MTStructureFactory

StructureFactory is used to create instances of class MTStructure (3.2). If automatic loading of PDB files from the mirrored directory hierarchy from RCSB (using PDBChainSaw) is envisaged, one must set the environment variable PDBDIR to point to its top directory.

Methods:

+(id)newStructure	This creates an empty structure
+(id)newStructureFromPDBDirectory: (NSString*)code	Read structure from directory (note that the environment variable PDBDIR must be defined)
+(id)newStructureFromPDBDirectory: (NSString*)code options: (long)opts	also pass options opts
+(id)newStructureFromPDBFile: (NSString*)fn	Read structure from the file system
+(id)newStructureFromPDBFile: (NSString*)fn options: (long)opts	also pass options opts

where opts is the sum of the options you want to pass to the parser:

PDBPARSER_ALL_NMRMODELS	1
PDBPARSER_IGNORE_SIDECHAINS	2
PDBPARSER_IGNORE_HETEROATOMS	4
PDBPARSER_IGNORE_SOLVENT	8
PDBPARSER_IGNORE_COMPOUND	16
PDBPARSER_IGNORE_SOURCE	32
PDBPARSER_IGNORE_KEYWORDS	64
PDBPARSER_IGNORE_EXPDTA	128
PDBPARSER_IGNORE_REMARK	256
PDBPARSER_IGNORE_REVDAT	512
PDBPARSER_DONT_VERIFYCONNECTIVITY	1024
PDBPARSER_IGNORE_SEQRES	2048
PDBPARSER_ALL_ALTERNATE_ATOMS	4096
PDBPARSER_IGNORE_HYDROGENS	8192

The methods without parameter opts implicitly pass no options (0) to the parser. Turning off some options in the parser affects the speed of parsing PDB files.

Example:

strx := MTStructureFactory newStructureFromPDBDirectory: '1ABC' .     " ask the default StructureFactory for a structure, which is received in the variable strx. "

strx2 := MTStructureFactory newStructureFromPDBFile: 'test_run/1ABC.pdb' options:(1024 + 8).     " load a structure from a file on disk, do not verify connectivity of residues and ignore solvent residues. "