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Michal Malý
WebMMB-php
Commits
90d72f06
Commit
90d72f06
authored
Jan 11, 2022
by
Michal Malý
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parent
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Types.inc
+53
-14
53 additions, 14 deletions
Types.inc
with
53 additions
and
14 deletions
Types.inc
+
53
−
14
View file @
90d72f06
<?php
<?php
// vim:
expandtab
sw=4 ts=4 sts=4 :
// vim:
set
sw=4 ts=4 sts=4
expandtab
:
/**
/**
* WebMMB PHP client
* WebMMB PHP client
...
@@ -460,9 +460,9 @@ class Mobilizer
...
@@ -460,9 +460,9 @@ class Mobilizer
}
}
/**
/**
* Defines NtC c
lass applicable to steps in a Compound
* Defines NtC c
onformation for a given step or range of steps
*/
*/
class
NtC
class
NtC
Conformation
{
{
/**
/**
* Name of the chain
* Name of the chain
...
@@ -524,6 +524,45 @@ class NtC
...
@@ -524,6 +524,45 @@ class NtC
}
}
}
}
/**
* Defines NtCs configuration
*/
class
NtCs
{
/**
* Array of all applied NtC conformations
* @var NtCConformation[] $conformations
*/
public
array
$conformations
;
/**
* Global scale factor of the NtC forces
* @var flaot $force_scale_factor;
*/
public
float
$force_scale_factor
;
public
function
__construct
(
array
$conformations
,
float
$force_scale_factor
)
{
$this
->
conformations
=
$conformations
;
$this
->
force_scale_factor
=
$force_scale_factor
;
}
public
static
function
fromArray
(
array
$data
)
{
try
{
$obj
=
new
self
([],
0
);
$obj
->
conformations
=
array_get
(
'conformations'
,
$data
);
$obj
->
force_scale_factor
=
array_get
(
'force_scale_factor'
,
$data
);
return
$obj
;
}
catch
(
\TypeError
$ex
)
{
throw
new
InvalidDataError
(
$ex
->
getMessage
());
}
}
}
/**
/**
* Defines residue number
* Defines residue number
*/
*/
...
@@ -687,9 +726,9 @@ class StandardCommands extends Commands
...
@@ -687,9 +726,9 @@ class StandardCommands extends Commands
/**
/**
* NtCs to be applied.
* NtCs to be applied.
* This shall be set explicitly after the object is constructed.
* This shall be set explicitly after the object is constructed.
* @var NtC
[]
$ntcs
* @var NtC
s
$ntcs
*/
*/
public
array
$ntcs
;
public
object
$ntcs
;
/**
/**
* Advanced job parametrers - currently unavailable
* Advanced job parametrers - currently unavailable
* @var $adv_params
* @var $adv_params
...
@@ -722,7 +761,7 @@ class StandardCommands extends Commands
...
@@ -722,7 +761,7 @@ class StandardCommands extends Commands
$this
->
compounds
=
[];
$this
->
compounds
=
[];
$this
->
double_helices
=
[];
$this
->
double_helices
=
[];
$this
->
base_interactions
=
[];
$this
->
base_interactions
=
[];
$this
->
ntcs
=
[]
;
$this
->
ntcs
=
new
NtCs
([],
0
)
;
$this
->
mobilizers
=
[];
$this
->
mobilizers
=
[];
$this
->
adv_params
=
new
AdvParams
();
$this
->
adv_params
=
new
AdvParams
();
$this
->
set_default_MD_parameters
=
false
;
$this
->
set_default_MD_parameters
=
false
;
...
@@ -743,9 +782,6 @@ class StandardCommands extends Commands
...
@@ -743,9 +782,6 @@ class StandardCommands extends Commands
[
'name'
=>
'base_interactions'
,
'initer'
=>
function
(
array
$data
)
{
[
'name'
=>
'base_interactions'
,
'initer'
=>
function
(
array
$data
)
{
return
BaseInteraction
::
fromArray
(
$data
);
return
BaseInteraction
::
fromArray
(
$data
);
}
],
}
],
[
'name'
=>
'ntcs'
,
'initer'
=>
function
(
array
$data
)
{
return
NtC
::
fromArray
(
$data
);
}
],
[
'name'
=>
'mobilizers'
,
'initer'
=>
function
(
array
$data
)
{
[
'name'
=>
'mobilizers'
,
'initer'
=>
function
(
array
$data
)
{
return
Mobilizer
::
fromArray
(
$data
);
return
Mobilizer
::
fromArray
(
$data
);
}
]
}
]
...
@@ -753,6 +789,8 @@ class StandardCommands extends Commands
...
@@ -753,6 +789,8 @@ class StandardCommands extends Commands
foreach
(
$ARRAY_PROPS_INIT
as
$init
)
{
foreach
(
$ARRAY_PROPS_INIT
as
$init
)
{
$obj
->
initializeArrayProperty
(
$init
[
'name'
],
$data
,
$init
[
'initer'
]);
$obj
->
initializeArrayProperty
(
$init
[
'name'
],
$data
,
$init
[
'initer'
]);
}
}
$obj
->
ntcs
=
NtCs
::
fromArray
(
array_get
(
'ntcs'
,
$data
));
// TODO: adv_params once we start to support them
// TODO: adv_params once we start to support them
$obj
->
set_default_MD_parameters
=
array_get
(
'set_default_MD_parameters'
,
$data
);
$obj
->
set_default_MD_parameters
=
array_get
(
'set_default_MD_parameters'
,
$data
);
...
@@ -794,9 +832,9 @@ class DensityFitCommands extends Commands
...
@@ -794,9 +832,9 @@ class DensityFitCommands extends Commands
/**
/**
* NtCs to be applied.
* NtCs to be applied.
* This shall be set explicitly after the object is constructed.
* This shall be set explicitly after the object is constructed.
* @var NtC
[]
$ntcs
* @var NtC
s
$ntcs
*/
*/
public
array
$ntcs
=
[]
;
public
object
$ntcs
;
/**
/**
* Whether to account for electrostatic and Lennard-Jones forces
* Whether to account for electrostatic and Lennard-Jones forces
* @var bool $set_default_MD_parameters
* @var bool $set_default_MD_parameters
...
@@ -834,6 +872,8 @@ class DensityFitCommands extends Commands
...
@@ -834,6 +872,8 @@ class DensityFitCommands extends Commands
throw
new
InvalidOperationError
(
'Invalid name of density map file'
);
throw
new
InvalidOperationError
(
'Invalid name of density map file'
);
}
}
$this
->
ntcs
=
new
NtCs
([],
0
);
$this
->
structure_file_name
=
$structure_file_name
;
$this
->
structure_file_name
=
$structure_file_name
;
$this
->
density_map_file_name
=
$density_map_file_name
;
$this
->
density_map_file_name
=
$density_map_file_name
;
}
}
...
@@ -847,9 +887,6 @@ class DensityFitCommands extends Commands
...
@@ -847,9 +887,6 @@ class DensityFitCommands extends Commands
[
'name'
=>
'compounds'
,
'initer'
=>
function
(
array
$data
)
{
[
'name'
=>
'compounds'
,
'initer'
=>
function
(
array
$data
)
{
return
Compound
::
fromArray
(
$data
);
return
Compound
::
fromArray
(
$data
);
}
],
}
],
[
'name'
=>
'ntcs'
,
'initer'
=>
function
(
array
$data
)
{
return
NtC
::
fromArray
(
$data
);
}
],
[
'name'
=>
'mobilizers'
,
'initer'
=>
function
(
array
$data
)
{
[
'name'
=>
'mobilizers'
,
'initer'
=>
function
(
array
$data
)
{
return
Mobilizer
::
fromArray
(
$data
);
return
Mobilizer
::
fromArray
(
$data
);
}
]
}
]
...
@@ -857,6 +894,8 @@ class DensityFitCommands extends Commands
...
@@ -857,6 +894,8 @@ class DensityFitCommands extends Commands
foreach
(
$ARRAY_PROPS_INIT
as
$init
)
{
foreach
(
$ARRAY_PROPS_INIT
as
$init
)
{
$obj
->
initializeArrayProperty
(
$init
[
'name'
],
$data
,
$init
[
'initer'
]);
$obj
->
initializeArrayProperty
(
$init
[
'name'
],
$data
,
$init
[
'initer'
]);
}
}
$obj
->
ntcs
=
NtCs
::
fromArray
(
array_get
(
'ntcs'
,
$data
));
$obj
->
structure_file_name
=
array_get
(
'structure_file_name'
,
$data
);
$obj
->
structure_file_name
=
array_get
(
'structure_file_name'
,
$data
);
$obj
->
density_map_file_name
=
array_get
(
'density_map_file_name'
,
$data
);
$obj
->
density_map_file_name
=
array_get
(
'density_map_file_name'
,
$data
);
$obj
->
set_default_MD_parameters
=
array_get
(
'set_default_MD_parameters'
,
$data
);
$obj
->
set_default_MD_parameters
=
array_get
(
'set_default_MD_parameters'
,
$data
);
...
...
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