PDB

Classes
struct	linetype
struct	linefield
struct	queery_set
struct	linedef
struct	charlist
struct	pdb_line_info
struct	pdb_line
Functions
assembly *	load_pdb (char *file_name)
int	howManyMolecules ()
assembly *	getAssembly ()
int	findTotalResidue (int start)
int	endOfMol (linedef *line)
int	isAtom (linedef *line)
int	getResInfo (residue *res, int start)
void	init_struct ()
linetype	get_type (char *)
void	pdb_def ()
void	rwm_line (int)
molecule	load_pdb_from_slurp (fileslurp in)
fileslurp	isolateInputPDB (fileslurp S)
fileslurp	isolateDockedPDB (fileslurp S)
void	init_struct_slurp (fileslurp S)
void	rwm_line_char (char *curLine, int rwmln)
molecule *	getMolecule (void)
void	set_assembly_atom_molbonds_from_PDB_CONECT (assembly *asmbl, linedef *ln, const char *file_name, int nlines)
void	set_assembly_residue_molbonds_from_PDB_LINK (assembly *asmbl, linedef *ln, const char *file_name, int nlines)
fileslurp	get_ensemble_PDB_ATOM_lines (ensemble *E, char isource, int savei, char raltname, int xs)
fileslurp	get_assembly_PDB_ATOM_lines (assembly *A, char isource, int savei, char raltname, int xs)
fileslurp	get_assembly_PDB_CONECT_lines (assembly *A, char isource, int savei)
fileslurp	get_molecule_PDB_CONECT_lines (molecule *m, int savei)
fileslurp	get_atom_PDB_CONECT_lines_assembly (assembly *A, atom *a, int savei)
const char *	get_PDB_line_for_ATOM (atom *a, residue *r, int ai, int ri, int asave, char raltname, int xs)
void	make_ATOM_HETATM (char *pdbline)
fileslurp	get_residue_PDB_ATOM_lines (residue *r, int ri, int ainit, int rsave, int asave, char raltname, int xs)
fileslurp	get_molecule_PDB_ATOM_lines (molecule *mol, int rinit, int ainit, int rsave, int asave, char oneres, char raltname, int xs)
void	outputMolPDB (molecule *, char *)
void	outputAsmblPDB (assembly *, char *)
Variables
FILE *	IN
linedef	line [1]
int	WARN
int	SILENT
char	froot [200]
char	suf [6]
char	sufc [20]
char	ACT
int	INWC
int	DATE
int	UNCUT
int	UNx
int	UNy
int	UNz
int	LASTRES
int	LASTOKX
int	LASTOKY
int	LASTOKZ
float	UNCTOL
float	CRYX
float	CRYY
float	CRYZ
float	LASTX
float	LASTY
float	LASTZ
int	DEBUG
pdb_line	pdb_a [6]
pdb_line	mod_a [6]
pdb_line	umod_a [6]
linedef *	ln
queery_set	QS

---

Function Documentation

int endOfMol

(

linedef *

line

)

Definition at line 555 of file load_pdb.c.

Referenced by findTotalResidue(), getAssembly(), getResInfo(), and howManyMolecules().

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int findTotalResidue

(

int

start

)

Definition at line 505 of file load_pdb.c.

References linefield::c, endOfMol(), linedef::f, INWC, isAtom(), and ln.

Referenced by getAssembly(), and getMolecule().

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fileslurp get_assembly_PDB_ATOM_lines	(	assembly *	A,
		char	isource,
		int	savei,
		char	raltname,
		int	xs
	)

Definition at line 9 of file writePDB.c.

References residue::a, deallocateFileslurp(), get_molecule_PDB_ATOM_lines(), atom::i, residue::i, fileslurp::L, assembly::m, mywhine(), fileslurp::n, residue::na, atom::nalt, atom::ni, residue::ni, assembly::nm, molecule::nr, and molecule::r.

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fileslurp get_assembly_PDB_CONECT_lines	(	assembly *	A,
		char	isource,
		int	savei
	)

fileslurp get_atom_PDB_CONECT_lines_assembly	(	assembly *	A,
		atom *	a,
		int	savei
	)

fileslurp get_ensemble_PDB_ATOM_lines	(	ensemble *	E,
		char	isource,
		int	savei,
		char	raltname,
		int	xs
	)

Definition at line 173 of file writePDB.c.

References residue::a, deallocateFileslurp(), get_molecule_PDB_ATOM_lines(), atom::i, residue::i, fileslurp::L, ensemble::m, mywhine(), fileslurp::n, residue::na, atom::nalt, atom::ni, residue::ni, ensemble::nm, molecule::nr, and molecule::r.

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fileslurp get_molecule_PDB_ATOM_lines	(	molecule *	mol,
		int	rinit,
		int	ainit,
		int	rsave,
		int	asave,
		char	oneres,
		char	raltname,
		int	xs
	)

Definition at line 548 of file writePDB.c.

References residue::a, get_residue_PDB_ATOM_lines(), fileslurp::L, atom::mb, mywhine(), fileslurp::n, residue::n, residue::na, atom::nmb, molecule::nr, molindex::r, molecule::r, and molbond::t.

Referenced by get_assembly_PDB_ATOM_lines(), get_ensemble_PDB_ATOM_lines(), outputAsmblPDB(), and outputMolPDB().

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fileslurp get_molecule_PDB_CONECT_lines	(	molecule *	m,
		int	savei
	)

const char* get_PDB_line_for_ATOM	(	atom *	a,
		residue *	r,
		int	ai,
		int	ri,
		int	asave,
		char	raltname,
		int	xs
	)

Definition at line 339 of file writePDB.c.

References get_char_string(), get_float_string(), atom::i, line, mywhine(), atom::n, and residue::n.

Referenced by get_residue_PDB_ATOM_lines().

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fileslurp get_residue_PDB_ATOM_lines	(	residue *	r,
		int	ri,
		int	ainit,
		int	rsave,
		int	asave,
		char	raltname,
		int	xs
	)

Definition at line 524 of file writePDB.c.

References residue::a, get_PDB_line_for_ATOM(), residue::i, fileslurp::L, fileslurp::n, atom::n, residue::n, and residue::na.

Referenced by get_molecule_PDB_ATOM_lines().

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linetype get_type

(

char *

)

Definition at line 6 of file get_type.c.

References linetype::a, linetype::b, and DEBUG.

Referenced by rwm_line(), and rwm_line_char().

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assembly* getAssembly

(

)

Definition at line 297 of file load_pdb.c.

References assembly::a, linefield::c, molecule::Des, endOfMol(), linedef::f, findTotalResidue(), getResInfo(), howManyMolecules(), initialize_residue(), INWC, isAtom(), ln, atom::m, assembly::m, mywhine(), atom::ni, assembly::nm, molecule::nr, and molecule::r.

Referenced by load_pdb().

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molecule* getMolecule

(

void

)

Definition at line 674 of file load_pdb.c.

References findTotalResidue(), getResInfo(), residue::IC, INWC, isAtom(), and ln.

Referenced by load_pdb_from_slurp().

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int getResInfo	(	residue *	res,
		int	start
	)

Definition at line 595 of file load_pdb.c.

References linefield::c, residue::cID, endOfMol(), linedef::f, residue::IC, INWC, isAtom(), ln, and residue::N.

Referenced by getAssembly(), and getMolecule().

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int howManyMolecules

(

)

Definition at line 274 of file load_pdb.c.

References endOfMol(), INWC, isAtom(), and ln.

Referenced by getAssembly().

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void init_struct

(

)

returns start line for next molecule

Definition at line 11 of file init_struct.c.

References linefield::c, DEBUG, linedef::f, linedef::ignore, IN, INWC, ln, linedef::m, linedef::n, and pdb_def().

Referenced by load_pdb().

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void init_struct_slurp

(

fileslurp

S

)

Definition at line 44 of file init_struct.c.

References linefield::c, linedef::f, linedef::ignore, INWC, ln, linedef::m, linedef::n, fileslurp::n, and pdb_def().

Referenced by load_pdb_from_slurp().

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int isAtom

(

linedef *

line

)

Definition at line 588 of file load_pdb.c.

Referenced by findTotalResidue(), getAssembly(), getMolecule(), getResInfo(), howManyMolecules(), and load_pdb_from_slurp().

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fileslurp isolateDockedPDB

(

fileslurp

S

)

Definition at line 252 of file load_pdb.c.

References fileslurp::L, and fileslurp::n.

Referenced by load_dlg_mol().

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fileslurp isolateInputPDB

(

fileslurp

S

)

Definition at line 222 of file load_pdb.c.

References fileslurp::L, and fileslurp::n.

Referenced by load_dlg_mol().

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assembly* load_pdb

(

char *

file_name

)

Definition at line 5 of file load_pdb.c.

References ACT, CRYX, CRYY, CRYZ, DATE, DEBUG, getAssembly(), IN, init_struct(), INWC, LASTOKX, LASTOKY, LASTOKZ, LASTRES, LASTX, LASTY, LASTZ, ln, myfopen(), rwm_line(), set_assembly_atom_molbonds_from_PDB_CONECT(), set_assembly_molindexes(), SILENT, suf, sufc, UNCTOL, UNCUT, UNx, UNy, UNz, and WARN.

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molecule load_pdb_from_slurp

(

fileslurp

in

)

Definition at line 74 of file load_pdb.c.

References getMolecule(), init_struct_slurp(), INWC, isAtom(), fileslurp::L, ln, fileslurp::n, and rwm_line_char().

Referenced by load_dlg_mol().

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void make_ATOM_HETATM

(

char *

pdbline

)

Definition at line 505 of file writePDB.c.

References mywhine().

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void outputAsmblPDB	(	assembly *	,
		char *
	)

Definition at line 75 of file outputPDB.c.

References deallocateFileslurp(), get_molecule_PDB_ATOM_lines(), coord_3D::i, coord_3D::j, coord_3D::k, fileslurp::L, myfopen(), mywhine(), fileslurp::n, atom::n, atom::N, assembly::nm, molecule::nr, spacing(), and atom::x.

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void outputMolPDB	(	molecule *	,
		char *
	)

Definition at line 8 of file outputPDB.c.

References get_molecule_PDB_ATOM_lines(), coord_3D::i, coord_3D::j, coord_3D::k, fileslurp::L, myfopen(), mywhine(), fileslurp::n, atom::n, atom::N, spacing(), and atom::x.

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void pdb_def

(

)

Definition at line 34 of file pdb_def.c.

References pdb_line::b, pdb_line_info::c, pdb_line_info::f, pdb_a, and pdb_line_info::t.

Referenced by init_struct(), and init_struct_slurp().

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void rwm_line

(

int

)

Definition at line 8 of file rwm_line.c.

References linetype::a, linedef::a, linetype::b, linedef::b, pdb_line::b, linefield::c, pdb_line_info::c, DEBUG, linedef::f, pdb_line_info::f, get_type(), IN, ln, pdb_a, and read_neek().

Referenced by load_pdb().

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void rwm_line_char	(	char *	curLine,
		int	rwmln
	)

Definition at line 107 of file rwm_line.c.

References linetype::a, linedef::a, linetype::b, linedef::b, pdb_line::b, linefield::c, pdb_line_info::c, DEBUG, linedef::f, pdb_line_info::f, get_type(), ln, pdb_a, and read_neek().

Referenced by load_pdb_from_slurp().

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void set_assembly_atom_molbonds_from_PDB_CONECT	(	assembly *	asmbl,
		linedef *	ln,
		const char *	file_name,
		int	nlines
	)

Definition at line 89 of file load_pdb.c.

References assembly::a, find_assembly_top_level_atoms_by_n(), molindex::i, atom::mb, atom::moli, mywhine(), atom::n, assembly::na, atom::nmb, molindex_set::nP, molindex_set::P, molbond::s, and molbond::t.

Referenced by load_pdb().

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void set_assembly_residue_molbonds_from_PDB_LINK	(	assembly *	asmbl,
		linedef *	ln,
		const char *	file_name,
		int	nlines
	)

Definition at line 216 of file load_pdb.c.

References mywhine().

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---

Variable Documentation

char ACT

Definition at line 43 of file load_pdb.h.

Referenced by load_pdb().

float CRYX

Definition at line 47 of file load_pdb.h.

Referenced by load_pdb().

float CRYY

Definition at line 47 of file load_pdb.h.

Referenced by load_pdb().

float CRYZ

Definition at line 47 of file load_pdb.h.

Referenced by load_pdb().

int DATE

Definition at line 44 of file load_pdb.h.

Referenced by load_pdb(), and mytime().

int DEBUG

Definition at line 48 of file load_pdb.h.

Referenced by get_type(), init_struct(), load_pdb(), rwm_line(), and rwm_line_char().

char froot[200]

Definition at line 42 of file load_pdb.h.

FILE* IN

Definition at line 39 of file load_pdb.h.

Referenced by init_struct(), load_pdb(), and rwm_line().

int INWC

Definition at line 44 of file load_pdb.h.

Referenced by findTotalResidue(), getAssembly(), getMolecule(), getResInfo(), howManyMolecules(), init_struct(), init_struct_slurp(), load_pdb(), and load_pdb_from_slurp().

int LASTOKX

Definition at line 46 of file load_pdb.h.

Referenced by load_pdb().

int LASTOKY

Definition at line 46 of file load_pdb.h.

Referenced by load_pdb().

int LASTOKZ

Definition at line 46 of file load_pdb.h.

Referenced by load_pdb().

int LASTRES

Definition at line 46 of file load_pdb.h.

Referenced by load_pdb().

float LASTX

Definition at line 47 of file load_pdb.h.

Referenced by load_pdb().

float LASTY

Definition at line 47 of file load_pdb.h.

Referenced by load_pdb().

float LASTZ

Definition at line 47 of file load_pdb.h.

Referenced by load_pdb().

linedef line[1]

Definition at line 40 of file load_pdb.h.

Referenced by findAD3Energies(), findAD4Energies(), get_PDB_line_for_ATOM(), load_atypes(), load_dlg_mol(), read_amber8_mden(), read_amber_prmtop_asis(), read_prep(), read_prepres(), and slurp_file().

linedef* ln

Definition at line 76 of file structures.h.

Referenced by findTotalResidue(), getAssembly(), getMolecule(), getResInfo(), howManyMolecules(), init_struct(), init_struct_slurp(), load_pdb(), load_pdb_from_slurp(), rwm_line(), and rwm_line_char().

pdb_line mod_a[6]

Definition at line 71 of file structures.h.

pdb_line pdb_a[6]

Definition at line 68 of file structures.h.

Referenced by pdb_def(), rwm_line(), and rwm_line_char().

queery_set QS

Definition at line 77 of file structures.h.

int SILENT

Definition at line 41 of file load_pdb.h.

Referenced by load_pdb().

char suf[6]

Definition at line 42 of file load_pdb.h.

Referenced by load_pdb().

char sufc[20]

Definition at line 42 of file load_pdb.h.

Referenced by load_pdb().

pdb_line umod_a[6]

Definition at line 74 of file structures.h.

float UNCTOL

Definition at line 47 of file load_pdb.h.

Referenced by load_pdb().

int UNCUT

Definition at line 45 of file load_pdb.h.

Referenced by load_pdb().

int UNx

Definition at line 45 of file load_pdb.h.

Referenced by load_pdb().

int UNy

Definition at line 45 of file load_pdb.h.

Referenced by load_pdb().

int UNz

Definition at line 45 of file load_pdb.h.

Referenced by load_pdb().

int WARN

Definition at line 41 of file load_pdb.h.

Referenced by load_pdb().