Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!

-pdb_seq_num is used instead of auth_seq_num in get_ressers_mappings. Now resser2pdbresser contains all residues even the unobserved ones. This has been changed in PdbasePdb and CiffilePdb classes.

-pdb_strand_id not needed in the query in read_seq in PdbasePdb class. Asym_id and pdb_strand_id have 1-1 mapping in case sensitive mode.

-comments have been added about the entity_id-asym_id-pdb_strand_id 1-1-1 mapping and some filters in queries that are no longer necessary.

added class PairwiseSequenceAlignment

Pdb code forced to lowercase in CiffilePdb

New method getMotifReducedAlphabet to get neighbourhood strings in Michael's reduced style (must pass a Graph with weights which indicate BB or SC domination)

started implementing a wrapper for the Maxcluster application (some related code is now in SimilarityGraph but should be moved to MaxClusterRunner in the future)

New method setSequence

deleted the print part in the checkCSA method in pdb class

NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError

MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
 * writeFasta
 
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class

class GraphFileFormatError:
- s. class CiffileFormatError

class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment

class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter

class PdbFileFormatError:
- s. class CifffileFormatError

hasCSA and getCSA methods added in Pdb.java

inSameSheet, isOther and getSheetSerial methods added in SecStrucElement

Methods added for:
-parsing CSA
-parsing EC
-parsing CONSURF-HSSP
-running & parsing Naccess
-parsing SCOP
-writing residues' info in a db table

Modifications have been also made in DSSP parsing:
-sheet serial is taken into account
-flexibility in reduced state preferred

added a new version of getDiffDistMap(...) that take a sequence alignment as an input to allow for residue mappings between two pdb-models of different size

redesign of TinkerRunner: added 2 reconstruct methods, one which generates normal tinker output for a given number of models, and one fully automatic one which simply returns one pdb object;
updated reconstruct.java to make use of the new TinkerRunner method;
updated GraphAverager: now assigning edgetype and cutoff to consensus graph

finally implemented the setCutoff method ;)

fixed nasty bug in constructor Graph(sequence) (residue indexing was wrong)

added method setCutoff() and some javadocs

Fixed bug: getContacts was not copying weights
Got rid of useless copyKeepingNodes(), made main Graph constructor public. Some new setters and getters

New method getEdge in EdgeSet, necessary since we introduced weights in the Edge class. To retrieve them we first need to retrieve the actual Edge object

Method writeUndirUnweightGraphToNetworkFiles added in Graph class

renamed precision to accuracy (in accordance with Casp)

Now weights are kept in the Edge objects rather than separately in a member variable in Graph

Graph,PredEval: added fields coverage and title to predEval (and evalPrediction)
GraphAverager: added method to return average graph (with weighted edges)
PdbfilePdb: fixed bug when reading from Casp prediction files

Fixed bug: now does correctly quoting for any of the 3 cases: "", '' or ;;. Does also correctly multiline parsing of ;; quoted fields. Passed testing on cullpdb 90 (more than 9000 pdb entries)

Fixed bug: wasn't tokenising well when first field in line was quoted

FIXED BUG: now doesn't fail with records that are delimited with \n; ;\n
Method tokeniseFields is now completely rewritten: is what does all the magic of parsing all the oddities of the mmcif format
Using RandomAccessFile to open the file only once and then seek to the positions we need to scan at each point. Might be slower due to the RandomAccessFile that does no buffering. Also maybe because the new tokenisation is not very optimal
Now parseCifFile does the whole parsing calling also the submethods instead of calling them in the constructor

Changed constructor with all parameters to protected, now shouldn't be used at all outside of package

Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.

Fixed documentation

Added two new constructors for Graph (sequence only and no parameters), changed interface of GraphAverager (pass target sequence instead of target graph), extracted constant DEFAULT_WEIGHT in Edge.

extracted constant NULL_CHAIN_CODE from ...Pdb classes, added copy() methods to NodeSet and EdgeSet, added some functionality to NodesAndEdges, new class SimilarityGraph

Now ConstraintsMaker works also for multi atom contact types (BB and SC) and crosses (either BB/SC or any cross to a single atom contact type)
New file aapairsBounds.dat with values for aminoacid side chains distance lower and upper bounds taken from statistics of a set of pdb representatives
New in AAinfo: aapairs2bounds and changed getUpperBoundDistance, getUpperBoundDistance to accomodate aapairs2bounds
PRMInfo: now for amber "OXT" gets transformed into "O"

New class NodesAndEdges (simple graph class), some added javadocs

added constructor for trivial alignment, renamed getSequence to getAlignedSequence

Better handling of graph averaging for different thresholds
Refactored predict to doAveraging, not returning anymore a Grap but rather modifying the reference

added a weight field to Edge class (set using alternative constructor, maintaining backwards compatibility)

Added GraphAverager class and PredEval class. GraphAverager copied from HomologyPredictor (in CMPredict): doing the averaging correctly now
Added method evaluatePrediction to Graph
Some refactoring in Alignment and better javadocs

First commit of ConstraintsMaker (and PRMInfo needed for it)
Does correct atom serial mapping when using amber prm files, except for some atoms of ASP, ARG, GLU, PHE, TYR (where there are some nomenclature differences between amber and pdb)
Does not work yet with multi atom contact types, should work fine for all single atom contact types and for crossed single atom contact types
The pdb/xyz atom mapping using coordinates (as in python) is commented out because it doesn't work due to rounding differences between java and fortran
Thus the PRMInfo class was needed, at the moment can read only amber prm files
Some new methods and better javadoc in Pdb.
Some new methods in AAinfo

Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat
New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file
Changed all references accordingly

added parsing of residue selection strings

2 new methods: getAllAtomSerials, getAtomCoord

Moved tinker stuff to its own package

Initial commit of TinkerRunner and exception class to go with it TinkerError

added calculation of difference distance map

added constructors for loading from online pdb

added some javadoc comments

Fixed some comments

Now parsing each element in different methods (re-opening the file). Parsing first pdbx_poly_seq_scheme so we get the chainCode that we can use for reading the rest
Now taking care of cases where struct_sheet_range is not a loop element
In tokeniseFields now also unquoting double-quoted strings
Tested on a set of 12000 entries

Checking number of fields per line in loop elements and throwing exception if count is not correect
Doing tokenisation of lines through new function that takes care of possible quoted string with spaces
New exception CiffileFormatError
Checking 1st line of cif file has correct format: data_1xxx, if not throwing exception

Fixed buf: sometimes struct_conf can be non-loop elements, now also taking care of that particular case

Bug with '?' in auth_seq_num was not really fixed. Now should be fine: behaviour is the same as PdbasePdb

Fixed bug: needed to read alt locs in advance in another scan of the file because the order of the elements in the cif file is not guaranteed. As read of atom_site needs of alt locs, we need to do first the parsing of atom_sites_alt

Fixed bugs:
- was reading HETATM lines as well as ATOM in atom_site
- auth_seq_num with '?' not taken now when populating the pdbresser2resser map (same behaviour as in PdbasePdb)
- now using chainCodeStr and auth_asym_id to identify chains in pdbx_poly_seq_scheme, struct_conf and struct_sheet_range. atom_site is not guaranteed to appear in file before all the others so we can't rely on having read a chainCode (asym_id) when parsing the other elements

Now taking indices for fields from parsed field names. Still only minimal testing

First implementation of mmCIF file parser. Tested minimally.

Got rid of useless (and potential bug) chainCode=getChainCode (self reference!)

changes to calcGridDensity, now also counts number of neighbouring non-empty grid cells

changed constant for unknown pdb code from "Unknown" to XXXX

Better checks for sequence equality in compare

Now also filling chain_pdb_code in write_graph_to_db

Fixed bug in  compare, wasn't assigning new weights

Introduced weights in Graph objects: we can read them from file or db and write them into file or db. On calling pdb.get_graph the weighs are taken as number of atom-edges per residue-edge (similar to Ioannis weights in chain_graph tables)

Wasn't deep copying secondary structure when passing it to Graph

Made get_graph a bit less memory hungry, by using a float[][] instead of double[][]
Not printing warnings about missing atoms anymore

fixed little bug in NodeNbh

changed internal implementation of runDssp method (not using getFullLength anymore)

Fixed bug in Graph constructor: was not getting correct fullLength (related to last bug fix)

Fixed bug with getFullLength when reading from pdb file
Now if SEQRES was missing then fullLength is maximum observed residue number instead of total number of observed residue numbers
New member variables obsLength and fullLength

Added secondary structure to write_graph_to_db
New method getNumSecStructureElements in SecondaryStructure

Fixed bug: wasn't taken into account OXT atoms in calculating the ALL graph

Added new SecondaryStructure object to Pdb and Graph

Fixed potential bug in regex for ATOM lines

Was still not fixed!, forgot to insert X for non standard aa

Fixed reading of SEQRES, was putting nulls for non-standard aas

Implemented write_graph_to_db
New member variable model in Graph, thus changed constructor
New methods to get degree of a node in Graph
New methos in NodeNbh to write other kinds of neighbourhood strings

completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes

Now reading sequence from SEQRES lines. This fixes bug in cmview window was not showing whole contact map because of size of contact map was set to number of observed residues size

fixed bugs in ATOM line export (atom names were wrongly aligned & added three more columns after coordinates), added method to run DSSP (still incomplete)

Added getNumAtoms

PdbfilePdb now also accepts Casp prediction files ('PFRMAT TS' instead of 'HEADER')

Made constructor public

added application to count grid density, suppressed warning for secondary structure reassignment

New methods containsContact and resetContacts

Added method hasTag

Made regex a constant and added | and \\-

Doing now everythin with maps (using seqTags) rather than arrays. Cleaned up, refactored, using more consistent naming

Added reverse map (from sequences serials to alignment serials) and did a bit of refactoring

Initial commit of Alignmnent, a class representing a multiple sequence alignment

Got rid of doneRes ArrayList in getRanks, was redundant

Now dealing correctly with ties.
Implemented getResiduesSortedByRank
Changed dist to be a TreeMap

Fixed bug in delEdge. Wasn't taking care of if contact was given as i>j in undirected case. Also recount of contacts and set of modified to true was wrong

Fixed bug in addEdge method. In case of undirected we need to check that the contact is inserted in the right order j>i

Optimised slightly the compareTo method in Edge

Now rmsd calculation works for 2 Pdb objects where there are missing residues (unobserved) or missing atoms
New Exception ConformationNotSameSizeError
Still not printing out individual distances between 2 conformations (altghough it is possible)
Can't specify yet a restricted range of residues to calculate rmsd only with them

Fixed bug. Was not doing correctly reflection along smallest principal axis in is_reflection case

Implemented rmsd calculation (based on Jama matrix package)
rmsd method still not taking care of unobserved or missing atoms. Also not returning individual distances between optimally superimposed structures (although it can calculate them in commented out code)

Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING: 
ContactList -> EdgeSet
Contact -> Edge

Added method getCopy

Now checking in addEdge that we don't duplicate edges
New methods: get2ndshell, copyKeepingNodes

added class NodeSet

Now calculate_dist_matrix returns the matrix with residue serials as indices (rather than atom serials)
Now AA.isValidSingleCT and AA.isValidMultiCT check also for crossed cases

Now can do crossed contacts also with geometric hashing
Renamed getGraphGeometricHashing to get_graph (so interface remains as it was before we introduced the geometric hashing)

First geometric hashing implementation for calculating graph (with new class Box). Only does non-crossed cts
Geometrich hashing graph calculation kept in a separate method than normal get_graph. Still either of the methods can be used.
Using javax.vectormath objects for the vectors (distance method also from that)
Using TreeMap for get_coords_for_ct

Now calculate distance matrix uses HashMap instead of TreeMap
Needed to change the hashCode function in Contact to make it faster

Added cross contacts to isValidCT

New secstruct2resinterval TreeMap to store secondary structure elements as a map of ss string ids to intervals
New class Interval

Now reading also secondary structure (in a map of residue serials to secondary structure identifiers)

now casting pdb codes to lower and pdb chain codes to upper in all constructors

Fixed bug: ATOM lines printing was locale dependant, thus was printing ',' for decimal separators in some locales

some clean up of exceptions in Pdb and Graph classes:
merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError,
created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead

Fixed bug in regex introduced in last revision

Fixed graph file format checking, was not working properly

Now throwing also SQLExceptions for individual queries, not just for connections

Throwing exception also in case graph file not in right format at all (no #AGLAPPE in 1st line)
Fixed bug: was not reading correctly #PDB CHAIN CODE

FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError

Restructured construction of Pdb and Graph objects: now subclasses for each case
Cleaned up and made consistent database connections
Now can also pass a MySQLConnection in all cases (as well as having default values for a default connection)
PdbaseInfo and MsdsdInfo classes removed: now merged into PdbasePdb and MsdsdPdb respectively
Updated following this changes testPdb and compareCMs

Major refactoring:
 accode -> pdbCode
 chaincode -> pdbChainCode
 chain -> chainCode
Major change of signatures (publics to privates)
Implemented getters for needed member variables
Major clean up

Using apache xmlrpc version 3.0 in PyMolServerOutputStream

MySQLConnection now throwing SQLException on connect
Many files changed following this: all calling classes now re-throwing or catching the SQLException

New isValidCT methods in AA
New method get_resser_from_atomser in Pdb

Implemented getRanks()

AA class is now db independent:
Hard coded getaas2atoms, not getting it anymore from db.

Added toString and getMotifFullGaps missing in EdgeNbh

Made contactTypes a String[]

Added contactTypes method and made private methods private

Moved motif static methods to Background class. They didn't belong here

Made contacts public

New method getAllEdgeNbhSizes

NEW FEATURE: mapping of pdb residue serials and internal serials in the Pdb object

Added basic compare method to the Graph class and test class compareCMs

FIXED BUG: The returned regex in motif2regex was wrong, needed a ".*" at the beginning

Implemented hashCode method in Contact and GenericContact. Was necessary to use these classes as keys in Maps
Fixed bug in equals method in GenericContact
Changed middle character from "\t" to " " in toString

New class GenericContact. To store a generic contact, i.e. a pair of residue types

Fixed bug: calculateEntropy was wrong when a pi was 0

FIXED BUG: the switch statement was missing the breaks
This was causing strange behaviour in counts NodeBackground getSize methods and also was making them being too slow

New class NbhProbDistribution
In NodeNbh implemented a few static classes to convert between different motifs and to match motifs using differing criteria

FIXED BUG: fixed restrictContactsToMax/MinRange. Couldn't delete contacts at the same time as looping in them
NEW CLASSES NodeNbh and EdgeNbh, now used in getNodeNbh and getEdgeNbh
New method getResidueType

Fixed bug in getMaxRange method, was not assigning to the max variable
Added toString method to Contact

FIXED BUG in initialisation of fullLength when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from new class ContactList
NEW FUNCTIONALITY in Graph:
-New member variable modified
-New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy
-Improved slightly the implementation of getEdgeNbh 
FIXED BUG in initialisation of fullLenght when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from ContactList
New class ContactList
NEW FUNCTIONALITY in Graph:
-New member variable modified
-New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy
-Improved slightly the implementation of getEdgeNbh 
New method getRange in Contact

Got rid of some unnecessary warnings

New functionality: added methods to get node/edge neighbours

made Graph.directed public

Moved ContactMap and EdgeState out of this repository. 
Extra functionality of ContactMap now in Graph:
- new member variables fullLength, obsLength, numContacts. New method getIntMatrix
- removed getCM method

FIXED BUG in get_db_graph_info, was not dealing well with the case of chaincode being NULL in the database

FIXED BUG: in getCM when directed was passing a reference to the contacts object and not deep copying it!

Now passing also chaincode from Pdb object to Graph object in get_graph

Fixed bug: wasn't initialising accode, chain and chaincode when reading to file. Now all set to "" when not present in file

Recoded chain reading in read_pdb_data_from_file to make it clearer, no change in functionality

NEW FUNCTIONALITY: Reading from pdb file given chain code or model serial fully implemented
Changed the chain that is dumped in dump2pdbfile directly to the Pdb.chain field i.e. internal chain identifier
Loads of new comments, including java doc for all constructors

FIXED 2 BUGS. NEW FEATURE reading graph from db given graph_id
Bugs:
- nodes TreeMap in read_graph_from_file contained one letter res codes, now three letter codes
- in getCM was passing residues as a TreeMap of nums to three letter residue types, now passing one letter residue types
New constructor for getting graph from db given graph_id, new method to go with that get_db_graph_info

Made cutoff and ct public

Made some fields public: sequence, accode, chaincode, model

NEW FEATURE: Read and write graphs from file fully implemented.

Refactored read_contacts_from_file to read_graph_from_file. Now can read other fields as well as contacts. Also gets nodes if sequence present
New method write_graph_to_file

FIXED BUG: last commit didn't fix bug correctly:
Changed the ContactMap constructor to put into residueNums and residueTypes nums from 1 to maximum of residues.keySet()

Made public accode and chain fields in Graph

FIXED BUG: getCM wasn't working well when reading from db and there were unobserved residues

Now setting the sequence to blank when reading from db. Also when reading from file (still nodes reading is not implemented)
In ContactMap constructor different handling when sequence is blank

Changed input in constructor for reading from db: chain->chaincode
Now getgraphid initialises too the internal chain code (pchain_code from graph db)

Made Pdb.acccode public

Changed default accode and chaincode to "Unknown" when reading from pdb file

FIXED BUG: wasn't setting the chain field when reading from msdsd

Made chain field in PDB class public

FIXED BUG: pdb data load from msdsd wasn't working for NULL chaincodes

NEW FUNCTIONALITY: reading of graph from db is fully implemented for all cases

New chain member variable in the Info classes, read in get_asym_id (Pdbase) and in get_chain_id (Msdsd)
Reading chain also in Pdb in read_pdb_data_from_file
Not reading chain anymore in read_atomData of PdbaseInfo
Added oneletter2threeletter and getoneletter2threeletter to AA class
Changes in Graph:
- added db static vars and getUserName method
- new member variables graphid and sm_id
- new method read_graph_from_db to read contacts, nodes (and sequence from nodes) from db
- new method getgraphid
New Exception class GraphIdNotFoundError

Implemented basic reading contacts from file

New functionality: now can create a Pdb object passing a model serial for NMR structures. Not implemented when reading from pdb files!

2 new convenience methods: getBoolMatrix and getIntMatrix
Got rid of method to print constraint equations, was useless

NEW FEATURE: reading pdb data from msdsd
New classes MsdsdInfo and its exception classes
FIXED BUG in dump2pdbfile in Pdb: was not sorting the atom lines

NEW FUNCTIONALITY: can retrieve now a ContactMap object from a Graph object
New method getCM in Graph. New member variables: sequence, accode, chain, nodes, directed
Passing more data from Pdb to Graph in get_graph
New constructor in ContactMap

ContactMap and EdgeState classes moved here from CMPredict repository

Implemented read of pdb data from pdb file.
FIXED BUG in dumping of pdb file. Was missing end of line in atom lines
Added more tests in testPdb

MYSQLUSER now taken from unix name with new getUserName method

Added error handling for PdbaseInfo: 2 new exception classes

Initial commit of the proteinstructure package. Contains classes to use pdb protein structures