called if flexible More...

Collaboration diagram for change_conformation:

Public Member Functions
subroutine	change_conformation (prot, tab_prot, geom, param_force_energy, param_metal, type_calc, dummy_array, hit, accepted, nb_overlap_flex, ptrf_energy)

subroutine	check_reaction_pair (prot1, prot2, rcriteria, visited_windows, escape, sum_time, first_time, time, dtnow, close)

subroutine	init_time (param_timestep, geom, dist, rhit, dm30, dtnow, hit)

subroutine	change_conformation (prot, tab_prot, geom, param_force_energy, param_metal, type_calc, dummy_array, hit, accepted, nb_overlap_flex, ptrf_energy)

subroutine	check_reaction_pair (prot1, prot2, rcriteria, visited_windows, escape, sum_time, first_time, time, dtnow, close)

subroutine	make_bd_move_2prot (prot1, prot2, geom, force, torque, torque1, dtnow, dist, rhit, hit, accept, escape, total_overlap, ignore_excl)

subroutine	init_time (param_timestep, geom, dist, rhit, dm30, dtnow, hit)

subroutine	change_conformation (prot, tab_prot, geom, param_force_energy, param_metal, type_calc, dummy_array, hit, accepted, nb_overlap_flex, ptrf_energy)

subroutine	make_bd_move_sdamm (tab_prot, geom, nb_prot, force, torque, dt)

subroutine	compute_rdf (resid_time, tab_protein, geom)

subroutine	check_reaction_pair_sdamm (tab_protein, set1, set2, rcriteria, geom, sum_time, dtnow, array_close, nclose, close)

subroutine	convert_to_record_format (array_energy, array_energy_1d, max_bit_energy)

Public Attributes
type(array_protein_type), target	tab_protein

type(react_criter)	rcriteria

type(record)	o_complexes

type(record)	trajectories

type(record), pointer	p_restart

type(geometry)	geom

type(residence_time)	resid_time

type(type_calculation)	type_calc

type(parameter_timestep)	param_timestep

type(probe_type)	param_probe

type(type_force_energy)	param_force_energy

type(parameter_analytic)	param_analytic

type(parameter_metaldesolv)	param_metaldesolv

real(kind=8)	timemax

real(kind=4)	rboost

integer	nrun

integer	nmax_overlap

type(mytimer)	timer_force

type(mytimer)	timer_energy

type(mytimer)	timer_reactpair

type(mytimer)	timer_exchk

type(mytimer)	timer_bd

type(mytimer)	timer_complexes

type(mytimer)	timer_flex

type(mytimer)	timer_update_rate

type(protein), pointer	protein1

type(protein), pointer	protein2

integer	max_energy_terms

real(kind=8), dimension(:,:), pointer	array_energy

real(kind=8)	total_energy

integer	size_array_energy

real(kind=8), dimension(:,:), pointer	array_energy_1d

logical	correct_format_energy

real(kind=8), dimension(3)	f

real(kind=8), dimension(3)	t

real(kind=8), dimension(3)	t1

real(kind=8), dimension(:,:), pointer	local_escape

integer, dimension(:), pointer	local_visited_windows

real(kind=4), dimension(:,:), pointer	local_sumtime

real(kind=4), dimension(:,:), pointer	local_fpt

integer, dimension(:), allocatable	steps_record

real(kind=8)	dm

real(kind=8)	dm30

real(kind=8)	time

real(kind=8)	time_all

real(kind=8)	time_per_run

real(kind=8)	timehit

real(kind=8)	dtnow

real(kind=4)	cut2

real(kind=4)	dist

real(kind=4)	rhit

integer	current_run

integer	run_done

integer	nstep_all

integer	current_step

integer	current_conf

integer	total_overlap

integer	nboost_all

integer	total_overlap_flex

integer	k

integer	nb_overlap

integer	ierr

integer	current_occur

integer	n_repeat_occur

integer	total_occur

type(one_complexe), pointer	p_tmp_onecomplexe

logical	overlap

logical	bool_escape

logical	print_step

logical	clos1

logical	hit

logical	accept

logical	iflex

logical	accepted_new_conf

character *32	steps_str

real(kind=8), dimension(:), pointer	dummy_array

integer	status

integer	io_err

type(array_protein_type), target	tab_protein_unique

type(record), target	o_complexes

type(record), target	trajectories

type(type_option_omp)	option_omp

type(array_protein_type), pointer	ptab_protein

type(record), pointer	p_local_complexe

integer, dimension(:), allocatable	global_steps_record

logical	rcrit_met

integer	total_test_change_conformation

integer	total_accepted_new_conf

type(array_protein_type)	tab_protein

type(mytimer)	timer_record

type(mytimer)	timer_rdf

integer	nb_protein

integer	i

integer	j

integer	n_rdfs

real(kind=8), dimension(:, :), pointer	array_energy_sdamm

real(kind=8), dimension(:, :), allocatable	force

real(kind=8), dimension(:, :), allocatable	torque

real(kind=4)	half_box

real(kind=8)	dt

logical	print_step_traj

logical	print_step_compl

integer	nb_overlap_flex

integer	nb_prot1

integer	nb_prot2

real(kind=8), dimension(:,:), pointer	array_energy_sda2prot

real(kind=8), dimension(:,:), pointer	array_energy_sda2prot_1d

real(kind=8), dimension(3)	pos_relat

integer	size_array_energy_sda2prot

integer	size_array_energy_sda2prot_1d

type(array_protein_type)	dummy_array_protein

real(kind=8), dimension(3, 3)	mrot

Detailed Description

called if flexible

Constructor & Destructor Documentation

◆ change_conformation() [1/3]

subroutine change_conformation::change_conformation	(	type ( protein )	prot,
		type ( array_protein_type ), intent(in), target	tab_prot,
		type ( geometry ), intent(in)	geom,
		type ( type_force_energy ), intent(in)	param_force_energy,
		type ( parameter_metaldesolv ), intent(in)	param_metal,
		type ( type_calculation ), intent(in)	type_calc,
		real ( kind=8 ), dimension( : ), intent(in), target	dummy_array,
		logical, intent(in)	hit,
		logical, intent(out)	accepted,
		integer	nb_overlap_flex,
			ptrf_energy
	)

◆ change_conformation() [2/3]

subroutine change_conformation::change_conformation	(	type ( protein )	prot,
		type ( array_protein_type ), intent(in), target	tab_prot,
		type ( geometry ), intent(in)	geom,
		type ( type_force_energy ), intent(in)	param_force_energy,
		type ( parameter_metaldesolv ), intent(in)	param_metal,
		type ( type_calculation ), intent(in)	type_calc,
		real ( kind=8 ), dimension( : ), intent(in), target	dummy_array,
		logical, intent(in)	hit,
		logical, intent(out)	accepted,
		integer	nb_overlap_flex,
			ptrf_energy
	)

◆ change_conformation() [3/3]

subroutine change_conformation::change_conformation	(	type ( protein )	prot,
		type ( array_protein_type ), intent(in), target	tab_prot,
		type ( geometry ), intent(in)	geom,
		type ( type_force_energy ), intent(in)	param_force_energy,
		type ( parameter_metaldesolv ), intent(in)	param_metal,
		type ( type_calculation ), intent(in)	type_calc,
		real ( kind=8 ), dimension( : ), intent(in), target	dummy_array,
		logical, intent(in)	hit,
		logical, intent(out)	accepted,
		integer	nb_overlap_flex,
			ptrf_energy
	)

Member Function/Subroutine Documentation

◆ check_reaction_pair() [1/2]

subroutine change_conformation::check_reaction_pair	(	type ( protein ), intent(in)	prot1,
		type ( protein ), intent(in)	prot2,
		type ( react_criter )	rcriteria,
		integer, dimension (:)	visited_windows,
		real ( kind=8 ), dimension (:,:)	escape,
		real ( kind=4 ), dimension(:,:)	sum_time,
		real ( kind=4 ), dimension(:,:)	first_time,
		real ( kind=4 )	time,
		real ( kind=4 )	dtnow,
		logical, intent(out)	close
	)

◆ check_reaction_pair() [2/2]

subroutine change_conformation::check_reaction_pair	(	type ( protein ), intent(in)	prot1,
		type ( protein ), intent(in)	prot2,
		type ( react_criter )	rcriteria,
		integer, dimension (:)	visited_windows,
		real ( kind=8 ), dimension (:,:)	escape,
		real ( kind=4 ), dimension(:,:)	sum_time,
		real ( kind=4 ), dimension(:,:)	first_time,
		real ( kind=4 )	time,
		real ( kind=4 )	dtnow,
		logical, intent(out)	close
	)

◆ check_reaction_pair_sdamm()

subroutine change_conformation::check_reaction_pair_sdamm	(	type ( array_protein_type )	tab_protein,
		integer	set1,
		integer	set2,
		type ( react_criter )	rcriteria,
		type ( geometry )	geom,
		real ( kind=4 ), dimension(:,:)	sum_time,
		real ( kind=4 )	dtnow,
		integer, dimension (:,:)	array_close,
		integer	nclose,
		logical, intent(out)	close
	)

◆ compute_rdf()

subroutine change_conformation::compute_rdf	(	type ( residence_time )	resid_time,
		type ( array_protein_type ), intent(in)	tab_protein,
		type ( geometry )	geom
	)

◆ convert_to_record_format()

subroutine change_conformation::convert_to_record_format	(	real(kind=8), dimension(:,:), intent(in)	array_energy,
		real(kind=8), dimension(:,:), intent(out)	array_energy_1d,
		integer, intent(in)	max_bit_energy
	)

◆ init_time() [1/2]

subroutine change_conformation::init_time	(	type ( parameter_timestep ), intent(in)	param_timestep,
		type ( geometry ), intent(in)	geom,
		real ( kind=4 ), intent(in)	dist,
		real ( kind=4 ), intent(in)	rhit,
		real ( kind=8 ), intent(in)	dm30,
		real ( kind=8 ), intent(out)	dtnow,
		logical, intent(out)	hit
	)

◆ init_time() [2/2]

subroutine change_conformation::init_time	(	type ( parameter_timestep ), intent(in)	param_timestep,
		type ( geometry ), intent(in)	geom,
		real ( kind=4 ), intent(in)	dist,
		real ( kind=4 ), intent(in)	rhit,
		real ( kind=8 ), intent(in)	dm30,
		real ( kind=8 ), intent(out)	dtnow,
		logical, intent(out)	hit
	)

◆ make_bd_move_2prot()

subroutine change_conformation::make_bd_move_2prot	(	type ( protein )	prot1,
		type ( protein )	prot2,
		type ( geometry ), intent(in)	geom,
		real ( kind=8 ), dimension ( 3 ), intent(in)	force,
		real ( kind=8 ), dimension ( 3 ), intent(in)	torque,
		real ( kind=8 ), dimension ( 3 ), intent(in)	torque1,
		real ( kind=8 ), intent(in)	dtnow,
		real ( kind=4 )	dist,
		real ( kind=4 )	rhit,
		logical, intent(out)	hit,
		logical, intent(out)	accept,
		logical, intent(out)	escape,
		integer	total_overlap,
		logical, intent(in)	ignore_excl
	)

◆ make_bd_move_sdamm()

subroutine change_conformation::make_bd_move_sdamm	(	type ( array_protein_type ), target	tab_prot,
		type ( geometry ), intent(in)	geom,
		integer, intent(in)	nb_prot,
		real ( kind=8 ), dimension(3 , nb_prot), intent(in)	force,
		real ( kind=8 ), dimension(3 , nb_prot), intent(in)	torque,
		real ( kind=8 ), intent(in)	dt
	)

Member Data Documentation

◆ accept

logical change_conformation::accept

◆ accepted_new_conf

logical change_conformation::accepted_new_conf

◆ array_energy

real ( kind=8 ), dimension(:,:), pointer change_conformation::array_energy

◆ array_energy_1d

real ( kind=8 ), dimension(:,:), pointer change_conformation::array_energy_1d

◆ array_energy_sda2prot

real ( kind=8 ), dimension(:,:), pointer change_conformation::array_energy_sda2prot

◆ array_energy_sda2prot_1d

real ( kind=8 ), dimension(:,:), pointer change_conformation::array_energy_sda2prot_1d

◆ array_energy_sdamm

real ( kind=8 ), dimension ( :, : ), pointer change_conformation::array_energy_sdamm

◆ bool_escape

logical change_conformation::bool_escape

◆ clos1

logical change_conformation::clos1

◆ correct_format_energy

logical change_conformation::correct_format_energy

◆ current_conf

integer change_conformation::current_conf

◆ current_occur

integer change_conformation::current_occur

◆ current_run

integer change_conformation::current_run

◆ current_step

integer change_conformation::current_step

◆ cut2

real ( kind=4 ) change_conformation::cut2

◆ dist

real ( kind=4 ) change_conformation::dist

◆ dm

real ( kind=8 ) change_conformation::dm

◆ dm30

real ( kind=8 ) change_conformation::dm30

◆ dt

real ( kind=8 ) change_conformation::dt

◆ dtnow

real ( kind=8 ) change_conformation::dtnow

◆ dummy_array

real ( kind=8 ), dimension( : ), pointer change_conformation::dummy_array

◆ dummy_array_protein

type ( array_protein_type ) change_conformation::dummy_array_protein

◆ f

real ( kind=8 ), dimension(3) change_conformation::f

◆ force

real ( kind=8 ), dimension ( :, : ), allocatable change_conformation::force

◆ geom

type ( geometry ) change_conformation::geom

◆ global_steps_record

integer, dimension(:), allocatable change_conformation::global_steps_record

◆ half_box

real ( kind=4 ) change_conformation::half_box

◆ hit

logical change_conformation::hit

◆ i

integer change_conformation::i

◆ ierr

integer change_conformation::ierr

◆ iflex

logical change_conformation::iflex

◆ io_err

integer change_conformation::io_err

◆ j

integer change_conformation::j

◆ k

integer change_conformation::k

◆ local_escape

real (kind=8), dimension(:,:), pointer change_conformation::local_escape

◆ local_fpt

real ( kind=4 ), dimension(:,:), pointer change_conformation::local_fpt

◆ local_sumtime

real ( kind=4 ), dimension(:,:), pointer change_conformation::local_sumtime

◆ local_visited_windows

integer, dimension(:), pointer change_conformation::local_visited_windows

◆ max_energy_terms

integer change_conformation::max_energy_terms

◆ mrot

real(kind=8), dimension(3,3) change_conformation::mrot

◆ n_rdfs

integer change_conformation::n_rdfs

◆ n_repeat_occur

integer change_conformation::n_repeat_occur

◆ nb_overlap

integer change_conformation::nb_overlap

◆ nb_overlap_flex

integer change_conformation::nb_overlap_flex

◆ nb_prot1

integer change_conformation::nb_prot1

◆ nb_prot2

integer change_conformation::nb_prot2

◆ nb_protein

integer change_conformation::nb_protein

◆ nboost_all

integer change_conformation::nboost_all

◆ nmax_overlap

integer change_conformation::nmax_overlap

◆ nrun

integer change_conformation::nrun

◆ nstep_all

integer change_conformation::nstep_all

◆ o_complexes [1/2]

type ( record ) change_conformation::o_complexes

◆ o_complexes [2/2]

type ( record ), target change_conformation::o_complexes

◆ option_omp

type ( type_option_omp ) change_conformation::option_omp

◆ overlap

logical change_conformation::overlap

◆ p_local_complexe

type ( record ), pointer change_conformation::p_local_complexe

◆ p_restart

type ( record ), pointer change_conformation::p_restart

◆ p_tmp_onecomplexe

type ( one_complexe ), pointer change_conformation::p_tmp_onecomplexe

◆ param_analytic

type ( parameter_analytic ) change_conformation::param_analytic

◆ param_force_energy

type ( type_force_energy ) change_conformation::param_force_energy

◆ param_metaldesolv

type ( parameter_metaldesolv ) change_conformation::param_metaldesolv

◆ param_probe

type ( probe_type ) change_conformation::param_probe

◆ param_timestep

type ( parameter_timestep ) change_conformation::param_timestep

◆ pos_relat

real (kind=8 ), dimension(3) change_conformation::pos_relat

◆ print_step

logical change_conformation::print_step

◆ print_step_compl

logical change_conformation::print_step_compl

◆ print_step_traj

logical change_conformation::print_step_traj

◆ protein1

type ( protein ), pointer change_conformation::protein1

◆ protein2

type ( protein ), pointer change_conformation::protein2

◆ ptab_protein

type ( array_protein_type ), pointer change_conformation::ptab_protein

◆ rboost

real ( kind=4 ) change_conformation::rboost

◆ rcrit_met

logical change_conformation::rcrit_met

◆ rcriteria

type ( react_criter ) change_conformation::rcriteria

◆ resid_time

type ( residence_time ) change_conformation::resid_time

◆ rhit

real ( kind=4 ) change_conformation::rhit

◆ run_done

integer change_conformation::run_done

◆ size_array_energy

integer change_conformation::size_array_energy

◆ size_array_energy_sda2prot

integer change_conformation::size_array_energy_sda2prot

◆ size_array_energy_sda2prot_1d

integer change_conformation::size_array_energy_sda2prot_1d

◆ status

integer change_conformation::status

◆ steps_record

integer, dimension(:), allocatable change_conformation::steps_record

◆ steps_str

character * change_conformation::steps_str

◆ t

real ( kind=8 ), dimension(3) change_conformation::t

◆ t1

real ( kind=8 ), dimension(3) change_conformation::t1

◆ tab_protein [1/2]

type ( array_protein_type ) change_conformation::tab_protein

◆ tab_protein [2/2]

type ( array_protein_type ), target change_conformation::tab_protein

◆ tab_protein_unique

type ( array_protein_type ), target change_conformation::tab_protein_unique

◆ time

real ( kind=8 ) change_conformation::time

◆ time_all

real ( kind=8 ) change_conformation::time_all

◆ time_per_run

real ( kind=8 ) change_conformation::time_per_run

◆ timehit

real ( kind=8 ) change_conformation::timehit

◆ timemax

real ( kind=8 ) change_conformation::timemax

◆ timer_bd

type ( mytimer ) change_conformation::timer_bd

◆ timer_complexes

type ( mytimer ) change_conformation::timer_complexes

◆ timer_energy

type ( mytimer ) change_conformation::timer_energy

◆ timer_exchk

type ( mytimer ) change_conformation::timer_exchk

◆ timer_flex

type ( mytimer ) change_conformation::timer_flex

◆ timer_force

type ( mytimer ) change_conformation::timer_force

◆ timer_rdf

type ( mytimer ) change_conformation::timer_rdf

◆ timer_reactpair

type ( mytimer ) change_conformation::timer_reactpair

◆ timer_record

type ( mytimer ) change_conformation::timer_record

◆ timer_update_rate

type ( mytimer ) change_conformation::timer_update_rate

◆ torque

real ( kind=8 ), dimension ( :, : ), allocatable change_conformation::torque

◆ total_accepted_new_conf

integer change_conformation::total_accepted_new_conf

◆ total_energy

real ( kind=8 ) change_conformation::total_energy

◆ total_occur

integer change_conformation::total_occur

◆ total_overlap

integer change_conformation::total_overlap

◆ total_overlap_flex

integer change_conformation::total_overlap_flex

◆ total_test_change_conformation

integer change_conformation::total_test_change_conformation

◆ trajectories [1/2]

type ( record ) change_conformation::trajectories

◆ trajectories [2/2]

type ( record ), target change_conformation::trajectories

◆ type_calc

type ( type_calculation ) change_conformation::type_calc

The documentation for this interface was generated from the following files:

Public Member Functions

Public Attributes