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Merge branch 'master' into PTMA-GBNO2-IBI-ff
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@ricalessandri
ricalessandri committed Oct 13, 2023
2 parents 1c33e62 + 357ebe3 commit 2c81ac2
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Showing 43 changed files with 10,982 additions and 966 deletions.
1 change: 0 additions & 1 deletion .github/workflows/pypi_deploy.yml
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Expand Up @@ -36,7 +36,6 @@ jobs:
token: ${{ secrets.CODECOV_TOKEN }}
files: ./coverage.xml
fail_ci_if_error: true
verbose: true

deploy:
needs: test
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6 changes: 3 additions & 3 deletions LIBRARY.md
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Expand Up @@ -21,9 +21,9 @@
|Polystyrene sulfonate |PSS | |[martini2](polyply/data/martini2/PSS.martini.2.itp) |
| | | |[martini3](polyply/data/martini3/PSS.martini3.ff) |
|Poly(para-phenylene ethynylene)|PPE | |[martini3](polyply/data/martini3/PPE.martini3.ff) |
|Poly(TEMPO methacrylate) |PTMA | |[martini3](polyply/data/martini3/PTMA.martini3.ff) |
| | | |[ibi_gbcg](polyply/data/ibi_gbcg/PTMA.gbno2.ibi.ff) |
|Poly(TEMPO methacrylate) |PTMA |[oplsaaLigParGen](polyply/data/oplsaaLigParGen/PTMA.oplsaa.LigParGen.ff)]|[martini3](polyply/data/martini3/PTMA.martini3.ff) |
| | | |[ibi_gbcg](polyply/data/ibi_gbcg/PTMA.gbno2.ibi.ff) |
|Dextran |DEX | |[martini3](polyply/data/martini3/dextran.martini3.ff) |
|DNA nucleobases |Dx, Tx5, Dx3 w/ x=T,G,A,C|[parmbsc1](polyply/data/parmbsc1/dna_final.ff) |[martini2](polyply/data/martini2/DNA_M2.ff) |
|Aminoacids |3 letter code | |[martini3](polyply/data/martini3/aminoacids.ff) |
|Polydimethylsiloxane |PDMS | |[martini3](polyply/data/martini3/PDMS.martini3.ff)
|Polydimethylsiloxane |PDMS | |[martini3](polyply/data/martini3/PDMS.martini3.ff) |
3 changes: 3 additions & 0 deletions bin/polyply
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Expand Up @@ -74,6 +74,9 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
help='A linear sequence of residue names.')
seq_group.add_argument('-seqf', dest='seq_file', type=Path,
help='A graph input file (JSON|TXT|FASTA|IG)')
dna_group = parser_gen_itp.add_argument_group('DNA specifc options')
dna_group.add_argument('-dsdna', dest='dsdna', action='store_true',
help='complement single sequence to dsDNA sequence')

parser_gen_itp.set_defaults(func=gen_itp)

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23 changes: 15 additions & 8 deletions polyply/__init__.py
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Expand Up @@ -19,16 +19,23 @@

# Find the data directory once.
try:
import pkg_resources
from importlib.resources import files, as_file
import atexit
from contextlib import ExitStack
except ImportError:
import os
DATA_PATH = os.path.join(os.path.dirname(__file__), 'data')
TEST_DATA = os.path.join(os.path.dirname(__file__), 'tests/test_data')
del os
from pathlib import Path
DATA_PATH = Path(__file__).parent / 'data'
TEST_DATA = Path(__file__).parent / 'tests/test_data'
del Path
else:
DATA_PATH = pkg_resources.resource_filename('polyply', 'data')
TEST_DATA = pkg_resources.resource_filename('polyply', 'tests/test_data')
del pkg_resources
ref_data = files('polyply') / 'data'
ref_test = files('polyply') / 'tests'/ 'test_data'
file_manager = ExitStack()
atexit.register(file_manager.close)
DATA_PATH = file_manager.enter_context(as_file(ref_data))
TEST_DATA = file_manager.enter_context(as_file(ref_test))

del files, as_file, atexit, ExitStack

del pbr

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25 changes: 25 additions & 0 deletions polyply/data/martini2/DNA_M2.ff
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Expand Up @@ -566,3 +566,28 @@ BB3 +BB2
BB2 BB3 +BB1 +BB2 1 180.00000 2 3 {"group": "link"}
BB3 +BB1 +BB2 +BB3 9 85.00000 2 2 {"group": "link", "version": "1"}
BB3 +BB1 +BB2 +BB3 9 160.00000 2 3 {"group": "link", "version": "2"}

;
; CIRCULAR MARTINI DNA
;

[ link ]
resname "DT|DG|DA|DC"
[ atoms ]
BB3 { }
>BB1 { }
[ bonds ]
BB3 >BB1 1 0.35300 10000 {"group": "link-circle", "edge": false}
[ angles ]
BB2 BB3 >BB1 2 102.00000 150 {"group": "backbone-circle", "edge": false}
BB3 >BB1 >BB2 2 106.00000 75 {"group": "backbone-circle", "edge": false}
[ exclusions ]
#meta {"edge": false}
BB2 >BB1
BB3 >BB2
[ dihedrals ]
BB2 BB3 >BB1 >BB2 1 180.00000 2 3 {"group": "link-circle", "edge": false}
BB3 >BB1 >BB2 >BB3 9 85.00000 2 2 {"group": "link-circle", "version": "1", "edge": false}
BB3 >BB1 >BB2 >BB3 9 160.00000 2 3 {"group": "link-circle", "version": "2", "edge": false}
[ edges ]
BB3 >BB1 {"linktype": "circle"}
45 changes: 45 additions & 0 deletions polyply/data/oplsaaLigParGen/CH3.ff
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@@ -0,0 +1,45 @@
;
;;;;;; "alpha" METHYL TERMINI for PTMA
;
[ moleculetype ]
; Name nrexcl
CH3a 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_135 1 CH3a C1 1 -0.3029 12.0110
2 opls_140 1 CH3a H2 2 0.0694 1.0080
3 opls_140 1 CH3a H3 3 0.0694 1.0080
4 opls_140 1 CH3a H4 4 0.0694 1.0080
[ bonds ]
; ai aj funct c0 c1
2 1 1 0.1090 284512.000
3 1 1 0.1090 284512.000
4 1 1 0.1090 284512.000
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1 107.800 276.144
3 1 4 1 107.800 276.144
2 1 4 1 107.800 276.144


;;;;;; "beta" METHYL TERMINI for PTMA
;
[ moleculetype ]
; Name nrexcl
CH3b 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_135 1 CH3b C1 1 -0.1854 12.0110
2 opls_140 1 CH3b H2 2 0.0386 1.0080
3 opls_140 1 CH3b H3 3 0.0386 1.0080
4 opls_140 1 CH3b H4 4 0.0386 1.0080
[ bonds ]
; ai aj funct c0 c1
2 1 1 0.1090 284512.000
3 1 1 0.1090 284512.000
4 1 1 0.1090 284512.000
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1 107.800 276.144
3 1 4 1 107.800 276.144
2 1 4 1 107.800 276.144
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