Tools

Files
file	genbox_subroutines.f90
file	mod_sda_input_tools.f90
file	utils_diffusion.f90

Functions/Subroutines
program	calc_solvaccess
	Program calc_accessibility. More...
program	cluster_sdamm
	Program cluster_sdammProgram for clustering the configurations of complexes formed between either two proteins or a protein and a surface. Used with SDAMM-type of trajectory. More...
program	contacts_sdamm
	Program contacts_sdammFinding contacts between protein pairs or protein and a surface. Used with SDAMM-type of trajectory. More...
program	convert_grid
	Extend formerprogram ascci2bin and bin2ascii, apbs2uhbd. More...
program	convert_traj_sdamm
	Program convert_traj_sdamm. More...
program	diffusion_calc
	Program diffusion_calc. More...
program	energy_analyze
	Extract energy from sdamm trajectory. More...
program	genbox
	Generate initial configuration for sdamm. More...
program	make_edhdlj_grid
	Prgram make_edhdlj_grid. More...
program	nos2rates
	Extract association rates, and compute average and dispersion from output files of sda_flex. More...
program	rdf
	Program rdf. More...
program	read_record
	Program read_record. More...
program	rot_diffusion
	Program rot_diffusion. More...
program	trans_diffusion
	Program trans_diffusion. More...
program	trajectory2dcd
	Program trajectory2dcd. More...

Detailed Description

Function/Subroutine Documentation

calc_solvaccess()

program calc_solvaccess

Program calc_accessibility.

Author

Neil Bruce

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cluster_sdamm()

program cluster_sdamm

Program cluster_sdammProgram for clustering the configurations of complexes formed between either two proteins or a protein and a surface. Used with SDAMM-type of trajectory.

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contacts_sdamm()

program contacts_sdamm

Program contacts_sdammFinding contacts between protein pairs or protein and a surface. Used with SDAMM-type of trajectory.

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convert_grid()

program convert_grid

Extend formerprogram ascci2bin and bin2ascii, apbs2uhbd.

Convert grid UHBD type between ascci and binary format can scale value (ex from kT to kcal/mol )
can conver to dx format, for pymol
note : do not make a real copy of the grid ( save memory ), copy is false copy by default, need to add an option

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convert_traj_sdamm()

program convert_traj_sdamm

Program convert_traj_sdamm.

Author

Neil Bruce

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diffusion_calc()

program diffusion_calc

Program diffusion_calc.

Compute the translational MSD and rotational MSD and ACF

Author

Neil Bruce

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energy_analyze()

program energy_analyze

Extract energy from sdamm trajectory.

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genbox()

program genbox

Generate initial configuration for sdamm.

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make_edhdlj_grid()

program make_edhdlj_grid

Prgram make_edhdlj_grid.

Regroup all the programs into one executable
Accept identical input file as sda6
Parameters specific to this tools are defined in mod_input_parameter.f90, under the type param_list_tools
Parrallelisaed with OpenMP

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nos2rates()

program nos2rates

Extract association rates, and compute average and dispersion from output files of sda_flex.

This is the original method in previous sda versions
It is updated with the bootstrap algorithm and the python auxiliary program

rdf()

program rdf

Program rdf.

Author

Neil Bruce

Need box information to retrieve the correct position of the solutes

Todo:

At present calculation not parallelised

Could add option to skip certain number of trajectory frames

Virial

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read_record()

program read_record

Program read_record.

General program for reading record
Multiple options :

• convert between binary and ascii
  
• extract energy terms : compute partial or total energy for sdamm
  
• split conformation : split a complex file with a flexible solute into n files
  to use with -format_cluster, it makes the format compatible with the clustering program

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rot_diffusion()

program rot_diffusion

Program rot_diffusion.

Correlation functions computed in parrallel with OpenMP
Different methods are implemented for fitting the diffusion coefficients

Common function are implemented in utils_diffusion.f90

2 methods acf : short time diffusion
msd : short and long time, it is an approximation, to try better
sdamm tool : acf_multyprot.f , use for rotational diffusion constant
rotdiff_msd_ensavg_multyprot.f : compute approximation to msd
msd_timeensavg_multyprot.f, use for translational diffusion coefficient
required :
flexibility ? certianly not
surface ? only z ? to do

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trajectory2dcd()

program trajectory2dcd

Program trajectory2dcd.

Read record (complexes or trajectory file ) and convert to pdb / dcd files
Support sda_2proteins / sdamm with flexible solutes

Consider trajectory by default in the backup, here want to transform complexes to pdbs ( or dcd ) exactly the same problem, prot1 to be prined ??, if pdb no need dummy atoms backup of trajectory, work with prot2 flexible, but link are wrong ( bad input pdb from Mykhylo ) correct bug in increasing array alternative : here put all atoms of all conformations in each dcd frame do not need to increase the size

Todo:

check possible bug, in allocating list_all_filename, when calling with explicit argument -pdb1/2

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trans_diffusion()

program trans_diffusion

Program trans_diffusion.

Need box information to retrieve the correct position of the solutes
Correlation functions computed in parrallel with OpenMP
Different methods are implemented for fitting the diffusion coefficients

Common function are implemented in utils_diffusion.f90

sdamm tool : acf_multyprot.f , use for rotational diffusion constant msd_timeensavg_multyprot.f, use for translational diffusion coefficient

2 versions in sdamm :

• space dependent translational diffusion, use of bins to discretize space msd_klm_ensavg
• multyprot, average over type of proteins, option z only

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