ajpdb

Enum AjECmapType

Enumerated value(s)

Name
ajECmapTypeNULL	NULL
ajECmapTypeIntra	Intra-molecular contact
ajECmapTypeInter	Inter-molecular contact
ajECmapTypeLigand	Ligand contact

Enum AjEPdbMethod

Enumerated value(s)

Name
ajEPdbMethodNULL	NULL
ajEPdbMethodXray	Structure was determined by X-ray crystallography
ajEPdbMethodNmr	Structure was determined by NMR or is a model

Enum AjEPdbMode

Enumerated value(s)

Name
ajEPdbModeNULL	NULL
ajEPdbModePdb	Original PDB residue numbering
ajEPdbModeIdx	Corrected residue numbering (index into SEQRES sequence)

Data type AjPAtom

Holds protein atom data

AjPAtom is implemented as a pointer to a C data structure.

Alias name(s)

Name
AjSAtom
AjOAtom

Attributes

Name	Type	Description
Mod	ajuint	Model number
Chn	ajuint	Chain number
Gpn	ajint	Group number
Idx	ajuint	Residue number - index into sequence.
Pdb	AjPStr	Residue number string from the original PDB file.
Id3	AjPStr	Residue or group identifier.
Atm	AjPStr	Atom identifier.
X	float	X coordinate.
Y	float	Y coordinate.
Z	float	Z coordinate.
O	float	Occupancy.
B	float	B value thermal factor.
Id1	char	Standard residue identifier or 'X' for unknown types or '.' for heterogens and water.
Type	char	'P' (protein atom), 'H' ("heterogens") or 'W' (water).
Padding	char[2]	Padding to alignment boundary

Constructor(s)

Name	Description
ajAtomNew	Default Atom constructor.

Destructor(s)

Name	Description
ajAtomDel	Default Atom destructor.

Assignment(s)

Name	Description
ajAtomCopy	Replicates an Atom object.
ajAtomListCopy	Replicates a list of Atom objects.

Operator(s)

Name	Description
embAtomInContact	Determines whether two atoms are in physical contact.
embAtomDistance	Returns the distance (Angstroms) between two atoms.
embVdwRad	Returns the van der Waals radius of an atom.

Other related data structure(s)

Name	Description
embPdbListHeterogens	Construct a list of arrays of Atom objects for ligands in the current Pdb object (a single array for each ligand).

Data type AjPResidue

Holds data for an amino acid residue.

AjPResidue is implemented as a pointer to a C data structure.

Alias name(s)

Name
AjSResidue
AjOResidue

Attributes

Name	Type	Description
Mod	ajuint	Model number
Chn	ajuint	Chain number
Idx	ajuint	Residue number. Can be used to index into the polypeptide sequence (the Seq element of an AjSChain object). Idx numbers start at 1 and run sequentially.
eNum	ajint	Element serial number (for secondary structure from the PDB file).
Pdb	AjPStr	Residue number string from the original PDB file.
Id3	AjPStr	3-letter residue identifier code.
eId	AjPStr	Element identifier (for secondary structure from the PDB file).
eClass	ajint	Class of helix, an int from 1-10, from http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html (for secondary structure from the PDB file).
eStrideNum	ajint	Number of the element: sequential count from N-term (for secondary structure from STRIDE).
Phi	float	Phi angle.
Psi	float	Psi angle.
Area	float	Residue solvent accessible area.
all_abs	float	Absolute accessibility, all atoms.
all_rel	float	Relative accessibility, all atoms.
side_abs	float	Absolute accessibility, atoms in side chain.
side_rel	float	Relative accessibility, atoms in side chain.
main_abs	float	Absolute accessibility, atoms in main chain.
main_rel	float	Relative accessibility, atoms in main chain.
npol_abs	float	Absolute accessibility, non-polar atoms.
npol_rel	float	Relative accessibility, non-polar atoms.
pol_abs	float	Absolute accessibility, polar atoms.
pol_rel	float	Relative accessibility, polar atoms.
Id1	char	Standard 1-letter residue identifier or 'X' for unknown types.
eType	char	Element type COIL ('C'), HELIX ('H'), SHEET ('E') or TURN ('T'). Has a default value of COIL (for secondary structure from the PDB file).
eStrideType	char	Element type: ALPHA HELIX ('H'), 3-10 HELIX ('G'), PI-HELIX ('I'), EXTENDED CONFORMATION ('E'), ISOLATED BRIDGE ('B' or 'b'), TURN ('T') or COIL (none of the above) ('C') (for secondary structure from STRIDE).
Padding	char[1]	Padding to alignment boundary

Constructor(s)

Name	Description
ajResidueNew	Default Residue constructor.

Destructor(s)

Name	Description
ajResidueDel	Default Residue destructor.

Assignment(s)

Name	Description
ajResidueCopy	Replicates a Residue object.
ajResidueListCopy	Replicates a list of Residue objects.

Operator(s)

Name	Description
ajResidueEnv1	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv2	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv3	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv4	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv5	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv6	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv7	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv8	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv9	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv10	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv11	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv12	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv13	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv14	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv15	Assigns environment based on side chain accessibility and secondary structure.
ajResidueEnv16	Assigns environment based on side chain accessibility and secondary structure.
ajResidueSSEnv	Assigns secondary structure environment of a residue.

Data type AjPChain

Holds protein chain data

AjPChain is implemented as a pointer to a C data structure.

Alias name(s)

Name
AjSChain
AjOChain

Attributes

Name	Type	Description
Nres	ajuint	Number of amino acid residues.
Nlig	ajuint	Number of groups which are non-covalently associated with the chain, excluding water ("heterogens").
numHelices	ajint	No. of helices in the chain according to the PDB file.
numStrands	ajint	No. of strands in the chain according to the PDB file.
Seq	AjPStr	Protein sequence as string.
Atoms	AjPList	List of Atom objects for (potentially multiple models) of the polypeptide chain and any groups (ligands) that could be uniquely associated with a chain.
Residues	AjPList	List of Residue objects for (potentially multiple models) of the polypeptide chain.
Id	char	Chain id, ('.' if one wasn't specified in the PDB file).
Padding	char[7]	Padding to alignment boundary

Constructor(s)

Name	Description
ajChainNew	Default Chain constructor.

Destructor(s)

Name	Description
ajChainDel	Default Chain destructor.

Data type AjPPdb

Holds arrays describing pdb data

AjPPdb is implemented as a pointer to a C data structure.

Alias name(s)

Name
AjSPdb
AjOPdb

Attributes

Name	Type	Description
Pdb	AjPStr	PDB code
Compnd	AjPStr	Text from COMPND records in PDB file
Source	AjPStr	Text from SOURCE records in PDB file
Method	AjEPdbMethod	AJAX PDB Method enumeration
Reso	float	Resolution of an XRAY structure or 0
Nmod	ajuint	Number of models (always 1 for XRAY structures)
Nchn	ajuint	Number of polypeptide chains
Chains	AjPChain*	Array of pointers to AjSChain structures
gpid	AjPChar	Array of chain (group) id's for groups that could not be uniquely associated with a chain.
Groups	AjPList	List of Atom objects for groups that could not be uniquely associated with a chain.
Water	AjPList	List of Atom objects for water molecules.
Ngp	ajuint	Number of groups that could not be uniquely associated with a chain in the SEQRES records.
Padding	char[4]	Padding to alignment boundary

Constructor(s)

Name	Description
ajPdbNew	Default Pdb constructor.
ajPdbReadRawNew	Pdb constructor from reading pdb format file.
ajPdbReadNew	Pdb constructor from reading CCF format file.
ajPdbReadFirstModelNew	Pdb constructor from reading CCF format file (retrieve data for 1st model only).
ajPdbReadoldNew	Pdb constructor from reading CCF format file lacking residue-level description in RE records.
ajPdbReadoldFirstModelNew	Pdb constructor from reading CCF format file lacking residue-level description in RE records.

Destructor(s)

Name	Description
ajPdbDel	Default Pdb destructor.

Assignment(s)

Name	Description
ajPdbCopy	Replicates a Pdb object.

Operator(s)

Name	Description
ajPdbGetEStrideType	Reads a Pdb object and writes a string with the secondary structure.
ajPdbChnidToNum	Finds the chain number for a given chain identifier.
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.
embPdbidToSp	Read a pdb identifier code and writes the equivalent swissprot identifier code.
embPdbidToAcc	Read a pdb identifier code and writes the equivalent accession number.
embPdbidToScop	Writes a list of scop identifier codes for the domains that a Pdb object contains.

Cast(s)

Name	Description
embPdbAtomIndexI	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.
embPdbAtomIndexICA	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.
embPdbAtomIndexCCA	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.

Output

Name	Description
ajPdbWriteDomainRecordRaw	Writes lines to a pdb format file for a domain.
ajPdbWriteRecordRaw	Writes lines to a pdb format file for a protein.
ajPdbWriteAllRaw	Writes a pdb-format file for a protein.
ajPdbWriteDomainRaw	Writes a pdb-format file for a SCOP domain.
ajPdbWriteAll	Writes a CCF-format file for a protein.
ajPdbWriteDomain	Writes a CCF-format file for a domain).
ajPdbWriteSegment	Writes a CCF-format file for a segment of a protein.

Cast(s)

Name	Description
embPdbListHeterogens	Construct a list of arrays of Atom objects for ligands in the current Pdb object (a single array for each ligand).

Data type AjPHetent

Holds a single entry from a dictionary of heterogen groups.

AjPHetent is implemented as a pointer to a C data structure.

Alias name(s)

Name
AjSHetent
AjOHetent

Attributes

Name	Type	Description
abv	AjPStr	3-letter abbreviation of heterogen.
syn	AjPStr	Synonym.
ful	AjPStr	Full name.
cnt	ajint	No. of occurrences (files) of this heterogen in a directory.
Padding	char[4]	Padding to alignment boundary

Constructor(s)

Name	Description
ajHetentNew	Default Hetent constructor.

Destructor(s)

Name	Description
ajHetentDel	Default Hetent destructor.

Data type AjPHet

AjPHet is implemented as a pointer to a C data structure.

Alias name(s)

Name
AjSHet
AjOHet

Attributes

Name	Type	Description
Entries	AjPHetent*	Array of AJAX Heterogen Entries
Number	ajuint	Number of entries
Padding	char[4]	Padding to alignment boundary

Constructor(s)

Name	Description
ajHetNew	Default Het constructor.
ajHetReadRawNew	Het constructor from reading dictionary of heterogen groups in raw format.
ajHetReadNew	Het constructor from reading dictionary of heterogen groups in embl-like format (see documentation for the EMBASSY DOMAINATRIX package).

Destructor(s)

Name	Description
ajHetDel	Default Het destructor.

Output

Name	Description
ajHetWrite	Write Het object to file in embl-like format (see documentation for the EMBASSY DOMAINATRIX package).

Data type AjPVdwres

Holds the Van der Waals radius for atoms in a residue

AjPVdwres is implemented as a pointer to a C data structure.

Alias name(s)

Name
AjSVdwres
AjOVdwres

Attributes

Name	Type	Description
Id3	AjPStr	3 character residue identifier.
Atm	AjPStr*	Array of atom identifiers.
Rad	float*	Array of van der Waals radii.
N	ajuint	Number of atoms in residue.
Id1	char	Standard residue identifier or 'X' for unknown.
Padding	char[3]	Padding to alignment boundary

Constructor(s)

Name	Description
ajVdwresNew	Default Vdwres constructor.

Destructor(s)

Name	Description
ajVdwresDel	Default Vdwres destructor.

Data type AjPVdwall

Holds the Van der Waals radii for all types of protein atoms

AjPVdwall is implemented as a pointer to a C data structure.

Alias name(s)

Name
AjSVdwall
AjOVdwall

Attributes

Name	Type	Description
Res	AjPVdwres*	Array of Vdwres structures.
N	ajuint	Number of residues.
Padding	char[4]	Padding to alignment boundary

Constructor(s)

Name	Description
ajVdwallNew	Default Vdwall constructor.
ajVdwallReadNew	Vdwall constructor from reading file in embl-like format (see documentation for the EMBASSY DOMAINATRIX package).

Destructor(s)

Name	Description
ajVdwallDel	Default Vdwall destructor.

Data type AjPCmap

Holds a contact map and associated data for a protein domain / chain (intra or inter-chain contacts) or between a protein / domain and a ligand. For ligand contacts, the first row / column only of the contact map is used.

AjPCmap is implemented as a pointer to a C data structure.

Alias name(s)

Name
AjSCmap
AjOCmap

Attributes

Name	Type	Description
Id	AjPStr	Protein id code.
Domid	AjPStr	Domain id code.
Ligid	AjPStr	Ligand id code.
Chn1	ajint	Chain number 1 (first chain)
Chn2	ajint	Chain number 2 (second chain if available)
Nres1	ajint	Number of residues in chain/domain 1
Nres2	ajint	Number of residues in chain/domain 2
Seq1	AjPStr	The sequence of the first domain or chain.
Seq2	AjPStr	The sequence of the second domain or chain.
Mat	AjPUint2d	Contact map.
Dim	ajint	Dimension of contact map.
Ncon	ajint	No. of contacts (1's in contact map).
en	ajint	Entry number.
ns	ajint	No. of sites (ajLIGAND only)
sn	ajint	Site number (ajLIGAND only)
Type	AjECmapType	AJAX Cmap Type enumeration
Desc	AjPStr	Description of ligand (ajLIGAND only)
Chid1	char	Chain identifier 1 (first chain)
Chid2	char	Chain identifier 2 (second chain if available)
Padding	char[6]	Padding to alignment boundary

Constructor(s)

Name	Description
ajCmapNew	Default Cmap constructor.
ajCmapReadINew	Cmap constructor from reading file in CON (embl-like)format (see documentation for the EMBASSY DOMAINATRIX package).
ajCmapReadCNew	Cmap constructor from reading file in CON format (see documentation for the EMBASSY DOMAINATRIX package).
ajCmapReadNew	Cmap constructor from reading file in CON format (see documentation for the EMBASSY DOMAINATRIX package).
ajCmapReadAllNew	Constructs list of Cmap objects from reading file in CON format (see documentation for the EMBASSY DOMAINATRIX package).

Destructor(s)

Name	Description
ajCmapDel	Default Cmap destructor.

Output

Name	Description
ajCmapWrite	Write Cmap object to file in CON format.

Data type AjPPdbtosp

Holds swissprot codes and accession numbers for a PDB code.

AjPPdbtosp is implemented as a pointer to a C data structure.

Alias name(s)

Name
AjSPdbtosp
AjOPdbtosp

Attributes

Name	Type	Description
Pdb	AjPStr	PDB code
Acc	AjPStr*	Accession numbers
Spr	AjPStr*	Swissprot codes
Number	ajuint	Number of entries for this pdb code
Padding	char[4]	Padding to alignment boundary

Constructor(s)

Name	Description
ajPdbtospNew	Default Pdbtosp constructor.
ajPdbtospReadAllRawNew	Pdbtosp constructor from reading swissprot- pdb equivalence table in raw format.
ajPdbtospReadNew	Pdbtosp constructor from reading file in embl-like format (see documentation for the EMBASSY DOMAINATRIX package).
ajPdbtospReadCNew	Pdbtosp constructor from reading file in embl-like format (see documentation for the EMBASSY DOMAINATRIX package).

Destructor(s)

Name	Description
ajPdbtospDel	Default Pdbtosp destructor.

Constructor(s)

Name	Description
ajPdbtospReadAllNew	Constructor for list of Pdbtosp objects from reading file in embl-like format (see documentation for the EMBASSY DOMAINATRIX package).

Output

Name	Description
ajPdbtospWrite	Write Pdbtosp object to file in embl-like format (see documentation for the EMBASSY DOMAINATRIX package).

Operator(s)

Name	Description
ajPdbtospArrFindPdbid	Binary search for Pdb element over array of Pdbtosp objects.