ResidueLookupElem Class Reference

#include <Molecule.h>

Public Member Functions
	ResidueLookupElem (void)
	~ResidueLookupElem (void)
int	lookup (const char *segid, int resid, int *begin, int *end) const
ResidueLookupElem *	append (const char *segid, int resid, int aid)

Public Attributes
char	mySegid [11]
ResidueLookupElem *	next
int	firstResid
int	lastResid
ResizeArray< int >	atomIndex

Detailed Description

Definition at line 89 of file Molecule.h.

Constructor & Destructor Documentation

ResidueLookupElem()

ResidueLookupElem::ResidueLookupElem ( void  )

inline

Definition at line 98 of file Molecule.h.

References firstResid, lastResid, and next.

{ next = 0; firstResid = -1; lastResid = -1; }

~ResidueLookupElem()

ResidueLookupElem::~ResidueLookupElem ( void  )

inline

Definition at line 99 of file Molecule.h.

References next.

{ delete next; }

Member Function Documentation

append()

ResidueLookupElem * ResidueLookupElem::append	(	const char *	segid,
		int	resid,
		int	aid
	)

Definition at line 94 of file Molecule.C.

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

                                               {
    ResidueLookupElem *rval = this;
    if ( firstResid == -1 ) {  // nothing added yet
      strcpy(mySegid,segid);
      firstResid = resid;
      lastResid = resid;
      atomIndex.add(aid);
      atomIndex.add(aid+1);
    } else if ( ! strcasecmp(mySegid,segid) ) {  // same segid
      if ( resid == lastResid ) {  // same resid
        atomIndex[lastResid - firstResid + 1] = aid + 1;
      } else if ( resid < lastResid ) {  // error
        // We can work around this by creating a new segment.
        iout << iWARN << "Residue " << resid <<
          " out of order in segment " << segid <<
          ", lookup for additional residues in this segment disabled.\n" << endi;
        rval = next = new ResidueLookupElem;
        next->append(segid,resid,aid);
      } else {  // new resid
        for ( ; lastResid < resid; ++lastResid ) atomIndex.add(aid);
        atomIndex[lastResid - firstResid + 1] = aid + 1;
      }
    } else {  // new segid
      rval = next = new ResidueLookupElem;
      next->append(segid,resid,aid);
    }
    return rval;
}

lookup()

int ResidueLookupElem::lookup	(	const char *	segid,
		int	resid,
		int *	begin,
		int *	end
	)		const

Definition at line 81 of file Molecule.C.

References atomIndex, firstResid, mySegid, and next.

Referenced by Molecule::prepare_qm().

                                                                  {
    const ResidueLookupElem *elem = this;
    int rval = -1;  // error
    while ( elem && strcasecmp(elem->mySegid,segid) ) elem = elem->next;
    if ( elem && (resid >= elem->firstResid) && (resid <= elem->lastResid) ) {
      *begin = elem->atomIndex[resid - elem->firstResid];
      *end = elem->atomIndex[resid - elem->firstResid + 1];
      rval = 0;  // no error
    }
    return rval;
}

Member Data Documentation

atomIndex

ResizeArray<int> ResidueLookupElem::atomIndex

Definition at line 96 of file Molecule.h.

Referenced by lookup().

firstResid

int ResidueLookupElem::firstResid

Definition at line 94 of file Molecule.h.

Referenced by lookup(), and ResidueLookupElem().

lastResid

int ResidueLookupElem::lastResid

Definition at line 95 of file Molecule.h.

Referenced by ResidueLookupElem().

mySegid

char ResidueLookupElem::mySegid[11]

Definition at line 92 of file Molecule.h.

Referenced by lookup().

next

ResidueLookupElem* ResidueLookupElem::next

Definition at line 93 of file Molecule.h.

Referenced by lookup(), ResidueLookupElem(), and ~ResidueLookupElem().

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

• Molecule.h
• Molecule.C