// ****************************************************************************
// Constructor: Atom::Atom
//
// Arguments:
// line the line of text in a PDB file
//
// Programmer: Jeremy Meredith
// Creation: March 23, 2006
//
// Modifications:
// Brad Whitlock, Fri Jun 2 13:15:47 PST 2006
// Added Jeremy's fix for yet another style of ATOM line.
//
// Jeremy Meredith, Mon Aug 28 17:58:02 EDT 2006
// Changed the scanning to (a) match the PDB spec document more
// effectively, (b) be faster, and (c) handle some missing elements
// (short lines) better.
//
// Jeremy Meredith, Wed Oct 17 11:27:10 EDT 2007
// Added compound support.
//
// ****************************************************************************
eavlPDBImporter::Atom::Atom(const char *line, int cmpnd)
{
char record[7];
int len = strlen(line);
ScanString(line, len, 1, 6, record);
ScanInt (line, len, 7, 11, &serial);
ScanString(line, len, 13, 16, name);
ScanChar (line, len, 17, &altloc);
ScanString(line, len, 18, 20, resname);
ScanChar (line, len, 22, &chainid);
ScanInt (line, len, 23, 26, &resseq);
ScanChar (line, len, 27, &icode);
ScanFloat (line, len, 31, 38, &x);
ScanFloat (line, len, 39, 46, &y);
ScanFloat (line, len, 47, 54, &z);
ScanFloat (line, len, 55, 60, &occupancy);
ScanFloat (line, len, 61, 66, &tempfactor);
ScanString(line, len, 73, 76, segid);
ScanString(line, len, 77, 78, element);
ScanString(line, len, 79, 80, charge);
// Left-justify element names
if (element[0] == ' ')
{
element[0] = element[1];
element[1] = '\0';
}
if((atomicnumber = ElementNameToAtomicNumber(element)) < 0)
{
// We have a weird file that does not keep the element name in
// the place designated by the ATOM record. Files like this seem
// to use the space for a line number. Check columns 12,13
// for the atom number.
if(line[12] == ' ' || (line[12] >= '0' && line[12] <= '9'))
{
element[0] = line[13];
element[1] = '\0';
}
else if (line[13] >= '0' && line[13] <= '9')
{
element[0] = line[12];
element[1] = '\0';
}
else
{
element[0] = line[12];
element[1] = line[13];
}
atomicnumber = ElementNameToAtomicNumber(element);
if (atomicnumber < 0 &&
element[1] != '\0')
{
element[1] = '\0';
atomicnumber = ElementNameToAtomicNumber(element);
}
if (atomicnumber < 0)
{
char msg[2000];
snprintf(msg, 2000, "Unknown element name <%s> in line: %s",
element, line);
THROW(eavlException, msg);
}
}
// Shift spaces out of the resname.
if(resname[0] == ' ')
{
if(resname[1] == ' ')
{
resname[0] = resname[2];
resname[1] = '\0';
}
else
{
resname[0] = resname[1];
resname[1] = resname[2];
resname[2] = '\0';
}
}
// Look up the residue number from the name.
if((residuenumber = ResiduenameToNumber(resname)) < 0)
{
residuenumber = 0;
}
backbone = false;
if (strcmp(name, " N ")==0 ||
strcmp(name, " C ")==0 ||
strcmp(name, " CA ")==0)
{
backbone = true;
}
compound = cmpnd;
}
void sXSILoader::ScanMatLib(sInt indent)
{
sChar chunk[XSISIZE];
sChar name[XSISIZE];
sChar texname[256];
sChar buffer[XSISIZE];
sChar pname[XSISIZE];
sChar tname[XSISIZE];
sChar tsup[2][XSISIZE];
sInt texena[2];
sXSIMaterial *mat;
sXSITexture *tex;
sInt i,max;
sInt pcount,ccount;
sInt ival;
sF32 fval;
ScanInt();
while(*Scan!=0 && *Scan!='}' && !Error)
{
ScanChunk(indent,chunk,name);
if(sCmpString(chunk,"SI_Material")==0)
{
mat = new sXSIMaterial;
sCopyString(mat->Name,name,sizeof(mat->Name));
mat->Flags |= 0;
Materials->Add(mat);
ScanFloat(); ScanFloat(); ScanFloat(); ScanFloat();
ScanFloat(); ScanFloat(); ScanFloat(); ScanFloat();
ScanFloat(); ScanFloat(); ScanFloat();
ScanInt();
ScanFloat(); ScanFloat(); ScanFloat();
sScanSpace(Scan);
while(*Scan!=0 && *Scan!='}' && !Error)
{
ScanChunk(indent+1,chunk,name);
if(sCmpString(chunk,"SI_Texture2D")==0)
{
ScanString(texname,sizeof(texname));
ScanInt(); ScanInt(); ScanInt(); ScanInt();
ScanInt(); ScanInt(); ScanInt(); ScanInt();
ScanInt(); ScanInt(); ScanInt(); ScanInt();
ScanFloat(); ScanFloat(); ScanFloat(); ScanFloat();
ScanFloat(); ScanFloat(); ScanFloat(); ScanFloat();
ScanFloat(); ScanFloat(); ScanFloat(); ScanFloat();
ScanFloat(); ScanFloat(); ScanFloat(); ScanFloat();
ScanFloat(); ScanFloat(); ScanFloat(); ScanFloat();
ScanInt();
ScanFloat(); ScanFloat(); ScanFloat(); ScanFloat();
ScanFloat(); ScanFloat(); ScanFloat();
EndChunk();
if(mat->Tex[0] == 0)
{
tex = FindTexture(texname);
if(tex)
mat->Tex[0] = tex;
}
}
else
{
SkipChunk();
}
sScanSpace(Scan);
}
EndChunk();
}
else if(sCmpString(chunk,"XSI_Material")==0)
{
mat = new sXSIMaterial;
sCopyString(mat->Name,name,sizeof(mat->Name));
mat->TFlags[0] = 0;
mat->TFlags[1] = 0;
mat->Flags |= 0;
sDPrintF("%08x:<%s>\n",Scan,name);
Materials->Add(mat);
max = ScanInt();
for(i=0;i<max;i++)
{
ScanString(buffer,sizeof(buffer));
ScanString(buffer,sizeof(buffer));
}
sScanSpace(Scan);
tsup[0][0]=0;
tsup[0][1]=0;
texena[0] = 0;
texena[1] = 0;
while(*Scan!=0 && *Scan!='}' && !Error)
{
ScanChunk(indent+1,chunk,name);
if(sCmpString(chunk,"XSI_Shader")==0)
{
ScanString(buffer,sizeof(buffer));
ScanInt();
pcount = ScanInt();
ccount = ScanInt();
for(i=0;i<pcount;i++)
{
ScanString(pname,sizeof(pname));
ScanString(tname,sizeof(tname));
if(sCmpString(tname,"STRING")==0)
{
ScanString(buffer,sizeof(buffer));
if(sCmpString(pname,"tspace_id1")==0) sCopyString(tsup[0],buffer,sizeof(tsup[0]));
if(sCmpString(pname,"tspace_id" )==0) sCopyString(tsup[0],buffer,sizeof(tsup[0]));
if(sCmpString(pname,"tspace_id2")==0) sCopyString(tsup[1],buffer,sizeof(tsup[1]));
}
else if(sCmpString(tname,"FLOAT")==0)
{
fval = ScanFloat();
ival = sRange<sInt>(255*fval,255,0);
if(sCmpString(pname,"Ambient.red")==0) mat->Ambient.r = ival;
if(sCmpString(pname,"Ambient.green")==0) mat->Ambient.g = ival;
if(sCmpString(pname,"Ambient.blue")==0) mat->Ambient.b = ival;
if(sCmpString(pname,"Diffuse.red")==0) mat->Diffuse.r = ival;
if(sCmpString(pname,"Diffuse.green")==0) mat->Diffuse.g = ival;
if(sCmpString(pname,"Diffuse.blue")==0) mat->Diffuse.b = ival;
if(sCmpString(pname,"Specular.red")==0) mat->Specular.r = ival;
if(sCmpString(pname,"Specular.green")==0) mat->Specular.g = ival;
if(sCmpString(pname,"Specular.blue")==0) mat->Specular.b = ival;
if(sCmpString(pname,"Shininess")==0) mat->Specularity = fval;
}
else if(sCmpString(tname,"INTEGER")==0)
{
ival = ScanInt();
}
else if(sCmpString(tname,"BOOLEAN")==0)
{
ival = ScanInt();
if(ival!=0)
{
// if(sCmpString(pname,"WrapS1")==0) mat->TFlags[0] |= sMTF_TILE;
// if(sCmpString(pname,"WrapT1")==0) mat->TFlags[0] |= sMTF_TILE;
if(sCmpString(pname,"Refmap1")==0) mat->TFlags[0] |= sMTF_UVENVI;
if(sCmpString(pname,"Texture_1_Enable")==0) texena[0]=1;
// if(sCmpString(pname,"WrapS2")==0) mat->TFlags[1] |= sMTF_TILE;
// if(sCmpString(pname,"WrapT2")==0) mat->TFlags[1] |= sMTF_TILE;
if(sCmpString(pname,"Refmap2")==0) mat->TFlags[1] |= sMTF_UVENVI;
if(sCmpString(pname,"Texture_2_Enable")==0) texena[1]=1;
}
else
{
if(sCmpString(pname,"Enable_Ambient")==0) mat->Ambient = 0xffffffff;
if(sCmpString(pname,"Enable_Diffuse")==0) mat->Diffuse = 0xffffffff;
if(sCmpString(pname,"Enable_Specular")==0) mat->Specular = 0xffffffff;
if(sCmpString(pname,"Enable_Shininess")==0) mat->Specularity = 0;
// if(sCmpString(pname,"Enable_Lighting")==0) mat->Flags &= ~sMF_LIGHTMASK;
}
}
else
{
Error = sTRUE;
}
}
for(i=0;i<ccount;i++)
{
ScanString(pname,sizeof(pname));
ScanString(buffer,sizeof(buffer));
ScanString(tname,sizeof(tname));
if(sCmpString(tname,"IMAGE")==0)
{
if((sCmpString(pname,"Texture_1")==0 || sCmpString(pname,"tex")==0) && texena[0])
{
if(mat->Tex[0] == 0
&& (tsup[0][0]!=0 || (mat->TFlags[0]&sMTF_UVMASK)==sMTF_UVENVI)
&& TSCount<sXSI_MAXTS)
{
tex = FindTexture(buffer);
if(tex)
{
mat->Tex[0] = tex;
mat->Mode = sMBM_TEX;
sCopyString(TSName[TSCount],tsup[0],XSISIZE);
mat->TUV[0] = TSCount++;
}
}
}
if(sCmpString(pname,"Texture_2")==0 && texena[1])
{
if(mat->Tex[1] == 0
&& (tsup[1][0]!=0 || (mat->TFlags[1]&sMTF_UVMASK)==sMTF_UVENVI)
&& TSCount<sXSI_MAXTS)
{
tex = FindTexture(buffer);
if(tex)
{
mat->Tex[1] = tex;
mat->Mode = sMBM_MUL;
// mat->TFlags[1] = sMTF_FILTER|sMTF_MIPMAP;//|sMTF_UVENVI;
sCopyString(TSName[TSCount],tsup[1],XSISIZE);
mat->TUV[1] = TSCount++;
}
}
}
}
}
sScanSpace(Scan);
while(*Scan!=0 && *Scan!='}' && !Error)
{
ScanChunk(indent+1,chunk,name);
SkipChunk();
sScanSpace(Scan);
}
EndChunk();
}
else
{
SkipChunk();
}
sScanSpace(Scan);
}
if((mat->TFlags[1] & sMTF_UVMASK)==0)
mat->TFlags[1] |= sMTF_UV1;
if(mat->Specularity>0.0001f || mat->Ambient!=0xffffffff
|| mat->Diffuse != 0xffffffff || mat->Specular != 0xffffffff)
{
// mat->Flags = (mat->Flags & (~sMF_LIGHTMASK)) | sMF_LIGHTMAT;
// sDPrintF("extlight: %08x %08x %08x\n",mat->Diffuse.Color,mat->Ambient.Color,mat->Specular.Color);
}
else
{
// mat->Flags |= sMF_COLBOTH;
}
mat->TFlags[0] |= sMTF_FILTERMIN | sMTF_FILTERMAG | sMTF_MIPMAP;
mat->TFlags[1] |= sMTF_FILTERMIN | sMTF_FILTERMAG | sMTF_MIPMAP;
EndChunk();
}
else
{
SkipChunk();
}
sScanSpace(Scan);
}
EndChunk();
}
void sXSILoader::ScanMesh(sInt indent,sXSIModel *model)
{
sChar buffer[256];
sChar chunk[XSISIZE];
sChar name[XSISIZE];
sChar *cmd;
sInt supports,i,j,k,max;
sInt fcount;
sInt vcount;
sXSICluster *cluster;
sInt cr,cg,cb,ca;
sInt set,set2;
sInt PosCount;
sVector *Pos;
sInt NormCount;
sVector *Norm;
sInt ColorCount;
sU32 *Color;
sInt UVCount[sXSI_MAXUV];
sF32 *UV[sXSI_MAXUV];
sChar UVName[sXSI_MAXUV][XSISIZE];
// init shape holder
PosCount = 0;
Pos = 0;
NormCount = 0;
Norm = 0;
ColorCount = 0;
Color = 0;
for(i=0;i<sXSI_MAXUV;i++)
{
UVCount[i] = 0;
UV[i] = 0;
}
while(*Scan!=0 && *Scan!='}' && !Error)
{
ScanChunk(indent,chunk,name);
if(sCmpString(chunk,"SI_Shape")==0)
{
supports = ScanInt();
ScanString(buffer,sizeof(buffer));
if(sCmpString(buffer,"ORDERED")!=0)
Error = sTRUE;
for(i=0;i<supports && !Error;i++)
{
max = ScanInt();
ScanString(buffer,sizeof(buffer));
if(sCmpString(buffer,"POSITION")==0)
{
sVERIFY(Pos==0);
PosCount = max;
Pos = new sVector[max];
for(j=0;j<max;j++)
{
Pos[j].x = ScanFloat();
Pos[j].y = ScanFloat();
Pos[j].z = ScanFloat();
}
}
else if(sCmpString(buffer,"NORMAL")==0)
{
sVERIFY(Norm==0);
NormCount = max;
Norm = new sVector[max];
for(j=0;j<max;j++)
{
Norm[j].x = ScanFloat();
Norm[j].y = ScanFloat();
Norm[j].z = ScanFloat();
}
}
else if(sCmpString(buffer,"COLOR")==0)
{
sVERIFY(Color==0);
ColorCount = max;
Color = new sU32[max];
for(j=0;j<max;j++)
{
cr = sRange<sInt>(ScanFloat()*255,255,0);
cg = sRange<sInt>(ScanFloat()*255,255,0);
cb = sRange<sInt>(ScanFloat()*255,255,0);
ca = sRange<sInt>(ScanFloat()*256,255,0);
Color[j] = (ca<<24)|(cb<<16)|(cg<<8)|(cr);
}
}
else if(sCmpString(buffer,"TEX_COORD_UV")==0)
{
set = 0;
sVERIFY(UV[set]==0);
UVCount[set] = max;
UV[set] = new sF32[max*2];
for(j=0;j<max;j++)
{
UV[set][j*2+0] = ScanFloat();
UV[set][j*2+1] = 1.0f-ScanFloat();
}
}
else if(sCmpMem(buffer,"TEX_COORD_UV",12)==0)
{
j=12;
set = 0;
while(buffer[j]>='0' && buffer[j]<='9')
set = set*10 + (buffer[j++]-'0');
sVERIFY(set>=0 && set<sXSI_MAXUV);
sVERIFY(UV[set]==0);
ScanString(UVName[set],sizeof(UVName[set]));
UVCount[set] = max;
UV[set] = new sF32[max*2];
for(j=0;j<max;j++)
{
UV[set][j*2+0] = ScanFloat();
UV[set][j*2+1] = 1.0f-ScanFloat();
}
}
else
{
Error = sTRUE;
}
}
EndChunk();
}
else if(sCmpString(chunk,"SI_PolygonList")==0)
{
cluster = new sXSICluster;
fcount = ScanInt();
sCopyString(buffer,"|POSITION|",sizeof(buffer));
i = sGetStringLen(buffer);
ScanString(buffer+i,sizeof(buffer)-i);
#if DUMPCHUNK
sDPrintF(" %s",buffer);
#endif
ScanString(name,sizeof(name));
cluster->Material = FindMaterial(name);
vcount = ScanInt();
cluster->VertexCount = vcount;
cluster->IndexCount = vcount;
cluster->Vertices = new sXSIVertex[vcount];
cluster->Faces = new sInt[vcount*2];
model->Clusters->Add(cluster);
j = 0;
for(i=0;i<fcount;i++)
{
max = ScanInt();
cluster->Vertices[j].Init();
cluster->Faces[j*2+0] = max;
cluster->Faces[j*2+1] = j;
j++;
for(k=1;k<max;k++)
{
cluster->Vertices[j].Init();
cluster->Faces[j*2+0] = 0;
cluster->Faces[j*2+1] = j;
j++;
}
}
sVERIFY(j==vcount);
cmd = buffer;
while(!Error && *cmd)
{
if(sCmpMem(cmd,"|POSITION",9)==0)
{
cmd+=9;
sVERIFY(Pos);
for(i=0;i<vcount;i++)
{
j = ScanInt();
cluster->Vertices[i].Pos = Pos[j];
cluster->Vertices[i].Index = j;
}
}
else if(sCmpMem(cmd,"|NORMAL",7)==0)
{
cmd+=7;
sVERIFY(Norm);
for(i=0;i<vcount;i++)
{
j = ScanInt();
cluster->Vertices[i].Normal = Norm[j];
cluster->Vertices[i].Normal.Init(0,0,0,1);
}
}
else if(sCmpMem(cmd,"|COLOR",6)==0)
{
cmd+=6;
sVERIFY(Color);
for(i=0;i<vcount;i++)
{
j = ScanInt();
cluster->Vertices[i].Color = Color[j];
}
}
else if(sCmpMem(cmd,"|TEX_COORD_UV",13)==0)
{
cmd+=13;
set = 0;
if(*cmd>='0' && *cmd<='9')
{
while(*cmd>='0' && *cmd<='9')
set = set*10 + ((*cmd++)-'0');
sVERIFY(set>=0 && set<sXSI_MAXUV);
sVERIFY(UV[set])
for(set2=0;set2<4;set2++)
if(sCmpString(TSName[cluster->Material->TUV[set2]],UVName[set])==0)
break;
}
else
{
set2 = 0;
}
for(i=0;i<vcount;i++)
{
j = ScanInt();
if(set2>=0 && set2<2)
{
cluster->Vertices[i].UV[set2][0] = 0.0f;// UV[set][j*2+0];
cluster->Vertices[i].UV[set2][1] = 0.0f;// UV[set][j*2+1];
}
}
}
else
{
void Lexer::ScanNumber()
{
PushBack(*--tp);
ScanInteger(10);
char ch = PeekAtChar();
// If they both read the same number of characters or the integer ended
// in a radix specifier then we got ourselves an integer but we'll need
// to check its in range later.
//
switch (ch)
{
case 'r':
{
if (m_tokenType != SmallIntegerConst)
return;
if (m_integer >= 2 && m_integer <= 36)
{
// Probably a short or long integer with a leading radix.
*tp++ = NextChar();
char* startSuffix = tp;
int radix = m_integer;
ScanInteger(radix);
if (tp == startSuffix)
{
m_integer = radix;
tp--;
PushBack(ch);
}
}
}
break;
case 's':
// A ScaledDecimal
*tp++ = NextChar();
// We must read over the trailing scale (optional)
while (isdigit(PeekAtChar()))
*tp++ = NextChar();
m_tokenType = ScaledDecimalConst;
break;
case '.':
// Its probably a floating value but might actually
// be the end of statement
ScanFloat();
if (PeekAtChar() == 's')
{
// Its a scaled decimal - include any trailing digits
*tp++ = NextChar();
while (isdigit(PeekAtChar()))
*tp++ = NextChar();
m_tokenType = ScaledDecimalConst;
}
break;
case 'e':
{
// Allow old St-80 exponent form, such as 1e6
ScanExponentInteger();
}
default:
break;
};
}
