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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 2000-2024 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 ! **************************************************************************************************
18 MODULE 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
31  CHARACTER(LEN=default_string_length), DIMENSION(:), POINTER :: element
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
39 CONTAINS
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 
163 END 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