Module: Sylfy::Utils

Defined in:
lib/sylfy/utils/keyhash.rb,
lib/sylfy/utils/reactionkey.rb

Defined Under Namespace

Modules: Keyhash

Constant Summary collapse

COFACTORS =

COFACTORS = [

["FAD-FADH2", ["VWWQXMAJTJZDQX-UYBVJOGSSA-N"], ["YPZRHBJKEMOYQH-UYBVJOGSSA-N"], "B"],
["FMN-FMNH2", ["FVTCRASFADXXNN-SCRDCRAPSA-N"], ["YTNIXZGTHTVJBW-SCRDCRAPSA-N"], "C"],
["NAD-NADH", ["BAWFJGJZGIEFAR-NNYOXOHSSA-O"], ["BOPGDPNILDQYTO-NNYOXOHSSA-N"], "D"],
["NADP-NADPH", ["XJLXINKUBYWONI-NNYOXOHSSA-O"], ["ACFIXJIJDZMPPO-NNYOXOHSSA-N"], "E"]

]

[]
PORTERS = 
[]

Class Method Summary collapse

Class Method Details

.reactionkey(leftin, rightin, direction = nil) ⇒ Object 



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# File 'lib/sylfy/utils/reactionkey.rb', line 68

def self.reactionkey(leftin, rightin, direction = nil)
			
    #key[:first].push(item[0][0..13])
    #key[:second].push(item[0][15..22])
    #key[:flag].push(item[0][23])
    #key[:ver].push(item[0][24])
    #key[:indicator].push(item[0][26])
    #
			#AAAAAAAAAAAAAA-BBBBBBBBFV-P
			#AAAAAAAAAAAAAA is the first hash block.
			#It is a 14-character hash encoding the basic (Mobile-H) InChI layer, that is, molecular skeleton (connectivity).
			#BBBBBBBB is the second hash block.
			#It is an 8-character hash of the remaining layers (except for the "/p" segment, which accounts for added or removed protons and is not hashed at all; instead, the number of protons is indicated at the end of the InChIKey). In all cases, this block encodes stereochemistry and isotopic substitution information, associated with molecular connectivity expressed by the first block. In case of Non-standard InChI, it also encodes information on the exact position of tautomeric hydrogens (if any), as well as on the related stereo/isotopic data.
			#F is a flag which indicates the kind of InChIKey.
			#It is 'S' for Standard InChIKey (produced out of Standard InChI) and 'N' for Non-standard.
			#V is an InChI version character.
			#It is 'A' for version 1 ( 'B' is reserved for version 2, etc. ).
			#P is a [de]protonation indicator.
			#
    #
    # input InChIKey;coef
    
    version = "A"
    
			reverse_sign = {'<=' => '=>', '=>' => '<=', '<=>' => '<=>', '<?>' => '<?>'}
			sign_symbol = {'<=' => 'B', '=>' => 'F', '<=>' => 'R', '<?>' => 'U'}
			
    both = []
    
    if direction && sign_symbol.keys.include?(direction) && leftin && rightin && !leftin.empty? && !rightin.empty? && leftin != rightin
				
				left = leftin.dup
				right = rightin.dup
				
				cofactor_symbol = "A"
				
				COFACTORS.each do |cofactor|
					if left.include_all?(cofactor[1]) && right.include_all?(cofactor[2])
						left.delete_if {|x| cofactor[1].include?(x.split(/;/)[0]) }
						right.delete_if {|x| cofactor[2].include?(x.split(/;/)[0]) }
						cofactor_symbol = cofactor[3]
					elsif left.include_all?(cofactor[2]) && right.include_all?(cofactor[1])
						left.delete_if {|x| cofactor[2].include?(x.split(/;/)[0]) }
						right.delete_if {|x| cofactor[1].include?(x.split(/;/)[0]) }
						cofactor_symbol = cofactor[3]
					end
				end
				
				if (left.sort <=> right.sort) < 0
					dsign = sign_symbol[direction]
					both = [left.sort, right.sort]
				else
					dsign = sign_symbol[reverse_sign[direction]]
					both = [right.sort, left.sort]
				end
				
			elsif leftin != rightin && ((leftin && !leftin.empty?) || (rightin && rightin.empty?))
				left = leftin ? leftin.dup : []
				right = rightin ? rightin.dup : []
				
				cofactor_symbol = "Z"
				
				PORTERS.each do |cofactor|
					if left.include_all?(cofactor[1]) && right.include_all?(cofactor[2])
						left.delete_if {|x| cofactor[1]._key_include?(x) }
						right.delete_if {|x| cofactor[2]._key_include?(x) }
						cofactor_symbol = cofactor[3]
					elsif left.include_all?(cofactor[2]) && right.include_all?(cofactor[1])
						left.delete_if {|x| cofactor[2]._key_include?(x) }
						right.delete_if {|x| cofactor[1]._key_include?(x) }
						cofactor_symbol = cofactor[3]
					end
				end
				
				if (left.sort <=> right.sort) < 0
					dsign = "A"
					both = [left.sort, right.sort]
				else
					dsign = "Z"
					both = [right.sort, left.sort]
				end
			else
				return nil
    end
    
    
    code = {:first => [], :second => [], :flag => [], :ver => [], :charge => [], :coef => []}
    both.each do |side|
				part = {:first => [], :second => [], :flag => [], :ver => [], :charge => [], :coef => []}
				side.each do |item|
					part[:first].push(item[0..13])
					part[:second].push(item[15..22])
					part[:flag].push(item[23])
					part[:ver].push(item[24])
					part[:charge].push(item[26])
					part[:coef].push(item.split(/;/)[1] ? item.split(/;/)[1].to_f : 1.0)
				end
				
				part.each_pair do |k, v|
					code[k].push([:first, :second].include?(k) ? v.join('+') : v)
				end
			end
			
			# construct code string
			codeString = {}
			codeString[:A] = Sylfy::Utils::Keyhash.key(code[:first].join('/'))
			codeString[:B] = Sylfy::Utils::Keyhash.key(code[:second].join('/'), false)
			codeString[:v] = code[:ver]._key_version?
			codeString[:F] = codeString[:version] != "X" ? code[:flag]._key_version? : "X"
			codeString[:H] = code[:charge]._key_cal_charge
			codeString[:E] = code[:coef]._key_cal_coef
			codeString[:CC] = "#{["A", "Z"].include?(dsign) ? "Z" : "A"}#{cofactor_symbol}"
				
			# construct key AAAAAAAAAAAAAA-BBBBBBBBFvV-HE-CC-D
    # A calculate from list of First part of InChIKey
    # B calculate from list of Second part of InChIKey
    # F Flag S for standard X for not
    # E sum of co-efficient
    # H charge B for balance and X for not
    # C indicate cofactor code
    # v indicate version of InChIKey
    # V indicate version of this key function
    # D indicate direction
			# return "#{codeString[:A]}-#{codeString[:B]}#{codeString[:F]}#{codeString[:v]}#{version}-#{codeString[:H]}#{codeString[:E]}-#{codeString[:CC]}-#{dsign}"
			return "#{codeString[:A]}-#{codeString[:B]}#{codeString[:F]}#{codeString[:v]}#{version}-#{codeString[:H]}#{codeString[:E]}-#{dsign}"
end