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mm_mapping_library.F
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1!--------------------------------------------------------------------------------------------------!
2! CP2K: A general program to perform molecular dynamics simulations !
3! Copyright 2000-2025 CP2K developers group <https://cp2k.org> !
4! !
5! SPDX-License-Identifier: GPL-2.0-or-later !
6!--------------------------------------------------------------------------------------------------!
7
8! **************************************************************************************************
9!> \brief Contains the mapping ATOM_KIND -> ELEMENT for the most
10!> common cases in CHARMM and AMBER
11!> This should avoid in most cases the need to provide the element
12!> column in the PDB if in the atom_name column of the PDB is provided
13!> instead the atom kind
14!> \par History
15!> 10.2006 created [tlaino]
16!> \author Teodoro Laino
17! **************************************************************************************************
18MODULE mm_mapping_library
19
20 USE kinds, ONLY: default_string_length
21#include "./base/base_uses.f90"
22
23 IMPLICIT NONE
24 PRIVATE
25 LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .true.
26 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'mm_mapping_library'
27
28! **************************************************************************************************
29 TYPE ff_map_type
30 CHARACTER(LEN=default_string_length), DIMENSION(:), POINTER :: kind => null()
31 CHARACTER(LEN=default_string_length), DIMENSION(:), POINTER :: element => null()
32 END TYPE ff_map_type
33
34 TYPE(ff_map_type), POINTER, PUBLIC :: amber_map, &
35 charmm_map, &
36 gromos_map
37 PUBLIC :: create_ff_map, &
38 destroy_ff_map
39CONTAINS
40
41! **************************************************************************************************
42!> \brief Initialize arrays for mapping KINDS <-> ELEMENTS
43!> for major elements in AMBER and CHARMM
44!> \param ff_type ...
45!> \par History
46!> 10.2006 created [tlaino]
47!> \author Teodoro Laino
48! **************************************************************************************************
49 SUBROUTINE create_ff_map(ff_type)
50 CHARACTER(LEN=*), INTENT(IN) :: ff_type
51
52 INTEGER, PARAMETER :: amb_imax = 66, chm_imax = 108, &
53 grm_imax = 22
54
55 SELECT CASE (ff_type)
56 CASE ("AMBER")
57 ALLOCATE (amber_map)
58 ! allocate substructures
59 ALLOCATE (amber_map%kind(amb_imax))
60 ALLOCATE (amber_map%element(amb_imax))
61
62 amber_map%kind = (/ &
63 "BR", "C ", "CA", "CB", "CC", "CD", "CI", "CK", "CP", "CM", &
64 "CS", "CN", "CQ", "CR", "CT", "CV", "CW", "C*", "CX", "CY", &
65 "CZ", "CO", "TG", "2C", "3C", "C0", "F ", "H ", "HC", "HA", &
66 "HO", "HS", "HW", "HP", "HZ", "I ", "IM", "IP", "IB", "MG", &
67 "N ", "NA", "NB", "NC", "N*", "NT", "NY", "ND", "NL", "TN", &
68 "OA", "O ", "OW", "OH", "OD", "OS", "OP", "P ", "S ", "SH", &
69 "CU", "FE", "Li", "K ", "Rb", "Cs"/)
70 amber_map%element = (/ &
71 "Br", "C ", "C ", "C ", "C ", "C ", "C ", "C ", "C ", "C ", &
72 "C ", "C ", "C ", "C ", "C ", "C ", "C ", "C ", "C ", "C ", &
73 "C ", "C ", "C ", "C ", "C ", "Ca", "F ", "H ", "H ", "H ", &
74 "H ", "H ", "H ", "H ", "H ", "I ", "Cl", "Na", "Na", "Mg", &
75 "N ", "N ", "N ", "N ", "N ", "N ", "N ", "N ", "N ", "N ", &
76 "O ", "O ", "O ", "O ", "O ", "O ", "O ", "P ", "S ", "S ", &
77 "Cu", "Fe", "Li", "K ", "Rb", "Cs"/)
78
79 CASE ("CHARMM")
80 ALLOCATE (charmm_map)
81 ! allocate substructures
82 ALLOCATE (charmm_map%kind(chm_imax))
83 ALLOCATE (charmm_map%element(chm_imax))
84
85 charmm_map%kind = (/ &
86 "CA ", "CAL ", "C ", "CC ", "CD ", "CE ", "CEL ", "CES ", "CLA ", "CL ", &
87 "CM ", "CN1A", "CN1T", "CN3A", "CN3B", "CN3C", "CN3D", "CN3T", "CN5G", "CN7B", &
88 "CN7C", "CN7D", "CN8B", "CNA ", "CN ", "CNE ", "CPA ", "CPB ", "CP ", "CPH ", &
89 "CPM ", "CPT ", "CS ", "CT ", "CTL ", "CY ", "DUM ", "FE ", "FNA ", "FN ", &
90 "HA ", "HAL ", "HB ", "HC ", "HCL ", "HE ", "HE ", "HEL ", "H ", "HL ", &
91 "HN3B", "HN3C", "HNE ", "HN ", "HNP ", "HOL ", "HP ", "HR ", "HS ", "HT ", &
92 "MG ", "NC ", "NE ", "NH3L", "NH ", "N ", "NN1C", "NN2B", "NN2C", "NN2G", &
93 "NN2U", "NN3A", "NN3G", "NN3I", "NN ", "NPH ", "NP ", "NR ", "NR ", "NTL ", &
94 "NY ", "O2L ", "OBL ", "OB ", "OCL ", "OC ", "OHL ", "OH ", "OM ", "ON1C", &
95 "ON2b", "ON6B", "ON ", "O ", "OSL ", "OS ", "OT ", "P2 ", "PL ", "POT ", &
96 "P ", "SL ", "SM ", "SOD ", "S ", "SS ", "ZN ", "CN6B"/)
97
98 charmm_map%element = (/ &
99 "C ", "Ca", "C ", "C ", "C ", "C ", "C ", "Cs", "Cl", "C ", &
100 "C ", "C ", "C ", "C ", "C ", "C ", "C ", "C ", "C ", "C ", &
101 "C ", "C ", "C ", "C ", "C ", "C ", "C ", "C ", "C ", "C ", &
102 "C ", "C ", "C ", "C ", "C ", "C ", "H ", "Fe", "F ", "F ", &
103 "H ", "H ", "H ", "H ", "H ", "H ", "He", "H ", "H ", "H ", &
104 "H ", "H ", "H ", "H ", "H ", "H ", "H ", "H ", "H ", "H ", &
105 "Mg", "N ", "Ne", "N ", "N ", "N ", "N ", "N ", "N ", "N ", &
106 "N ", "N ", "N ", "N ", "N ", "N ", "N ", "N ", "N ", "N ", &
107 "N ", "O ", "O ", "O ", "O ", "O ", "O ", "O ", "O ", "O ", &
108 "O ", "O ", "O ", "O ", "O ", "O ", "O ", "P ", "P ", "K ", &
109 "P ", "S ", "S ", "Na", "S ", "S ", "Zn", "C "/)
110
111 CASE ("GROMOS")
112 ALLOCATE (gromos_map)
113 ! allocate substructures
114 ALLOCATE (gromos_map%kind(grm_imax))
115 ALLOCATE (gromos_map%element(grm_imax))
116
117 gromos_map%kind = (/ &
118 "H1 ", "CA ", "HA ", "SD ", "OG ", "CG ", "HD ", "SG ", &
119 "CZ ", "OH ", "C2 ", "H8 ", "O4* ", "O5* ", "PA ", "O1A ", &
120 "MG ", "Na ", "Cl ", "OW ", "HW ", "HW "/)
121
122 gromos_map%element = (/ &
123 "H ", "C ", "H ", "S ", "O ", "C ", "H ", "S ", &
124 "C ", "O ", "C ", "H ", "O ", "O ", "P ", "O ", &
125 "Mg", "Na", "Cl", "O ", "H ", "H "/)
126
127 END SELECT
128
129 END SUBROUTINE create_ff_map
130
131! **************************************************************************************************
132!> \brief Deallocates the arrays used for mapping
133!> \param ff_type ...
134!> \par History
135!> 10.2006 created [tlaino]
136!> \author Teodoro Laino
137! **************************************************************************************************
138 SUBROUTINE destroy_ff_map(ff_type)
139 CHARACTER(LEN=*), INTENT(IN) :: ff_type
140
141 SELECT CASE (ff_type)
142 CASE ("AMBER")
143 ! deallocate substructures
144 DEALLOCATE (amber_map%kind)
145 DEALLOCATE (amber_map%element)
146 ! deallocate main
147 DEALLOCATE (amber_map)
148 CASE ("CHARMM")
149 ! deallocate substructures
150 DEALLOCATE (charmm_map%kind)
151 DEALLOCATE (charmm_map%element)
152 ! deallocate main
153 DEALLOCATE (charmm_map)
154 CASE ("GROMOS")
155 ! deallocate substructures
156 DEALLOCATE (gromos_map%kind)
157 DEALLOCATE (gromos_map%element)
158 ! deallocate main
159 DEALLOCATE (gromos_map)
160 END SELECT
161 END SUBROUTINE destroy_ff_map
162
163END MODULE mm_mapping_library
kinds
Defines the basic variable types.
Definition kinds.F:23
kinds::default_string_length
integer, parameter, public default_string_length
Definition kinds.F:57
mm_mapping_library
Contains the mapping ATOM_KIND -> ELEMENT for the most common cases in CHARMM and AMBER This should a...
Definition mm_mapping_library.F:18
mm_mapping_library::charmm_map
type(ff_map_type), pointer, public charmm_map
Definition mm_mapping_library.F:34
mm_mapping_library::create_ff_map
subroutine, public create_ff_map(ff_type)
Initialize arrays for mapping KINDS <-> ELEMENTS for major elements in AMBER and CHARMM.
Definition mm_mapping_library.F:50
mm_mapping_library::gromos_map
type(ff_map_type), pointer, public gromos_map
Definition mm_mapping_library.F:34
mm_mapping_library::destroy_ff_map
subroutine, public destroy_ff_map(ff_type)
Deallocates the arrays used for mapping.
Definition mm_mapping_library.F:139
mm_mapping_library::amber_map
type(ff_map_type), pointer, public amber_map
Definition mm_mapping_library.F:34