version_5.1.txt

Changes from ProFlex v.5 to v.5.1:
-----------------------------------------------

An improved rainbow color scheme for showing flexibility index results in 
PyMol has been implemented in v. 5.1, when users choose that ProFlex option. 
The color scheme ranges from red (most flexible) to orange, yellow, then 
grey (isostatic, or just barely rigid), to light blue to dark blue (most rigid).

If you currently have a license for ProFlex v.5 and wish to upgrade to 
v.5.1, please contact the ProFlex Development Team for an upgrade patch and
installation instructions by sending an email to: kuhnlab@msu.edu.

License holders for versions of ProFlex prior to v.5 can also contact the
Development Team for a complete v.5.1 package for a fresh install.


Global changes from ProFlex v.4 to ProFlex v.5:
-----------------------------------------------

1) The environment variable $FIRSTPTB was substituted by $PROFLEX_HOME

2) All the sourcecode in 

   <$PROFLEX_HOME>/hbdilute/
   <$PROFLEX_HOME>/first/src/c++/
   <$PROFLEX_HOME>/first/src/fortran/

   has been updated to reflect the latest version (v5.0) and copyright 
   info (1997 - 2008).

3) Names/format of some of the output files has been changed:
   
    a) _FIRSTdataset    -> _proflexdataset
    b) _h-bonds.        -> _h-bonds_SEfilt. (stereochemically & 
                        energy filtered h-bond list)

4) Six new files are output in v5.0:
    
    a) preacptr_info
    
        - preacceptor atom numbers of all the H-bonds listed in
          the _proflexdataset

    b) _h-phobs_SEfilt.xxxx

        - Bond indices from _proflexdataset that correspond to the
          tether atoms. The _h-bonds_SEfilt.xxxx file will not contain
          any tether information unlike v4.0.  

    c) _flex_0001.pdb

        - A PDB format file with all the atom records including the 
          tethers used as an input to the program that writes out
          the PyMol scripts. The atom number field replaced by a 
          unique index mapping each atom to a unique rigid or flexibile
          cluster and b-value field is replaced by a flex_index score 
          that indicates the relative flexibility of each residue
          on a scale of 0 through 99 (0 - most rigid, 99 - most flexible,
          49-50 - isostatic) 

    d) <protein>_flex_0001.pml, <protein>_RC_0001.pml, and <protein>_FC_0001.pml

        - PyMol scripts for visualizing the protein flexibility 
          based on flex_index values, rigid cluster decomposition,
          and collectively moving clusters respectively.

List of output files from flexibility analysis:
===============================================

v5.0                v4.0        
----                ----    
<protein>_allbond.0001      <protein>_allbond.0001
<protein>_analysis.all      <protein>_analysis.all
<protein>_h-bonds_SEfilt.0001   <protein>_h-bonds.0001
<protein>_h-phobs_SEfilt.0001       -
<protein>_proflexdataset    <protein>_FIRSTdataset
<protein>_flex_0001.pdb         -
preacptr_info               -
    -           <protein>_bond_wt.0001
    -           <protein>_fig_0001.htm
    -           <protein>_fdecomp.0001
    -           <protein>_sdecomp.0001
    -           <protein>_rdecomp.0001
    -           <protein>_fig_0001.pdb
    -           <protein>_graphic.0001
    -           <protein>_Rscript.0001
    -           <protein>_txt_0001.htm

List of output files from H-bond dilution:
==========================================

v5.0                v4.0
----                ----
<protein>_h-bonds.ps        <protein>_h-bonds.ps
decomp_list         decomp_list
<protein>_h-bonds_SEfilt.0001   <protein>_h-bonds.0001
<protein>_h-phobs_SEfilt.0001       -


###########################################################################

            CODE CHANGES
           =====================

List of files changed:
----------------------

1) <$PROFLEX_HOME>/first/include/class.h

2) <$PROFLEX_HOME>/first/src/c++/main.cpp

3) <$PROFLEX_HOME>/first/src/c++/find_hbonds.cpp

4) <$PROFLEX_HOME>/first/src/c++/pick_hbonds.cpp

5) <$PROFLEX_HOME>/first/src/c++/makechem.cpp

6) <$PROFLEX_HOME>/first/src/c++/transitions.cpp

7) <$PROFLEX_HOME>/first/src/fortran/first.f

8) <$PROFLEX_HOME>/first/src/fortran/getfiles.f

9) <$PROFLEX_HOME>/first/src/fortran/hbdilute.f

10) <$PROFLEX_HOME>/first/src/fortran/outputfirst.f

11) <$PROFLEX_HOME>/first/src/fortran/read_hb_list.f

12) <$PROFLEX_HOME>/util/flex_index.cpp 

13) <$PROFLEX_HOME>/hbdilute/include/types.h

14) <$PROFLEX_HOME>/hbdilute/src/hbdilute.c

15) <$PROFLEX_HOME>/hbdilute/src/hbfunctions.c

16) <$PROFLEX_HOME>/hbdilute/src/postscript.c

17) <$PROFLEX_HOME>/hbdilute/include/postscript.h, hbfunctions.h, hbdilute.h

18) <$PROFLEX_HOME>/first/src/c++/fix_babel.cpp

19) <$PROFLEX_HOME>/../Makefile

----------------------------------------------------------------------

1) class.h

a) Changed maxnopt from 19 to 5
b) Changed donor-hydrogen maximum length from 2.6 to 2.5 A and
   acceptor-hydrogen length from 3.6 to 3.5 A to maintain consistency
   among various softwares (SLIDE, ROCK, ProFlex) designed by PSA lab.
c) Changed the minimum donor-hydrogen-acceptor (theta) angle from 80 to 110
d) Added the minimum hydrogen-acceptor-preacptr (delta) angle, set to 90
e) Changed the prototype for pick_hbonds() from (int) to (int,int)

-----------------------------------------------------------------------

2) main.cpp

a) OUTPUT MESSAGE CHANGED: 

  If wrong or no options specified then the old menu was:

  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

   Usage : ./proflex [-r] [-e] [-non] <-h|{-p|-pw}> <filename>

   <filename> Expected to have a .pdb or .PDB file extension.
              With the -p or -pw option the extension may be _FIRSTdataset.


      Option definitions:

      -non   Use for non-interactive hydrogen bond dilution.

      -h     Use with a PDB file including polar hydrogens (required by default).
             Hydrogens can be added explicitly by programs like WhatIf.

      -r     Distance between van der Waals surfaces of atoms participating
             in a hydrophobic interaction. 0.5 is default.

      -e     Max energy a hydrogen bond can have to be included in the analysis
            ( E.g. -0.1 for including only H-bonds with energy < -0.1 kcal/mol.
             Default = -0.1 kcal/mol)

      -p     Use when the original PDB file has been previously processed to 
         assign all bonds. *proflexdataset file from previous run must 
         exist in the same directory.

      -pw    Same as [-p] except previous warning messages are re-displayed.

   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

   The correponding new output is as follows:

   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    Usage : proflex [-r] [-e] [-nonh|nonf] <-h|{-p|-pw}> <filename>

    <filename> Expected to have a .pdb or .PDB file extension.
               With the -p or -pw option the input file may instead be the 
        _proflexdataset.


     Option definitions:

     -nonh   Use for non-interactive hydrogen bond dilution
     -nonf  Use for non-interactive flexibility analysis

            **NOTE: Any filtering using stereochemical, energy,
                    hydrophobic, side chain, and water criteria from the
                    previous ProFlex run generating the proflex_dataset file
                    are not applied in -non mode.  Only the default 
            stereochemical criteria are applied. Be sure to only 
            include buried water molecules in the input PDB file.**

     -h     Use with a PDB file having hydrogens
            Hydrogens can be added explicitly by programs like WhatIf.

     -r     Distance between van der Waal's surfaces of atoms participating
            in a hydrophobic interaction. 0.5 is default.

     -e     Maximum energy a hydrogen bond can have to be included in the analysis

     -p     Use when the original PDB file has been previously processed.
            *proflexdataset file from previous run must exist in the same 
        directory.

     -pw    Same as [-p] except previous warning messages are re-displayed.

   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

b) Changed "FIRSTdataset" to "proflexdataset" and also changed string lengths
   appropriately at multiple locations.
c) Changed the environment variable.
d) Added -nonf option to reflect Kevin Keating's changes for making ProFlex output
   compatible with StoneHinge
e) Added input validation for -r and -e options
f) The addition of stereochemical filters required some additional 
   user-interaction, which had to be eliminated for -nonh option.

-----------------------------------------------------------------------

3) find_hbonds.cpp

a) Added necessary code to extract the preacceptor atom number and stored it
   in the previously unused but allocated "hbond[][0]" array.

b) Implemented/rectified the mandatory stereochemical filters.

   The constraints that have to be satisfied for a H-bond to be included in
   the bond network for further processing are the hydrogen-acceptor and
   donor-acceptor distances and the theta (donor-H-acceptor) and delta 
   (H-acceptor-preacceptor) angles. Screen output showing each filtered
   H-bond with the specific constraint unsatisfied is generated and also
   written out into "filtered_Hbonds_log" file.

c) Fix for H-bonds without preacptr information formed due to water molecules
   with 'H' atoms missing in the input PDB file is that we identify such cases
   when the PDB file is read and the user is prompted to re-run ProFlex
   with a modified input PDB file with all the requisite data in the file.

d) For H-bonds involving waters, the pre-acceptor atom can be either one of
   the water hydrogens. We pick the H atom that makes a more obtuse delta 
   angle.

-----------------------------------------------------------------------

4) pick_hbonds.cpp

a) Added the following output:

   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    The following stereochemical rules serve as default selection criteria:

        Hydrogen-Acceptor distance  <= 2.5 Angstroms
                 with Sulphur atom  <= 3.0 Angstroms
                   for Salt-bridge  <= 3.5 Angstroms

        Donor-Acceptor distance     <= 3.5 Angstroms
              with Sulphur atom     <= 4.0 Angstroms
                for Salt-bridge     <= 4.5 Angstroms

        Theta (D-H-A angle)         >= 110 Degrees
        Delta (H-A-P angle)         >= 90  Degrees

    Do you wish to impose more stringent rules? (y/n):

   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

b) Implemented the more stringent rules and thorough input validation.

c) Added the following menu and implemented each of the individual filters.


   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

                        NON-COVALENT BOND SCREENING OPTIONS MENU

         1 : Keep *ALL* H-bonds involving WATER
                (Select this ONLY if you have included only
                 buried water molecules in the input PDB file)
         2 : Remove *ALL* H-bonds involving sidechain atoms
         3 : Remove *ALL* H-bonds involving non-water HETATOMs
         4 : Remove hydrophobic tethers
         5 : Use defaults (keep all hydrophobic tethers and H-bonds except 
        those including water)

         f : Finished selecting options; Continue to next step
         s : Stop program

        Enter Option:
   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

2006:04:10     
    - Changes to all the H-bond filters
    - sidechain-non-water HETATM filter added

            ~ This matters when the user only selects to remove 
        nonwater-HETATM H-bonds as this set of bonds were being 
        left out unscreened.

        - The atom name field format is as follows:

        '[][][atom-tye][position][label]' e.g.'  NH1','  CD '

          So, the filter should just check for the atom-type and 
      not the whole atom name

d) Added the new energy-based filter and the following menu:

   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

   Number of H-bonds remaining: 160

   Number of H-phobic tethers remaining: 109

                 Filter on Hydrogen Bond Energy:
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

        All current hydrogen bonds have energies between:
           -10.0000 Kcal/Mol  to  5.1156 Kcal/Mol

        Enter a maximum acceptable hydrogen bond energy (in Kcal/Mol): -1
   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


e) The corresponding old menu was:

   ========================================================================
                *OLD* Menu

                    H-BOND SCREENING OPTIONS MENU

         1 : Keep all hydrogen bonds ----> Default assumption
         2 : Keep mainchain-mainchain hydrogen bonds
         3 : Keep mainchain-sidechain hydrogen bonds
         4 : Keep mainchain-Non_water HETATM hydrogen bonds
         5 : Keep mainchain-WATER_atom hydrogen bonds
         6 : Keep sidechain-sidechain hydrogen bonds
         7 : Keep sidechain-Non_water HETATM hydrogen bonds
         8 : Keep sidechain-WATER_atom hydrogen bonds
         9 : Keep HETATM_atom-Non_water HETATM hydrogen bonds
        10 : Keep WATER_atom-WATER_atom hydrogen bonds
        11 : Interactively identify hydrogen bonds to keep
        12 : Filter on Donor-Hydrogen-Acceptor angle
        13 : Filter on Donor-Acceptor distance
        14 : Filter on Hydrogen-Acceptor distance
        15 : Filter on Hydrogen bond energy
        18 : Interactively identify hydrogen bonds to discard
        19 : Discard all hydrogen bonds

         f : Finished selection
         s : Stop program

        The "Keep" selections are subjected to post Filtering.
        Select one Option:  (Multiple selections are possible)

        Enter Option:
    ======================================================================

f) Added code to produce the following information.

   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

                          SELECTION CRITERIA

        Hydrogen bond geometric selection criteria:
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        Donor-Acceptor distance <= 3.5 Ang. without sulfur
        Donor-Acceptor distance <= 4 Ang. with sulfur
        Donor-Acceptor distance <= 4.5 Ang. Salt Bridge
        Hydrogen-Acceptor distance <= 2.5 Ang. without sulfur
        Hydrogen-Acceptor distance <= 3 Ang. with sulfur
        Hydrogen-Acceptor distance <= 3.5 Ang. Salt Bridge
        Donor-Hydrogen-Acceptor angle >= 110 Deg.
        Hydrogen-Acceptor-Preacceptor angle >= 90 Deg.

        Hydrogen bond energetic selection criteria:
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        Maximum allowed hydrogen bonding energy = -1 Kcal/Mol

        Criteria A = Donor-Acceptor Distance
        Criteria B = Hydrogen-Acceptor Distance
        Criteria C = Donor-Hydrogen-Acceptor Angle
        Criteria D = Hydrogen-Acceptor-Preacceptor Angle
        Criteria E = Relative H-bond energy top percentile
        Criteria F = H-bond energy
        Select bond when: [A .AND. B .AND. C .AND. D] .AND. (E .AND. F) = TRUE

        Non-covalent bond selection criteria:
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        Default: Remove *ALL* H-bonds involving waters
   ---------------------------------------------------------------------
   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

g) Added code to compute preacceptor-acceptor-H angle and perform H-bond 
   filtering based on it

h) Salt bridges do not have to be subjected to angular check and can be 
   accepted if H-A or D-A distance is acceptable

i) Added code to suppress user-interactive code when -non (hbdilution) and 
   -nonf (flexibility analysis) option is selected

-----------------------------------------------------------------------

5) makechem.cpp and (6) transitions.cpp

a) Examined and tested (with help from Maria) makechem.cpp 
    - In case, multiple residue or side-chain conformers exist in the 
   input PDB file ProFlex scans for a maximum occupancy conformer. 
   If it fails to find one then it looks for a low mobility conformer.

b) Implemented all the file name changes and changed the code that
   extracts the common prefix for each of the file names including
   the sizes of the filename holder variables.

c) (i) Incorporated code to change 'D'euterium atoms to 'H' atoms and
   process them, (ii) added a fix to handle 'ANISOU'tropic records 
   present in input PDB file

d) Missing polar hydrogens on any of the residues and waters are detected
   and the user is prompted to take necessary action before program terminates.
   This test has been revised to check each chain in the input and only for
   the standard residue types.

-----------------------------------------------------------------------

7) first.f

a) Modified the following analysis menu.

   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
                *NEW* Menu

    ANALYSIS MENU

   What would you like to perform:

    (1) Flexibility and Rigidity Analysis.
    (2) Hydrogen Bond Dilution.
   
   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

   ========================================================================
                *OLD* Menu
       ANALYSIS MENU

     What would you like to perform:

       (1) Flexibility and Rigidity Analysis.
       (2) Hydrogen Bond Dilution.
       (3) Bond Stripping.

   =========================================================================

b) Changed the input validation code accordingly, i.e., option choices 
   less than 1 and greater than 2 are flagged as erroneous and a message
   is output to the user.
   
c) Added fix to process -nonf option. (StoneHinge compatibility)

-----------------------------------------------------------------------

8) getfiles.f

a) Rewrote this file to ensure correct renaming of files by changing the
   naming logic.

-----------------------------------------------------------------------

9) hbdilute.f

a) Added following new menu:

   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
                *NEW* Menu

   Which hydrogen bond dilution analysis would you like?

   (1) Standard hydrogen bond dilution.

   (2) Random dilution over all H-bonds.
       NOTE: This option is not *recommended*;
             It may be used to probe the influence of H-bond
             density, as opposed to strength, on rigidity

   (3) Flexible region and rigid cluster analysis at a
       specific energy in the H-bond dilution.

   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   ========================================================================
                *OLD* Menu

   Which hydrogen bond dilution analysis would you like?

    (1) Standard Hydrogen Bond Dilution.

    (2) Random dilution over all bonds.

    (3) Rigid Cluster Analysis output files at a specific
       point in standard dilution.

   ========================================================================

b) Examined each of the above options for correctness and tested them.
   Also, made some changes to ensure consistency in output files produced
   for each of the options. Also, added code to produce separate h-bond and
   h-phob (hydrophobic tether) files.

c) Rewrote code for option 3 to allow filtering with respect to an energy
   cutoff rather than an H-bond number. One of the changes is to handle
   the hbond list correctly that was previously sorted in the ascending order
   of energy.

d) Changed code corresponding to fetching files from a user-specified
   "PROFLEX" directory and changes to account for the filename changes
   such as "FIRSTdataset" to "proflexdataset".

e) Detected a bug in h-bond count being passed to another function,
   which resulted in out-of-bound memory access, and fixed it.

f) Added fix to suppress some output in -non option. 

-----------------------------------------------------------------------

10) outputfirst.f

a) Added code to output (or suppress) tether info into hphob-file and 
   h-bonds into h-bond file based on user-selected options.

b) Added code to output the correct number of h-bonds and tethers into
   the "_analysis_" file and the display.

c) Added a fix for processing the -nonf option added by Kevin for StoneHinge.

-----------------------------------------------------------------------

11) read_hb_list.f

a) Minor addition of code to make a note of any tethers being processed

-----------------------------------------------------------------------

12) flex_index.cpp 

a) Updated MAXATM from 10000 to 100000
b) Changed "FIRSTdataset" to "proflexdataset"
c) Made changes to fix Linux g++ file opening problem

d) The old flex_index.cpp program assigned flexibility index (called flexindex
   hereon) to an atom by calculating the average of the flexindex values 
   of all the bonds in which the atom participates. The previous assignment 
   could result in varying flexindex values within a side-chain ring or 
   within a hydrophobic tether for instance. Further, flex_index.cpp used 
   the "bond_wt" file as the input, which did not have information abount
   all the bonds. To remedy the observed discrepancy, the revised 
   flex_index.cpp program picks the minimum flexindex among all the bonds 
   that it participates in as that atom's flexindex. The program uses the 
   "allbonds" file as its input instead of the "bond_wt" file as it is a 
   more comprehensive collection of bonds with an additional column that
   indicated the rigid or flexible cluster label.

   Flexindex is assigned to individual atoms with values ranging between 
   -1 and +1 where -1 represents maximum rigidity. To facilitate 
   flexibility-based visualization of proteins the program maps the -1 to +1 
   values onto 0 to 99 and stores those values in the b-value column of the 
   input protein's PDB file as most of the 3D visualization softwares use the 
   temperature factor column of PDB file to color code the protein. To visualize 
   the protein in InsightII, it requires a spectrum file that maps ranges of
   b-values onto various colors. We provide a spectrum file called 
   "flexindex.spect" in the "$PROFLEX_HOME/../util/" directory, which maps the
   b-values as follows: 

    The 0 to 99 range of values is split into 13 bins with one representing 
    b-values < 40 (colored blue for rigid), one for b-values > 60 (colored
    red for flexible) and 11 bins between 40 and 60, colored as follows:
    five bins between 40 and 49 color coded starting with dark blue, 
    indicating least flexibility, and progressively wanning out into light 
    green; one central bin (49 to 50) colored grey to represent isostatic, 
    and five bins between 50 and 60 color coded starting with yellow and 
    progressively gaining in the extent of redness and ending up in dark 
    red at the maximum value of 60 indicating maximum flexibility. 

   Individual proteins may have varied flexibilities. flex_index.cpp was 
   faulty in that the minimum and maximum of any protein's flexibility 
   values, such as (-0.6,+0.4), were being mapped on to 0 to 99, 
   (i.e., -0.6 equivalent to 0 and +0.4 mapped on to 99), thus
   blurring the variation of flexibility across multiple proteins 
   (some of which are more rigid than the others).

   Users who use a visualization software other than InsightII are advised
   to adopt a similar color coding scheme.

e) The changes in flex-index.cpp cause minimal differences in mainchain
   flexibility assignments while resulting in more representative assignments 
   for side-chain groups.

f) Added a -1 option from Kevin Keating's fixes for StoneHinge to output 
   flexibility index on a -1 to +1 scale. This is named the noscaling option.

g) Added code to process the _allbonds_ file to generate a new PDB file 
   that contains all the atoms including the tethers and has in it all
   the necessary information required for creating PyMol scripts for
   coloring the protein by (a) flexindex, (b) rigid cluster decomposition,
   and (c) flexible clusters that indulge in collective motions.
   This results in four new files (refer to the first section of this
   document for the details).

-----------------------------------------------------------------------

13) types.h

a) Added MAXATOMS, FILE_LIST_SIZE and MAX_CLUSTER_COUNT macros

-----------------------------------------------------------------------

14) hbdilute.c

a) Updated "bulk_atom_label" and "atom_label" array sizes wit MAXATOMS
b) Updated file_list[] array size with FILE_LIST_SIZE
c) Updated sizes of various arrays corresponding to clusters to
   MAX_CLUSTER_COUNT
d) Updated some loop counters (for loop) to MAX_CLUSTER_COUNT
e) Added a NULL memory allocation check

f) New variables added to capture missing and inserted residue information
   and appropriate initialization statements added
    --- min_max_rsd, missing_rsd_list, missing_rsd_count,
        insertions_prior_donor, insertions_prior_acptr,
            donor_insertion_code,acptr_insertion_code,
        acptr_chain_index,donor_chain_index

g) Function interfaces updates:
    1) read_chem_file, print_decomp 
        --- min_max_rsd, missing_rsd_list, missing_rsd_count
    2) print_landscape_footer 
        --- scale_factor
    3) print_current_Hbond_info_landscape, 
       print_current_Hbond_info_landscape_multipage
        --- insertions_prior_donor, insertions_prior_acptr,
            donor_insertion_code,acptr_insertion_code

h) Added code to compute insertions_prior_<donor or acptr>

i) Disabled portrait output function calls and made landscape output mode
   to be triggered for those calls

-----------------------------------------------------------------------

15) hbfunctions.c

a) Same as (a-d) for hbdilute.c
b) read_chem_file(): Added code to declare, initialize, and compute 
   min_max_rsd, missing_rsd_list, missing_rsd_count, which are later 
   used in hbdilute.c

-----------------------------------------------------------------------

16) postscript.c

a) Same as (a-d) for hbdilute.c
b) Added more than 700 lines of code/comments to correct the hbdilution
   plot display in single and multi-page output formats. The following
   is the list of corrections:

   i)   Distinguish between multiple chains and display legibly the boundaries,
        the chain-IDs, and residue numbers of each chain

   ii)  Rectified the logic that computes the starting position of each chain

   iii) Account for insertions in each chain:
        --- print_decomp(), print_multi_decomp()
    - Display various inserted residues with their insertion codes at
      the top of the plot
    - Change the resdiue number displayed to reflect the PDB residue 
      number accurately and adjust the spacing between any two residue
      indices displayed to account for insertions
      
   iv)  Account for missing residues in each chain 
    - Display missing residues indicated by an 'X' at the top of the plot

   v)   Change in the fonts of various text elements on the plot
        --- print_header()
    - Times to Arial for left legend (H-bonds left, energy, and r)
    - Times to Arial for broken H-bond information to the right
    - Times to CourierNew for the insertions and missing residues displayed 
      on the top

   vi)  Change in the format of broken H-bond information to the right. Also,
    rectified the broken H-bond indicator (triangles) position computation.
        --- print_current_Hbond_info_landscape()
        --- print_current_Hbond_info_landscape_multipage()

    - <H|M|S|W> <rsd> <chain-id> --> <H|M|S|W> <chain-id> <rsd> <ins code>

   vii) Corrected the display color in the bottom legend (donor)
    and added new statements that explain the format of the right
    legend.
        --- print_landscape_footer(), print_data_headings()

   viii)Rectified a bug for singlepage output case when an H-bond that occurs
    between two different chains is broken.
   

-----------------------------------------------------------------------

17) postscript.h, hbfunctions.h, hbdilute.h

a) Updated the function interfaces

-----------------------------------------------------------------------

18) fix_babel.cpp

a) To ensure correct inter-atomic distance measurement for specific metal atoms, 
   we check for the atom-type of the input atom matching the following
   list of metals: Co, Cu, Fe, K, Mn, Mg, Na, Ni, Zn, and calcium CA and
   then look up for their corresponding vander Waals radii stored in a
   lookup table.
   
   Minor changes in the conditions being checked on line numbers 
   1060 & 1218 to ensure right sequence of valency checks is being performed.

-----------------------------------------------------------------------

19) Makefile in the proflex/ directory:

a) Added all the changes that Kevin Keating had made in StoneHinge to support 
   proflex execution without setting any environment variable.

%%%%%%%%%%%%%%%%%%%%%%%%%% END OF FILE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%