forked from lijiext/lammps
1928 lines
35 KiB
Plaintext
1928 lines
35 KiB
Plaintext
! mcff_templates
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! Template file of potential type assignment templates for the mcff
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! forcefield (March-1995)
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!
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type: ?
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! anything
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template: (>*)
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end_type
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type: lp
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!lone pair
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template: (>L (-*))
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end_type
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type:c
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! generic SP3 carbon
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template: (>C)
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atom_test:1
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hybridization:SP3
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end_test
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end_type
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type: c3
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! sp3 carbon with 3 h's 1 heavy
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template: (>C(-H)(-H)(-H)(-*))
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atom_test:5
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disallowed_elements:H
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end_test
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end_type
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type:c2
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! sp3 carbon with 2 H's, 2 Heavy's
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template:(>C(-H)(-H)(-*)(-*))
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atom_test:4
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disallowed_elements:H
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end_test
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atom_test:5
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disallowed_elements:H
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end_test
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end_type
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type:co
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! sp3 carbon in acetals
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template:(>C(-O)(-O)(-*)(-*))
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end_type
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type:coh
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! sp3 carbon in acetals with hydrogen
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template:(>C(-O)(-O)(-H)(-*))
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end_type
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type: c1
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! sp3 carbon with 1 H 3 heavies
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template: (>C(-H)(-*)(-*)(-*))
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atom_test:3
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disallowed_elements:H
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end_test
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atom_test:4
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disallowed_elements:H
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end_test
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atom_test:5
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disallowed_elements:H
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end_test
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end_type
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type: c3m
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! sp3 carbon in 3-membered ring
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template: (>C)
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atom_test:1
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hybridization:SP3
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ring:PLANAR(3)
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type: c4m
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! sp3 carbon in 4-membered ring
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template: (>C)
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atom_test:1
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hybridization:SP3
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ring:NON_PLANAR(4)
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type: c4m
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! sp3 carbon in 4-membered ring
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template: (>C)
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atom_test:1
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hybridization:SP3
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ring:PLANAR(4)
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type: c3h
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! sp3 carbon in 3-membered ring with hydrogens
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template: (>C(-H))
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atom_test:1
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hybridization:SP3
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ring:PLANAR(3)
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type: c4h
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! sp3 carbon in 4-membered ring with hydrogens
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template: (>C(-H))
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atom_test:1
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hybridization:SP3
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ring:NON_PLANAR(4)
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type: c4h
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! sp3 carbon in 4-membered ring
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template: (>C(-H))
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atom_test:1
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hybridization:SP3
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ring:PLANAR(4)
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type:c_a
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!general amino acid alpha carbon (sp3)
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template: (>C(-N(-*))(-C[~O])(~*)(~*))
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end_type
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type: cg
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! sp3 alpha carbon in glycine
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template: (>C(-H)(-H)(-C[~O])(-N(-H)))
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end_type
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type: c=2
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! non aromatic doubly bonded carbon
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template: (>C(=*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type: c=
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! non aromatic end doubly bonded carbon
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template: (>C(=*)(-*)(-N(-*)(-*)))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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atom_test:2
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disallowed_elements:O,S
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end_test
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atom_test:3
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disallowed_elements:N,C
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end_test
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end_type
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type: c=
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! non aromatic end doubly bonded carbon
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template: (>C(=*)(-N(-*)(-*))(-N(-*)(-*)))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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atom_test:2
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disallowed_elements:O,S
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end_test
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end_type
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type: c=
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! non aromatic end doubly bonded carbon
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template: (>C(=*)(-N(-*)(-*))(-C(-*)(-*)(-*)))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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atom_test:2
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disallowed_elements:O,S
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end_test
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end_type
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type: c=
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! non aromatic end doubly bonded carbon
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template: (>C(=*)(-*)(-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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atom_test:2
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disallowed_elements:O,S
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end_test
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atom_test:3
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disallowed_elements:N,C
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end_test
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atom_test:4
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disallowed_elements:N,C
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end_test
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end_type
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type: c=
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! non aromatic end doubly bonded carbon
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template: (>C(=*)(-*)(-C))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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atom_test:2
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disallowed_elements:O,S
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end_test
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atom_test:3
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disallowed_elements:N,C
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end_test
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atom_test:4
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hybridization:SP3
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end_test
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end_type
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type: c=
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! non aromatic end doubly bonded carbon
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template: (>C(=*)(-C)(-C))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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atom_test:2
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disallowed_elements:O,S
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end_test
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atom_test:3
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hybridization:SP3
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end_test
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atom_test:4
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hybridization:SP3
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end_test
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end_type
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type: c=1
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! non aromatic, next to end doubly bonded carbon
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template: (>C(=C(-*)(-N(-*)(-*)))(-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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atom_test:3
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disallowed_elements:N,C
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end_test
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end_type
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type: c=1
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! non aromatic, next to end doubly bonded carbon
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template:(>C(=C(-N(-*)(-*))(-N(-*)(-*)))(-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type: c=1
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! non aromatic, next to end doubly bonded carbon
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template:(>C(=C(-N(-*)(-*))(-C(-*)(-*)(-*)))(-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type: c=1
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! non aromatic, next to end doubly bonded carbon
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template:(>C(=C(-*)(-*))(-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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atom_test:3
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disallowed_elements:N,C
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end_test
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atom_test:4
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disallowed_elements:N,C
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end_test
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end_type
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type: c=1
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! non aromatic, next to end doubly bonded carbon
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template:(>C(=C(-C)(-*))(-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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atom_test:3
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hybridization:SP3
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end_test
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atom_test:4
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disallowed_elements:N,C
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end_test
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end_type
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type: c=1
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! non aromatic, next to end doubly bonded carbon
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template:(>C(=C(-C)(-C))(-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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atom_test:3
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hybridization:SP3
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end_test
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atom_test:4
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hybridization:SP3
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end_test
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end_type
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type: c=1
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! non aromatic carbon doubly bonded to an end nitrogen
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template: (>C[=N(-N(-*)(-*))](-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type: c=1
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! non aromatic carbon doubly bonded to an end nitrogen
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template: (>C[=N(-C(-*)(-*)(-*))](-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type: c=1
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! non aromatic carbon doubly bonded to an end nitrogen
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template: (>C[=N(-*)](-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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atom_test:3
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disallowed_elements:N,C
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end_test
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end_type
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type: c=1
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! non aromatic carbon doubly bonded to an end nitrogen
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template: (>C(=N(-N(-*)(-*))(-N(-*)(-*)))(-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type: c=1
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! non aromatic carbon doubly bonded to an end nitrogen
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template: (>C(=N(-C(-*)(-*)(-*))(-C(-*)(-*)(-*)))(-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type: c=1
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! non aromatic carbon doubly bonded to an end nitrogen
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template: (>C(=N(-C(-*)(-*)(-*))(-N(-*)(-*)))(-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type: c=1
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! non aromatic carbon doubly bonded to an end nitrogen
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template: (>C(=N(-*)(-*))(-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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atom_test:3
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disallowed_elements:N,C
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end_test
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atom_test:4
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disallowed_elements:N,C
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end_test
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end_type
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type: c=1
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! non aromatic carbon doubly bonded to an end nitrogen
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template: (>C(=N(-*)(-N(-*)(-*)))(-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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atom_test:3
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disallowed_elements:N,C
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end_test
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end_type
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type: c=1
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! non aromatic carbon doubly bonded to an end nitrogen
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template: (>C(=N(-*)(-C(-*)(-*)(-*)))(-*))
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atom_test:1
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aromaticity:NON_AROMATIC
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end_test
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atom_test:3
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disallowed_elements:N,C
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end_test
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end_type
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type:cp
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! SP2 aromatic carbon with partial double bond
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template:(>C)
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atom_test:1
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hybridization: SP2
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aromaticity:AROMATIC
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end_test
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end_type
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type:cp
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! This is used for aromatic carbons that fail the aromaticity test because
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! the current ring checker is to lame to figure on a ring with more than
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! seven or eight sides. The NON_AROMATIC test is to eliminate the conflict
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! with the above 'cp' definition. This can be removed when the ring checker
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! is made more robust.
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template: [>C(-*)(:*)(:*)]
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atom_test:1
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hybridization:SP2
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aromaticity:NON_AROMATIC
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end_test
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end_type
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type: c5
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! Sp2 aromatic carbon in 5-membered ring
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template:(>C)
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atom_test:1
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hybridization:SP2
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aromaticity:AROMATIC
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ring:PLANAR(5)
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end_test
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end_type
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type:ci
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! sp2 aromatic carbon in charged imidazole ring (His+)
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template: (>C(:N(-H)(:C))(:N(-H)(:C)))
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atom_test:1
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hybridization:SP2
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aromaticity:AROMATIC
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ring:PLANAR(5)
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end_test
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atom_test:2
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hybridization:SP2
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aromaticity:AROMATIC
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ring:PLANAR(5)
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end_test
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atom_test:4
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hybridization: SP2
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aromaticity:AROMATIC
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ring:PLANAR(5)
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end_test
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atom_test:5
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hybridization:SP2
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aromaticity:AROMATIC
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ring:PLANAR(5)
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end_test
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atom_test:6
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hybridization: SP2
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aromaticity:AROMATIC
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ring:PLANAR(5)
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end_test
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atom_test:7
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hybridization: SP2
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aromaticity:AROMATIC
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ring:PLANAR(5)
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end_test
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end_type
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type: ci
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! Carbon in charged imidazole ring
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template:(>C(=N(-C(=C(-N)))(-H)))
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atom_test:1
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ring:PLANAR(5)
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end_test
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atom_test:2
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ring:PLANAR(5)
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end_test
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atom_test:3
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ring:PLANAR(5)
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end_test
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atom_test:4
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ring:PLANAR(5)
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end_test
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atom_test:5
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ring:PLANAR(5)
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end_test
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end_type
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type: ci
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! Carbon in charged imidazole ring
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template:(>C(-N(-C(=N(-H)(-C)))))
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atom_test:1
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ring:PLANAR(5)
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end_test
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atom_test:2
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ring:PLANAR(5)
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end_test
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atom_test:3
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ring:PLANAR(5)
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end_test
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atom_test:4
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ring:PLANAR(5)
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end_test
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atom_test:6
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ring:PLANAR(5)
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end_test
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end_type
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type: ci
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! Carbon in charged imidazole ring
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template:(>C(=C(-N(-C(=N(-C)(-H))))))
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atom_test:1
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ring:PLANAR(5)
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end_test
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atom_test:2
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ring:PLANAR(5)
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end_test
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atom_test:3
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ring:PLANAR(5)
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end_test
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atom_test:4
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ring:PLANAR(5)
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end_test
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atom_test:5
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ring:PLANAR(5)
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end_test
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atom_test:6
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ring:PLANAR(5)
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end_test
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end_type
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type: cs
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! SP2 aromatic carbon in 5 membered ring next to S
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template:(>C(~S))
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atom_test:1
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hybridization:SP2
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aromaticity:AROMATIC
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ring:PLANAR(5)
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end_test
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atom_test:2
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hybridization:SP2
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aromaticity:AROMATIC
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ring:PLANAR(5)
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end_test
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end_type
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type: cr
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! c in neutral arginine
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template: (>C (=N(-*)) (-N(-H)(-H)) (-N(-H)(-H)) )
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end_type
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type: c+
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! c in guanidinium group
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template: (>C (=N(-*)(-*)) (-N(-H)(-H)) (-N(-H)(-H)) )
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end_type
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type: c+
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! c in guanidinium group
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template: (>C (:N(-*)(-*)) (:N(-H)(-H)) (:N(-H)(-H)) )
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end_type
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type: c-
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! c in charged carboxylate
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template: [>C[:O][:O](-*)]
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end_type
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type: c-
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! c in charged carboxylate
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! How do we indicate that the second O has nothing bonded to it ?
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! what makes it not match COOH ?
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template: [>C[=O][-O](-*)]
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end_type
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type: ct
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! sp carbon involved in a triple bond
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template: (>C(#*))
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end_type
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type: na
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! sp3 nitrogen in amines
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template: (>N (-*)(-*)(-*))
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atom_test:1
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hybridization:SP3
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end_test
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end_type
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type: n+
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! sp3 nitrogen in protonated amines
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template: (>N(-H)(-*)(-*)(-*))
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atom_test:1
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hybridization:SP3
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end_test
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end_type
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type: n4
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! sp3 nitrogen with 4 substituents
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template: (>N(-*)(-*)(-*)(-*))
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atom_test:1
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hybridization:SP3
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end_test
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atom_test:2
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disallowed_elements:H
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end_test
|
|
atom_test:3
|
|
disallowed_elements:H
|
|
end_test
|
|
atom_test:4
|
|
disallowed_elements:H
|
|
end_test
|
|
atom_test:5
|
|
disallowed_elements:H
|
|
end_test
|
|
end_type
|
|
|
|
type: nb
|
|
! sp2 nitrogen in aromatic amines
|
|
template: (>N(~C)(-*)(-*))
|
|
atom_test: 1
|
|
hybridization: SP2
|
|
Aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test: 2
|
|
hybridization: SP2
|
|
Aromaticity: AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type: nb
|
|
! sp2 nitrogen in aromatic amines
|
|
template: (>N(~C(:*)(:*))(-*)(-*))
|
|
atom_test: 1
|
|
hybridization: SP2
|
|
Aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:2
|
|
hybridization: SP2
|
|
Aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type: n
|
|
! generic sp2 nitrogen (in amids))
|
|
template: (>N(-*))
|
|
atom_test: 1
|
|
hybridization: SP2
|
|
aromaticity: NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type: n3m
|
|
! sp3 nitrogen in 3- membered ring
|
|
template: (>N(-*)(-*)(-*))
|
|
atom_test: 1
|
|
hybridization: SP3
|
|
aromaticity: NON_AROMATIC
|
|
ring:PLANAR(3)
|
|
end_test
|
|
end_type
|
|
|
|
type: n4m
|
|
! sp3 nitrogen in 4- membered ring
|
|
template: (>N(-*)(-*)(-*))
|
|
atom_test: 1
|
|
hybridization: SP3
|
|
aromaticity: NON_AROMATIC
|
|
ring:PLANAR(4)
|
|
end_test
|
|
end_type
|
|
|
|
type: n4m
|
|
! sp3 nitrogen in 4- membered ring
|
|
template: (>N(-*)(-*)(-*))
|
|
atom_test: 1
|
|
hybridization: SP3
|
|
aromaticity: NON_AROMATIC
|
|
ring:NON_PLANAR(4)
|
|
end_test
|
|
end_type
|
|
|
|
type: n3n
|
|
! sp2 nitrogen in 3- membered ring
|
|
template: (>N(~*)(-*)(-*))
|
|
atom_test: 1
|
|
hybridization: SP2
|
|
aromaticity: NON_AROMATIC
|
|
ring:PLANAR(3)
|
|
end_test
|
|
end_type
|
|
|
|
type: n4n
|
|
! sp2 nitrogen in 3- membered ring
|
|
template: (>N(~*)(-*)(-*))
|
|
atom_test: 1
|
|
hybridization: SP2
|
|
aromaticity: NON_AROMATIC
|
|
ring:PLANAR(4)
|
|
end_test
|
|
end_type
|
|
|
|
type: n4n
|
|
! sp2 itrogen in 4- membered ring
|
|
template: (>N(~*)(-*)(-*))
|
|
atom_test: 1
|
|
hybridization: SP2
|
|
aromaticity: NON_AROMATIC
|
|
ring:NON_PLANAR(4)
|
|
end_test
|
|
end_type
|
|
|
|
type: np
|
|
! sp2 nitrogen in 5- or 6- membered ring
|
|
! not bonded to hydrogen
|
|
template: [>N(~*)(~*)]
|
|
atom_test:1
|
|
hybridization:SP2
|
|
aromaticity:AROMATIC
|
|
end_test
|
|
atom_test:2
|
|
disallowed_elements:P H
|
|
end_test
|
|
atom_test:3
|
|
disallowed_elements:P H
|
|
end_test
|
|
end_type
|
|
|
|
type: np
|
|
! sp2 nitrogen in 5- or 6- membered ring
|
|
! not bonded to hydrogen
|
|
template: [>N(:*)(:*)]
|
|
atom_test:1
|
|
hybridization: SP2
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:2
|
|
hybridization: SP2
|
|
aromaticity:NON_AROMATIC
|
|
disallowed_elements:P H
|
|
end_test
|
|
atom_test:3
|
|
hybridization: SP2
|
|
aromaticity:NON_AROMATIC
|
|
disallowed_elements:P H
|
|
end_test
|
|
end_type
|
|
|
|
type: npc
|
|
! sp2 nitrogen in 5- or 6- membered ring
|
|
! bonded to a heavy atom
|
|
template: [>N(~*)(~*)(~*)]
|
|
atom_test:1
|
|
hybridization:SP2
|
|
aromaticity:AROMATIC
|
|
end_test
|
|
atom_test:2
|
|
disallowed_elements:H
|
|
end_test
|
|
atom_test:3
|
|
disallowed_elements:H
|
|
end_test
|
|
atom_test:4
|
|
disallowed_elements:H
|
|
end_test
|
|
end_type
|
|
|
|
type: npc
|
|
! sp2 nitrogen in 5- or 6- membered ring
|
|
! bonded to a heavy atom
|
|
template: [>N(:*)(:*)(~*)]
|
|
atom_test:1
|
|
hybridization: SP2
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:2
|
|
hybridization: SP2
|
|
aromaticity:NON_AROMATIC
|
|
disallowed_elements:H
|
|
end_test
|
|
atom_test:3
|
|
hybridization: SP2
|
|
aromaticity:NON_AROMATIC
|
|
disallowed_elements:H
|
|
end_test
|
|
atom_test:4
|
|
disallowed_elements:H
|
|
end_test
|
|
end_type
|
|
|
|
type: nh
|
|
! sp2 nitrogen in 5-or 6- membered ring
|
|
! with hydrogen attached
|
|
template: (>N(-H))
|
|
atom_test: 1
|
|
hybridization: SP2
|
|
aromaticity: AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type: nh+
|
|
! protonated nitrogen in 6- membered ring
|
|
! with hydrogen attached
|
|
template: (>N(-H))
|
|
atom_test: 1
|
|
hybridization: SP2
|
|
aromaticity: AROMATIC
|
|
ring:PLANAR(6)
|
|
end_test
|
|
end_type
|
|
|
|
type: nho
|
|
! sp2 nitrogen in 6- membered ring
|
|
! next to a carbonyl group and with a hydrogen
|
|
! attached
|
|
template: (>N(~C[=O])(-H))
|
|
atom_test: 1
|
|
hybridization: SP2
|
|
aromaticity: AROMATIC
|
|
ring:PLANAR(6)
|
|
end_test
|
|
end_type
|
|
|
|
type: nho
|
|
! sp2 nitrogen in 6- membered ring
|
|
! next to a carbonyl group and with a hydrogen
|
|
! attached
|
|
template: (>N(~C[:O])(-H))
|
|
atom_test: 1
|
|
hybridization: SP2
|
|
aromaticity: AROMATIC
|
|
ring:PLANAR(6)
|
|
end_test
|
|
end_type
|
|
|
|
|
|
type: n2
|
|
!sp2 nitrogen (NH2) in guanidinium group (HN=C(NH2)2)
|
|
template: (>N(-H)(-H)(-C(=N(-*))(-N(-H)(-H))))
|
|
atom_test: 1
|
|
aromaticity: NON_AROMATIC
|
|
hybridization:SP2
|
|
end_test
|
|
end_type
|
|
|
|
type: n=2
|
|
! sp2 nitrogen in neutral arginine (double bond)
|
|
template: (>N(=*))
|
|
atom_test: 1
|
|
hybridization:SP2
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type: n=
|
|
! non aromatic end double bonded nitrogen
|
|
template: [>N(=*)(-N(-*)(-*))]
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:2
|
|
disallowed_elements:O,S
|
|
end_test
|
|
end_type
|
|
|
|
type: n=
|
|
! non aromatic end double bonded nitrogen
|
|
template: [>N(=*)(-C(-*)(-*)(-*))]
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:2
|
|
disallowed_elements:O,S
|
|
end_test
|
|
end_type
|
|
|
|
type: n=
|
|
! non aromatic end double bonded nitrogen
|
|
template: [>N(=*)(-*)]
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:2
|
|
disallowed_elements:O,S
|
|
end_test
|
|
atom_test:3
|
|
disallowed_elements:N,C
|
|
end_test
|
|
end_type
|
|
|
|
type: n=
|
|
! non aromatic end double bonded nitrogen
|
|
template: (>N(=*)(-N(-*)(-*))(-N(-*)(-*)))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:2
|
|
disallowed_elements:O,S
|
|
end_test
|
|
end_type
|
|
|
|
type: n=
|
|
! non aromatic end double bonded nitrogen
|
|
template: (>N(=*)(-C(-*)(-*)(-*))(-C(-*)(-*)(-*)))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:2
|
|
disallowed_elements:O,S
|
|
end_test
|
|
end_type
|
|
|
|
type: n=
|
|
! non aromatic end double bonded nitrogen
|
|
template: (>N(=*)(-C(-*)(-*)(-*))(-N(-*)(-*)))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:2
|
|
disallowed_elements:O,S
|
|
end_test
|
|
end_type
|
|
|
|
type: n=
|
|
! non aromatic end double bonded nitrogen
|
|
template: (>N(=*)(-*)(-*))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:2
|
|
disallowed_elements:O,S
|
|
end_test
|
|
atom_test:3
|
|
disallowed_elements:N,C
|
|
end_test
|
|
atom_test:4
|
|
disallowed_elements:N,C
|
|
end_test
|
|
end_type
|
|
|
|
type: n=
|
|
! non aromatic end double bonded nitrogen
|
|
template: (>N(=*)(-*)(-N(-*)(-*)))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:2
|
|
disallowed_elements:O,S
|
|
end_test
|
|
atom_test:3
|
|
disallowed_elements:N,C
|
|
end_test
|
|
end_type
|
|
|
|
type: n=
|
|
! non aromatic end double bonded nitrogen
|
|
template: (>N(=*)(-*)(-C(-*)(-*)(-*)))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:2
|
|
disallowed_elements:O,S
|
|
end_test
|
|
atom_test:3
|
|
disallowed_elements:N,C
|
|
end_test
|
|
end_type
|
|
|
|
type: n=
|
|
! phosphazene nitrogen
|
|
template: [>N(:P)(:P)]
|
|
end_type
|
|
|
|
type: n=1
|
|
! non aromatic, next to end doubly bonded carbon
|
|
template: (>N(=C(-*)(-N(-*)(-*))))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:3
|
|
disallowed_elements:N,C
|
|
end_test
|
|
end_type
|
|
|
|
type: n=1
|
|
! non aromatic, next to end doubly bonded carbon
|
|
template:(>N(=C(-N(-*)(-*))(-N(-*)(-*))))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type: n=1
|
|
! non aromatic, next to end doubly bonded carbon
|
|
template:(>N(=C(-N(-*)(-*))(-C(-*)(-*)(-*)))(-*))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type: n=1
|
|
! non aromatic, next to end doubly bonded carbon
|
|
template:(>N(=C(-*)(-*))(-*))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:3
|
|
disallowed_elements:N,C
|
|
end_test
|
|
atom_test:4
|
|
disallowed_elements:N,C
|
|
end_test
|
|
end_type
|
|
|
|
type: n=1
|
|
! non aromatic, next to end doubly bonded carbon
|
|
template:(>N(=C(-C)(-*))(-*))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:3
|
|
hybridization:SP3
|
|
end_test
|
|
atom_test:4
|
|
disallowed_elements:N,C
|
|
end_test
|
|
end_type
|
|
|
|
type: n=1
|
|
! non aromatic, next to end doubly bonded carbon
|
|
template:(>N(=C(-C)(-C))(-*))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:3
|
|
hybridization:SP3
|
|
end_test
|
|
atom_test:4
|
|
hybridization:SP3
|
|
end_test
|
|
end_type
|
|
|
|
|
|
type: n=1
|
|
! non aromatic nitrogen doubly bonded to an end nitrogen
|
|
template: (>N(=N(-N(-*)(-*)))(-*))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type: n=1
|
|
! non aromatic nitrogen doubly bonded to an end nitrogen
|
|
template: (>N(=N(-C(-*)(-*)(-*)))(-*))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type: n=1
|
|
! non aromatic nitrogen doubly bonded to an end nitrogen
|
|
template: (>N(=N(-*))(-*))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:3
|
|
disallowed_elements:N,C
|
|
end_test
|
|
end_type
|
|
|
|
type: n1
|
|
!sp2 nitrogen in charged arginine
|
|
template: (>N(-*)(-*)(=C(-N(-H)(-H))(-N(-H)(-H))))
|
|
atom_test:1
|
|
hybridization:SP2
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
|
|
type: ni
|
|
! Nitrogen in charged imidazole ring
|
|
template:(>N(-H)(:C)(:C(:N(-H))))
|
|
atom_test:1
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:3
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:4
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:5
|
|
ring:PLANAR(5)
|
|
end_test
|
|
end_type
|
|
|
|
type: ni
|
|
! Nitrogen in charged imidazole ring
|
|
template:[>N(=C(-N(-C(=C))))(-H)(-C)]
|
|
atom_test:1
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:2
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:3
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:4
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:5
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:7
|
|
ring:PLANAR(5)
|
|
end_test
|
|
end_type
|
|
|
|
|
|
type: ni
|
|
! Nitrogen in charged imidazole ring
|
|
template:(>N(-C(=C(-N(=C)(-H))))(-C)(-*))
|
|
atom_test:1
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:2
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:3
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:4
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:5
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:7
|
|
ring:PLANAR(5)
|
|
end_test
|
|
end_type
|
|
|
|
type:nt
|
|
! sp nitrogen involved in a triple bond
|
|
template:(>N(#*))
|
|
end_type
|
|
|
|
type:nz
|
|
! sp nitrogen in N2
|
|
template:[>N[#N]]
|
|
end_type
|
|
|
|
type:o
|
|
! generic SP3 oxygen in alcohol, ether,or acid group
|
|
template (>O)
|
|
atom_test:1
|
|
end_test
|
|
end_type
|
|
|
|
type oh
|
|
! oxygen bonded to hydrogen
|
|
template: (>O(-H)(-*))
|
|
end_type
|
|
|
|
type:oc
|
|
! SP3 oxygen in ether or acetals
|
|
template (>O(-C)(-C))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type:oe
|
|
! SP3 oxygen in ester
|
|
template (>O(-C(=O))(-C))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type:oe
|
|
! SP3 oxygen in ester
|
|
template (>O(:C[:O])(-C))
|
|
atom_test:1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type:o3e
|
|
! SP3 oxygen in three membered ring
|
|
template (>O(-C)(-C))
|
|
atom_test:1
|
|
ring:PLANAR(3)
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type:o4e
|
|
! SP3 oxygen in non-planar four membered ring
|
|
template (>O(-C)(-C))
|
|
atom_test:1
|
|
ring:NON_PLANAR(4)
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type:o4e
|
|
! SP3 oxygen in planar four memberedd ring
|
|
template (>O(-C)(-C))
|
|
atom_test:1
|
|
ring:PLANAR(4)
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type: o=
|
|
! oxygen double bonded to O, N,C,S,P
|
|
template: (>O(=*))
|
|
atom_test:2
|
|
allowed_elements: O,N,C,S,P
|
|
end_test
|
|
end_type
|
|
|
|
type: o-
|
|
! partial double oxygen bonded to something then bonded to
|
|
! another partial double oxygen
|
|
template: [>O(:*[:O])]
|
|
atom_test:2
|
|
allowed_elements: C,P
|
|
end_test
|
|
end_type
|
|
|
|
type: o-
|
|
! double bonded oxygen in charged carboxylate COO-
|
|
! or charged phosphate POO-
|
|
template: [>O(=*[-O])]
|
|
atom_test:2
|
|
allowed_elements: C,P
|
|
end_test
|
|
end_type
|
|
|
|
type: o-
|
|
! single bonded oxygen in charged carboxylate COO-
|
|
! or charged phosphate POO-
|
|
template: [>O[-*[=O]]]
|
|
atom_test:2
|
|
allowed_elements: C,P
|
|
end_test
|
|
end_type
|
|
|
|
type: op
|
|
! SP2 aromatic in 5 membered ring
|
|
template:(>O)
|
|
atom_test:1
|
|
hybridization: SP2
|
|
aromaticity:AROMATIC
|
|
ring:PLANAR(5)
|
|
end_test
|
|
end_type
|
|
|
|
type: op
|
|
! SP2 aromatic in 5 membered ring
|
|
template:(>O(:*)(:*))
|
|
atom_test:1
|
|
hybridization:SP2
|
|
aromaticity:NON_AROMATIC
|
|
ring:PLANAR(5)
|
|
end_test
|
|
end_type
|
|
|
|
type: o*
|
|
!oxygen in water
|
|
template (>O(-H)(-H))
|
|
end_type
|
|
|
|
type:h
|
|
! generic hydrogen
|
|
template: (>H (-*) )
|
|
atom_test:2
|
|
allowed_elements:C,Si,H
|
|
end_test
|
|
end_type
|
|
|
|
type:hc
|
|
! hydrogen bonded to carbon
|
|
template: (>H (-C) )
|
|
end_type
|
|
|
|
type:hs
|
|
! hydrogen bonded to sulfur
|
|
template: (>H (-S) )
|
|
end_type
|
|
|
|
type:hsi
|
|
! hydrogen bonded to silicon
|
|
template: (>H (-Si) )
|
|
end_type
|
|
|
|
type:hp
|
|
! hydrogen bonded to phosphorus
|
|
template: (>H (-P) )
|
|
end_type
|
|
|
|
type:h*
|
|
! hydrogen bonded to fluorine, nitrogen, Oxygen
|
|
template: (>H(-*))
|
|
atom_test:2
|
|
allowed_elements:O,N,F
|
|
end_test
|
|
end_type
|
|
|
|
type:ho
|
|
! hydrogen bonded to oxygen
|
|
template: (>H(-O))
|
|
end_type
|
|
|
|
type: hi
|
|
! Hydrogen in charged imidazole ring
|
|
template:(>H(-N(:C)(:C(:N(-*)))))
|
|
atom_test:2
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:3
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:4
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:5
|
|
ring:PLANAR(5)
|
|
end_test
|
|
end_type
|
|
|
|
type: hi
|
|
! Hydrogen in charged imidazole ring
|
|
template:(>H(-N(=C(-N(-H)(-C(=C))))(-C)))
|
|
atom_test:2
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:3
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:4
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:6
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:7
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:8
|
|
ring:PLANAR(5)
|
|
end_test
|
|
end_type
|
|
|
|
type: hi
|
|
! Hydrogen in charged imidazole ring
|
|
template:(>H(-N(-C(=C(-N(=C)(-H))))(-C)))
|
|
atom_test:2
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:3
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:4
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:5
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:6
|
|
ring:PLANAR(5)
|
|
end_test
|
|
atom_test:8
|
|
ring:PLANAR(5)
|
|
end_test
|
|
end_type
|
|
|
|
type:hw
|
|
! hydrogen in water
|
|
template: (>H(-O(-H)))
|
|
end_type
|
|
|
|
|
|
type:hn
|
|
! hydrogen bonded to nitrogen
|
|
template: (>H (-N) )
|
|
end_type
|
|
|
|
type:h+
|
|
! charged hydrogen in cations
|
|
template: (>H (-N(-*)(-*)(-*)) )
|
|
end_type
|
|
|
|
type:dw
|
|
! deuterium in heivy water
|
|
template: (>D(-O(-D)))
|
|
end_type
|
|
|
|
|
|
type:s
|
|
! sp3 sulfur
|
|
template: (>S)
|
|
end_type
|
|
|
|
type:sc
|
|
! sp3 sulfur in methionines (C-S-C) group
|
|
template: (>S(-C)(-C))
|
|
end_type
|
|
|
|
type:s3e
|
|
! sulfur in three membered ring
|
|
template (>S(-C)(-C))
|
|
atom_test:1
|
|
ring:PLANAR(3)
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type:s4e
|
|
! sulfur in four membered ring
|
|
template (>S(-C)(-C))
|
|
atom_test:1
|
|
ring:PLANAR(4)
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type:s4e
|
|
! sulfur in three membered ring
|
|
template (>S(-C)(-C))
|
|
atom_test:1
|
|
ring:NON_PLANAR(4)
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
end_type
|
|
|
|
type:s1
|
|
! sp3 sulfur involved in (S-S) group of disulfides
|
|
template: (>S(-S))
|
|
end_type
|
|
|
|
type:sh
|
|
! sp3 sulfur in sulfhydryl (-SH) group (e.g. cysteine)
|
|
template: (>S(-H)(-*))
|
|
atom_test:3
|
|
disallowed_elements:S
|
|
end_test
|
|
end_type
|
|
|
|
type: sp
|
|
! sulfur in an aromatic ring (e.g. thiophene)
|
|
template: (>S)
|
|
atom_test:1
|
|
aromaticity: AROMATIC
|
|
hybridization:SP2
|
|
ring: PLANAR(5)
|
|
end_test
|
|
end_type
|
|
|
|
type: sp
|
|
! sulfur in an aromatic ring (e.g. thiophene)
|
|
template: (>S(:*)(:*))
|
|
atom_test:1
|
|
hybridization:SP2
|
|
aromaticity:NON_AROMATIC
|
|
ring: PLANAR(5)
|
|
end_test
|
|
end_type
|
|
|
|
type: s'
|
|
! S in thioketone group
|
|
template: (>S(=*))
|
|
atom_test:2
|
|
allowed_elements: C,P,N,O
|
|
end_test
|
|
end_type
|
|
|
|
type: sf
|
|
! S in sulfonate group
|
|
template: (>S(=O)(=O)(-*)(-*))
|
|
atom_test:1
|
|
hybridization:SP3
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test:4
|
|
disallowed_elements:S
|
|
end_test
|
|
atom_test:5
|
|
disallowed_elements:S
|
|
end_test
|
|
end_type
|
|
|
|
type: s-
|
|
! partial double sulfur bonded to something then bonded to
|
|
! another partial double oxygen or sulfur
|
|
template: [>S(:*[:*])]
|
|
atom_test:2
|
|
allowed_elements: C,P
|
|
end_test
|
|
atom_test:3
|
|
allowed_elements: O,S
|
|
end_test
|
|
end_type
|
|
|
|
type: s-
|
|
! double bonded sulfur in charged phosphate PSS- or PSO-
|
|
template: [>S(=*[-*])]
|
|
atom_test:2
|
|
allowed_elements: C,P
|
|
end_test
|
|
atom_test:3
|
|
allowed_elements: O,S
|
|
end_test
|
|
end_type
|
|
|
|
type: s-
|
|
! single bonded sulfur in charged phosfur PSS- or PSO-
|
|
template: [>S[-*[=*]]]
|
|
atom_test:2
|
|
allowed_elements: C,P
|
|
end_test
|
|
atom_test:3
|
|
allowed_elements: O,S
|
|
end_test
|
|
end_type
|
|
|
|
|
|
type: ca+
|
|
! calcium ion
|
|
template: [>Ca]
|
|
end_type
|
|
|
|
type: f
|
|
!fluorine atom
|
|
template: (>F (-*))
|
|
end_type
|
|
|
|
type: cl
|
|
!chlorine atom
|
|
template: (>Cl (-*))
|
|
end_type
|
|
|
|
type: Cl
|
|
!chlorine ion
|
|
template: [>Cl]
|
|
end_type
|
|
|
|
type: br
|
|
!bromine atom
|
|
template: (>Br (-*))
|
|
end_type
|
|
|
|
type: Br
|
|
!bromine ion
|
|
template: [>Br]
|
|
end_type
|
|
|
|
type: i
|
|
!iodine atom
|
|
template: (>I (-*))
|
|
end_type
|
|
|
|
type: p
|
|
! General phosphorous atom
|
|
template: (>P)
|
|
end_type
|
|
|
|
type: p=
|
|
! phopsphorous with double bond
|
|
template: [>P (=*) (-*) (-*) (-*)]
|
|
atom_test: 2
|
|
allowed_elements: O,S,N
|
|
end_test
|
|
end_type
|
|
|
|
type: p=
|
|
! phopsphorous with double bond
|
|
template: [>P (:N) (:N) (-*) (-*)]
|
|
end_type
|
|
|
|
type: si
|
|
!silicon atom
|
|
template: (>Si)
|
|
end_type
|
|
|
|
!
|
|
! THE FOLLOWING DEFINITIONS ARE TAKEN FROM PFF
|
|
!
|
|
|
|
type: o_1
|
|
! carbonyl oxygen
|
|
template: (>O (=C(~*)(~*)) )
|
|
end_type
|
|
|
|
type: oo
|
|
! carbonyl oxygen of carbonates
|
|
template: (>O (=C(-O)(-O)) )
|
|
end_type
|
|
|
|
type: o_2
|
|
! ester oxygen
|
|
template: (>O (-C (=O)) (-*))
|
|
atom_test: 4
|
|
allowed_elements: C, H
|
|
end_test
|
|
end_type
|
|
|
|
type: oz
|
|
! ester oxygen in carbonate
|
|
template: (>O (-C (=O)(-O)) (-*))
|
|
atom_test: 5
|
|
allowed_elements: C, H
|
|
end_test
|
|
end_type
|
|
|
|
type:c_0
|
|
! aldehydes and ketones carbonyl carbon
|
|
template: (>C (=O) (-*) (-*))
|
|
atom_test:1
|
|
hybridization:sp2
|
|
end_test
|
|
atom_test:2
|
|
allowed_elements: O,S
|
|
end_test
|
|
atom_test:3
|
|
allowed_elements: C, H
|
|
end_test
|
|
atom_test:4
|
|
allowed_elements: C, H
|
|
end_test
|
|
end_type
|
|
|
|
type:c_1
|
|
! amide, acid and ester carbonyl carbon
|
|
template: (>C (=O) (~*) (~*))
|
|
atom_test:1
|
|
hybridization:sp2
|
|
end_test
|
|
atom_test:2
|
|
allowed_elements: O,S
|
|
end_test
|
|
atom_test:3
|
|
allowed_elements: C, H
|
|
end_test
|
|
atom_test:4
|
|
allowed_elements: O, N
|
|
end_test
|
|
end_type
|
|
|
|
type:c_2
|
|
! carbamate, urea carbonyl carbon
|
|
template: (>C (=O) (~*) (~*))
|
|
atom_test:1
|
|
hybridization:sp2
|
|
end_test
|
|
atom_test:3
|
|
allowed_elements: N
|
|
end_test
|
|
atom_test:4
|
|
allowed_elements: O, N
|
|
end_test
|
|
end_type
|
|
|
|
type:cz
|
|
! carbonate carbonyl carbon
|
|
template: (>C (=O) (-O) (-O))
|
|
atom_test:1
|
|
hybridization:sp2
|
|
end_test
|
|
end_type
|
|
|
|
type: n_2
|
|
! nitrogen in carbamate
|
|
template: (>N (~C(=O)) (-H) (~*))
|
|
atom_test: 1
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test: 5
|
|
allowed_elements: C, H
|
|
end_test
|
|
end_type
|
|
|
|
type:hn2
|
|
! hydrogen bonded to nitrogen
|
|
template: (>H (-N (~C(=O)(-*)) (~*)))
|
|
atom_test: 2
|
|
aromaticity:NON_AROMATIC
|
|
end_test
|
|
atom_test: 5
|
|
allowed_elements: O, N, C, H
|
|
end_test
|
|
atom_test: 6
|
|
allowed_elements: C, H
|
|
end_test
|
|
end_type
|
|
|
|
type:ho2
|
|
! hydroxyl hydrogen
|
|
template: (>H (-O (-C(=O)) ) )
|
|
end_type
|
|
|
|
type: osi
|
|
! oxygen in siloxane
|
|
template: (>O (-Si) (-*) )
|
|
atom_test: 3
|
|
allowed_elements: Si, H
|
|
end_test
|
|
end_type
|
|
|
|
type: sio
|
|
! siloxane silicon
|
|
template: (>SI (-O) (-*) (-*) (-*) )
|
|
atom_test: 3
|
|
allowed_elements: O, C, H
|
|
end_test
|
|
atom_test: 4
|
|
allowed_elements: O, C, H
|
|
end_test
|
|
atom_test: 5
|
|
allowed_elements: O, C, H
|
|
end_test
|
|
end_type
|
|
|
|
type: he
|
|
! Helium
|
|
template: (>He)
|
|
end_type
|
|
|
|
type: ne
|
|
! Neon atom
|
|
template: (>Ne)
|
|
end_type
|
|
|
|
type: ar
|
|
! Argon atom
|
|
template: (>Ar)
|
|
end_type
|
|
|
|
type: kr
|
|
! Krypton atom
|
|
template: (>Kr)
|
|
end_type
|
|
|
|
type: xe
|
|
! Xenon atom
|
|
template: (>Xe)
|
|
end_type
|
|
|
|
type: sz
|
|
! silicon atom in zeolites (SiO4 tetrahedron)
|
|
template: (>Si(-O)(-O)(-O)(-O))
|
|
end_type
|
|
|
|
type: az
|
|
! aluminium atom in zeolites (AlO4 tetrahedron)
|
|
template: (>Al(-O)(-O)(-O)(-O))
|
|
end_type
|
|
|
|
type:ob
|
|
! oxygen in a Al-(OH)-Si bridge
|
|
template: [>O(-Al)(-Si)(-H)]
|
|
end_type
|
|
|
|
type:oas
|
|
! oxygen in an Al-O-Si bridge
|
|
template: [>O(-Al)(-Si)]
|
|
end_type
|
|
|
|
type:oss
|
|
! oxygen in a Si-O-Si bridge
|
|
template: [>O(-Si(-O)(-O)(-O))(-Si(-O)(-O)(-O))]
|
|
end_type
|
|
|
|
type:osh
|
|
! oxygen in silanol groups
|
|
template: [>O(-Si(-O)(-O)(-O))(-H)]
|
|
end_type
|
|
|
|
type:oah
|
|
! oxygen in AlOH groups
|
|
template: [>O(-Al)(-H)]
|
|
end_type
|
|
|
|
type:hos
|
|
! hydrogen in silanol groups
|
|
template: (>H [-O(-Si(-O)(-O)(-O))] )
|
|
end_type
|
|
|
|
type:hoa
|
|
! hydrogen in AlOH groups
|
|
template: (>H [-O(-Al)] )
|
|
end_type
|
|
|
|
type:hb
|
|
! hydrogen in bridging OH groups
|
|
template: (>H [-O(-Al)(-Si)] )
|
|
end_type
|
|
|
|
type: Al
|
|
! Aluminium Metal
|
|
template: (>Al)
|
|
end_type
|
|
|
|
type: Na
|
|
! Sodium Metal
|
|
template: (>Na)
|
|
end_type
|
|
|
|
type: Pt
|
|
! Platinum Metal
|
|
template: (>Pt)
|
|
end_type
|
|
|
|
type: Pd
|
|
! Palladium Metal
|
|
template: (>Pd)
|
|
end_type
|
|
|
|
type: Au
|
|
! Gold Metal
|
|
template: (>Au)
|
|
end_type
|
|
|
|
type: Ag
|
|
! Silver Metal
|
|
template: (>Ag)
|
|
end_type
|
|
|
|
type: Sn
|
|
! Tin Metal
|
|
template: (>Sn)
|
|
end_type
|
|
|
|
type: K
|
|
! Potassium Metal
|
|
template: (>K)
|
|
end_type
|
|
|
|
type: Li
|
|
! Lithium Metal
|
|
template: (>Li)
|
|
end_type
|
|
|
|
type: Mo
|
|
! Molybdenum Metal
|
|
template: (>Mo)
|
|
end_type
|
|
|
|
type: Fe
|
|
! Iron Metal
|
|
template: (>Fe)
|
|
end_type
|
|
|
|
type: W
|
|
! Tungsten Metal
|
|
template: (>W)
|
|
end_type
|
|
|
|
type: Ni
|
|
! Nickel Metal
|
|
template: (>Ni)
|
|
end_type
|
|
|
|
type: Cr
|
|
! Chromium Metal
|
|
template: (>Cr)
|
|
end_type
|
|
|
|
type: Cu
|
|
! Copper Metal
|
|
template: (>Cu)
|
|
end_type
|
|
|
|
type: Pb
|
|
! Lead Metal
|
|
template: (>Pb)
|
|
end_type
|
|
|
|
|
|
precedence:
|
|
(?
|
|
(h(hsi)(hc))
|
|
(hs)
|
|
(hp)
|
|
(h*(ho(hw)(ho2)(hos)(hoa)(hb))(hn(hn2)(h+(hi))(hi)))
|
|
(cp(c5(ci(c_0)(c_1)(c_2)(cz))(c_0)(c_1)(c_2)(cz)(cs(c_0)(c_1)(c_2)(cz)))(c_0)(c_1)(c_2)(cz)(c-))
|
|
(c=2(ci(c_0)(c_1)(c_2)(cz))(c_0)(c_1)(c_2)(cz)(c-) (cr(c+))) (cr(c+)) (c+)
|
|
(c=2(c=1(c=(cr(c+))))(c=(cr(c+)))(cr(c+)))
|
|
(c_0)(c_1)(c_2)(cz)(c-)(ct)(ci)
|
|
(c(c1(c_a(c3m(c3h))(c4m(c3m)(c4h(c3h))))(co(coh))(c3m(c3h))(c4m(c3m)(c4h(c3h)))))
|
|
(c(c2(c_a(cg(c3m(c3h))(c4m(c3m)(c4h(c3h)))))(co(coh))(c3m(c3h))(c4m(c3m)(c4h(c3h)))))
|
|
(c(c3)(c_a(c3m(c3h))(c4m(c3m)(c4h(c3h))))(co(coh))(c3m(c3h))(c4m(c3m)(c4h(c3h))))
|
|
(o(osi(oss)(osi(osh)))(oas)(oh(o_2(oz))(o*)(osi(ob))(osi(oss)(osh(osi)))(oas)(oah))(oc(oe(o_2(oz)))(o3e)(o4e))(oe(o_2(oz)))(o3e)(o4e)(op)(o=(o-)(o_1(oo)))(o-))(o3e)(o4e)(op)(o=(o-))(o-)(oh(o_2(oz)))
|
|
(na(n+)(n4)(n3m)(n4m)) (n(n3n)(n4n)(nb(n_2)(n3n)(n4n))) (nb(n_2)(n3n)(n4n))
|
|
(np) (nh(ni)(nh+(nho))) (n2) (ni) (nt(nz)) (na(npc)) (npc) (n(npc))
|
|
(n(np(ni))(nh(ni)(nh+(nho)))(ni)(n2)(nb(n_2)(np(ni))(nh(ni)(nh+(nho)))(ni)))
|
|
(n=2(n=1(n=(n1)))(n=(n1))(n1))(n1)
|
|
(n(n_2)(n=2(n=1(n=(n1)))(n=(n1)))(n1))(n1)
|
|
(n=)
|
|
(s(sc(s'(sf))(sp)(s3e)(s4e)(sh(s'(sf))(s3e)(s4e))(s1(s3e)(s4e)))(sh(s'(sf))(s3e)(s4e))(s1(s3e)(s4e))(s'(sf))(sp))
|
|
(p(p=))
|
|
(si(sio(sz)))
|
|
(ca+)
|
|
(f)
|
|
(cl)(Cl)
|
|
(br)(Br)
|
|
(i)
|
|
(he)
|
|
(ne)
|
|
(ar)
|
|
(kr)
|
|
(xe)
|
|
(lp)
|
|
(dw)
|
|
(Al(az))
|
|
(Na)
|
|
(Pt)
|
|
(Pd)
|
|
(Au)
|
|
(Ag)
|
|
(Sn)
|
|
(K)
|
|
(Li)
|
|
(Mo)
|
|
(Fe)
|
|
(W)
|
|
(Ni)
|
|
(Cr)
|
|
(Cu)
|
|
(Pb)
|
|
)
|
|
end_precedence
|
|
|