pdb++ (3) - A C++ class for manipulating Brookhaven Protein DataBank records

PDB++(3)

NAME

pdb++ - A C++ class for manipulating Brookhaven Protein DataBank records

SYNOPSIS

#include <pdb++.h>

     ....
          PDB  record;

          while (cin >> record) {
               switch (record.type()) {
               case PDB::ATOM:
                    cout << record.atom.xyz[0] << ' ' << record.atom.xyz[0]
                         << ' ' << record.atom.xyz[0] << endl;
                    ....
                    break;
               }
          }
     ....

DESCRIPTION

The routines listed below are available in the pdb++ library; the include file is typically found in /usr/local/midas/include/pdb++.h and the library archive is in /usr/local/midas/lib/libpdb.a.

The PDB class provides methods for parsing Brookhaven Protein DataBank (PDB) records (lines from a PDB file) into structures and expanding those structures back into PDB records. Rather than provide access functions for each possible field, the structure containing the parsed record is publicly available. The field names are listed in the header file.

The PDB class has several enhancements to the Brookhaven Protein DataBank specification: four character residue names, the PDBRUN set of scene annotation records (see reference in the SEE ALSO section), and atom serial number overflow protection. Four character residue names work because everywhere in the specification a three character residue name appears, there is a blank afterwards. Atom serial number overflow protection works for ATOM, HETATM, and SIGATM records, by assigning an unique serial number over 10000. Unfortunately, it is not possible to fix PDB records that refer to atom serial numbers, such as CONECT records.

MEMBER CONSTANTS

BufLen: The maximum length of a generated PDB record string (including the null byte).

PDBRUNVersion: The default version of the PDBRUN scene annotation records.

There are also constants for each known PDB record type (e.g., ATOM, HETATM, etc.), and the constant UNKNOWN for an unknown PDB record.

The following constants are for each PDBRUN scene annotation record type: USER_PDBRUN, USER_EYEPOS, USER_ATPOS, USER_WINDOW, USER_FOCUS, USER_VIEWPORT, USER_BGCOLOR, USER_ANGLE, USER_DISTANCE, USER_FILE, USER_MARKNAME, USER_MARK, USER_CNAME, USER_COLOR, USER_RADIUS, USER_OBJECT, USER_ENDOBJ, USER_CHAIN, USER_GFX_BEGIN, USER_GFX_END, USER_GFX_COLOR, USER_GFX_NORMAL, USER_GFX_VERTEX, USER_GFX_FONT, USER_GFX_TEXTPOS, and USER_GFX_LABEL.

The following constants are for the various graphics primitives supported in scenes: GFX_UNKNOWN, GFX_POINTS, GFX_MARKERS, GFX_LINES, GFX_LINE_STRIP, GFX_LINE_LOOP, GFX_TRIANGLES, GFX_TRIANGLE_STRIP, GFX_TRIANGLE_FAN, GFX_QUADS, GFX_QUAD_STRIP, and GFX_POLYGON.

MEMBER TYPES

typedef char Date[10]: A text field containing a date, typically day-month-year, where day is numeric, month is a three-letter abbreviation, and year is the last two digits of the year.

typedef char AName[5]: A PDB atom name, e.g., NO2*.

typedef char RName[5]: Residue name, e.g., ALA.

typedef char PName[5]: PDB name, e.g., 9lyz.

typedef char Id[4]: Generic short id field.

typedef double Real: Size of floating point numbers read and written.

struct Residue: A Residue consists of a residue name (name), a chain identifier (chainId), a sequence number (seqNum), and an insertion code (insertCode).

MEMBER FUNCTIONS

     pdb()
     pdb(RecordType t)
     pdb(const char *buf)
          Constructors.  The first two above construct a zeroed
          instance of the given record type (default UNKNOWN).
          The last constructor above fills in all of the fields
          of the instance from the given PDB record text.

RecordType type() const: Return the type of PDB instance.

void type(RecordType t): Change the PDB record type of the instance and reinitialize all the fields to default values (zero in all cases except for an ATOM's occupancy which defaults to 1.0).

const char *chars() const;: Return a string containing the PDB record in textual form.

static int PdbrunInputVersion(): Return the current PDBRUN scene annotation version used to parse text records.

static int PdbrunOutputVersion(): Return the current PDBRUN scene annotation version used to create text records.

static void PdbrunInputVersion(int v): Set the current PDBRUN scene annotation version used to parse text records.

static void PdbrunOutputVersion(int v): Set the current PDBRUN scene annotation version used to create text records.

static recordType getType(const char *buf): Return the PDB record type for the given line of text.

static GfxType getGfxType(const char *buf)

static const char *gfxChars(GfxType gt)

static int sscanf(const char *, const char *, ...): A version of sscanf(3) whose format's behave like FORTRAN formats where field widths are sacrosanct. If the input line is short, then the rest of the fields are initialized to default values. Any literal characters in the format must match the input. The format characters are: space, ignore input character; c, character (array), default to a space; d, integer, default zero; f, double, default zero; s, get a C string, trailing spaces are stripped and it is null terminated, default an empty string. sscanf returns the number of input fields converted (may be less than expected if the input line is short) or -1 if an error is found.

static int sprintf(char *, const char *, ...): A version of sprintf(3) whose format's behave like FORTRAN formats where field widths are sacrosanct. Literal characters are copied as is. If the text or number to be printed is larger than the given field width, then the field is filled in with asterisks. The format characters are: d, integer; D, integer where zero is written as spaces; s, right-justified string (a negative field width left-justifies); c, character (array), zero characters are converted to spaces; f, floating point, normal printf precisions are used.

I/O FUNCTIONS

ostream &operator<<(ostream &s, const PDB &p): Output the current PDB record on the given output stream.

istream &operator>>(istream &s, PDB &p): Read a line from the given input stream and convert to a PDB record.

NOTES

The subtype field of USERxx structure tells what the xx part was. The rest of the line, up to the card sequence portion, is the text field.

Due to the way Brookhaven encodes their files, atom names often have leading blanks and sometimes have embedded blanks. Residue names occasionally have leading blanks too. To be entirely consistent with the PDB format, the programmer should put those blanks in before using the chars member function.

BUGS

Routines are needed to convert to and from PDB typesetting conventions in COMPND, SOURCE, AUTHOR, and JRNL records.

COPYRIGHT

Redistribution and use in source and binary forms are permitted provided that the above copyright notice and this paragraph are duplicated in all such forms and that any documentation, advertising materials, and other materials related to such distribution and use acknowledge that the software was developed by the University of California, San Francisco. The name of the University may not be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.