embpdb.c

Section: Operators

These functions use the contents of an instance but do not make any changes.

Functions: embPdbidToSp embPdbidToAcc embPdbidToScop embAtomInContact embAtomDistance

Function embPdbidToSp

Read a pdb identifier code and writes the equivalent swissprot identifier code. Relies on list of Pdbtosp objects sorted by PDB code, which is usually obtained by a call to ajPdbtospReadAllNew.

Synopsis

Prototype

AjBool embPdbidToSp (
      const AjPStr pdb,
      AjPStr* spr,
      const AjPList list
);

Type Name Read/Write Description

const AjPStr pdb Input Pdb identifier code

AjPStr* spr Output Swissprot identifier code

const AjPList list Input Sorted list of Pdbtosp objects

AjBool RETURN True if a swissprot identifier code was found for the Pdb code.

Type	Name	Read/Write	Description
const AjPStr	pdb	Input	Pdb identifier code
AjPStr*	spr	Output	Swissprot identifier code
const AjPList	list	Input	Sorted list of Pdbtosp objects
AjBool		RETURN	True if a swissprot identifier code was found for the Pdb code.

Input

pdb:	(Input)	Pdb identifier code
list:	(Input)	Sorted list of Pdbtosp objects

Output

spr:

(Output)

Swissprot identifier code

Returns

AjBool:

True if a swissprot identifier code was found for the Pdb code.

Description

Read a pdb identifier code and writes the equivalent swissprot identifier code. Relies on list of Pdbtosp objects sorted by PDB code, which is usually obtained by a call to ajPdbtospReadAllNew.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPdbidToAcc

Read a pdb identifier code and writes the equivalent accession number. Relies on list of Pdbtosp objects sorted by PDB code, which is usually obtained by a call to ajPdbtospReadAllNew.

Synopsis

Prototype

AjBool embPdbidToAcc (
      const AjPStr pdb,
      AjPStr* acc,
      const AjPList list
);

Type Name Read/Write Description

const AjPStr pdb Input Pdb identifier code

AjPStr* acc Output Accession number

const AjPList list Input Sorted list of Pdbtosp objects

AjBool RETURN True if a swissprot identifier code was found for the Pdb code.

Type	Name	Read/Write	Description
const AjPStr	pdb	Input	Pdb identifier code
AjPStr*	acc	Output	Accession number
const AjPList	list	Input	Sorted list of Pdbtosp objects
AjBool		RETURN	True if a swissprot identifier code was found for the Pdb code.

Input

pdb:	(Input)	Pdb identifier code
list:	(Input)	Sorted list of Pdbtosp objects

Output

acc:

(Output)

Accession number

Returns

AjBool:

True if a swissprot identifier code was found for the Pdb code.

Description

Read a pdb identifier code and writes the equivalent accession number. Relies on list of Pdbtosp objects sorted by PDB code, which is usually obtained by a call to ajPdbtospReadAllNew.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPdbidToScop

Writes a list of scop identifier codes for the domains that a Pdb object contains. The domain data is taken from a list of scop objects.

Synopsis

Prototype

AjBool embPdbidToScop (
      const AjPPdb pdb,
      const AjPList list_allscop,
      AjPList* list_pdbscopids
);

Type Name Read/Write Description

const AjPPdb pdb Input Pointer to pdb object

const AjPList list_allscop Input Pointer to SCOP list of SCOP classification objects

AjPList* list_pdbscopids Output Pointer to list of scop domain ids in the current pdb object

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
const AjPPdb	pdb	Input	Pointer to pdb object
const AjPList	list_allscop	Input	Pointer to SCOP list of SCOP classification objects
AjPList*	list_pdbscopids	Output	Pointer to list of scop domain ids in the current pdb object
AjBool		RETURN	ajTrue on success

Input

pdb:	(Input)	Pointer to pdb object
list_allscop:	(Input)	Pointer to SCOP list of SCOP classification objects

Output

list_pdbscopids:

(Output)

Pointer to list of scop domain ids in the current pdb object

Returns

AjBool:

ajTrue on success

Description

Writes a list of scop identifier codes for the domains that a Pdb object contains. The domain data is taken from a list of scop objects.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embAtomInContact

Determines whether two atoms are in physical contact

Synopsis

Prototype

AjBool embAtomInContact (
      const AjPAtom atm1,
      const AjPAtom atm2,
      float thresh,
      const AjPVdwall vdw
);

Type Name Read/Write Description

const AjPAtom atm1 Input Atom 1 object

const AjPAtom atm2 Input Atom 1 object

float thresh Input Threshold contact distance

const AjPVdwall vdw Input Vdwall object Contact between two atoms is defined as when the van der Waals surface of the first atom comes within the threshold contact distance (thresh) of the van der Waals surface of the second atom.

AjBool RETURN True if the two atoms form contact

Type	Name	Read/Write	Description
const AjPAtom	atm1	Input	Atom 1 object
const AjPAtom	atm2	Input	Atom 1 object
float	thresh	Input	Threshold contact distance
const AjPVdwall	vdw	Input	Vdwall object Contact between two atoms is defined as when the van der Waals surface of the first atom comes within the threshold contact distance (thresh) of the van der Waals surface of the second atom.
AjBool		RETURN	True if the two atoms form contact

Input

atm1:	(Input)	Atom 1 object
atm2:	(Input)	Atom 1 object
thresh:	(Input)	Threshold contact distance
vdw:	(Input)	Vdwall object Contact between two atoms is defined as when the van der Waals surface of the first atom comes within the threshold contact distance (thresh) of the van der Waals surface of the second atom.

Returns

AjBool:

True if the two atoms form contact

Description

Determines whether two atoms are in physical contact

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embAtomDistance

Returns the distance (Angstroms) between two atoms.

Synopsis

Prototype

float embAtomDistance (
      const AjPAtom atm1,
      const AjPAtom atm2,
      const AjPVdwall vdw
);

Type Name Read/Write Description

const AjPAtom atm1 Input Atom 1 object

const AjPAtom atm2 Input Atom 1 object

const AjPVdwall vdw Input Vdwall object Returns the distance (Angstroms) between the van der Waals surface of two atoms.

float RETURN Distance (Angstroms) between two atoms.

Type	Name	Read/Write	Description
const AjPAtom	atm1	Input	Atom 1 object
const AjPAtom	atm2	Input	Atom 1 object
const AjPVdwall	vdw	Input	Vdwall object Returns the distance (Angstroms) between the van der Waals surface of two atoms.
float		RETURN	Distance (Angstroms) between two atoms.

Input

atm1:	(Input)	Atom 1 object
atm2:	(Input)	Atom 1 object
vdw:	(Input)	Vdwall object Returns the distance (Angstroms) between the van der Waals surface of two atoms.

Returns

float:

Distance (Angstroms) between two atoms.

Description

Returns the distance (Angstroms) between two atoms.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Section: Reporters

These functions return the contents of an instance but do not make any changes.

Functions: embVdwRad embPdbToIdx

Function embVdwRad

Returns the van der Waals radius of an atom. Returns 1.2 as default.

Synopsis

Prototype

float embVdwRad (
      const AjPAtom atm,
      const AjPVdwall vdw
);

Type Name Read/Write Description

const AjPAtom atm Input Atom object

const AjPVdwall vdw Input Vdwall object

float RETURN van der Waals radius of the atom

Type	Name	Read/Write	Description
const AjPAtom	atm	Input	Atom object
const AjPVdwall	vdw	Input	Vdwall object
float		RETURN	van der Waals radius of the atom

Input

atm:	(Input)	Atom object
vdw:	(Input)	Vdwall object

Returns

float:

van der Waals radius of the atom

Description

Returns the van der Waals radius of an atom. Returns 1.2 as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPdbToIdx

Reads a Pdb object and writes an integer which gives the index into the protein sequence for a residue with a specified pdb residue number and a specified chain number.

Synopsis

Prototype

AjBool embPdbToIdx (
      ajint* idx,
      const AjPPdb pdb,
      const AjPStr res,
      ajint chn
);

Type Name Read/Write Description

ajint* idx Output Residue number (index into sequence)

const AjPPdb pdb Input Pdb object

const AjPStr res Input Residue number (PDB numbering)

ajint chn Input Chain number

AjBool RETURN True on succcess (res was found in pdb object)

Type	Name	Read/Write	Description
ajint*	idx	Output	Residue number (index into sequence)
const AjPPdb	pdb	Input	Pdb object
const AjPStr	res	Input	Residue number (PDB numbering)
ajint	chn	Input	Chain number
AjBool		RETURN	True on succcess (res was found in pdb object)

Input

pdb:	(Input)	Pdb object
res:	(Input)	Residue number (PDB numbering)
chn:	(Input)	Chain number

Output

idx:

(Output)

Residue number (index into sequence)

Returns

AjBool:

True on succcess (res was found in pdb object)

Description

Reads a Pdb object and writes an integer which gives the index into the protein sequence for a residue with a specified pdb residue number and a specified chain number.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Section: Miscellaneous

These functions may have diverse functions that do not fit into the other categories.

Functions: embPdbListHeterogens embPdbResidueIndexI embPdbResidueIndexC embPdbResidueIndexICA embPdbResidueIndexCCA embStrideToThree

Function embPdbListHeterogens

Function to create a list of arrays of Atom objects for ligands in the current Pdb object (a single array for each ligand). An array of int's giving the number of Atom objects in each array, is also written. The number of ligands is also written.

Synopsis

Prototype

AjBool embPdbListHeterogens (
      const AjPPdb pdb,
      AjPList* list_heterogens,
      AjPInt* siz_heterogens,
      ajint* nhet,
      AjPFile logfile
);

Type Name Read/Write Description

const AjPPdb pdb Input Pointer to pdb object

AjPList* list_heterogens Output Pointer to list of heterogen Atom arrays

AjPInt* siz_heterogens Output Pointer to integer array of sizes (number of Atom objects in each array).

ajint* nhet Output Number of arrays in the list that was written.

AjPFile logfile Modify Log file for error messages

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
const AjPPdb	pdb	Input	Pointer to pdb object
AjPList*	list_heterogens	Output	Pointer to list of heterogen Atom arrays
AjPInt*	siz_heterogens	Output	Pointer to integer array of sizes (number of Atom objects in each array).
ajint*	nhet	Output	Number of arrays in the list that was written.
AjPFile	logfile	Modify	Log file for error messages
AjBool		RETURN	ajTrue on success

Input

pdb:

(Input)

Pointer to pdb object

Output

list_heterogens:	(Output)	Pointer to list of heterogen Atom arrays
siz_heterogens:	(Output)	Pointer to integer array of sizes (number of Atom objects in each array).
nhet:	(Output)	Number of arrays in the list that was written.

Input & Output

logfile:

(Modify)

Log file for error messages

Returns

AjBool:

ajTrue on success

Description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPdbResidueIndexI

Reads a Pdb object and writes an integer array which gives the index into the protein sequence for structured residues (residues for which electron density was determined) for a given chain. The array length is of course equal to the number of structured residues.

Synopsis

Prototype

AjBool embPdbResidueIndexI (
      const AjPPdb pdb,
      ajint chn,
      AjPInt* idx
);

Type Name Read/Write Description

const AjPPdb pdb Input Pdb object

ajint chn Input Chain number

AjPInt* idx Output Index array

AjBool RETURN True on succcess

Type	Name	Read/Write	Description
const AjPPdb	pdb	Input	Pdb object
ajint	chn	Input	Chain number
AjPInt*	idx	Output	Index array
AjBool		RETURN	True on succcess

Input

pdb:	(Input)	Pdb object
chn:	(Input)	Chain number

Output

idx:

(Output)

Index array

Returns

AjBool:

True on succcess

Description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPdbResidueIndexC

Synopsis

Prototype

AjBool embPdbResidueIndexC (
      const AjPPdb pdb,
      char chn,
      AjPInt* idx
);

Type Name Read/Write Description

const AjPPdb pdb Input Pdb object

char chn Input Chain identifier

AjPInt* idx Output Index array

AjBool RETURN True on succcess

Type	Name	Read/Write	Description
const AjPPdb	pdb	Input	Pdb object
char	chn	Input	Chain identifier
AjPInt*	idx	Output	Index array
AjBool		RETURN	True on succcess

Input

pdb:	(Input)	Pdb object
chn:	(Input)	Chain identifier

Output

idx:

(Output)

Index array

Returns

AjBool:

True on succcess

Description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPdbResidueIndexICA

Reads a Pdb object and writes an integer array which gives the index into the protein sequence for structured residues (residues for which electron density was determined) for a given chain, EXCLUDING those residues for which CA atoms are missing. The array length is of course equal to the number of structured residues.

Synopsis

Prototype

AjBool embPdbResidueIndexICA (
      const AjPPdb pdb,
      ajint chn,
      AjPUint* idx,
      ajint* nres
);

Type Name Read/Write Description

const AjPPdb pdb Input Pdb object

ajint chn Input Chain number

AjPUint* idx Output Index array

ajint* nres Output Array length

AjBool RETURN True on succcess

Type	Name	Read/Write	Description
const AjPPdb	pdb	Input	Pdb object
ajint	chn	Input	Chain number
AjPUint*	idx	Output	Index array
ajint*	nres	Output	Array length
AjBool		RETURN	True on succcess

Input

pdb:	(Input)	Pdb object
chn:	(Input)	Chain number

Output

idx:	(Output)	Index array
nres:	(Output)	Array length

Returns

AjBool:

True on succcess

Description

Reads a Pdb object and writes an integer array which gives the index into the protein sequence for structured residues (residues for which electron density was determined) for a given chain, EXCLUDING those residues for which CA atoms are missing. The array length is of course equal to the number of structured residues.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPdbResidueIndexCCA

Reads a Pdb object and writes an integer array which gives the index into the protein sequence for structured residues (residues for which electron density was determined) for a given chain, EXCLUDING those residues for which CA atoms are missing. The array length is of course equal to the number of structured residues.

Synopsis

Prototype

AjBool embPdbResidueIndexCCA (
      const AjPPdb pdb,
      char chn,
      AjPUint* idx,
      ajint* nres
);

Type Name Read/Write Description

const AjPPdb pdb Input Pdb object

char chn Input Chain identifier

AjPUint* idx Output Index array

ajint* nres Output Array length

AjBool RETURN True on succcess

Type	Name	Read/Write	Description
const AjPPdb	pdb	Input	Pdb object
char	chn	Input	Chain identifier
AjPUint*	idx	Output	Index array
ajint*	nres	Output	Array length
AjBool		RETURN	True on succcess

Input

pdb:	(Input)	Pdb object
chn:	(Input)	Chain identifier

Output

idx:	(Output)	Index array
nres:	(Output)	Array length

Returns

AjBool:

True on succcess

Description

Reads a Pdb object and writes an integer array which gives the index into the protein sequence for structured residues (residues for which electron density was determined) for a given chain, EXCLUDING those residues for which CA atoms are missing. The array length is of course equal to the number of structured residues.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embStrideToThree

Reads a string that contains an 8-state STRIDE secondary structure assignment and writes a string with the corresponding 3-state assignment. The 8 states used in STRIDE are 'H' (alpha helix), 'G' (3-10 helix), 'I' (Pi-helix), 'E' (extended conformation), 'B' or 'b' (isolated bridge), 'T' (turn) or 'C' (coil, i.e. none of the above). The 3 states used are 'H' (STRIDE 'H', 'G' or 'I'), 'E' (STRIDE 'E', 'B' or 'b') and 'C' (STRIDE 'T' or 'C'). The string is allocated if necessary.

Synopsis

Prototype

AjBool embStrideToThree (
      AjPStr* to,
      const AjPStr from
);

Type Name Read/Write Description

AjPStr* to Output String to write

const AjPStr from Input String to read

AjBool RETURN True on succcess

Type	Name	Read/Write	Description
AjPStr*	to	Output	String to write
const AjPStr	from	Input	String to read
AjBool		RETURN	True on succcess

Input

from:

(Input)

String to read

Output

to:

(Output)

String to write

Returns

AjBool:

True on succcess

Description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

embpdb.c

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