Difference between revisions of "pdbFile(API)"
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==== Append ==== | ==== Append ==== | ||
| − | Create new data to | + | Create new data to next of '''pdb->PDB'''.<br> |
Create new data allocating memory. Then set it to current data, original data to previous data, and original next data to next data. | Create new data allocating memory. Then set it to current data, original data to previous data, and original next data to next data. | ||
extern pdbRecord* pdbFileAppend(pdbFile* pdb); | extern pdbRecord* pdbFileAppend(pdbFile* pdb); | ||
| Line 631: | Line 631: | ||
extern void pdbFileOneProteinCopy(pdbFile* dst, pdbFile* src, long num); | extern void pdbFileOneProteinCopy(pdbFile* dst, pdbFile* src, long num); | ||
| − | === | + | ===Secondary Structure=== |
| − | ==== | + | ==== Read ==== |
| − | pdb->PDB-> | + | Read Secondary Structure from '''pdb->PDB->FullRecord''', and store to '''second'''. |
extern int pdbSecondaryStructureSetFromPDB(pdbFile* pdb, pdbFileSecondaryStructure* second); | extern int pdbSecondaryStructureSetFromPDB(pdbFile* pdb, pdbFileSecondaryStructure* second); | ||
| − | pdb->PDB-> | + | Read alpha carbon which is out of Secondary Structure from '''pdb->PDB->FullRecord''', and store to '''second'''. |
extern int pdbNoSecondaryStructureSetFromPDB(pdbFile* pdb, pdbFileSecondaryStructure* second); | extern int pdbNoSecondaryStructureSetFromPDB(pdbFile* pdb, pdbFileSecondaryStructure* second); | ||
==== Write ==== | ==== Write ==== | ||
| − | + | Write Secondary Structure '''second''' to file '''fpt''' as [[PDB]]. (Repeat to use '''pdbFileSecondaryStructureRecordPrint''') | |
extern void pdbFileWriteSecondaryStructure(FILE* fpt, pdbFileSecondaryStructure* second); | extern void pdbFileWriteSecondaryStructure(FILE* fpt, pdbFileSecondaryStructure* second); | ||
| − | + | Write 1 line Secondary Structure '''second''' to file '''fpt''' as [[PDB]]. | |
extern pdbFileSecondaryStructureRecord* pdbFileSecondaryStructureRecordPrint(FILE* fpt, pdbFileSecondaryStructureRecord* second); | extern pdbFileSecondaryStructureRecord* pdbFileSecondaryStructureRecordPrint(FILE* fpt, pdbFileSecondaryStructureRecord* second); | ||
| − | ==== | + | ==== Append ==== |
| − | + | Create new Secondary Structure data to '''second''', allocating memory. | |
extern int pdbSecondaryStructureAppend(pdbFileSecondaryStructure* second); | extern int pdbSecondaryStructureAppend(pdbFileSecondaryStructure* second); | ||
| − | + | If second->nSecondaryStructure=0, set it to top data. In addition, set NULL to the previous and the next data.<br> | |
| − | + | Otherwise, set it to current data, original data to previous data, and original next data to next data. | |
==== data判定 ==== | ==== data判定 ==== | ||
| − | + | If Secondary Structure(HELIX, SHEET, TURN), return 1. Otherwise, return 0. | |
extern long pdbFileIsSecondaryStructure(pdbFile* pdb); | extern long pdbFileIsSecondaryStructure(pdbFile* pdb); | ||
| − | + | If Helix Structure(HELIX), return 1. Otherwise, return 0. | |
extern long pdbFileIsHelix(pdbFile* pdb); | extern long pdbFileIsHelix(pdbFile* pdb); | ||
| − | + | If Sheet Structure(SHEET), return 1. Otherwise, return 0. | |
extern long pdbFileIsSheet(pdbFile* pdb); | extern long pdbFileIsSheet(pdbFile* pdb); | ||
| − | + | If Turn Structure(TURN), return 1. Otherwise, return 0. | |
extern long pdbFileIsTurn(pdbFile* pdb); | extern long pdbFileIsTurn(pdbFile* pdb); | ||
| − | pdb-> | + | If '''pdb->PDB''' is included by '''second->SecondaryStructure''', return the Secondary Structure data. Otherwise, return '''pdbFileSecondaryStructureModeNo'''. |
extern pdbFileSecondaryStructureMode pdbFileWithSecondaryStructure(pdbFile* pdb, pdbFileSecondaryStructure* second); | extern pdbFileSecondaryStructureMode pdbFileWithSecondaryStructure(pdbFile* pdb, pdbFileSecondaryStructure* second); | ||
Revision as of 07:48, 7 October 2014
DataManip/pdbFile is API to treat PDB file.
Contents
constant
Syntax for PDB file
String length definition
#define PDB_FILE_RECORD_FULL_LENGTH (80) #define PDB_FILE_RECORD_START (0) #define PDB_FILE_RECORD_LENGTH (6) #define PDB_FILE_ATOM_NUMBER_START (6) #define PDB_FILE_ATOM_NUMBER_LENGTH (5) #define PDB_FILE_ATOM_NAME_START (12) #define PDB_FILE_ATOM_NAME_LENGTH (4) #define PDB_FILE_LOCATION_START (16) #define PDB_FILE_LOCATION_LENGTH (1) #define PDB_FILE_RESIDUE_START (17) #define PDB_FILE_RESIDUE_LENGTH (3) #define PDB_FILE_CHAIN_IDENT_START (21) #define PDB_FILE_CHAIN_IDENT_LENGTH (1) #define PDB_FILE_RESNUM_START (22) #define PDB_FILE_RESNUM_LENGTH (4) #define PDB_FILE_INSERTION_START (26) #define PDB_FILE_INSERTION_LENGTH (1) #define PDB_FILE_X_START (30) #define PDB_FILE_X_LENGTH (8) #define PDB_FILE_Y_START (38) #define PDB_FILE_Y_LENGTH (8) #define PDB_FILE_Z_START (46) #define PDB_FILE_Z_LENGTH (8) #define PDB_FILE_OCCUPANCY_START (54) #define PDB_FILE_OCCUPANCY_LENGTH (6) #define PDB_FILE_TEMPERATURE_START (60) #define PDB_FILE_TEMPERATURE_LENGTH (6) #define PDB_FILE_FOOT_START (67) #define PDB_FILE_FOOT_LENGTH (3) #define PDB_FILE_FOOTNOTE_START (70) #define PDB_FILE_FOOTNOTE_LENGTH (10) #define MAX_RESIDUE_NUMBER (20) #define RESIDUE_ONECHAR_MODE (1) #define RESIDUE_THREECHAR_MODE (3)
String definition
#define pdbRecordAtom ("ATOM ")
#define pdbRecordHeteroAtom ("HETATM")
#define pdbRecordHelix ("HELIX ")
#define pdbRecordSheet ("SHEET ")
#define pdbRecordTurn ("TURN ")
#define pdbRecordEnd ("END ")
Residue Name
residueName3: 3 characters, residueName1: 1 character
typedef struct residueName {
char residueName3[4];
char residueName1[2];
} residueName;
Define the struct in header file, and define residue name in /pdbFile/src/pdbGet.c.
static residueName residue[MAX_RESIDUE_NUMBER] = {
"ALA","A", "VAL","V", "PHE","F", "PRO","P",
"MET","M", "ILE","I", "LEU","L", "ASP","D",
"GLU","E", "LYS","K", "ARG","R", "SER","S",
"THR","T", "TYR","Y", "HIS","H", "CYS","C",
"ASN","N", "GLN","Q", "TRP","W", "GLY","G"
};
| Element No. | residueName3 | residueName1 |
|---|---|---|
| 0 | ALA | A |
| 1 | VAL | V |
| 2 | PHE | F |
| 3 | PRO | P |
| 4 | MET | M |
| 5 | ILE | I |
| 6 | LEU | L |
| 7 | ASP | D |
| 8 | GLU | E |
| 9 | LYS | K |
| 10 | ARG | R |
| 11 | SER | S |
| 12 | THR | T |
| 13 | TYR | Y |
| 14 | HIS | H |
| 15 | CYS | C |
| 16 | ASN | N |
| 17 | GLN | Q |
| 18 | TRP | W |
| 19 | GLY | G |
Secondary Structure
Secondary Structure Mode
typedef enum pdbFileSecondaryStructureMode {
pdbFileSecondaryStructureModeNo = 0,
pdbFileSecondaryStructureModeHelix = 1,
pdbFileSecondaryStructureModeSheet = 2,
pdbFileSecondaryStructureModeTurn = 3
} pdbFileSecondaryStructureMode;
Helix Structure
typedef enum pdbSecondaryStructureHelixClass {
HelixClassRightHandedAlpha = 1,
HelixClassRightHandedOmega = 2,
HelixClassRightHandedPi = 3,
HelixClassRightHandedGammda= 4,
HelixClassRightHanded310 = 5,
HelixClassLeftHandedAlpha = 6,
HelixClassLeftHandedOmega = 7,
HelixClassLeftHandedGammda = 9,
HelixClassPolyProline = 10,
} pdbSecondaryStructureHelixClass;
struct
Management Data
This is struct to manage PDB data and Secondary Structure data.
typedef struct pdbFile {
pdbRecord* top;
pdbRecord* PDB;
pdbFileParaTypeInteger nAtom;
pdbFileSecondaryStructure second;
} pdbFile;
| Member | Description |
|---|---|
| top | Top PDB data(Pointer) |
| PDB | Current PDB data(Pointer) |
| nAtom | Number of PDB data |
| second | Secondary Structure data |
Management Secondary Structure data
typedef struct pdbFileSecondaryStructure {
int nSecondaryStructure;
pdbFileSecondaryStructureRecord* top;
pdbFileSecondaryStructureRecord* SecondaryStructure;
} pdbFileSecondaryStructure;
| Member | Description |
|---|---|
| nSecondaryStructure | Number of Secondary Structure data |
| top | Top Secondary Structure data(Pointer) |
| SecondaryStructure | Current Secondary Structure data(Pointer) |
PDB data
This is struct to store PDB data. Manage by list, and correspond one line PDB file data.
typedef struct pdbRecord pdbRecord;
struct pdbRecord {
pdbFileParaTypeCharacter FullRecord[PDB_FILE_RECORD_FULL_LENGTH+1];
pdbFileParaTypeCharacter Record[PDB_FILE_RECORD_LENGTH+1];
/* ATOM and HETATM Record */
pdbFileParaTypeInteger AtomSerialNumber;
pdbFileParaTypeCharacter AtomName[PDB_FILE_ATOM_NAME_LENGTH+1];
pdbFileParaTypeCharacter LocationIndicator;
pdbFileParaTypeCharacter ResidueName[PDB_FILE_RESIDUE_LENGTH+1];
pdbFileParaTypeCharacter ChainIdentifier;
pdbFileParaTypeInteger ResidueSequenceNumber;
pdbFileParaTypeCharacter InsertionCode;
pdbCoord Coord;
pdbFileParaTypeReal Occupancy;
pdbFileParaTypeReal TemperatureFactor;
pdbFileParaTypeInteger FootnoteNumber;
pdbFileParaTypeCharacter Footnote[PDB_FILE_FOOTNOTE_LENGTH+1];
pdbRecord* prev;
pdbRecord* next;
};
| Member | Description |
|---|---|
| FullRecord | One line PDB data |
| Record | One line PDB data as Atom Information |
| AtomSerialNumber | |
| AtomName | Atom Name |
| LocationIndicator | |
| ResidueName | Residue Name |
| ChainIdentifier | Chain ID |
| ResidueSequenceNumber | Residue Sequence Number |
| InsertionCode | |
| Coord | Coordinates of Atom |
| Occupancy | Occupancy |
| TemperatureFactor | Temperature Factor |
| FootnoteNumber | |
| Footnote | |
| prev | Previous data |
| next | Next data |
typedef char pdbFileParaTypeCharacter; typedef long pdbFileParaTypeInteger; typedef float pdbFileParaTypeReal;
Coordinates of PDB data
typedef struct pdbCoord {
pdbFileParaTypeReal x;
pdbFileParaTypeReal y;
pdbFileParaTypeReal z;
} pdbCoord;
Secondary Structure
This is struct to store Secondary Structure data.Manage by list, and correspond one line Secondary Structure.
typedef struct pdbFileSecondaryStructureRecord pdbFileSecondaryStructureRecord;
struct pdbFileSecondaryStructureRecord {
pdbFileSecondaryStructureMode mode;
pdbSecondaryStructureHelix* helix;
pdbSecondaryStructureSheet* sheet;
pdbSecondaryStructureTurn* turn;
pdbSecondaryStructureNo* no;
pdbFileSecondaryStructureRecord* prev;
pdbFileSecondaryStructureRecord* next;
};
| Member | Description |
|---|---|
| mode | Secondary Structure Mode |
| helix | Helix Structure data |
| sheet | Sheet Structure data |
| turn | Turn Structure data |
| no | Non Secondary Structure data |
| prev | Previous data |
| next | Next data |
Helix Structure
typedef struct pdbSecondaryStructureHelix {
int serNum; /* Serial Number */
char* helixID; /* HelixID : Three alpahnumeric characters */
/* informtion for the initial residue */
char* initResName;/* Name of the initial residue : Three alpahnumeric characters */
char initChainID; /* Chain identifier */
int initSeqNum; /* Sequence number of the initial residue */
char initICode;
/* informtion for the terminal residue */
char* endResName;/* Name of the initial residue : Three alpahnumeric characters */
char endChainID; /* Chain identifier */
int endSeqNum; /* Sequence number of the initial residue */
char endICode;
pdbSecondaryStructureHelixClass helixClass;
char* comment;
int length;
} pdbSecondaryStructureHelix;
Sheet Structure
typedef struct pdbSecondaryStructureSheet {
int strand; /* Strand number which starts 1 for eache strand wihtin a sheet and increases by one */
char* sheetID; /* Sheet ID */
int numStrands; /* Number of strands in sheet */
/* initial residue */
char* initResName;/* Name of the initial residue : Three alpahnumeric characters */
char initChainID; /* Chain identifier */
int initSeqNum; /* Sequence number of the initial residue */
char initICode;
/* informtion for the terminal residue */
char* endResName;/* Name of the initial residue : Three alpahnumeric characters */
char endChainID; /* Chain identifier */
int endSeqNum; /* Sequence number of the initial residue */
char endICode;
int sense; /* 0: first strand, 1: parallel, -1: anti-paralle */
char* curAtom; /* Registration. Atom name in current strand */
char* curResName; /* Registration. Residue name in current strand */
char curChainID; /* Registration. Chain ID in current strand */
int curResSeq; /* Registration. Res sequence in current strand */
char curICode; /* Registration. Insertion code in current strand */
char* prevAtom; /* Registration. Atom name in current strand */
char* prevResName; /* Registration. Residue name in current strand */
char prevChainID; /* Registration. Chain ID in current strand */
int prevResSeq; /* Registration. Res sequence in current strand */
char prevICode; /* Registration. Insertion code in current strand */
}pdbSecondaryStructureSheet;
Turn Structure
typedef struct pdbSecondaryStructureTurn {
int serNum; /* Serial Number */
char* turnID; /* Turn ID : Three alpahnumeric characters */
/* informtion for the initial residue */
char* initResName;/* Name of the initial residue : Three alpahnumeric characters */
char initChainID; /* Chain identifier */
int initSeqNum; /* Sequence number of the initial residue */
char initICode;
/* informtion for the terminal residue */
char* endResName;/* Name of the initial residue : Three alpahnumeric characters */
char endChainID; /* Chain identifier */
int endSeqNum; /* Sequence number of the initial residue */
char endICode;
char* comment;
}pdbSecondaryStructureTurn;
Non Secondary Structure
typedef struct pdbSecondaryStructureNo {
int serNum; /* Serial Number */
char* noID; /* Turn ID : Three alpahnumeric characters */
/* informtion for the initial residue */
char* initResName;/* Name of the initial residue : Three alpahnumeric characters */
char initChainID; /* Chain identifier */
int initSeqNum; /* Sequence number of the initial residue */
char initICode;
/* informtion for the terminal residue */
char* endResName;/* Name of the initial residue : Three alpahnumeric characters */
char endChainID; /* Chain identifier */
int endSeqNum; /* Sequence number of the initial residue */
char endICode;
char* comment;
}pdbSecondaryStructureNo;
API
File Management
Read
Read data in file fpt, and store to manage data pdb.
extern void pdbFileRead(FILE* fpt, pdbFile* pdb);
Write
Write manage data pdb to file fpt as PDB. (Repeat to use pdbFileRecordPrint)
extern void pdbFileWrite(FILE* fpt, pdbFile* pdb);
Write manage data pdb to file fpt as tsv. (Repeat to use pdbFileRecordTablePrint)
extern void pdbFileTableWrite(FILE* fpt, pdbFile* pdb);
Write coordinates list in manage data pdb to file fpt.
extern void pdbFileWriteCoord(FILE* fpt, pdbFile* pdb);
Treat PDB data
New Create
Create new data to pdb->PDB.
Create new data allocating memory. Then set it to top data. In addition, set NULL to the previous and the next data.
extern pdbRecord* pdbFileNew(pdbFile* pdb);
Append
Create new data to next of pdb->PDB.
Create new data allocating memory. Then set it to current data, original data to previous data, and original next data to next data.
extern pdbRecord* pdbFileAppend(pdbFile* pdb);
Release
Release all of PDB data in pdb.
extern pdbRecord* pdbFileFree(pdbFile* pdb);
Write
Write pdb->PDB to file fpt as PDB.
extern pdbRecord* pdbFileRecordPrint(FILE* fpt, pdbFile* pdb);
Write pdb->PDB to file fpt as tsv.
extern pdbRecord* pdbFileRecordTablePrint(FILE* fpt, pdbFile* pdb);
Pointer move
Move to top data.
extern pdbRecord* pdbFileTop(pdbFile* pdb);
Return pointer of top data to pdb->top.
extern pdbRecord* pdbFileTopPointer(pdbFile* pdb);
Move to next data.(If don't correspond, return NULL.)
extern pdbRecord* pdbFileNext(pdbFile* pdb);
Move to next Atom data.(If don't correspond, return NULL.)
extern pdbRecord* pdbFileNextAtom(pdbFile* pdb);
Move to next alpha carbon data.(If don't correspond, return NULL.)
extern pdbRecord* pdbFileNextCA(pdbFile* pdb);
Move to previous data.(If don't correspond, return NULL.)
extern pdbRecord* pdbFilePrev(pdbFile* pdb);
Move to previous Atom data.(If don't correspond, return NULL.)
extern pdbRecord* pdbFilePrevAtom(pdbFile* pdb);
Move to previous alpha carbon data.(If don't correspond, return NULL.)
extern pdbRecord* pdbFilePrevCA(pdbFile* pdb);
Move to end data.
extern long pdbFileGoToEnd(pdbFile* pdb);
Check Data
If end data, return 1. Otherwise, return 0.
extern long pdbFileEnd(pdbFile* pdb);
If pdb->PDB->Record is end character(END), return 1. Otherwise, return 0.
extern long pdbFileIsEndLine(pdbFile* pdb);
If pdb->PDB->Record is Atom, return 1. Otherwise, return 0.
extern long pdbFileIsAtom(pdbFile* pdb);
If pdb->PDB->AtomName is alpha carbon( CA ), return 1. Otherwise, return 0.
extern long pdbFileIsCA(pdbFile* pdb);
Return Z value from pdb->PDB->AtomName. If don't correspond, return 6 as carbon.
extern pdbFileParaTypeInteger pdbZValueGet(pdbFile* pdb);
If residue name of pdb->PDB is "D" or "E", return 1. Otherwise, return 0.
extern long pdbFileIsNegative(pdbFile* pdb);
If residue name of pdb->PDB is "K" or "R", return 1. Otherwise, return 0.
extern long pdbFileIsPositive(pdbFile* pdb);
If residue name of pdb->PDB is "K", "R", "D", or "E", return 1. Otherwise, return 0.
extern long pdbFileIsCharge(pdbFile* pdb);
If records have same ChainID and their sequence number difference is 1, return 1. Otherwise, return 0.
extern long pdbRecordIsNearby(pdbRecord record1,pdbRecord record2);
Set data
Set (x, y, z) to pdb->PDB->Coord.
extern long pdbFileCoordSet(pdbFile* pdb, pdbFileParaTypeReal x, pdbFileParaTypeReal y, pdbFileParaTypeReal z);
Set temp to pdb->PDB->TemperatureFactor.
extern void pdbFileTemperatureFactorSet(pdbFile* pdb, double temp);
Set c to pdb->PDB->ChainIdentifier.
extern void pdbFileChainIdentifierSet(pdbFile* pdb, unsigned char c);
Set c to all Chain ID in pdb.
extern void pdbFileChainIdentifierSetAll(pdbFile* pdb, unsigned char c);
Set temp to pdb->PDB->Occupancy.
extern void pdbFileOccupancySet(pdbFile* pdb, double temp);
Get data
Output pdb->PDB->Coord to (x, y, z).
extern long pdbFileCoordGet(pdbFile* pdb, pdbFileParaTypeReal* x, pdbFileParaTypeReal* y, pdbFileParaTypeReal* z);
Return pdb->PDB->ResidueSequenceNumber.
extern long pdbFileResidueSequenceNumberGet(pdbFile* pdb);
Return residue name. (If mode=RESIDUE_THREECHAR_MODE, 3 characters. Otherwise, 1 character)
extern char* pdbFileResidueNameGet(pdbFile* pdb,int mode);
Return pdb->PDB->TemperatureFactor.
extern pdbFileParaTypeReal pdbFileTemperatureFactorGet(pdbFile* pdb);
Return pdb->PDB->ChainIdentifier.
extern unsigned char pdbFileChainIdentifierGet(pdbFile* pdb);
Return pdb->PDB->Occupancy.
extern pdbFileParaTypeReal pdbFileOccupancyGet(pdbFile* pdb);
Increase
Increase pdb->PDB->ResidueSequenceNumber by 1..
extern void pdbFileResidueSequenceNumberIncrement(pdbFile* pdb, int n);
Increase all Residue Sequence Number in pdb by 1.
extern void pdbFileResidueSequenceNumberIncrementAll(pdbFile* pdb, int n);
Copy
Copy src->PDB to dst->PDB.
Then, keep the relation to previous and next data, and return dst->PDB.
extern pdbRecord* pdbFileOneRecordCopy(pdbFile* dst, pdbFile* src);
Copy all PDB data in src to dst with overwrite.
Copy calling pdbFileNew for dst. So, you must release dst by pdbFileFree , before using it.
extern void pdbFileCopyAll(pdbFile* dst, pdbFile* src);
Append all PDB data in src, to next of dst->PDB.
extern void pdbFileAppendAll(pdbFile* dst, pdbFile* src);
If src->PDB is alpha carbon, copy it to dst->PDB.
Then, keep the relation to previous and next data, and if the copy is succeed, return dst->PDB. Otherwise, return NULL.
extern pdbRecord* pdbFileCAOnlyCopy(pdbFile* pdb, pdbFile* src);
Copy all alpha carbon data in src to dst with overwrite.
Copy calling pdbFileNew for dst. So, you must release dst by pdbFileFree , before using it.
extern void pdbFileCAOnlyCopyAll(pdbFile* pdb, pdbFile* src);
Copy src to dst as one protein data.
You must initialize dst by pdbFileNew , before using it.
extern void pdbFileOneProteinCopy(pdbFile* dst, pdbFile* src, long num);
Secondary Structure
Read
Read Secondary Structure from pdb->PDB->FullRecord, and store to second.
extern int pdbSecondaryStructureSetFromPDB(pdbFile* pdb, pdbFileSecondaryStructure* second);
Read alpha carbon which is out of Secondary Structure from pdb->PDB->FullRecord, and store to second.
extern int pdbNoSecondaryStructureSetFromPDB(pdbFile* pdb, pdbFileSecondaryStructure* second);
Write
Write Secondary Structure second to file fpt as PDB. (Repeat to use pdbFileSecondaryStructureRecordPrint)
extern void pdbFileWriteSecondaryStructure(FILE* fpt, pdbFileSecondaryStructure* second);
Write 1 line Secondary Structure second to file fpt as PDB.
extern pdbFileSecondaryStructureRecord* pdbFileSecondaryStructureRecordPrint(FILE* fpt, pdbFileSecondaryStructureRecord* second);
Append
Create new Secondary Structure data to second, allocating memory.
extern int pdbSecondaryStructureAppend(pdbFileSecondaryStructure* second);
If second->nSecondaryStructure=0, set it to top data. In addition, set NULL to the previous and the next data.
Otherwise, set it to current data, original data to previous data, and original next data to next data.
data判定
If Secondary Structure(HELIX, SHEET, TURN), return 1. Otherwise, return 0.
extern long pdbFileIsSecondaryStructure(pdbFile* pdb);
If Helix Structure(HELIX), return 1. Otherwise, return 0.
extern long pdbFileIsHelix(pdbFile* pdb);
If Sheet Structure(SHEET), return 1. Otherwise, return 0.
extern long pdbFileIsSheet(pdbFile* pdb);
If Turn Structure(TURN), return 1. Otherwise, return 0.
extern long pdbFileIsTurn(pdbFile* pdb);
If pdb->PDB is included by second->SecondaryStructure, return the Secondary Structure data. Otherwise, return pdbFileSecondaryStructureModeNo.
extern pdbFileSecondaryStructureMode pdbFileWithSecondaryStructure(pdbFile* pdb, pdbFileSecondaryStructure* second);
Matrixによるアフィン変換
file処理
Matrix3D(API)#file処理を使用して,fileの処理を行います.
extern void pdbMatrixFileFormat(FILE* fpt); extern void pdbMatrixFileRead(FILE* fpt, Matrix3D Matrix); extern void pdbMatrixFileWrite(FILE* fpt, Matrix3D Matrix);
アフィン変換
MatrixMatrixを使用して,pdbにアフィン変換を行います.
extern void pdbTrans(pdbFile* pdb, Matrix3D Matrix); extern void pdbTransCuda(float* hv, int n, Matrix3D Matrix);
Matrix3D(API)#アフィンMatrixを使用してMatrixをCreateし,pdbを回転します.
Euler Angleを使用した回転
extern void pdbRotationFollowingEulerAngle(pdbFile* pdb, char Mode[4], pdbFileParaTypeReal rot1, pdbFileParaTypeReal rot2, pdbFileParaTypeReal rot3); extern void pdbRotationFollowingEulerAngleInverse(pdbFile* pdb, char Mode[4], pdbFileParaTypeReal rot1, pdbFileParaTypeReal rot2, pdbFileParaTypeReal rot3);
指定したAxisの順番で回転
extern void pdbRotationXYZ(pdbFile* pdb, pdbFileParaTypeReal rotx, pdbFileParaTypeReal roty, pdbFileParaTypeReal rotz); extern void pdbRotationZYX(pdbFile* pdb, pdbFileParaTypeReal rotx, pdbFileParaTypeReal roty, pdbFileParaTypeReal rotz); extern void pdbRotationZXY(pdbFile* pdb, pdbFileParaTypeReal rotx, pdbFileParaTypeReal roty, pdbFileParaTypeReal rotz); extern void pdbRotationYXZ(pdbFile* pdb, pdbFileParaTypeReal rotx, pdbFileParaTypeReal roty, pdbFileParaTypeReal rotz);
