| Name | virialize JSON |
| Version |
0.1.3
JSON |
| download |
| home_page | None |
| Summary | Calculates the osmotic second virial coefficient (B2), and dissociation constant (Kd), for two rigid (macro)molecules, e.g. globular proteins. Done by explicit summation of the partition function in six dimensions (angular space and rigid-body separation). Calvados 3 parameters for use with coarsed grained amino acids are provided, but any pair-wise additivie potential can be used. |
| upload_time | 2024-12-02 20:16:23 |
| maintainer | None |
| docs_url | None |
| author | Mikael Lund <lyssky@icloud.com> |
| requires_python | None |
| license | Apache-2.0 |
| keywords |
pairwise_interaction
bioinformatics
virial_coefficient
dissociation_constant
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# Angular Scan
This iterates over all intermolecular poses between two rigid molecules.
For each pose, defined by two quaternions and a mass center separation, the
intermolecular interaction energy is calculated.
For each mass center separation, _r_, the partition function,
$Q(r) = \sum e^{-\beta u(r)}$, is explicitly
evaluated, whereby we can obtain the free energy, $w(r) = -kT \ln \langle e^{-\beta u(r)} \rangle$ and
the thermally averaged energy, $u(r) = \sum u(r)e^{-\beta u(r)} / Q$.
## Usage
The command-line tool `virialize` does the 6D scanning and calculates the potential of mean force, w(r) which
is used to derive the 2nd virial coefficient and twobody dissociation constant.
Two input structures are requires (`.xyz` format) and all particle types must be defined in the topology file.
The topology files also defines the particular pair-potential to use. Note that currently, a coulomb potential
is automatically added and should hence not be specified in the topology.
```console
virialize scan --icotable -1 cppm-p18.xyz -2 cppm-p00.xyz --rmin 40.5 --rmax 60 --dr 1.0 --top topology.yaml --resolution 0.6 --molarity 0.05
```
## Create `pip` package using Maturin
This is for development purposes only.
```console
pip install ziglang pipx
pipx install maturin # on ubuntu; then restart shell
maturin publish --target=x86_64-unknown-linux-gnu --zig
```
Raw data
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"description": "# Angular Scan\n\nThis iterates over all intermolecular poses between two rigid molecules.\nFor each pose, defined by two quaternions and a mass center separation, the\nintermolecular interaction energy is calculated.\n\nFor each mass center separation, _r_, the partition function,\n$Q(r) = \\sum e^{-\\beta u(r)}$, is explicitly\nevaluated, whereby we can obtain the free energy, $w(r) = -kT \\ln \\langle e^{-\\beta u(r)} \\rangle$ and\nthe thermally averaged energy, $u(r) = \\sum u(r)e^{-\\beta u(r)} / Q$.\n\n\n\n## Usage\n\nThe command-line tool `virialize` does the 6D scanning and calculates the potential of mean force, w(r) which\nis used to derive the 2nd virial coefficient and twobody dissociation constant.\nTwo input structures are requires (`.xyz` format) and all particle types must be defined in the topology file.\nThe topology files also defines the particular pair-potential to use. Note that currently, a coulomb potential\nis automatically added and should hence not be specified in the topology.\n\n```console\nvirialize scan --icotable -1 cppm-p18.xyz -2 cppm-p00.xyz --rmin 40.5 --rmax 60 --dr 1.0 --top topology.yaml --resolution 0.6 --molarity 0.05\n```\n\n## Create `pip` package using Maturin\n\nThis is for development purposes only.\n\n```console\npip install ziglang pipx\npipx install maturin # on ubuntu; then restart shell\nmaturin publish --target=x86_64-unknown-linux-gnu --zig\n```\n\n",
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