ajpdb.c

Constructors

All constructors return a pointer to a new instance. It is the responsibility of the user to first destroy any previous instance. The target pointer does not need to be initialised to NULL, but it is good programming practice to do so anyway.

Function ajPdbtospReadAllRawNew

Reads the swissprot:pdb equivalence table available at URL (1) (1) http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt and returns the data as a list of Pdbtosp objects.

Synopsis

Prototype

AjPList ajPdbtospReadAllRawNew (
      AjPFile inf
);

Input & Output

inf:(Modify)Input file

Returns

AjPList:List of Pdbtosp objects.

Description

Reads the swissprot:pdb equivalence table available at URL (1) (1) http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt and returns the data as a list of Pdbtosp objects.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbtospReadNew

Read a Pdbtosp object from a file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application).

Synopsis

Prototype

AjPPdbtosp ajPdbtospReadNew (
      AjPFile inf,
      const AjPStr entry
);

Input

entry:(Input)Pdb id

Input & Output

inf:(Modify)Input file stream

Returns

AjPPdbtosp:True on success

Description

Read a Pdbtosp object from a file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application).

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbtospReadCNew

Read a Pdbtosp object from a file in embl-like format. Memory for the object is allocated.

Synopsis

Prototype

AjPPdbtosp ajPdbtospReadCNew (
      AjPFile inf,
      const char* entry
);

Input

entry:(Input)Pdb id

Input & Output

inf:(Modify)Input file stream

Returns

AjPPdbtosp:True on success

Description

Read a Pdbtosp object from a file in embl-like format. Memory for the object is allocated.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbtospReadAllNew

Read all the Pdbtosp objects in a file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application) and writes a list of these objects. It then sorts the list by PDB id.

Synopsis

Prototype

AjPList ajPdbtospReadAllNew (
      AjPFile inf
);

Input & Output

inf:(Modify)Input file stream

Returns

AjPList:List of Pdbtosp objects.

Description

Read all the Pdbtosp objects in a file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application) and writes a list of these objects. It then sorts the list by PDB id.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajCmapReadINew

Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). Takes the chain identifier as an integer. If the arguments mod and chn are both 0, the function will read the next Cmap in the file.

Synopsis

Prototype

AjPCmap ajCmapReadINew (
      AjPFile inf,
      ajint chn,
      ajint mod
);

Input

chn:(Input)Chain number
mod:(Input)Model number

Input & Output

inf:(Modify)Input file stream

Returns

AjPCmap:Pointer to new Cmap object.

Description

Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). Takes the chain identifier as an integer. If the arguments mod and chn are both 0, the function will read the next Cmap in the file.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajCmapReadCNew

Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). Takes the chain identifier as a character.

Synopsis

Prototype

AjPCmap ajCmapReadCNew (
      AjPFile inf,
      char chn,
      ajint mod
);

Input

chn:(Input)Chain number
mod:(Input)Model number

Input & Output

inf:(Modify)Input file stream

Returns

AjPCmap:Pointer to new Cmap object.

Description

Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). Takes the chain identifier as a character.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajCmapReadAllNew

Read every Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application) and returns a list of these objects.

Synopsis

Prototype

AjPList ajCmapReadAllNew (
      AjPFile inf
);

Input & Output

inf:(Modify)Input file stream

Returns

AjPList:List of Cmap objects.

Description

Read every Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application) and returns a list of these objects.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajCmapReadNew

Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). This is not usually called by the user, who uses ajCmapReadINew or ajCmapReadCNew instead. If mode==CMAP_MODE_I, chn==0 and mod==0, the function will read the next Cmap in the file.

Synopsis

Prototype

AjPCmap ajCmapReadNew (
      AjPFile inf,
      ajint mode,
      ajint chn,
      ajint mod
);

Input

mode:(Input)Mode, either CMAP_MODE_I (treat chn arg as an integer) or CMAP_MODE_C (treat chn arg as a character).
chn:(Input)Chain identifier / number.
mod:(Input)Model number.

Input & Output

inf:(Modify)Input file stream.

Returns

AjPCmap:True on success (an object read)

Description

Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). This is not usually called by the user, who uses ajCmapReadINew or ajCmapReadCNew instead. If mode==CMAP_MODE_I, chn==0 and mod==0, the function will read the next Cmap in the file.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajVdwallReadNew

Read a Vdwall object from a file in embl-like format (see documentation for the EMBASSY DOMAINATRIX package).

Synopsis

Prototype

AjPVdwall ajVdwallReadNew (
      AjPFile inf
);

Input & Output

inf:(Modify)Input file stream

Returns

AjPVdwall:Pointer to Vdwall object.

Description

Read a Vdwall object from a file in embl-like format (see documentation for the EMBASSY DOMAINATRIX package).

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajHetReadNew

Read heterogen dictionary, the Het object is allocated.

Synopsis

Prototype

AjPHet ajHetReadNew (
      AjPFile inf
);

Input & Output

inf:(Modify)Pointer to Het file

Returns

AjPHet:Het object.

Description

Read heterogen dictionary, the Het object is allocated.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajHetReadRawNew

Reads a dictionary of heterogen groups available at http://pdb.rutgers.edu/het_dictionary.txt and writes a Het object.

Synopsis

Prototype

AjPHet ajHetReadRawNew (
      AjPFile inf
);

Input & Output

inf:(Modify)Pointer to dictionary

Returns

AjPHet:True on success

Description

Reads a dictionary of heterogen groups available at http://pdb.rutgers.edu/het_dictionary.txt and writes a Het object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbReadFirstModelNew

Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for the first model only is read in.

Synopsis

Prototype

AjPPdb ajPdbReadFirstModelNew (
      AjPFile inf
);

Input & Output

inf:(Modify)Pointer to clean coordinate file

Returns

AjPPdb:Pointer to Pdb object.

Description

Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for the first model only is read in.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbReadAllModelsNew

Reads a clean coordinate file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for all models is read.

Synopsis

Prototype

AjPPdb ajPdbReadAllModelsNew (
      AjPFile inf
);

Input & Output

inf:(Modify)Pointer to clean coordinate file

Returns

AjPPdb:Pointer to Pdb object.

Description

Reads a clean coordinate file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for all models is read.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbReadNew

Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for the first model only is read in.

Synopsis

Prototype

AjPPdb ajPdbReadNew (
      AjPFile inf,
      ajint mode
);

Input

mode:(Input)Mode. 0==Read first model only. 1==Read all models.

Input & Output

inf:(Modify)Pointer to clean coordinate file

Returns

AjPPdb:Pointer to Pdb object.

Description

Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for the first model only is read in.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbReadoldNew

Reads a clean coordinate file (see documentation for DOMAINATRIX "pdbparse" application) lacking residue-level description in RE records and writes a filled Pdb object.

Synopsis

Prototype

AjPPdb ajPdbReadoldNew (
      AjPFile inf
);

Input & Output

inf:(Modify)Pointer to clean coordinate file

Returns

AjPPdb:Pointer to Pdb object.

Description

Reads a clean coordinate file (see documentation for DOMAINATRIX "pdbparse" application) lacking residue-level description in RE records and writes a filled Pdb object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbReadoldFirstModelNew

Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) lacking residue-level description in RE records and writes a filled Pdb object. Data for the first model only is read in.

Synopsis

Prototype

AjPPdb ajPdbReadoldFirstModelNew (
      AjPFile inf
);

Input & Output

inf:(Modify)Pointer to clean coordinate file

Returns

AjPPdb:Pointer to Pdb object.

Description

Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) lacking residue-level description in RE records and writes a filled Pdb object. Data for the first model only is read in.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajAtomNew

Atom object constructor. This is normally called by the ajChainNew function.

Synopsis

Prototype

AjPAtom ajAtomNew (
      void
);

Returns

AjPAtom:Pointer to an atom object

Description

Atom object constructor. This is normally called by the ajChainNew function.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueNew

Residue object constructor. This is normally called by the ajChainNew function.

Synopsis

Prototype

AjPResidue ajResidueNew (
      void
);

Returns

AjPResidue:Pointer to a Residue object

Description

Residue object constructor. This is normally called by the ajChainNew function.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajChainNew

Chain object constructor. This is normally called by the ajPdbNew function

Synopsis

Prototype

AjPChain ajChainNew (
      void
);

Returns

AjPChain:Pointer to a chain object

Description

Chain object constructor. This is normally called by the ajPdbNew function

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbNew

Pdb object constructor. Fore-knowledge of the number of chains is required. This is normally called by the functions that read PDB files or clean coordinate files (see embpdb.c & embpdbraw.c).

Synopsis

Prototype

AjPPdb ajPdbNew (
      ajint n
);

Input

n:(Input)Number of chains in this pdb file

Returns

AjPPdb:Pointer to a pdb object

Description

Pdb object constructor. Fore-knowledge of the number of chains is required. This is normally called by the functions that read PDB files or clean coordinate files (see embpdb.c & embpdbraw.c).

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajHetentNew

Hetent object constructor.

Synopsis

Prototype

AjPHetent ajHetentNew (
      void
);

Returns

AjPHetent:Pointer to a Hetent object

Description

Hetent object constructor.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajHetNew

Het object constructor.

Synopsis

Prototype

AjPHet ajHetNew (
      ajint n
);

Input

n:(Input)Number of entries in dictionary.

Returns

AjPHet:Pointer to a Het object

Description

Het object constructor.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajVdwallNew

Vdwall object constructor. This is normally called by the ajVdwallReadNew function. Fore-knowledge of the number of residues is required.

Synopsis

Prototype

AjPVdwall ajVdwallNew (
      ajint n
);

Input

n:(Input)Number of residues

Returns

AjPVdwall:Pointer to a Vdwall object

Description

Vdwall object constructor. This is normally called by the ajVdwallReadNew function. Fore-knowledge of the number of residues is required.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajVdwresNew

Vdwres object constructor. This is normally called by the ajVdwallReadNew function. Fore-knowledge of the number of atoms is required.

Synopsis

Prototype

AjPVdwres ajVdwresNew (
      ajint n
);

Input

n:(Input)Number of atoms

Returns

AjPVdwres:Pointer to a Vdwres object

Description

Vdwres object constructor. This is normally called by the ajVdwallReadNew function. Fore-knowledge of the number of atoms is required.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajCmapNew

Cmap object constructor. This is normally called by the ajCmapReadNew function. Fore-knowledge of the dimension (number of residues) for the contact map is required.

Synopsis

Prototype

AjPCmap ajCmapNew (
      ajint n
);

Input

n:(Input)Dimenion of contact map

Returns

AjPCmap:Pointer to a Cmap object

Description

Cmap object constructor. This is normally called by the ajCmapReadNew function. Fore-knowledge of the dimension (number of residues) for the contact map is required.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbtospNew

Pdbtosp object constructor. Fore-knowledge of the number of entries is required. This is normally called by the ajPdbtospReadCNew / ajPdbtospReadNew functions.

Synopsis

Prototype

AjPPdbtosp ajPdbtospNew (
      ajint n
);

Input

n:(Input)Number of entries

Returns

AjPPdbtosp:Pointer to a Pdbtosp object

Description

Pdbtosp object constructor. Fore-knowledge of the number of entries is required. This is normally called by the ajPdbtospReadCNew / ajPdbtospReadNew functions.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Destructors

All destructor functions receive the address of the instance to be deleted. The original pointer is set to NULL so is ready for re-use.

Function ajAtomDel

Destructor for atom object.

Synopsis

Prototype

void ajAtomDel (
      AjPAtom* ptr
);

Output

ptr:(Delete)Atom object pointer

Returns

void:No return value

Description

Destructor for atom object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueDel

Destructor for residue object.

Synopsis

Prototype

void ajResidueDel (
      AjPResidue* ptr
);

Output

ptr:(Delete)Residue object pointer

Returns

void:No return value

Description

Destructor for residue object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajChainDel

Destructor for chain object.

Synopsis

Prototype

void ajChainDel (
      AjPChain* ptr
);

Output

ptr:(Delete)Chain object pointer

Returns

void:No return value

Description

Destructor for chain object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbDel

Destructor for pdb object.

Synopsis

Prototype

void ajPdbDel (
      AjPPdb* ptr
);

Output

ptr:(Delete)Pdb object pointer

Returns

void:No return value

Description

Destructor for pdb object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajHetentDel

Destructor for Hetent object.

Synopsis

Prototype

void ajHetentDel (
      AjPHetent* ptr
);

Output

ptr:(Delete)Hetent object pointer

Returns

void:No return value

Description

Destructor for Hetent object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajHetDel

Destructor for Het object.

Synopsis

Prototype

void ajHetDel (
      AjPHet* ptr
);

Output

ptr:(Delete)Het object pointer

Returns

void:No return value

Description

Destructor for Het object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajVdwallDel

Destructor for Vdwall object.

Synopsis

Prototype

void ajVdwallDel (
      AjPVdwall* ptr
);

Output

ptr:(Delete)Vdwall object pointer

Returns

void:No return value

Description

Destructor for Vdwall object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajVdwresDel

Destructor for Vdwres object.

Synopsis

Prototype

void ajVdwresDel (
      AjPVdwres* ptr
);

Output

ptr:(Delete)Vdwres object pointer

Returns

void:No return value

Description

Destructor for Vdwres object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajCmapDel

Destructor for Cmap object.

Synopsis

Prototype

void ajCmapDel (
      AjPCmap* ptr
);

Output

ptr:(Delete)Cmap object pointer

Returns

void:No return value

Description

Destructor for Cmap object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbtospDel

Destructor for Pdbtosp object.

Synopsis

Prototype

void ajPdbtospDel (
      AjPPdbtosp* ptr
);

Output

ptr:(Delete)Pdbtosp object pointer

Returns

void:No return value

Description

Destructor for Pdbtosp object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Assignments

These functions overwrite the instance provided as the first argument A NULL value is always acceptable so these functions are often used to create a new instance by assignment.

Function ajAtomCopy

Copies the data from an Atom object to an Atom object; the new object is created if needed.

IMPORTANT - THIS DOES NOT COPY THE eNum & eType ELEMENTS, WHICH ARE SET TO ZERO and '.' INSTEAD.

Synopsis

Prototype

AjBool ajAtomCopy (
      AjPAtom* to,
      const AjPAtom from
);

Input

from:(Input)Atom object pointer

Output

to:(Output)Atom object pointer

Returns

AjBool:True on success

Description

Copies the data from an Atom object to an Atom object; the new object is created if needed.

IMPORTANT - THIS DOES NOT COPY THE eNum & eType ELEMENTS, WHICH ARE SET TO ZERO and '.' INSTEAD.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueCopy

Copies the data from a Residue object to an Residue object; the new object is created if needed.

IMPORTANT - THIS DOES NOT COPY THE eNum & eType ELEMENTS, WHICH ARE SET TO ZERO and '.' INSTEAD.

Synopsis

Prototype

AjBool ajResidueCopy (
      AjPResidue* to,
      const AjPResidue from
);

Input

from:(Input)Residue object pointer

Output

to:(Output)Residue object pointer

Returns

AjBool:True on success

Description

Copies the data from a Residue object to an Residue object; the new object is created if needed.

IMPORTANT - THIS DOES NOT COPY THE eNum & eType ELEMENTS, WHICH ARE SET TO ZERO and '.' INSTEAD.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajAtomListCopy

Read a list of Atom structures and writes a copy of the list. The data are copied and the list is created if necessary.

Synopsis

Prototype

AjBool ajAtomListCopy (
      AjPList* to,
      const AjPList from
);

Input

from:(Input)List of Atom objects to read

Output

to:(Output)List of Atom objects to write

Returns

AjBool:True if list was copied ok.

Description

Read a list of Atom structures and writes a copy of the list. The data are copied and the list is created if necessary.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueListCopy

Read a list of Residue structures and writes a copy of the list. The data are copied and the list is created if necessary.

Synopsis

Prototype

AjBool ajResidueListCopy (
      AjPList* to,
      const AjPList from
);

Input

from:(Input)List of Residue objects to read

Output

to:(Output)List of Residue objects to write

Returns

AjBool:True if list was copied ok.

Description

Read a list of Residue structures and writes a copy of the list. The data are copied and the list is created if necessary.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbCopy

Copies data from one Pdb object to another; the new object is always created.

Synopsis

Prototype

AjBool ajPdbCopy (
      AjPPdb* to,
      const AjPPdb from
);

Input

from:(Input)Pdb object pointer

Output

to:(Output)Pdb object pointer

Returns

AjBool:True on success

Description

Copies data from one Pdb object to another; the new object is always created.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Operators

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

Function ajResidueSSEnv

Assigns secondary structure environment of a residue

Synopsis

Prototype

AjBool ajResidueSSEnv (
      const AjPResidue res,
      char* SEnv,
      AjPFile logf
);

Input

res:(Input)Residue object

Output

SEnv:(Output)Character for the Secondary structure environment
logf:(Output)Log file

Returns

AjBool:ajTrue on success

Description

Assigns secondary structure environment of a residue

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv1

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv1 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv2

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv2 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv3

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv3 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv4

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv4 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv5

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv5 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv6

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv6 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv7

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv7 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv8

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv8 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv9

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv9 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv10

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv10 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv11

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv11 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv12

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv12 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv13

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv13 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv14

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv14 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv15

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv15 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajResidueEnv16

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Synopsis

Prototype

ajint ajResidueEnv16 (
      const AjPResidue res,
      char SEnv,
      AjPStr* OEnv,
      AjPFile logf
);

Input

res:(Input)Residue object
SEnv:(Input)Secondary structure environment code

Output

OEnv:(Output)Character for the overall environment class
logf:(Output)Log file

Returns

ajint:Number of environments

Description

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbGetEStrideType

Reads a Pdb object and writes a string with the secondary structure. The string that is written is the same length as the full-length chain (regardless of whether coordinates for a residue were available or not) therefore it can be indexed into using residue numbers. The string is allocated if necessary. If secondary structure assignment was not available for a residue a '.' is given in the string.

Synopsis

Prototype

ajint ajPdbGetEStrideType (
      const AjPPdb obj,
      ajint chn,
      AjPStr* EStrideType
);

Input

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

Output

EStrideType:(Output)String to hold secondary structure

Returns

ajint:Length (residues) of array that was written or -1 (for an error)

Description

Reads a Pdb object and writes a string with the secondary structure. The string that is written is the same length as the full-length chain (regardless of whether coordinates for a residue were available or not) therefore it can be indexed into using residue numbers. The string is allocated if necessary. If secondary structure assignment was not available for a residue a '.' is given in the string.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Reporters

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

Function ajPdbChnidToNum

Finds the chain number for a given chain identifier in a pdb structure

Synopsis

Prototype

AjBool ajPdbChnidToNum (
      char id,
      const AjPPdb pdb,
      ajint* chn
);

Input

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

Output

chn:(Output)Chain number

Returns

AjBool:True on succcess

Description

Finds the chain number for a given chain identifier in a pdb structure

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbtospArrFindPdbid

Performs a binary search for a PDB code over an array of Pdbtosp structures (which of course must first have been sorted). This is a case-insensitive search.

Synopsis

Prototype

ajint ajPdbtospArrFindPdbid (
      const AjPPdbtosp* arr,
      ajint siz,
      const AjPStr id
);

Input

arr:(Input)Array of AjOPdbtosp objects
siz:(Input)Size of array
id:(Input)Search term

Returns

ajint:Index of first Pdbtosp object found with an PDB code matching id, or -1 if id is not found.

Description

Performs a binary search for a PDB code over an array of Pdbtosp structures (which of course must first have been sorted). This is a case-insensitive search.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Input & output

These functions are used for formatted input and output to file.

Function ajPdbWriteAll

Writes a clean coordinate file for a protein.

Synopsis

Prototype

AjBool ajPdbWriteAll (
      AjPFile outf,
      const AjPPdb obj
);

Input

obj:(Input)Pdb object

Output

outf:(Output)Output file stream

Returns

AjBool:True on success

Description

Writes a clean coordinate file for a protein.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbWriteSegment

Writes a clean coordinate file for a segment, e.g. a domain. The segment corresponds to a sequence that is passed to the function. In the clean coordinate file, the coordinates are presented as belonging to a single chain. Coordinates for heterogens are NOT written to file.

Synopsis

Prototype

AjBool ajPdbWriteSegment (
      AjPFile outf,
      const AjPPdb pdb,
      const AjPStr segment,
      char chnid,
      const AjPStr domain,
      AjPFile errf
);

Input

pdb:(Input)Pdb object
segment:(Input)Sequence of segment to print out.
chnid:(Input)Chain id of segment
domain:(Input)Domain code for segment

Output

outf:(Output)Output file stream
errf:(Output)Output file stream for error messages

Returns

AjBool:True on success

Description

Writes a clean coordinate file for a segment, e.g. a domain. The segment corresponds to a sequence that is passed to the function. In the clean coordinate file, the coordinates are presented as belonging to a single chain. Coordinates for heterogens are NOT written to file.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajHetWrite

Writes the contents of a Het object to file.

Synopsis

Prototype

AjBool ajHetWrite (
      AjPFile outf,
      const AjPHet obj,
      AjBool dogrep
);

Input

obj:(Input)Het object
dogrep:(Input)Flag (True if we are to write element of the Het object to file).

Output

outf:(Output)Output file

Returns

AjBool:True on success

Description

Writes the contents of a Het object to file.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbtospWrite

Reads a list of Pdbtosp objects, e.g. taken from the swissprot:pdb equivalence table available at URL: (1) http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt) and writes the list out to file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application).

Synopsis

Prototype

AjBool ajPdbtospWrite (
      AjPFile outf,
      const AjPList list
);

Input

list:(Input)List of Pdbtosp objects

Output

outf:(Output)Output file

Returns

AjBool:True of file was written ok.

Description

Reads a list of Pdbtosp objects, e.g. taken from the swissprot:pdb equivalence table available at URL: (1) http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt) and writes the list out to file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application).

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajCmapWrite

Write a Cmap object to file in CON format (see documentation for DOMAINATRIX "contacts" application).

Synopsis

Prototype

AjBool ajCmapWrite (
      AjPFile outf,
      const AjPCmap cmap
);

Input

cmap:(Input)Cmap object pointer.

Input & Output

outf:(Modify)Output file stream.

Returns

AjBool:True on success (object was written succesfully)

Description

Write a Cmap object to file in CON format (see documentation for DOMAINATRIX "contacts" application).

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0