Class MTChain

Inherits from:

NSObject

Declared in:

../libmoltalk/MTChain.oh

Class Hierarchy

    NSObject
      |
      +---MTChain

Last modified:

16-May-2006 (../libmoltalk/MTChain.m)

Instance Variables

protected NSString *source

protected NSString *compound

protected NSString *eccode

protected NSString *seqres

protected char code

protected MTStructure *strx

protected NSMutableDictionary *solventKeys

protected NSMutableArray *solvent

protected NSMutableDictionary *heterogenKeys

protected NSMutableArray *heterogens

protected NSMutableDictionary *residueKeys

protected NSMutableArray *residues

protected NSMutableDictionary *residuehash

protected unsigned int hashingbits

protected double hash_value_offset

Method Index

• naming
  

  -(char)code

  -(NSNumber*)codeNumber

  -(NSString*)description

  -(NSString*)fullPDBCode

  -(NSString*)name

• readonly access
  

  -(NSString*)compound

  -(NSString*)eccode

  -(NSString*)source

• reference to parent structure
  

  -(id)orderResidues

  -(MTStructure*)structure

• transform all residues/atoms in this chain by the given matrix
  

  -(id)rotateBy:(MTMatrix44*)r

  -(id)transformBy:(MTMatrix53*)m

  -(id)translateBy:(MTCoordinates*)v

• enumerator over residues, heterogens, solvent, respectively
  

  -(NSEnumerator*)allHeterogens

  -(NSEnumerator*)allResidues

  -(NSEnumerator*)allSolvent

• count of residues, heterogens, solvent, respectively
  

  -(int)countHeterogens

  -(int)countResidues

  -(int)countSolvent

  -(int)countStandardAminoAcids

• access a residue, heterogen, solvent, respectively, for the given identifying number (eventually, plus an insertion code, single character)
  

  -(MTResidue*)getHeterogen:(NSString*)nr

  -(MTResidue*)getResidue:(NSString*)nr

  -(MTResidue*)getSolvent:(NSString*)nr

• add a residue, heterogen, solvent, respectively, to this chain
  

  -(id)addHeterogen:(MTResidue*)het

  -(id)addResidue:(MTResidue*)res

  -(id)addSolvent:(MTResidue*)sol

• remove a residue
  

  -(void)removeResidue:(MTResidue*)p_res

• derive amino acid sequence
  

  -(NSString*)get3DSequence

  -(NSString*)getSEQRES

  -(NSString*)getSequence

• geometric hash of all residues in this Chain
  

  -(NSArray*)findResiduesCloseTo:(MTCoordinates*)p_coords

  -(void)prepareResidueHash:(float)binwidth

• compute hash key value
  

  -(NSNumber*)mkCoordinatesHashX:(double)x Y:(double)y Z:(double)z

• complex utilities
  

  -(MTChain*)deepCopy

  -(MTChain*)deepCopyCA

  -(NSArray*)selectResiduesCloseTo:(MTChain*)other maxDistance:(float)maxdist

Methods

-(id)addHeterogen:(MTResidue*)het

add hetero group

-(id)addResidue:(MTResidue*)res

add residue

-(id)addSolvent:(MTResidue*)sol

add solvent

-(NSEnumerator*)allHeterogens

return enumerator over all hetero groups

-(NSEnumerator*)allResidues

return enumerator over all residues

-(NSEnumerator*)allSolvent

return enumerator over all solvent

-(char)code

return character code of this chain

-(NSNumber*)codeNumber

return numerical character code of this chain

-(NSString*)compound

return compound name

-(int)countHeterogens

count hetero groups

-(int)countResidues

count residues

-(int)countSolvent

count solvent

-(int)countStandardAminoAcids

count residues which are of the 20 standard amino acids

-(MTChain*)deepCopy

complex utilities

-(MTChain*)deepCopyCA

-(NSString*)description

see -name

-(NSString*)eccode

return E.C. code (if possible)

-(NSArray*)findResiduesCloseTo:(MTCoordinates*)p_coords

returns a list of residues which are close to the given coordinates
must compute the hash table first using: -prepareResidueHash:

-(NSString*)fullPDBCode

return concatenation of the structure's code and this one's code

-(NSString*)get3DSequence

derive sequence of present standard amino acids

-(MTResidue*)getHeterogen:(NSString*)nr

find hetero for key

-(MTResidue*)getResidue:(NSString*)nr

find residue for key

-(NSString*)getSEQRES

return parsed SEQRES sequence

-(NSString*)getSequence

derive amino acid sequence from coordinates. wherever there is a gap in the mainchain and in the number of the residues, insert as many neutral elements 'X' as necessary.

-(MTResidue*)getSolvent:(NSString*)nr

find solvent for key

-(NSNumber*)mkCoordinatesHashX:(double)p_x Y:(double)p_y Z:(double)p_z

compute hash key value

-(NSString*)name

return code of this chain as string

-(id)orderResidues

-(void)prepareResidueHash:(float)gridsize

computes the hash of all residues

-(void)removeResidue:(MTResidue*)p_res

remove residue (either real residue, or hetero group, or solvent)

-(id)rotateBy:(MTMatrix44*)m

apply rotation to this chain

-(NSArray*)selectResiduesCloseTo:(MTChain*)other maxDistance:(float)maxdist

select all residues in both chains which are at most maxdist separated, return in selections

-(NSString*)source

return source organism

-(MTStructure*)structure

give access to the Structure we are part of

-(id)transformBy:(MTMatrix53*)m

apply transformation matrix to this chain

-(id)translateBy:(MTCoordinates*)v

apply translation to this chain