Cell lookup(Cell var, Cell env) {
while (!is_null(env)) {
Cell frame = car(env);
Cell vars = car(frame);
Cell vals = cdr(frame);
while (!is_null(vars)) {
if (is_eq(car(vars), var)) {
return car(vals);
}
vars = cdr(vars);
vals = cdr(vals);
}
env = cdr(env);
}
return atom("#<unbound>");
}
void Parser::pattern_pkg() {
if (tokens[look].type == OPENPAREN) {
pattern_group();
} else {
atom();
if (tokens[look].type == OPENBRACE) {
match(OPENBRACE);
atoms[atoms.size()-1].interval_from = Number(tokens[look].value);
match(NUM);
match(COMMA);
atoms[atoms.size()-1].interval_to = Number(tokens[look].value);
match(NUM);
match(CLOSEBRACE);
}
}
}
void XfitMan::setIconGeometry(Window _wid, QRect* rect) const
{
Atom net_wm_icon_geometry = atom("_NET_WM_ICON_GEOMETRY");
if(!rect)
XDeleteProperty(QX11Info::display(), _wid, net_wm_icon_geometry);
else
{
long data[4];
data[0] = rect->x();
data[1] = rect->y();
data[2] = rect->width();
data[3] = rect->height();
XChangeProperty(QX11Info::display(), _wid, net_wm_icon_geometry,
XA_CARDINAL, 32, PropModeReplace, (unsigned char*)data, 4);
}
}
void testLiteral()
{
tryLiteralOk("true ", [](const JSONAtom &atom) { assertTrue(atom.asBool()); });
tryLiteralOk("false ", [](const JSONAtom &atom) { assertFalse(atom.asBool()); });
tryLiteralOk("null ", [](const JSONAtom &atom) { assertNull(atom.asNull()); });
const char *const json = "invalid ";
memoryStream_t stream(const_cast<char *const>(json), length(json));
JSONParser parser(stream);
try
{
std::unique_ptr<JSONAtom> atom(literal(parser));
fail("The parser failed to throw an exception on invalid literal");
}
catch (const JSONParserError &err) { }
}
/**
* @brief returns the window that currently has inputfocus
*/
Window XfitMan::getActiveWindow() const
{
unsigned long len;
unsigned long *data;
if (!getWindowProperty(root, atom("_NET_ACTIVE_WINDOW"), XA_WINDOW,
&len, (unsigned char**) &data)
)
return 0;
Window result = 0;
if (len)
result = data[0];
XFree(data);
return result;
}
PDBChain DNAMutator::mutate(const std::string& seq, const PDBChain& chain) const
{
if(seq.size() != chain.size())
throw std::invalid_argument("sequence and chain have different size");
std::size_t index = 0;
PDBChain mutated;
for(auto residue = chain.cbegin(); residue != chain.cend(); ++residue)
{
std::shared_ptr<PDBResidue> res(new PDBResidue);
for(auto iter = (*residue)->cbegin();
iter != (*residue)->cend(); ++iter)
{
// deep copy
std::shared_ptr<PDBAtom> atom(new PDBAtom(**iter));
res->push_back(atom);
}
ax::Vector3d B(0e0);
ax::Vector3d S(0e0);
for(auto atom = res->cbegin(); atom != res->cend(); ++atom)
{
if((*atom)->atom() == "DB ")
B = (*atom)->pos();
else if((*atom)->atom() == "DS ")
S = (*atom)->pos();
}
const ax::Vector3d direction = (B - S) / length(B - S);
const ax::Vector3d B_newpos = S +
direction * this->SBlength.at(seq.at(index));
for(auto atom = res->cbegin(); atom != res->cend(); ++atom)
{
(*atom)->residue() = std::string("D") + seq.at(index) + std::string(" ");
if((*atom)->atom() == "DB ") (*atom)->pos() = B_newpos;
else if((*atom)->atom() == "DS ") S = (*atom)->pos();
}
mutated.push_back(res);
index++;
}
return mutated;
}
double atom()
{
double res = NAN;
if(isdigit(top())) {
res = literal();
} else if(top() == '(') {
next();
res = addexpr();
next();
} else if(top() == '-') {
next();
res = -atom();
}
return res;
}
/// ( )
void eval_expr5(parser &p, float &value)
{
MSG("EVAL5\n");
if(p.tokens[p.index].type == PARENTHESIS_LEFT) {
p.index++;
eval_expr(p, value);
if(p.tokens[p.index].type != PARENTHESIS_RIGHT) {
MSG("expected )\n");
return;
}
p.index++;
} else {
atom(p, value);
}
}
void delayed_reply(const actor_ptr& to,
const Duration& rel_time,
message_id_t id,
any_tuple data ) {
CPPA_REQUIRE(!id.valid() || id.is_response());
if (id.valid()) {
auto tup = make_any_tuple(atom("REPLY"),
util::duration{rel_time},
to,
id,
std::move(data));
delayed_send_helper()->enqueue(self, std::move(tup));
}
else {
this->delayed_send(to, rel_time, std::move(data));
}
}
Cell set(Cell var, Cell val, Cell env) {
while (!is_null(env)) {
Cell frame = car(env);
Cell vars = car(frame);
Cell vals = cdr(frame);
while (!is_null(vars)) {
if (is_eq(car(vars), var)) {
set_car(vals, val);
return atom("#<void>");
}
vars = cdr(vars);
vals = cdr(vals);
}
env = cdr(env);
}
fprintf(stderr, "unbound variable\n");
}
void tryNumberOk(const char *const json, void tests(const JSONAtom &))
{
try
{
memoryStream_t stream(const_cast<char *const>(json), length(json));
JSONParser parser(stream);
std::unique_ptr<JSONAtom> atom(number(parser));
assertNotNull(atom.get());
tests(*atom);
}
catch (const JSONParserError &err)
{ fail(err.error()); }
catch (const JSONTypeError &err)
{ fail(err.error()); }
catch (const std::bad_alloc &err)
{ fail(err.what()); }
}
/*
* ISO 9660 file names must be uppercase, digits, or underscore.
* We use lowercase, digits, and underscore, translating lower to upper
* in mkisostring, and upper to lower in isostring.
* Files with uppercase letters in their names are thus nonconforming.
* Conforming files also must have a basename
* at most 8 letters and at most one suffix of at most 3 letters.
*/
char*
isostring(uchar *buf, int len)
{
char *p, *q;
p = emalloc(len+1);
memmove(p, buf, len);
p[len] = '\0';
while(len > 0 && p[len-1] == ' ')
p[--len] = '\0';
for(q=p; *q; q++)
*q = tolower(*q);
q = atom(p);
free(p);
return q;
}
Expression read_from_tokens(InputIterator& first, InputIterator& last) {
if (first == last) {
throw std::runtime_error("Syntax error: unexpected EOF while reading");
}
if ("(" == *first) {
List out;
while ( *(++first) != ")" ) {
out.push_back(read_from_tokens(first,last));
}
return out;
} else if (")" == *first) {
throw std::runtime_error("Syntax error: unexpected ')'");
}
else {
return atom(*first);
}
}
void
FilterTotalFormalCharge::Calculate(OpenBabel::OBMol* mol)
{
_result = 0;
for(OpenBabel::OBMolAtomIter atom(mol); atom; ++atom)
{
_result += atom->GetFormalCharge();
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}
void
FilterCarbons::Calculate(OpenBabel::OBMol* mol)
{
_result = 0;
for(OpenBabel::OBMolAtomIter atom(mol); atom; ++atom)
{
if (atom->IsCarbon()) ++_result;
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}
void default_actor_addressing::put(const process_information& node,
actor_id aid,
const actor_proxy_ptr& proxy) {
auto& submap = m_proxies[node];
auto i = submap.find(aid);
if (i == submap.end()) {
submap.insert(make_pair(aid, proxy));
m_parent->enqueue(node,
{nullptr, nullptr},
make_any_tuple(atom("MONITOR"),
process_information::get(),
aid));
}
else {
CPPA_LOGMF(CPPA_ERROR, self, "proxy for " << aid << ":"
<< to_string(node) << " already exists");
}
}
DEM redu (DEM x)
{
int forme_Sfg;
DEM rf, ra, f1, a1, x1, r1, r2, t1, t2, t3, t4, t5, t6, r, rr1;
trace_dem ("redu", x);
if (atom(x))
{
trace_dem ("atom: return", x);
return x;
}
trace_dem ("not atom", x);
rf = redu (fnc(x)); trace_dem ("", rf);
ra = redu (arg(x)); trace_dem ("", ra);
f1 = right (rf); trace_dem ("", f1);
a1 = right (ra); trace_dem ("", a1);
trace_dem ("", x);
if (fnc(x)==f1 && arg(x)==a1)
{
r1 = redu1 (x); trace_dem ("", r1);
rr1 = right(r1); trace_dem ("", rr1);
if (rr1 == x)
{
trace_dem ("return", r1);
return r1;
}
trace_dem ("", rr1);
r2 = redu (rr1); trace_dem ("", r2);
if (left(r2) == right(r2))
return r1;
if (left(r1) == right(r1))
return r2;
r = trans (r1, r2); trace_dem ("", r);
return r;
}
x1 = ap (f1, a1); trace_dem ("", x1);
r1 = redu1 (x1); trace_dem ("", r1);
if (right(r1) == x)
r2 = r1;
r2 = redu (right(r1)); trace_dem ("", r2);
t3 = ap (rf, ra); trace_dem ("", t3);
t4 = trans (t3, r1); trace_dem ("", t4);
t5 = trans (t4, r2); trace_dem ("", t5);
return t5;
}
int script_parse(const char *script, const char *_arg) {
char *arg = NULL;
int a, b;
if (script == NULL)
return(0);
if (_arg != NULL)
_arg = arg = strdup(_arg);
for (a = 0; (a < 50) && (arg != NULL); a++) {
char buf[1024], *tmp;
tmp = atom(arg);
snprintf(buf, sizeof(buf), "args%i*", a+1);
secs_setvar(buf, tmp);
arg = firstwhite(arg);
snprintf(buf, sizeof(buf), "arg%i", a+1);
secs_setvar(buf, tmp);
}
for (b = a; b < 50; b++) {
char buf[1024];
snprintf(buf, sizeof(buf), "args%i*", b+1);
secs_setvar(buf, "");
snprintf(buf, sizeof(buf), "arg%i", b+1);
secs_setvar(buf, "");
}
secs_script_parse(script);
while (a > 0) {
char buf[1024];
snprintf(buf, sizeof(buf), "arg%i", a);
secs_setvar(buf, "");
snprintf(buf, sizeof(buf), "args%i*", a);
secs_setvar(buf, "");
a--;
}
if (_arg != NULL)
free((void *)_arg);
return(1);
}
bool actor::establish_backlink(const actor_ptr& other) {
std::uint32_t reason = exit_reason::not_exited;
if (other && other != this) {
guard_type guard{m_mtx};
reason = m_exit_reason;
if (reason == exit_reason::not_exited) {
auto i = std::find(m_links.begin(), m_links.end(), other);
if (i == m_links.end()) {
m_links.push_back(other);
return true;
}
}
}
// send exit message without lock
if (reason != exit_reason::not_exited) {
send_as(this, other, make_any_tuple(atom("EXIT"), reason));
}
return false;
}
bool parser::parse_atom(utf8str::iterator& it, utf8str::iterator& it_end, shared_ptr<expr>& result)
{
if (it != it_end)
{
uint32_t ch = utf8::peek_next(it, it_end);
if (is_atom_char(ch))
{
utf8::unchecked::next(it);
shared_ptr<utf8str> atom(new utf8str());
atom->append(ch);
while (it != it_end)
{
ch = utf8::peek_next(it, it_end);
if (is_atom_char(ch))
{
utf8::unchecked::next(it);
atom->append(ch);
}
else
{
break;
}
}
try
{
cout << "Trying to coerce value to integer" << std::endl;
int intValue = boost::lexical_cast<int>(atom->get_string());
result = shared_ptr<expr>(new expr(intValue));
}
catch(boost::bad_lexical_cast& e)
{
cout << "Not an integer, than symbol" << std::endl;
result = shared_ptr<expr>(new expr(atom));
}
return true;
}
else
{
return false;
}
}
return false;
}
List Factory::convert(Data::Geometry& geometry)
{
List list;
Atoms* atoms(new Atoms());
Bonds* bonds(new Bonds());
list.append(atoms);
list.append(bonds);
unsigned nAtoms(geometry.nAtoms());
OpenBabel::OBMol obMol;
obMol.BeginModify();
AtomMap atomMap;
for (unsigned i = 0; i < nAtoms; ++i) {
unsigned Z(geometry.atomicNumber(i));
qglviewer::Vec position(geometry.position(i));
Atom* atom(new Atom(geometry.atomicNumber(i)));
atom->setPosition(geometry.position(i));
atoms->appendLayer(atom);
OpenBabel::OBAtom* obAtom(obMol.NewAtom());
obAtom->SetAtomicNum(Z);
obAtom->SetVector(position.x, position.y, position.z);
atomMap.insert(obAtom, atom);
}
obMol.SetTotalCharge(geometry.charge());
obMol.SetTotalSpinMultiplicity(geometry.multiplicity());
obMol.EndModify();
obMol.ConnectTheDots();
obMol.PerceiveBondOrders();
for (OpenBabel::OBMolBondIter obBond(&obMol); obBond; ++obBond) {
Atom* begin(atomMap.value(obBond->GetBeginAtom()));
Atom* end(atomMap.value(obBond->GetEndAtom()));
Bond* bond(new Bond(begin, end));
bond->setOrder(obBond->GetBondOrder());
bonds->appendLayer(bond);
}
return list;
}
char*
jolietstring(uchar *buf, int len)
{
char *p, *q;
int i;
Rune *rp;
rp = emalloc(sizeof(Rune)*(len/2+1));
p = emalloc(UTFmax*(len/2+1));
for(i=0; i<len/2; i++)
rp[i] = (buf[2*i]<<8) | buf[2*i+1];
rp[i] = (Rune)'\0';
snprint(p, UTFmax*(len/2+1), "%S", rp);
q = atom(p);
free(p);
return q;
}
namespace riac {
/// Used to query all known nodes from nexus
using list_nodes = atom_constant<atom("listNodes")>;
/// Used to query meta information about a particular node.
using get_node = atom_constant<atom("getNode")>;
/// Used to query all peers of a particular node.
using list_peers = atom_constant<atom("listPeers")>;
/// Used to query system load information on a particular node.
using get_sys_load = atom_constant<atom("getSysLoad")>;
/// Used to query RAM usage on a particular node.
using get_ram_usage = atom_constant<atom("getRam")>;
/// Used to query all known actors on a particular node.
using list_actors = atom_constant<atom("listActors")>;
/// Used to query a single actor on a particular node.
using get_actor = atom_constant<atom("getActor")>;
struct nexus_proxy_state {
riac::probe_data_map data;
std::list<node_id> visited_nodes;
};
using nexus_proxy_type =
nexus_type::extend<
reacts_to<probe_data_map>,
replies_to<list_nodes>::with<std::vector<node_id>>,
replies_to<list_nodes, std::string>::with<std::vector<node_id>>,
replies_to<get_node, node_id>::with<node_info>,
replies_to<list_peers, node_id>::with<std::vector<node_id>>,
replies_to<get_sys_load, node_id>::with<work_load>,
replies_to<get_ram_usage, node_id>::with<ram_usage>,
replies_to<list_actors, node_id>::with<std::vector<strong_actor_ptr>>,
replies_to<get_actor, node_id, actor_id>::with<strong_actor_ptr>
>;
nexus_proxy_type::behavior_type
nexus_proxy(nexus_proxy_type::stateful_pointer<nexus_proxy_state> self);
} // namespace riac
/**
* @brief gets a client list
*/
WindowList XfitMan::getClientList() const
{
//initialize the parameters for the XGetWindowProperty call
unsigned long length, *data;
length=0;
/**
* @todo maybe support multiple desktops here!
*/
QList<Window> output;
if (getRootWindowProperty(atom("_NET_CLIENT_LIST"), (Atom)AnyPropertyType, &length, (unsigned char**) &data))
{
for (unsigned int i = 0; i < length; i ++)
output.append(data[i]);
XFree(data);
}
return output;
}
object *eval (object *o)
{
/* printf("%s: Trying to eval object type: %d\n", __func__, o->type); */
if (is_truthy (atom (o))) {
if (symbol_p (o)) {
/* printf("%s: Looking for symbol\n", __func__); */
return env_find_symbol_value (current_env, o);
} else {
/* printf("%s: Not eval-ing\n", __func__); */
return o;
}
} else {
/* printf("%s: Function call\n", __func__); */
object *symbol = car (o);
object *arguments = cdr (o);
return call_function (symbol, arguments);
}
}
void Parser::parseAtoms() {
int id;
char buff[1024];
while(true) {
in >> id;
switch(id) {
case 0:
return;
default:
assert(id > 0);
in.getline(buff, 1024);
Atom atom(program, id);
assert(buff[0] = ' ');
atom.setName(string(buff+1));
break;
}
}
}
static void test_common()
{
try
{
std::size_t actor_num = 10;
context ctx;
threaded_actor base = spawn(ctx);
for (std::size_t a=0; a<5; ++a)
{
for (std::size_t i=0; i<actor_num; ++i)
{
aid_t aid = spawn(
base,
boost::bind(&coro_ut::my_actor, _arg1, base.get_aid()),
monitored
);
}
std::size_t i=0;
while (i < actor_num)
{
message msg;
aid_t sender = base.recv(msg);
match_t type = msg.get_type();
if (type == atom("echo"))
{
base.send(sender, msg);
}
else
{
++i;
}
}
}
}
catch (std::exception& ex)
{
std::cerr << ex.what() << std::endl;
}
}
void cESBTL::pdbTranslate(const std::string& fileIn, const std::string& fileOut, const cVector3<double>& offset)
{
checkExtension(fileIn);
checkExtension(fileOut);
// input
ESBTL::PDB_line_selector pdbSelector;
std::vector<ESBTL::Default_system> pdbSystems;
ESBTL::All_atom_system_builder<ESBTL::Default_system> pdbBuilder(pdbSystems, pdbSelector.max_nb_systems());
require(ESBTL::read_a_pdb_file(fileIn, pdbSelector, pdbBuilder, Occupancy_policy_all()), "cannot read PDB file");
require(!pdbSystems.empty(), "No PDB system");
require( pdbSystems.size() == 1, "More than one PDB system: pdbSystems.size() = " + num2str(pdbSystems.size()));
require(!pdbSystems[0].has_no_model(), "No model in 1st PDB system");
require( pdbSystems[0].number_of_models() == 1, "More than one model in 1st PDB system: pdbSystems[0].number_of_models() = "
+ num2str(pdbSystems[0].number_of_models()));
// output
std::ofstream output(fileOut.c_str());
assure(output);
// translate
for (ESBTL::Default_system::Models_iterator iterModel = pdbSystems[0].models_begin();
iterModel != pdbSystems[0].models_end();
iterModel++) {
const ESBTL::Default_system::Model& model = *iterModel;
for (ESBTL::Default_system::Model::Atoms_const_iterator iterAtom = model.atoms_begin();
iterAtom != model.atoms_end();
iterAtom++) {
ESBTL::Default_system::Atom atom(*iterAtom);
atom.x() += offset[0];
atom.y() += offset[1];
atom.z() += offset[2];
output << ESBTL::PDB::get_atom_pdb_format(atom) << "\n";
}
}
}
void
FilterLipinskiDonors::Calculate(OpenBabel::OBMol* mol)
{
_result = 0;
for(OpenBabel::OBMolAtomIter atom(mol); atom; ++atom)
{
if (atom->IsOxygen() || atom->IsNitrogen())
{
_result += atom->GetImplicitValence() - atom->GetHvyValence();
}
}
if ((_minLimit && (_result < _min)) || (_maxLimit && (_result > _max)))
{
_passed = false;
}
else
{
_passed = true;
}
}
/**
* @brief rejects a window from beeing listed
*/
bool XfitMan::acceptWindow(Window window) const
{
{
AtomList types = getWindowType(window);
AtomList ignoreList;
ignoreList << atom("_NET_WM_WINDOW_TYPE_DESKTOP")
<< atom("_NET_WM_WINDOW_TYPE_DOCK")
<< atom("_NET_WM_WINDOW_TYPE_SPLASH")
<< atom("_NET_WM_WINDOW_TYPE_TOOLBAR")
<< atom("_NET_WM_WINDOW_TYPE_MENU")
// for qlipper - using qpopup as a main window
<< atom("_NET_WM_WINDOW_TYPE_POPUP_MENU");
// issue #284: qmmp its not registered in window list panel
// qmmp has _KDE_NET_WM_WINDOW_TYPE_OVERRIDE in its
// _NET_WM_WINDOW_TYPE(ATOM) = _KDE_NET_WM_WINDOW_TYPE_OVERRIDE, _NET_WM_WINDOW_TYPE_NORMAL
// Let's expect that _KDE_NET_WM_WINDOW_TYPE_OVERRIDE can be set for
// regular windows too. If it should be hidden we should expect
// one of atoms listed above.
// << atom("_KDE_NET_WM_WINDOW_TYPE_OVERRIDE");
foreach (Atom i, ignoreList)
{
if (types.contains(i))
return false;
}
WindowState state = getWindowState(window);
if (state.SkipTaskBar) return false;
}
Window transFor = None;
// WM_TRANSIENT_FOR hint not set - normal window
if (!XGetTransientForHint(QX11Info::display(), window, &transFor))
return true;
if (transFor == 0) return true;
if (transFor == window) return true;
if (transFor == root) return true;
AtomList transForTypes = getWindowType(transFor);
return !transForTypes.contains(atom("_NET_WM_WINDOW_TYPE_NORMAL"));
}