CCP4 Coordinate Library Project
         Object interface: Querying the Coordinate Hierarchy.
         
         
         
            This section presents a collection of different functions for
            querying the coordinate hierarchy.
            Only non-specific querying functions are listed here. Querying
            functions which relate closely to subjects of other sections of
            this Manual (e.g., retrieving the description of an error code,
            type of input file etc.), are described in those sections.
            
         
         
         
         
         
         
         
         
         
         
         
            PURPOSEObtaining the entry ID (or a PDB ID code).
         
RETURN
            The function returns pointer to a string containing
            the entry ID. If no entry ID was set or read from coordinate
            file, the return will be "XXXX".
            
         
         
         
         
         
         
         
         
            PURPOSEObtaining the total number of atoms in the
            coordinate hierarchy.
         
RETURN
            The function returns total number of atoms, which are currently
            contained in the coordinate hierarchy.
            
         
         
         
         
         
         
         
         
            PURPOSEObtaining the number of models in the
            coordinate hierarchy.
         
RETURN
            The function returns the number of models, which are currently
            contained in the coordinate hierarchy.
            
         
         
         
         
         
         
         
         
            PURPOSEChecking on the presence of crystallographic information
            in coordinate hierarchy.
            
         
RETURN
            The function returns True if cell parameters
            a, b, c,
            alpha, beta and
            gamma were read from coordinate file or
            otherwise set up in the hierarchy.
            
         
         
         
         
         
         
         
         
            PURPOSEChecking on the presence of the name of space symmetry
            group in coordinate hierarchy.
            
         
RETURN
            The function returns True if name of space
            group of symmetry was read from coordinate file or otherwise set
            up in the hierarchy.
            
         
         
         
         
         
         
         
         
            PURPOSEChecking on the presence of the
            orthogonalising/fractionalising matrices.
            
         
RETURN
            The function returns True if the
            orthogonalising/fractionalising matrices were successfully
            calculated. The calculations are performed automatically
            when cell parameters are read from a coordinate file or
            set up by application.
            
         
         
         
         
         
         
         
         
            PURPOSEChecking on the presence of orthogonal-fractional
            transformation matrix in
            coordinate hierarchy.
            
         
RETURN
            The function returns True if the 
            orthogonal-fractional transformation matrix (PDB records
            SCALEn) was read from coordinate file or otherwise set
            up in the hierarchy.
            
         
         
         
         
         
         
         
         
            PURPOSEChecking on the presence of non-crystallographic
            symmetry transformation matrices in
            coordinate hierarchy.
            
         
RETURN
            The function returns True if the 
            non-crystallographic symmetry transformation matrices
            (PDB records MTRIXn) were read from coordinate file or
            otherwise set up in the hierarchy.
            
         
         
         
         
         
         
         
         
            PURPOSEChecking on quality and completeness of 
            crystallographic information set up in
            coordinate hierarchy.
            
         
RETURN
            The function returns a non-negative value if crystallographic
            information is usable. Positive return is interpreted as a
            combination of the following flags:
            
            
            
            
               
                  | Flag | Value | Description | 
               
                  | CRRDY_Complete | 0 | Crystallographic information is complete | 
               
                  | CRRDY_NotPrecise | 0x00000001 | The newly set up crystallographic information
                        somewhat differ from the previous setting or
                        from what was read from a coordinate file | 
               
                  | CRRDY_isTranslation | 0x00000002 | The orthogonal-to-fractional transformation matrix
                        contains translational component(s) | 
               
                  | CRRDY_NoOrthCode | 0x00000004 | The orthogonalization code was not supplied or
                        could not be established | 
            
            
            
            Negative return codes indicate more serious problems:
            
            
            
            
               
                  | Code | Value | Description | 
               
                  | CRRDY_NoTransfMatrices | -1 | No orthogonal-to-fractional transformation matrix
                        was read from coordinate file or otherwise
                        set up in the hierarchy | 
               
                  | CRRDY_Unchecked | -2 | The crystallographic information (cell parameter and/or
                        transformation matrices) was not properly set up
                        in the coordinate hierarchy (e.g. not all SCALEn
                        cards were supplied or part of cell parameters is
                        missing) | 
               
                  | CRRDY_Ambiguous | -3 | The newly set up crystallographic information
                        differ considerably from the previous setting or
                        from what was read from a coordinate file | 
               
                  | CRRDY_NoCell | -4 | No cell parameters were read from a coordinate file
                        or otherwise set up in the coordinate hierarchy | 
            
            
         
         
         
         
         
         
         
         
            PURPOSEObtaining the number of symmetry operations.
            
         
RETURN
            The function returns the number of symmetry operations that
            are present in the space symmetry group currently set up in
            the coordinate hierarchy.
            
            
            The function returns 0 if no space symmetry group is defined.
            
         
         
         
         
         
         
         
         
            PURPOSEObtaining the symmetry transformation matrix.
            
         
ARGUMENTS
            mat44 &  TMatrix
Matrix to accept the transformation matrix.
            
int  Nop
Number of the space group symmetry operation. It should
            be in the range of 0..NumberOfSymOps-1,
            where NumberOfSymOps is returned by
            CMMDBManager::GetNumberOfSymOps.
            
int  cellshift_a
Shift of the unit cell in a-directions in a-periods.
            
int  cellshift_b
Shift of the unit cell in b-directions in b-periods.
            
int  cellshift_c
Shift of the unit cell in c-directions in c-periods.
            
DESCRIPTION
            The function calculates and returns the symmetry transformation
            matrix, which transforms from the principal orthogonal
            coordinates found in a coordinate file, into orthogonal
            coordinates of a symmetry mate generated by
            Nopth symmetry operation of the current
            space symmetry group in the unit cell shifted by
            cellshift_a a-periods, 
            cellshift_b b-periods and
            cellshift_c c-periods from the principal
            unit cell of coordinate file.
            
         
RETURN
            The function returns 0 if no problems were encountered.
            Other returns indicate:
            
            
               
                  | 1 | Nop is not in the right range
                        or space symmetry group was not set up | 
               
                  | 2 | fractionalizing/orthogonalizing matrices were not
                        calculated (lack of crystallographic data
                        in the file) | 
               
                  | 3 | cell parameters a,
                        b, c,
                        alpha, beta,
                        gamma were not set up | 
            
            
         
         NOTE : 
            First symmetry operation Nop=0 is the
            identity.
            
         
         
         
         
         
         
         
         
         
            PURPOSECalculating the averaged properties of all atoms in the
            coordinate hierarchy.
            
         
ARGUMENTS
            RSAtomStat  AS
Reference to structure
            SAtomStat
               , which returns the average results.
            
DESCRIPTION
            The function performs an actual calculation of averaged atom properties,
            none of them are stored as variables. It is therefore advised to avoid
            unnecessary calls to this function.
            
         
         
         
         
         
         
         
         
            PURPOSECalculating the mass center of a set of atoms.
            
         
ARGUMENTS
            PPCAtom  A
Array of atoms. This array may conveniently
            come from selection functions.
            
int  nA
Number of atoms in array A. The array is
            indexed as 0..nA-1 .
            
realtype &  xmc
X-coordinate of mass center.
            
realtype &  ymc
Y-coordinate of mass center.
            
realtype &  zmc
Z-coordinate of mass center.
            
DESCRIPTION
            The function calculates the mass center of atoms given in array
            A, with atomic weights peculiar to the
            element type taken into account.
            
         
         
         
         
         
         
         
         
         
         
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