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Martin Kurečka
Plumed AlphaFold
Commits
e2627636
There was an error fetching the commit references. Please try again later.
Commit
e2627636
authored
6 years ago
by
Giovanni Bussi
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unique_ptr: MultiDomainRMSD
parent
93618442
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Changes
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2 changed files
src/reference/MultiDomainRMSD.cpp
+1
-5
1 addition, 5 deletions
src/reference/MultiDomainRMSD.cpp
src/reference/MultiDomainRMSD.h
+1
-2
1 addition, 2 deletions
src/reference/MultiDomainRMSD.h
with
2 additions
and
7 deletions
src/reference/MultiDomainRMSD.cpp
+
1
−
5
View file @
e2627636
...
@@ -35,10 +35,6 @@ MultiDomainRMSD::MultiDomainRMSD( const ReferenceConfigurationOptions& ro ):
...
@@ -35,10 +35,6 @@ MultiDomainRMSD::MultiDomainRMSD( const ReferenceConfigurationOptions& ro ):
{
{
}
}
MultiDomainRMSD
::~
MultiDomainRMSD
()
{
for
(
unsigned
i
=
0
;
i
<
domains
.
size
();
++
i
)
delete
domains
[
i
];
}
void
MultiDomainRMSD
::
read
(
const
PDB
&
pdb
)
{
void
MultiDomainRMSD
::
read
(
const
PDB
&
pdb
)
{
unsigned
nblocks
=
pdb
.
getNumberOfAtomBlocks
();
unsigned
nblocks
=
pdb
.
getNumberOfAtomBlocks
();
if
(
nblocks
<
2
)
error
(
"multidomain RMSD only has one block of atoms"
);
if
(
nblocks
<
2
)
error
(
"multidomain RMSD only has one block of atoms"
);
...
@@ -60,7 +56,7 @@ void MultiDomainRMSD::read( const PDB& pdb ) {
...
@@ -60,7 +56,7 @@ void MultiDomainRMSD::read( const PDB& pdb ) {
parse
(
"UPPER_CUTOFF"
+
num
,
upper
,
true
);
parse
(
"UPPER_CUTOFF"
+
num
,
upper
,
true
);
nopbc
=
false
;
parseFlag
(
"NOPBC"
+
num
,
nopbc
);
nopbc
=
false
;
parseFlag
(
"NOPBC"
+
num
,
nopbc
);
}
}
domains
.
push
_back
(
metricRegister
().
create
<
SingleDomainRMSD
>
(
ftype
)
);
domains
.
emplace
_back
(
metricRegister
().
create
<
SingleDomainRMSD
>
(
ftype
)
);
positions
.
resize
(
blocks
[
i
]
-
blocks
[
i
-
1
]
);
positions
.
resize
(
blocks
[
i
]
-
blocks
[
i
-
1
]
);
align
.
resize
(
blocks
[
i
]
-
blocks
[
i
-
1
]
);
align
.
resize
(
blocks
[
i
]
-
blocks
[
i
-
1
]
);
displace
.
resize
(
blocks
[
i
]
-
blocks
[
i
-
1
]
);
displace
.
resize
(
blocks
[
i
]
-
blocks
[
i
-
1
]
);
...
...
This diff is collapsed.
Click to expand it.
src/reference/MultiDomainRMSD.h
+
1
−
2
View file @
e2627636
...
@@ -37,10 +37,9 @@ private:
...
@@ -37,10 +37,9 @@ private:
/// Blocks containing start and end points for all the domains
/// Blocks containing start and end points for all the domains
std
::
vector
<
unsigned
>
blocks
;
std
::
vector
<
unsigned
>
blocks
;
/// Each of the domains we are calculating the distance from
/// Each of the domains we are calculating the distance from
std
::
vector
<
SingleDomainRMSD
*
>
domains
;
std
::
vector
<
std
::
unique_ptr
<
SingleDomainRMSD
>
>
domains
;
public:
public:
explicit
MultiDomainRMSD
(
const
ReferenceConfigurationOptions
&
ro
);
explicit
MultiDomainRMSD
(
const
ReferenceConfigurationOptions
&
ro
);
~
MultiDomainRMSD
();
/// Read in the input from a pdb
/// Read in the input from a pdb
void
read
(
const
PDB
&
);
void
read
(
const
PDB
&
);
/// Set the input from an analysis object (don't know how this will work yet so currently just a plumed_error)
/// Set the input from an analysis object (don't know how this will work yet so currently just a plumed_error)
...
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