diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml index 908b1c22..c08200df 100644 --- a/.github/workflows/build-docs.yml +++ b/.github/workflows/build-docs.yml @@ -34,7 +34,10 @@ jobs: commit_user_name: "github-actions[bot]" commit_user_email: "github-actions[bot]@users.noreply.github.com" commit_author: "github-actions[bot] " + file_pattern: "docs/ _inv/ _reference/ _freeze/" + push_options: "--force" - uses: peaceiris/actions-gh-pages@v3 with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: docs + diff --git a/_reference/kmc.qmd b/_reference/kmc.qmd index ce53cb46..bd64d84a 100644 --- a/_reference/kmc.qmd +++ b/_reference/kmc.qmd @@ -18,7 +18,7 @@ and because we have one reactant molecule ### KMCResult { #kimmdy.kmc.KMCResult } -`kmc.KMCResult(recipe=field(default_factory=lambda : Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)` +`kmc.KMCResult(recipe=field(default_factory=lambda: Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)` The result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction. diff --git a/_reference/topology.atomic.qmd b/_reference/topology.atomic.qmd index 312d5450..7385fd79 100644 --- a/_reference/topology.atomic.qmd +++ b/_reference/topology.atomic.qmd @@ -26,8 +26,8 @@ See [gromacs manual](https://manual.gromacs.org/current/reference-manual/topolog | [PositionRestraint](#kimmdy.topology.atomic.PositionRestraint) | Information about one position restraint. | | [ResidueAtomSpec](#kimmdy.topology.atomic.ResidueAtomSpec) | Information about one atom in a residue | | [ResidueBondSpec](#kimmdy.topology.atomic.ResidueBondSpec) | Information about one bond in a residue | -| [ResidueImproperSpec](#kimmdy.topology.atomic.ResidueImproperSpec) | Information about one imroper dihedral in a residue | -| [ResidueProperSpec](#kimmdy.topology.atomic.ResidueProperSpec) | Information about one imroper dihedral in a residue | +| [ResidueImproperSpec](#kimmdy.topology.atomic.ResidueImproperSpec) | Information about one improper dihedral in a residue | +| [ResidueProperSpec](#kimmdy.topology.atomic.ResidueProperSpec) | Information about one proper dihedral in a residue | | [ResidueType](#kimmdy.topology.atomic.ResidueType) | Information about one residuetype from aminoacids.rtp | | [Settle](#kimmdy.topology.atomic.Settle) | Information about one settles | @@ -215,19 +215,19 @@ Information about one bond in a residue ### ResidueImproperSpec { #kimmdy.topology.atomic.ResidueImproperSpec } -`topology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, q0, cq)` +`topology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)` -Information about one imroper dihedral in a residue +Information about one improper dihedral in a residue -; atom1 atom2 atom3 atom4 q0 cq +; atom1 atom2 atom3 atom4 c0(q0) c1(cp) c2(mult) ### ResidueProperSpec { #kimmdy.topology.atomic.ResidueProperSpec } -`topology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, q0)` +`topology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)` -Information about one imroper dihedral in a residue +Information about one proper dihedral in a residue -; atom1 atom2 atom3 atom4 q0 cq +; atom1 atom2 atom3 atom4 c0(q0) c1(cq) c2 ### ResidueType { #kimmdy.topology.atomic.ResidueType } diff --git a/docs/_reference/kmc.html b/docs/_reference/kmc.html index 6500bd4f..88259513 100644 --- a/docs/_reference/kmc.html +++ b/docs/_reference/kmc.html @@ -511,7 +511,7 @@

Classes

KMCResult

-

kmc.KMCResult(recipe=field(default_factory=lambda : Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)

+

kmc.KMCResult(recipe=field(default_factory=lambda: Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)

The result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.

Attributes

diff --git a/docs/_reference/topology.atomic.html b/docs/_reference/topology.atomic.html index 1b69a87d..b52de320 100644 --- a/docs/_reference/topology.atomic.html +++ b/docs/_reference/topology.atomic.html @@ -563,11 +563,11 @@

Classes

ResidueImproperSpec -Information about one imroper dihedral in a residue +Information about one improper dihedral in a residue ResidueProperSpec -Information about one imroper dihedral in a residue +Information about one proper dihedral in a residue ResidueType @@ -689,15 +689,15 @@

Res

ResidueImproperSpec

-

topology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, q0, cq)

-

Information about one imroper dihedral in a residue

-

; atom1 atom2 atom3 atom4 q0 cq

+

topology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)

+

Information about one improper dihedral in a residue

+

; atom1 atom2 atom3 atom4 c0(q0) c1(cp) c2(mult)

ResidueProperSpec

-

topology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, q0)

-

Information about one imroper dihedral in a residue

-

; atom1 atom2 atom3 atom4 q0 cq

+

topology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)

+

Information about one proper dihedral in a residue

+

; atom1 atom2 atom3 atom4 c0(q0) c1(cq) c2

ResidueType

diff --git a/docs/guide/explanation/index.html b/docs/guide/explanation/index.html index 49a90693..590f97de 100644 --- a/docs/guide/explanation/index.html +++ b/docs/guide/explanation/index.html @@ -537,7 +537,7 @@

Explanations

- + Visualize Topologies diff --git a/docs/guide/how-to/index.html b/docs/guide/how-to/index.html index 8d08824b..65441beb 100644 --- a/docs/guide/how-to/index.html +++ b/docs/guide/how-to/index.html @@ -537,7 +537,7 @@

How-To

- + Contribute @@ -545,7 +545,7 @@

How-To

  - + Examples @@ -553,7 +553,7 @@

How-To

  - + High Performance Computing @@ -561,7 +561,7 @@

How-To

  - + Install Machine Learning Plugins @@ -569,7 +569,7 @@

How-To

  - + Reaction only diff --git a/docs/guide/tutorials/getting-started.html b/docs/guide/tutorials/getting-started.html index 279cf195..8237d998 100644 --- a/docs/guide/tutorials/getting-started.html +++ b/docs/guide/tutorials/getting-started.html @@ -603,7 +603,7 @@

Setup the Simulation<

Our starting structure is a simple ACE/NME-capped Alanine molecule in a box of water. Note, how it has a missing hydrogen atom on the alpha carbon. This is a radical. We will use the builtin hat_reaction to simulate hydrogen atom transfer reactions from nearby hydrogens to the radical position.

diff --git a/docs/guide/tutorials/index.html b/docs/guide/tutorials/index.html index 8a6c412a..a81cc205 100644 --- a/docs/guide/tutorials/index.html +++ b/docs/guide/tutorials/index.html @@ -507,7 +507,7 @@

Tutorials

-
+

@@ -539,7 +539,7 @@

-
+

@@ -571,7 +571,7 @@

-
+

 

diff --git a/docs/search.json b/docs/search.json index 408869a8..1813ad70 100644 --- a/docs/search.json +++ b/docs/search.json @@ -256,14 +256,14 @@ "href": "_reference/kmc.html", "title": "kmc", "section": "", - "text": "kmc\nKinetic Monte Carlo (KMC) classes and functions.\nIn our system, the reaction rate r = (deterministic) reaction constant k = stochastic reaction constant c (from gillespie 1977) = propensity a (from Anderson 2007) because of the fundamental premise of chemical kinetics and because we have one reactant molecule\n\n\n\n\n\nName\nDescription\n\n\n\n\nKMCResult\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nkmc.KMCResult(recipe=field(default_factory=lambda : Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nrecipe\nRecipe\nSingle sequence of RecipeSteps to build product\n\n\nreaction_probability\nOptional[list[float]]\nIntegral of reaction propensity with respect to time\n\n\ntime_delta\nOptional[float]\nMC time jump during which the reaction occurs [ps]\n\n\ntime_start\nOptional[float]\nTime, from which the reaction starts. The reaction changes the geometry/topology of this timestep and continues from there. [ps]\n\n\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nextrande\nExtrande KMC\n\n\nextrande_mod\nModified Extrande KMC\n\n\nfrm\nFirst Reaction Method variant of Kinetic Monte Carlo.\n\n\nrf_kmc\nRejection-Free Monte Carlo.\n\n\n\n\n\nkmc.extrande(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nExtrande KMC\nImplemented as in Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.extrande_mod(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nModified Extrande KMC\nImproved implementation of Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923 Changes: The considered time window is chosen to be a window containing constant rates. This prevents very small tau caused by a spike in the rate at a later point. As a side effect, the upper rate bound b and current rate a0 are the same, and the ‘extra’ side channel can not be triggered anymore.\nThis should be more efficient given a limited number of time windows containing constant rates.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.frm(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng(), MD_time=None)\nFirst Reaction Method variant of Kinetic Monte Carlo. takes RecipeCollection and choses a recipe based on which reaction would occur.\nCompare e.g. Wikipedia KMC - time dependent\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nto generate random numbers in the KMC step\ndefault_rng()\n\n\nMD_time\nOptional[float]\ntime [ps] to compare conformational events with reaction events in the time domain\nNone\n\n\n\n\n\n\n\nkmc.rf_kmc(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng())\nRejection-Free Monte Carlo. Takes RecipeCollection and choses a recipe based on the relative propensity of the events. The ‘start’ time of the reaction is the time of the highest rate of the accepted reaction.\nCompare e.g. Wikipedia KMC - rejection free\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()" + "text": "kmc\nKinetic Monte Carlo (KMC) classes and functions.\nIn our system, the reaction rate r = (deterministic) reaction constant k = stochastic reaction constant c (from gillespie 1977) = propensity a (from Anderson 2007) because of the fundamental premise of chemical kinetics and because we have one reactant molecule\n\n\n\n\n\nName\nDescription\n\n\n\n\nKMCResult\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nkmc.KMCResult(recipe=field(default_factory=lambda: Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nrecipe\nRecipe\nSingle sequence of RecipeSteps to build product\n\n\nreaction_probability\nOptional[list[float]]\nIntegral of reaction propensity with respect to time\n\n\ntime_delta\nOptional[float]\nMC time jump during which the reaction occurs [ps]\n\n\ntime_start\nOptional[float]\nTime, from which the reaction starts. The reaction changes the geometry/topology of this timestep and continues from there. [ps]\n\n\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nextrande\nExtrande KMC\n\n\nextrande_mod\nModified Extrande KMC\n\n\nfrm\nFirst Reaction Method variant of Kinetic Monte Carlo.\n\n\nrf_kmc\nRejection-Free Monte Carlo.\n\n\n\n\n\nkmc.extrande(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nExtrande KMC\nImplemented as in Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.extrande_mod(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nModified Extrande KMC\nImproved implementation of Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923 Changes: The considered time window is chosen to be a window containing constant rates. This prevents very small tau caused by a spike in the rate at a later point. As a side effect, the upper rate bound b and current rate a0 are the same, and the ‘extra’ side channel can not be triggered anymore.\nThis should be more efficient given a limited number of time windows containing constant rates.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.frm(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng(), MD_time=None)\nFirst Reaction Method variant of Kinetic Monte Carlo. takes RecipeCollection and choses a recipe based on which reaction would occur.\nCompare e.g. Wikipedia KMC - time dependent\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nto generate random numbers in the KMC step\ndefault_rng()\n\n\nMD_time\nOptional[float]\ntime [ps] to compare conformational events with reaction events in the time domain\nNone\n\n\n\n\n\n\n\nkmc.rf_kmc(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng())\nRejection-Free Monte Carlo. Takes RecipeCollection and choses a recipe based on the relative propensity of the events. The ‘start’ time of the reaction is the time of the highest rate of the accepted reaction.\nCompare e.g. Wikipedia KMC - rejection free\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()" }, { "objectID": "_reference/kmc.html#classes", "href": "_reference/kmc.html#classes", "title": "kmc", "section": "", - "text": "Name\nDescription\n\n\n\n\nKMCResult\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nkmc.KMCResult(recipe=field(default_factory=lambda : Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nrecipe\nRecipe\nSingle sequence of RecipeSteps to build product\n\n\nreaction_probability\nOptional[list[float]]\nIntegral of reaction propensity with respect to time\n\n\ntime_delta\nOptional[float]\nMC time jump during which the reaction occurs [ps]\n\n\ntime_start\nOptional[float]\nTime, from which the reaction starts. The reaction changes the geometry/topology of this timestep and continues from there. [ps]" + "text": "Name\nDescription\n\n\n\n\nKMCResult\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nkmc.KMCResult(recipe=field(default_factory=lambda: Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nrecipe\nRecipe\nSingle sequence of RecipeSteps to build product\n\n\nreaction_probability\nOptional[list[float]]\nIntegral of reaction propensity with respect to time\n\n\ntime_delta\nOptional[float]\nMC time jump during which the reaction occurs [ps]\n\n\ntime_start\nOptional[float]\nTime, from which the reaction starts. The reaction changes the geometry/topology of this timestep and continues from there. [ps]" }, { "objectID": "_reference/kmc.html#functions", @@ -480,14 +480,14 @@ "href": "_reference/topology.atomic.html", "title": "topology.atomic", "section": "", - "text": "topology.atomic\nAtomic datatypes for the topology such as Atom, Bond, Angle, Dihedral, etc. The order of the fields comes from the gromacs topology file format. See gromacs manual\n\n\n\n\n\nName\nDescription\n\n\n\n\nAngle\nInformation about one angle\n\n\nAngleType\nInformation about one angletype\n\n\nAtom\nInformation about one atom\n\n\nAtomType\nInformation about one atom type\n\n\nBond\nInformation about one bond\n\n\nBondType\nInformation about one bondtype\n\n\nDihedral\nInformation about one proper or improper dihedral\n\n\nDihedralRestraint\nInformation about one dihedral restraint.\n\n\nDihedralType\nInformation about one dihedraltype\n\n\nExclusion\nInformation about one exclusion\n\n\nMultipleDihedralTypes\nMultiple DihedralTypess with the same ai, aj, ak, al\n\n\nMultipleDihedrals\nMultiple Dihedrals with the same ai, aj, ak, al\n\n\nPair\nInformation about one pair\n\n\nPositionRestraint\nInformation about one position restraint.\n\n\nResidueAtomSpec\nInformation about one atom in a residue\n\n\nResidueBondSpec\nInformation about one bond in a residue\n\n\nResidueImproperSpec\nInformation about one imroper dihedral in a residue\n\n\nResidueProperSpec\nInformation about one imroper dihedral in a residue\n\n\nResidueType\nInformation about one residuetype from aminoacids.rtp\n\n\nSettle\nInformation about one settles\n\n\n\n\n\ntopology.atomic.Angle(ai, aj, ak, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angle\nA class containing angle information as in the angles section of the topology.\nFrom gromacs topology: ; ai aj ak funct c0 c1 c2 c3 With aj < ai < ak\n\n\n\ntopology.atomic.AngleType(i, j, k, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angletype\nA class containing angle type information as in the angletypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j k func th0 cth\n\n\n\ntopology.atomic.Atom(nr, type, resnr, residue, atom, cgnr, charge, mass=None, typeB=None, chargeB=None, massB=None, bound_to_nrs=field(default_factory=list), is_radical=False)\nInformation about one atom\nA class containing atom information as in the atoms section of the topology. An atom keeps a list of which atoms it is bound to and its radical state.\nFrom gromacs topology: ; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n\n\n\ntopology.atomic.AtomType(type, id_sym, at_num, mass, charge, ptype, sigma, epsilon, id)\nInformation about one atom type\nA class containing atom type information as in the atomtypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; name at.num mass charge ptype sigma epsilon\n\n\n\ntopology.atomic.Bond(ai, aj, funct, c0=None, c1=None, c2=None, c3=None, c4=None, c5=None)\nInformation about one bond\nA class containing bond information as in the bonds section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3 c4 c5 With ai < aj\n\n\n\ntopology.atomic.BondType(i, j, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one bondtype\nA class containing bond information as in the bondtype section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j func b0 kb Where i and j are atomtypes\n\n\n\ntopology.atomic.Dihedral(ai, aj, ak, al, funct, c0=None, c1=None, periodicity='', c3=None, c4=None, c5=None)\nInformation about one proper or improper dihedral\nA class containing dihedral information as in the dihedrals section of the topology. Improper dihedrals have funct 4. Proper dihedrals have funct != 4, mostly funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity.\nFrom gromacs topology: ; ai aj ak al funct c0 c1 c2 c3 c4 c5 For proper dihedrals (funct 9): aj < ak\n\n\n\ntopology.atomic.DihedralRestraint(ai, aj, ak, al, type, phi, dphi, fc)\nInformation about one dihedral restraint.\nA class containing information as in the dihedral_restraints section of the topology.\nFrom gromacs topology: ; ai aj ak al type phi dphi fc\n\n\n\ntopology.atomic.DihedralType(i, j, k, l, id, id_sym, funct, c0, c1, periodicity, c3=None, c4=None, c5=None)\nInformation about one dihedraltype\nA class containing dihedral type information as in the dihedraltypes section of the forcefield. Improper dihedrals have funct 4. Proper dihedrals have funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity and part of the id.\nFrom gromacs version of the amber* ff: ; i j k l func phase kd pn\n\n\n\ntopology.atomic.Exclusion(ai, aj, ak=None, al=None)\nInformation about one exclusion\nA class containing atom information as in the exclusions section of the topology.\nFrom gromacs topology: ; ai aj ak al\n\n\n\ntopology.atomic.MultipleDihedralTypes(ai, aj, ak, al, funct, dihedral_types)\nMultiple DihedralTypess with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is > 1. The key of the dihedral_types dict is the periodicity (c2).\n\n\n\ntopology.atomic.MultipleDihedrals(ai, aj, ak, al, funct, dihedrals)\nMultiple Dihedrals with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is > 1. The key of the dihedrals dict is the periodicity (c2).\n\n\n\ntopology.atomic.Pair(ai, aj, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one pair\nA class containing pair information as in the pair section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3\n\n\n\ntopology.atomic.PositionRestraint(ai, funct, fc, condition=None)\nInformation about one position restraint.\nA class containing information as in the position_restraints section of the topology.\nFrom gromacs topology: ; ai funct fc(x,y,z)\n\n\n\ntopology.atomic.ResidueAtomSpec(name, type, charge, cgrp)\nInformation about one atom in a residue\n; name type charge chargegroup\n\n\n\ntopology.atomic.ResidueBondSpec(atom1, atom2, b0=None, kb=None)\nInformation about one bond in a residue\n; atom1 atom2 b0 kb\n\n\n\ntopology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, q0, cq)\nInformation about one imroper dihedral in a residue\n; atom1 atom2 atom3 atom4 q0 cq\n\n\n\ntopology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, q0)\nInformation about one imroper dihedral in a residue\n; atom1 atom2 atom3 atom4 q0 cq\n\n\n\ntopology.atomic.ResidueType(residue, atoms, bonds, proper_dihedrals, improper_dihedrals)\nInformation about one residuetype from aminoacids.rtp\n\n\n\ntopology.atomic.Settle(nr, funct, doh, dhh)\nInformation about one settles\nA class containing atom information as in the settle section of the topology.\nFrom gromacs topology: ; nr funct doh dhh" + "text": "topology.atomic\nAtomic datatypes for the topology such as Atom, Bond, Angle, Dihedral, etc. The order of the fields comes from the gromacs topology file format. See gromacs manual\n\n\n\n\n\nName\nDescription\n\n\n\n\nAngle\nInformation about one angle\n\n\nAngleType\nInformation about one angletype\n\n\nAtom\nInformation about one atom\n\n\nAtomType\nInformation about one atom type\n\n\nBond\nInformation about one bond\n\n\nBondType\nInformation about one bondtype\n\n\nDihedral\nInformation about one proper or improper dihedral\n\n\nDihedralRestraint\nInformation about one dihedral restraint.\n\n\nDihedralType\nInformation about one dihedraltype\n\n\nExclusion\nInformation about one exclusion\n\n\nMultipleDihedralTypes\nMultiple DihedralTypess with the same ai, aj, ak, al\n\n\nMultipleDihedrals\nMultiple Dihedrals with the same ai, aj, ak, al\n\n\nPair\nInformation about one pair\n\n\nPositionRestraint\nInformation about one position restraint.\n\n\nResidueAtomSpec\nInformation about one atom in a residue\n\n\nResidueBondSpec\nInformation about one bond in a residue\n\n\nResidueImproperSpec\nInformation about one improper dihedral in a residue\n\n\nResidueProperSpec\nInformation about one proper dihedral in a residue\n\n\nResidueType\nInformation about one residuetype from aminoacids.rtp\n\n\nSettle\nInformation about one settles\n\n\n\n\n\ntopology.atomic.Angle(ai, aj, ak, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angle\nA class containing angle information as in the angles section of the topology.\nFrom gromacs topology: ; ai aj ak funct c0 c1 c2 c3 With aj < ai < ak\n\n\n\ntopology.atomic.AngleType(i, j, k, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angletype\nA class containing angle type information as in the angletypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j k func th0 cth\n\n\n\ntopology.atomic.Atom(nr, type, resnr, residue, atom, cgnr, charge, mass=None, typeB=None, chargeB=None, massB=None, bound_to_nrs=field(default_factory=list), is_radical=False)\nInformation about one atom\nA class containing atom information as in the atoms section of the topology. An atom keeps a list of which atoms it is bound to and its radical state.\nFrom gromacs topology: ; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n\n\n\ntopology.atomic.AtomType(type, id_sym, at_num, mass, charge, ptype, sigma, epsilon, id)\nInformation about one atom type\nA class containing atom type information as in the atomtypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; name at.num mass charge ptype sigma epsilon\n\n\n\ntopology.atomic.Bond(ai, aj, funct, c0=None, c1=None, c2=None, c3=None, c4=None, c5=None)\nInformation about one bond\nA class containing bond information as in the bonds section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3 c4 c5 With ai < aj\n\n\n\ntopology.atomic.BondType(i, j, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one bondtype\nA class containing bond information as in the bondtype section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j func b0 kb Where i and j are atomtypes\n\n\n\ntopology.atomic.Dihedral(ai, aj, ak, al, funct, c0=None, c1=None, periodicity='', c3=None, c4=None, c5=None)\nInformation about one proper or improper dihedral\nA class containing dihedral information as in the dihedrals section of the topology. Improper dihedrals have funct 4. Proper dihedrals have funct != 4, mostly funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity.\nFrom gromacs topology: ; ai aj ak al funct c0 c1 c2 c3 c4 c5 For proper dihedrals (funct 9): aj < ak\n\n\n\ntopology.atomic.DihedralRestraint(ai, aj, ak, al, type, phi, dphi, fc)\nInformation about one dihedral restraint.\nA class containing information as in the dihedral_restraints section of the topology.\nFrom gromacs topology: ; ai aj ak al type phi dphi fc\n\n\n\ntopology.atomic.DihedralType(i, j, k, l, id, id_sym, funct, c0, c1, periodicity, c3=None, c4=None, c5=None)\nInformation about one dihedraltype\nA class containing dihedral type information as in the dihedraltypes section of the forcefield. Improper dihedrals have funct 4. Proper dihedrals have funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity and part of the id.\nFrom gromacs version of the amber* ff: ; i j k l func phase kd pn\n\n\n\ntopology.atomic.Exclusion(ai, aj, ak=None, al=None)\nInformation about one exclusion\nA class containing atom information as in the exclusions section of the topology.\nFrom gromacs topology: ; ai aj ak al\n\n\n\ntopology.atomic.MultipleDihedralTypes(ai, aj, ak, al, funct, dihedral_types)\nMultiple DihedralTypess with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is > 1. The key of the dihedral_types dict is the periodicity (c2).\n\n\n\ntopology.atomic.MultipleDihedrals(ai, aj, ak, al, funct, dihedrals)\nMultiple Dihedrals with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is > 1. The key of the dihedrals dict is the periodicity (c2).\n\n\n\ntopology.atomic.Pair(ai, aj, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one pair\nA class containing pair information as in the pair section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3\n\n\n\ntopology.atomic.PositionRestraint(ai, funct, fc, condition=None)\nInformation about one position restraint.\nA class containing information as in the position_restraints section of the topology.\nFrom gromacs topology: ; ai funct fc(x,y,z)\n\n\n\ntopology.atomic.ResidueAtomSpec(name, type, charge, cgrp)\nInformation about one atom in a residue\n; name type charge chargegroup\n\n\n\ntopology.atomic.ResidueBondSpec(atom1, atom2, b0=None, kb=None)\nInformation about one bond in a residue\n; atom1 atom2 b0 kb\n\n\n\ntopology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)\nInformation about one improper dihedral in a residue\n; atom1 atom2 atom3 atom4 c0(q0) c1(cp) c2(mult)\n\n\n\ntopology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)\nInformation about one proper dihedral in a residue\n; atom1 atom2 atom3 atom4 c0(q0) c1(cq) c2\n\n\n\ntopology.atomic.ResidueType(residue, atoms, bonds, proper_dihedrals, improper_dihedrals)\nInformation about one residuetype from aminoacids.rtp\n\n\n\ntopology.atomic.Settle(nr, funct, doh, dhh)\nInformation about one settles\nA class containing atom information as in the settle section of the topology.\nFrom gromacs topology: ; nr funct doh dhh" }, { "objectID": "_reference/topology.atomic.html#classes", "href": "_reference/topology.atomic.html#classes", "title": "topology.atomic", "section": "", - "text": "Name\nDescription\n\n\n\n\nAngle\nInformation about one angle\n\n\nAngleType\nInformation about one angletype\n\n\nAtom\nInformation about one atom\n\n\nAtomType\nInformation about one atom type\n\n\nBond\nInformation about one bond\n\n\nBondType\nInformation about one bondtype\n\n\nDihedral\nInformation about one proper or improper dihedral\n\n\nDihedralRestraint\nInformation about one dihedral restraint.\n\n\nDihedralType\nInformation about one dihedraltype\n\n\nExclusion\nInformation about one exclusion\n\n\nMultipleDihedralTypes\nMultiple DihedralTypess with the same ai, aj, ak, al\n\n\nMultipleDihedrals\nMultiple Dihedrals with the same ai, aj, ak, al\n\n\nPair\nInformation about one pair\n\n\nPositionRestraint\nInformation about one position restraint.\n\n\nResidueAtomSpec\nInformation about one atom in a residue\n\n\nResidueBondSpec\nInformation about one bond in a residue\n\n\nResidueImproperSpec\nInformation about one imroper dihedral in a residue\n\n\nResidueProperSpec\nInformation about one imroper dihedral in a residue\n\n\nResidueType\nInformation about one residuetype from aminoacids.rtp\n\n\nSettle\nInformation about one settles\n\n\n\n\n\ntopology.atomic.Angle(ai, aj, ak, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angle\nA class containing angle information as in the angles section of the topology.\nFrom gromacs topology: ; ai aj ak funct c0 c1 c2 c3 With aj < ai < ak\n\n\n\ntopology.atomic.AngleType(i, j, k, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angletype\nA class containing angle type information as in the angletypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j k func th0 cth\n\n\n\ntopology.atomic.Atom(nr, type, resnr, residue, atom, cgnr, charge, mass=None, typeB=None, chargeB=None, massB=None, bound_to_nrs=field(default_factory=list), is_radical=False)\nInformation about one atom\nA class containing atom information as in the atoms section of the topology. An atom keeps a list of which atoms it is bound to and its radical state.\nFrom gromacs topology: ; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n\n\n\ntopology.atomic.AtomType(type, id_sym, at_num, mass, charge, ptype, sigma, epsilon, id)\nInformation about one atom type\nA class containing atom type information as in the atomtypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; name at.num mass charge ptype sigma epsilon\n\n\n\ntopology.atomic.Bond(ai, aj, funct, c0=None, c1=None, c2=None, c3=None, c4=None, c5=None)\nInformation about one bond\nA class containing bond information as in the bonds section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3 c4 c5 With ai < aj\n\n\n\ntopology.atomic.BondType(i, j, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one bondtype\nA class containing bond information as in the bondtype section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j func b0 kb Where i and j are atomtypes\n\n\n\ntopology.atomic.Dihedral(ai, aj, ak, al, funct, c0=None, c1=None, periodicity='', c3=None, c4=None, c5=None)\nInformation about one proper or improper dihedral\nA class containing dihedral information as in the dihedrals section of the topology. Improper dihedrals have funct 4. Proper dihedrals have funct != 4, mostly funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity.\nFrom gromacs topology: ; ai aj ak al funct c0 c1 c2 c3 c4 c5 For proper dihedrals (funct 9): aj < ak\n\n\n\ntopology.atomic.DihedralRestraint(ai, aj, ak, al, type, phi, dphi, fc)\nInformation about one dihedral restraint.\nA class containing information as in the dihedral_restraints section of the topology.\nFrom gromacs topology: ; ai aj ak al type phi dphi fc\n\n\n\ntopology.atomic.DihedralType(i, j, k, l, id, id_sym, funct, c0, c1, periodicity, c3=None, c4=None, c5=None)\nInformation about one dihedraltype\nA class containing dihedral type information as in the dihedraltypes section of the forcefield. Improper dihedrals have funct 4. Proper dihedrals have funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity and part of the id.\nFrom gromacs version of the amber* ff: ; i j k l func phase kd pn\n\n\n\ntopology.atomic.Exclusion(ai, aj, ak=None, al=None)\nInformation about one exclusion\nA class containing atom information as in the exclusions section of the topology.\nFrom gromacs topology: ; ai aj ak al\n\n\n\ntopology.atomic.MultipleDihedralTypes(ai, aj, ak, al, funct, dihedral_types)\nMultiple DihedralTypess with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is > 1. The key of the dihedral_types dict is the periodicity (c2).\n\n\n\ntopology.atomic.MultipleDihedrals(ai, aj, ak, al, funct, dihedrals)\nMultiple Dihedrals with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is > 1. The key of the dihedrals dict is the periodicity (c2).\n\n\n\ntopology.atomic.Pair(ai, aj, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one pair\nA class containing pair information as in the pair section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3\n\n\n\ntopology.atomic.PositionRestraint(ai, funct, fc, condition=None)\nInformation about one position restraint.\nA class containing information as in the position_restraints section of the topology.\nFrom gromacs topology: ; ai funct fc(x,y,z)\n\n\n\ntopology.atomic.ResidueAtomSpec(name, type, charge, cgrp)\nInformation about one atom in a residue\n; name type charge chargegroup\n\n\n\ntopology.atomic.ResidueBondSpec(atom1, atom2, b0=None, kb=None)\nInformation about one bond in a residue\n; atom1 atom2 b0 kb\n\n\n\ntopology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, q0, cq)\nInformation about one imroper dihedral in a residue\n; atom1 atom2 atom3 atom4 q0 cq\n\n\n\ntopology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, q0)\nInformation about one imroper dihedral in a residue\n; atom1 atom2 atom3 atom4 q0 cq\n\n\n\ntopology.atomic.ResidueType(residue, atoms, bonds, proper_dihedrals, improper_dihedrals)\nInformation about one residuetype from aminoacids.rtp\n\n\n\ntopology.atomic.Settle(nr, funct, doh, dhh)\nInformation about one settles\nA class containing atom information as in the settle section of the topology.\nFrom gromacs topology: ; nr funct doh dhh" + "text": "Name\nDescription\n\n\n\n\nAngle\nInformation about one angle\n\n\nAngleType\nInformation about one angletype\n\n\nAtom\nInformation about one atom\n\n\nAtomType\nInformation about one atom type\n\n\nBond\nInformation about one bond\n\n\nBondType\nInformation about one bondtype\n\n\nDihedral\nInformation about one proper or improper dihedral\n\n\nDihedralRestraint\nInformation about one dihedral restraint.\n\n\nDihedralType\nInformation about one dihedraltype\n\n\nExclusion\nInformation about one exclusion\n\n\nMultipleDihedralTypes\nMultiple DihedralTypess with the same ai, aj, ak, al\n\n\nMultipleDihedrals\nMultiple Dihedrals with the same ai, aj, ak, al\n\n\nPair\nInformation about one pair\n\n\nPositionRestraint\nInformation about one position restraint.\n\n\nResidueAtomSpec\nInformation about one atom in a residue\n\n\nResidueBondSpec\nInformation about one bond in a residue\n\n\nResidueImproperSpec\nInformation about one improper dihedral in a residue\n\n\nResidueProperSpec\nInformation about one proper dihedral in a residue\n\n\nResidueType\nInformation about one residuetype from aminoacids.rtp\n\n\nSettle\nInformation about one settles\n\n\n\n\n\ntopology.atomic.Angle(ai, aj, ak, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angle\nA class containing angle information as in the angles section of the topology.\nFrom gromacs topology: ; ai aj ak funct c0 c1 c2 c3 With aj < ai < ak\n\n\n\ntopology.atomic.AngleType(i, j, k, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angletype\nA class containing angle type information as in the angletypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j k func th0 cth\n\n\n\ntopology.atomic.Atom(nr, type, resnr, residue, atom, cgnr, charge, mass=None, typeB=None, chargeB=None, massB=None, bound_to_nrs=field(default_factory=list), is_radical=False)\nInformation about one atom\nA class containing atom information as in the atoms section of the topology. An atom keeps a list of which atoms it is bound to and its radical state.\nFrom gromacs topology: ; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n\n\n\ntopology.atomic.AtomType(type, id_sym, at_num, mass, charge, ptype, sigma, epsilon, id)\nInformation about one atom type\nA class containing atom type information as in the atomtypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; name at.num mass charge ptype sigma epsilon\n\n\n\ntopology.atomic.Bond(ai, aj, funct, c0=None, c1=None, c2=None, c3=None, c4=None, c5=None)\nInformation about one bond\nA class containing bond information as in the bonds section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3 c4 c5 With ai < aj\n\n\n\ntopology.atomic.BondType(i, j, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one bondtype\nA class containing bond information as in the bondtype section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j func b0 kb Where i and j are atomtypes\n\n\n\ntopology.atomic.Dihedral(ai, aj, ak, al, funct, c0=None, c1=None, periodicity='', c3=None, c4=None, c5=None)\nInformation about one proper or improper dihedral\nA class containing dihedral information as in the dihedrals section of the topology. Improper dihedrals have funct 4. Proper dihedrals have funct != 4, mostly funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity.\nFrom gromacs topology: ; ai aj ak al funct c0 c1 c2 c3 c4 c5 For proper dihedrals (funct 9): aj < ak\n\n\n\ntopology.atomic.DihedralRestraint(ai, aj, ak, al, type, phi, dphi, fc)\nInformation about one dihedral restraint.\nA class containing information as in the dihedral_restraints section of the topology.\nFrom gromacs topology: ; ai aj ak al type phi dphi fc\n\n\n\ntopology.atomic.DihedralType(i, j, k, l, id, id_sym, funct, c0, c1, periodicity, c3=None, c4=None, c5=None)\nInformation about one dihedraltype\nA class containing dihedral type information as in the dihedraltypes section of the forcefield. Improper dihedrals have funct 4. Proper dihedrals have funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity and part of the id.\nFrom gromacs version of the amber* ff: ; i j k l func phase kd pn\n\n\n\ntopology.atomic.Exclusion(ai, aj, ak=None, al=None)\nInformation about one exclusion\nA class containing atom information as in the exclusions section of the topology.\nFrom gromacs topology: ; ai aj ak al\n\n\n\ntopology.atomic.MultipleDihedralTypes(ai, aj, ak, al, funct, dihedral_types)\nMultiple DihedralTypess with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is > 1. The key of the dihedral_types dict is the periodicity (c2).\n\n\n\ntopology.atomic.MultipleDihedrals(ai, aj, ak, al, funct, dihedrals)\nMultiple Dihedrals with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is > 1. The key of the dihedrals dict is the periodicity (c2).\n\n\n\ntopology.atomic.Pair(ai, aj, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one pair\nA class containing pair information as in the pair section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3\n\n\n\ntopology.atomic.PositionRestraint(ai, funct, fc, condition=None)\nInformation about one position restraint.\nA class containing information as in the position_restraints section of the topology.\nFrom gromacs topology: ; ai funct fc(x,y,z)\n\n\n\ntopology.atomic.ResidueAtomSpec(name, type, charge, cgrp)\nInformation about one atom in a residue\n; name type charge chargegroup\n\n\n\ntopology.atomic.ResidueBondSpec(atom1, atom2, b0=None, kb=None)\nInformation about one bond in a residue\n; atom1 atom2 b0 kb\n\n\n\ntopology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)\nInformation about one improper dihedral in a residue\n; atom1 atom2 atom3 atom4 c0(q0) c1(cp) c2(mult)\n\n\n\ntopology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)\nInformation about one proper dihedral in a residue\n; atom1 atom2 atom3 atom4 c0(q0) c1(cq) c2\n\n\n\ntopology.atomic.ResidueType(residue, atoms, bonds, proper_dihedrals, improper_dihedrals)\nInformation about one residuetype from aminoacids.rtp\n\n\n\ntopology.atomic.Settle(nr, funct, doh, dhh)\nInformation about one settles\nA class containing atom information as in the settle section of the topology.\nFrom gromacs topology: ; nr funct doh dhh" }, { "objectID": "_reference/plugins.html", diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 3ebfcbbf..c19746e3 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -2,154 +2,154 @@ http://hits-mbm-dev.github.io/kimmdy/guide/explanation/topology.html - 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