/*
/*	(C)1992 Institute for New Generation Computer Technology
/*		$BG[I[$=$NB>$O(BCOPYRIGHT$B%U%!%$%k$r;2>H$7$F2<$5$$(B
/*		(Read COPYRIGHT for detailed information.)
 */
Edited by GniiBE Thu May 14 11:51:20 1992

Message-Id: <9205121053.AA26620@mrigwa.mri.co.jp>
From: nak@mri.co.jp (Kazuo Nakata)
To: gniibe@mri.co.jp
Subject: pdb-kappa I/F spec
Date: Tue, 12 May 92 19:53:54 JST

PIR,PDB-Kappa VIF УģѸɽˡ

- 

[̾]
	ID_CODEʰ켡
[]
	q_form : term
	       | 'and(' term ',' q_form ')'
	term   : field '=[' value ']'
	field  : 'id_code'			<- pir  ID-Code б
	       | 'func_name'			<- pir  Molec б
	       | 'compound'			<- pir  Keyword б
	       | 'source'			<- pir  Life б
	value  : string
	       | string ',' value
	string : '"' ank_char '"'
	       | '"' ank_char '*' '"'
[ﵭ]
	id_code"1*"⤷"2*"
	source"HUMAN*"(Ƭ"HUMAN")
	func_name"C*"⤷"G*"ξ
		q_form : and(and(id_code=["1*","2*"],
				 source="HUMAN*"),
			     func_name=["C*","H*"])

[̽񼰻ؼ]
	(pdb_gen(id_code))			<- pir  ID-Code б
[̽(one)]
	result : '{' '"' ank_char '"' '}'
[(one)]
	{"2IL8"}
[̽(all)]
	result : '[' value ']'
	value  : '{' '"' ank_char '"' '}'
	       | '{' '"' ank_char '"' '}' ',' value
[(all)]
	[{"1HLA"},{"1UBQ"},{"2CAB"},{"2HLA"},{"2I1B"},{"2IL8"}]

̤γˡȤơޤǤΡ֣ƤӽФ->(one)פ¾
  ֣ƤӽФ->(all)פɲäޤ id_code 
  κݤˤϡall ǤƲ(pir, pdb )

	int KappaReadAll(kps, format, buffer, length)
	KPS *	kps;			/* KPS¤ΤؤΥݥ */
	char *	format;			/* ̽Ͻ */
	char *	buffer;			/* ɤ߹ߥХåե */
	int	length;			/* ɤ߹ߥХåեĹ */

	 one ϡޤޤ̤Ǥ


- ɽ

ɽ̤ˤϡ켡ǳ id_code ˤäơpdb_gen, pdb_seq 򸡺
̤ɽޤ

[̾]
	PDB_GENʥ˼ pdb_gen
[]
	q_form : term
	term   : field '=[' value ']'
	field  : 'id_code'			<- pir  ID-Code б
	value  : string
	       | string ',' value
	string : '"' ank_char '"'
[ﵭ]
	q_form : id_code=["1HLA","1UBQ","2CAB"]
[̽񼰻ؼ]
	(pdb_gen(id_code,func_name,date,compound,source,sid_code))
[̽(one)]
	result      : '{' pdb_gen '}'
	pdb_gen     : id_code ',' func_name ',' date ',' compound ','
		      source ',' sid_code
	id_code     : string			<- pir  ID-Code б
	func_name   : string			<- pir  Molec б
	compound    : string			<- pir  Keyword б
	source      : string			<- pir  Life б
	sid_code    : list   PDB ξ硢ȥʣǡ
			       ϿƤ礬롣 pdb_gen 
			       ȥ б pdb_seq  ID-Code 
			       
	date        : datelist			<- pir  ***_Date б
	string      : 
		    | 'nil'
		    | '"' ank_char '"'
	list        : '[' stlist ']'
	stlist      | string
		    | string ',' stlist
	datelist    : '[' dtlist ']'
	dtlist      : '{' string ',' string '}'
		    | '{' string ',' string '}' ',' dtlint

	 func_name, source -> ᥤɽ̤
	   date -> "INITIAL"  "ALL" ɽ̤ Attr Window 
		INITIAL <- pir  entry_date б
		ALL     <- pir  seq_date б
	   compound -> ɽ̤ Attr Window  (pir  alter_name б)
	   id_code ϡpdb_seq ¦ sid_code ɽޤ

[(one)]
	{"1HLA","HISTOCOMPATIBILITY ANTIGEN",
	 [{"15-OCT-87","INITIAL"},{"15-JUL-90","REMARK"},
	  {"15-APR-90","REMARK"},{"16-JAN-88","ALL"}],
	 "HUMAN CLASS I HISTOCOMPATIBILITY ANTIGEN A2 (/HLA-A2$,HUMAN LEUCOCYTE
	 ANTIGEN)",
	 "HUMAN (HOMO $SAPIENS) LYMPHOBLASTOID CELL LINE /JY$",
	["1HLA(A)","1HLA(M)"]}

[̾]
	PDB_SEQʥ˼ pdb_seq
[]
	q_form : term
	term   : field '=[' value ']'
	field  : 'sid_code'		<- pir  ID-Code Ʊ
	value  : string
	       | string ',' value
	string : '"' ank_char '"'
[ﵭ]
	q_form : sid_code=["1HLA(A)","1HLA(M)"]
[̽񼰻ؼ]
	(pdb_seq(sid_code,sequence,helix,sheet,turn,ssbond))
[̽(one)]
	result      : '{' pdb_seq '}'
	pdb_seq     : sid_code ',' sequence ',' helix ',' sheet ',' turn ','
		      ssbond

	sid_code    : string

	sequence    : '{' length ',' seq_data '}'
	length      : integer
	seq_data    : string

	helix       : '[' hel_list ']'
	hel_list    : hel_value
	            | hel_value ',' hel_list
	hel_value   : '{' helix_id ',' start_num ',' dummy, ',' end_num ','
		      dummy ',' type ',' comment
	helix_id    : string
	start_num   : string
	end_num     : string
	type        : string
	comment     : string
	dummuy      : nil

	sheet       : '[' sh_list ']'
	sh_list     : sh_value
	            | sh_value ',' sh_list
	sh_value    : '{' sheet_id ',' '[' sh_sub_list ']' '}'
	sheet_id    : string
	sh_sub_list : sh_sub_value
	            | sh_sub_value ',' sh_sub_list
	sh_sub_value: '{'
                      sh_idx ','
                      start_num ','
                      dummy ','
                      end_num ','
                      dummy ','
                      xyz ','
                      dummy ','
                      dummy ','
                      dummy ','
                      dummy ','
                      dummy ','
                      dummy
                      '}'
	sh_idx      : integer
	start_num   : string
	end_num     : string
	xyz         : integer
	dummuy      : nil

	turn        : '[' turn_list ']'
	turn_list   : turn_value
	            | turn_value ',' turn_list
	turn_value  : '{' turn_id ',' start_num ',' dummy, ',' end_num ','
		      dummy ',' comment
	turn_id     : string
	start_num   : string
	end_num     : string
	comment     : string
	dummuy      : nil

	ssbond      : '[' ss_list ']'
	ss_lis      : ss_value
	            | ss_value ',' ss_list
	ss_value    : '{' start_num ',' dummy, ',' end_num ','dummy '}'
	start_num   : string
	end_num     : string
	dummuy      : nil

	 sid_code -> ᥤɽ̤
	   length  -> ᥤɽ̤ (pir  Length б)
	   seq_data -> ᥤɽ̤
	   helix, sheet, turn, ssbond -> ᥤɽ̤

[(one)]
	{"1UBQ",
	 {76,"MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKES
	     TLHLVLRLRGG"},
	 [{"H1","23",nil,"34",nil,"1",nil},
	  {"H2","56",nil,"59",nil,"5",nil}],
	 [{"BET",[{1,"10",nil,"17",nil,0,nil,nil,nil,nil,nil,nil},
		  {2,"1",nil,"7",nil,-1,nil,nil,nil,nil,nil,nil},
		  {3,"64",nil,"72",nil,1,nil,nil,nil,nil,nil,nil},
		  {4,"40",nil,"45",nil,-1,nil,nil,nil,nil,nil,nil},
		  {5,"48",nil,"50",nil,-1,nil,nil,nil,nil,nil,nil}]
	  }],
	 [{"T1","7",nil,"10",nil,"TYPE I"},
	  {"T2","18",nil,"21",nil,"TYPE I"},
	  {"T3","37",nil,"40",nil,"TYPE III"},
	  {"T4","45",nil,"48",nil,"TYPE III(PRIME)"},
	  {"T5","51",nil,"54",nil,"TYPE I"},
	  {"T6","55",nil,"58",nil,"TYPE III"},
	  {"T7","56",nil,"59",nil,"TYPE III"},
	  {"T8","57",nil,"60",nil,"TYPE I"},
	  {"T9","62",nil,"65",nil,"TYPE II"}],
	[{"101",nil,"164",nil},{"203",nil,"259",nil}]}

Уģ¤°ɽ

  pir_fea °(Modified-site, Seq-comment, ...) бΤ
  pdb_seq  helix, sheet, turn, ssbond Ǥ°ϰʲι¤
  ɽ̤Ρ֥ꥹȥܥåפˤϰʲΤ褦ɽޤ

	helix  : helix_id, ֡start->end,  
		ɽ : Helix (helix_id) 	֤ seq ɽ
	sheet  : sheet_id ֡start1->end1, start2->end2, ...
		ɽ : Sheet (sheet_id) 		֤ seq ɽ
	turn   : turn_id, ֡start->end,  
		ɽ : Turn (turnx_id) 		֤ seq ɽ
	ssbond : ֡start1->end1, start2->end2, ...
		ɽ : SSBond 				֤ seq ɽ

ꥹȥܥåɽ

	-----------------------------------------
	|Helix (H1) 				|
	|Helix (H2) 				|
	|Helix (H3) 				|
	|Sheet (BET)				|
	|Turn  (T1) TYPE I			|
	|Turn  (T2) TYPE I			|
	|Turn  (T3) TYPE III			|
	|Turn  (T4) TYPE III(PRIME)		|
	|					|
	|					|
	|SSBond					|
	-----------------------------------------


