CAtomList *DecodeList( const string &x, unsigned long iStart )
{
unsigned long i = iStart + 1;
CAtomList *pList = new CAtomList( );
while( i < x.size( ) && x[i] != 'e' )
{
CAtom *pAtom = Decode( x, i );
if( pAtom )
{
i += pAtom->EncodedLength( );
pList->addItem( pAtom );
}
else
{
UTIL_LogPrint( "error decoding list - error decoding list item, discarding list\n" );
delete pList;
return NULL;
}
}
return pList;
}
static PyObject*
CAtom_new( PyTypeObject* type, PyObject* args, PyObject* kwargs )
{
PyDictPtr membersptr( PyObject_GetAttr( pyobject_cast( type ), atom_members ) );
if( !membersptr )
return 0;
if( !membersptr.check_exact() )
return py_bad_internal_call( "atom members" );
PyObjectPtr selfptr( PyType_GenericNew( type, args, kwargs ) );
if( !selfptr )
return 0;
CAtom* atom = catom_cast( selfptr.get() );
uint32_t count = static_cast<uint32_t>( membersptr.size() );
if( count > 0 )
{
if( count > MAX_MEMBER_COUNT )
return py_type_fail( "too many members" );
size_t size = sizeof( PyObject* ) * count;
void* slots = PyObject_MALLOC( size );
if( !slots )
return PyErr_NoMemory();
memset( slots, 0, size );
atom->slots = reinterpret_cast<PyObject**>( slots );
atom->set_slot_count( count );
}
atom->set_notifications_enabled( true );
return selfptr.release();
}
static PyObject*
Member_del_slot( Member* self, PyObject* object )
{
if( !CAtom::TypeCheck( object ) )
return py_expected_type_fail( object, "CAtom" );
CAtom* atom = catom_cast( object );
if( self->index >= atom->get_slot_count() )
return py_no_attr_fail( object, PyString_AsString( self->name ) );
atom->set_slot( self->index, 0 );
Py_RETURN_NONE;
}
CAtomDicti *DecodeDicti( const string &x, unsigned long iStart )
{
unsigned long i = iStart + 1;
CAtomDicti *pDicti = new CAtomDicti( );
while( i < x.size( ) && x[i] != 'e' )
{
CAtom *pKey = Decode( x, i );
if( pKey && dynamic_cast<CAtomString *>( pKey ) )
{
i += pKey->EncodedLength( );
string strKey = pKey->toString( );
delete pKey;
if( i < x.size( ) )
{
CAtom *pValue = Decode( x, i );
if( pValue )
{
i += pValue->EncodedLength( );
pDicti->setItem( strKey, pValue );
}
else
{
UTIL_LogPrint( "error decoding dictionary - error decoding value, discarding dictionary\n" );
delete pDicti;
return NULL;
}
}
}
else
{
UTIL_LogPrint( "error decoding dictionary - error decoding key, discarding dictionary\n" );
delete pDicti;
return NULL;
}
}
return pDicti;
}
static PyObject*
Member_set_slot( Member* self, PyObject* args )
{
if( PyTuple_GET_SIZE( args ) != 2 )
return py_type_fail( "set_slot() takes exactly 2 arguments" );
PyObject* object = PyTuple_GET_ITEM( args, 0 );
PyObject* value = PyTuple_GET_ITEM( args, 1 );
if( !CAtom::TypeCheck( object ) )
return py_expected_type_fail( object, "CAtom" );
CAtom* atom = catom_cast( object );
if( self->index >= atom->get_slot_count() )
return py_no_attr_fail( object, PyString_AsString( self->name ) );
atom->set_slot( self->index, value );
Py_RETURN_NONE;
}
void CState::fillBoxes()
{
cout << "CState::fillBoxes()" << endl;
vec3 atomPosition;
ivec3 boxIndex;
CAtom* atomptr;
for (int i = 0; i < nAtoms; i++)
{
atomptr = atoms[i];
atomPosition = atomptr->getPosition();
for (int j = 0; j < 3; j++)
{
boxIndex(j) = int(floor(atomPosition(j)/boxDimensions(j)));
}
boxes[calculate_box_number(boxIndex, NBoxes)]->addAtom(atomptr);
}
cout << "Exiting CState::fillBoxes()" << endl << endl;
}
void CState::makeAtoms(ivec3 N, vec3 L, mat r, double sites_per_cell, string atomType)
{
cout << "CState::makeAtoms" << endl;
vec3 cellPos;
atoms = vector<CAtom*>();
atoms.reserve(nAtoms); // don't want resize, since we're using "push_back" to add item
for (int ix = 0; ix < N(0); ix++)
{
for (int iy = 0; iy < N(1); iy++)
{
for (int iz = 0; iz < N(2); iz++)
{
for (int i = 0; i < sites_per_cell; i++)
{
CAtom* atom = new CAtom;
cellPos << L(0)*ix << L(1)*iy << L(2)*iz;
atom->setPosition(cellPos + r.row(i).t());
atom->setAtomType(atomType);
if (atom->matrixAtom)
{
nMatrixAtoms++;
atoms.push_back(atom);
}
else
{
nMovingAtoms++;
movingAtoms.push_back(atom);
atoms.push_back(atom);
}
}
}
}
}
cout << "Exiting CState::makeAtoms" << endl;
}
void CTracker :: serverResponseSignupLilyPOST( struct request_t *pRequest, struct response_t *pResponse, CAtomList *pPost )
{
// Set the start time
const struct bnbttv btv( UTIL_CurrentTime( ) );
// Verify that the IP is permitted to access the tracker
if( m_ucIPBanMode != 0 )
if( IsIPBanned( pRequest, pResponse, btv, gmapLANG_CFG["signup_page"], string( CSS_SIGNUP ), NOT_INDEX ) )
return;
string cstrLogin = string( );
string cstrLilyID = string( );
if( pPost )
{
// Initialise segment dictionary
CAtomDicti *pSegment = 0;
CAtom *pDisposition = 0;
CAtom *pData = 0;
CAtom *pName = 0;
CAtom *pFile = 0;
// Get the segments from the post
vector<CAtom *> vecSegments = pPost->getValue( );
// Loop through the segments
for( unsigned long ulCount = 0; ulCount < vecSegments.size( ); ulCount++ )
{
// Is the segment a dictionary?
if( vecSegments[ulCount]->isDicti( ) )
{
// Get the segment dictionary
pSegment = (CAtomDicti *)vecSegments[ulCount];
// Get the disposition and the data from the segment dictionary
pDisposition = pSegment->getItem( "disposition" );
pData = pSegment->getItem( "data" );
// Did we get a disposition that is a dictionary and has data?
if( pDisposition && pDisposition->isDicti( ) && pData )
{
// Get the content name from the disposition
pName = ( (CAtomDicti *)pDisposition )->getItem( "name" );
// Did we get a content name?
if( pName )
{
// What is the content name to be tested?
string strName = pName->toString( );
if( strName == "us_login")
cstrLogin = pData->toString( );
else if( strName == "us_lilyid")
cstrLilyID = UTIL_ToLower( pData->toString( ) );
}
else
{
// Output common HTML head
HTML_Common_Begin( pRequest, pResponse, gmapLANG_CFG["signup_page"], string( CSS_SIGNUP ), string( ), NOT_INDEX, CODE_400 );
// failed
pResponse->strContent += "<p class=\"failed\">" + gmapLANG_CFG["failed"] + "</p>\n";
// Signal a bad request
pResponse->strContent += "<p class=\"body_upload\">400 " + gmapLANG_CFG["server_response_400"] + "</p>\n";
// Output common HTML tail
HTML_Common_End( pRequest, pResponse, btv, NOT_INDEX, string( CSS_SIGNUP ) );
if( gbDebug )
UTIL_LogPrint( "Login Warning - Bad request (no users name)\n" );
return;
}
}
}
}
}
else
{
// Output common HTML head
HTML_Common_Begin( pRequest, pResponse, gmapLANG_CFG["signup_page"], string( CSS_SIGNUP ), string( ), NOT_INDEX, CODE_400 );
// failed
pResponse->strContent += "<p class=\"failed\">" + gmapLANG_CFG["failed"] + "</p>\n";
// Signal a bad request
pResponse->strContent += "<p class=\"body_upload\">400 " + gmapLANG_CFG["server_response_400"] + "</p>\n";
// Output common HTML tail
HTML_Common_End( pRequest, pResponse, btv, NOT_INDEX, string( CSS_SIGNUP ) );
if( gbDebug )
UTIL_LogPrint( "Upload Warning - Bad request (no post received)\n" );
return;
}
if( pRequest->user.ucAccess & ACCESS_SIGNUP )
{
HTML_Common_Begin( pRequest, pResponse, gmapLANG_CFG["signup_page"], string( CSS_SIGNUP ), string( ), NOT_INDEX, CODE_200 );
if( !cstrLogin.empty( ) && !cstrLilyID.empty( ) )
{
// if( cstrLogin[0] == ' ' || cstrLogin[cstrLogin.size( ) - 1] == ' ' || cstrLogin.size( ) > m_uiNameLength )
if( cstrLogin.find( ' ' ) != string :: npos || cstrLogin.find( '.' ) != string :: npos || cstrLogin.find( '%' ) != string :: npos || cstrLogin.find( '&' ) != string :: npos || cstrLilyID.find( ' ' ) != string :: npos || cstrLilyID.find( '.' ) != string :: npos || cstrLilyID.find( '%' ) != string :: npos || cstrLilyID.find( '&' ) != string :: npos || cstrLogin.size( ) > m_uiNameLength )
{
// Unable to signup. Your name must be less than " + CAtomInt( m_uiNameLength ).toString( ) + " characters long and it must not start or end with spaces.
pResponse->strContent += "<p class=\"signup_failed\">" + UTIL_Xsprintf( gmapLANG_CFG["signup_name_error"].c_str( ), CAtomInt( m_uiNameLength ).toString( ).c_str( ), string( "<a title=\"" + gmapLANG_CFG["navbar_signup"] + "\" href=\"" + RESPONSE_STR_SIGNUP_LILY_HTML + "\">" ).c_str( ), "</a>" ) + "</p>\n\n";
// Output common HTML tail
HTML_Common_End( pRequest, pResponse, btv, NOT_INDEX, string( CSS_SIGNUP ) );
return;
}
time_t tNow = time( 0 );
char pTime[256];
memset( pTime, 0, sizeof( pTime ) / sizeof( char ) );
strftime( pTime, sizeof( pTime ) / sizeof( char ), "%Y %m/%d %H:%M:%S", localtime( &tNow ) );
const string cstrA1( cstrLogin + ":" + gstrRealm + ":" + pTime );
unsigned char szMD5[16];
memset( szMD5, 0, sizeof( szMD5 ) / sizeof( unsigned char ) );
MD5_CTX md5;
MD5Init( &md5 );
MD5Update( &md5, (const unsigned char *)cstrA1.c_str( ), (unsigned int)cstrA1.size( ) );
MD5Final( szMD5, &md5 );
const string cstrPass = UTIL_HashToString( string( (char *)szMD5, sizeof( szMD5 ) / sizeof( unsigned char ) ) ).substr( 0, 8 );
const string cstrMail = cstrLilyID + "@bbs.nju.edu.cn";
if( !getUser( cstrLogin, m_ucGuestAccess ).strLogin.empty( ) )
{
// Unable to signup. The user \"" + UTIL_RemoveHTML( cstrLogin ) + "\" already exists.
pResponse->strContent += "<p class=\"signup_failed\">" + UTIL_Xsprintf( gmapLANG_CFG["signup_exists_error"].c_str( ), UTIL_RemoveHTML( cstrLogin ).c_str( ), string( "<a title=\"" + gmapLANG_CFG["navbar_signup"] + "\" href=\"" + RESPONSE_STR_SIGNUP_LILY_HTML + "\">" ).c_str( ), "</a>" ) + "</p>\n\n";
}
else
{
CMySQLQuery *pQuery = new CMySQLQuery( "SELECT blilyid FROM lily WHERE blilyid=\'" + UTIL_StringToMySQL( cstrLilyID ) + "\'" );
if( pQuery->nextRow( ).size( ) == 1 )
{
pResponse->strContent += "<p class=\"signup_failed\">" + UTIL_Xsprintf( gmapLANG_CFG["signup_exists_error_lily"].c_str( ), UTIL_RemoveHTML( cstrLogin ).c_str( ), UTIL_RemoveHTML( cstrLilyID ).c_str( ), string( "<a title=\"" + gmapLANG_CFG["navbar_signup"] + "\" href=\"" + RESPONSE_STR_SIGNUP_LILY_HTML + "\">" ).c_str( ), "</a>" ) + "</p>\n\n";
}
else
{
if( addUser( cstrLogin, cstrPass, m_ucMemberAccess, cstrMail ) )
{
CMySQLQuery mq01( "INSERT INTO lily (blilyid,busername,bpassword) VALUES(\'" + UTIL_StringToMySQL( cstrLilyID ) + "\',\'" + UTIL_StringToMySQL( cstrLogin ) + "\',\'" + UTIL_StringToMySQL( cstrPass ) + "\')" );
system( string( "echo \"ID: " + cstrLogin + " Password: "******"\" | mutt -s \"ZiJingBT\" " + cstrMail ).c_str( ) );
// Thanks! You've successfully signed up!
pResponse->strContent += "<p class=\"signup_ok\">" + UTIL_Xsprintf( gmapLANG_CFG["signup_success_lily"].c_str( ), UTIL_RemoveHTML( cstrLilyID ).c_str( ), string( "<a title=\"" + gmapLANG_CFG["navbar_signup"] + "\" href=\"" + RESPONSE_STR_LOGIN_HTML + "\">" ).c_str( ), "</a>" ) + "</p>\n\n";
}
else
pResponse->strContent += "<p class=\"signup_failed\">" + UTIL_Xsprintf( gmapLANG_CFG["users_max_create_fail"].c_str( ), string( "<a title=\"" + gmapLANG_CFG["navbar_users"] + "\" href=\"" + RESPONSE_STR_USERS_HTML + "\">" ).c_str( ), "</a>" ) + "</p>\n";
}
delete pQuery;
}
HTML_Common_End( pRequest, pResponse, btv, NOT_INDEX, string( CSS_SIGNUP ) );
}
}
else
{
//Unable to signup. You must fill in all the fields.
pResponse->strContent += "<p class=\"signup_failed\">" + UTIL_Xsprintf( gmapLANG_CFG["signup_fields_error"].c_str( ), string( "<a title=\"" + gmapLANG_CFG["navbar_signup"] + "\" href=\"" + RESPONSE_STR_SIGNUP_LILY_HTML + "\">" ).c_str( ), "</a>" ) + "</p>\n\n";
// Output common HTML tail
HTML_Common_End( pRequest, pResponse, btv, NOT_INDEX, string( CSS_SIGNUP ) );
return;
}
}
static Residue::eAtomClassification ClassifyAtom(const Residue *residue, const CAtom& atom)
{
if (!atom.IsSetIupac_code()) return Residue::eUnknownAtom;
string code = atom.GetIupac_code().front();
CAtom::EElement element = atom.GetElement();
if (residue->IsAminoAcid()) {
// amino acid C-alpha
if (element==CAtom::eElement_c && code==" CA ")
return Residue::eAlphaBackboneAtom;
// amino acid partial backbone
if (
(element==CAtom::eElement_c && code==" C ") ||
(element==CAtom::eElement_n && code==" N ")
)
return Residue::ePartialBackboneAtom;
// amino acid complete backbone (all backbone that's not part of "partial")
// including both GLY alpha hydrogens and terminal COOH and NH3+
if (
(element==CAtom::eElement_o &&
(code==" O " || code==" OXT")) ||
(element==CAtom::eElement_h &&
(code==" H " || code==" HA " || code=="1HA " || code=="2HA " ||
code==" HXT" || code=="1H " || code=="2H " || code=="3H "))
)
return Residue::eCompleteBackboneAtom;
// anything else is side chain
return Residue::eSideChainAtom;
} else if (residue->IsNucleotide()) {
// nucleic acid Phosphorus
if (element==CAtom::eElement_p && code==" P ")
return Residue::eAlphaBackboneAtom;
// nucleic acid partial backbone
if (
(element==CAtom::eElement_c && (code==" C5*" || code==" C4*" || code==" C3*")) ||
(element==CAtom::eElement_o && (code==" O5*" || code==" O3*")) ||
(element==CAtom::eElement_h && (code==" H3T" || code==" H5T"))
)
return Residue::ePartialBackboneAtom;
// nucleic acid complete backbone (all backbone that's not part of "partial")
if (
(element==CAtom::eElement_o &&
(code==" O1P" || code==" O2P" || code==" O4*" || code==" O2*")) ||
(element==CAtom::eElement_c && (code==" C2*" || code==" C1*")) ||
(element==CAtom::eElement_h &&
(code=="1H5*" || code=="2H5*" || code==" H4*" || code==" H3*" ||
code==" H2*" || code==" H1*" || code==" H1P" || code==" H2P" ||
code==" HO2" || code=="1H2*" || code=="2H2*"))
)
return Residue::eCompleteBackboneAtom;
// anything else is side chain
return Residue::eSideChainAtom;
}
return Residue::eUnknownAtom;
}
void CInventory::Update()
{
// add an atom to the beaker when selected from the inventory
int touchX = 0;
int touchY = 0;
if (g_Game.getGameState() == GS_Playing && s3ePointerGetState(S3E_POINTER_BUTTON_SELECT) & S3E_POINTER_STATE_PRESSED)
{
touchX = s3ePointerGetX();
touchY = s3ePointerGetY();
for (int i = 0; i < inventoryCount; i++)
{
if (atomObjs[i]->isTouched(touchX, touchY))
{
if (g_Beaker.getAtomSymbol() != NULL && !strcmp(atomObjs[i]->getSymbol(), g_Beaker.getAtomSymbol()))
{
// Early-terminate because the same inventory item was clicked more than once & can be ignored
break;
}
if (atomCount[i] == 1)
{
// hide atom to indicate zero are left
atomObjs[i]->setVisible(false);
// HASAN - new to display the inventory count image
atomCountImages[i]->setVisible(false);
}
// create new CAtom object to be held in the beaker, so inventory atom can remain unchanged
CAtom* newAtom = new CAtom();
newAtom->Init(atomObjs[i]->getSymbol());
CAtom* prevAtom = g_Beaker.setAtom(newAtom);
if (prevAtom != NULL)
{
// replacing previously selected atom in the beaker, so moving previous one back into this inventory
// 1 - find previous atom slot in inventory
// 2 - if previously zero count, then set back to visible
// 3 - increment the atom counter
for (int j = 0; j < inventoryCount; j++)
{
if (!strcmp(prevAtom->getSymbol(), atomObjs[j]->getSymbol()))
{
// match found
if (atomCount[j] <= 0)
{
atomObjs[j]->setVisible(true);
atomCountImages[j]->setVisible(true);
}
atomCount[j]++;
// This was a clone of the object in the inventory, need to delete it (happens inside the sprite manager) when it's being replaced and not shot into the environment
g_Game.getSpriteManager()->removeSprite(prevAtom);
break;
}
}
}
atomCount[i]--;
}
}
}
}
void CInventory::AddAtoms(char* i_strAtomSymbol, int i_nCount)
{
bool bMatchFound = false;
int matchIndex = -1;
if (inventoryCount == 0)
{
// HASAN - debug
//s3eDebugOutputString("Adding inventory sprite to sprite manager.");
// add the inventory to the sprite manager when the first atom is added
g_Game.getSpriteManager()->addSprite(inventory_sprite);
}
if (inventoryCount > 0)
{
for (int i = 0; i < MAX_COUNT; i++)
{
if (!strcmp(atoms[i], i_strAtomSymbol))
{
bMatchFound = true;
matchIndex = i;
break;
}
}
}
if (!bMatchFound)
{
// match
strcpy(atoms[inventoryCount], i_strAtomSymbol);
atomCount[inventoryCount] += i_nCount;
CAtom* atom = new CAtom();
atom->Init(i_strAtomSymbol);
// horizontal center, same as inventory graphic
int posX = (Iw2DGetSurfaceWidth() / 2) - (IMAGE_SIZE_WIDTH / 2);
int posY = Iw2DGetSurfaceHeight() - (IMAGE_SIZE_HEIGHT / 2);
// offset inventory horizontally to fit in the container
posX = posX + (10 + (64 / 2)); // NOTE: 64 = atom size, 10 = border + spacing
if (inventoryCount > 0)
{
posX = posX + (inventoryCount * (64 + 15)); // NOTE: 64 = atom size, 15 = spacing + border + spacing
}
atom->setPosAngScale(posX, posY, 0, IW_GEOM_ONE);
atom->setVelocity(0,0);
// HASAN - new to create/show the inventory count images
CIw2DImage* inventoryCountImage = Iw2DCreateImageResource("inventory_number");
CSprite* inventoryCountSprite = new CSprite();
inventoryCountSprite->setImage(inventoryCountImage, "inventory_number");
// NOTE: image width & height = 25 & font width & height = 30
inventoryCountSprite->setPosition(posX + 13 + (30 / 2), posY + (30 / 2) + 3);
inventoryCountSprite->setDestSize(30, 30); // make larger than source to fit behind the text properly
g_Game.getSpriteManager()->addSprite(inventoryCountSprite);
atomCountImages[inventoryCount] = inventoryCountSprite;
atomObjs[inventoryCount] = atom;
inventoryCount++;
}
else
{
atomCount[matchIndex] += i_nCount;
}
}
