait_until_end_of_move();
analogWrite(FAN_PIN, 0);
digitalWrite(FAN_PIN, LOW);
break;
case 80: // M81 - ATX Power On
wait_until_end_of_move();
if(PS_ON_PIN > -1) pinMode(PS_ON_PIN,OUTPUT); //GND
break;
case 81: // M81 - ATX Power Off
wait_until_end_of_move();
if(PS_ON_PIN > -1) pinMode(PS_ON_PIN,INPUT); //Floating
break;
case 82:
relative_mode_e = false;
break;
case 83:
relative_mode_e = true;
break;
case 84:
if(GCODE_HAS_S(com)) {
stepper_inactive_time = com->S * 1000;
}
else {
wait_until_end_of_move();
kill(true);
}
break;
case 85: // M85
if(GCODE_HAS_S(com))
max_inactive_time = (long)com->S * 1000;
else
max_inactive_time = 0;
break;
case 92: // M92
if(GCODE_HAS_X(com)) axis_steps_per_unit[0] = com->X;
if(GCODE_HAS_Y(com)) axis_steps_per_unit[1] = com->Y;
if(GCODE_HAS_Z(com)) axis_steps_per_unit[2] = com->Z;
if(GCODE_HAS_E(com)) current_extruder->stepsPerMM = com->E;
update_ramps_parameter();
break;
case 111:
if(GCODE_HAS_S(com)) debug_level = com->S;
if(DEBUG_DRYRUN) { // simulate movements without printing
extruder_set_temperature(0);
#if HEATED_BED_TYPE!=0
target_bed_raw = 0;
#endif
}
break;
case 115: // M115
out.println_P(PSTR("FIRMWARE_NAME:Repetier FIRMWARE_URL:https://github.com/repetier/Repetier-Firmware/ PROTOCOL_VERSION:1.0 MACHINE_TYPE:Mendel EXTRUDER_COUNT:1 REPETIER_PROTOCOL:1"));
break;
case 114: // M114
out.print_float_P(PSTR("X:"),printer_state.currentPositionSteps[0]*inv_axis_steps_per_unit[0]*(unit_inches?0.03937:1));
out.print_float_P(PSTR(" Y:"),printer_state.currentPositionSteps[1]*inv_axis_steps_per_unit[1]*(unit_inches?0.03937:1));
out.print_float_P(PSTR(" Z:"),printer_state.currentPositionSteps[2]*inv_axis_steps_per_unit[2]*(unit_inches?0.03937:1));
out.println_float_P(PSTR(" E:"),printer_state.currentPositionSteps[3]*inv_axis_steps_per_unit[3]*(unit_inches?0.03937:1));
break;
case 119: // M119
wait_until_end_of_move();
#if (X_MIN_PIN > -1)
out.print_P(PSTR("x_min:"));
out.print_P((digitalRead(X_MIN_PIN)^ENDSTOPS_INVERTING)?PSTR("H "):PSTR("L "));
#endif
#if (X_MAX_PIN > -1)
out.print_P(PSTR("x_max:"));
out.print_P((digitalRead(X_MAX_PIN)^ENDSTOPS_INVERTING)?PSTR("H "):PSTR("L "));
#endif
#if (Y_MIN_PIN > -1)
out.print_P(PSTR("y_min:"));
out.print_P((digitalRead(Y_MIN_PIN)^ENDSTOPS_INVERTING)?PSTR("H "):PSTR("L "));
#endif
#if (Y_MAX_PIN > -1)
out.print_P(PSTR("y_max:"));
out.print_P((digitalRead(Y_MAX_PIN)^ENDSTOPS_INVERTING)?PSTR("H "):PSTR("L "));
#endif
#if (Z_MIN_PIN > -1)
out.print_P(PSTR("z_min:"));
out.print_P((digitalRead(Z_MIN_PIN)^ENDSTOPS_INVERTING)?PSTR("H "):PSTR("L "));
#endif
#if (Z_MAX_PIN > -1)
out.print_P(PSTR("z_max:"));
out.print_P((digitalRead(Z_MAX_PIN)^ENDSTOPS_INVERTING)?PSTR("H "):PSTR("L "));
#endif
out.println();
break;
#ifdef RAMP_ACCELERATION
case 201: // M201
if(GCODE_HAS_X(com)) axis_steps_per_sqr_second[0] = com->X * axis_steps_per_unit[0];
if(GCODE_HAS_Y(com)) axis_steps_per_sqr_second[1] = com->Y * axis_steps_per_unit[1];
if(GCODE_HAS_Z(com)) axis_steps_per_sqr_second[2] = com->Z * axis_steps_per_unit[2];
if(GCODE_HAS_E(com)) axis_steps_per_sqr_second[3] = com->E * axis_steps_per_unit[3];
break;
case 202: // M202
if(GCODE_HAS_X(com)) axis_travel_steps_per_sqr_second[0] = com->X * axis_steps_per_unit[0];
if(GCODE_HAS_Y(com)) axis_travel_steps_per_sqr_second[1] = com->Y * axis_steps_per_unit[1];
if(GCODE_HAS_Z(com)) axis_travel_steps_per_sqr_second[2] = com->Z * axis_steps_per_unit[2];
if(GCODE_HAS_E(com)) axis_travel_steps_per_sqr_second[3] = com->E * axis_steps_per_unit[3];
break;
#endif
case 203: // M203 Temperature monitor
if(GCODE_HAS_S(com)) manage_monitor = com->S;
if(manage_monitor==100) manage_monitor=NUM_EXTRUDER; // Set 100 to heated bed
break;
case 205: // M205 Show EEPROM settings
epr_output_settings();
break;
case 206: // M206 T[type] P[pos] [Sint(long] [Xfloat] Set eeprom value
#if EEPROM_MODE!=0
epr_update(com);
#else
out.println_P(PSTR("Error: No EEPROM support compiled."));
#endif
break;
case 222: //M222 F_CPU / S
if(GCODE_HAS_S(com))
out.println_long_P(PSTR("F_CPU/x="),CPUDivU2(com->S));
break;
case 223:
if(GCODE_HAS_S(com)) {
extruder_enable();
printer_state.extruderStepsNeeded+=(int)com->S;
out.println_int_P(PSTR("Added to:"),printer_state.extruderStepsNeeded);
}
break;
#ifdef USE_ADVANCE
case 232:
out.print_int_P(PSTR("Max advance="),maxadv);
if(maxadv>0)
out.println_float_P(PSTR(", speed="),maxadvspeed);
else
out.println();
maxadv=0;
maxadvspeed=0;
break;
#endif
#if USE_OPS==1
case 231: // M231 S<OPS_MODE> X<Min_Distance> Y<Retract> Z<Backslash> F<ReatrctMove>
if(GCODE_HAS_S(com) && com->S>=0 && com->S<3)
printer_state.opsMode = com->S;
if(GCODE_HAS_X(com) && com->X>=0)
printer_state.opsMinDistance = com->X;
if(GCODE_HAS_Y(com) && com->Y>=0)
printer_state.opsRetractDistance = com->Y;
if(GCODE_HAS_Z(com) && com->Z>=-printer_state.opsRetractDistance)
printer_state.opsRetractBackslash = com->Z;
if(GCODE_HAS_F(com) && com->F>=0 && com->F<=100)
printer_state.opsMoveAfter = com->F;
extruder_select(current_extruder->id);
if(printer_state.opsMode==0) {
out.println_P(PSTR("OPS disabled"));
} else {
if(printer_state.opsMode==1)
out.print_P(PSTR("OPS classic mode:"));
else
out.print_P(PSTR("OPS fast mode:"));
out.print_float_P(PSTR("min distance = "),printer_state.opsMinDistance);
out.print_float_P(PSTR(", retract = "),printer_state.opsRetractDistance);
out.print_float_P(PSTR(", backslash = "),printer_state.opsRetractDistance);
if(printer_state.opsMode==2)
out.print_float_P(PSTR(", move after = "),printer_state.opsMoveAfter);
out.println();
}
#ifdef DEBUG_OPS
out.println_int_P(PSTR("Timer diff"),printer_state.timer0Interval);
out.println_int_P(PSTR("Ret. steps:"),printer_state.opsRetractSteps);
out.println_int_P(PSTR("PushBack Steps:"),printer_state.opsPushbackSteps);
out.println_int_P(PSTR("Move after steps:"),printer_state.opsMoveAfterSteps);
#endif
break;
#endif
}
} else if(GCODE_HAS_T(com)) { // Process T code
wait_until_end_of_move();
extruder_select(com->T);
} else {
if(DEBUG_ERRORS) {
out.print_P(PSTR("Unknown command:"));
gcode_print_command(com);
out.println();
}
}
#ifdef ECHO_ON_EXECUTE
if(DEBUG_ECHO) {
out.print_P(PSTR("Echo:"));
gcode_print_command(com);
out.println();
}
#endif
gcode_command_finished(); // free command cache
}
void BS_Camera::update_camera()
{
matrix_position = glm::vec3(get_coordinates('x'), get_coordinates('y'), get_coordinates('z'));
LookAtMatrix = glm::lookAt(matrix_position, matrix_position + matrix_direction, matrix_up);
}
void update_type_two_coordinate_and_velocity(int tree, int i, int centralgal)
{
int j, p;
float tmppos;
double Scale_V, dv;
p=i;
//printf("updating type 2 treenr =%d\n",tree);
#ifdef GUO10
if(HaloGal[i].Type == 2) /* Update positions of type 2's */
#else
if(Gal[i].Type == 2) /* Update positions of type 2's */
#endif
{
#ifdef GUO10
int snapnum = HaloGal[i].SnapNum;
#else
int snapnum = Gal[i].SnapNum;
#endif
Nids = CountIDs_snaptree[snapnum * Ntrees + tree];
OffsetIDs = OffsetIDs_snaptree[snapnum * Ntrees + tree];
size_t header_offset = 4 * sizeof(int) + 2 * TotSnaps * sizeof(int) + 2 * TotSnaps * Ntrees * sizeof(int) + 2
* sizeof(int) * NtotHalos;
IdList = (long long *) (TreeAuxData + header_offset);
PosList = (float *) (TreeAuxData + header_offset + TotIds * sizeof(long long));
VelList = (float *) (TreeAuxData + header_offset + TotIds * sizeof(long long) + TotIds * 3 * sizeof(float));
IdList += OffsetIDs;
PosList += 3 * OffsetIDs;
VelList += 3 * OffsetIDs;
#ifdef GUO10
get_coordinates(HaloGal[i].Pos, HaloGal[i].Vel, HaloGal[i].MostBoundID, tree, HaloGal[i].HaloNr,
HaloGal[i].SnapNum);
#else
get_coordinates(Gal[i].Pos, Gal[i].Vel, Gal[i].MostBoundID, tree, Gal[i].HaloNr,
Gal[i].SnapNum);
#endif
//#ifdef SCALE_COSMOLOGY
#ifdef GUO10
for(j = 0; j < 3; j++)
HaloGal[i].Pos[j] *= ScalePos;
#else
for(j = 0; j < 3; j++)
Gal[i].Pos[j] *= ScalePos;
#endif
//#endif
#ifdef GUO10
for(j = 0; j < 3; j++)
{
tmppos = wrap(-HaloGal[p].MergCentralPos[j] + HaloGal[p].Pos[j],BoxSize);
tmppos *= sqrt(HaloGal[p].MergTime/HaloGal[p].OriMergTime);
HaloGal[p].Pos[j]=HaloGal[p].MergCentralPos[j] + tmppos;
if(HaloGal[p].Pos[j] < 0)
HaloGal[p].Pos[j] = BoxSize + HaloGal[p].Pos[j];
if(HaloGal[p].Pos[j] > BoxSize)
HaloGal[p].Pos[j] = HaloGal[p].Pos[j] - BoxSize;
}
#else
for(j = 0; j < 3; j++)
{
tmppos = wrap(-Gal[p].MergCentralPos[j] + Gal[p].Pos[j],BoxSize);
#ifndef HT09_DISRUPTION
tmppos *= (Gal[p].MergTime/Gal[p].OriMergTime);
#else
tmppos *= (Gal[p].MergRadius/Gal[p].OriMergRadius);
#endif
Gal[p].Pos[j]=Gal[p].MergCentralPos[j] + tmppos;
if(Gal[p].Pos[j] < 0)
Gal[p].Pos[j] = BoxSize + Gal[p].Pos[j];
if(Gal[p].Pos[j] > BoxSize)
Gal[p].Pos[j] = Gal[p].Pos[j] - BoxSize;
}
#endif
#ifdef GUO10
//#ifdef SCALE_COSMOLOGY
//add by Qi. 06/04/2012 to account for the scale of velocity field
Scale_V = scale_v_cen(Halo[HaloGal[centralgal].HaloNr].SnapNum);
for (j = 0; j < 3 ; j++)
{
dv = HaloGal[p].Vel[j] - HaloGal[centralgal].Vel[j]/Scale_V;
dv *=sqrt(ScaleMass/ScalePos) * sqrt(AA_OriginalCosm[Halo[HaloGal[centralgal].HaloNr].SnapNum]/AA[Halo[HaloGal[centralgal].HaloNr].SnapNum]);
HaloGal[p].Vel[j] = HaloGal[centralgal].Vel[j] + dv;
}
//#endif
#else
Scale_V = scale_v_cen(Halo[Gal[centralgal].HaloNr].SnapNum);
for (j = 0; j < 3 ; j++)
{
dv = Gal[p].Vel[j] - Gal[centralgal].Vel[j]/Scale_V;
dv *=sqrt(ScaleMass/ScalePos) * sqrt(AA_OriginalCosm[Halo[Gal[centralgal].HaloNr].SnapNum]/AA[Halo[Gal[centralgal].HaloNr].SnapNum]);
Gal[p].Vel[j] = Gal[centralgal].Vel[j] + dv;
}
#endif
}
}
int main(int argc, char* argv[])
{
if(argc == 1)
{
printf("Usage: calculate_rmsd [options] alpha.xyz beta.xyz\n");
exit(0);
}
if(argc < 3)
{
printf ("Not enough arguments\n");
exit(EXIT_FAILURE);
}
bool output = false;
int a = 0;
int b = 0;
for(int i=1; i < argc; i++)
{
if(strcmp(argv[i], "-o") == 0 || strcmp(argv[i], "--output") == 0)
{
output = true;
continue;
}
if(a==0)
{
a = i;
}
else
{
b = i;
}
}
const std::string p_file = argv[a];
const std::string q_file = argv[b];
unsigned int n_atoms {0};
std::valarray<std::string> p_atoms;
std::valarray<std::string> q_atoms;
matrix p_coord;
matrix q_coord;
std::valarray<double> p_center;
std::valarray<double> q_center;
std::tie(p_atoms, p_coord, n_atoms) = get_coordinates(p_file);
std::tie(q_atoms, q_coord, n_atoms) = get_coordinates(q_file);
// find the center of the structures
p_center = kabsch::centroid(p_coord);
q_center = kabsch::centroid(q_coord);
// Recenter molecules in origin
for(unsigned int i = 0; i < n_atoms; i++) {
for(unsigned int d = 0; d < 3; d++) {
p_coord[3*i + d] -= p_center[d];
q_coord[3*i + d] -= q_center[d];
}
}
if(output)
{
matrix p_rotated = kabsch::kabsch_rotate(p_coord, q_coord, n_atoms);
// Center coordinates P on Q
for(unsigned int i = 0; i < n_atoms; i++) {
for(unsigned int d = 0; d < 3; d++) {
p_rotated[3*i + d] += q_center[d];
}
}
// print the structure in XYZ format
std::cout << n_atoms << std::endl << std::endl;
print_coordinates(p_rotated, p_atoms, n_atoms);
return 0;
}
// rotate and calculate rmsd
double krmsd = kabsch::kabsch_rmsd(p_coord, q_coord, n_atoms);
printf( "%.10lf \n", krmsd);
} // main
static PyObject *mmeval_vdwenergy(PyObject *self, PyObject *args)
{
// Get the AmberSystem
PyObject *mol;
if(!PyArg_ParseTuple(args, "O", &mol))
return NULL;
// Extract atom type and L-J parameters from the prmtop
int header_size = 0;
int *header = get_block_as_int_array(mol, "POINTERS", &header_size);
if(header == NULL)
return NULL;
int nb_parm_index_size = 0;
int *nb_parm_index = get_block_as_int_array(mol, "NONBONDED_PARM_INDEX", &nb_parm_index_size);
if(nb_parm_index == NULL)
{
free(header);
return NULL;
}
int atom_type_index_size = 0;
int *atom_type_index = get_block_as_int_array(mol, "ATOM_TYPE_INDEX", &atom_type_index_size);
if(atom_type_index == NULL)
{
free(nb_parm_index);
free(header);
return NULL;
}
int lj_a_size = 0;
float *lj_a = get_block_as_float_array(mol, "LENNARD_JONES_ACOEF", &lj_a_size);
if(lj_a == NULL)
{
free(atom_type_index);
free(nb_parm_index);
free(header);
return NULL;
}
int lj_b_size = 0;
float *lj_b = get_block_as_float_array(mol, "LENNARD_JONES_BCOEF", &lj_b_size);
if(lj_b == NULL)
{
free(lj_a);
free(atom_type_index);
free(nb_parm_index);
free(header);
return NULL;
}
// Extract coordinate arrays
float *x, *y, *z;
int num_atoms = get_coordinates(mol, &x, &y, &z);
int num_atom_types = header[1];
float Evdw = 0.0f;
Evdw = calc_vdw_energy(
atom_type_index,
nb_parm_index,
lj_a,
lj_b,
x,
y,
z,
num_atoms,
num_atom_types);
free(lj_b);
free(lj_a);
free(x);
free(y);
free(z);
free(atom_type_index);
free(nb_parm_index);
free(header);
return Py_BuildValue("f", Evdw);
}
bool OSystem_PalmBase::pollEvent(Event &event) {
::EventType ev;
Boolean handled;
UInt32 keyCurrentState;
Coord x, y;
battery_handler();
timer_handler();
sound_handler();
for(;;) {
#if defined(COMPILE_OS5) && defined(PALMOS_ARM)
SysEventGet(&ev, evtNoWait);
#else
EvtGetEvent(&ev, evtNoWait);
#endif
// check for hardkey repeat for mouse emulation
keyCurrentState = KeyCurrentState();
// check_hard_keys();
if (!(keyCurrentState & _keyMouseMask)) {
_lastKeyRepeat = 0;
} else {
if (getMillis() >= (_keyMouseRepeat + _keyMouseDelay)) {
_keyMouseRepeat = getMillis();
if (gVars->arrowKeys) {
if (keyCurrentState & _keyMouse.bitUp)
event.kbd.keycode = 273;
else if (keyCurrentState & _keyMouse.bitDown)
event.kbd.keycode = 274;
else if (keyCurrentState & _keyMouse.bitLeft)
event.kbd.keycode = 276;
else if (keyCurrentState & _keyMouse.bitRight)
event.kbd.keycode = 275;
else if (keyCurrentState & _keyMouse.bitButLeft)
event.kbd.keycode = chrLineFeed;
event.type = EVENT_KEYDOWN;
event.kbd.ascii = event.kbd.keycode;
event.kbd.flags = 0;
} else {
Int8 sx = 0;
Int8 sy = 0;
if (keyCurrentState & _keyMouse.bitUp)
sy = -1;
else if (keyCurrentState & _keyMouse.bitDown)
sy = +1;
if (keyCurrentState & _keyMouse.bitLeft)
sx = -1;
else if (keyCurrentState & _keyMouse.bitRight)
sx = +1;
if (sx || sy) {
simulate_mouse(event, sx, sy, &x, &y);
event.type = EVENT_MOUSEMOVE;
_lastKey = kKeyMouseMove;
} else {
x = _mouseCurState.x;
y = _mouseCurState.y;
if (keyCurrentState & _keyMouse.bitButLeft) {
event.type = EVENT_LBUTTONDOWN;
_lastKey = kKeyMouseLButton;
} else if (_lastKey == kKeyMouseLButton) {
event.type = EVENT_LBUTTONUP;
_lastKey = kKeyNone;
}
}
event.mouse.x = x;
event.mouse.y = y;
warpMouse(x, y);
// updateCD();
}
return true;
}
}
if (ev.eType == keyDownEvent) {
switch (ev.data.keyDown.chr) {
// ESC key
case vchrLaunch:
_lastKey = kKeyNone;
event.type = EVENT_KEYDOWN;
event.kbd.keycode = 27;
event.kbd.ascii = 27;
event.kbd.flags = 0;
return true;
// F5 = menu
case vchrMenu:
_lastKey = kKeyNone;
event.type = EVENT_KEYDOWN;
event.kbd.keycode = 319;
event.kbd.ascii = 319;
event.kbd.flags = 0;
return true;
// if hotsync pressed, etc...
case vchrHardCradle:
case vchrHardCradle2:
case vchrLowBattery:
case vchrFind:
// case vchrBrightness: // volume control on Zodiac, let other backends disable it
case vchrContrast:
// do nothing
_lastKey = kKeyNone;
return true;
}
}
if (check_event(event, &ev))
return true;
_lastKey = kKeyNone;
// prevent crash when alarm is raised
handled = ((ev.eType == keyDownEvent) &&
(ev.data.keyDown.modifiers & commandKeyMask) &&
((ev.data.keyDown.chr == vchrAttnStateChanged) ||
(ev.data.keyDown.chr == vchrAttnUnsnooze)));
// graffiti strokes, auto-off, etc...
if (!handled)
if (SysHandleEvent(&ev))
continue;
switch(ev.eType) {
case penMoveEvent:
get_coordinates(&ev, x, y);
if (y > _screenHeight || y < 0 || x > _screenWidth || x < 0)
return false;
if (_lastEvent != penMoveEvent && (abs(y - event.mouse.y) <= 2 || abs(x - event.mouse.x) <= 2)) // move only if
return false;
_lastEvent = penMoveEvent;
event.type = EVENT_MOUSEMOVE;
event.mouse.x = x;
event.mouse.y = y;
warpMouse(x, y);
return true;
case penDownEvent:
get_coordinates(&ev, x, y);
// indy fight mode
if (_useNumPad && !_overlayVisible) {
char num = '1';
num += 9 -
(3 - (3 * x / _screenWidth )) -
(3 * (3 * y / _screenHeight));
event.type = EVENT_KEYDOWN;
event.kbd.keycode = num;
event.kbd.ascii = num;
event.kbd.flags = 0;
_lastEvent = keyDownEvent;
return true;
}
_lastEvent = penDownEvent;
if (y > _screenHeight || y < 0 || x > _screenWidth || x < 0)
return false;
event.type = ((gVars->stylusClick || _overlayVisible) ? EVENT_LBUTTONDOWN : EVENT_MOUSEMOVE);
event.mouse.x = x;
event.mouse.y = y;
warpMouse(x, y);
return true;
case penUpEvent:
get_coordinates(&ev, x, y);
event.type = ((gVars->stylusClick || _overlayVisible) ? EVENT_LBUTTONUP : EVENT_MOUSEMOVE);
if (y > _screenHeight || y < 0 || x > _screenWidth || x < 0)
return false;
event.mouse.x = x;
event.mouse.y = y;
warpMouse(x, y);
return true;
case keyDownEvent:
if (ev.data.keyDown.chr == vchrCommand &&
(ev.data.keyDown.modifiers & commandKeyMask)) {
_lastKeyModifier++;
_lastKeyModifier %= kModifierCount;
if (_lastKeyModifier)
draw_osd((kDrawKeyState + _lastKeyModifier - 1), 2, _screenDest.h + 2, true);
else
draw_osd(kDrawKeyState, 2, _screenDest.h + 2, false);
return false;
}
char mask = 0;
UInt16 key = ev.data.keyDown.chr;
if (_lastKeyModifier == kModifierNone) {
// for keyboard mode
if (ev.data.keyDown.modifiers & shiftKeyMask) mask |= KBD_SHIFT;
if (ev.data.keyDown.modifiers & controlKeyMask) mask |= KBD_CTRL;
if (ev.data.keyDown.modifiers & optionKeyMask) mask |= KBD_ALT;
if (ev.data.keyDown.modifiers & commandKeyMask) mask |= KBD_CTRL|KBD_ALT;
} else {
// for grafiti mode
if (_lastKeyModifier == kModifierCommand) mask = KBD_CTRL|KBD_ALT;
if (_lastKeyModifier == kModifierAlt) mask = KBD_ALT;
if (_lastKeyModifier == kModifierCtrl) mask = KBD_CTRL;
}
if (_lastKeyModifier)
draw_osd(kDrawKeyState, 2, _screenDest.h + 2, false);
_lastKeyModifier = kModifierNone;
// F1 -> F10 key
if (key >= '0' && key <= '9' && mask == (KBD_CTRL|KBD_ALT)) {
key = (key == '0') ? 324 : (315 + key - '1');
mask = 0;
// exit
} else if ((key == 'z' && mask == KBD_CTRL) || (mask == KBD_ALT && key == 'x')) {
event.type = EVENT_QUIT;
return true;
// num pad (indy fight mode)
} else if (key == 'n' && mask == (KBD_CTRL|KBD_ALT) && !_overlayVisible) {
_useNumPad = !_useNumPad;
draw_osd(kDrawFight, _screenDest.w - 34, _screenDest.h + 2, _useNumPad, 1);
displayMessageOnOSD(_useNumPad ? "Fight mode on." : "Fight mode off.");
return false;
}
// other keys
event.type = EVENT_KEYDOWN;
event.kbd.keycode = key;
event.kbd.ascii = key;
event.kbd.flags = mask;
return true;
default:
return false;
};
}
}
IMP_FOREACH(Pair pp, local_) {
IMP_LOG_VERBOSE("Loading local coordinates for "
<< m->get_particle_name(pp.second) << std::endl);
algebra::Vector3D rf(get_coordinates(fh.get_node(pp.first), ip_factory_));
core::RigidBodyMember(m, pp.second).set_internal_coordinates(rf);
}
void cigma::VtkReader::
get_coordinates(const char *loc, double **coordinates, int *nno, int *nsd)
{
get_coordinates(coordinates, nno, nsd);
}
int main(int argc, char **argv)
{
struct GModule *module;
struct
{
struct Option *text;
struct Option *size;
struct Option *fgcolor;
struct Option *bgcolor;
struct Option *line;
struct Option *at;
struct Option *rotation;
struct Option *align;
struct Option *linespacing;
struct Option *font;
struct Option *path;
struct Option *charset;
struct Option *input;
} opt;
struct
{
struct Flag *p;
struct Flag *g;
struct Flag *b;
struct Flag *r;
struct Flag *s;
} flag;
/* options and flags */
char *text;
double size;
double x, y;
int line;
double rotation;
char align[3];
double linespacing;
char bold;
/* window info */
struct rectinfo win;
/* command file */
FILE *cmd_fp;
char buf[512];
int first_text;
int linefeed;
int set_l;
double orig_x, orig_y;
double prev_x, prev_y;
double set_x, set_y;
double east, north;
int do_background, fg_color, bg_color;
/* initialize the GIS calls */
G_gisinit(argv[0]);
module = G_define_module();
G_add_keyword(_("display"));
G_add_keyword(_("cartography"));
module->description =
_("Draws text in the active display frame on the graphics monitor using the current font.");
opt.text = G_define_option();
opt.text->key = "text";
opt.text->type = TYPE_STRING;
opt.text->required = NO;
opt.text->description = _("Text to display");
opt.text->guisection = _("Input");
opt.input = G_define_standard_option(G_OPT_F_INPUT);
opt.input->required = NO;
opt.input->description = _("Input file");
opt.input->guisection = _("Input");
opt.fgcolor = G_define_option();
opt.fgcolor->key = "color";
opt.fgcolor->type = TYPE_STRING;
opt.fgcolor->answer = DEFAULT_COLOR;
opt.fgcolor->required = NO;
opt.fgcolor->description =
_("Text color, either a standard GRASS color or R:G:B triplet");
opt.fgcolor->gisprompt = "old_color,color,color";
opt.fgcolor->guisection = _("Text");
opt.bgcolor = G_define_option();
opt.bgcolor->key = "bgcolor";
opt.bgcolor->type = TYPE_STRING;
opt.bgcolor->required = NO;
opt.bgcolor->description =
_("Text background color, either a standard GRASS color or R:G:B triplet");
opt.bgcolor->gisprompt = "old_color,color,color";
opt.bgcolor->guisection = _("Text");
opt.rotation = G_define_option();
opt.rotation->key = "rotation";
opt.rotation->type = TYPE_DOUBLE;
opt.rotation->required = NO;
opt.rotation->answer = "0";
opt.rotation->description =
_("Rotation angle in degrees (counter-clockwise)");
opt.rotation->guisection = _("Text");
opt.linespacing = G_define_option();
opt.linespacing->key = "linespacing";
opt.linespacing->type = TYPE_DOUBLE;
opt.linespacing->required = NO;
opt.linespacing->answer = "1.25";
opt.linespacing->description = _("Line spacing");
opt.linespacing->guisection = _("Text");
opt.at = G_define_option();
opt.at->key = "at";
opt.at->key_desc = "x,y";
opt.at->type = TYPE_DOUBLE;
opt.at->required = NO;
opt.at->description =
_("Screen position at which text will begin to be drawn (percentage, [0,0] is lower left)");
opt.at->guisection = _("Position");
opt.line = G_define_option();
opt.line->key = "line";
opt.line->required = NO;
opt.line->type = TYPE_INTEGER;
opt.line->options = "1-1000";
opt.line->description =
_("The screen line number on which text will begin to be drawn");
opt.line->guisection = _("Position");
opt.align = G_define_option();
opt.align->key = "align";
opt.align->type = TYPE_STRING;
opt.align->required = NO;
opt.align->answer = "ll";
opt.align->options = "ll,lc,lr,cl,cc,cr,ul,uc,ur";
opt.align->description = _("Text alignment");
opt.align->guisection = _("Position");
opt.font = G_define_option();
opt.font->key = "font";
opt.font->type = TYPE_STRING;
opt.font->required = NO;
opt.font->description = _("Font name");
opt.font->guisection = _("Font settings");
opt.size = G_define_option();
opt.size->key = "size";
opt.size->type = TYPE_DOUBLE;
opt.size->required = NO;
opt.size->answer = "5";
opt.size->options = "0-100";
opt.size->description =
_("Height of letters in percentage of available frame height");
opt.size->guisection = _("Font settings");
opt.path = G_define_standard_option(G_OPT_F_INPUT);
opt.path->key = "path";
opt.path->required = NO;
opt.path->description = _("Path to font file");
opt.path->gisprompt = "old,font,file";
opt.path->guisection = _("Font settings");
opt.charset = G_define_option();
opt.charset->key = "charset";
opt.charset->type = TYPE_STRING;
opt.charset->required = NO;
opt.charset->description =
_("Text encoding (only applicable to TrueType fonts)");
opt.charset->guisection = _("Font settings");
flag.p = G_define_flag();
flag.p->key = 'p';
flag.p->description = _("Screen position in pixels ([0,0] is top left)");
flag.p->guisection = _("Position");
flag.g = G_define_flag();
flag.g->key = 'g';
flag.g->description = _("Screen position in geographic coordinates");
flag.g->guisection = _("Position");
flag.b = G_define_flag();
flag.b->key = 'b';
flag.b->description = _("Use bold text");
flag.b->guisection = _("Text");
flag.r = G_define_flag();
flag.r->key = 'r';
flag.r->description = _("Use radians instead of degrees for rotation");
flag.r->guisection = _("Text");
flag.s = G_define_flag();
flag.s->key = 's';
flag.s->description = _("Font size is height in pixels");
flag.s->guisection = _("Font settings");
/* check command line */
if (G_parser(argc, argv))
exit(1);
/* parse and check options and flags */
if ((opt.line->answer && opt.at->answer) ||
(flag.p->answer && flag.g->answer))
G_fatal_error(_("Please choose only one placement method"));
text = opt.text->answer;
line = (opt.line->answer ? atoi(opt.line->answer) : 1);
/* calculate rotation angle in radian */
rotation = atof(opt.rotation->answer);
if (!flag.r->answer)
rotation *= M_PI / 180.0;
rotation = fmod(rotation, 2.0 * M_PI);
if (rotation < 0.0)
rotation += 2.0 * M_PI;
strncpy(align, opt.align->answer, 2);
linespacing = atof(opt.linespacing->answer);
bold = flag.b->answer;
D_open_driver();
if (opt.font->answer)
D_font(opt.font->answer);
else if (opt.path->answer)
D_font(opt.path->answer);
if (opt.charset->answer)
D_encoding(opt.charset->answer);
D_setup_unity(0);
/* figure out where to put text */
D_get_src(&win.t, &win.b, &win.l, &win.r);
if (flag.s->answer)
size = atof(opt.size->answer);
else
#ifdef BACKWARD_COMPATIBILITY
size = atof(opt.size->answer) / 100.0 * (win.b - win.t) / linespacing;
#else
size = atof(opt.size->answer) / 100.0 * (win.b - win.t);
#endif
fg_color = D_parse_color(opt.fgcolor->answer, TRUE);
if (opt.bgcolor->answer) {
do_background = 1;
bg_color = D_parse_color(opt.bgcolor->answer, TRUE);
if (bg_color == 0) /* ie color="none" */
do_background = 0;
} else
do_background = 0;
set_color(opt.fgcolor->answer);
orig_x = orig_y = 0;
if (opt.at->answer) {
if (get_coordinates(&x, &y, &east, &north,
win, opt.at->answers,
flag.p->answer, flag.g->answer))
G_fatal_error(_("Invalid coordinates"));
orig_x = x;
orig_y = y;
}
else {
x = win.l + (size * linespacing + 0.5) - size; /* d.text: +5 */
y = win.t + line * (size * linespacing + 0.5);
}
prev_x = x;
prev_y = y;
D_text_size(size, size);
D_text_rotation(rotation * 180.0 / M_PI);
if (text) {
double x2, y2;
x2 = x;
y2 = y;
if (text[0])
draw_text(text, &x2, &y2, size, align, rotation, bold, do_background, fg_color, bg_color);
/* reset */
D_text_size(5, 5);
D_text_rotation(0.0);
D_save_command(G_recreate_command());
D_close_driver();
exit(EXIT_SUCCESS);
}
if (!opt.input->answer || strcmp(opt.input->answer, "-") == 0)
cmd_fp = stdin;
else {
cmd_fp = fopen(opt.input->answer, "r");
if (!cmd_fp)
G_fatal_error(_("Unable to open input file <%s>"), opt.input->answer);
}
if (isatty(fileno(cmd_fp)))
fprintf(stderr,
_("\nPlease enter text instructions. Enter EOF (ctrl-d) on last line to quit\n"));
set_x = set_y = set_l = 0;
first_text = 1;
linefeed = 1;
/* do the plotting */
while (fgets(buf, sizeof(buf), cmd_fp)) {
int buf_len;
char *buf_ptr, *ptr;
buf_len = strlen(buf) - 1;
for (; buf[buf_len] == '\r' || buf[buf_len] == '\n'; buf_len--) ;
buf[buf_len + 1] = 0;
if (buf[0] == '.' && buf[1] != '.') {
int i;
double d;
G_squeeze(buf); /* added 6/91 DBS @ CWU */
for (buf_ptr = buf + 2; *buf_ptr == ' '; buf_ptr++) ;
buf_len = strlen(buf_ptr);
switch (buf[1] & 0x7f) {
case 'F':
/* font */
if ((ptr = strchr(buf_ptr, ':')))
*ptr = 0;
D_font(buf_ptr);
if (ptr)
D_encoding(ptr + 1);
break;
case 'C':
/* color */
set_color(buf_ptr);
fg_color = D_parse_color(buf_ptr, 1);
break;
case 'G':
/* background color */
bg_color = D_parse_color(buf_ptr, 1);
do_background = 1;
break;
case 'S':
/* size */
i = 0;
if (strchr("+-", buf_ptr[0]))
i = 1;
d = atof(buf_ptr);
if (buf_ptr[buf_len - 1] != 'p')
#ifdef BACKWARD_COMPATIBILITY
d *= (win.b - win.t) / 100.0 / linespacing;
#else
d *= (win.b - win.t) / 100.0;
#endif
size = d + (i ? size : 0);
D_text_size(size, size);
break;
case 'B':
/* bold */
bold = (atoi(buf_ptr) ? 1 : 0);
break;
case 'A':
/* align */
strncpy(align, buf_ptr, 2);
break;
case 'R':
/* rotation */
i = 0;
if (strchr("+-", buf_ptr[0]))
i = 1;
d = atof(buf_ptr);
if (buf_ptr[buf_len - 1] != 'r')
d *= M_PI / 180.0;
d += (i ? rotation : 0.0);
rotation = fmod(d, 2.0 * M_PI);
if (rotation < 0.0)
rotation += 2.0 * M_PI;
D_text_rotation(rotation * 180.0 / M_PI);
break;
case 'I':
/* linespacing */
linespacing = atof(buf_ptr);
break;
case 'X':
/* x */
set_l = 0;
set_x = 1;
i = 0;
if (strchr("+-", buf_ptr[0]))
i = 1;
d = atof(buf_ptr);
if (buf_ptr[buf_len - 1] == '%')
/* percentage */
d *= (win.r - win.l) / 100.0;
else if (buf_ptr[buf_len - 1] != 'p')
/* column */
d = (d - 1) * size * linespacing + 0.5;
x = prev_x = d + (i ? x : orig_x);
break;
case 'Y':
/* y */
set_l = 0;
set_y = 1;
i = 0;
if (strchr("+-", buf_ptr[0]))
i = 1;
d = atof(buf_ptr);
if (buf_ptr[buf_len - 1] == '%')
/* percentage */
d = win.b - d * (win.b - win.t) / 100.0;
else if (buf_ptr[buf_len - 1] != 'p')
/* row */
d *= size * linespacing + 0.5;
y = prev_y = d + (i ? y : orig_y);
break;
case 'L':
/* linefeed */
set_l = 1;
linefeed = (atoi(buf_ptr) ? 1 : 0);
break;
case 'E':
i = 0;
if (strchr("+-", buf_ptr[0]))
i = 1;
d = atof(buf_ptr);
if (buf_ptr[buf_len - 1] == '%')
d *= (win.r - win.l) / 100.0;
else if (buf_ptr[buf_len - 1] != 'p')
d = D_u_to_d_col(d);
x = prev_x = orig_x = d + (i ? orig_x : win.l);
break;
case 'N':
i = 0;
if (strchr("+-", buf_ptr[0]))
i = 1;
d = atof(buf_ptr);
if (buf_ptr[buf_len - 1] == '%')
d *= (win.b - win.t) / 100.0;
else if (buf_ptr[buf_len - 1] != 'p')
d = D_u_to_d_row(d);
y = prev_y = orig_y = d + (i ? orig_y : win.t);
break;
}
}
else {
buf_ptr = buf;
if (buf[0] == '.' && buf[1] == '.')
buf_ptr++;
if (!first_text && (linefeed || set_l)) {
/* if x is not given, increment x */
if (!set_x)
x = prev_x +
(size * linespacing + 0.5) * sin(rotation);
/* if y is not given, increment y */
if (!set_y)
y = prev_y +
(size * linespacing + 0.5) * cos(rotation);
prev_x = x;
prev_y = y;
}
set_x = set_y = set_l = first_text = 0;
draw_text(buf_ptr, &x, &y, size, align, rotation, bold, do_background, fg_color, bg_color);
}
}
if (cmd_fp != stdin)
fclose(cmd_fp);
/* reset */
D_text_size(5, 5);
D_text_rotation(0.0);
D_close_driver();
exit(EXIT_SUCCESS);
}
IMP_FOREACH(Pair pp, global_) {
IMP_LOG_VERBOSE("Loading global coordinates for "
<< m->get_particle_name(pp.second) << std::endl);
algebra::Vector3D rf(get_coordinates(fh.get_node(pp.first), ip_factory_));
core::XYZ(m, pp.second).set_coordinates(rf);
}