" INSTALLATION:

  below you will find a line like:
	pq := PostgreSQL connectTo:'mydb' on:'localhost' at:'5432'.
  change the database name, hostname and port number to the values where 
  MolTalk will find your local PostgreSQL database server.

  That's all.
"


  
[|
	"Read a PDB structure and derive some information"
	"everything gets entered into a relational database"


main
	| sname arg s1 override |

	sname := nil.	"holds the name of the structure file"
	override := 0.	"0=do not override structure already in the db, 1=do reload into database"

	1 to: (ARGS count) - 1 do: [ :argc |
		arg := (ARGS objectAtIndex:(argc intValue)).
		"Transcript showLine:('argument: ',argc stringValue, ' ', arg)."
		"check for input file name"
		(arg = '-i') ifTrue: [ targc := argc + 1. sname := (ARGS objectAtIndex:(targc)). ].
		(arg = '-f') ifTrue: [ override := 1. ].
	].

	(sname isNil)
	ifTrue: [ Transcript showLine:('no PDB code was given (parameter -i). Abort'). ^self ]
	ifFalse: [ s1 := self loadStrx:sname doOverride:override. ].


	Transcript showLine:('all done.').
	^self
!





" load the structure with the given name "
loadStrx:sname doOverride:override
	| pq |
	"connect to the database"

" >>>> >>>> >>>> >>>>  change it here !!! "
	pq := PostgreSQL connectTo:'mydb' on:'localhost' at:'5432'.
" <<<< <<<< <<<< <<<< "

	(pq notNil) ifTrue: [ 
		pq query: ('select code from chsaw_pdb where code=\'',sname,'\' union select pdb from chsaw_chain where pdb=\'',sname,'\';').
		(pq rows > 0)	"check for structure-chains already in db"
		ifTrue: [
			Transcript showLine: ('already have structure ',sname,' in database.').
			(override=1) ifTrue: [ 
				Transcript showLine: 'we do override!'.
				"remove current structure-chains in db"
				pq query: ('delete from chsaw_chain where pdb=\'',sname,'\';').
				pq query: ('delete from chsaw_pdb where code=\'',sname,'\';').
				"reload"
				self parseStrx:sname intoDB:pq.
			].
		]
		ifFalse: [
			"load structure-chains into db"
			self parseStrx:sname intoDB:pq.
		].
	]
	ifFalse: [ Transcript showLine:'failed to connect to database server.' ].
	pq disconnect.
	^strx
!





" parse information contained in structure "
parseStrx:sname intoDB:pq
	| strx t1 |
	[ strx := StructureFactory newStructureFromPDBDirectory:sname. ]
	handler: [ :except | Transcript showLine:('EXCEPTION: ',except reason). ].
	"load structure-chains into db"
	(strx notNil) ifTrue: [ 
		Transcript showLine:('Structure:  ', strx pdbcode).
		Transcript showLine:('Title:      ', strx title).
		Transcript showLine:('Resolution: ', strx resolution stringValue).
		Transcript showLine:('Date:       ', strx date description).
		Transcript showLine:('Rev. Date:  ', strx revdate description).
		Transcript showLine:('Experiment: ', strx expdata stringValue).
		pq query:('insert into chsaw_pdb (code,deposited,lastrev,experiment,resolution,header,title) values(\'',strx pdbcode,'\',\'',strx date description,'\',\'',strx revdate description,'\',\'',strx expdata stringValue,'\',\'',strx resolution stringValue,'\',\'',strx header quoted,'\',\'',strx title quoted,'\');').
		strx allChains allObjects do: [ :chain |
				self parseChain:chain intoDB:pq.
		].
	].
	^self
!



" give information about chain "
parseChain:chain intoDB:pq
	| c1 |
	Transcript showLine:('    Chain:      ', chain code stringValue, ' \'', chain name, '\'').
	Transcript showLine:('    Source:     ', chain source).
	Transcript showLine:('    Compound:   ', chain compound).
	Transcript showLine:('    E.C. code:  ', chain eccode).
	Transcript showLine:('    Residues:   ', chain countResidues stringValue).
	Transcript showLine:('    Amino Ac.:  ', chain countStandardAminoAcids stringValue).
	Transcript showLine:('    Heterogens: ', chain countHeterogens stringValue).
	Transcript showLine:('    Solvent:    ', chain countSolvent stringValue).
	Transcript showLine:('    Sequence:   ', chain getSequence).
	Transcript showLine:''.
	pq query:('insert into chsaw_chain (pdb,code,residues,aminoacids,heterogens,solvent,sequence,organism,compound,eccode,chainid,chainid2) values(\'',chain structure pdbcode,'\',\'',chain name,'\',\'',chain countResidues stringValue,'\',\'',chain countStandardAminoAcids stringValue,'\',\'',chain countHeterogens stringValue,'\',\'',chain countSolvent stringValue,'\',\'',chain getSequence,'\',\'',chain source quoted,'\',\'',chain compound quoted,'\',\'',chain eccode,'\',\'',chain structure pdbcode,chain name,'\',\'',chain structure pdbcode,chain code stringValue,'\');').
	^self



]