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James Graham
pycgtool
Commits
d4fabd07
Commit
d4fabd07
authored
8 years ago
by
James Graham
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Add test for itp
parent
384cfaee
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3 changed files
pycgtool/bondset.py
+8
-5
8 additions, 5 deletions
pycgtool/bondset.py
test/data/sugar_out.itp
+43
-0
43 additions, 0 deletions
test/data/sugar_out.itp
test/test_bondset.py
+16
-0
16 additions, 0 deletions
test/test_bondset.py
with
67 additions
and
5 deletions
pycgtool/bondset.py
+
8
−
5
View file @
d4fabd07
...
@@ -226,26 +226,29 @@ class BondSet:
...
@@ -226,26 +226,29 @@ class BondSet:
e
.
args
=
(
"
Bead(s) {0} do(es) not exist in residue {1}
"
.
format
(
missing
,
mol
),)
e
.
args
=
(
"
Bead(s) {0} do(es) not exist in residue {1}
"
.
format
(
missing
,
mol
),)
raise
raise
def
write_itp
(
self
,
filename
,
mapping
):
def
write_itp
(
self
,
filename
,
mapping
,
exclude
=
set
()
):
"""
"""
Output a GROMACS .itp file containing atoms/beads and bonded terms.
Output a GROMACS .itp file containing atoms/beads and bonded terms.
:param filename: Name of output file
:param filename: Name of output file
:param mapping: AA->CG Mapping from which to collect bead properties
:param mapping: AA->CG Mapping from which to collect bead properties
:param exclude: Set of molecule names to be excluded from itp
"""
"""
self
.
_populate_atom_numbers
(
mapping
)
self
.
_populate_atom_numbers
(
mapping
)
backup_file
(
filename
,
verbose
=
True
)
backup_file
(
filename
,
verbose
=
True
)
def
write_bond_angle_dih
(
bonds
,
section_header
,
itp
,
fconst
=
True
):
def
write_bond_angle_dih
(
bonds
,
section_header
,
itp
,
fconst
=
True
,
multiplicity
=
None
):
if
bonds
:
if
bonds
:
print
(
"
\n
[ {0:s} ]
"
.
format
(
section_header
),
file
=
itp
)
print
(
"
\n
[ {0:s} ]
"
.
format
(
section_header
),
file
=
itp
)
for
bond
in
bonds
:
for
bond
in
bonds
:
# Factor is usually 1, unless doing correction
# Factor is usually 1, unless doing correction
eqm
=
bond
.
eqm
*
self
.
_empirical_correction_factor
eqm
=
bond
.
eqm
*
self
.
_empirical_correction_factor
line
=
"
"
.
join
([
"
{0:4d}
"
.
format
(
atnum
+
1
)
for
atnum
in
bond
.
atom_numbers
])
line
=
"
"
.
join
([
"
{0:4d}
"
.
format
(
atnum
+
1
)
for
atnum
in
bond
.
atom_numbers
])
line
+=
"
{0:12.5f}
"
.
format
(
eqm
)
line
+=
"
{0:
4d} {1:
12.5f}
"
.
format
(
1
,
eqm
)
if
fconst
:
if
fconst
:
line
+=
"
{0:12.5f}
"
.
format
(
bond
.
fconst
)
line
+=
"
{0:12.5f}
"
.
format
(
bond
.
fconst
)
if
multiplicity
is
not
None
:
line
+=
"
{0:4d}
"
.
format
(
multiplicity
)
print
(
line
,
file
=
itp
)
print
(
line
,
file
=
itp
)
with
open
(
filename
,
"
w
"
)
as
itp
:
with
open
(
filename
,
"
w
"
)
as
itp
:
...
@@ -258,7 +261,7 @@ class BondSet:
...
@@ -258,7 +261,7 @@ class BondSet:
print
(
header
,
file
=
itp
)
print
(
header
,
file
=
itp
)
# Print molecule
# Print molecule
for
mol
in
self
.
_molecules
:
for
mol
in
filter
(
lambda
mol
:
mol
not
in
exclude
,
self
.
_molecules
)
:
print
(
"
\n
[ moleculetype ]
"
,
file
=
itp
)
print
(
"
\n
[ moleculetype ]
"
,
file
=
itp
)
print
(
"
{0:4s} {1:4d}
"
.
format
(
mol
,
1
),
file
=
itp
)
print
(
"
{0:4s} {1:4d}
"
.
format
(
mol
,
1
),
file
=
itp
)
...
@@ -271,7 +274,7 @@ class BondSet:
...
@@ -271,7 +274,7 @@ class BondSet:
write_bond_angle_dih
(
self
.
get_bond_lengths
(
mol
),
"
bonds
"
,
itp
)
write_bond_angle_dih
(
self
.
get_bond_lengths
(
mol
),
"
bonds
"
,
itp
)
write_bond_angle_dih
(
self
.
get_bond_angles
(
mol
),
"
angles
"
,
itp
)
write_bond_angle_dih
(
self
.
get_bond_angles
(
mol
),
"
angles
"
,
itp
)
write_bond_angle_dih
(
self
.
get_bond_dihedrals
(
mol
),
"
dihedrals
"
,
itp
)
write_bond_angle_dih
(
self
.
get_bond_dihedrals
(
mol
),
"
dihedrals
"
,
itp
,
multiplicity
=
1
)
write_bond_angle_dih
(
self
.
get_bond_length_constraints
(
mol
),
"
constraints
"
,
itp
,
fconst
=
False
)
write_bond_angle_dih
(
self
.
get_bond_length_constraints
(
mol
),
"
constraints
"
,
itp
,
fconst
=
False
)
def
apply
(
self
,
frame
):
def
apply
(
self
,
frame
):
...
...
This diff is collapsed.
Click to expand it.
test/data/sugar_out.itp
0 → 100644
+
43
−
0
View file @
d4fabd07
;
; Topology prepared automatically using PyCGTOOL
; James Graham <J.A.Graham@soton.ac.uk> 2016
; University of Southampton
; https://github.com/jag1g13/pycgtool
;
[ moleculetype ]
ALLA 1
[ atoms ]
1 P3 1 ALLA C1 1 0.000
2 P3 1 ALLA C2 2 0.000
3 P3 1 ALLA C3 3 0.000
4 P3 1 ALLA C4 4 0.000
5 P2 1 ALLA C5 5 0.000
6 P4 1 ALLA O5 6 0.000
[ bonds ]
2 3 1 0.21998 35162.10022
3 4 1 0.21648 65545.10313
4 5 1 0.26454 19022.17121
5 6 1 0.20452 53457.20659
[ angles ]
1 2 3 1 77.69557 383.16060
2 3 4 1 115.59599 262.66648
3 4 5 1 108.51038 698.56915
4 5 6 1 81.23827 1098.41706
5 6 1 1 146.49898 48.08599
6 1 2 1 99.84045 1571.73513
[ dihedrals ]
1 2 3 4 1 -85.45004 234.10405 1
2 3 4 5 1 65.21378 117.46132 1
3 4 5 6 1 -22.73796 94.20175 1
4 5 6 1 1 55.18087 37.92107 1
5 6 1 2 1 -96.52349 40.73340 1
6 1 2 3 1 73.82477 259.20126 1
[ constraints ]
1 2 1 0.22209
6 1 1 0.17931
This diff is collapsed.
Click to expand it.
test/test_bondset.py
+
16
−
0
View file @
d4fabd07
import
unittest
import
unittest
import
filecmp
from
pycgtool.bondset
import
BondSet
from
pycgtool.bondset
import
BondSet
from
pycgtool.frame
import
Frame
from
pycgtool.frame
import
Frame
...
@@ -103,3 +104,18 @@ class BondSetTest(unittest.TestCase):
...
@@ -103,3 +104,18 @@ class BondSetTest(unittest.TestCase):
for
bond
in
bondset
.
get_bond_lengths
(
"
ETH
"
,
True
):
for
bond
in
bondset
.
get_bond_lengths
(
"
ETH
"
,
True
):
self
.
assertAlmostEqual
(
1.
,
bond
.
eqm
)
self
.
assertAlmostEqual
(
1.
,
bond
.
eqm
)
self
.
assertEqual
(
float
(
"
inf
"
),
bond
.
fconst
)
self
.
assertEqual
(
float
(
"
inf
"
),
bond
.
fconst
)
def
test_full_itp_sugar
(
self
):
measure
=
BondSet
(
"
test/data/sugar.bnd
"
,
DummyOptions
)
frame
=
Frame
(
"
test/data/sugar.gro
"
,
xtc
=
"
test/data/sugar.xtc
"
)
mapping
=
Mapping
(
"
test/data/sugar.map
"
,
DummyOptions
)
cgframe
=
mapping
.
apply
(
frame
)
while
frame
.
next_frame
():
cgframe
=
mapping
.
apply
(
frame
,
cgframe
=
cgframe
,
exclude
=
{
"
SOL
"
})
measure
.
apply
(
cgframe
)
measure
.
boltzmann_invert
()
measure
.
write_itp
(
"
sugar_out.itp
"
,
mapping
,
exclude
=
{
"
SOL
"
})
self
.
assertTrue
(
filecmp
.
cmp
(
"
sugar_out.itp
"
,
"
test/data/sugar_out.itp
"
))
This diff is collapsed.
Click to expand it.
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