NAME
gdb \- NMRWish TCL Generic Database Tools
HIERARCHY
. (root)
dBase1 ................ dBaseN
table1 ...... tableN text
text variable... entry...
cell... cell...
KEY
() type of data returned by a function.
[] optional argument.
"" keyword.
| separates mutually exclusive options.
{} a single item or proper TCL list.
Elements such as names and keywords are case-sensitive.
TABLE FORMAT
Keywords in a table file consist of the following:
# comment
REMARK comment
DATA [information]
VARS [variableNameList]
FORMAT [variableFormatList]
Empty lines are ignored.
All other lines are treated as table entries, regardless
of where they are in the file.
Each entry should have as many elements as there are
variable names listed in the VARS line.
Currently, spaces are not allowed within an item (i.e.,
within a text string or format); this will be changed in
future versions.
Variable names must begin with a letter or underscore,
and contain only letters, numerals, or underscores.
INITIALIZE THE DATABASE SYSTEM
(handle) gdbInit
CHECK THE INTEGRITY OF THE DATABASE
(int) gdbCheck [-verb]
Checks all database info; returns error count.
(int) gdbCheck [handleList]
Returns valid handles or zeros for bad handles.
CREATE AN OBJECT
(handle) gdbCreate "dBase" | "table" | "variable" | "entry"
[-name objectName]
[-parent parentHandle]
[-result resultHandle]
-varType variableType
-varFmt variableFormat
Arguments -varType and -varFmt are required for
creation of variables, and are ignored in other cases.
READ A TABLE OR DATABASE
(handle) gdbRead "dBase" | "table"
-in fileOrDirName
-name objectName
[-parent parentHandle]
[-result resultHandle]
[-pdb]
Argument -in should be a directory name when reading
a database (dBase), and a file name when reading a table.
Option -pdb is only valid when reading a PDB format file
as a table.
WRITE A TABLE OR DATABASE
(boolean) gdbWrite dBaseHandle | tableHandle
[outName]
The outName should be a directory name when writing
a database, and a file name when writining a table. If
the
outName argument is omitted, the data will be written
to standard error.
DESTROY AN OBJECT
Returns count of items destroyed.
(int) gdbDestroy handleList
[-verb]
APPEND TABLES
Appends rows of source to destination.
Returns the handle to the result table.
(handle) gdbAppend
[-dest destHandle]
-src srcTableHandleList
If the -dest argument is a table, this table will
modified by the appending the source table to it.
If the -dest arguement is a dBase, a new table will
be created in this dBase, and the source table copied to
it.
JOIN TABLES
Appends columns of source to destination.
Returns the handle to the result table.
(handle) gdbJoin
[-dest destHandle]
-src srcTableHandleList
If the -dest argument is a table, this table will
modified by the appending the source table to it.
If the -dest arguement is a dBase, a new table will
be created in this dBase, and the source table copied to
it.
QUERY TABLES
(result) gdbSelect
-from tableList
[-inPlace]
[-tcl | -M]
[-cond condition]
[-vars varsSelectedList]
[-using varsLoadedList]
[-destSuffix [dSufixList]]
[-querySuffix [qSuffixList]]
[-suffix [suffixList]]
[-name tableName]
[-result resultVar]
[-parent dBaseHandle]
Selects TCL (default) or M format query.
Result is list of entries from input.
Default: all entries.
Default: all variables.
Default: variables in unsubstituted condition.
Maps input vars to output vars.
Maps input vars to query vars.
Sets both suffix lists.
Sets name of result table.
Tcl variable; destroys previous object.
Desired dBase for result, if different from first input
table.
If no suffix list is given, _0, _1 etc
is used. Keyword 'None' in a suffix list
means no suffix will be applied.
SORT A TABLE
(boolean) gdbSort [<|>]varNameOrHandleList
[-proc tclSortProc]
The TCL sort procedure should return -1, 0, or 1
when two entries are compared:
proc sortProc {entry1ValList entry2ValList} ...
FIND AN OBJECT BY NAME
(handleList) gdbFind parentHandle name
[-all]
Use . for root handle
Older command gdbFindByName is equivalent to gdbFind.
GET FIRST/LAST ITEM OF AN OBJECT
(infoList) gdbFirst handle
(infoList) gdbLast handle
For root, same as: gdbGetInfo -parms dBase
For dBase, same as: gdbGetInfo -parms table
For table, same as: gdbGetInfo -parms entry
GET INFORMATION ABOUT AN OBJECT
(infoList) gdbGetInfo handle
[-array tclArrayName]
[-parms parmNameList]
Types: dBase table variable entry text cell
dBase: text: root: table:
type type type type
handle handle handle handle
name next dBase name
next prev dBaseN varCount
prev parent {dBases} entryCount
table value var
tableN entry
tabCount varN
text entryN
textN next
parent prev
{tables} parent
text
textN
{vars}
{varNames}
{entries}
variable: entry: cell:
type type type
handle handle handle
name next north
varFmt prev south
varType cell east
next cellN west
prev parent value
cell {cells} empty
cellN {values} var
parent entry
{cells}
{values}
SET PROPERTIES OF AN OBJECT
(boolean) gdbSetInfo handle
[-name objectName]
[-varFmt varFmt] (variable only)
[-value {val}] (cell or text only)
GET VALUES FROM TABLES
(string) gdbGet entry varNameOrHandleList
[-notrim]
(string) gdbGetVal cellList [-notrim]
TEST FOR DEFINED VALUES IN TABLES
(string) gdbTest entry varNameOrHandleList
(string) gdbTestVal cellList
SET VALUES IN TABLES
(int) gdbSet entry {varNameList} {valueList}
(int) gdbSetVal {cellList} {valueList}
Older command gdbSetValByVar is equivalent to gdbSet.
GET THE NTH ITEM
Returns the next, previous, or Nth item in a linked list.
(handleList) gdbNext {handleList} [n | "last"]
(handleList) gdbPrev {handleList} [n | "last"]
(handleList) gdbEast {cellList} [n | "last"]
(handleList) gdbWest {cellList} [n | "last"]
(handleList) gdbNorth {cellList} [n | "last"]
(handleList) gdbSouth {cellList} [n | "last"]
SWAP TWO ITEMS
(boolean) gdbSwap handle1 handle2
Swaps two items in a linked list;
Not implemented yet.
REVERSE THE ORDER
(handle) gdbReverse listBase
Reverses the order of items in a linked list;
Not implemented yet.
MANIPULATE ANNOTATIONS
(boolean) gdbDeleteAnnotation
dbaHandle | tableHandle
(boolean) gdbAddAnnotation
dbaHandle | tableHandle {textValue}
PDB TABLES
(float) pdbCoords entry
Returns X,Y,Z coords of an ATOM entry.
(float) pdbDist entry1 entry2
Returns distance between ATOMs 1, and 2.
(float) pdbAngle entry1 entry2 entry3
Returns angle formed by ATOMs 1, 2, and 3
(float) pdbAngle entry1 entry2 entry3
Returns dihedral formed by ATOMs 1, 2, 3, and 4.