Functions to prepare the force field XML files from the sources in atomes
Functions to read the force field XML files. More...

#include "global.h"
#include "interface.h"
#include "dlp_field.h"
#include "force_fields.h"
#include <libxml/xmlreader.h>

Include dependency graph for force_fields.c:

Go to the source code of this file.

Data Structures
struct	f_bond

struct	f_angl

Macros
#define	N_FIELDS 21

#define	N_PARAMS

#define	ALL_PARAMS 9

#define	FATS 0

#define	FEQI 1

#define	FBDS 2

#define	FANG 3

#define	FDIH 4

#define	FIMP 5

#define	FINV 6

#define	FNBD 7

#define	FINC 8

#define	USE_ATOMS

Typedefs
typedef struct f_bond	f_bond

typedef struct f_angl	f_angl

Functions
xmlNodePtr	findnode (xmlNodePtr startnode, char *nname)
	find XML node

int	clean_xml_data (xmlDoc *doc, xmlTextReaderPtr reader)
	free XML data

int	get_pdim (int fid, int prop, int col)
	retrieve number of parameters for property in force field database

int	get_fkey (int fid, int prop, int col)
	retrieve key for property in force field database

int	find_atom_id (int print, char *keyw)
	find atom id in force field database

gchar *	find_atom_key (int fid, int prop, char *keyw)
	retrieve property key in force field database for atom

int	find_atom_z (char *keyw)
	find atom Z

void	print_object_dim_and_key_tables (int fid)
	print tables dimensions and keys to file

void	set_data (int pid, int obj, int oid, int faid)
	save retrieved force field data

int	get_z (int faid)
	get field atom Z

int	get_atoms (int z)
	retrieve all field atom(s) with matching Z

int	get_bond (int faid, int bid)
	retrieve all bonding parameter(s) for this field atom

int	get_angle (int faid, int aid)
	retrieve all angle parameter(s) for this field atom

int	get_apex (int faid, int aid)
	retrieve all angle apex parameter(s) for this field atom

int	get_torsion (int faid, int tid, int a, int b)
	retrieve all torsion parameter(s) for this field atom

int	get_improper (int faid, int a, int b)
	retrieve all improper parameter(s) for this field atom

int	get_vdw (int faid)
	retrieve all VdW parameter(s) for this field atom

void	field_has_element (int aid)
	retrieve force field parameters for this atom

void	print_atom_table (int fid)
	print force field atom data to file

gboolean	not_done (int eid, int a, int b)
	was this case already considered ?

void	print_this_bond (int eid, int h, int fid, int inum, char at_a, char at_b, char **the_bond)
	print this bond to file

void	print_bond_table (int fid, int inum)
	print force field bond table to file

gboolean	not_done_an (int eid, int a, int b, int c)
	was this case already considered ?

void	print_this_angle (int eid, int h, int fid, int inum, int ub, char at_a, char at_b, char at_c, char *the_angle)
	print this angle to file

void	print_angle_table (int fid, int inum)
	print angle(s) table to file

void	print_dihedral_table (int fid, int inum)
	print dihedral(s) table to file

void	print_improper_table (int fid, int inum)
	print improper(s) table to file

void	print_inversion_table (int fid, int inum)
	print inversion(s) table to file

void	print_vdw_table (int fid, int inum)
	print VdW table to file

int	field_find_atoms ()
	retrieve matching atom from force field data base

gboolean	is_a_match (int *data, int num, int val[4])
	is this a match ?

void	find_object_ijkl (int hid, int foid, int oid, int sa, int za, int sb, int zb, int sc, int zc, int sd, int zd)
	retrieve parameter from force field database

void	field_find_bonds ()
	retrieve available bond parameters in force field database

void	field_find_angles ()
	retrieve available angle parameters in force field database

void	field_find_dihedrals (int id)
	retrieve available dihedral parameters in force field database

void	field_find_vdw ()
	retrieve available VdW parameters in force field database

float	get_force_field_atom_mass (int sp, int num)
	get force field atomic mass

void	clean_this_field_data (xmlDoc *doc, xmlTextReaderPtr reader)
	free force field XML file data

gchar *	open_field_file (int field)
	open force field XML file

G_MODULE_EXPORT void	setup_this_force_field (int id)
	setup force field parameters

Variables
char *	field_keyw [N_FIELDS]

char *	field_ffl [N_FIELDS]

char *	field_name [N_FIELDS]

char *	field_acro [N_FIELDS]

char ***	field_atoms

char ***	field_equi [2]

char ***	field_bonds [3]

char ***	field_angles [2]

char ***	field_dihedrals [2]

char ***	field_inversions

char ***	field_impropers

char ***	field_vdw

int *	field_objects

int *	field_dim

gboolean	is_99

int *	atoms_id

int **	atoms_id_list

int **	extraz_id

FILE *	fp

gchar *	ffo_file [21]

gchar *	prop_name [11]

gchar *	table_name [11] = {"qbonds", "sbonds", "mbonds", "qangles", "sangles", "dih", "tor", "inv", "imp", "vdw", "bdi"}

int	ffdim [14][2] = {{1, 0}, {1, 1}, {1, 1}, {2, 2}, {2, 4}, {2, 3}, {3, 2}, {3, 4}, {4, 3}, {4, 4}, {4, 2}, {4, 3}, {1, 2}, {2, 0}}

int	ffpot [N_FIELDS][10]

field_object_match **	all_data [10]

field_object_match *	om_tmp

f_bond *	the_bonds [2]

f_bond *	tmpbd

f_angl *	the_angles [2]

f_angl *	tmpan

field_object_match *	field_objects_id [6] = {NULL, NULL, NULL, NULL, NULL, NULL}

field_object_match *	tmp_obj_id

char ***	ff_atoms

field_data *	ff_bonds [3]

field_data *	ff_angles [2]

field_data *	ff_dih [2]

field_data *	ff_imp

field_data *	ff_inv

field_data *	ff_vdw

int	ff_unit

int *	ff_objects

int *	ff_dim

int *	ff_info

int *	ff_key

int	is_extra

gchar *	filetoread

Detailed Description

Functions to prepare the force field XML files from the sources in atomes
Functions to read the force field XML files.

Author: Sébastien Le Roux sebas.nosp@m.tien.nosp@m..lero.nosp@m.ux@i.nosp@m.pcms..nosp@m.unis.nosp@m.tra.f.nosp@m.r

Definition in file force_fields.c.

Macro Definition Documentation

◆ ALL_PARAMS

#define ALL_PARAMS 9

Definition at line 95 of file force_fields.c.

◆ FANG

#define FANG 3

Definition at line 102 of file force_fields.c.

◆ FATS

#define FATS 0

Definition at line 99 of file force_fields.c.

◆ FBDS

#define FBDS 2

Definition at line 101 of file force_fields.c.

◆ FDIH

#define FDIH 4

Definition at line 103 of file force_fields.c.

◆ FEQI

#define FEQI 1

Definition at line 100 of file force_fields.c.

◆ FIMP

#define FIMP 5

Definition at line 104 of file force_fields.c.

◆ FINC

#define FINC 8

Definition at line 107 of file force_fields.c.

◆ FINV

#define FINV 6

Definition at line 105 of file force_fields.c.

◆ FNBD

#define FNBD 7

Definition at line 106 of file force_fields.c.

◆ N_FIELDS

#define N_FIELDS 21

Definition at line 93 of file force_fields.c.

◆ N_PARAMS

#define N_PARAMS

Definition at line 94 of file force_fields.c.

◆ USE_ATOMS

#define USE_ATOMS

Definition at line 109 of file force_fields.c.

Typedef Documentation

◆ f_angl

typedef struct f_angl f_angl

Definition at line 1302 of file force_fields.c.

◆ f_bond

typedef struct f_bond f_bond

Definition at line 1062 of file force_fields.c.

Function Documentation

◆ clean_this_field_data()

void clean_this_field_data	(	xmlDoc *	doc,
		xmlTextReaderPtr	reader )

free force field XML file data

Parameters

doc	the xmlDoc pointer to free
reader	the XML reader to free

Definition at line 2314 of file force_fields.c.

◆ clean_xml_data()

int clean_xml_data	(	xmlDoc *	doc,
		xmlTextReaderPtr	reader )

extern

free XML data

Parameters

doc	the XML doc pointer to free
reader	the XML reader to free

Definition at line 322 of file w_library.c.

◆ field_find_angles()

void field_find_angles ( )

retrieve available angle parameters in force field database

Definition at line 2173 of file force_fields.c.

◆ field_find_atoms()

int field_find_atoms ( )

retrieve matching atom from force field data base

Definition at line 1963 of file force_fields.c.

◆ field_find_bonds()

void field_find_bonds ( )

retrieve available bond parameters in force field database

Definition at line 2139 of file force_fields.c.

◆ field_find_dihedrals()

void field_find_dihedrals ( int id )

retrieve available dihedral parameters in force field database

Parameters

id	0 = dihedral(s), 1 = improper(s), 2 = inversion(s)

Definition at line 2207 of file force_fields.c.

◆ field_find_vdw()

void field_find_vdw ( )

retrieve available VdW parameters in force field database

Definition at line 2247 of file force_fields.c.

◆ field_has_element()

void field_has_element ( int aid )

retrieve force field parameters for this atom

Parameters

aid	the target atom id

Definition at line 1013 of file force_fields.c.

◆ find_atom_id()

int find_atom_id	(	int	print,
		char *	keyw )

find atom id in force field database

Parameters

print	print debug information ?
keyw	the key entry for atom in the force field database

Definition at line 612 of file force_fields.c.

◆ find_atom_key()

gchar * find_atom_key	(	int	fid,
		int	prop,
		char *	keyw )

retrieve property key in force field database for atom

Parameters

fid	the force field id
prop	the type of property
keyw	the key entry for atom in the force field database

Definition at line 636 of file force_fields.c.

◆ find_atom_z()

int find_atom_z ( char * keyw )

find atom Z

Parameters

keyw	the element name

Definition at line 677 of file force_fields.c.

◆ find_object_ijkl()

void find_object_ijkl	(	int	hid,
		int	foid,
		int	oid,
		int	sa,
		int	za,
		int	sb,
		int	zb,
		int	sc,
		int	zc,
		int	sd,
		int	zd )

retrieve parameter from force field database

Parameters

hid	iteration parameter
foid	force table id
oid	type of structural element
sa	1st chemical species
za	1st Z
sb	2nd chemical species
zb	2nd Z
sc	3rd chemical species, if any
zc	3rd Z, if any
sd	4th chemical species, if any
zd	4th Z, if any

Definition at line 2046 of file force_fields.c.

◆ findnode()

xmlNodePtr findnode	(	xmlNodePtr	startnode,
		char *	nname )

extern

find XML node

Parameters

startnode	Starting node
nname	Node name to find

Definition at line 546 of file read_isaacs.c.

◆ get_angle()

int get_angle	(	int	faid,
		int	aid )

retrieve all angle parameter(s) for this field atom

Parameters

faid	the field atom id
aid	the structural element id

Definition at line 856 of file force_fields.c.

◆ get_apex()

int get_apex	(	int	faid,
		int	aid )

retrieve all angle apex parameter(s) for this field atom

Parameters

faid	the field atom id
aid	the structural element id

Definition at line 882 of file force_fields.c.

◆ get_atoms()

int get_atoms ( int z )

retrieve all field atom(s) with matching Z

Parameters

z	the target Z

Definition at line 807 of file force_fields.c.

◆ get_bond()

int get_bond	(	int	faid,
		int	bid )

retrieve all bonding parameter(s) for this field atom

Parameters

faid	the field atom id
bid	the structural element id

Definition at line 830 of file force_fields.c.

◆ get_fkey()

int get_fkey	(	int	fid,
		int	prop,
		int	col )

retrieve key for property in force field database

Parameters

fid	the force field id
prop	the property id
col	the column id

Definition at line 307 of file force_fields.c.

◆ get_force_field_atom_mass()

float get_force_field_atom_mass	(	int	sp,
		int	num )

get force field atomic mass

Parameters

sp	the target chemical species
num	the atom id

Definition at line 2289 of file force_fields.c.

◆ get_improper()

int get_improper	(	int	faid,
		int	a,
		int	b )

retrieve all improper parameter(s) for this field atom

Parameters

faid	the field atom id
a	1st atom position
b	2nd atom position

Definition at line 937 of file force_fields.c.

◆ get_pdim()

int get_pdim	(	int	fid,
		int	prop,
		int	col )

retrieve number of parameters for property in force field database

Parameters

fid	the force field id
prop	the type of property
col	the column id

Definition at line 289 of file force_fields.c.

◆ get_torsion()

int get_torsion	(	int	faid,
		int	tid,
		int	a,
		int	b )

retrieve all torsion parameter(s) for this field atom

Parameters

faid	the field atom id
tid	the structural element id
a	1st atom position
b	2nd atom position

Definition at line 910 of file force_fields.c.

◆ get_vdw()

int get_vdw ( int faid )

retrieve all VdW parameter(s) for this field atom

Parameters

faid	the field atom id

Definition at line 962 of file force_fields.c.

◆ get_z()

int get_z ( int faid )

get field atom Z

Parameters

faid	the field atom id

Definition at line 790 of file force_fields.c.

◆ is_a_match()

gboolean is_a_match	(	int *	data,
		int	num,
		int	val[4] )

is this a match ?

Parameters

data	the set of parameter(s)
num	the number of parameter
val	the target value(s)

Definition at line 2018 of file force_fields.c.

◆ not_done()

gboolean not_done	(	int	eid,
		int	a,
		int	b )

was this case already considered ?

Parameters

eid	equivalence id (not used for the time being)
a	1st atom id
b	2nd atom id

Definition at line 1084 of file force_fields.c.

◆ not_done_an()

gboolean not_done_an	(	int	eid,
		int	a,
		int	b,
		int	c )

was this case already considered ?

Parameters

eid	equivalence id (not used for the time being)
a	1st atom id
b	2nd atom id
c	3rd atom id

Definition at line 1326 of file force_fields.c.

◆ open_field_file()

gchar * open_field_file ( int field )

open force field XML file

Parameters

field the id of the force field to open

Definition at line 2373 of file force_fields.c.

◆ print_angle_table()

void print_angle_table	(	int	fid,
		int	inum )

print angle(s) table to file

Parameters

fid	the field id
inum	the object id

Definition at line 1433 of file force_fields.c.

◆ print_atom_table()

void print_atom_table ( int fid )

print force field atom data to file

Parameters

fid	the force field id

Definition at line 1045 of file force_fields.c.

◆ print_bond_table()

void print_bond_table	(	int	fid,
		int	inum )

print force field bond table to file

Parameters

fid	the force field id
inum	the structural element id

Definition at line 1185 of file force_fields.c.

◆ print_dihedral_table()

void print_dihedral_table	(	int	fid,
		int	inum )

print dihedral(s) table to file

Parameters

fid	the force field id
inum	the object id

Definition at line 1683 of file force_fields.c.

◆ print_improper_table()

void print_improper_table	(	int	fid,
		int	inum )

print improper(s) table to file

Parameters

fid	the force field id
inum	the object id

Definition at line 1752 of file force_fields.c.

◆ print_inversion_table()

void print_inversion_table	(	int	fid,
		int	inum )

print inversion(s) table to file

Parameters

fid	the force field id
inum	the object id

Definition at line 1815 of file force_fields.c.

◆ print_object_dim_and_key_tables()

void print_object_dim_and_key_tables ( int fid )

print tables dimensions and keys to file

Parameters

fid	the force field id

Definition at line 709 of file force_fields.c.

◆ print_this_angle()

void print_this_angle	(	int	eid,
		int	h,
		int	fid,
		int	inum,
		int	ub,
		char *	at_a,
		char *	at_b,
		char *	at_c,
		char **	the_angle )

print this angle to file

Parameters

eid	equivalence id (not used for the time being)
h	0 = angle, 1 = angle restraints
fid	the force field id
inum	the structural element id
ub	Urey-Bradley parameter for the CHARRM FF, 2 for CHARMM FF, 0 otherwise
at_a	1st atom name
at_b	2nd atom name
at_c	3rd atom name
the_angle	the force field parameter(s) for this angle

Definition at line 1353 of file force_fields.c.

◆ print_this_bond()

void print_this_bond	(	int	eid,
		int	h,
		int	fid,
		int	inum,
		char *	at_a,
		char *	at_b,
		char **	the_bond )

print this bond to file

Parameters

eid	equivalence id (not used for the time being)
h	the bond type
fid	the force field id
inum	the structural element id
at_a	1st atom name
at_b	2nd atom name
the_bond	the force field parameter(s) for this bond

Definition at line 1109 of file force_fields.c.

◆ print_vdw_table()

void print_vdw_table	(	int	fid,
		int	inum )

print VdW table to file

Parameters

fid	the force field id
inum	the object id

Definition at line 1856 of file force_fields.c.

◆ set_data()

void set_data	(	int	pid,
		int	obj,
		int	oid,
		int	faid )

save retrieved force field data

Parameters

pid	the type of structural element
obj	the element id
oid	the parameter id the force field database
faid	the field atom id

Definition at line 766 of file force_fields.c.

◆ setup_this_force_field()

G_MODULE_EXPORT void setup_this_force_field ( int id )

setup force field parameters

Parameters

id	the force field id

Definition at line 2823 of file force_fields.c.

Variable Documentation

◆ all_data

field_object_match** all_data[10]

Definition at line 753 of file force_fields.c.

◆ atoms_id

int* atoms_id

Definition at line 238 of file force_fields.c.

◆ atoms_id_list

int** atoms_id_list

Definition at line 239 of file force_fields.c.

◆ extraz_id

int** extraz_id

Definition at line 240 of file force_fields.c.

◆ ff_angles

field_data* ff_angles[2]

Definition at line 1946 of file force_fields.c.

◆ ff_atoms

char*** ff_atoms

Definition at line 1942 of file force_fields.c.

◆ ff_bonds

field_data* ff_bonds[3]

Definition at line 1945 of file force_fields.c.

◆ ff_dih

field_data* ff_dih[2]

Definition at line 1947 of file force_fields.c.

◆ ff_dim

int* ff_dim

Definition at line 1954 of file force_fields.c.

◆ ff_imp

field_data* ff_imp

Definition at line 1948 of file force_fields.c.

◆ ff_info

int* ff_info

Definition at line 1955 of file force_fields.c.

◆ ff_inv

field_data* ff_inv

Definition at line 1949 of file force_fields.c.

◆ ff_key

int* ff_key

Definition at line 1956 of file force_fields.c.

◆ ff_objects

int* ff_objects

Definition at line 1953 of file force_fields.c.

◆ ff_unit

int ff_unit

Definition at line 1952 of file force_fields.c.

◆ ff_vdw

field_data* ff_vdw

Definition at line 1950 of file force_fields.c.

◆ ffdim

int ffdim[14][2] = {{1, 0}, {1, 1}, {1, 1}, {2, 2}, {2, 4}, {2, 3}, {3, 2}, {3, 4}, {4, 3}, {4, 4}, {4, 2}, {4, 3}, {1, 2}, {2, 0}}

Definition at line 255 of file force_fields.c.

◆ ffo_file

gchar* ffo_file[21]

Initial value:

={"parm94.dat", "parm96.dat", "parm98.dat", "parm99.dat",
                      "par_all22_prot.prm", "par_all22_prot_metals.prm", "par_all35_ethers.prm",
                      "par_all36_carb.prm", "par_all36_cgenff.prm", "par_all36_lipid.prm", "par_all36_na.prm",
                      "par_all36_prot.prm", "par_all36m_prot.prm", "par_all_silicates.prm",
                      "CVFF.frc", "CVFF_aug.frc", "CFF91.frc", "PCFF.frc", "compass.frc",  "par_opls_aam.inp", "par_opls_rna.inp"}

Definition at line 244 of file force_fields.c.

◆ ffpot

int ffpot[N_FIELDS][10]

Initial value:

={{1, 0, 0, 1, 0, 1, 0, 1, 0, 1},
                        {1, 0, 0, 1, 0, 1, 0, 1, 0, 1},
                        {1, 0, 0, 1, 0, 1, 0, 1, 0, 1},
                        {1, 0, 0, 1, 0, 1, 0, 1, 0, 1},
                        {1, 0, 0, -1, 0, 1, 0, 2, 0, -1},
                        {1, 0, 0, -1, 0, 1, 0, 2, 0, -1},
                        {1, 0, 0, -1, 0, 1, 0, 2, 0, -1},
                        {1, 0, 0, -1, 0, 1, 0, 2, 0, -1},
                        {1, 0, 0, -1, 0, 1, 0, 2, 0, -1},
                        {1, 0, 0, -1, 0, 1, 0, 2, 0, -1},
                        {1, 0, 0, -1, 0, 1, 0, 2, 0, -1},
                        {1, 0, 0, -1, 0, 1, 0, 2, 0, -1},
                        {1, 0, 0, -1, 0, 1, 0, 2, 0, -1},
                        {1, 0, 0, -1, 0, 1, 0, 2, 0, -1},
                        {1, 0, 2, 1, 0, 1, -4, 1, 0, 1},
                        {1, 0, 2, 1, 0, 1, -4, 1, 0, 0},
                        {1, 6, 0, 0, 2, 1, -4, 0, 2, 0},
                        {1, 6, 0, 1, 2, 1, -4, 0, 2, 0},
                        {0, 6, 0, 0, 2, 0, -4, 0, 2, -2},
                        {1, 0, 0, 1, 0, 1, 0, 1, 0, 1},
                        {1, 0, 0, 1, 0, 1, 0, 1, 0, 1}}

Definition at line 257 of file force_fields.c.

◆ field_acro

char* field_acro[N_FIELDS]

Initial value:

= {"AMBER 94",
                               "AMBER 96",
                               "AMBER 98",
                               "AMBER 99",
                               "CHARMM 22 Proteins",
                               "CHARMM 22 Proteins and metals",
                               "CHARMM 35 Ethers",
                               "CHARMM 36 Carbohydrates",
                               "CHARMM 36 General",
                               "CHARMM 36 Lipids",
                               "CHARMM 36 Nucleid acids",
                               "CHARMM 36 Proteins",
                               "CHARMM 36 Proteins and metals",
                               "CHARMM Silicates",
                               "CVFF",
                               "CVFF Augmented",
                               "CFF 91",
                               "PCFF",
                               "COMPASS",
                               "OPLS All-atoms for proteins",
                               "OPLS All-atoms for RNA"}

Definition at line 200 of file force_fields.c.

◆ field_angles

char*** field_angles[2]

Definition at line 227 of file force_fields.c.

◆ field_atoms

char*** field_atoms

Definition at line 222 of file force_fields.c.

◆ field_bonds

char*** field_bonds[3]

Definition at line 225 of file force_fields.c.

◆ field_dihedrals

char*** field_dihedrals[2]

Definition at line 228 of file force_fields.c.

◆ field_dim

int* field_dim

Definition at line 234 of file force_fields.c.

◆ field_equi

char*** field_equi[2]

Definition at line 223 of file force_fields.c.

◆ field_ffl

char* field_ffl[N_FIELDS]

Initial value:

= {"amber94",
                              "amber96",
                              "amber98",
                              "amber99",
                              "charmm-prot_22",
                              "charmm-prot_metals_22",
                              "charmm-ethers_35",
                              "charmm-carb_36",
                              "charmm-cgenff_36",
                              "charmm-lipid_36",
                              "charmm-na_36",
                              "charmm-prot_36",
                              "charmm-prot_metals_36",
                              "charmm-silicates",
                              "cvff",
                              "cvff_aug",
                              "cff91",
                              "pcff",
                              "compass",
                              "oplsaap",
                              "oplsaar"}

Definition at line 156 of file force_fields.c.

◆ field_impropers

char*** field_impropers

Definition at line 230 of file force_fields.c.

◆ field_inversions

char*** field_inversions

Definition at line 229 of file force_fields.c.

◆ field_keyw

char* field_keyw[N_FIELDS]

Initial value:

= {"amber94",
                               "amber96",
                               "amber98",
                               "amber99",
                               "prot_22",
                               "prot_metals_22",
                               "ethers_35",
                               "carb_36",
                               "cgenff_36",
                               "lipid_36",
                               "na_36",
                               "prot_36",
                               "prot_metals_36",
                               "silicates",
                               "CVFF",
                               "CVFF_Aug",
                               "CFF91",
                               "PCFF",
                               "Compass",
                               "OPLSAAP",
                               "OPLSAAR"}

Definition at line 134 of file force_fields.c.

◆ field_name

char* field_name[N_FIELDS]

Initial value:

= {"Assisted Model Building with Energy Refinement 94",
                               "Assisted Model Building with Energy Refinement 96",
                               "Assisted Model Building with Energy Refinement 98",
                               "Assisted Model Building with Energy Refinement 99",
                               "Chemistry at HARvard Macromolecular Mechanics 22 Proteins",
                               "Chemistry at HARvard Macromolecular Mechanics 22 Proteins and metals",
                               "Chemistry at HARvard Macromolecular Mechanics 35 Ethers",
                               "Chemistry at HARvard Macromolecular Mechanics 36 Carbohydrates",
                               "Chemistry at HARvard Macromolecular Mechanics 36 General",
                               "Chemistry at HARvard Macromolecular Mechanics 36 Lipids",
                               "Chemistry at HARvard Macromolecular Mechanics 36 Nucleid acids",
                               "Chemistry at HARvard Macromolecular Mechanics 36 Proteins",
                               "Chemistry at HARvard Macromolecular Mechanics 36 proteins and metals",
                               "Chemistry at HARvard Macromolecular Mechanics Silicates",
                               "Consistent Valence Force Field",
                               "Consistent Valence Force Field Augmented",
                               "Consistent Force Field 91",
                               "Polymer Consistent Force Field",
                               "Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies",
                               "Optimized Potentials for Liquid Simulation All-atoms for Proteins",
                               "Optimized Potentials for Liquid Simulation All-atoms for Proteins, Nucleosides, and Nucleotides"}

Definition at line 178 of file force_fields.c.

◆ field_objects

int* field_objects

Definition at line 233 of file force_fields.c.

◆ field_objects_id

field_object_match* field_objects_id[6] = {NULL, NULL, NULL, NULL, NULL, NULL}

Definition at line 1939 of file force_fields.c.

◆ field_vdw

char*** field_vdw

Definition at line 231 of file force_fields.c.

◆ filetoread

gchar* filetoread

Definition at line 2304 of file force_fields.c.

◆ fp

FILE* fp

Definition at line 242 of file force_fields.c.

◆ is_99

gboolean is_99

Definition at line 236 of file force_fields.c.

◆ is_extra

int is_extra

Definition at line 2007 of file force_fields.c.

◆ om_tmp

field_object_match* om_tmp

Definition at line 754 of file force_fields.c.

◆ prop_name

gchar* prop_name[11]

Initial value:

= {"Quadratic bonds", "Quartic bonds", "Morse bonds", "Quadratic angles", "Quartic angles",

"Dihedrals", "Torsions 3", "Inversions", "Impropers", "Non-bonded", "Bond increments"}

Definition at line 250 of file force_fields.c.

◆ table_name

gchar* table_name[11] = {"qbonds", "sbonds", "mbonds", "qangles", "sangles", "dih", "tor", "inv", "imp", "vdw", "bdi"}

Definition at line 253 of file force_fields.c.

◆ the_angles

f_angl* the_angles[2]

Definition at line 1313 of file force_fields.c.

◆ the_bonds

f_bond* the_bonds[2]

Definition at line 1072 of file force_fields.c.

◆ tmp_obj_id

field_object_match* tmp_obj_id

Definition at line 1940 of file force_fields.c.

◆ tmpan

f_angl* tmpan

Definition at line 1314 of file force_fields.c.

◆ tmpbd

f_bond* tmpbd

Definition at line 1073 of file force_fields.c.

Data Structures

Macros

Typedefs

Functions

Variables

Detailed Description

Macro Definition Documentation

◆ ALL_PARAMS

◆ FANG

◆ FATS

◆ FBDS

◆ FDIH

◆ FEQI

◆ FIMP

◆ FINC

◆ FINV

◆ FNBD

◆ N_FIELDS

◆ N_PARAMS

◆ USE_ATOMS

Typedef Documentation

◆ f_angl

◆ f_bond

Function Documentation

◆ clean_this_field_data()

◆ clean_xml_data()

◆ field_find_angles()

◆ field_find_atoms()

◆ field_find_bonds()

◆ field_find_dihedrals()

◆ field_find_vdw()

◆ field_has_element()

◆ find_atom_id()

◆ find_atom_key()

◆ find_atom_z()

◆ find_object_ijkl()

◆ findnode()

◆ get_angle()

◆ get_apex()

◆ get_atoms()

◆ get_bond()

◆ get_fkey()

◆ get_force_field_atom_mass()

◆ get_improper()

◆ get_pdim()

◆ get_torsion()

◆ get_vdw()

◆ get_z()

◆ is_a_match()

◆ not_done()

◆ not_done_an()

◆ open_field_file()

◆ print_angle_table()

◆ print_atom_table()

◆ print_bond_table()

◆ print_dihedral_table()

◆ print_improper_table()

◆ print_inversion_table()

◆ print_object_dim_and_key_tables()

◆ print_this_angle()

◆ print_this_bond()

◆ print_vdw_table()

◆ set_data()

◆ setup_this_force_field()

Variable Documentation

◆ all_data

◆ atoms_id

◆ atoms_id_list

◆ extraz_id

◆ ff_angles

◆ ff_atoms

◆ ff_bonds

◆ ff_dih

◆ ff_dim

◆ ff_imp

◆ ff_info

◆ ff_inv

◆ ff_key

◆ ff_objects

◆ ff_unit