FreeEnergyParse.C File Reference

#include <ctype.h>
#include <string.h>
#include <stdlib.h>
#include "common.h"
#include "InfoStream.h"
#include "FreeEnergyEnums.h"
#include "FreeEnergyAssert.h"
#include "Vector.h"
#include "FreeEnergyVector.h"
#include "FreeEnergyGroup.h"
#include "FreeEnergyRestrain.h"
#include "FreeEnergyRMgr.h"
#include "FreeEnergyLambda.h"
#include "FreeEnergyLambdMgr.h"
#include "NamdTypes.h"
#include "GlobalMaster.h"
#include "GlobalMasterFreeEnergy.h"
#include "FreeEnergyParse.h"

Go to the source code of this file.

Functions
void	ProblemParsing (const char *Message, const char *Str, Bool_t Terminate)
void	CheckParentheses (const char *Str)
void	ReadInput (char *Str, ARestraintManager &RMgr, ALambdaManager &LMgr, GlobalMasterFreeEnergy &CFE, double dT)
int	ReadPmfBlock (char *Str, ALambdaControl &PmfBlock, double dT)
double	GetTime (double Val, TimeUnits_t Units)
int	ReadTimeUnits (char *Str, TimeUnits_t &Units, TimeUnits_t DefaultUnits)
int	ReadTaskType (char *Str, feptask_t &Task)
int	ReadNextPmfSpec (char *Str, pmf_t &PmfSpec)
int	ReadRestraints (char *Str, ARestraintManager &AllRestraints, GlobalMasterFreeEnergy &CFE)
ARestraint *	GetRestraint (char *Str, int &NumChars, GlobalMasterFreeEnergy &CFE)
int	ReadBound (char *Str, Bound_t &Bound)
int	ReadAValue (char *Str, double &Value, Bool_t ErrMsg)
int	ReadChar (char *Str, char Char, Bool_t ErrMsg)
int	ReadWord (const char *Str, const char *Word, Bool_t ErrMsg)
restr_t	ReadNextRestraintType (char *Str, int &NumChars)
int	AddAtoms (AGroup &Group, char *Str, GlobalMasterFreeEnergy &CFE)
void	AddAtomsInResidues (AGroup &Group, char *AtomNames, char *ResRange, GlobalMasterFreeEnergy &CFE)
void	AddResidues (AGroup &Group, char *ResRange, GlobalMasterFreeEnergy &CFE)
void	AddAtom (AGroup &Group, char *Atom, GlobalMasterFreeEnergy &CFE)
void	AddAtom (AGroup &Group, char *ResRange, char *AtomName, GlobalMasterFreeEnergy &CFE)
void	GetResRange (char *ResRange, int &ResNum1, int &ResNum2)
int	GetSegName (char *Str, char *SegName)
int	GetResNum (char *Str, int &ResNum)
int	GetAtomName (char *Str, char *AtomName)
item_t	ReadNextItem (char *Str, int &NumChars)
int	IsStartGroup (char *Str)
int	IsEndGroup (char *Str)
int	IsAtomName (char *Str)
int	IsAtomNameList (char *Str)
int	IsAtom (char *Str)
int	IsResidueRange (char *Str)
int	IsResidue (char *Str)
int	IsAResidue (char *Str)
int	ReadParentheses (const char *Str)
int	ReadAlpha (const char *Str)
int	ReadAlphaNum (const char *Str)
int	ReadDigits (const char *Str)
int	ReadWhite (const char *Str)
void	ToLower (char *Str)

---

Function Documentation

void AddAtom	(	AGroup &	Group,
		char *	ResRange,
		char *	AtomName,
		GlobalMasterFreeEnergy &	CFE
	)

Definition at line 1024 of file FreeEnergyParse.C.

References AGroup::Add(), GlobalMasterFreeEnergy::getAtomID(), GetResRange(), GetSegName(), ProblemParsing(), and GlobalMasterFreeEnergy::requestAtom().

                                          {
//-------------------------------------------------------------------
// Group contains a list of int's representing AtomID's.
// ResRange should be "(segname, resnum) to (segname, resnum)"
//                 or "(segname, resnum)"
// AtomName is specified separately.
// get the atomID, and add it to Group.
//-------------------------------------------------------------------
  char  SegName[21];
  int   ResNum, ResNum1, ResNum2, AtomID, RetVal;

  // convert "(segname, resnum1) to (segname, resnum2)"
  //  -> SegName, ResNum1, ResNum2
  GetSegName(ResRange, SegName);
  GetResRange(ResRange, ResNum1, ResNum2);

  // get atomID for each atom in the specified residue range
  // register it, add it to Group
  for (ResNum=ResNum1; ResNum<=ResNum2; ResNum++) {
    AtomID = CFE.getAtomID(SegName, ResNum, AtomName);
    if (AtomID < 0) { ProblemParsing("Invalid AtomID", ResRange); }
    RetVal = CFE.requestAtom(AtomID);
    if (RetVal < 0) { ProblemParsing("Unable to requestAtom", ResRange); }
    Group.Add(AtomID);
  }
}

void AddAtom	(	AGroup &	Group,
		char *	Atom,
		GlobalMasterFreeEnergy &	CFE
	)

Definition at line 1011 of file FreeEnergyParse.C.

References AddAtom(), and GetAtomName().

Referenced by AddAtom(), AddAtoms(), and AddAtomsInResidues().

                                                                     {
//-------------------------------------------------------------------
// Group contains a list of int's representing AtomID's.
// Atom should be "(segname, resnum, atomname)"
// get the atomID for Atom, and add it to Group.
//-------------------------------------------------------------------
  char  AtomName[21];

  GetAtomName(Atom, AtomName);
  AddAtom(Group, Atom, AtomName, CFE);
}

int AddAtoms	(	AGroup &	Group,
		char *	Str,
		GlobalMasterFreeEnergy &	CFE
	)

Definition at line 875 of file FreeEnergyParse.C.

References AddAtom(), AddAtomsInResidues(), AddResidues(), kAtom, kAtomName, kAtomNameList, kEndGroup, kFalse, kResidue, kResidueRange, kStartGroup, kTrue, ProblemParsing(), ReadNextItem(), and ReadWhite().

Referenced by GetRestraint().

                                                                    {
//----------------------------------------------------------------------------
// Str contains specifications for which atoms to add to Group.
// The atoms may be:
//   a) a single atom, b) all atoms of a residue, c) a list of atoms
//   d) all atoms in a list of residues, e) all atoms in a range of residues,
//   e) one or more atomnames in a list of residues, or
//   f) one or more atomnames in a range of residues
// Add the AtomID's for these specified atoms to Group.
// return the number of characters in Str that were read.
//----------------------------------------------------------------------------
  int     NumChars;
  int     RetNumChars = 0;
  Bool_t  GroupMode = kFalse;
  Bool_t  AtomList =  kFalse;
  Bool_t  Finished =  kFalse;
  char*   SavePtr = 0;

  while (!Finished) {
    switch(ReadNextItem(Str, NumChars)) {
      case kStartGroup:
        GroupMode = kTrue;
        break;
      case kEndGroup:
        Finished = kTrue;
        break;
      case kAtom:
        AddAtom(Group, Str, CFE);
        if (!GroupMode) {
          Finished = kTrue;
        }
        break;
      case kAtomName:
      case kAtomNameList:
        AtomList = kTrue;
        SavePtr = Str;
        break;
      case kResidue:
      case kResidueRange:
        if (AtomList) {
          AddAtomsInResidues(Group, SavePtr, Str, CFE);
        }
        else {
          AddResidues(Group, Str, CFE);
        }
        if (!GroupMode) {
          Finished = kTrue;
        }
        break;
      default:
        Finished = kTrue;
        ProblemParsing("Can't Read Atoms", Str);
        break;
    }
    Str += NumChars;
    RetNumChars += NumChars;
  }
  RetNumChars += ReadWhite(Str);
  return(RetNumChars);
}

void AddAtomsInResidues	(	AGroup &	Group,
		char *	AtomNames,
		char *	ResRange,
		GlobalMasterFreeEnergy &	CFE
	)

Definition at line 937 of file FreeEnergyParse.C.

References AddAtom(), AddResidues(), ReadAlphaNum(), and ReadWhite().

Referenced by AddAtoms().

                                                     {
//-------------------------------------------------------------------
// Group contains a list of int's representing AtomID's.
// ResRange should be "(segname, resnum) to (segname, resnum)"
//                 or "(segname, resnum)"
// AtomNames should be "(atomname, atomname, ...):" or "atomname:"
// get the atomID's for each atomname in ResRange, add them to Group.
//-------------------------------------------------------------------
  int   Count, ArrayIndex, i;
  char  AtomNamesArray[21][30];

  // skip to start of first atomname
  if (AtomNames[0] == '(') {
    AtomNames++;
    Count = ReadWhite(AtomNames);
    AtomNames += Count;
  }
  // put each atomname into the array, finish when ':' or ')' is found
  ArrayIndex = 0;
  while ( (AtomNames[0]!=':') && (AtomNames[0]!=')') ) {
    Count = ReadAlphaNum(AtomNames);
    strncpy(AtomNamesArray[ArrayIndex], AtomNames, Count);
    AtomNamesArray[ArrayIndex][Count] = '\0';
    AtomNames += Count;
    Count = ReadWhite(AtomNames);
    AtomNames += Count;
    ArrayIndex++;
  }
  // now add each atomname of Res to Group.
  // if "all" is specified, add all atoms of Res to Group.
  for (i=0; i<ArrayIndex; i++) {
    if (strcmp(AtomNamesArray[i], "all") == 0) {
      AddResidues(Group, ResRange, CFE);
    }
    else {
      AddAtom(Group, ResRange, AtomNamesArray[i], CFE);
    }
  }
}

void AddResidues	(	AGroup &	Group,
		char *	ResRange,
		GlobalMasterFreeEnergy &	CFE
	)

Definition at line 979 of file FreeEnergyParse.C.

References AGroup::Add(), GlobalMasterFreeEnergy::getAtomID(), GlobalMasterFreeEnergy::getNumAtoms(), GetResRange(), GetSegName(), ProblemParsing(), and GlobalMasterFreeEnergy::requestAtom().

Referenced by AddAtoms(), and AddAtomsInResidues().

                                                                             {
//-------------------------------------------------------------------
// Group contains a list of int's representing AtomID's.
// ResRange should be "(segname, resnum) to (segname, resnum)"
//                 or "(segname, resnum)"
// get the atomID's for each atom of ResRange, and add them to Group.
//-------------------------------------------------------------------
  char  SegName[21];
  int   ResNum1, ResNum2, ResNum;
  int   i, NumAtoms, AtomID, RetVal;

  // get start and stop residue numbers
  GetSegName(ResRange, SegName);
  GetResRange(ResRange, ResNum1, ResNum2);

  // for each residue of residue range
  for (ResNum=ResNum1; ResNum<=ResNum2; ResNum++) {
    // for each atom of residue
    NumAtoms = CFE.getNumAtoms(SegName, ResNum);
    if (NumAtoms < 1) { ProblemParsing("No Atoms in Residue", ResRange); }
    for (i=0; i<NumAtoms; i++) {
      // get atomID, register it, add it to Group
      AtomID = CFE.getAtomID(SegName, ResNum, i);
      if (AtomID < 0) { ProblemParsing("Invalid AtomID", ResRange); }
      RetVal = CFE.requestAtom(AtomID);
      if (RetVal < 0) { ProblemParsing("Unable to requestAtom", ResRange); }
      Group.Add(AtomID);
    }
  }
}

void CheckParentheses

(

const char *

Str

)

Definition at line 54 of file FreeEnergyParse.C.

References ProblemParsing().

Referenced by ReadInput().

                                       {
//----------------------------------------------------------------------------
// check for balanced '(' ')' and '{' '}'
//----------------------------------------------------------------------------
  int  ParenthesesCount = 0;
  int  CurlyBracketCount = 0;

  for (unsigned int i=0; i<strlen(Str); i++) {
    if (Str[i] == '(') {ParenthesesCount++;}
    if (Str[i] == ')') {ParenthesesCount--;}
    if (Str[i] == '{') {CurlyBracketCount++;}
    if (Str[i] == '}') {CurlyBracketCount--;}
    if ((ParenthesesCount<0) || (CurlyBracketCount<0)) {
      ProblemParsing("Mismatched Parentheses", Str+i);
    }
  }
}

int GetAtomName	(	char *	Str,
		char *	AtomName
	)

Definition at line 1134 of file FreeEnergyParse.C.

References GetResNum(), ProblemParsing(), ReadAlphaNum(), and ReadWhite().

Referenced by AddAtom().

                                           {
//-------------------------------------------------------------------
// Str should be (segname, resnum, atomname)
// put atomname into AtomName
// return the number of characters from start-of-Str thru ')'
//-------------------------------------------------------------------
  int    Count, ResNum;
  char*  FullString=Str;

  Str += GetResNum(Str, ResNum);
  Str += ReadWhite(Str);
  Count = ReadAlphaNum(Str);
  if (Count == 0)    {ProblemParsing("Missing Atom Name", Str);}
  strncpy(AtomName, Str, Count);
  AtomName[Count] = '\0';
  Str += Count;
  Str += ReadWhite(Str);
  if (Str[0] != ')') {ProblemParsing("Missing )", Str);}
  Str += 1;
  return(Str-FullString);
}

int GetResNum	(	char *	Str,
		int &	ResNum
	)

Definition at line 1114 of file FreeEnergyParse.C.

References GetSegName(), ProblemParsing(), ReadDigits(), and ReadWhite().

Referenced by GetAtomName(), and GetResRange().

                                       {
//-------------------------------------------------------------------
// Str should be (segname, resnum) or (segname, resnum, atomname)
// convert resnum to an int and return it
// return the number of characters from start-of-Str thru resnum
//-------------------------------------------------------------------
  int    Count;
  char   SegName[21];
  char*  FullString=Str;

  Str += GetSegName(Str, SegName);
  Str += ReadWhite(Str);
  ResNum = (int) strtol(Str, NULL, 10);
  Count = ReadDigits(Str);
  if (Count == 0) {ProblemParsing("Missing Residue Number", Str);}
  Str += Count;
  return(Str-FullString);
}

void GetResRange	(	char *	ResRange,
		int &	ResNum1,
		int &	ResNum2
	)

Definition at line 1053 of file FreeEnergyParse.C.

References GetResNum(), GetSegName(), ProblemParsing(), ReadAlphaNum(), ReadParentheses(), and ReadWhite().

Referenced by AddAtom(), and AddResidues().

                                                             {
//-------------------------------------------------------------------
// ResRange should be "(segname, resnum1) to (segname, resnum2)"
// return ResNum1 & ResNum2
// if "to" is missing, return resnum1 in both ResNum1 & ResNum2
//-------------------------------------------------------------------
  char SegName1[21], SegName2[21];

  // get start residue number
  GetSegName(ResRange, SegName1);
  GetResNum(ResRange, ResNum1);

  // skip to where "to" should appear
  ResRange += ReadParentheses(ResRange);
  ResRange += ReadWhite(ResRange);

  // if "to" is found
  if (strncmp(ResRange, "to", 2) == 0) {
    //skip to next residue
    ResRange += ReadAlphaNum(ResRange);
    ResRange += ReadWhite(ResRange);
    // get final residue number
    GetSegName(ResRange, SegName2);
    GetResNum(ResRange, ResNum2);
    // do some checks
    if (strcmp(SegName1, SegName2)!=0) {
      ProblemParsing("SegNames Differ", ResRange);
    }
    if (ResNum2 < ResNum1) {
      ProblemParsing("Decreasing Residues", ResRange);
    }
  }

  // otherwise, ResNum2 = ResNum1
  else {
    ResNum2 = ResNum1;
  }
}

ARestraint* GetRestraint	(	char *	Str,
		int &	NumChars,
		GlobalMasterFreeEnergy &	CFE
	)

Definition at line 410 of file FreeEnergyParse.C.

References A, AddAtoms(), ASSERT, kAngle, kAngleBound, kAnglePMF, kDihe, kDiheBound, kDihePMF, kDist, kDistBound, kDistPMF, kPi, kPosi, kPosiBound, kPosiPMF, kTrue, kUnknownRestr, ProblemParsing(), ReadAValue(), ReadBound(), ReadChar(), ReadNextRestraintType(), ReadWord(), ARestraint::SetBound(), ARestraint::SetGroups(), ARestraint::SetIntervalAngle(), ARestraint::SetKf(), ARestraint::SetLowerAngle(), ARestraint::SetRefAngle(), ARestraint::SetRefDist(), ARestraint::SetRefPos(), ARestraint::SetStartAngle(), ARestraint::SetStartDist(), ARestraint::SetStartPos(), ARestraint::SetStopAngle(), ARestraint::SetStopDist(), ARestraint::SetStopPos(), and ARestraint::SetUpperAngle().

Referenced by ReadRestraints().

                                                                                {
//----------------------------------------------------------------------------
// read spec's for a restraint, from the input string.
// allocate space for and initialize a restraint object with these specs.
// note:  memory is allocated here, and free'd elsewhere.
//
// return a pointer to this object.
// return the number of characters to read past these specs.
// return NumChars=0 for illegal restraint specs.
//----------------------------------------------------------------------------
  AGroup      Group1, Group2, Group3, Group4;
  ARestraint* pRestraint = NULL;
  restr_t     Restraint;
  Bound_t     Bound;
  int         Count;
  double      Kf;
  double      D,   D0,   D1;
  double      A=0, A0=0, A1=0, A2=0;
  AVector     Pos, Pos0, Pos1;
  char*       FullStr;
  char*       TempStr;

  const Bool_t  kPrintErrMsg=kTrue; // kNoErrMsg=kFalse;

  // save pointer to full string
  FullStr = Str;
  NumChars = 0;

  // get restraint type
  Restraint = ReadNextRestraintType(Str, Count);
  if (Count == 0) {
    ProblemParsing("Can't Read Restraint Type", Str);
    return(pRestraint);
  }

  // skip past restraint type
  ASSERT(Restraint != kUnknownRestr);
  Str += Count;
  
  // read in appropriate number of atoms or groups-of-atoms for
  // this restraint type, put the atoms in Group1 thru Group4
  switch (Restraint) {
    case kDihe:  case kDiheBound:  case kDihePMF:
      Str += AddAtoms(Group4, Str, CFE);
    case kAngle: case kAngleBound: case kAnglePMF:
      Str += AddAtoms(Group3, Str, CFE);
    case kDist:  case kDistBound:  case kDistPMF:
      Str += AddAtoms(Group2, Str, CFE);
    case kPosi:  case kPosiBound:  case kPosiPMF:
      Str += AddAtoms(Group1, Str, CFE);
    default: ;
  }

  // for dihedrals, allow keywords of "barr=", "gap=", OR "kf="
  // for other restraints, just allow "kf="
  TempStr = Str;
  switch(Restraint) {
    case kDihe:
    case kDiheBound:
    case kDihePMF:
      Str += ReadWord(Str, "barr");
      Str += ReadWord(Str, "gap");
    default:
      Str += ReadWord(Str, "kf");
      // make sure the word "barr", "gap", or "kf" was read
      if (Str==TempStr) {
        ProblemParsing("Word Missing: barr, gap, or kf", Str);
      }
      Str += ReadChar(Str, '=');
  }
  // get the Kf value
  Str += ReadAValue(Str, Kf,          kPrintErrMsg);
  
  // read the reference positions, distances or angles
  switch (Restraint) {
    case kPosi:  
      Str += ReadWord(Str, "ref",    kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadChar(Str, '(');
      Str += ReadAValue(Str, Pos[0],  kPrintErrMsg);
      Str += ReadAValue(Str, Pos[1],  kPrintErrMsg);
      Str += ReadAValue(Str, Pos[2],  kPrintErrMsg);
      Str += ReadChar(Str, ')');
      break;
    case kDist:
      Str += ReadWord(Str, "ref",    kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadAValue(Str, D,       kPrintErrMsg);
      break;
    case kAngle:
      Str += ReadWord(Str, "ref",    kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadAValue(Str, A,       kPrintErrMsg);
      break;
    case kDihe:
      Str += ReadWord(Str, "ref",    kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadAValue(Str, A,       kPrintErrMsg);
      break;
    case kPosiBound:
      if (ReadBound(Str, Bound) == 0) {ProblemParsing("Missing Bound", Str);}
      Str += ReadWord(Str, "low");
      Str += ReadWord(Str, "hi");
      Str += ReadChar(Str, '=');
      Str += ReadChar(Str, '(');
      Str += ReadAValue(Str, Pos[0],  kPrintErrMsg);
      Str += ReadAValue(Str, Pos[1],  kPrintErrMsg);
      Str += ReadAValue(Str, Pos[2],  kPrintErrMsg);
      Str += ReadAValue(Str, D,       kPrintErrMsg);
      Str += ReadChar(Str, ')');
      break;
    case kDistBound:
      if (ReadBound(Str, Bound) == 0) {ProblemParsing("Missing Bound", Str);}
      Str += ReadWord(Str, "low");
      Str += ReadWord(Str, "hi");
      Str += ReadChar(Str, '=');
      Str += ReadAValue(Str, D,       kPrintErrMsg);
      break;
    case kAngleBound:
      if (ReadBound(Str, Bound) == 0) {ProblemParsing("Missing Bound", Str);}
      Str += ReadWord(Str, "low");
      Str += ReadWord(Str, "hi");
      Str += ReadChar(Str, '=');
      Str += ReadAValue(Str, A,       kPrintErrMsg);
      break;
    case kDiheBound:
      Str += ReadWord(Str, "low",    kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadAValue(Str, A0,      kPrintErrMsg);
      Str += ReadWord(Str, "hi",     kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadAValue(Str, A1,      kPrintErrMsg);
      Str += ReadWord(Str, "delta",  kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadAValue(Str, A2,      kPrintErrMsg);
      break;
    case kPosiPMF:
      Str += ReadWord(Str, "low",    kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadChar(Str, '(');
      Str += ReadAValue(Str, Pos0[0], kPrintErrMsg);
      Str += ReadAValue(Str, Pos0[1], kPrintErrMsg);
      Str += ReadAValue(Str, Pos0[2], kPrintErrMsg);
      Str += ReadChar(Str, ')');
      Str += ReadWord(Str, "hi",     kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadChar(Str, '(');
      Str += ReadAValue(Str, Pos1[0], kPrintErrMsg);
      Str += ReadAValue(Str, Pos1[1], kPrintErrMsg);
      Str += ReadAValue(Str, Pos1[2], kPrintErrMsg);
      Str += ReadChar(Str, ')');
      break;
    case kDistPMF:
      Str += ReadWord(Str, "low",    kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadAValue(Str, D0,      kPrintErrMsg);
      Str += ReadWord(Str, "hi",     kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadAValue(Str, D1,      kPrintErrMsg);
      break;
    case kAnglePMF:
      Str += ReadWord(Str, "low",    kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadAValue(Str, A0,      kPrintErrMsg);
      Str += ReadWord(Str, "hi",     kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadAValue(Str, A1,      kPrintErrMsg);
      break;
    case kDihePMF:
      Str += ReadWord(Str, "low",    kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadAValue(Str, A0,      kPrintErrMsg);
      Str += ReadWord(Str, "hi",     kPrintErrMsg);
      Str += ReadChar(Str, '=');
      Str += ReadAValue(Str, A1,      kPrintErrMsg);
      break;
    default: ;
  }

  // convert degrees to radians
  A  *= (kPi/180);
  A0 *= (kPi/180);
  A1 *= (kPi/180);
  A2 *= (kPi/180);

  // initialize the restraint
  switch (Restraint) {
    case kPosi:
      pRestraint = new AFixedPosRestraint;
      pRestraint->SetKf(Kf);
      pRestraint->SetGroups(Group1);
      pRestraint->SetRefPos(Pos);
      break;
    case kDist:
      pRestraint = new AFixedDistRestraint;
      pRestraint->SetKf(Kf);
      pRestraint->SetGroups(Group2, Group1);
      pRestraint->SetRefDist(D);
      break;
    case kAngle:
      pRestraint = new AFixedAngleRestraint;
      pRestraint->SetKf(Kf);
      pRestraint->SetGroups(Group3, Group2, Group1);
      pRestraint->SetRefAngle(A);
      break;
    case kDihe:
      pRestraint = new AFixedDiheRestraint;
      pRestraint->SetKf(Kf);
      pRestraint->SetGroups(Group4, Group3, Group2, Group1);
      pRestraint->SetRefAngle(A);
      break;
    case kPosiBound:
      pRestraint = new ABoundPosRestraint;
      pRestraint->SetKf(Kf);
      pRestraint->SetGroups(Group1);
      pRestraint->SetRefPos(Pos);
      pRestraint->SetRefDist(D);
      pRestraint->SetBound(Bound);
      break;
    case kDistBound:
      pRestraint = new ABoundDistRestraint;
      pRestraint->SetKf(Kf);
      pRestraint->SetGroups(Group2, Group1);
      pRestraint->SetRefDist(D);
      pRestraint->SetBound(Bound);
      break;
    case kAngleBound:
      pRestraint = new ABoundAngleRestraint;
      pRestraint->SetKf(Kf);
      pRestraint->SetGroups(Group3, Group2, Group1);
      pRestraint->SetRefAngle(A);
      pRestraint->SetBound(Bound);
      break;
    case kDiheBound:
      pRestraint = new ABoundDiheRestraint;
      pRestraint->SetKf(Kf);
      pRestraint->SetGroups(Group4, Group3, Group2, Group1);
      pRestraint->SetLowerAngle(A0);
      pRestraint->SetUpperAngle(A1);
      pRestraint->SetIntervalAngle(A2);
      break;
    case kPosiPMF:
      pRestraint = new AForcingPosRestraint;
      pRestraint->SetKf(Kf);
      pRestraint->SetGroups(Group1);
      pRestraint->SetStartPos(Pos0);
      pRestraint->SetStopPos(Pos1);
      break;
    case kDistPMF:
      pRestraint = new AForcingDistRestraint;
      pRestraint->SetKf(Kf);
      pRestraint->SetGroups(Group2, Group1);
      pRestraint->SetStartDist(D0);
      pRestraint->SetStopDist(D1);
      break;
    case kAnglePMF:
      pRestraint = new AForcingAngleRestraint;
      pRestraint->SetKf(Kf);
      pRestraint->SetGroups(Group3, Group2, Group1);
      pRestraint->SetStartAngle(A0);
      pRestraint->SetStopAngle(A1);
      break;
    case kDihePMF:
      pRestraint = new AForcingDiheRestraint;
      pRestraint->SetKf(Kf);
      pRestraint->SetGroups(Group4, Group3, Group2, Group1);
      pRestraint->SetStartAngle(A0);
      pRestraint->SetStopAngle(A1);
      break;
    default: ;
  }
  // calc number of chars to read restraint specs
  NumChars = Str-FullStr;
  return(pRestraint);
}

int GetSegName	(	char *	Str,
		char *	SegName
	)

Definition at line 1093 of file FreeEnergyParse.C.

References ProblemParsing(), ReadAlphaNum(), and ReadWhite().

Referenced by AddAtom(), AddResidues(), GetResNum(), and GetResRange().

                                         {
//-------------------------------------------------------------------
// Str should be (segname, resnum) or (segname, resnum, atomname)
// put segname into SegName
// return the number of characters from start-of-Str thru segname
//-------------------------------------------------------------------
  int    Count;
  char*  FullString=Str;

  if (Str[0] != '(') {ProblemParsing("Missing (", Str);}
  Str += 1;
  Str += ReadWhite(Str);
  Count = ReadAlphaNum(Str);
  if (Count == 0)    {ProblemParsing("Missing Segment Name", Str);}
  strncpy(SegName, Str, Count);
  SegName[Count] = '\0';
  Str += Count;
  return(Str-FullString);
}

double GetTime	(	double	Val,
		TimeUnits_t	Units
	)

Definition at line 261 of file FreeEnergyParse.C.

References ASSERT, k_fs, k_ns, k_ps, and kFalse.

Referenced by ReadPmfBlock().

                                              {
//----------------------------------------------------------------------------
// convert (Val Units) to fs, where Units is either fs, ps, or ns
//----------------------------------------------------------------------------
  switch (Units) {
    case k_fs:  return(Val);
    case k_ps:  return(Val*1000);
    case k_ns:  return(Val*1000000);
    default:
      ASSERT(kFalse);
      return(Val);
  }
}

int IsAResidue

(

char *

Str

)

Definition at line 1366 of file FreeEnergyParse.C.

References IsAtomNameList(), ReadAlphaNum(), ReadDigits(), and ReadWhite().

Referenced by IsResidue(), and IsResidueRange().

                          {
//------------------------------------------------------------------------
// see if Str starts with "(segname, resnum)"
// return:    the number of characters, including white space.
//            0, if Str does not start with "(segname, resnum)"
//------------------------------------------------------------------------
  int    Count;
  char*  FullString=Str;

  // if char following the parentheses is ':', this isn't a residue
  if (IsAtomNameList(Str)) {
    return(0);
  }
  // Str must contain the following in sequence to be a legit residue
  // <ws> = optional white-space
  // '(', <ws>, alphanumeric, <ws>, numeric, <ws>, ')'
  if (Str[0] == '(') {
    Str += 1;
    Str += ReadWhite(Str);
    Count = ReadAlphaNum(Str);
    if (Count) {
      Str += Count;
      Str += ReadWhite(Str);
      Count = ReadDigits(Str);
      if (Count) {
        Str += Count;
        Str += ReadWhite(Str);
        if (Str[0] == ')') {
          Str += 1;
          return(Str-FullString);
        }
      }
    }
  }
  return(0);
}

int IsAtom

(

char *

Str

)

Definition at line 1273 of file FreeEnergyParse.C.

References IsAtomNameList(), ReadAlphaNum(), ReadDigits(), and ReadWhite().

Referenced by ReadNextItem().

                      {
//------------------------------------------------------------------------
// see if Str starts with "(segname, resnum, atomname)"
// return:    the number of characters, including white space.
//            0, if Str does not start with "(segname, resnum, atomname)"
//------------------------------------------------------------------------
  int    Count;
  char*  FullString=Str;

  // if char following the parentheses is ':', this isn't an atom
  if (IsAtomNameList(Str)) {
    return(0);
  }
  // Str must contain the following in sequence to be a legit atom
  // <ws> = optional white-space
  // '(', <ws>, alphanumeric, <ws>, numeric, <ws>, alphanumeric, <ws>, ')'
  if (Str[0] == '(') {
    Str += 1;
    Str += ReadWhite(Str);
    Count = ReadAlphaNum(Str);
    if (Count) {
      Str += Count;
      Str += ReadWhite(Str);
      Count = ReadDigits(Str);
      if (Count) {
        Str += Count;
        Str += ReadWhite(Str);
        Count = ReadAlphaNum(Str);
        if (Count) {
          Str += Count;
          Str += ReadWhite(Str);
          if (Str[0] == ')') {
            Str += 1;
            return(Str-FullString);
          }
        }
      }
    }
  }
  return(0);
}

int IsAtomName

(

char *

Str

)

Definition at line 1227 of file FreeEnergyParse.C.

References ReadAlphaNum(), and ReadWhite().

Referenced by ReadNextItem().

                          {
//-------------------------------------------------------------------
// see if Str starts with "atomname:"
// return:    the number of characters, including white space.
//            0, if Str does not start with "atomname:"
//-------------------------------------------------------------------
  int    Count;
  char*  FullString=Str;

  Count = ReadAlphaNum(Str);
  if (Count) {
    Str += Count;
    Str += ReadWhite(Str);
    if (Str[0] == ':') {
      Str += 1;
      return(Str-FullString);
    }
  }
  return(0);
}

int IsAtomNameList

(

char *

Str

)

Definition at line 1249 of file FreeEnergyParse.C.

References ReadParentheses(), and ReadWhite().

Referenced by IsAResidue(), IsAtom(), and ReadNextItem().

                              {
//------------------------------------------------------------------------
// see if Str starts with "(atomname, atomname, ...):"
// return:    the number of characters, including white space.
//            0, if Str does not start with "(atomname, atomname, ...):"
//------------------------------------------------------------------------
  int    Count;
  char*  FullString=Str;

  // Str will be considered an atom-name-list if it contains the following:
  // '(', anything, ')', ':'
  Count = ReadParentheses(Str);
  if (Count > 0) {
    Str += Count;
    Str += ReadWhite(Str);
    if (Str[0] == ':') {
      Str += 1;
      return(Str-FullString);
    }
  }
  return(0);
}

int IsEndGroup

(

char *

Str

)

Definition at line 1214 of file FreeEnergyParse.C.

Referenced by ReadNextItem().

                          {
//-------------------------------------------------------------------
// see if Str starts with "}"
// return:    the number of characters, including white space.
//            0, if Str does not start with "}"
//-------------------------------------------------------------------
  if (Str[0] == '}') {
    return(1);
  }
  return(0);
}

int IsResidue

(

char *

Str

)

Definition at line 1346 of file FreeEnergyParse.C.

References IsAResidue(), and IsResidueRange().

Referenced by ReadNextItem().

                         {
//------------------------------------------------------------------------
// see if Str starts with "(segname, resnum)"
// but not "(segname, resnum) to (segname, resnum)"
//------------------------------------------------------------------------
  int Count;

  Count = IsAResidue(Str);
  if (Count) {
    if (IsResidueRange(Str)) {
      return(0);
    }
    else {
      return(Count);
    }
  }
  return(0);
}

int IsResidueRange

(

char *

Str

)

Definition at line 1316 of file FreeEnergyParse.C.

References IsAResidue(), and ReadWhite().

Referenced by IsResidue(), and ReadNextItem().

                              {
//------------------------------------------------------------------------
// see if Str starts with "(segname, resnum) to (segname, resnum)"
// return:    the number of characters, including white space.
//            0, if Str does not start with "(sn, rn) to (sn, rn)"
//------------------------------------------------------------------------
  int    Count;
  char*  FullString=Str;

  // Str must contain the following in sequence to be a legit res range
  // <ws> = optional white-space
  // residue, <ws>, "to", <ws>, residue
  Count = IsAResidue(Str);
  if (Count) {
    Str += Count;
    Str += ReadWhite(Str);
    if (strncmp(Str, "to", 2) == 0) {
      Str += 2;
      Str += ReadWhite(Str);
      Count = IsAResidue(Str);
      if (Count) {
        Str += Count;
        return(Str-FullString);
      }
    }
  }
  return(0);
}

int IsStartGroup

(

char *

Str

)

Definition at line 1194 of file FreeEnergyParse.C.

References ReadWhite().

Referenced by ReadNextItem().

                            {
//-------------------------------------------------------------------
// see if Str starts with "group {"
// return:     the number of characters, including white space.
//             0, if Str does not start with "group {"
//-------------------------------------------------------------------
  char*  FullString=Str;

  if (strncmp(Str, "group", 5) == 0) {
    Str += 5;
    Str += ReadWhite(Str);
    if (Str[0] == '{') {
      Str += 1;
      return(Str-FullString);
    }
  }
  return(0);
}

void ProblemParsing	(	const char *	Message,
		const char *	Str,
		Bool_t	Terminate
	)

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 31 of file FreeEnergyParse.C.

References endi(), iout, and NAMD_die().

Referenced by AddAtom(), AddAtoms(), AddResidues(), CheckParentheses(), GetAtomName(), GetResNum(), GetResRange(), GetRestraint(), GetSegName(), ReadAValue(), ReadChar(), ReadInput(), ReadPmfBlock(), and ReadWord().

                                                                            {
//----------------------------------------------------------------------------
// print this message if there's a problem parsing
//----------------------------------------------------------------------------
  iout << "FreeEnergy: " << std::endl << endi;
  iout << "FreeEnergy: ";
  iout << "Problem parsing input parameters" << std::endl << endi;
  iout << "FreeEnergy: ";
  if (Terminate) {
    iout << "  Error:       " << Message << std::endl << endi;
  }
  else {
    iout << "  Warning:     " << Message << std::endl << endi;
  }
  iout << "FreeEnergy: ";
  iout << "  Read Until:  " << Str << std::endl << endi;
  iout << "FreeEnergy: " << std::endl << endi;
  if (Terminate) {
    NAMD_die("FreeEnergy: Fatal Parsing Error");
  }
}

int ReadAlpha

(

const char *

Str

)

Definition at line 1424 of file FreeEnergyParse.C.

Referenced by ReadNextPmfSpec(), ReadTaskType(), ReadTimeUnits(), and ReadWord().

                               {
//-------------------------------------------------------------------
// determine the leading number of alphabetic characters in Str.
//-------------------------------------------------------------------
  int  i=0;

  while (1) {
    if (isalpha(Str[i]) || Str[i]=='\'' || Str[i]=='\"' || Str[i] == '*') {
      i++;
    }
    else {
      break;
    }
  }
  return(i);
}

int ReadAlphaNum

(

const char *

Str

)

Definition at line 1442 of file FreeEnergyParse.C.

Referenced by AddAtomsInResidues(), GetAtomName(), GetResRange(), GetSegName(), IsAResidue(), IsAtom(), IsAtomName(), and ReadNextRestraintType().

                                  {
//-------------------------------------------------------------------
// determine the leading number of alphanumeric characters in Str.
//-------------------------------------------------------------------
  int  i=0;

  while (1) {
    if (isalnum(Str[i]) || Str[i]=='\'' || Str[i]=='\"' || Str[i] == '*') {
      i++;
    }
    else {
      break;
    }
  }
  return(i);
}

int ReadAValue	(	char *	Str,
		double &	Value,
		Bool_t	ErrMsg
	)

Definition at line 712 of file FreeEnergyParse.C.

References ProblemParsing(), and ReadWhite().

Referenced by GetRestraint(), and ReadPmfBlock().

                                                        {
//----------------------------------------------------------------------------
// Str should start with a floating point number.  convert it to a double.
// also, return the number of chars to read past the value + white-space
// return NumChars = 0 if Str does not start with a valid fp number.
// Print an error message if ErrMsg is kTrue, and no value is read.
//----------------------------------------------------------------------------
  int    NumChars;
  char*  NewStr;

  // read f.p. number and trailing white-space
  Value = strtod(Str, &NewStr);
  if (NewStr != Str) {
    NewStr += ReadWhite(NewStr);
  }
  NumChars = NewStr - Str;

  // if no number was read, and ErrMsg is kTrue, print a message
  if ((NumChars==0) && (ErrMsg)) {
    ProblemParsing("Floating Point Number Expected", Str);
  }

  return(NumChars);
}

int ReadBound	(	char *	Str,
		Bound_t &	Bound
	)

Definition at line 687 of file FreeEnergyParse.C.

References kLower, kUnknownBound, kUpper, and ReadWord().

Referenced by GetRestraint().

                                         {
//----------------------------------------------------------------------------
// Str should start with "low" or "hi".  determine which it is and
// count the number of characters to read past this word + white-space.
// return NumChars=0 if Str does not start with "low" or "hi"
//----------------------------------------------------------------------------
  int  Count;

  Bound = kUnknownBound;
  Count = ReadWord(Str, "low");
  if (Count) {
    Bound=kLower;
    return(Count);
  }

  Count = ReadWord(Str, "hi");
  if (Count) {
    Bound=kUpper;
    return(Count);
  }

  return(Count);  // Count will be 0 if "low" or "hi" wasn't found
}

int ReadChar	(	char *	Str,
		char	Char,
		Bool_t	ErrMsg
	)

Definition at line 738 of file FreeEnergyParse.C.

References ProblemParsing(), and ReadWhite().

Referenced by GetRestraint(), ReadPmfBlock(), and ReadRestraints().

                                                  {
//----------------------------------------------------------------------------
// Str should start with Char plus trailing white space.
// return the number of chars, including the white space, to read past Char
// return 0 if Str does not start with Char.
// Print an error message if ErrMsg is kTrue, and Char is not read.
//----------------------------------------------------------------------------
  int    NumChars;
  char*  FullString=Str;
  char   Message[64];
  
  // initial part of Message
  strcpy(Message, "Character Missing:  ");

  // read char and trailing white-space
  if (Str[0] == Char) {
    Str += 1;
    Str += ReadWhite(Str);
  }
  NumChars = Str - FullString;

  // if Char was not read, and ErrMsg is kTrue, print a message
  if ((NumChars==0) && (ErrMsg)) {
    // add the character that's missing to Message
    Message[strlen(Message)-1] = Char;
    ProblemParsing(Message, Str);
  }

  return(NumChars);
}

int ReadDigits

(

const char *

Str

)

Definition at line 1460 of file FreeEnergyParse.C.

Referenced by GetResNum(), IsAResidue(), and IsAtom().

                                {
//-------------------------------------------------------------------
// determine the leading number of numeric characters in Str.
//-------------------------------------------------------------------
  int  i=0;

  while (1) {
    if (isdigit(Str[i])) {
      i++;
    }
    else {
      break;
    }
  }
  return(i);
}

void ReadInput	(	char *	Str,
		ARestraintManager &	RMgr,
		ALambdaManager &	LMgr,
		GlobalMasterFreeEnergy &	CFE,
		double	dT
	)

Definition at line 73 of file FreeEnergyParse.C.

References ALambdaManager::Add(), CheckParentheses(), ALambdaControl::Init(), kFalse, ProblemParsing(), ReadPmfBlock(), ReadRestraints(), ReadWhite(), and ToLower().

                                     {
//----------------------------------------------------------------------------
// parse the input string.  Add restraints to RMgr.  Add PmfBlocks to LMgr.
//----------------------------------------------------------------------------
  int             Count;
  char*           OldStr=NULL;   //make sure it's not equal Str to start
  ALambdaControl  PmfBlock, OldPmfBlock;
  // Bool_t          Terminate;

  // read from Str until can't read anymore
  ToLower(Str);
  CheckParentheses(Str);
  Str += ReadWhite(Str);
  while (OldStr != Str) {
    OldStr = Str;
    // add restraints to restraint manager
    Str += ReadRestraints(Str, RMgr, CFE);
    // read a single PmfBlock
    Count = ReadPmfBlock(Str, PmfBlock, dT);
    if (Count) {
      Str += Count;
      // add it to the Lambda manger
      LMgr.Add(PmfBlock);
      // initialize the default parameters of the next PmfBlock
      OldPmfBlock = PmfBlock;
      PmfBlock.Init(OldPmfBlock);
    }
  }
  Str += ReadWhite(Str);
  if (strlen(Str) > 0) {
    ProblemParsing("Unable to Read Entire Input File", Str, /* Terminate= */ kFalse);
  }
}

item_t ReadNextItem	(	char *	Str,
		int &	NumChars
	)

Definition at line 1157 of file FreeEnergyParse.C.

References IsAtom(), IsAtomName(), IsAtomNameList(), IsEndGroup(), IsResidue(), IsResidueRange(), IsStartGroup(), kAtom, kAtomName, kAtomNameList, kEndGroup, kResidue, kResidueRange, kStartGroup, kUnknownItem, and ReadWhite().

Referenced by AddAtoms().

                                              {
//-------------------------------------------------------------------
// Figure out what the next item in Str is, and how many characters
// long it is.  The next item should be one of the following:
//   1.  kStartGroup:       Group {
//   2.  kEndGroup:         }
//   3.  kAtomName:         atomname:
//   4.  kAtomNameList:     (atomname, atomname, ... ):
//   5.  kAtom:             (segname, resno, atomname)
//   6.  kResidue:          (segname, resno)
//   7.  kResidueRange:     (segname, resno) to (segname, resno)
// The following assumptions may be made:
//   1. Str is all lowercase
//   2. There are NO leading white-char's
// Return:
//   The length of the next item, plus the white space that follows.
//-------------------------------------------------------------------
  int     Num;
  item_t  RetVal=kUnknownItem;

  Num=IsStartGroup(Str);     if (Num)  {RetVal=kStartGroup;   goto Found;}
  Num=IsEndGroup(Str);       if (Num)  {RetVal=kEndGroup;     goto Found;}
  Num=IsAtomName(Str);       if (Num)  {RetVal=kAtomName;     goto Found;}
  Num=IsAtomNameList(Str);   if (Num)  {RetVal=kAtomNameList; goto Found;}
  Num=IsAtom(Str);           if (Num)  {RetVal=kAtom;         goto Found;}
  Num=IsResidue(Str);        if (Num)  {RetVal=kResidue;      goto Found;}
  Num=IsResidueRange(Str);   if (Num)  {RetVal=kResidueRange; goto Found;}

  // add the white-space after the item to the length of the item.
Found:
  NumChars = Num;
  Str += NumChars;
  NumChars += ReadWhite(Str);
  return(RetVal);
}

int ReadNextPmfSpec	(	char *	Str,
		pmf_t &	PmfSpec
	)

Definition at line 337 of file FreeEnergyParse.C.

References kAccumTime, kEquilTime, kLambda, kLambdaT, kNoPrint, kNumRepeats, kPrint, kTask, kTime, kUnknownPmf, ReadAlpha(), and ReadWhite().

Referenced by ReadPmfBlock().

                                               {
//----------------------------------------------------------------------------
// Str should start with the next spec for a pmf or mcti block, one of:
//   "task", "time", "lambda", "lambdaT", "print",
//   "equiltime", "accumtime", "numsteps"
//
// Return an identifier of the above.
// Return number of characters, including trailing white space to read past
// this word.  Return NumChars=0 if Str does not begin with one of the above.
//----------------------------------------------------------------------------
  char*  FullString=Str;

  PmfSpec = kUnknownPmf;
  if (strncmp(Str,"task",4)==0)    {PmfSpec=kTask;       goto GotIt;}
  if (strncmp(Str,"time",4)==0)    {PmfSpec=kTime;       goto GotIt;}
  // check for lambdat first, else PmfSpec will be kLambda for "lambdat"
  if (strncmp(Str,"lambdat",7)==0) {PmfSpec=kLambdaT;    goto GotIt;}
  if (strncmp(Str,"lambda",6)==0)  {PmfSpec=kLambda;     goto GotIt;}
  if (strncmp(Str,"print",5)==0)   {PmfSpec=kPrint;      goto GotIt;}
  if (strncmp(Str,"nopr",4)==0)    {PmfSpec=kNoPrint;    goto GotIt;}
  if (strncmp(Str,"equil",5)==0)   {PmfSpec=kEquilTime;  goto GotIt;}
  if (strncmp(Str,"accum",5)==0)   {PmfSpec=kAccumTime;  goto GotIt;}
  if (strncmp(Str,"numstep",7)==0) {PmfSpec=kNumRepeats; goto GotIt;}
  return(0);

GotIt:
  Str += ReadAlpha(Str);
  Str += ReadWhite(Str);
  return(Str-FullString);
}

restr_t ReadNextRestraintType	(	char *	Str,
		int &	NumChars
	)

Definition at line 809 of file FreeEnergyParse.C.

References kAngle, kAngleBound, kAnglePMF, kDihe, kDiheBound, kDihePMF, kDist, kDistBound, kDistPMF, kPosi, kPosiBound, kPosiPMF, kUnknownRestr, ReadAlphaNum(), and ReadWhite().

Referenced by GetRestraint().

                                                        {
//----------------------------------------------------------------------------
// Str should start with the next restraint type (no leading white space),
// namely one of:
// 
//   "posi",       "dist",       "angle",       "dihe"
//   "posi bound", "dist bound", "angle bound", "dihe bound"
//   "posi pmf",   "dist pmf",   "angle pmf",   "dihe pmf"
//
// figure out which it is.
// also, return the number of characters, including trailing white space.
// return NumChars=0 for an illegal restraint-type
//
// the words "pos*", "dist*", "angle*", "dihe*", "bound*", and "pmf*"
// are all recognized.
//----------------------------------------------------------------------------
  restr_t  RestraintType=kUnknownRestr;
  char*    FullString=Str;

  // check if Str starts with "pos", "dist", "angl", or "dihe"
  if (strncmp(Str,"pos", 3)==0)  {RestraintType=kPosi;  goto GotIt;}
  if (strncmp(Str,"dist",4)==0)  {RestraintType=kDist;  goto GotIt;}
  if (strncmp(Str,"angl",4)==0)  {RestraintType=kAngle; goto GotIt;}
  if (strncmp(Str,"dihe",4)==0)  {RestraintType=kDihe;  goto GotIt;}
  NumChars = 0;
  return(RestraintType);

  // skip to the end of the white space following this word
GotIt:
  Str += 3;
  Str += ReadAlphaNum(Str);
  Str += ReadWhite(Str);

  // check if the next word is "bound", skip to the end of this word
  if (strncmp(Str,"bound",5)==0) {
    switch (RestraintType) {
      case kPosi:   RestraintType=kPosiBound;   break;
      case kDist:   RestraintType=kDistBound;   break;
      case kAngle:  RestraintType=kAngleBound;  break;
      case kDihe:   RestraintType=kDiheBound;   break;
      default: break;
    }
    Str += 5;
    Str += ReadAlphaNum(Str);
  }

  // check if the next word is "pmf", skip to the end of this word
  if (strncmp(Str,"pmf",3)==0) {
    switch (RestraintType) {
      case kPosi:   RestraintType=kPosiPMF;   break;
      case kDist:   RestraintType=kDistPMF;   break;
      case kAngle:  RestraintType=kAnglePMF;  break;
      case kDihe:   RestraintType=kDihePMF;   break;
      default: break;
    }
    Str += 3;
    Str += ReadAlphaNum(Str);
  }

  // skip past trailing white space, calcuate num chars string has been advanced
  Str += ReadWhite(Str);
  NumChars = Str-FullString;
  return(RestraintType);
}

int ReadParentheses

(

const char *

Str

)

Definition at line 1404 of file FreeEnergyParse.C.

Referenced by GetResRange(), and IsAtomNameList().

                                     {
//-------------------------------------------------------------------
// count the number of characters from the leading '('
// to the first ')' of Str (inclusive).
//     no leading '('  =>  return  0
//     no closing ')'  =>  return -1
//-------------------------------------------------------------------
  const char* Str2;

  if (Str[0] != '(') {
    return(0);
  }
  Str2 = strchr(Str, ')');
  if (Str2 == NULL) {
    return(-1);
  }
  return((Str2-Str)+1);
}

int ReadPmfBlock	(	char *	Str,
		ALambdaControl &	PmfBlock,
		double	dT
	)

Definition at line 111 of file FreeEnergyParse.C.

References ASSERT, ALambdaControl::GetTask(), GetTime(), k_ps, kAccumTime, kALittle, kDown, kEquilTime, kFade, kFalse, kGrow, kLambda, kLambdaT, kNoGrow, kNoPrint, kNumRepeats, kPrint, kStepDown, kStepFade, kStepGrow, kStepUp, kStop, kTask, kTime, kTrue, kUnknownTask, kUp, ProblemParsing(), ReadAValue(), ReadChar(), ReadNextPmfSpec(), ReadTaskType(), ReadTimeUnits(), ReadWord(), ALambdaControl::SetLambdaKf(), ALambdaControl::SetLambdaRef(), ALambdaControl::SetNumAccumSteps(), ALambdaControl::SetNumEquilSteps(), ALambdaControl::SetNumPrintSteps(), ALambdaControl::SetNumRepeats(), ALambdaControl::SetNumSteps(), and ALambdaControl::SetTask().

Referenced by ReadInput().

                                                                 {
//----------------------------------------------------------------------------
// if str starts with "pmf" or "mcti", read all the specs for this block
// and initialize PmfBlock.
//
// PmfBlock will already have default values for all parameters.
// The parameters that are read will be used to override the defaults.
// LambdaKf and LambdaRef are initialized after all parameters have been
// read, because the meaning of these parameters depends upon the task.
//
// If time-units (fs, ps, ns) are not specified, use ps
//
// return the number of chars to read past this block.
// return 0 if Str does not start with "pmf" or "mcti"
//----------------------------------------------------------------------------
  int     Count, Count1, Count2;
  Bool_t  Finished=kFalse;
  char*   FullString=Str;
  char*   TempStr;
  pmf_t   PmfSpec;
  // if time-units are not specified, then they're in ps.
  TimeUnits_t  TimeUnits;
  TimeUnits_t  DefaultTimeUnits = k_ps;
  // illegal default value.  user will have to specify this.
  feptask_t  Task=kUnknownTask;
  double  Lambda=-1, LambdaT=-1, Time;
  double  Dummy;
  int     NumRepeats=-1;

  const Bool_t  kPrintErrMsg=kTrue; // kNoErrMsg=kFalse;

  // if Str does not begin with "pmf" or "mcti" return 0
  Count1 = ReadWord(Str, "pmf");
  Count2 = ReadWord(Str, "mcti");
  Count = Count1 + Count2;
  if (Count==0) {
    return(0);
  }

  // skip past "pmf" or "mcti"
  Str += Count;
  // skip past "{"
  Str += ReadChar(Str, '{');
  // read spec's until "}" is found or can't read a spec
  do {
    Count = ReadNextPmfSpec(Str, PmfSpec);
    Str += Count;
    if (Count==0) {
      ProblemParsing("Unable to Read PMF Specification", Str);
    }
    // skip past "="
    Str += ReadChar(Str, '=');
    switch (PmfSpec) {
      case kTask:
        TempStr = Str;
        Str += ReadTaskType(Str, Task);
        if (Str == TempStr) {
          ProblemParsing("Can't Read Task", Str);
        }
        PmfBlock.SetTask(Task);
        break;
      case kTime:
        Str += ReadAValue(Str, Time, kPrintErrMsg);
        Str += ReadTimeUnits(Str, TimeUnits, DefaultTimeUnits);
        Time = GetTime(Time, TimeUnits);
        PmfBlock.SetNumSteps((int)(Time/dT));
        break;
      case kLambda:
        Str += ReadAValue(Str, Lambda, kPrintErrMsg);
        break;
      case kLambdaT:
        Str += ReadAValue(Str, LambdaT, kPrintErrMsg);
        break;
      case kPrint:
        Str += ReadAValue(Str, Time, kPrintErrMsg);
        Str += ReadTimeUnits(Str, TimeUnits, DefaultTimeUnits);
        Time = GetTime(Time, TimeUnits);
        PmfBlock.SetNumPrintSteps((int)(Time/dT));
        break;
      case kNoPrint:
        PmfBlock.SetNumPrintSteps(-1);
        break;
      case kEquilTime:
        Str += ReadAValue(Str, Time, kPrintErrMsg);
        Str += ReadTimeUnits(Str, TimeUnits, DefaultTimeUnits);
        Time = GetTime(Time, TimeUnits);
        PmfBlock.SetNumEquilSteps((int)(Time/dT));
        break;
      case kAccumTime:
        Str += ReadAValue(Str, Time, kPrintErrMsg);
        Str += ReadTimeUnits(Str, TimeUnits, DefaultTimeUnits);
        Time = GetTime(Time, TimeUnits);
        PmfBlock.SetNumAccumSteps((int)(Time/dT));
        break;
      case kNumRepeats:
        Str += ReadAValue(Str, Dummy, kPrintErrMsg);
        NumRepeats = (int)Dummy;
        PmfBlock.SetNumRepeats(NumRepeats);
        break;
      default:
        ASSERT(kFalse);
    }
    Count = ReadChar(Str, '}');
    Str += Count;
    // if "}" was read, then we're finished
    if (Count!=0) {Finished=kTrue;}
  }
  while(!Finished);

  // if Task was not specified above, then use PmfBlock's default task
  if (Task==kUnknownTask) {
    Task = PmfBlock.GetTask();
  }
  // if Task wasn't specified earlier, die.
  if (Task==kUnknownTask) {
    ProblemParsing("Must Specify Task", FullString);
  }

  // set LambdaKf and LambdaRef, using Lambda and LambdaT
  // (the former is the internal representation, the latter is the user's)
  // there's no need to set them if they haven't been read in this routine
  switch(Task) {
    case kStop:
      PmfBlock.SetLambdaKf(1.0);
      if (Lambda >= -kALittle) {
        PmfBlock.SetLambdaRef(Lambda);
      }
      break;
    case kNoGrow:
      if (Lambda >= -kALittle) {
        PmfBlock.SetLambdaKf(Lambda);
      }
    case kGrow:
    case kFade:
    case kStepGrow:
    case kStepFade:
      if (LambdaT >= -kALittle) {
        PmfBlock.SetLambdaRef(LambdaT);
      }
      break;
    default:
      ASSERT((Task==kUp)||(Task==kDown)||(Task==kStepUp)||(Task==kStepDown));
      PmfBlock.SetLambdaKf(1.0);
      break;
  }
  
  return(Str-FullString);
}

int ReadRestraints	(	char *	Str,
		ARestraintManager &	AllRestraints,
		GlobalMasterFreeEnergy &	CFE
	)

Definition at line 369 of file FreeEnergyParse.C.

References ARestraintManager::Add(), GetRestraint(), kFalse, kTrue, ReadChar(), and ReadWord().

Referenced by ReadInput().

                                                           {
//----------------------------------------------------------------------------
// if Str starts with "urestr", read each restraint spec, create
// a restraint, and put a pointer to the restraint into AllRestraints
//
// return the number of chars to read past all restraints
// return 0 if Str does not start with "urestr"
//----------------------------------------------------------------------------
  int          Count;
  Bool_t       Finished=kFalse;
  char*        FullString=Str;
  ARestraint*  pRestraint;

  Count = ReadWord(Str, "urest");
  // when "urestraint" is found
  if (Count) {
    // skip past "urest..."
    Str += Count;
    // skip past "{"
    Str += ReadChar(Str, '{');
    // read restraints until "}" is found or can't read a restraint
    do {
      pRestraint = GetRestraint(Str, Count, CFE);
      Str += Count;
      // if a restraint could not be read, then we're finished
      if (Count==0) {Finished=kTrue;}
      if (!Finished) {
        AllRestraints.Add(pRestraint);
        Count = ReadChar(Str, '}');
        Str += Count;
        // if "}" was read, then we're finished
        if (Count!=0) {Finished=kTrue;}
      }
    }
    while(!Finished);
  }
  return(Str-FullString);
}

int ReadTaskType	(	char *	Str,
		feptask_t &	Task
	)

Definition at line 305 of file FreeEnergyParse.C.

References kDown, kFade, kGrow, kNoGrow, kStepDown, kStepFade, kStepGrow, kStepUp, kStop, kUnknownTask, kUp, ReadAlpha(), and ReadWhite().

Referenced by ReadPmfBlock().

                                             {
//----------------------------------------------------------------------------
// Str should start with a task, one of:
//   "up", "down", "stop", "grow", "fade", "nogrow",
//   "stepup", "stepdown", "stepgrow", "stepfade"
//
// return an identifer for the above.
// return the number of chars to read past the task.  return 0 if Str does
// not start with one of the above.
//----------------------------------------------------------------------------
  char*   FullString=Str;

  Task = kUnknownTask;
  if (strncmp(Str,"up",2)==0)       {Task=kUp;       goto GotIt;}
  if (strncmp(Str,"down",4)==0)     {Task=kDown;     goto GotIt;}
  if (strncmp(Str,"stop",4)==0)     {Task=kStop;     goto GotIt;}
  if (strncmp(Str,"grow",4)==0)     {Task=kGrow;     goto GotIt;}
  if (strncmp(Str,"fade",4)==0)     {Task=kFade;     goto GotIt;}
  if (strncmp(Str,"nogrow",6)==0)   {Task=kNoGrow;   goto GotIt;}
  if (strncmp(Str,"stepup",6)==0)   {Task=kStepUp;   goto GotIt;}
  if (strncmp(Str,"stepdown",8)==0) {Task=kStepDown; goto GotIt;}
  if (strncmp(Str,"stepgrow",8)==0) {Task=kStepGrow; goto GotIt;}
  if (strncmp(Str,"stepfade",8)==0) {Task=kStepFade; goto GotIt;}
  return(0);

GotIt:
  Str += ReadAlpha(Str);
  Str += ReadWhite(Str);
  return(Str-FullString);
}

int ReadTimeUnits	(	char *	Str,
		TimeUnits_t &	Units,
		TimeUnits_t	DefaultUnits
	)

Definition at line 276 of file FreeEnergyParse.C.

References k_fs, k_ns, k_ps, kFalse, kTrue, ReadAlpha(), and ReadWhite().

Referenced by ReadPmfBlock().

                                                                           {
//----------------------------------------------------------------------------
// Str should start with one of:
//   "fs", "ps", or "ns"
//
// If Str starts with one of the above, return an identifier for the above.
// if Str does not start with one of the above, set Units to DefaultUnits.
//
// return the number of chars to read past the time units.  return 0 if
// Str does not start with one of the above.
//----------------------------------------------------------------------------
  char*   FullString=Str;
  Bool_t  FoundIt=kFalse;

  if (strncmp(Str,"fs",2)==0) {Units=k_fs; FoundIt=kTrue;}
  if (strncmp(Str,"ps",2)==0) {Units=k_ps; FoundIt=kTrue;}
  if (strncmp(Str,"ns",2)==0) {Units=k_ns; FoundIt=kTrue;}

  if (FoundIt) {
    Str += ReadAlpha(Str);
    Str += ReadWhite(Str);
  }
  else {
    Units = DefaultUnits;
  }
  return(Str-FullString);
}

int ReadWhite

(

const char *

Str

)

Definition at line 1478 of file FreeEnergyParse.C.

Referenced by AddAtoms(), AddAtomsInResidues(), GetAtomName(), GetResNum(), GetResRange(), GetSegName(), IsAResidue(), IsAtom(), IsAtomName(), IsAtomNameList(), IsResidueRange(), IsStartGroup(), ReadAValue(), ReadChar(), ReadInput(), ReadNextItem(), ReadNextPmfSpec(), ReadNextRestraintType(), ReadTaskType(), ReadTimeUnits(), and ReadWord().

                               {
//-------------------------------------------------------------------
// determine the leading number of white characters in Str.
// a white char is:
//   space, tab, linefeed, carriage-return, formfeed,
//   vertical-tab, and newline characters.
// a white char is also (for the sake of this program):
//   comma, semi-colon, and period.
//-------------------------------------------------------------------
  int  i=0;

  // count the number of white-char's.  break at first non-white-char.
  while (1) {
    if (
         (Str[i] == 9)   ||      // tab
         (Str[i] == 10)  ||      // LF
         (Str[i] == 11)  ||      // vertical-tab
         (Str[i] == 12)  ||      // form-feed
         (Str[i] == 13)  ||      // CR
         (Str[i] == 32)  ||      // space
         (Str[i] == ',') ||      // comma
         (Str[i] == ';')         // semi-colon
//         (Str[i] == '.')         // period  (took this out in case of =.4, eg)
       )
    {    
      i++;
    }
    else {
      break;
    }
  }
  return(i);
}

int ReadWord	(	const char *	Str,
		const char *	Word,
		Bool_t	ErrMsg
	)

Definition at line 770 of file FreeEnergyParse.C.

References ProblemParsing(), ReadAlpha(), and ReadWhite().

Referenced by GetRestraint(), ReadBound(), ReadPmfBlock(), and ReadRestraints().

                                                               {
//----------------------------------------------------------------------------
// Str should start with Word plus, perhaps, some extra alphabetic
// characters, plus trailing white space.
//
// (do NOT read past numeric characters which follow Word, so that
//  this routine can be used on the following:  ReadWord(Str, "="),
//  where Str is, for example, "=123 ...")
//
// return the number of chars, including the white space, to read past Word
// return 0 if Str does not start with Word.
//
// Print an error message if ErrMsg is kTrue, and word is not read.
//----------------------------------------------------------------------------
  const char*  FullString=Str;
  int    NumChars, StrLen;
  char   Message[64];
  
  // initial part of message
  strcpy(Message, "Word Missing: ");

  StrLen = strlen(Word);
  if (strncmp(Str, Word, StrLen) == 0) {
    Str += StrLen;
    Str += ReadAlpha(Str);
    Str += ReadWhite(Str);
  }
  NumChars = Str - FullString;

  // if Word was not read, and ErrMsg is kTrue, print a message
  if ((NumChars==0) && (ErrMsg)) {
    strcat(Message, Word);
    ProblemParsing(Message, Str);
  }

  return(NumChars);
}

void ToLower

(

char *

Str

)

Definition at line 1513 of file FreeEnergyParse.C.

Referenced by ReadInput().

                        {
//-------------------------------------------------------------------
// convert Str to all lower case
//-------------------------------------------------------------------
  for (unsigned int i=0; i<strlen(Str); i++) {
    Str[i] = (char)tolower(Str[i]);
  }
}