ajpdb

Data type AjPAtom

Holds protein atom data

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

Alias name(s)

Name	Description
AjSAtom
AjOAtom

Attributes

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

Attributes

Name	Type	Description
Mod	Model number.
Chn	Chain number.
Idx	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	Element serial number (for secondary structure from the PDB file).
Pdb	Residue number string from the original PDB file.
Id3	3-letter residue identifier code.
eId	Element identifier (for secondary structure from the PDB file).
eClass	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	Number of the element: sequential count from N-term (for secondary structure from STRIDE).
Phi	Phi angle.
Psi	Psi angle.
Area	Residue solvent accessible area.
all_abs	Absolute accessibility, all atoms.
all_rel	Relative accessibility, all atoms.
side_abs	Absolute accessibility, atoms in sidechain.
side_rel	Relative accessibility, atoms in sidechain.
main_abs	Absolute accessibility, atoms in mainchain.
main_rel	Relative accessibility, atoms in mainchain.
npol_abs	Absolute accessibility, nonpolar atoms.
npol_rel	Relative accessibility, nonpolar atoms.
pol_abs	Absolute accessibility, polar atoms.
pol_rel	Relative accessibility, polar atoms.
Id1	Standard 1-letter residue identifier or 'X' for unknown types.
eType	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	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	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	Description
AjSChain
AjOChain

Attributes

Name	Type	Description
Nres	No. of amino acid residues.
Nlig	No. of groups which are non-covalently associated with the chain, excluding water ("heterogens").
numHelices	No. of helices in the chain according to the PDB file.
numStrands	No. of strands in the chain according to the PDB file.
Seq	Protein sequence as string.
Atoms	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	List of Residue objects for (potentially multiple models) of the polypeptide chain.
Id	Chain id, ('.' if one wasn't specified in the PDB file).
Padding	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	Description
AjSPdb
AjOPdb

Attributes

Name	Type	Description
Pdb	PDB code.
Compnd	Text from COMPND records in PDB file.
Source	Text from SOURCE records in PDB file.
Method	Experiment type, either XRAY or NMR.
Reso	Resolution of an XRAY structure or 0.
Nmod	No. of models (always 1 for XRAY structures).
Nchn	No. polypeptide chains.
Chains	Array of pointers to AjSChain structures.
gpid	Array of chain (group) id's for groups that could not be uniquely associated with a chain.
Groups	List of Atom objects for groups that could not be uniquely associated with a chain.
Water	List of Atom objects for water molecules.
Ngp	No. groups that could not be uniquely associated with a chain in the SEQRES records.
Padding	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 (retrive 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	Description
AjSHetent
AjOHetent

Attributes

Name	Type	Description
abv	3-letter abbreviation of heterogen.
syn	Synonym.
ful	Full name.
cnt	No. of occurences (files) of this heterogen in a directory.
Padding	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	Description
AjSHet
AjOHet

Attributes

Name	Type	Description
entries	Array of entries.
n	Number of entries.
Padding	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	Description
AjSVdwres
AjOVdwres

Attributes

Name	Type	Description
Id3	3 character residue identifier.
Atm	Array of atom identifiers.
Rad	Array of van der Waals radii.
N	Nummber of atoms in residue.
Id1	Standard residue identifier or 'X' for unknown.
Padding	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	Description
AjSVdwall
AjOVdwall

Attributes

Name	Type	Description
Res	Array of Vdwres structures.
N	Number of residues.
Padding	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	Description
AjSCmap
AjOCmap	for intra-chain, inter-chain and chain-ligand contacts respectively.

Attributes

Name	Type	Description
Id	Protein id code.
Domid	Domain id code.
Ligid	Ligand id code.
Chn1	Chain number 1 (first chain)
Chn2	Chain number 2 (second chain if available)
Nres1	Number of residues in chain/domain 1
Nres2	Number of residues in chain/domain 2
Seq1	The sequence of the first domain or chain.
Seq2	The sequence of the second domain or chain.
Mat	Contact map.
Dim	Dimension of contact map.
Ncon	No. of contacts (1's in contact map).
en	Entry number.
ns	No. of sites (ajLIGAND only)
sn	Site number (ajLIGAND only)
Type	Type of contact, either ajINTRA, ajINTER or ajLIGAND
Desc	Description of ligand (ajLIGAND only)
Chid1	Chain identifier 1 (first chain)
Chid2	Chain identifier 2 (second chain if available)
Padding	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	Description
AjSPdbtosp
AjOPdbtosp

Attributes

Name	Type	Description
Pdb	PDB code
Acc	Accession numbers
Spr	Swissprot codes
n	No. entries for this pdb code
Padding	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.