embpdb.c

Section: Operators

Functions:

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.
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.
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.
embAtomInContact	Determines whether two atoms are in physical contact
embAtomDistance	Returns the distance (Angstroms) between two atoms.

Function embPdbidToSp

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.

From EMBOSS 2.9.0

Function embPdbidToAcc

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.

From EMBOSS 2.9.0

Function embPdbidToScop

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

From EMBOSS 2.9.0

Function embAtomInContact

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

From EMBOSS 2.9.0

Function embAtomDistance

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.

From EMBOSS 2.9.0

Section: Reporters

Functions:

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

Function embVdwRad

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

From EMBOSS 2.9.0

Function embPdbToIdx

Prototype

AjBool embPdbToIdx (
      ajint* idx,
      const AjPPdb pdb,
      const AjPStr res,
      ajuint 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)
ajuint	chn	Input	Chain number
AjBool		RETURN	True on succcess (res was found in pdb object)

From EMBOSS 2.9.0

Section: Miscellaneous

Functions:

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.
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.
embPdbResidueIndexC	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.
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.
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.
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.

Function embPdbListHeterogens

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

From EMBOSS 2.9.0

Function embPdbResidueIndexI

Prototype

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

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

From EMBOSS 3.0.0

Function embPdbResidueIndexC

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

From EMBOSS 3.0.0

Function embPdbResidueIndexICA

Prototype

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

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

From EMBOSS 3.0.0

Function embPdbResidueIndexCCA

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

From EMBOSS 3.0.0

Function embStrideToThree

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

From EMBOSS 2.9.0