System* MolecularFileDialog::readPDBFile(String filename, String system_name)
{
setStatusbarText((String)tr("reading PDB file..."), true);
System* system = new System();
try
{
PDBFile pdb_file(filename);
if(read_all_pdb_models_) {
pdb_file.selectAllModels();
}
pdb_file >> *system;
pdb_file.close();
}
catch(Exception::GeneralException& e)
{
Log.error() << e << std::endl;
setStatusbarText((String)tr("Reading of PDB file failed, see logs!"), true);
delete system;
return 0;
}
if (!finish_(filename, system_name, system)) return 0;
return system;
}
int
modentry(int boot, Module m, void *ptr)
{
switch (boot) {
case 0:
return setup_(m);
break;
case 1:
return boot_(m);
break;
case 2:
return cleanup_(m);
break;
case 3:
return finish_(m);
break;
case 4:
return features_(m, (char ***)ptr);
break;
case 5:
return enables_(m, (int **)ptr);
break;
default:
zerr("bad call to modentry");
return 1;
break;
}
}
// ------------------------------------------------------------------------------------------------------
// Master Transmit - blocking routine with timeout, transmits Tx buffer to slave. i2c_stop parameter can be used
// to indicate if command should end with a STOP(I2C_STOP) or not (I2C_NOSTOP).
// return: 0=success, 1=data too long, 2=recv addr NACK, 3=recv data NACK, 4=other error
// parameters:
// i2c_stop = I2C_NOSTOP, I2C_STOP
// timeout = timeout in microseconds
//
uint8_t i2c_t3::endTransmission(i2c_stop sendStop, uint32_t timeout)
{
sendTransmission_(i2c, sendStop);
// wait for completion or timeout
finish_(i2c, timeout);
return getError();
}
// ------------------------------------------------------------------------------------------------------
// Master Receive - blocking routine with timeout, requests length bytes from slave at address. Receive data will
// be placed in the Rx buffer. i2c_stop parameter can be used to indicate if command should end
// with a STOP (I2C_STOP) or not (I2C_NOSTOP).
// return: #bytes received = success, 0=fail (0 length request, NAK, timeout, or bus error)
// parameters:
// address = target 7bit slave address
// length = number of bytes requested
// i2c_stop = I2C_NOSTOP, I2C_STOP
// timeout = timeout in microseconds
//
size_t i2c_t3::requestFrom_(struct i2cStruct* i2c, uint8_t addr, size_t len, i2c_stop sendStop, uint32_t timeout)
{
// exit immediately if request for 0 bytes
if(len == 0) return 0;
sendRequest_(i2c, addr, len, sendStop);
// wait for completion or timeout
if(finish_(i2c, timeout))
return i2c->rxBufferLength;
else
return 0; // NAK, timeout or bus error
}
System* MolecularFileDialog::readHINFile(String filename, String system_name)
{
bool has_periodic_boundary = false;
SimpleBox3 bounding_box;
setStatusbarText((String)tr("reading HIN file..."), true);
System* system = new System();
try
{
HINFile hin_file(filename);
hin_file >> *system;
has_periodic_boundary = hin_file.hasPeriodicBoundary();
bounding_box = hin_file.getPeriodicBoundary();
hin_file.close();
}
catch(Exception::GeneralException& e)
{
Log.error() << e << std::endl;
setStatusbarText((String)tr("Reading of HIN file failed, see logs!"), true);
delete system;
return 0;
}
// generating bounding box if exists
if (has_periodic_boundary)
{
/*
Box3* simple_box = new Box3;
Vector3 first, second;
bounding_box.get(first.x, first.y, first.z, second.x, second.y, second.z);
Log.info() << "> creating bounding box (" << first << ", " << second << ")" << std::endl;
simple_box->setVertex1(first);
simple_box->setVertex2(second);
simple_box->setColor("ff0000a0");
simple_box->setName("BoundingBox");
simple_box->setProperty(BALL::VIEW::GeometricObject::PROPERTY__OBJECT_TRANSPARENT);
*/
}
if (!finish_(filename, system_name, system)) return 0;
return system;
}
System* MolecularFileDialog::readXYZFile(String filename, String system_name)
{
setStatusbarText((String)tr("reading XYZ file..."), true);
System* system = new System();
try
{
XYZFile sd_file(filename);
sd_file >> *system;
sd_file.close();
}
catch(Exception::GeneralException& e)
{
setStatusbarText((String)tr("Reading of XYZ file failed, see logs!"), true);
delete system;
return 0;
}
if (!finish_(filename, system_name, system)) return 0;
return system;
}
System* MolecularFileDialog::readMOL2File(String filename, String system_name)
{
setStatusbarText((String)tr("reading MOL2 file..."), true);
System* system = new System();
try
{
MOL2File mol2_file(filename);
mol2_file >> *system;
mol2_file.close();
}
catch(Exception::GeneralException& e)
{
setStatusbarText(tr("Reading of MOL2 file failed, see logs!"), true);
Log.error() << e << std::endl;
delete system;
return 0;
}
if (!finish_(filename, system_name, system)) return 0;
return system;
}
