embpdb.c

Operators

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

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embAtomDistance

Returns the distance (Angstroms) between two atoms.

Synopsis

Prototype

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

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

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 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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

Miscellaneous

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

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 logf
);

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

logf:(Modify)Log file for error messages

Returns

AjBool:ajTrue on success

Description

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.

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 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
);

Input

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

Output

idx:(Output)Index array

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. 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

See Also

See other functions in this section

Availability

In release 3.0.0

Function 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.

Synopsis

Prototype

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

Input

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

Output

idx:(Output)Index array

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. 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

See Also

See other functions in this section

Availability

In release 3.0.0

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,
      AjPInt* idx,
      ajint* nres
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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,
      AjPInt* idx,
      ajint* nres
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

Input

from:(Input)String to read

Output

to:(Output)String to write

Returns

AjBool:True on succcess

Description

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.

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