src/common/open_prospect.h File Reference

#include <stdlib.h>
#include <math.h>
#include <assert.h>

Go to the source code of this file.

Data Structures

class AlignFeatures

class ResidueAtoms

struct TemplateResidue

The data structure for a single template residue. More...

class TargetResidue

Information for a single residue in a target sequence. More...

struct InteractionElement

Data type to hold 2/3/4 body interaction information. More...

struct TemplateCoreDefinition

The geographic chararcteristics of a core. More...

struct DfireStruct

This structure holds the information from the defire energy function. More...

class ParamElement

struct ResidueInfoElement

This is the original residue structure information rotamer torision angles are applied to this original model of the residue in order obtain the side chains. More...

struct AtomDataElement

class AtomData

struct PopsParamsElement

class PopsParam

struct RotamerElement

This structure is designed to store one possible rotamer conformation. More...

struct RotamerArray

This structure holds the array of rotamers for a single residue. More...

class ProspectParam

The ProspectParam Object is designed to be a common loading place for tabled data that has been stored in parameter files installed with the open_prospect installation (typically in $PREFIX/share/open_prospect). More...

class ScoreStruct

struct TargetDistConstraint

class TargetStruct

This structure holds data related to protein sequence that is to be threaded. More...

class TemplateStruct

Primary data structure for Template Data. More...

class AlignmentStruct

Output of threading program. More...

class TargetAlignmentStruct

struct ThreaderDesc

This structure describes the characteristics of a threading functions. More...

struct RotamerMask

class DynamicAlign

class ProspectDynamicAlign

class ProspectDynamicCoreAlign

class ProspectThreadingInfo

class ProspectOutput

struct feature_parse_op

class ThreadFeatureParse

class SasaCalc

class PopsSasa

class PopsRSasa

class SimpleSasa

class DsspSasa

Defines

#define TEMPLATELIST_DEFAULT   "default.list"

name of file that contains the default template list

#define TEMPLATELIST_FSSP   "fssp.list"

#define TEMPLATELIST_SCOP   "scop.list"

#define FUNCTIONLIST   "function.list"

#define SINGLETON_FILE   "singleton.param"

name of file that contains values for singleton energy term

#define PAIRWISE_FILE   "pair.param"

name of file that contains values for pairwise energy term

#define ALIGNMENT_FILE   "alignment.dat"

#define CONTACT_FILE   "contact_count.param"

#define GONNETMATRIX_FILE   "gonnet.param"

#define RESIDUELIB_FILE   "residues.lib"

#define BBIND_FILE   "bbind02.May.lib"

#define ATOMDATA_FILE   "atoms.dat"

#define DEFIRE_CB_DATA   "dfire_cb.dat"

#define DEFIRE_BIN_DATA   "dfire_bin_info.dat"

#define WEIGHT_CONF_FILE   "weights.conf"

#define PairDistCutoff   58.0

#define PairDistCutoffSqrt   7.61577310586

#define MinDistTwoBody   4

#define MaxContactCount   25

#define StructTypeCount   3

#define ResidueTypeCount   20

#define HELIX   2

#define SHEET   1

#define LOOP   0

#define pValType   float

Datatype for prospect calculations. Can hypothetically be switched to double.

#define e_mutation   0

#define e_mutationfull   1

#define e_mutationlog   2

#define e_mutscore   3

#define e_singleton   4

#define e_sec_struct   5

#define e_twobody_frozen   6

#define e_twobody   7

#define e_distconst   8

#define e_dfire   9

#define e_contact   10

#define e_gapopen   11

#define e_gapconst   12

#define e_coredel   13

#define e_tsingledel   14

#define e_tsingleins   15

#define e_qsingledel   16

#define e_qsingleins   17

#define e_contactdel   18

#define e_count   19

#define e_mask(x)   ((0x00000001) << (x))

#define et_gap   0

#define et_single   1

#define et_pair   2

#define f_count   13

Alignment Features///.

#define anN   0

#define anCa   1

#define anC   2

#define anO   3

#define anBBcount   4

#define anCb   4

#define kMaxResAtoms   24

#define vUp   1

#define vLeft   2

#define vMatch   3

#define FPOP_SET   1

#define FPOP_GET   2

#define FPOP_ADD   3

#define FPOP_SUB   4

#define FPOP_MUL   5

#define FPOP_DIV   6

#define FPOP_POW   7

#define FPOP_SRT   8

#define FPOP_LOG   9

#define FPOP_SIN   10

#define FPOP_COS   11

#define FPOP_NEG   12

#define FPOP_ABS   13

#define FPOP_RES   14

Typedefs

typedef pValType EnergyArray [e_count]

typedef pValType WeightArray [e_count]

typedef float vec3 [3]

typedef float mat3 [3][3]

typedef char *(* threading_function )(struct ProspectParam *, WeightArray, struct TemplateStruct *, struct TargetStruct *, struct AlignmentStruct *)

Function pointer type for a threading function.

typedef char *(* scoring_function )(ProspectParam *, WeightArray, TemplateStruct *, TargetStruct *, AlignmentStruct *)

Function pointer type for a scoring function.

Functions

int ResidueAtoms_CalcCb (ResidueAtoms *res)

pValType calc_LRET (vec3 a, vec3 b, pValType ra, pValType rb)

int Prospect_Target_Rotamer (ProspectParam *param, ResidueAtoms *structure, char residue, int rotamer_number)

pValType rot_mask_pairscore_get (RotamerMask *mask, long vertex_1, long vertex_2, long state_1, long state_2)

void rot_mask_pairscore_set (RotamerMask *mask, long vertex_1, long vertex_2, long state_1, long state_2, pValType score)

int Prospect_Target_RotamerMask_Init (ProspectParam *param, TargetStruct *target_data, RotamerMask *rotamer_mask)

void Prospect_Target_RotamerMask_Free (RotamerMask *mask)

int Prospect_RotamerMask_DEE (RotamerMask *mask)

int Prospect_RotamerMask_DEE_Split (RotamerMask *mask)

int Prospect_RotamerMask_TreeDecomp (RotamerMask *mask)

pValType calc_raw_score (WeightArray weights, EnergyArray energies)

pValType calc_single_energy (ProspectParam *param, WeightArray weights, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num, int target_res_num)

This function call and sums togeather all single residue energy functions.

pValType calc_pair_energy (ProspectParam *param, WeightArray weights, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num_1, int template_res_num_2, int target_res_num_1, int target_res_num_2)

This function call and sums togeather all residue pair energy functions.

pValType calc_del_val (ProspectParam *param, WeightArray weights, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num, int target_res_num)

pValType calc_ins_val (ProspectParam *param, WeightArray weights, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num, int target_res_num)

pValType calc_coredel (ProspectParam *param, TemplateStruct *template_data, int template_res_num)

pValType calc_contactdel (ProspectParam *param, TemplateStruct *template_data, int template_res_num)

pValType calc_mutation (ProspectParam *param, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num, int target_res_num)

Calculate the mutation energy from mutation profile vectors.

pValType calc_mutationlog (ProspectParam *param, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num, int target_res_num)

pValType calc_mutationfull (ProspectParam *param, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num, int target_res_num)

pValType calc_sec_struct (ProspectParam *param, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num, int target_res_num)

Caclulate the secondary structure energy.

pValType calc_singleton (ProspectParam *param, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num, int target_res_num)

Calculate the singleton energy.

pValType calc_mutscore (ProspectParam *param, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num, int target_res_num)

Calculate the mutation energy based on the gonnet energy function.

pValType calc_twobody_frozen (ProspectParam *param, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num, int target_res_num)

Calculate the energy of the pairwise cutoff term assuming the residues for the other pairs are the same as the table.

pValType calc_contact_frozen (ProspectParam *param, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num, int target_res_num)

pValType calc_twobody (ProspectParam *param, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num_1, int template_res_num_2, int target_res_num_1, int target_res_num_2)

Returns the two body energy between to aligned points.

pValType calc_twobody_val (ProspectParam *param, TargetStruct *target_data, int template_res_num_1, int template_res_num_2)

pValType calc_dfire (ProspectParam *param, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num_1, int template_res_num_2, int target_res_num_1, int target_res_num_2)

Returns the two body energy from the defire function between to aligned points.

pValType calc_dfire (ProspectParam *param, char res_a, char res_b, float dist)

pValType calc_distconst (ProspectParam *param, TemplateStruct *template_data, TargetStruct *target_data, int template_res_num_1, int template_res_num_2, int target_res_num_1, int target_res_num_2)

Returns the value of the pair placement given the constraint information that has been inputed.

pValType calc_singledel (ProspectParam *param, TemplateStruct *template_data, int template_res_num)

pValType calc_singleins (ProspectParam *param, TemplateStruct *template_data, int template_res_num)

int ss_filter (ProspectParam *param, TemplateStruct *template_data, TargetStruct *target_data, int core_num, int core_position)

Returns zero if the core position is not predicted to be possible.

char AA3toAA1 (char *res)

Turn the amino acid character into a number (0-19, 20 for X).

void AA1toAA3 (char res, char *res_name)

int AA1toAANum (char a)

char AANumtoAA1 (int a)

int SS1toSSNum (char a)

int PDBAtomtoNum (char *atom_name)

int solvent_acc (char a, int template_acc)

int solvent_sec_struct (TemplateStruct *template_data, int template_res_num)

void shuffle_seq (TargetStruct *q, TargetStruct *s_q)

Variables

char pdb_atomname [288][4]

char e_names [e_count][40]

char e_types [e_count]

Detailed Description

Definition in file open_prospect.h.

Typedef Documentation

typedef char*(* threading_function)(struct ProspectParam *, WeightArray, struct TemplateStruct *, struct TargetStruct *, struct AlignmentStruct *)

Function pointer type for a threading function.
New threading functions added to the OpenProspect library need to follow this format. The function pointer provided can later be looked up with the Prospect_Threader_Find function.
Parameters:

ProspectParam Prospect parameter information for energy functions and generic data. This is passed to prospect energy functions, usually as the first argument

WeightStruct The weight co-efficient set that is used to scale various energy functions.

TemplateStruct The data structure for the known protein structure which is used to model a new protein sequence.

TargetStruct The data structure for the sequence with an unknown structure that is to be threaded against the template.

AlignmentWholeStruct The structure contains the output alignment from the threading function

Definition at line 363 of file open_prospect.h.

Function Documentation

char AA3toAA1 ( char * res )

Turn the amino acid character into a number (0-19, 20 for X).

Parameters:

a The amino acid character

Definition at line 135 of file seq_tools.cc.
References AA3toAA1().
Referenced by AA3toAA1(), PopsParam::LoadParam(), and TargetStruct::LoadPDB().

pValType calc_dfire ( ProspectParam * param,

TemplateStruct * template_data,

TargetStruct * target_data,

int template_res_num_1,

int template_res_num_2,

int target_res_num_1,

int target_res_num_2

)

Returns the two body energy from the defire function between to aligned points.

Parameters:

param Prospect variables and data

template_data The template information

target_data The target information

template_res_num_1 Which template position is the first residue in the alignment

template_res_num_2 Which template position is the second residue in the alignment

target_res_num_1 Which target position is the first residue in the alignment

target_res_num_2 Which target position is the first residue in the alignment

Definition at line 495 of file energy_functions.cc.
References AA1toAANum(), DfireStruct::bin, DfireStruct::bin_count, DfireStruct::bin_max, DfireStruct::bin_min, TemplateStruct::cb_dist, ProspectParam::dfire, pValType, TargetStruct::residue, and TargetResidue::RS.

pValType calc_distconst ( ProspectParam * param,

TemplateStruct * template_data,

TargetStruct * target_data,

int template_res_num_1,

int template_res_num_2,

int target_res_num_1,

int target_res_num_2

)

Returns the value of the pair placement given the constraint information that has been inputed.

Parameters:

param Prospect variables and data

template_data The template information

target_data The target information

template_res_num_1 Which template position is the first residue in the alignment

template_res_num_2 Which template position is the second residue in the alignment

target_res_num_1 Which target position is the first residue in the alignment

target_res_num_2 Which target position is the first residue in the alignment

Definition at line 537 of file energy_functions.cc.
References TargetDistConstraint::aa, TemplateStruct::cb_dist, TargetDistConstraint::dist, TargetStruct::distconst, TargetStruct::distconst_count, pValType, and TargetDistConstraint::var.

pValType calc_mutation ( ProspectParam * param,

TemplateStruct * template_data,

TargetStruct * target_data,

int template_res_num,

int target_res_num

)

Calculate the mutation energy from mutation profile vectors.

Parameters:

param Prospect variables and data

template_data The template information

target_data The target information

template_res_num Which template position is in the alignment

target_res_num Which target residue is aligned

Definition at line 126 of file energy_functions.cc.
References TargetResidue::FREQ, pValType, and TargetStruct::residue.

pValType calc_mutscore ( ProspectParam * param,

TemplateStruct * template_data,

TargetStruct * target_data,

int template_res_num,

int target_res_num

)

Calculate the mutation energy based on the gonnet energy function.

Parameters:

param Prospect variables and data

template_data The template information

target_data The target information

template_res_num Which template position is in the alignment

target_res_num Which target residue is aligned

Definition at line 270 of file energy_functions.cc.
References AA1toAANum(), TargetStruct::residue, TargetResidue::RS, TemplateResidue::Score, and TemplateStruct::t_residue_info.

pValType calc_pair_energy ( ProspectParam * param,

WeightArray weights,

TemplateStruct * template_data,

TargetStruct * target_data,

int template_res_num_1,

int template_res_num_2,

int target_res_num_1,

int target_res_num_2

)

This function call and sums togeather all residue pair energy functions.

Parameters:

param

weights

template_data

target_data

template_res_num_1

template_res_num_2

target_res_num_1

target_res_num_2

Definition at line 65 of file energy_functions.cc.
References e_dfire, e_distconst, e_twobody, and pValType.

pValType calc_sec_struct ( ProspectParam * param,

TemplateStruct * template_data,

TargetStruct * target_data,

int template_res_num,

int target_res_num

)

Caclulate the secondary structure energy.

Parameters:

param Prospect variables and data

template_data The template information

target_data The target information

template_res_num Which template position is in the alignment

target_res_num Which target residue is aligned

Definition at line 278 of file energy_functions.cc.
References HELIX, LOOP, pValType, TargetStruct::residue, SHEET, TargetResidue::SS, and TargetResidue::SS_PROB.

pValType calc_single_energy ( ProspectParam * param,

WeightArray weights,

TemplateStruct * template_data,

TargetStruct * target_data,

int template_res_num,

int target_res_num

)

This function call and sums togeather all single residue energy functions.

Parameters:

param

weights

template_data

target_data

template_res_num

target_res_num

Definition at line 24 of file energy_functions.cc.
References e_contact, e_mutation, e_mutationlog, e_mutscore, e_sec_struct, e_singleton, and pValType.

pValType calc_singleton ( ProspectParam * param,

TemplateStruct * template_data,

TargetStruct * target_data,

int template_res_num,

int target_res_num

)

Calculate the singleton energy.

Parameters:

param Prospect variables and data

template_data The template information

target_data The target information

template_res_num Which template position is in the alignment

target_res_num Which target residue is aligned

Definition at line 298 of file energy_functions.cc.
References TargetResidue::FREQ, pValType, TargetStruct::residue, and ProspectParam::SINGLETON.

pValType calc_twobody ( ProspectParam * param,

TemplateStruct * template_data,

TargetStruct * target_data,

int template_res_num_1,

int template_res_num_2,

int target_res_num_1,

int target_res_num_2

)

Returns the two body energy between to aligned points.
Note, this assumes that the positions are within the cutoff range, sqrt(56). Usuallly just cycles through the TemplateStruct twobody_interactions list and apply it to those residue pairs.
Parameters:

param Prospect variables and data

template_data The template information

target_data The target information

template_res_num_1 Which template position is the first residue in the alignment

template_res_num_2 Which template position is the second residue in the alignment

target_res_num_1 Which target position is the first residue in the alignment

target_res_num_2 Which target position is the first residue in the alignment

Definition at line 457 of file energy_functions.cc.
References TemplateStruct::cb_dist, TargetStruct::len, MinDistTwoBody, TargetResidue::orig_num, PairDistCutoffSqrt, TargetStruct::residue, and TargetStruct::twobody.

pValType calc_twobody_frozen ( ProspectParam * param,

TemplateStruct * template_data,

TargetStruct * target_data,

int template_res_num,

int target_res_num

)

Calculate the energy of the pairwise cutoff term assuming the residues for the other pairs are the same as the table.

Parameters:

param Prospect variables and data

template_data The template information

target_data The target information

template_res_num Which template position is in the alignment

target_res_num Which target residue is aligned

Definition at line 407 of file energy_functions.cc.
References AA1toAANum(), InteractionElement::core_number, ProspectParam::PAIR_POT, pValType, TargetStruct::residue, InteractionElement::residue_number, TargetResidue::RS, TemplateStruct::twobody_count, and TemplateStruct::twobody_interactions.

int ss_filter ( ProspectParam * param,

TemplateStruct * template_data,

TargetStruct * target_data,

int core_num,

int core_position

)

Returns zero if the core position is not predicted to be possible.
Note, this is a heuristic, it is not guarenteed to be accurate in all cases.
Parameters:

param Prospect Information.

template_data

target_data

core_num

core_position

Definition at line 738 of file energy_functions.cc.

Generated on Wed Apr 11 16:50:50 2007 for open_prospect by

1.4.6


Data Structures
class	AlignFeatures
class	ResidueAtoms
struct	TemplateResidue
	The data structure for a single template residue. More...
class	TargetResidue
	Information for a single residue in a target sequence. More...
struct	InteractionElement
	Data type to hold 2/3/4 body interaction information. More...
struct	TemplateCoreDefinition
	The geographic chararcteristics of a core. More...
struct	DfireStruct
	This structure holds the information from the defire energy function. More...
class	ParamElement
struct	ResidueInfoElement
	This is the original residue structure information rotamer torision angles are applied to this original model of the residue in order obtain the side chains. More...
struct	AtomDataElement
class	AtomData
struct	PopsParamsElement
class	PopsParam
struct	RotamerElement
	This structure is designed to store one possible rotamer conformation. More...
struct	RotamerArray
	This structure holds the array of rotamers for a single residue. More...
class	ProspectParam
	The ProspectParam Object is designed to be a common loading place for tabled data that has been stored in parameter files installed with the open_prospect installation (typically in $PREFIX/share/open_prospect). More...
class	ScoreStruct
struct	TargetDistConstraint
class	TargetStruct
	This structure holds data related to protein sequence that is to be threaded. More...
class	TemplateStruct
	Primary data structure for Template Data. More...
class	AlignmentStruct
	Output of threading program. More...
class	TargetAlignmentStruct
struct	ThreaderDesc
	This structure describes the characteristics of a threading functions. More...
struct	RotamerMask
class	DynamicAlign
class	ProspectDynamicAlign
class	ProspectDynamicCoreAlign
class	ProspectThreadingInfo
class	ProspectOutput
struct	feature_parse_op
class	ThreadFeatureParse
class	SasaCalc
class	PopsSasa
class	PopsRSasa
class	SimpleSasa
class	DsspSasa
Defines
#define	TEMPLATELIST_DEFAULT "default.list"
	name of file that contains the default template list
#define	TEMPLATELIST_FSSP "fssp.list"
#define	TEMPLATELIST_SCOP "scop.list"
#define	FUNCTIONLIST "function.list"
#define	SINGLETON_FILE "singleton.param"
	name of file that contains values for singleton energy term
#define	PAIRWISE_FILE "pair.param"
	name of file that contains values for pairwise energy term
#define	ALIGNMENT_FILE "alignment.dat"
#define	CONTACT_FILE "contact_count.param"
#define	GONNETMATRIX_FILE "gonnet.param"
#define	RESIDUELIB_FILE "residues.lib"
#define	BBIND_FILE "bbind02.May.lib"
#define	ATOMDATA_FILE "atoms.dat"
#define	DEFIRE_CB_DATA "dfire_cb.dat"
#define	DEFIRE_BIN_DATA "dfire_bin_info.dat"
#define	WEIGHT_CONF_FILE "weights.conf"
#define	PairDistCutoff 58.0
#define	PairDistCutoffSqrt 7.61577310586
#define	MinDistTwoBody 4
#define	MaxContactCount 25
#define	StructTypeCount 3
#define	ResidueTypeCount 20
#define	HELIX 2
#define	SHEET 1
#define	LOOP 0
#define	pValType float
	Datatype for prospect calculations. Can hypothetically be switched to double.
#define	e_mutation 0
#define	e_mutationfull 1
#define	e_mutationlog 2
#define	e_mutscore 3
#define	e_singleton 4
#define	e_sec_struct 5
#define	e_twobody_frozen 6
#define	e_twobody 7
#define	e_distconst 8
#define	e_dfire 9
#define	e_contact 10
#define	e_gapopen 11
#define	e_gapconst 12
#define	e_coredel 13
#define	e_tsingledel 14
#define	e_tsingleins 15
#define	e_qsingledel 16
#define	e_qsingleins 17
#define	e_contactdel 18
#define	e_count 19
#define	e_mask(x) ((0x00000001) << (x))
#define	et_gap 0
#define	et_single 1
#define	et_pair 2
#define	f_count 13
	Alignment Features///.
#define	anN 0
#define	anCa 1
#define	anC 2
#define	anO 3
#define	anBBcount 4
#define	anCb 4
#define	kMaxResAtoms 24
#define	vUp 1
#define	vLeft 2
#define	vMatch 3
#define	FPOP_SET 1
#define	FPOP_GET 2
#define	FPOP_ADD 3
#define	FPOP_SUB 4
#define	FPOP_MUL 5
#define	FPOP_DIV 6
#define	FPOP_POW 7
#define	FPOP_SRT 8
#define	FPOP_LOG 9
#define	FPOP_SIN 10
#define	FPOP_COS 11
#define	FPOP_NEG 12
#define	FPOP_ABS 13
#define	FPOP_RES 14
Typedefs
typedef pValType	EnergyArray [e_count]
typedef pValType	WeightArray [e_count]
typedef float	vec3 [3]
typedef float	mat3 [3][3]
typedef char (	threading_function )(struct ProspectParam , WeightArray, struct TemplateStruct , struct TargetStruct , struct AlignmentStruct )
	Function pointer type for a threading function.
typedef char (	scoring_function )(ProspectParam , WeightArray, TemplateStruct , TargetStruct , AlignmentStruct )
	Function pointer type for a scoring function.
Functions
int	ResidueAtoms_CalcCb (ResidueAtoms *res)
pValType	calc_LRET (vec3 a, vec3 b, pValType ra, pValType rb)
int	Prospect_Target_Rotamer (ProspectParam param, ResidueAtoms structure, char residue, int rotamer_number)
pValType	rot_mask_pairscore_get (RotamerMask *mask, long vertex_1, long vertex_2, long state_1, long state_2)
void	rot_mask_pairscore_set (RotamerMask *mask, long vertex_1, long vertex_2, long state_1, long state_2, pValType score)
int	Prospect_Target_RotamerMask_Init (ProspectParam param, TargetStruct target_data, RotamerMask *rotamer_mask)
void	Prospect_Target_RotamerMask_Free (RotamerMask *mask)
int	Prospect_RotamerMask_DEE (RotamerMask *mask)
int	Prospect_RotamerMask_DEE_Split (RotamerMask *mask)
int	Prospect_RotamerMask_TreeDecomp (RotamerMask *mask)
pValType	calc_raw_score (WeightArray weights, EnergyArray energies)
pValType	calc_single_energy (ProspectParam param, WeightArray weights, TemplateStruct template_data, TargetStruct *target_data, int template_res_num, int target_res_num)
	This function call and sums togeather all single residue energy functions.
pValType	calc_pair_energy (ProspectParam param, WeightArray weights, TemplateStruct template_data, TargetStruct *target_data, int template_res_num_1, int template_res_num_2, int target_res_num_1, int target_res_num_2)
	This function call and sums togeather all residue pair energy functions.
pValType	calc_del_val (ProspectParam param, WeightArray weights, TemplateStruct template_data, TargetStruct *target_data, int template_res_num, int target_res_num)
pValType	calc_ins_val (ProspectParam param, WeightArray weights, TemplateStruct template_data, TargetStruct *target_data, int template_res_num, int target_res_num)
pValType	calc_coredel (ProspectParam param, TemplateStruct template_data, int template_res_num)
pValType	calc_contactdel (ProspectParam param, TemplateStruct template_data, int template_res_num)
pValType	calc_mutation (ProspectParam param, TemplateStruct template_data, TargetStruct *target_data, int template_res_num, int target_res_num)
	Calculate the mutation energy from mutation profile vectors.
pValType	calc_mutationlog (ProspectParam param, TemplateStruct template_data, TargetStruct *target_data, int template_res_num, int target_res_num)
pValType	calc_mutationfull (ProspectParam param, TemplateStruct template_data, TargetStruct *target_data, int template_res_num, int target_res_num)
pValType	calc_sec_struct (ProspectParam param, TemplateStruct template_data, TargetStruct *target_data, int template_res_num, int target_res_num)
	Caclulate the secondary structure energy.
pValType	calc_singleton (ProspectParam param, TemplateStruct template_data, TargetStruct *target_data, int template_res_num, int target_res_num)
	Calculate the singleton energy.
pValType	calc_mutscore (ProspectParam param, TemplateStruct template_data, TargetStruct *target_data, int template_res_num, int target_res_num)
	Calculate the mutation energy based on the gonnet energy function.
pValType	calc_twobody_frozen (ProspectParam param, TemplateStruct template_data, TargetStruct *target_data, int template_res_num, int target_res_num)
	Calculate the energy of the pairwise cutoff term assuming the residues for the other pairs are the same as the table.
pValType	calc_contact_frozen (ProspectParam param, TemplateStruct template_data, TargetStruct *target_data, int template_res_num, int target_res_num)
pValType	calc_twobody (ProspectParam param, TemplateStruct template_data, TargetStruct *target_data, int template_res_num_1, int template_res_num_2, int target_res_num_1, int target_res_num_2)
	Returns the two body energy between to aligned points.
pValType	calc_twobody_val (ProspectParam param, TargetStruct target_data, int template_res_num_1, int template_res_num_2)
pValType	calc_dfire (ProspectParam param, TemplateStruct template_data, TargetStruct *target_data, int template_res_num_1, int template_res_num_2, int target_res_num_1, int target_res_num_2)
	Returns the two body energy from the defire function between to aligned points.
pValType	calc_dfire (ProspectParam *param, char res_a, char res_b, float dist)
pValType	calc_distconst (ProspectParam param, TemplateStruct template_data, TargetStruct *target_data, int template_res_num_1, int template_res_num_2, int target_res_num_1, int target_res_num_2)
	Returns the value of the pair placement given the constraint information that has been inputed.
pValType	calc_singledel (ProspectParam param, TemplateStruct template_data, int template_res_num)
pValType	calc_singleins (ProspectParam param, TemplateStruct template_data, int template_res_num)
int	ss_filter (ProspectParam param, TemplateStruct template_data, TargetStruct *target_data, int core_num, int core_position)
	Returns zero if the core position is not predicted to be possible.
char	AA3toAA1 (char *res)
	Turn the amino acid character into a number (0-19, 20 for X).
void	AA1toAA3 (char res, char *res_name)
int	AA1toAANum (char a)
char	AANumtoAA1 (int a)
int	SS1toSSNum (char a)
int	PDBAtomtoNum (char *atom_name)
int	solvent_acc (char a, int template_acc)
int	solvent_sec_struct (TemplateStruct *template_data, int template_res_num)
void	shuffle_seq (TargetStruct q, TargetStruct s_q)
Variables
char	pdb_atomname [288][4]
char	e_names [e_count][40]
char	e_types [e_count]