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raw_species_find_algorithms.clj

; bridge
(defn find [anchor]
  (if (is anchor 3)
    (if (havent anchor BRIDGE 3)
      (def nbrs (cross_110 (crystal anchor) anchor))
      (if (and (all nbrs) (is nbrs[0] 6) (is nbrs[1] 6)
            (has_bond anchor nbrs[0]) (has_bond anchor nbrs[1]))
        (def atoms [anchor nbrs[0] nbrs[1]])
        (create BRIDGE atoms)))))

; -------------------------------------------------------------------------------------

; bridge(ct: *, ct: i)
(defn find [parent]
  (def anchor (atom parent 0))
  (if (is anchor 28)
    (if (havent anchor BRIDGE_CTSI 28)
      (create BRIDGE_CTSI parent))))

; bridge(cr: *, ct: i, cl: i)
(defn find [parent]
  (def anchors [(atom parent 0) (atom parent 1) (atom parent 2)])
  (if (and (is anchors[0] 0) (is anchors[1] 5) (is anchors[2] 4))
    (if (or (havent anchors[0] BRIDGE_CRS_CTI_CLI 0)
          (havent anchors[1] BRIDGE_CRS_CTI_CLI 5)
          (havent anchors[2] BRIDGE_CRS_CTI_CLI 4))
      (create BRIDGE_CRS_CTI_CLI parent))))

; methyl_on_bridge
(defn find [parent]
  (def anchor (atom parent 0))
  (if (is anchor 9)
    (if (havent anchor METHYL_ON_BRIDGE 9)
      (def amorph1 (amorph_neighbour anchor))
      (if (is amorph1 14)
        (create METHYL_ON_BRIDGE amorph1 parent)))))

; -------------------------------------------------------------------------------------

; bridge(cr: i)
(defn find [parent]
  (each_symmetry parent (fn [specie]
    (def anchor (atom specie 1))
    (if (is anchor 4)
      (if (havent anchor BRIDGE_CRI 4)
        (create BRIDGE_CRI specie))))))

; -------------------------------------------------------------------------------------

; dimer
(defn find [anchor]
  (if (is anchor 22)
    (if (havent anchor DIMER 22)
      (each_neighbour anchor front_100 (fn [neighbour]
        (if (and (is neighbour 22) (has_bond anchor neighbour))
          (def parents [(spec_by_role anchor BRIDGE 3) (spec_by_role neighbour BRIDGE 3)])
          (create DIMER parents)))))))

; methyl_on_dimer
(defn find [anchor]
  (if (is anchor 23)
    (if (havent anchor METHYL_ON_DIMER 23)
      (each_neighbour anchor front_100 (fn [neighbour]
        (if (and (is neighbour 22) (has_bond anchor neighbour))
          (def parents [(spec_by_role anchor METHYL_ON_BRIDGE 9) (spec_by_role neighbour BRIDGE 3)])
          (create METHYL_ON_DIMER parents)))))
    (if (is anchor 22)
      (if (havent anchor METHYL_ON_DIMER 22)
        (each_neighbour anchor front_100 (fn [neighbour]
          (if (and (is neighbour 23) (has_bond anchor neighbour))
            (def parents [(spec_by_role neighbour METHYL_ON_BRIDGE 9) (spec_by_role anchor BRIDGE 3)])
            (create METHYL_ON_DIMER parents))))))))

; -------------------------------------------------------------------------------------

; cross_bridge_on_bridges
(defn find [anchor]
  (if (is anchor 10)
    (if (havent anchor CROSS_BRIDGE_ON_BRIDGES 10)
      (def species (specs_by_role anchor METHYL_ON_BRIDGE 2 14))
      (if (all species)
        (def atoms [(atom species[0] 1) (atom species[1] 1)])
        (each_neighbour atoms[0] cross_100 (fn [neighbour])
          (if (and (== atoms[1] neighbour) (not (has_bond atoms[0], neighbour)))
            (def parents [species[0] species[1]])
            (create CROSS_BRIDGE_ON_BRIDGES parents)))))))

; three_bridges
(defn find [anchor]
  (if (is anchor 24)
    (if (havent anchor THREE_BRIDGES 24)
      (each_spec_by_role anchor BRIDGE 6 (fn [target1]
        (each_symmetry target1 (fn [specie1]
          (if (== (atom specie1 1) anchor)
            (each_spec_by_role anchor BRIDGE 6 (fn [target2]
              (if (== target2 target1)
                (each_symmetry target2 (fn [specie2]
                  (if (== (atom specie2 2) anchor)
                    (def atom1 (atom specie1 2))
                    (def specie3 (specs_by_role atom1 BRIDGE 3))
                    (def parents [specie1 specie2 specie3])
                    (create THREE_BRIDGES parents)))))))))))))))

; bridge_with_dimer
(defn find [anchor]
  (if (is anchor 32)
    (if (havent anchor BRIDGE_WITH_DIMER 32)
      (each_spec_by_role anchor DIMER 22 (fn [target1]
        (each_symmetry target1 (fn [specie1]
          (if (== (atom specie1 3) anchor)
            (each_spec_by_role anchor BRIDGE 6 (fn [target2]
              (each_symmetry target2 (fn [specie2]
                (if (== (atom specie2 1) anchor)
                  (def atom1 (atom specie2 2))
                  (def specie3 (specs_by_role atom1 BRIDGE 3))
                  (def parents [specie1 specie2 specie3])
                  (create THREE_BRIDGES parents))))))))))))))