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lammps/tools/msi2lmp/biosym_frc_files/pcff_templates.dat
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pcff_templates.dat
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! mcff_templates
! Template file of potential type assignment templates for the mcff
! forcefield (March-1995)
!
type: ?
! anything
template: (>*)
end_type
type: lp
!lone pair
template: (>L (-*))
end_type
type:c
! generic SP3 carbon
template: (>C)
atom_test:1
hybridization:SP3
end_test
end_type
type: c3
! sp3 carbon with 3 h's 1 heavy
template: (>C(-H)(-H)(-H)(-*))
atom_test:5
disallowed_elements:H
end_test
end_type
type:c2
! sp3 carbon with 2 H's, 2 Heavy's
template:(>C(-H)(-H)(-*)(-*))
atom_test:4
disallowed_elements:H
end_test
atom_test:5
disallowed_elements:H
end_test
end_type
type:co
! sp3 carbon in acetals
template:(>C(-O)(-O)(-*)(-*))
end_type
type:coh
! sp3 carbon in acetals with hydrogen
template:(>C(-O)(-O)(-H)(-*))
end_type
type: c1
! sp3 carbon with 1 H 3 heavies
template: (>C(-H)(-*)(-*)(-*))
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: c3m
! sp3 carbon in 3-membered ring
template: (>C)
atom_test:1
hybridization:SP3
ring:PLANAR(3)
aromaticity:NON_AROMATIC
end_test
end_type
type: c4m
! sp3 carbon in 4-membered ring
template: (>C)
atom_test:1
hybridization:SP3
ring:NON_PLANAR(4)
aromaticity:NON_AROMATIC
end_test
end_type
type: c4m
! sp3 carbon in 4-membered ring
template: (>C)
atom_test:1
hybridization:SP3
ring:PLANAR(4)
aromaticity:NON_AROMATIC
end_test
end_type
type: c3h
! sp3 carbon in 3-membered ring with hydrogens
template: (>C(-H))
atom_test:1
hybridization:SP3
ring:PLANAR(3)
aromaticity:NON_AROMATIC
end_test
end_type
type: c4h
! sp3 carbon in 4-membered ring with hydrogens
template: (>C(-H))
atom_test:1
hybridization:SP3
ring:NON_PLANAR(4)
aromaticity:NON_AROMATIC
end_test
end_type
type: c4h
! sp3 carbon in 4-membered ring
template: (>C(-H))
atom_test:1
hybridization:SP3
ring:PLANAR(4)
aromaticity:NON_AROMATIC
end_test
end_type
type:c_a
!general amino acid alpha carbon (sp3)
template: (>C(-N(-*))(-C[~O])(~*)(~*))
end_type
type: cg
! sp3 alpha carbon in glycine
template: (>C(-H)(-H)(-C[~O])(-N(-H)))
end_type
type: c=2
! non aromatic doubly bonded carbon
template: (>C(=*))
atom_test:1
aromaticity:NON_AROMATIC
end_test
end_type
type: c=
! non aromatic end doubly bonded carbon
template: (>C(=*)(-*)(-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: c=
! non aromatic end doubly bonded carbon
template: (>C(=*)(-N(-*)(-*))(-N(-*)(-*)))
atom_test:1
aromaticity:NON_AROMATIC
end_test
atom_test:2
disallowed_elements:O,S
end_test
end_type
type: c=
! non aromatic end doubly bonded carbon
template: (>C(=*)(-N(-*)(-*))(-C(-*)(-*)(-*)))
atom_test:1
aromaticity:NON_AROMATIC
end_test
atom_test:2
disallowed_elements:O,S
end_test
end_type
type: c=
! non aromatic end doubly bonded carbon
template: (>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
atom_test:4
disallowed_elements:N,C
end_test
end_type
type: c=
! non aromatic end doubly bonded carbon
template: (>C(=*)(-*)(-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
atom_test:4
hybridization:SP3
end_test
end_type
type: c=
! non aromatic end doubly bonded carbon
template: (>C(=*)(-C)(-C))
atom_test:1
aromaticity:NON_AROMATIC
end_test
atom_test:2
disallowed_elements:O,S
end_test
atom_test:3
hybridization:SP3
end_test
atom_test:4
hybridization:SP3
end_test
end_type
type: c=1
! non aromatic, next to end doubly bonded carbon
template: (>C(=C(-*)(-N(-*)(-*)))(-*))
atom_test:1
aromaticity:NON_AROMATIC
end_test
atom_test:3
disallowed_elements:N,C
end_test
end_type
type: c=1
! non aromatic, next to end doubly bonded carbon
template:(>C(=C(-N(-*)(-*))(-N(-*)(-*)))(-*))
atom_test:1
aromaticity:NON_AROMATIC
end_test
end_type
type: c=1
! non aromatic, next to end doubly bonded carbon
template:(>C(=C(-N(-*)(-*))(-C(-*)(-*)(-*)))(-*))
atom_test:1
aromaticity:NON_AROMATIC
end_test
end_type
type: c=1
! non aromatic, next to end doubly bonded carbon
template:(>C(=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: c=1
! non aromatic, next to end doubly bonded carbon
template:(>C(=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: c=1
! non aromatic, next to end doubly bonded carbon
template:(>C(=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: c=1
! non aromatic carbon doubly bonded to an end nitrogen
template: (>C[=N(-N(-*)(-*))](-*))
atom_test:1
aromaticity:NON_AROMATIC
end_test
end_type
type: c=1
! non aromatic carbon doubly bonded to an end nitrogen
template: (>C[=N(-C(-*)(-*)(-*))](-*))
atom_test:1
aromaticity:NON_AROMATIC
end_test
end_type
type: c=1
! non aromatic carbon doubly bonded to an end nitrogen
template: (>C[=N(-*)](-*))
atom_test:1
aromaticity:NON_AROMATIC
end_test
atom_test:3
disallowed_elements:N,C
end_test
end_type
type: c=1
! non aromatic carbon doubly bonded to an end nitrogen
template: (>C(=N(-N(-*)(-*))(-N(-*)(-*)))(-*))
atom_test:1
aromaticity:NON_AROMATIC
end_test
end_type
type: c=1
! non aromatic carbon doubly bonded to an end nitrogen
template: (>C(=N(-C(-*)(-*)(-*))(-C(-*)(-*)(-*)))(-*))
atom_test:1
aromaticity:NON_AROMATIC
end_test
end_type
type: c=1
! non aromatic carbon doubly bonded to an end nitrogen
template: (>C(=N(-C(-*)(-*)(-*))(-N(-*)(-*)))(-*))
atom_test:1
aromaticity:NON_AROMATIC
end_test
end_type
type: c=1
! non aromatic carbon doubly bonded to an end nitrogen
template: (>C(=N(-*)(-*))(-*))
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: c=1
! non aromatic carbon doubly bonded to an end nitrogen
template: (>C(=N(-*)(-N(-*)(-*)))(-*))
atom_test:1
aromaticity:NON_AROMATIC
end_test
atom_test:3
disallowed_elements:N,C
end_test
end_type
type: c=1
! non aromatic carbon doubly bonded to an end nitrogen
template: (>C(=N(-*)(-C(-*)(-*)(-*)))(-*))
atom_test:1
aromaticity:NON_AROMATIC
end_test
atom_test:3
disallowed_elements:N,C
end_test
end_type
type:cp
! SP2 aromatic carbon with partial double bond
template:(>C)
atom_test:1
hybridization: SP2
aromaticity:AROMATIC
end_test
end_type
type:cp
! This is used for aromatic carbons that fail the aromaticity test because
! the current ring checker is to lame to figure on a ring with more than
! seven or eight sides. The NON_AROMATIC test is to eliminate the conflict
! with the above 'cp' definition. This can be removed when the ring checker
! is made more robust.
template: [>C(-*)(:*)(:*)]
atom_test:1
hybridization:SP2
aromaticity:NON_AROMATIC
end_test
end_type
type: c5
! Sp2 aromatic carbon in 5-membered ring
template:(>C)
atom_test:1
hybridization:SP2
aromaticity:AROMATIC
ring:PLANAR(5)
end_test
end_type
type:ci
! sp2 aromatic carbon in charged imidazole ring (His+)
template: (>C(:N(-H)(:C))(:N(-H)(:C)))
atom_test:1
hybridization:SP2
aromaticity:AROMATIC
ring:PLANAR(5)
end_test
atom_test:2
hybridization:SP2
aromaticity:AROMATIC
ring:PLANAR(5)
end_test
atom_test:4
hybridization: SP2
aromaticity:AROMATIC
ring:PLANAR(5)
end_test
atom_test:5
hybridization:SP2
aromaticity:AROMATIC
ring:PLANAR(5)
end_test
atom_test:6
hybridization: SP2
aromaticity:AROMATIC
ring:PLANAR(5)
end_test
atom_test:7
hybridization: SP2
aromaticity:AROMATIC
ring:PLANAR(5)
end_test
end_type
type: ci
! Carbon in charged imidazole ring
template:(>C(=N(-C(=C(-N)))(-H)))
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
end_type
type: ci
! Carbon in charged imidazole ring
template:(>C(-N(-C(=N(-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:6
ring:PLANAR(5)
end_test
end_type
type: ci
! Carbon in charged imidazole ring
template:(>C(=C(-N(-C(=N(-C)(-H))))))
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:6
ring:PLANAR(5)
end_test
end_type
type: cs
! SP2 aromatic carbon in 5 membered ring next to S
template:(>C(~S))
atom_test:1
hybridization:SP2
aromaticity:AROMATIC
ring:PLANAR(5)
end_test
atom_test:2
hybridization:SP2
aromaticity:AROMATIC
ring:PLANAR(5)
end_test
end_type
type: cr
! c in neutral arginine
template: (>C (=N(-*)) (-N(-H)(-H)) (-N(-H)(-H)) )
end_type
type: c+
! c in guanidinium group
template: (>C (=N(-*)(-*)) (-N(-H)(-H)) (-N(-H)(-H)) )
end_type
type: c+
! c in guanidinium group
template: (>C (:N(-*)(-*)) (:N(-H)(-H)) (:N(-H)(-H)) )
end_type
type: c-
! c in charged carboxylate
template: [>C[:O][:O](-*)]
end_type
type: c-
! c in charged carboxylate
! How do we indicate that the second O has nothing bonded to it ?
! what makes it not match COOH ?
template: [>C[=O][-O](-*)]
end_type
type: ct
! sp carbon involved in a triple bond
template: (>C(#*))
end_type
type: na
! sp3 nitrogen in amines
template: (>N (-*)(-*)(-*))
atom_test:1
hybridization:SP3
end_test
end_type
type: n+
! sp3 nitrogen in protonated amines
template: (>N(-H)(-*)(-*)(-*))
atom_test:1
hybridization:SP3
end_test
end_type
type: n4
! sp3 nitrogen with 4 substituents
template: (>N(-*)(-*)(-*)(-*))
atom_test:1
hybridization:SP3
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
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
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