int main()
{
char s[81];
gets(s);
removeSpace(s);
printf("%s", s);
return 0;
}
int main(int argc, char * argv[]) {
/* must be defined as an array */
/* if defined as a pont, it will be read only space */
char str[] = " hello world ";
removeSpace(str);
printf("%s\n", str);
return 1;
}
//if true return true, and also set the path
bool plainconf::isInclude(const char *sLine, AutoStr2 &path)
{
if (strncasecmp(sLine, "include", 7) == 0)
{
char *p = (char *)sLine + 7;
removeSpace(p, 0);
path = p;
return true;
}
return false;
}
int main (int argc, const char * argv[]) {
char string[100];
char ch;
int i = 0;
printf("Enter input: \n");
while (gets(string) && string[0] != '\0') {
removeSpace(string);
printf("The new sentence: %s\n", string);
}
return 0;
}
int main(int argc, char* argv[]) { //表达式求值（入口）
for (int i=1; i<argc; i++) { //逐一处理各命令行参数（表达式）
/*DSA*/system("cls"); printf("\nPress any key to evaluate: [%s]\a\n", argv[i]); getchar();
char* rpn = (char*)malloc(sizeof(char)*1); rpn[0] = '\0'; //逆波兰表达式
float value = evaluate(removeSpace(argv[i]), rpn); //求值
/*DSA*/printf("EXPR\t: %s\n", argv[i]); //输出原表达式
/*DSA*/printf("RPN\t: [ %s]\n", rpn); //输出RPN
/*DSA*/printf("Value\t= %.1f = %d\n", value, (int)value); //输出表达式的值
free(rpn); rpn = NULL;
/*DSA*/getchar();
}
return 0;
}
Node makeNodeElements(Node new_node, char* string, int i) {
char* value_for_insertion = removeSpace(string);
switch (i){
case 0:
strcpy(new_node->name, value_for_insertion);
break;
case 1:
strcpy(new_node->route->bus_line, value_for_insertion);
break;
case 2:
strcpy(new_node->start_time, value_for_insertion);
break;
}
return new_node;
}
void ParseAsset(const char* filename) {
FILE* file = fopen(filename, "r");
char* start;
char* end;
char raw_line[256];
char line[256];
printf("Parsing...\n");
void* gameAssetPointer; //just so I remeber that we'll need such a pointer
void* compoundAssetPointer; //ditto
while (fgets(raw_line, 256, file) != NULL) {
strncpy(line, removeSpace(raw_line), 256); //filter out whitespace
if (strchr(raw_line, '#') != NULL) { //filter out comments
end = strchr(raw_line, '#');
*end = '\0';
}
if (line[0] == '[') { //define a section
if (strchr(line, ']') == NULL) { //make sure the syntax is correct
printf("Error, bad syntax in: %s\n", line);
exit(1);
}
*strchr(line, ']') = '\0';
printf("Section: %s\n", line + 1);
}
else if (strchr(line, ':') != NULL) { //define a param/value pair
end = strchr(line, ':');
*end = '\0';
//if (strpbrk(line, "Texture") == NULL)
if (!strcmp(line, "Texture"))
printf("Got Texture: %s\n", end + 1);
else if (!strcmp(line, "Offset"))
printf("Got Offset: %s\n", end + 1);
else if (!strcmp(line, "Origin"))
printf("Got Origin: %s\n", end + 1);
}
}
}
void listInstruction(char *filepath, int n) {
FILE *fp;
fp = fopen(filepath,"r");
char *buffer = (char *) malloc(BUFFER_SIZE * sizeof(char));
if (fp==NULL) {
perror("ERROR in opening file");
exit(EXIT_FAILURE);
}
while (!feof(fp) &&0<n ){
memset(buffer, 0, ((sizeof(char))*BUFFER_SIZE));
fgets (buffer, BUFFER_SIZE, fp);
if(strlen(buffer)>1) n--;
}
if(n==0) {
printf("%s", removeSpace(buffer));
}
else{
perror("End of file reached before line");
}
free(buffer);
fclose(fp);
}
//----------------------------------------------------------------------//
void CIO::commVecPDB(const vector<string>& strCommPDB)
{
string strLine,strSubLine,strHeader,strX,strY,strZ;
delphi_integer iAtomIndex = 0;
CAtomPdb tmpAtomObj;
for (int i = 0; i < strCommPDB.size(); ++i)
{
strLine = strCommPDB[i];
// to ignore possible empty lines
strSubLine = removeSpace(strLine);
if (0 == strSubLine.compare(0,1,"")) continue;
strHeader = strLine.substr(0,6); strHeader = toUpperCase(strHeader);
if (0 == strHeader.compare("ATOM ") || 0 == strHeader.compare("HETATM"))
{
tmpAtomObj.setAtInf(strLine.substr(11,15));
strX = strLine.substr(30,8); strX = removeSpace(strX);
strY = strLine.substr(38,8); strY = removeSpace(strY);
strZ = strLine.substr(46,8); strZ = removeSpace(strZ);
tmpAtomObj.setPose( atof(strX.c_str()),atof(strY.c_str()),atof(strZ.c_str()) );
strSubLine = strLine.substr(54,8); strSubLine = removeSpace(strSubLine);
tmpAtomObj.setCharge( (delphi_real)atof(strSubLine.c_str()) );
strSubLine = strLine.substr(62,7); strSubLine = removeSpace(strSubLine);
tmpAtomObj.setRadius( (delphi_real)atof(strSubLine.c_str()) );
vctapAtomPdb.push_back(tmpAtomObj);
vctiAtomMediaNum.push_back(iObjectMediaNum);
iAtomIndex += 1;
}
else
continue;
}
}
void readFASTA(
const std::string& inPath,
const std::string& outPath,
const int maxLength,
const int overlapLength) {
std::ifstream ifs(inPath.c_str());
std::string buf;
std::string label;
std::string sequence;
while(ifs && std::getline(ifs, buf)) {
if(buf.find(">") != std::string::npos) {
if(!label.empty()) {
splitFASTA(label, sequence, outPath, maxLength, overlapLength);
eraseData(label, sequence);
}
label = buf;
} else if(buf.empty()) {
if(!label.empty()) {
splitFASTA(label, sequence, outPath, maxLength, overlapLength);
eraseData(label, sequence);
}
} else {
if(!label.empty()) {
removeSpace(buf);
sequence += buf;
}
}
}
if(ifs.eof()) {
if(!label.empty()) {
splitFASTA(label, sequence, outPath, maxLength, overlapLength);
eraseData(label, sequence);
}
}
}
//-----------------------------------------------------------------------//
void CIO::readModFile1(ifstream& ifPdbFileStream)
{
int iObjectType = 0; // objecttype, 1-sphere, 2-cylinder
delphi_real fInDielec = 0.0; // repsintmp
string strLine,strSubLine,strHeader,strX,strY,strZ;
delphi_integer iObjectIndex = 0,iAtomIndex = 0;
ifPdbFileStream.clear(); ifPdbFileStream.seekg(0); // rewind
CAtomPdb tmpAtomObj;
while (!ifPdbFileStream.eof())
{
getline(ifPdbFileStream,strLine);
// to ignore possible empty lines
strSubLine = removeSpace(strLine);
if (0 == strSubLine.compare(0,1,"")) continue;
strHeader = strLine.substr(0,6); strHeader = toUpperCase(strHeader);
if (0 == strHeader.compare("MEDIA "))
// # of media has been read during first file reading
continue;
else if (0 == strHeader.compare("OBJECT"))
{
strSubLine = strLine.substr(7,3); strSubLine = removeSpace(strSubLine);
iObjectIndex = atoi( strSubLine.c_str() );
strSubLine = strLine.substr(11,3); strSubLine = removeSpace(strSubLine);
iObjectType = atoi( strSubLine.c_str() );
strSubLine = strLine.substr(15,3); strSubLine = removeSpace(strSubLine);
iObjectMediaNum = atoi( strSubLine.c_str() );
strSubLine = strLine.substr(19,8); strSubLine = removeSpace(strSubLine);
fInDielec = atof( strSubLine.c_str() );
// entries of vctfMediaEps have been initialized to be 1/epkt
vctfMediaEps.push_back(fInDielec/fEPKT);
if (0 != iObjectType)
{
bOnlyMolecule = false;
// dataobject(iObjectIndex,1) and dataobject(iObjectIndex,2)
vctstrObject.push_back(strLine);
vctstrObject.push_back(string(" "));
}
else
{
// dataobject(iObjectIndex,1) and dataobject(iObjectIndex,2)
vctstrObject.push_back(string("is a molecule 0"));
vctstrObject.push_back(string(" "));
prgiObjectMediaNum.push_back(iObjectMediaNum);
}
}
else if (0 == strHeader.compare("CRGDST"))
throw CUnsupportedCRGDST(strLine);
else if (0 == strHeader.compare("ATOM ") || 0 == strHeader.compare("HETATM"))
{
tmpAtomObj.setAtInf(strLine.substr(11,15));
strX = strLine.substr(30,8); strX = removeSpace(strX);
strY = strLine.substr(38,8); strY = removeSpace(strY);
strZ = strLine.substr(46,8); strZ = removeSpace(strZ);
tmpAtomObj.setPose( atof(strX.c_str()),atof(strY.c_str()),atof(strZ.c_str()) );
strSubLine = strLine.substr(54,6); strSubLine = removeSpace(strSubLine);
tmpAtomObj.setRadius( (delphi_real)atof(strSubLine.c_str()) );
strSubLine = strLine.substr(60,7); strSubLine = removeSpace(strSubLine);
tmpAtomObj.setCharge( (delphi_real)atof(strSubLine.c_str()) );
vctapAtomPdb.push_back(tmpAtomObj);
vctiAtomMediaNum.push_back(iObjectMediaNum);
iAtomIndex += 1;
}
else
continue;
} // ---------- end of while (!ifPdbFileStream.eof())
}
//-----------------------------------------------------------------------//
// atom(a6),residue(a3),radius(f8.4) or charge(f8.4)
// aaaaaarrrfff.ffff
void CIO::readFileInNotPKFormat(ifstream& ifFileStream, const int& iFileType)
{
//getForceFileRecordNum(ifFileStream,iFileType);
vector<CForce> * prgaf; // pointer to an array fo CForce
if (SIZEFILE == iFileType) { prgaf = &prgas; }
else if (CHARGEFILE == iFileType) { prgaf = &prgac; }
string strLine, strSubLine;
ifFileStream.clear(); ifFileStream.seekg(0); // rewind
while (!ifFileStream.eof()) // skip comments and header
{
getline(ifFileStream,strLine);
strSubLine = removeSpace(strLine);
if (0 == strSubLine.compare(0,1,"")) continue; // ignore possible empty lines
if ('!' != strLine[0]) break; // header
}
CForce tmpForceObj;
while (!ifFileStream.eof())
{
getline(ifFileStream, strLine);
if ('!' == strLine[0]) continue; // skip commented line
// to ignore possible empty lines
strSubLine = removeSpace(strLine);
if (0 == strSubLine.compare(0,1,"")) continue;
strSubLine = strLine.substr(0,6); // atom name, 6 characters
if (0 != strSubLine.compare(0,6," "))
{
strSubLine = removeSpace(strSubLine);
strSubLine = toUpperCase(strSubLine);
}
else
strSubLine = " ";
tmpForceObj.setAtom(strSubLine);
strSubLine = strLine.substr(6,3); // residue name, 3 characters
if (0 != strSubLine.compare(0,3," "))
{
strSubLine = removeSpace(strSubLine);
strSubLine = toUpperCase(strSubLine);
}
else
strSubLine = " ";
tmpForceObj.setResidue(strSubLine);
tmpForceObj.setResidueNum(" "); // residue number
tmpForceObj.setChain(" "); // subunit name
strSubLine = strLine.substr(9,8); // radius or charge
strSubLine = removeSpace(strSubLine);
tmpForceObj.setValue( atof(strSubLine.c_str()) );
prgaf->push_back(tmpForceObj);
} // ---------- end of while (!ifFileStream.eof())
}
void plainconf::parseLine(const char *fileName, int lineNumber,
const char *sLine)
{
const int MAX_NAME_LENGTH = 4096;
char name[MAX_NAME_LENGTH] = {0};
char value[MAX_NAME_LENGTH] = {0};
const char *attr = NULL;
XmlNode *pNode = NULL;
XmlNode *pCurNode = (XmlNode *)gModuleList.back();
const char *p = sLine;
const char *pEnd = sLine + strlen(sLine);
bool bNameSet = false;
for (; p < pEnd; ++p)
{
//"{" is a beginning of a block only if it is the last char of a line
if (*p == '{' && pEnd - p == 1)
{
if (strlen(name) > 0)
{
const char *pRealname = getRealName(name);
if (pRealname)
{
pNode = new XmlNode;
pNode->init(pRealname, &attr);
//Remove space in the end of the value such as "module cache {", value will be "cache"
removeSpace(value, 1);
if (strlen(value) > 0)
pNode->setValue(value, strlen(value));
pCurNode->addChild(pNode->getName(), pNode);
gModuleList.push_back(pNode);
pCurNode = pNode;
clearNameAndValue(name, value);
break;
}
else
{
logToMem(LOG_LEVEL_ERR,
"parseline find block name [%s] is NOT keyword in %s:%d", name, fileName,
lineNumber);
break;
}
}
else
{
logToMem(LOG_LEVEL_ERR,
"parseline found '{' without a block name in %s:%d", fileName, lineNumber);
break;
}
}
else if (*p == '}' && p == sLine)
{
if (gModuleList.size() > 1)
{
gModuleList.pop_back();
clearNameAndValue(name, value);
if (*(p + 1))
{
++p;
trimWhiteSpace(&p);
parseLine(fileName, lineNumber, p);
break;
}
}
else
{
logToMem(LOG_LEVEL_ERR, "parseline found more '}' in %s:%d", fileName,
lineNumber);
clearNameAndValue(name, value);
break;
}
}
else if ((*p == ' ' || *p == '\t') && value[0] == 0)
{
bNameSet = true;
continue;
}
else
{
if (!bNameSet)
strcatchr(name, *p, MAX_NAME_LENGTH);
else
strcatchr(value, *p, MAX_NAME_LENGTH);
}
}
if (name[0] != 0)
{
const char *pRealname = getRealName(name);
if (pRealname)
{
assert(pNode == NULL);
pNode = new XmlNode;
pNode->init(pRealname, &attr);
if (strlen(value) > 0)
pNode->setValue(value, strlen(value));
pCurNode->addChild(pNode->getName(), pNode);
}
else
{
//There is no special case in server level
//if (memcmp(pCurNode->getName(), SERVER_ROOT_XML_NAME, sizeof(SERVER_ROOT_XML_NAME) - 1) != 0)
saveUnknownItems(fileName, lineNumber, pCurNode, name, value);
//else
// logToMem(LOG_LEVEL_ERR, "%s Server level find unknown keyword [%s], ignored.", SERVER_ROOT_XML_NAME, name );
}
}
}
//This function may be recruse called
void plainconf::loadConfFile(const char *path)
{
logToMem(LOG_LEVEL_INFO, "start parsing file %s", path);
int type = checkFiletype(path);
if (type == 0)
return;
else if (type == 2)
loadDirectory(path, NULL);
else if (type == 3)
{
AutoStr2 prefixPath = path;
const char *p = strrchr(path, '/');
if (p)
prefixPath.setStr(path, p - path);
struct stat sb;
//removed the wildchar filename, should be a directory if exist
if (stat(prefixPath.c_str(), &sb) == -1)
{
logToMem(LOG_LEVEL_ERR, "LoadConfFile error 1, path:%s directory:%s",
path, prefixPath.c_str());
return ;
}
if ((sb.st_mode & S_IFMT) != S_IFDIR)
{
logToMem(LOG_LEVEL_ERR, "LoadConfFile error 2, path:%s directory:%s",
path, prefixPath.c_str());
return ;
}
loadDirectory(prefixPath.c_str(), p + 1);
}
else //existed file
{
//gModuleList.push_back();
//XmlNode *xmlNode = new XmlNode;
FILE *fp = fopen(path, "r");
if (fp == NULL)
{
logToMem(LOG_LEVEL_ERR, "Cannot open configuration file: %s", path);
return;
}
const int MAX_LINE_LENGTH = 8192;
char sLine[MAX_LINE_LENGTH];
char *p;
char sLines[MAX_LINE_LENGTH] = {0};
int lineNumber = 0;
const int MAX_MULLINE_SIGN_LENGTH = 128;
char sMultiLineModeSign[MAX_MULLINE_SIGN_LENGTH] = {0};
size_t nMultiLineModeSignLen = 0; //>0 is mulline mode
while (fgets(sLine, MAX_LINE_LENGTH, fp), !feof(fp))
{
++lineNumber;
p = sLine;
if (nMultiLineModeSignLen)
{
//Check if reach the END of the milline mode
size_t len = 0;
const char *pLineStart = getStrNoSpace(p, len);
if (len == nMultiLineModeSignLen &&
strncasecmp(pLineStart, sMultiLineModeSign, nMultiLineModeSignLen) == 0)
{
nMultiLineModeSignLen = 0;
removeSpace(sLines,
1); //Remove the last \r\n so that if it is one line, it will still be one line
parseLine(path, lineNumber, sLines);
sLines[0] = 0x00;
}
else
strcat(sLines, p);
continue;
}
removeSpace(p, 0);
removeSpace(p, 1);
if (!isValidline(p))
continue;
AutoStr2 pathInclude;
if (isInclude(p, pathInclude))
{
char achBuf[512] = {0};
getIncludeFile(pathInclude.c_str(), achBuf);
loadConfFile(achBuf);
}
else
{
nMultiLineModeSignLen = checkMultiLineMode(p, sMultiLineModeSign,
MAX_MULLINE_SIGN_LENGTH);
if (nMultiLineModeSignLen > 0)
strncat(sLines, p, strlen(p) - (3 + nMultiLineModeSignLen));
//need to continue
else if (isChunkedLine(p))
{
strncat(sLines, p, strlen(p) - 1);
//strcatchr(sLines, ' ', MAX_LINE_LENGTH); //add a space at the end of the line which has a '\\'
}
else
{
strcat(sLines, p);
parseLine(path, lineNumber, sLines);
sLines[0] = 0x00;
}
}
}
fclose(fp);
//Parsed, check in it
checkInFile(path);
}
}
//-----------------------------------------------------------------------//
void CIO::readForceFile(const string & strFile)
{
ifstream ifFileStream;
// open the file with name strParamFile
ifFileStream.open(strFile.c_str());
// if the file doesnt exists, exit
if (!ifFileStream.is_open()) throw CUnknownIOFile(strFile);
string strLine, strSubLine;
while (!ifFileStream.eof()) // skip comments and empty lines till the header
{
getline(ifFileStream,strLine);
strSubLine = removeSpace(strLine);
if (0 == strSubLine.compare(0,1,"")) continue; // ignore possible empty lines
if ('!' != strLine[0]) break; // header
}
if ( 0 == strLine.find("atom__res_radius") || 0 == strLine.find("atom__resnumbc_radius_") )
cout << "\n" << "atom radii read from file " << strFile << "\n";
else if ( 0 == strLine.find("atom__res_charge") || 0 == strLine.find("atom__resnumbc_charge_") )
cout << "\n" << "atomic charges read from file " << strFile << "\n";
else
throw CUnknownForceFileHeader(strFile,strLine);
ifFileStream.clear(); ifFileStream.seekg(0); // rewind
while (!ifFileStream.eof()) // skip and print comments (start with !) till the header
{
getline(ifFileStream,strLine);
strSubLine = removeSpace(strLine);
if (0 == strSubLine.compare(0,1,"")) continue; // ignore possible empty lines
if ('!' != strLine[0]) break; // header
cout << strLine << endl; // print comments
}
// determine file format
// isPK = false:
// atom(a6),residue(a3),radius(f8.4): aaaaaarrrfff.ffff
// isPK = true:
// atom(a6),residue(a3),residue_number(a4),subunit(a1),radius(f8.4):
// aaaaaarrrnnnncfff.ffff
if (0 == strLine.find("atom__res_radius") || 0 == strLine.find("atom__resnumbc_radius_"))
{
if (0 == strLine.find("atom__res_radius"))
{
readFileInNotPKFormat(ifFileStream,SIZEFILE);
#ifdef DEBUG_IO_SIZE
printForce(SIZEFILE);
#endif
}
else if (0 == strLine.find("atom__resnumbc_radius_"))
{
cout << "reading pK style radius file \n";
readFileInPKFormat(ifFileStream,SIZEFILE);
#ifdef DEBUG_IO_SIZE
printForce(SIZEFILE);
#endif
}
iRadiusNum = prgas.size(); // # of entries in radius file
cout << "# of radius parameter records: \t\t" << iRadiusNum << "\n";
}
else // 0 == strLine.find("atom__res_charge") ||
// 0 == strLine.find("atom__resnumbc_charge_")
{
if (0 == strLine.find("atom__res_charge"))
{
readFileInNotPKFormat(ifFileStream,CHARGEFILE);
#ifdef DEBUG_IO_CHARGE
printForce(CHARGEFILE);
#endif
}
else if (0 == strLine.find("atom__resnumbc_charge_"))
{
cout << "reading pK style charge file \n";
readFileInPKFormat(ifFileStream,CHARGEFILE);
#ifdef DEBUG_IO_CHARGE
printForce(CHARGEFILE);
#endif
}
iCrgNum = prgac.size(); // # of entries in charge file
cout << "# of charge parameter records: \t\t" << iCrgNum << "\n";
}
ifFileStream.close();
}
void CIO::readPdbFile(const string& strPdbFile, const int& iPdbFormat, const bool& bPdbUnformatIn,
const vector<string>& strCommPDB)
{
if (CommPDB == iPdbFormat) {
bExistRadiiInfo = true;
bool bPostProcess = true;
vctfMediaEps.push_back(0.0); // medeps(0)
commVecPDB(strCommPDB);
iAtomNum = vctapAtomPdb.size();
if (bPostProcess)
{
if (0 == vctfMediaEps.size()) vctfMediaEps.push_back(0.0); // medeps(0)
cout << "You are not reading from an object file! \n";
cout << "Assuming having only molecules, and one medium \n";
vctfMediaEps.push_back(fDielec/fEPKT); // medeps(1)=repsin/epkt
// dataobject(1,1) and dataobject(1,2)
vctstrObject.push_back(string("is a molecule 0"));
vctstrObject.push_back(string(" "));
prgiObjectMediaNum.push_back(iObjectMediaNum);
}
iObjectNum = vctstrObject.size()/2;
iMediaNum = vctfMediaEps.size()-1;
// regardless of being a molecule or not, iatmmed has a field to say which is its medium
if (0 != prgiObjectMediaNum.size())
{
for (unsigned i=0; i < prgiObjectMediaNum.size(); i++)
vctiAtomMediaNum.push_back(prgiObjectMediaNum[i]);
prgiObjectMediaNum.clear();
}
}
else
{
bExistRadiiInfo = false; // iatrad, whether there is radius info
ifstream ifPdbFileStream;
ifPdbFileStream.open(strPdbFile.c_str());
if (!ifPdbFileStream.is_open()) throw CUnknownIOFile(strPdbFile);
bool bPostProcess = true;
int iFormatID = 0; // idfrm
if(!bPdbUnformatIn) // ---------- formatted pdb file ---------- //
{
string strLine, strSubLine, strHeader;
cout << "\nopening formatted file: " << strPdbFile << endl;
// Now only delphi mod type pdb files have keyword "DELPHI PDB", other pdb files
// such as standard, mod4 and pqr pdb files do not check the keyword any more
if (MODPDB == iPdbFormat) // mod pdb file
{
getline(ifPdbFileStream,strLine); // read the 1st line
string strHeadFirst = strLine.substr(0,6);
strHeadFirst = removeSpace(strHeadFirst);
strHeadFirst = toUpperCase(strHeadFirst);
if (0 == strHeadFirst.compare(0,5,"MEDIA")) bPostProcess = false;
if (string::npos != strLine.find("DELPHI")) // find keyword "DELPHI"
{
if (string::npos == strLine.find("PDB")) // no keyword "PDB" is found
throw CUnknownDelphiPdb(strPdbFile);
cout << "Reading a Delphi-style pdb file \n";
getline(ifPdbFileStream,strLine); // read the 2nd line
size_t found = strLine.find_first_of('=');
strSubLine = strLine.substr(found+1,strLine.size()-found-1);
strSubLine = removeSpace(strSubLine);
iFormatID = atoi(strSubLine.c_str());
cout << "Read Delphi Format Number = " << iFormatID << endl;
if (1 != iFormatID && 4 != iFormatID)
throw CUnknownModPdb(strPdbFile,iFormatID);
}
}
else
{
ifPdbFileStream.clear(); ifPdbFileStream.seekg(0); // rewind
cout << "No DELPHI keyword, assuming Delphi Format number = " << iFormatID << endl;
}
if (STDPDB == iPdbFormat) bExistRadiiInfo = false; // standard pdb
else bExistRadiiInfo = true; // others
// medeps(0:nmediamax)
vctfMediaEps.push_back(0.0); // medeps(0)
switch (iPdbFormat)
{
case STDPDB: // standard pdb
readStdPdbFile(ifPdbFileStream);
break;
case MODPDB: // mod pdb
if (1 == iFormatID) readModFile1(ifPdbFileStream);
else readModFile4(ifPdbFileStream); // 4 == iFormatID
break;
case PQRPDB: // pqr pdb
readPqrFile(ifPdbFileStream);
break;
case MOD4PDB: // mod4 pdb
readMod4File(ifPdbFileStream);
break;
case PQR4PDB: // pqr4 pdb
readPqr4File(ifPdbFileStream);
break;
}
iAtomNum = vctapAtomPdb.size();
cout << "number of atoms read in = " << iAtomNum << " formatted \n";
}
else // ---------- unformatted pdb file ---------- //
{
int iUnformatID = 0; // idfrm
char cLine[80]; // line
bExistRadiiInfo = true;
ifPdbFileStream.read(cLine,80); // header
string strHeader(cLine); // string to be converted from cLine for simpler manipulation
if (string::npos != strHeader.find("DELPHI")) // find keyword "DELPHI"
{
if (string::npos == strHeader.find("PDB")) // no keyword "PDB" is found
throw CUnknownDelphiPdb(strPdbFile);
cout << "Reading a Delphi-style pdb file \n";
}
ifPdbFileStream.read( reinterpret_cast<char*>(&iUnformatID), sizeof(int) ); // idfrm
if (0 != iUnformatID && 1 != iUnformatID) throw CUnknownUnformattedPdb(strPdbFile);
readUnformattedPdb(strPdbFile,ifPdbFileStream,bPostProcess);
}
#ifdef DEBUG_IO_PDB
printPDB();
#endif
// Some post-processing
if (bPostProcess)
{
if (0 == vctfMediaEps.size()) vctfMediaEps.push_back(0.0); // medeps(0)
cout << "You are not reading from an object file! \n";
cout << "Assuming having only molecules, and one medium \n";
vctfMediaEps.push_back(fDielec/fEPKT); // medeps(1)=repsin/epkt
// dataobject(1,1) and dataobject(1,2)
vctstrObject.push_back(string("is a molecule 0"));
vctstrObject.push_back(string(" "));
prgiObjectMediaNum.push_back(iObjectMediaNum);
}
iObjectNum = vctstrObject.size()/2;
iMediaNum = vctfMediaEps.size()-1;
// regardless of being a molecule or not, iatmmed has a field to say which is its medium
if (0 != prgiObjectMediaNum.size())
{
for (unsigned i=0; i < prgiObjectMediaNum.size(); i++)
vctiAtomMediaNum.push_back(prgiObjectMediaNum[i]);
prgiObjectMediaNum.clear();
}
ifPdbFileStream.close();
}
}
void CSite::writeSite(const int& iisitsf)
{
//---------------------------------------------------------------------------------------------//
bool isita = bAtomInSite, isiti = bSaltInSite, isitmd = bMDInSite, isitpot = bPotentialInSite,
isitx = bAtomCoordInSite, isitq = bCrgInSite, isitf = bFieldInSite, isitp = bGridPotentialInSite,
isitr = bReactPotentialInSite, isitc = bCoulombPotentialInSite, isitap = bAtomPotentialInSite, isitdeb = bDebyeFractionInSite,
isitsf = bSurfCrgInSite, isittf = bTotalForceInSite, isitrf = bReactForceInSite, isitt = bTotalPotentialInSite,
isitcf = bCoulombForceInSite, iself = bPDB2FRCInSite;
//----- ifrm is true if ANY of the flags for special output have been set
bool ifrm = isita || isitq || isitp || isitf || isitr || isitt || isitc || isitx || isiti || isitrf || isitcf || isitap ||
isittf || isitdeb;
bool isitmp1 = ifrm; ifrm = ifrm || isitsf;
bool ofrm = true;
if (isitmd || isitpot) {iFrcFormatOut = -1; ofrm = false;}
if (!ifrm && (0 == iFrcFormatOut || 3 == iFrcFormatOut))
{
isitx = true; isitq = true; isitf = true; isitp = true;
}
switch (iFrcFormatOut)
{
case 1: isitx = true; isitq = true; isitr = true; isitc = true; break;
case 2: isitx = true; isitq = true; isitr = true; break;
case 3: ofrm = false; break;
}
string vrow(80,' '),datum(65,' '); int j = 0, k = 0;
if (isita)
{
vrow.replace(j,15,"ATOM DESCRIPTOR"); datum.replace(k,5,"ATOM ");
j += 20; k += 5;
}
if (isitx)
{
vrow.replace(j+4,24,"ATOM COORDINATES (X,Y,Z)"); datum.replace(k,12,"COORDINATES ");
j += 30; k += 12;
}
if (isitq)
{
vrow.replace(j+3,6,"CHARGE"); datum.replace(k,7,"CHARGE ");
j += 10; k += 7;
}
if (isitp)
{
vrow.replace(j+2,8,"GRID PT."); datum.replace(k,11,"POTENTIALS ");
j += 10; k += 11;
}
if (isiti)
{
vrow.replace(j+1,8,"SALT CON"); datum.replace(k,5,"SALT ");
j += 10; k += 5;
}
if (80 <= j)
{
isitr = false; isitc = false; isitap = false; isitdeb = false; isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitr)
{
vrow.replace(j,10," REAC. PT."); datum.replace(k,9,"REACTION ");
j += 10; k += 9;
}
if (80 <= j)
{
isitc = false; isitap = false; isitdeb = false; isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitc)
{
vrow.replace(j,10," COUL. POT"); datum.replace(k,10,"COULOMBIC ");
j += 10; k += 10;
}
if (80 <= j)
{
isitap = false; isitdeb = false; isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitap)
{
vrow.replace(j+2,8,"ATOM PT."); datum.replace(k,11,"ATOMIC PT. ");
j += 10; k += 11;
}
if (80 <= j)
{
isitdeb = false; isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitdeb)
{
vrow.replace(j+3,11,"DEBFRACTION"); datum.replace(k,12,"DEBFRACTION ");
j += 14; k += 12;
}
if (60 <= j)
{
isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitf)
{
vrow.replace(j+4,25,"GRID FIELDS: (Ex, Ey, Ez)"); datum.replace(k,7,"FIELDS ");
j += 30;
}
if (60 <= j)
{
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitrf)
{
vrow.replace(j+4,25,"REAC. FORCE: (Rx, Ry, Rz)"); datum.replace(k,7,"RFORCE ");
j += 30;
}
if (60 <= j)
{
isitsf = false; isittf = false; isitcf = false; isitt = false;
}
if (isitcf)
{
vrow.replace(j+4,25,"COUL. FORCE: (Cx, Cy, Cz)"); datum.replace(k,7,"CFORCE ");
j += 30;
}
if (60 <= j)
{
isitsf = false; isittf = false; isitt = false;
}
if (isittf)
{
vrow.replace(j+4,25,"TOTAL FORCE: (Tx, Ty, Tz)"); datum.replace(k,7,"TFORCE ");
j += 30;
}
if (70 <= j)
{
isitt = false;
}
if (isitt)
{
vrow.replace(j+4,6," TOTAL"); datum.replace(k,6,"TOTAL ");
j += 10;
}
if (50 <= j) isitsf = false;
if (isitsf)
{
vrow.replace(j+4,65,"sCharge, x y z urf.E°n,surf. E[kT/(qA)]");
datum.replace(k,35,"SCh, x, y, z, surf En, surf. E");
j += 50;
}
//---------------------------------------------------------------------------------------------//
/*
* if site potentials required and unformatted read/write, skip during formatted frc file read/write can write unformatted frc.pdb
*/
bool ifrm2 = false, iqass = true;
ifstream ifFileStream;
vector<bool> residsf(iResidueNum,false);
if (!(isitmd || isitpot)) cout << "\nwriting potentials at given sites...\n";
if (iself)
{
cout << "using the current pdb file\n";
ifrm2 = true; iqass = false;
}
else
{
if (!isitpot)
{
ifFileStream.open(strFrciFile.c_str()); // just inquire whether the file exists or not
if (!ifFileStream.is_open())
{
CUnknownInFrcFile warning(strFrciFile);
ifFileStream.close();
return;
}
else
{
cout << "coordinates, etc for potential output read from file " << strFrciFile << endl;
ifrm2 = checkFileFormat(strFrciFile);
}
ifFileStream.close();
}
}
//----- if unformatted may not contain all the info needed for all options, i.e atom info
if (!ifrm2 && isita)
{
CNoAtomInfo warning(strFrciFile);
isita = false; iqass = false;
}
if (!ifrm2) iqass = false;
if (!iself && !isitpot)
{
if (ifrm2) ifFileStream.open(strFrciFile.c_str());
else ifFileStream.open(strFrciFile.c_str(),ios::binary);
if (!ifFileStream.is_open()) CUnknownInFrcFile warning(strFrciFile);
}
if (isitsf) //----- isitsf assumes ifrm2=.true.
{
ifstream ifFileStream15;
string strLine,strHead;
int iresnum;
ifFileStream15.open(strFrciFile.c_str()); // just inquire whether the file exists or not
if (!ifFileStream15.is_open())
{
CUnknownInFrcFile warning(strFrciFile);
}
else
{
cout << "coordinates, etc for potential output read from file " << strFrciFile << endl;
while (!ifFileStream15.eof()) // loop D302
{
getline(ifFileStream15,strLine);
strHead = strLine.substr(0,6);
if (0 != strHead.compare(" ")) strHead = toUpperCase(strHead);
if (0 != strHead.compare("ATOM ") && 0 != strHead.compare("HETATM")) continue;
iresnum = atoi(strLine.substr(23,4).c_str());
residsf[iresnum-1] = true;
}
}
ifFileStream15.close();
}
//---------------------------------------------------------------------------------------------//
ofstream ofFileStream;
if (ofrm) ofFileStream.open(strFrcFile.c_str());
if(!(ofrm || isitmd || isitpot)) ofFileStream.open(strFrcFile.c_str(),ios::binary);
if (!isitmd && !isitpot) cout << "potentials written to file " << strFrcFile << endl << endl;
if (ofrm)
{
ofFileStream << "DELPHI SITE POTENTIAL FILE\n";
ofFileStream << "grid size,percent fill: " << iGrid << " " << fPercentageFill << endl;
ofFileStream << "outer diel. and first one assigned : " << fExDielec << " " << vctfMediaEps[1]*fEPKT << endl;
ofFileStream << "ionic strength (M): " << fIonStrength << endl;
ofFileStream << "ion excl., probe radii: " << fIonRadius << " " << rgfProbeRadius[0] << " " << rgfProbeRadius[1] << endl;
ofFileStream << "linear, nolinear iterations: " << iLinIterateNum << " " << iNonIterateNum << endl;
ofFileStream << "boundary condition: " << iBndyType << endl;
ofFileStream << "Data Output: " << datum << endl;
ofFileStream << "title: " << rgcFileMap << endl;
ofFileStream << "\n\n";
ofFileStream << vrow << endl;
}
if (!ofrm && (!(isitmd || isitpot)))
{
ofFileStream << fixed << setprecision(4);
string strLine;
strLine = "DELPHI FRC FILE"; ofFileStream << strLine << endl;
strLine = "FORMAT NUMBER=1"; ofFileStream << strLine << endl;
strLine = "DATA="; strLine.append(datum); ofFileStream << strLine << endl;
ofFileStream << setw(5) << right << iGrid << setw(10) << right << fPercentageFill << setw(10) << right << fExDielec
<< setw(10) << right << fIonStrength << endl;
for (int i = 1; i <= iMediaNum; i++)
ofFileStream << "dielectric in medium nr. " << i << ": " << vctfMediaEps[i]*fEPKT << endl;
ofFileStream << setw(10) << right << fIonRadius << setw(10) << right << rgfProbeRadius[0] << setw(10) << right << rgfProbeRadius[1]
<< setw(5) << right << iLinIterateNum << setw(5) << right << iNonIterateNum << setw(5) << right << iBndyType << endl;
ofFileStream.unsetf(ios_base::floatfield);
}
if (!iself && (isitrf || isitmd || isittf))
{
CCalcReactForceError warning;
isitrf = false; isittf = false; isitmd = false;
}
vector< SGrid<real> > rfield;
if (isitrf || isitmd || isittf)
{
if (1 == iMediaNum && fZero > abs(vctfMediaEps[1]*fEPKT-1.0))
rfield = rforceeps1();
else
rfield = rforce();
}
//---------------------------------------------------------------------------------------------//
integer nnatom,inum,ncrgs;
SGrid<real> cxyz = {0.0,0.0,0.0},xo,xn,fu,fl,xo2,fxyz,vtemp,xu2,xu,rxyz;
real chrgv,radu,goff,vphi,aphi,etot,phiv,temp,phii,debyefraction,phirt,phict,phir,phias,tcrgs,dist,phirtt,crgs,phiat,phic,phiac,eps,phiact,phit;
real sdist,ff,fn;
string atm,res,rnum,chn,crdstr,atnum,atdes(16,' '),strLine,strHead;
bool isitmp;
int iFound,iresnum,idist,ncrg,jtmp;
vector<bool> atmsf(iAtomNum*iisitsf,false);
vector<real> sold,scomp;
char otemp[10];
string oline(80,' ');
nnatom = 0; chrgv = 0.0; goff = ((real)iGrid+1.0)/2.0; etot = 0.0; phirt = 0.0; phict =0.0;
if (isitpot)
{
CSitePhiError warning;
}
else
{
do // beginning of the big loop on natom
{
if(iself)
{
if (iAtomNum == nnatom) break;
xo = prgfgAtomCoordA[nnatom];
chrgv = vctapAtomPdb[nnatom].getCharge();
radu = vctapAtomPdb[nnatom].getRadius()*fScale;
atm = vctapAtomPdb[nnatom].getAtInf().substr(0,4);
res = vctapAtomPdb[nnatom].getAtInf().substr(6,3);
rnum = vctapAtomPdb[nnatom].getAtInf().substr(11,4);
chn = vctapAtomPdb[nnatom].getAtInf().substr(10,1);
}
else
{
//if (!ifFileStream.is_open()) break;
if(ifrm2) // formatted reading
{
getline(ifFileStream,strLine);
if (ifFileStream.eof()) break;
strHead = strLine.substr(0,6); strHead = toUpperCase(strHead);
if (0 != strHead.compare("ATOM ") && 0 != strHead.compare("HETATM")) continue;
crdstr = strLine.substr(30,24);
atnum = strLine.substr(6,5);
xo.nX = atof(crdstr.substr(0,8).c_str()); xo.nY = atof(crdstr.substr(8,8).c_str()); xo.nZ = atof(crdstr.substr(16,8).c_str());
inum = atoi(atnum.c_str());
}
else // unformatted (binary) reading
{
ifFileStream.read( reinterpret_cast<char*>(&xo.nX),sizeof(real) );
ifFileStream.read( reinterpret_cast<char*>(&xo.nY),sizeof(real) );
ifFileStream.read( reinterpret_cast<char*>(&xo.nZ),sizeof(real) );
ifFileStream.read( reinterpret_cast<char*>(&radu), sizeof(real) );
ifFileStream.read( reinterpret_cast<char*>(&chrgv),sizeof(real) );
}
} //----- end of atom reading
nnatom++;
isitmp = (isitq && iqass) || isitap || isitp;
if((isita || isitmp) && !iself)
{
atm = strLine.substr(11,5);
res = strLine.substr(17,3);
rnum = strLine.substr(22,4);
chn = strLine.substr(21,1);
if (0 != atm.compare(" ")) {atm = removeSpace(atm); atm = toUpperCase(atm);}
if (0 != res.compare(" ")) {res = removeSpace(res); res = toUpperCase(res);}
if (0 != rnum.compare(" ")) {rnum = removeSpace(rnum); rnum = toUpperCase(rnum);}
if (0 != chn.compare(" ")) {chn = removeSpace(chn); chn = toUpperCase(chn);}
}
xn = (xo-fgBoxCenter)*fScale+goff; // scale atoms to grid space
if (isita)
{
atdes.assign(16,' ');
atdes.replace( 0,atm.size(),atm);
atdes.replace( 5,res.size(),res);
atdes.replace( 9,chn.size(),chn);
atdes.replace(11,rnum.size(),rnum);
}
/*
* assign charge to atom, searching for decreasingly specific specification
* note if no charge record found, is assumed to be 0.0
*/
if(!iself && ifrm2 && isitmp)
{
chrgv = 0.0;
iFound = FindRecord(atm,res,rnum,chn,CHARGEFILE,chrgv);
if(isitap) iFound = FindRecord(atm,res,rnum,chn,SIZEFILE,radu);
radu = radu*fScale;
}
if (isitsf)
{
iresnum = atoi(rnum.c_str());
atmsf[nnatom-1] = false;
if (residsf[iresnum-1]) atmsf[nnatom-1] = true;
}
if(isitap && fZero < abs(chrgv))
{
real rads = min(radu,fPotentialUpperBond*fScale);
SGrid<real> xt;
xt = xn; xt.nX += rads;
vphi = interpl(iGrid,phimap,xt);
aphi = vphi;
xt = xn; xt.nX -= rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
xt = xn; xt.nY += rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
xt = xn; xt.nY -= rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
xt = xn; xt.nZ += rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
xt = xn; xt.nZ -= rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
aphi = aphi/6.0;
}
if (isitp || isiti || (isitap && fZero > abs(chrgv)))
{
vphi = interpl(iGrid,phimap,xn);
if (isitap && fZero > abs(chrgv)) aphi = vphi;
if (isitp) { etot += chrgv*vphi; phiv = vphi; }
if (isiti)
{
CNoIDebMap warning;
/*
* we have changed the iconc action so that the phimap has NOT been converted to salt concentrations. therefore
*/
if (0 != iNonIterateNum)
{
temp = vphi*fTaylorCoeff5+fTaylorCoeff4; temp = vphi*temp+fTaylorCoeff3;
temp = vphi*temp+fTaylorCoeff2; temp = vphi*temp+fTaylorCoeff1;
phii = vphi*temp;
}
else
phii = -fIonStrength*2.0*vphi;
}
} //----- end if isitp or isiti, salt and or potentials
if (isitdeb) // it calculates the fraction of closest grid points that are in solution
{
cout << "Calculating Debye Fraction\n";
debyefraction = boolinterpl(iGrid,prgbDielecMap,xn);
}
if (isitf)
{
xn.nX += 1.0; fu.nX = interpl(iGrid,phimap,xn);
xn.nX -= 2.0; fl.nX = interpl(iGrid,phimap,xn);
xn.nX += 1.0; xn.nY += 1.0; fu.nY = interpl(iGrid,phimap,xn);
xn.nY -= 2.0; fl.nY = interpl(iGrid,phimap,xn);
xn.nY += 1.0; xn.nZ += 1.0; fu.nZ = interpl(iGrid,phimap,xn);
xn.nZ -= 2.0; fl.nZ = interpl(iGrid,phimap,xn);
xn.nZ += 1.0;
fxyz = (fl-fu)*0.5*fScale; // the electric field is opposite the potential gradient so I change the sign
}
/*
* check if this point is within the box.
*/
if (isitt)
{
SExtrema<real> bedge;
bedge.nMin = fgBoxCenter-0.5*(iGrid-1)/fScale; bedge.nMax = fgBoxCenter+0.5*(iGrid-1)/fScale;
int it = 0;
if ( optORLT<real>(xo,bedge.nMin) || optORGT<real>(xo,bedge.nMax) ) it = 1;
if (0 == it)
{
xo2 = (xo-fgBoxCenter)*fScale+goff;
/*
* first find reaction field from surface elements inside of the box..
*/
phir=0.0; phias=0.0; ncrgs=0; tcrgs=0.0; sold.assign(30,0.0);
for (integer i = 0; i < iDielecBndySum; i++)
{
vtemp = xo - prgfgSurfCrgA[i]; dist = sqrt(optDot(vtemp,vtemp));
//----- first find reaction field from surface elements inside of the box
ncrgs++; tcrgs += prgfSurfCrgE[i]; phirtt = prgfSurfCrgE[i]/dist;
//----- medeps either epsin contain the 561.0 factor....
phirtt = phirtt*fEPKT; phir += phirtt;
xu2.nX = (real)prgigBndyGrid[i].nX; xu2.nY = (real)prgigBndyGrid[i].nY; xu2.nZ = (real)prgigBndyGrid[i].nZ;
crgs = prgfSurfCrgE[i];
//----- took place of repsin because eps is no more included in schrg , surface charge
phiat = tops(xu2,xo2,crgs,1.0,1); phiat = phiat*2.0; phias += phiat;
idist = (int)dist; sold[idist] += phiat - phirtt;
}
temp = 0.0;
cout << "Writing sold(1:30) and temp \n";
for (integer i = 0; i < 30; i++)
{
temp += sold[i];
cout << sold[i] << " " << temp;
}
cout << endl;
/*
* next find the colombic potential for that site from charges within the box
*/
phic = 0.0; phiac = 0.0; ncrg = 0;
for (integer i = 0; i < iCrgGridNum; i++)
{
it = 0;
if (optORLT<real>(prgfgCrgPoseA[i],bedge.nMin) || optORGT<real>(prgfgCrgPoseA[i],bedge.nMax)) it = 1;
if (0 == it)
{
ncrg++;
vtemp = xo - prgfgCrgPoseA[i]; dist = sqrt(optDot(vtemp,vtemp));
if (5.0 > dist)
{
if (fZero < dist) {temp = prggvAtomicCrg[i].nValue/dist; phic += temp/prgfAtomEps[i];}
//----- find analytic potential from this real charge..=phiac
xu = prgfgCrgPoseA[i]; crgs = prggvAtomicCrg[i].nValue;
xu2 = (xu-fgBoxCenter)*fScale+goff;
eps = prgfAtomEps[i]*fEPKT;
phiact = tops(xu2,xo2,crgs,eps,1);
phiac += phiact;
}
}
}
/*
* medeps, either epsin contain the 561.0 factor....
*/
phiac = phiac*2.0;
/*
* find the grid potentials..
*/
phiv = interpl(iGrid,phimap,xn);
string strFileName7 = "extra.dat";
ofstream ofFileSteam7;
ofFileSteam7.open(strFileName7.c_str());
ofFileSteam7 << phic << " " << phir << " " << phiv << " " << phias << " " << phiac << " "<< ncrg << " "
<< ncrgs << " " << tcrgs << endl;
ofFileSteam7.close();
phit = phic + phir + phiv - phias - phiac;
}
else
phit = 0.0;
/*
* phit contains the total corrected potential
*/
}
if (isitr)
{
scomp.assign(30,0.0); sold.assign(30,0.0); phir = 0.0;
for (integer i = 0; i < iDielecBndySum; i++)
{
vtemp = xo - prgfgSurfCrgA[i]; dist = sqrt(optDot(vtemp,vtemp));
idist = (int)dist;
if (30 > idist) sold[idist] += fEPKT*prgfSurfCrgE[i]/dist;
phir += prgfSurfCrgE[i]/dist;
}
/*
* medeps either epsin contains the 561.0 factor....
*/
phir = phir*fEPKT;
for (integer i = 0; i < 30; i++)
{
if (0 == i) scomp[i] = sold[i];
if (0 != i) scomp[i] = scomp[i-1]+sold[i];
}
phirt += phir*chrgv;
}
/*
* medeps either epsin contains the 561.0 factor....
*/
if (isitrf || isitmd || isittf) rxyz = rfield[nnatom-1]*fEPKT;
if(isitcf || isitmd || isittf)
{
cxyz.nX = 0.0; cxyz.nY = 0.0; cxyz.nZ = 0.0;
if (fZero < abs(chrgv))
{
for (integer i = 0; i < iCrgGridNum; i++)
{
vtemp = xo - prgfgCrgPoseA[i]; dist = optDot(vtemp,vtemp);
if (fZero < dist)
{
sdist = sqrt(dist)*dist;
temp = prggvAtomicCrg[i].nValue/(prgfAtomEps[i]*sdist);
cxyz = cxyz + vtemp*temp;
}
}
/*
* atmeps and medeps and epsin contain the 561.0 factor....
*/
cxyz = cxyz*chrgv;
}
}
if (isitc)
{
phic = 0.0;
for (integer i = 0; i < iCrgGridNum; i++)
{
vtemp = xo - prgfgCrgPoseA[i]; dist = optDot(vtemp,vtemp);
if (fZero < dist)
{
sdist = sqrt(dist);
temp = prggvAtomicCrg[i].nValue/sdist;
phic += temp/prgfAtomEps[i];
}
}
/*
* atmeps and medeps and epsin contain the 561.0 factor....
*/
phict += phic*chrgv;
}
//---------------------------------------------------------------------------------------//
/*
* write out calculated/assigned charges
*
* need otemp cos can not write into a substring apparently
* otemp needs to be at least 15 long to avoid an error!!
*/
oline.assign(80,' '); // reset oline
j = 0;
if (isita)
{
oline.replace(j,16,atdes.substr(0,16));
j += 20;
}
if (isitx)
{
sprintf(otemp,"%10.4f",xo.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",xo.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",xo.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isitq)
{
sprintf(otemp,"%10.4f",chrgv); oline.replace(j,10,otemp); j += 10;
}
if (isitp)
{
sprintf(otemp,"%10.4f",phiv); oline.replace(j,10,otemp); j += 10;
#ifdef MCCE
mcce_phiv.push_back(phiv);
#endif
}
if (isiti)
{
sprintf(otemp,"%10.4f",phii); oline.replace(j,10,otemp); j += 10;
}
if (isitr)
{
sprintf(otemp,"%10.4f",phir); oline.replace(j,10,otemp); j += 10;
}
if (isitc)
{
sprintf(otemp,"%10.4f",phic); oline.replace(j,10,otemp); j += 10;
}
if (isitap)
{
sprintf(otemp,"%10.4f",aphi); oline.replace(j,10,otemp); j += 10;
}
if (isitdeb)
{
sprintf(otemp,"%10.4f",debyefraction); oline.replace(j,10,otemp); j += 10;
}
if (isitf)
{
sprintf(otemp,"%10.4f",fxyz.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",fxyz.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",fxyz.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isitrf)
{
sprintf(otemp,"%10.4f",rxyz.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",rxyz.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",rxyz.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isitcf)
{
sprintf(otemp,"%10.4f",cxyz.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",cxyz.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",cxyz.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isittf)
{
vtemp = rxyz + cxyz;
sprintf(otemp,"%10.4f",vtemp.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",vtemp.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",vtemp.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isitmd)
{
vtemp = rxyz + cxyz;
cout << "atom: " << nnatom << " rx= " << rxyz.nX << " cx= " << cxyz.nX << " tx= " << vtemp.nX << endl;
cout << "atom: " << nnatom << " ry= " << rxyz.nY << " cy= " << cxyz.nY << " ty= " << vtemp.nY << endl;
cout << "atom: " << nnatom << " rz= " << rxyz.nZ << " cz= " << cxyz.nZ << " tz= " << vtemp.nZ << endl;
}
if (isitt)
{
sprintf(otemp,"%10.4f",phit); oline.replace(j,10,otemp); j += 10;
}
if (ofrm && isitmp1) ofFileStream << oline << endl;
if (!ofrm && isitmp1)
{
if (isita) ofFileStream << atdes << endl;
if (isitx) ofFileStream << xo << endl;
if (isitq) ofFileStream << chrgv << endl;
if (isitp) ofFileStream << phiv << endl;
if (isiti) ofFileStream << phii << endl;
if (isitr) ofFileStream << phir << endl;
if (isitc) ofFileStream << phic << endl;
if (isitap) ofFileStream << aphi << endl;
if (isitf) ofFileStream << fxyz << endl;
if (isitrf) ofFileStream << rxyz << endl;
if (isitcf) ofFileStream << cxyz << endl;
if (isittf) { vtemp = rxyz + cxyz; ofFileStream << vtemp << endl;}
}
} while(true); // end of the big loop on natom
}
if (isitsf)
{
for (integer jj = 0; jj < iBndyGridNum; jj++)
{
integer i = prgiAtSurf[jj];
if (atmsf[i-1] && (0 < prgiAtNdx[jj]))
{
/*
* if the bgp belongs to the interesting site
* attention: using always radprb(1), in some case might be inappropriate
*/
xo = prgfgSurfCrgA[jj]+rgfProbeRadius[0]*prgfgSurfCrgE[jj];
xn = (xo-fgBoxCenter)*fScale+goff;
xn.nX += 1.0; fu.nX = interpl(iGrid,phimap,xn);
xn.nX -= 2.0; fu.nX = interpl(iGrid,phimap,xn);
xn.nX += 1.0; xn.nY += 1.0; fu.nY = interpl(iGrid,phimap,xn);
xn.nY -= 2.0; fu.nY = interpl(iGrid,phimap,xn);
xn.nY += 1.0; xn.nZ += 1.0; fu.nZ = interpl(iGrid,phimap,xn);
xn.nZ -= 2.0; fu.nZ = interpl(iGrid,phimap,xn);
xn.nZ += 1.0;
fxyz = fl - fu;
fn = 0.5*fScale*(optDot(fxyz,prgfgSurfCrgE[jj]));
ff = 0.5*fScale*(optDot(fxyz,fxyz));
if (ofrm)
{
jtmp = j;
sprintf(otemp,"%10.4f",prgfSurfCrgE[jj]); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",xo.nX); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",xo.nY); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",xo.nZ); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",fn); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",ff); oline.replace(jtmp,10,otemp); jtmp += 10;
ofFileStream << oline << endl;
}
if (!ofrm) ofFileStream << prgfSurfCrgE[jj] << " " << fn << endl;
}
}
}
if(!iself) ifFileStream.close();
#ifdef VERBOSE
cout << "\n number of atom coordinates read : " << nnatom << endl << endl;
#endif
etot = etot/2.0;
if (ofrm)
{
if (0 == iFrcFormatOut)
{
ofFileStream << "total energy = " << etot << " kt\n";
if (isitr) ofFileStream << "corrected reaction field energy= " << phirt/2.0 << " kt\n";
if (isitap) ofFileStream << "Atomic potential for charged atoms is averaged over a spherical surface of less than "
<< fPotentialUpperBond << " A\n";
}
if (1 == iFrcFormatOut)
{
ofFileStream << "corrected reaction field energy= " << phirt/2.0 << " kt\n";
ofFileStream << "total coulombic energy = " << phict/2.0 << " kt\n";
if (isitap) ofFileStream << "Atomic potential for charged atoms is averaged over a spherical surface of less than "
<< fPotentialUpperBond << " A\n";
}
if (2 == iFrcFormatOut)
{
ofFileStream << "corrected reaction field energy= " << phirt/2.0 << " kt\n";
if (isitap) ofFileStream << "Atomic potential for charged atoms is averaged over a spherical surface of less than "
<< fPotentialUpperBond << " A\n";
}
}
/*
* end of formatted frc read/write and unformatted frc write
* end of unformatted frc.pdb read and frc write
*/
if (ofFileStream.is_open()) ofFileStream.close();
#ifdef VERBOSE
cout << "frc stuff now done at "; pTimer->showTime(); cout << endl;
#endif
}
