GroupRestraintParam Class Reference

#include <GroupRestraintsParam.h>

Public Member Functions
	GroupRestraintParam (void)
	~GroupRestraintParam (void)
void	SetGroup1AtomFileIndices (const char *fileName)
void	SetGroup1AtomListIndices (const char *list)
void	SetGroup1RefPosition (const char *vec)
void	SetGroup2AtomFileIndices (const char *fileName)
void	SetGroup2AtomListIndices (const char *list)
void	SetGroupName (const char *name)
void	SetForce (const BigReal force)
void	SetExponent (const int exponent)
void	SetResCenter (const char *vec)
void	SetResDirection (const char *status, const int component)
void	SetUseDistMagnitude (const char *status)
void	CheckParam (void)
void	PrintSummary ()
const char *	GetGroupName () const
int	GetExponent () const
double	GetForce () const
Vector	GetGroupRes1Position () const
Vector	GetResDirection () const
Vector	GetResCenter () const
const std::vector< int > &	GetGroup1AtomIndex () const
const std::vector< int > &	GetGroup2AtomIndex () const
bool	GetUseDistMagnitude () const

Detailed Description

Group restraint parameter class. Stores parameters required for harmonic restraints. Make sure that all necessary parameters are provided. Read atom indicies from file. Print summary of parameters.

Definition at line 18 of file GroupRestraintsParam.h.

Constructor & Destructor Documentation

GroupRestraintParam()

GroupRestraintParam::GroupRestraintParam

(

void

)

< Default restraint exponent is 2




< Default force



< Default reference COM position for group 1


< Default restraint in X,Y, and Z direction

< Default center of restraint
< Default is to use vector distance, not magnitude

Definition at line 5 of file GroupRestraintsParam.C.

                                             {
    groupNameDefined = false;
    restraintForceDefined = false;
    group1RefPositionDefined = false;
    restraintCenterDefined = false;
    groupName = NULL;
    group1Idx.clear();
    group2Idx.clear();
    restraintExp = 2;          
    restraintForce = 0.0;      
    group1RefPosition = 0.0;   
    restraintDir = 1.0;        
    restraintCenter = 0.0;     
    useDistanceMagnitude = false; 
}

~GroupRestraintParam()

GroupRestraintParam::~GroupRestraintParam

(

void

)

Definition at line 21 of file GroupRestraintsParam.C.

                                              {
    if (groupName) delete [] groupName;
}

Member Function Documentation

CheckParam()

void GroupRestraintParam::CheckParam

(

void

)

Check all necessary parameters in group restraint are set

Check all necessary parameters are set

Definition at line 275 of file GroupRestraintsParam.C.

References Vector::length2(), and NAMD_die().

                                         {
    char err_msg[512];

    if (!groupNameDefined) {
        sprintf(err_msg, "Group restraints: Key or tag name is not defined!\n");
        NAMD_die(err_msg);
    }

    if (!restraintForceDefined) {
        sprintf(err_msg, "Group restraints: Restraint Force constant is not defined for %s!\n", groupName);
        NAMD_die(err_msg);
    }

    if (!restraintCenterDefined) {
        sprintf(err_msg, "Group restraints: Restraint center is not defined for %s!\n", groupName);
        NAMD_die(err_msg);
    }

    if (!(restraintExp > 0)) {
        sprintf(err_msg, "Group restraints: Restraint exponent must be positive value for %s!\n", groupName);
        NAMD_die(err_msg);
    }

    if (restraintExp % 2) {
        sprintf(err_msg, "Group restraints: Restraint exponent must be an even number for %s!\n", groupName);
        NAMD_die(err_msg);
    }

    if (!(restraintForce > 0)) {
        sprintf(err_msg, "Group restraints: Restraint Force constant must be positive value for %s!\n", groupName);
        NAMD_die(err_msg);
    }

    if (!group1RefPositionDefined && !group1Idx.size()) {
        sprintf(err_msg, "Group restraints: Either reference COM position or atom indices for group 1 must be defined for %s!\n", groupName);
        NAMD_die(err_msg);
    }

    if (group1RefPositionDefined && group1Idx.size()) {
        sprintf(err_msg, "Group restraints: Reference COM position and atom indices for group 1 cannot be defined together for %s!\n", groupName);
        NAMD_die(err_msg);
    }

    if (!(group2Idx.size())) {
        sprintf(err_msg, "Group restraints: No atom is defined for group 2 to be restrained for %s!\n", groupName);
        NAMD_die(err_msg);
    }

    if (!(restraintDir.length2())) {
        sprintf(err_msg, "Group restraints: At least one component of restraint distance "
            "must be selected for %s!\n", groupName);
        NAMD_die(err_msg);
    }
}

GetExponent()

int GroupRestraintParam::GetExponent ( ) const

inline

Get the restraint exponent

Definition at line 68 of file GroupRestraintsParam.h.

{return restraintExp;}

GetForce()

double GroupRestraintParam::GetForce ( ) const

inline

Get the restraint force constant

Definition at line 71 of file GroupRestraintsParam.h.

{return restraintForce;}

GetGroup1AtomIndex()

const std::vector<int>& GroupRestraintParam::GetGroup1AtomIndex ( ) const

inline

Get reference to restrained atom indicies in group 1

Definition at line 83 of file GroupRestraintsParam.h.

{return group1Idx;}

GetGroup2AtomIndex()

const std::vector<int>& GroupRestraintParam::GetGroup2AtomIndex ( ) const

inline

Get reference to restrained atom indicies in group 2

Definition at line 86 of file GroupRestraintsParam.h.

{return group2Idx;}

GetGroupName()

const char* GroupRestraintParam::GetGroupName ( ) const

inline

Get restraint group name

Definition at line 65 of file GroupRestraintsParam.h.

{return groupName;}

GetGroupRes1Position()

Vector GroupRestraintParam::GetGroupRes1Position ( ) const

inline

Get the reference COM position for group 1

Definition at line 74 of file GroupRestraintsParam.h.

{return group1RefPosition;}

GetResCenter()

Vector GroupRestraintParam::GetResCenter ( ) const

inline

Get the center of restraint

Definition at line 80 of file GroupRestraintsParam.h.

{return restraintCenter;}

GetResDirection()

Vector GroupRestraintParam::GetResDirection ( ) const

inline

Get restraint vector component (X, Y, Z)

Definition at line 77 of file GroupRestraintsParam.h.

{return restraintDir;}

GetUseDistMagnitude()

bool GroupRestraintParam::GetUseDistMagnitude ( ) const

inline

Definition at line 89 of file GroupRestraintsParam.h.

{return useDistanceMagnitude;}

PrintSummary()

void GroupRestraintParam::PrintSummary

(

)

Print summary of parameters in group restraint

Definition at line 331 of file GroupRestraintsParam.C.

References endi(), iINFO(), iout, Vector::length(), Vector::x, Vector::y, and Vector::z.

                                       {
    iout << iINFO << "GROUP RESTRAINT KEY                  " << groupName << "\n" << endi;
    if (useDistanceMagnitude) {
        iout << iINFO << "       RESTRAINT DISTANCE MAGNITUDE  " << "ACTIVE\n" << endi;
        iout << iINFO << "       RESTRAINT CENTER              " << restraintCenter.length() << "\n" << endi;
    } else {
        iout << iINFO << "       RESTRAINT DISTANCE VECTOR     " << "ACTIVE\n" << endi;
        iout << iINFO << "       RESTRAINT CENTER              " << restraintCenter << "\n" << endi;
    }
    iout << iINFO << "       RESTRAINT FORCE               " << restraintForce << "\n" << endi;
    iout << iINFO << "       RESTRAINT EXPONENT            " << restraintExp << "\n" << endi;
    iout << iINFO << "       RESTRAINT COMPONENT X         " << (restraintDir.x ? "YES" : "NO") << "\n" << endi;
    iout << iINFO << "       RESTRAINT COMPONENT Y         " << (restraintDir.y ? "YES" : "NO") << "\n" << endi;
    iout << iINFO << "       RESTRAINT COMPONENT Z         " << (restraintDir.z ? "YES" : "NO") << "\n" << endi;
    iout << iINFO << "       RESTRAINED ATOMS IN GROUP 2   " << group2Idx.size() << "\n" << endi;
    if (group1RefPositionDefined) {
        iout << iINFO << "       COM REF. POSITION IN GROUP 1  " << group1RefPosition << "\n" << endi;
    } else {
        iout << iINFO << "       RESTRAINED ATOMS IN GROUP 1   " << group1Idx.size() << "\n" << endi;
    }
}

SetExponent()

void GroupRestraintParam::SetExponent

(

const int

exponent

)

Set the restraint exponent

Definition at line 207 of file GroupRestraintsParam.C.

Referenced by GroupRestraintList::SetExponent().

                                                        {
    restraintExp = exponent; 
}

SetForce()

void GroupRestraintParam::SetForce

(

const BigReal

force

)

Set the restraint force constant

Definition at line 195 of file GroupRestraintsParam.C.

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

Referenced by GroupRestraintList::SetForce().

                                                      {
    char err_msg[512]; //  Buffer for error message
    if (restraintForceDefined) {
        sprintf(err_msg, "Group restraints: Redefining restraint force for %s!\n",
            groupName);
        iout << iWARN << err_msg << "\n" << endi;   
    }
    restraintForce = force; 
    restraintForceDefined = true;
}

SetGroup1AtomFileIndices()

void GroupRestraintParam::SetGroup1AtomFileIndices

(

const char *

fileName

)

Read the restrained atom indicies for group 1 from file and store it

Read the restrained atom indices for group 1 from file and store it

Definition at line 26 of file GroupRestraintsParam.C.

References endi(), iINFO(), iout, iWARN(), NAMD_blank_string(), NAMD_die(), and NAMD_read_line().

Referenced by GroupRestraintList::SetGroup1AtomFileIndices().

                                                                       {
    char err_msg[512]; //  Buffer for error message
    char buffer[512];  //  Buffer for file reading

    if(group1Idx.size()) {
        group1Idx.clear();
        sprintf(err_msg, "Group restraints: Redefining existing group 1 indices for %s!\n",
            groupName);
        iout << iWARN << err_msg << "\n" << endi;   
    }

    if (! fileName) {
        sprintf(err_msg, "Group restraints: No group 1 restraint file is defined for '%s'!\n", groupName);
        NAMD_die(err_msg); 
    }

    FILE *file = fopen(fileName, "r");
    if (!file) {
        sprintf(err_msg, "Group restraints: Unable to open group 1 restraint file '%s'!\n", fileName);
        NAMD_die(err_msg); 
    } else {
        iout << iINFO << "Reading group 1 restraint file " << fileName << " for group " <<
                groupName << "\n" << endi; 
    }

    while (true) {
        int index;
        int badLine = 0;
        int return_code = 0;
        do {
            return_code = NAMD_read_line(file, buffer, 512);
        } while ( (return_code == 0) && (NAMD_blank_string(buffer)) );

        if (return_code) {
            break;
        }
        if (sscanf(buffer, "%d", &index) != 1) {
            sprintf(err_msg, "Group restraints: Bad line in group 1 restraint file '%s': %s!\n", fileName, buffer);
            NAMD_die(err_msg);
        } else {
            group1Idx.push_back(index);
        }
    }
    fclose(file);
}

SetGroup1AtomListIndices()

void GroupRestraintParam::SetGroup1AtomListIndices

(

const char *

list

)

Set the restrained atom indicies for group 1 from a list

Set the restrained atom indices for group 1 from a list

Definition at line 120 of file GroupRestraintsParam.C.

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

Referenced by GroupRestraintList::SetGroup1AtomListIndices().

                                                                   {
    char err_msg[512]; //  Buffer for error message
    int index, numRead;
    int i = 0;

    if(group1Idx.size()) {
        group1Idx.clear();
        sprintf(err_msg, "Group restraints: Redefining existing group 1 restraint indices for %s!\n",
            groupName);
        iout << iWARN << err_msg << "\n" << endi;   
    }

    // Get the length of string
    int strLength = strlen(list);
    // Read the index and advance the number of read char
    // until we reach to the end of it
    while (i < strLength) {
        if(sscanf(list,"%d%n", &index, &numRead) != 1) {
            sprintf(err_msg, "Group restraints: Bad line in group 1 restraint list for '%s': %s!\n",
                groupName, list);
            NAMD_die(err_msg);
        } else {
            list += numRead + 1;
            i += numRead + 1;
            group1Idx.push_back(index);
        }
    } 
}

SetGroup1RefPosition()

void GroupRestraintParam::SetGroup1RefPosition

(

const char *

vec

)

Set the reference COM position for group 1

Definition at line 212 of file GroupRestraintsParam.C.

References endi(), iout, iWARN(), NAMD_die(), and Vector::set().

Referenced by GroupRestraintList::SetGroup1RefPosition().

                                                              {
    char err_msg[512]; //  Buffer for error message
    if (group1RefPositionDefined) {
        sprintf(err_msg, "Group restraints: Redefining group 1 reference COM position for %s!\n",
            groupName);
        iout << iWARN << err_msg << "\n" << endi;   
    }

    if(group1RefPosition.set(vec)) {
        group1RefPositionDefined = true; 
    } else {
        sprintf(err_msg, "Group restraints: Bad reference COM position for %s: { %s }. %s\n",
            groupName, vec, "Expect a {x y z} vector.");
        NAMD_die(err_msg);
    }
}

SetGroup2AtomFileIndices()

void GroupRestraintParam::SetGroup2AtomFileIndices

(

const char *

fileName

)

Read the restained atom indicies for group 2 from file and store it

Read the restrained atom indices for group 2 from file and store it

Definition at line 73 of file GroupRestraintsParam.C.

References endi(), iINFO(), iout, iWARN(), NAMD_blank_string(), NAMD_die(), and NAMD_read_line().

Referenced by GroupRestraintList::SetGroup2AtomFileIndices().

                                                                       {
    char err_msg[512]; //  Buffer for error message
    char buffer[512];  //  Buffer for file reading

    if(group2Idx.size()) {
        group2Idx.clear();
        sprintf(err_msg, "Group restraints: Redefining existing group 2 indices for %s!\n",
            groupName);
        iout << iWARN << err_msg << "\n" << endi;   
    }

    if (! fileName) {
        sprintf(err_msg, "Group restraints: No group 2 restraint file is defined for '%s'!\n", groupName);
        NAMD_die(err_msg); 
    }

    FILE *file = fopen(fileName, "r");
    if (!file) {
        sprintf(err_msg, "Group restraints: Unable to open group 2 restraint file '%s'!\n", fileName);
        NAMD_die(err_msg); 
    } else {
        iout << iINFO << "Reading group 2 restraint file " << fileName << " for group " <<
                groupName << "\n" << endi; 
    }

    while (true) {
        int index;
        int badLine = 0;
        int return_code = 0;
        do {
            return_code = NAMD_read_line(file, buffer, 512);
        } while ( (return_code == 0) && (NAMD_blank_string(buffer)) );

        if (return_code) {
            break;
        }
        if (sscanf(buffer, "%d", &index) != 1) {
            sprintf(err_msg, "Group restraints: Bad line in group 2 restraint file '%s': %s!\n", fileName, buffer);
            NAMD_die(err_msg);
        } else {
            group2Idx.push_back(index);
        }
    }
    fclose(file);
}

SetGroup2AtomListIndices()

void GroupRestraintParam::SetGroup2AtomListIndices

(

const char *

list

)

Set the restrained atom indicies for group 2 from a list

Set the restrained atom indices for group 2 from a list

Definition at line 150 of file GroupRestraintsParam.C.

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

Referenced by GroupRestraintList::SetGroup2AtomListIndices().

                                                                   {
    char err_msg[512]; //  Buffer for error message
    int index, numRead;
    int i = 0;

    if(group2Idx.size()) {
        group2Idx.clear();
        sprintf(err_msg, "Group restraints: Redefining existing group 2 restraint indices for %s!\n",
            groupName);
        iout << iWARN << err_msg << "\n" << endi;   
    }

    // Get the length of string
    int strLength = strlen(list);
    // Read the index and advance the number of read char
    // until we reach to the end of it
    while (i < strLength) {
        if(sscanf(list,"%d%n", &index, &numRead) != 1) {
            sprintf(err_msg, "Group restraints: Bad line in group 2 restraint list for '%s': %s!\n",
                groupName, list);
            NAMD_die(err_msg);
        } else {
            list += numRead + 1;
            i += numRead + 1;
            group2Idx.push_back(index);
        }
    } 
}

SetGroupName()

void GroupRestraintParam::SetGroupName

(

const char *

name

)

Set restraint group name

Definition at line 180 of file GroupRestraintsParam.C.

References NAMD_die().

                                                       {
    char err_msg[512]; //  Buffer for error message
    if (groupName) {
        sprintf(err_msg, "Group restraints: Redefining existing group restraint name from %s to %s!\n",
            groupName, name);
        NAMD_die(err_msg);
    } else {
        groupNameDefined = true;
        int nameLength = strlen(name);
        groupName = new char[nameLength + 1];
        strncpy(groupName, name, nameLength + 1);
    }
}

SetResCenter()

void GroupRestraintParam::SetResCenter

(

const char *

vec

)

Set the center of equilibrium value of restraint

Set the center or equilibrium value of restraint

Definition at line 230 of file GroupRestraintsParam.C.

References endi(), iout, iWARN(), NAMD_die(), and Vector::set().

Referenced by GroupRestraintList::SetResCenter().

                                                      {
    char err_msg[512]; //  Buffer for error message
    if (restraintCenterDefined) {
        sprintf(err_msg, "Group restraints: Redefining restraint center for %s!\n",
            groupName);
        iout << iWARN << err_msg << "\n" << endi;   
    }

    if(restraintCenter.set(vec)) {
        restraintCenterDefined = true; 
    } else {
        sprintf(err_msg, "Group restraints: Bad restraint center value for %s: { %s }. %s\n",
            groupName, vec, "Expect a {x y z} vector.");
        NAMD_die(err_msg);
    }
}

SetResDirection()

void GroupRestraintParam::SetResDirection	(	const char *	status,
		const int	component
	)

Set restraint vector component (X, Y, Z)

Definition at line 248 of file GroupRestraintsParam.C.

References NAMD_die(), Vector::x, Vector::y, and Vector::z.

Referenced by GroupRestraintList::SetResDirectionX(), GroupRestraintList::SetResDirectionY(), and GroupRestraintList::SetResDirectionZ().

                                                                                 {
    // Only modify the resDir if we turn off the specific component
    // because the default behaviour is that we apply restraint in
    // all direction 
    BigReal value = this->CheckStatus<BigReal>(status);

    switch (component) {
        case 0 :
            restraintDir.x = value;
            break;
        case 1 :
            restraintDir.y = value;
            break; 
        case 2 :
            restraintDir.z = value;
            break;   
        default :
            NAMD_die("Group restraints: Unknown vector component in SetResDirection function! \n");
    }
}

SetUseDistMagnitude()

void GroupRestraintParam::SetUseDistMagnitude

(

const char *

status

)

Set restraint distance mode (magnitude or vector)

Definition at line 270 of file GroupRestraintsParam.C.

Referenced by GroupRestraintList::SetUseDistMagnitude().

                                                                {
    useDistanceMagnitude = this->CheckStatus<bool>(status); 
}

---

The documentation for this class was generated from the following files:

• GroupRestraintsParam.h
• GroupRestraintsParam.C