original_docstring: Creates a new structure containing a single amino acid. The type and
  	geometry of the amino acid are determined by the argument, which has to be
  	either a geometry object or a single-letter amino acid code.
  	The amino acid will be placed into chain A of model 0.
docstring: Creates a new structure containing a single amino acid. The type and
  geometry of the amino acid are determined by the argument, which has to be
  either a geometry object or a single-letter amino acid code.
  The amino acid will be placed into chain A of model 0.
docstring_tokens: Creates a new structure containing a single amino acid . The type and geometry of the amino acid are determined by the argument which has to be either a geometry object or a single - letter amino acid code . The amino acid will be placed into chain A of model 0 .
code: def initialize_res(residue):
  	'''Creates a new structure containing a single amino acid. The type and
  	geometry of the amino acid are determined by the argument, which has to be
  	either a geometry object or a single-letter amino acid code.
  	The amino acid will be placed into chain A of model 0.'''
  	
  	if isinstance( residue, Geo ):
  		geo = residue
  	else:
  		geo=geometry(residue) 
  	
  	segID=1
  	AA= geo.residue_name
  	CA_N_length=geo.CA_N_length
  	CA_C_length=geo.CA_C_length
  	N_CA_C_angle=geo.N_CA_C_angle
  	
  	#
  	#      |   aa -1  |  aa i     |
  	#      |          |           |
  	#      | phi-1    |      psi  |
  	#      | N---CA   |    CA---C |  
  	#omega-1//    \psi-1  /.    .\\omega+1 
  	#      //      \     /phi   . \\ 
  	#  ...C         C===N  .    .  N...
  	#               omega  .    .
  	#                      .    .
  	#                      |----|
  	#                     CA_C_length
  	#
  	CA_coord = numpy.array([0.,0.,0.])
  	C_coord  = numpy.array([CA_C_length,0.0,0.0])
  	N_coord  = numpy.array([CA_N_length*math.cos(N_CA_C_angle*(math.pi/180.0)),CA_N_length*math.sin(N_CA_C_angle*(math.pi/180.0)),0])
  	
  	N= Atom("N",   N_coord, 0.0 , 1.0, " " , " N" , 0 , "N")
  	CA=Atom("CA", CA_coord, 0.0 , 1.0, " " , " CA", 0 , "C")
  	C= Atom("C",   C_coord, 0.0 , 1.0, " " , " C" , 0 , "C")
  	
  	##Create Carbonyl atom (to be moved later)
  	C_O_length=geo.C_O_length
  	CA_C_O_angle=geo.CA_C_O_angle
  	N_CA_C_O_diangle=geo.N_CA_C_O_diangle
  	
  	
  	carbonyl=calculateCoordinates(N, CA, C, C_O_length, CA_C_O_angle, N_CA_C_O_diangle)
  	O= Atom("O",carbonyl , 0.0 , 1.0, " "," O", 0, "O")
  	
  	if(AA=='G'):
  		res=makeGly(segID, N, CA, C, O, geo)
  	elif(AA=='A'):
  		res=makeAla(segID, N, CA, C, O, geo)
  	elif(AA=='S'):
  		res=makeSer(segID, N, CA, C, O, geo)
  	elif(AA=='C'):
  		res=makeCys(segID, N, CA, C, O, geo)
  	elif(AA=='V'):
  		res=makeVal(segID, N, CA, C, O, geo)
  	elif(AA=='I'):
  		res=makeIle(segID, N, CA, C, O, geo)
  	elif(AA=='L'):
  		res=makeLeu(segID, N, CA, C, O, geo)
  	elif(AA=='T'):
  		res=makeThr(segID, N, CA, C, O, geo)
  	elif(AA=='R'):
  		res=makeArg(segID, N, CA, C, O, geo)
  	elif(AA=='K'):
  		res=makeLys(segID, N, CA, C, O, geo)
  	elif(AA=='D'):
  		res=makeAsp(segID, N, CA, C, O, geo)
  	elif(AA=='E'):
  		res=makeGlu(segID, N, CA, C, O, geo)
  	elif(AA=='N'):
  		res=makeAsn(segID, N, CA, C, O, geo)
  	elif(AA=='Q'):
  		res=makeGln(segID, N, CA, C, O, geo)
  	elif(AA=='M'):
  		res=makeMet(segID, N, CA, C, O, geo)
  	elif(AA=='H'):
  		res=makeHis(segID, N, CA, C, O, geo)
  	elif(AA=='P'):
  		res=makePro(segID, N, CA, C, O, geo)
  	elif(AA=='F'):
  		res=makePhe(segID, N, CA, C, O, geo)
  	elif(AA=='Y'):
  		res=makeTyr(segID, N, CA, C, O, geo)
  	elif(AA=='W'):
  		res=makeTrp(segID, N, CA, C, O, geo)
  	elif(AA=='SAR'):
  		res=makeSar(segID, N, CA, C, O, geo)
  	else:
  		res=makeGly(segID, N, CA, C, O, geo)
  	cha= Chain('A')
  	cha.add(res)
  	
  	mod= Model(0)
  	mod.add(cha)
  
  	struc= Structure('X')
  	struc.add(mod)
  	return struc
code_tokens: def initialize_res ( residue ) : if isinstance ( residue , Geo ) : geo = residue else : geo = geometry ( residue ) segID = 1 AA = geo . residue_name CA_N_length = geo . CA_N_length CA_C_length = geo . CA_C_length N_CA_C_angle = geo . N_CA_C_angle CA_coord = numpy . array ( [ 0. , 0. , 0. ] ) C_coord = numpy . array ( [ CA_C_length , 0.0 , 0.0 ] ) N_coord = numpy . array ( [ CA_N_length * math . cos ( N_CA_C_angle * ( math . pi / 180.0 ) ) , CA_N_length * math . sin ( N_CA_C_angle * ( math . pi / 180.0 ) ) , 0 ] ) N = Atom ( "N" , N_coord , 0.0 , 1.0 , " " , " N" , 0 , "N" ) CA = Atom ( "CA" , CA_coord , 0.0 , 1.0 , " " , " CA" , 0 , "C" ) C = Atom ( "C" , C_coord , 0.0 , 1.0 , " " , " C" , 0 , "C" ) C_O_length = geo . C_O_length CA_C_O_angle = geo . CA_C_O_angle N_CA_C_O_diangle = geo . N_CA_C_O_diangle carbonyl = calculateCoordinates ( N , CA , C , C_O_length , CA_C_O_angle , N_CA_C_O_diangle ) O = Atom ( "O" , carbonyl , 0.0 , 1.0 , " " , " O" , 0 , "O" ) if ( AA == 'G' ) : res = makeGly ( segID , N , CA , C , O , geo ) elif ( AA == 'A' ) : res = makeAla ( segID , N , CA , C , O , geo ) elif ( AA == 'S' ) : res = makeSer ( segID , N , CA , C , O , geo ) elif ( AA == 'C' ) : res = makeCys ( segID , N , CA , C , O , geo ) elif ( AA == 'V' ) : res = makeVal ( segID , N , CA , C , O , geo ) elif ( AA == 'I' ) : res = makeIle ( segID , N , CA , C , O , geo ) elif ( AA == 'L' ) : res = makeLeu ( segID , N , CA , C , O , geo ) elif ( AA == 'T' ) : res = makeThr ( segID , N , CA , C , O , geo ) elif ( AA == 'R' ) : res = makeArg ( segID , N , CA , C , O , geo ) elif ( AA == 'K' ) : res = makeLys ( segID , N , CA , C , O , geo ) elif ( AA == 'D' ) : res = makeAsp ( segID , N , CA , C , O , geo ) elif ( AA == 'E' ) : res = makeGlu ( segID , N , CA , C , O , geo ) elif ( AA == 'N' ) : res = makeAsn ( segID , N , CA , C , O , geo ) elif ( AA == 'Q' ) : res = makeGln ( segID , N , CA , C , O , geo ) elif ( AA == 'M' ) : res = makeMet ( segID , N , CA , C , O , geo ) elif ( AA == 'H' ) : res = makeHis ( segID , N , CA , C , O , geo ) elif ( AA == 'P' ) : res = makePro ( segID , N , CA , C , O , geo ) elif ( AA == 'F' ) : res = makePhe ( segID , N , CA , C , O , geo ) elif ( AA == 'Y' ) : res = makeTyr ( segID , N , CA , C , O , geo ) elif ( AA == 'W' ) : res = makeTrp ( segID , N , CA , C , O , geo ) elif ( AA == 'SAR' ) : res = makeSar ( segID , N , CA , C , O , geo ) else : res = makeGly ( segID , N , CA , C , O , geo ) cha = Chain ( 'A' ) cha . add ( res ) mod = Model ( 0 ) mod . add ( cha ) struc = Structure ( 'X' ) struc . add ( mod ) return struc
short_docstring: Creates a new structure containing a single amino acid.
short_docstring_tokens: Creates a new structure containing a single amino acid .
comment: '''Creates a new structure containing a single amino acid. The type and
  	geometry of the amino acid are determined by the argument, which has to be
  	either a geometry object or a single-letter amino acid code.
  	The amino acid will be placed into chain A of model 0.'''$SEP$#$SEP$#      |   aa -1  |  aa i     |$SEP$#      |          |           |$SEP$#      | phi-1    |      psi  |$SEP$#      | N---CA   |    CA---C |  $SEP$#omega-1//    \psi-1  /.    .\\omega+1 $SEP$#      //      \     /phi   . \\ $SEP$#  ...C         C===N  .    .  N...$SEP$#               omega  .    .$SEP$#                      .    .$SEP$#                      |----|$SEP$#                     CA_C_length$SEP$#$SEP$##Create Carbonyl atom (to be moved later)