diff --git a/dev/.buildinfo b/dev/.buildinfo index 1d5feec..643151b 100644 --- a/dev/.buildinfo +++ b/dev/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 8e6d2975566a474f18332d2d4e2dc774 +config: 357d9b14b45985ea0c943f0164441803 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/dev/_static/documentation_options.js b/dev/_static/documentation_options.js index a186a95..985722f 100644 --- a/dev/_static/documentation_options.js +++ b/dev/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '1.1dev_90984d5', + VERSION: '1.1dev_3ca70f0', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/dev/api.html b/dev/api.html index 8d0d2bf..b29e88d 100644 --- a/dev/api.html +++ b/dev/api.html @@ -8,7 +8,7 @@ - API — OpenMM ML 1.1dev_90984d5 documentation + API — OpenMM ML 1.1dev_3ca70f0 documentation @@ -35,7 +35,7 @@ - + diff --git a/dev/generated/openmmml.MLPotential.html b/dev/generated/openmmml.MLPotential.html index ebfc6bf..0d7e59b 100644 --- a/dev/generated/openmmml.MLPotential.html +++ b/dev/generated/openmmml.MLPotential.html @@ -8,7 +8,7 @@ - openmmml.MLPotential — OpenMM ML 1.1dev_90984d5 documentation + openmmml.MLPotential — OpenMM ML 1.1dev_3ca70f0 documentation @@ -35,7 +35,7 @@ - + diff --git a/dev/generated/openmmml.mlpotential.MLPotentialImpl.html b/dev/generated/openmmml.mlpotential.MLPotentialImpl.html index 8f0d9d5..a116a75 100644 --- a/dev/generated/openmmml.mlpotential.MLPotentialImpl.html +++ b/dev/generated/openmmml.mlpotential.MLPotentialImpl.html @@ -8,7 +8,7 @@ - openmmml.mlpotential.MLPotentialImpl — OpenMM ML 1.1dev_90984d5 documentation + openmmml.mlpotential.MLPotentialImpl — OpenMM ML 1.1dev_3ca70f0 documentation @@ -35,7 +35,7 @@ - + diff --git a/dev/generated/openmmml.mlpotential.MLPotentialImplFactory.html b/dev/generated/openmmml.mlpotential.MLPotentialImplFactory.html index b0e3d3d..6370884 100644 --- a/dev/generated/openmmml.mlpotential.MLPotentialImplFactory.html +++ b/dev/generated/openmmml.mlpotential.MLPotentialImplFactory.html @@ -8,7 +8,7 @@ - openmmml.mlpotential.MLPotentialImplFactory — OpenMM ML 1.1dev_90984d5 documentation + openmmml.mlpotential.MLPotentialImplFactory — OpenMM ML 1.1dev_3ca70f0 documentation @@ -35,7 +35,7 @@ - + diff --git a/dev/generated/openmmml.models.anipotential.ANIPotentialImpl.html b/dev/generated/openmmml.models.anipotential.ANIPotentialImpl.html index aa9ba51..de04277 100644 --- a/dev/generated/openmmml.models.anipotential.ANIPotentialImpl.html +++ b/dev/generated/openmmml.models.anipotential.ANIPotentialImpl.html @@ -8,7 +8,7 @@ - openmmml.models.anipotential.ANIPotentialImpl — OpenMM ML 1.1dev_90984d5 documentation + openmmml.models.anipotential.ANIPotentialImpl — OpenMM ML 1.1dev_3ca70f0 documentation @@ -35,7 +35,7 @@ - + diff --git a/dev/genindex.html b/dev/genindex.html index c4ead05..330e207 100644 --- a/dev/genindex.html +++ b/dev/genindex.html @@ -7,7 +7,7 @@ - Index — OpenMM ML 1.1dev_90984d5 documentation + Index — OpenMM ML 1.1dev_3ca70f0 documentation @@ -34,7 +34,7 @@ - + diff --git a/dev/index.html b/dev/index.html index 8170ef4..5eee862 100644 --- a/dev/index.html +++ b/dev/index.html @@ -8,7 +8,7 @@ - OpenMM-ML — OpenMM ML 1.1dev_90984d5 documentation + OpenMM-ML — OpenMM ML 1.1dev_3ca70f0 documentation @@ -35,7 +35,7 @@ - + diff --git a/dev/search.html b/dev/search.html index 96c72c4..fee62e0 100644 --- a/dev/search.html +++ b/dev/search.html @@ -6,7 +6,7 @@ - Search - OpenMM ML 1.1dev_90984d5 documentation + Search - OpenMM ML 1.1dev_3ca70f0 documentation @@ -33,7 +33,7 @@ - + diff --git a/dev/searchindex.js b/dev/searchindex.js index 72a24fd..bc3dbc1 100644 --- a/dev/searchindex.js +++ b/dev/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["api", "generated/openmmml.MLPotential", "generated/openmmml.mlpotential.MLPotentialImpl", "generated/openmmml.mlpotential.MLPotentialImplFactory", "generated/openmmml.models.anipotential.ANIPotentialImpl", "index", "userguide"], "filenames": ["api.rst", "generated/openmmml.MLPotential.rst", "generated/openmmml.mlpotential.MLPotentialImpl.rst", "generated/openmmml.mlpotential.MLPotentialImplFactory.rst", "generated/openmmml.models.anipotential.ANIPotentialImpl.rst", "index.rst", "userguide.rst"], "titles": ["API", "openmmml.MLPotential", "openmmml.mlpotential.MLPotentialImpl", "openmmml.mlpotential.MLPotentialImplFactory", "openmmml.models.anipotential.ANIPotentialImpl", "OpenMM-ML", "User Guide"], "terms": {"class": [1, 2, 3, 4], "name": [1, 2, 3, 4, 6], "str": [1, 3, 4], "arg": [1, 2, 3, 4], "A": [1, 4], "potenti": [1, 2, 3, 4, 6], "function": [1, 2, 3, 4, 6], "can": [1, 4, 6], "us": [1, 2, 3, 4, 6], "simul": [1, 6], "To": [1, 6], "thi": [1, 2, 3, 4, 6], "creat": [1, 2, 3, 4, 6], "specifi": [1, 2, 3, 4, 6], "you": [1, 2, 3, 4, 6], "call": [1, 3, 6], "createsystem": [1, 2, 4, 6], "system": [1, 2, 4, 6], "object": [1, 2, 3, 4, 6], "For": [1, 6], "exampl": [1, 6], "ani2x": [1, 4, 6], "topologi": [1, 2, 4, 6], "altern": [1, 6], "createmixedsystem": [1, 6], "where": [1, 6], "part": [1, 6], "i": [1, 2, 3, 4, 6], "model": [1, 5, 6], "rest": [1, 6], "convent": [1, 6], "forc": [1, 2, 4, 6], "field": [1, 6], "As": [1, 6], "an": [1, 3, 6], "suppos": [1, 6], "contain": [1, 6], "three": [1, 6], "chain": [1, 6], "0": [1, 6], "protein": [1, 6], "1": [1, 6], "ligand": [1, 6], "2": [1, 6], "solvent": [1, 6], "The": [1, 4, 6], "follow": [1, 6], "code": [1, 6], "which": [1, 2, 4, 6], "intern": [1, 6], "energi": [1, 6], "comput": [1, 6], "while": [1, 6], "everyth": [1, 6], "els": [1, 6], "includ": [1, 6], "interact": [1, 6], "between": [1, 6], "amber14": [1, 6], "forcefield": [1, 6], "all": [1, 4, 6], "xml": [1, 6], "tip3pfb": [1, 6], "mm_system": [1, 6], "list": [1, 6], "ml_atom": [1, 6], "atom": [1, 2, 4, 6], "index": [1, 6], "ml_system": [1, 6], "__init__": [1, 2, 3, 4], "paramet": [1, 2, 3, 4], "built": 1, "support": [1, 4, 6], "current": [1, 4, 6], "provid": [1, 2, 3, 4], "ani1ccx": [1, 4], "other": 1, "mai": 1, "ad": [1, 2, 4], "registerimplfactori": [1, 3], "particular": 1, "defin": [1, 2, 3], "addit": [1, 2, 3, 4], "argument": [1, 2, 3, 4], "custom": [1, 2, 3, 4], "them": 1, "see": 1, "document": 1, "specif": 1, "more": [1, 4], "inform": 1, "method": [1, 2, 3, 4], "run": 1, "return": [1, 3], "type": [1, 3], "newli": [1, 2, 4], "iter": [1, 2, 4], "int": [1, 2, 4], "removeconstraint": 1, "bool": 1, "true": 1, "forcegroup": [1, 2, 4], "interpol": 1, "fals": 1, "partli": 1, "first": 1, "entir": [1, 2, 4], "pass": [1, 2, 3, 4], "along": 1, "indic": [1, 2, 4], "ml": 1, "subset": 1, "It": 1, "new": [1, 2, 3, 6], "ident": 1, "origin": 1, "one": [1, 4], "except": 1, "chang": 1, "remov": 1, "bond": 1, "angl": 1, "torsion": 1, "ar": [1, 2, 3, 4, 6], "everi": 1, "nonbondedforc": 1, "customnonbondedforc": 1, "exclus": 1, "prevent": 1, "from": [1, 2, 4, 6], "each": 1, "option": [1, 2, 4], "constraint": 1, "both": [1, 4], "necessari": 1, "smoothli": 1, "In": [1, 6], "case": 1, "customcvforc": 1, "were": [1, 2, 3, 4], "abov": 1, "correspond": 1, "custombondforc": 1, "nonbond": 1, "within": 1, "global": 1, "lambda_interpol": 1, "two": 1, "when": [1, 2, 3], "set": [1, 6], "its": 1, "valu": 1, "setparamet": 1, "context": 1, "whose": 1, "should": [1, 2, 4], "pair": 1, "group": [1, 2, 4], "": 1, "place": 1, "static": 1, "factori": [1, 2, 3], "mlpotentialimplfactori": [1, 2], "regist": [1, 2, 3], "constructor": [1, 3], "mlpotentialimpl": [1, 3, 4], "abstract": [2, 3], "interfac": [2, 3], "implement": [2, 3, 4, 6], "If": [2, 3], "need": [2, 3], "subclass": [2, 3, 4], "user": [2, 5], "look": 2, "up": [2, 6], "ha": 2, "been": 2, "appropri": 2, "addforc": [2, 4], "none": [2, 4], "add": [2, 4, 6], "invok": [2, 3, 4], "must": [2, 3, 4], "request": [2, 3, 4], "being": [2, 4], "appli": [2, 4], "ani": [2, 3, 4, 6], "keyword": [2, 3, 4], "allow": [2, 3, 4], "behavior": [2, 3, 4], "base": [2, 3, 4], "extra": [2, 3, 4], "instanc": 3, "createimpl": 3, "correct": 3, "wa": 3, "torchani": [4, 6], "build": 4, "pytorch": 4, "torchforc": 4, "openmm": 4, "version": 4, "ensembl": 4, "eight": 4, "averag": 4, "over": 4, "lead": 4, "slightli": 4, "accur": 4, "result": 4, "than": [4, 6], "individu": 4, "onli": [4, 6], "singl": 4, "modelindex": 4, "select": 4, "larg": 4, "improv": 4, "speed": 4, "cost": 4, "small": [4, 6], "decreas": 4, "accuraci": 4, "nnpop": 4, "mlpotenti": [4, 5, 6], "guid": 5, "api": [5, 6], "openmmml": [5, 6], "develop": 5, "high": 6, "level": 6, "machin": 6, "learn": 6, "With": 6, "just": 6, "few": 6, "line": 6, "standard": 6, "pretrain": 6, "repres": 6, "some": 6, "releas": 6, "1ccx": 6, "2x": 6, "thei": 6, "suitabl": 6, "molecul": 6, "involv": 6, "limit": 6, "element": 6, "charg": 6, "futur": 6, "much": 6, "wider": 6, "rang": 6, "conda": 6, "mamba": 6, "c": 6, "forg": 6, "we": 6, "recommend": 6, "sinc": 6, "faster": 6, "less": 6, "buggi": 6, "packag": 6, "import": 6}, "objects": {"openmmml": [[1, 0, 1, "", "MLPotential"]], "openmmml.MLPotential": [[1, 1, 1, "", "__init__"], [1, 1, 1, "", "createMixedSystem"], [1, 1, 1, "", "createSystem"], [1, 1, 1, "", "registerImplFactory"]], "openmmml.mlpotential": [[2, 0, 1, "", "MLPotentialImpl"], [3, 0, 1, "", "MLPotentialImplFactory"]], "openmmml.mlpotential.MLPotentialImpl": [[2, 1, 1, "", "__init__"], [2, 1, 1, "", "addForces"]], "openmmml.mlpotential.MLPotentialImplFactory": [[3, 1, 1, "", "__init__"], [3, 1, 1, "", "createImpl"]], "openmmml.models.anipotential": [[4, 0, 1, "", "ANIPotentialImpl"]], "openmmml.models.anipotential.ANIPotentialImpl": [[4, 1, 1, "", "__init__"], [4, 1, 1, "", "addForces"]]}, "objtypes": {"0": "py:class", "1": "py:method"}, "objnames": {"0": ["py", "class", "Python class"], "1": ["py", "method", "Python method"]}, "titleterms": {"api": 0, "develop": 0, "model": [0, 4], "openmmml": [1, 2, 3, 4], "mlpotenti": [1, 2, 3], "mlpotentialimpl": 2, "mlpotentialimplfactori": 3, "anipotenti": 4, "anipotentialimpl": 4, "openmm": [5, 6], "ml": [5, 6], "user": 6, "guid": 6, "instal": 6, "usag": 6}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx": 60}, "alltitles": {"API": [[0, "api"]], "Developer API": [[0, "developer-api"]], "Models": [[0, "models"]], "openmmml.MLPotential": [[1, "openmmml-mlpotential"]], "openmmml.mlpotential.MLPotentialImpl": [[2, "openmmml-mlpotential-mlpotentialimpl"]], "openmmml.mlpotential.MLPotentialImplFactory": [[3, "openmmml-mlpotential-mlpotentialimplfactory"]], "openmmml.models.anipotential.ANIPotentialImpl": [[4, "openmmml-models-anipotential-anipotentialimpl"]], "OpenMM-ML": [[5, "openmm-ml"], [6, "openmm-ml"]], "User Guide": [[6, "user-guide"]], "Installation": [[6, "installation"]], "Usage": [[6, "usage"]]}, "indexentries": {"mlpotential (class in openmmml)": [[1, "openmmml.MLPotential"]], "__init__() (openmmml.mlpotential method)": [[1, "openmmml.MLPotential.__init__"]], "createmixedsystem() (openmmml.mlpotential method)": [[1, "openmmml.MLPotential.createMixedSystem"]], "createsystem() (openmmml.mlpotential method)": [[1, "openmmml.MLPotential.createSystem"]], "registerimplfactory() (openmmml.mlpotential static method)": [[1, "openmmml.MLPotential.registerImplFactory"]], "mlpotentialimpl (class in openmmml.mlpotential)": [[2, "openmmml.mlpotential.MLPotentialImpl"]], "__init__() (openmmml.mlpotential.mlpotentialimpl method)": [[2, "openmmml.mlpotential.MLPotentialImpl.__init__"]], "addforces() (openmmml.mlpotential.mlpotentialimpl method)": [[2, "openmmml.mlpotential.MLPotentialImpl.addForces"]], "mlpotentialimplfactory (class in openmmml.mlpotential)": [[3, "openmmml.mlpotential.MLPotentialImplFactory"]], "__init__() (openmmml.mlpotential.mlpotentialimplfactory method)": [[3, "openmmml.mlpotential.MLPotentialImplFactory.__init__"]], "createimpl() (openmmml.mlpotential.mlpotentialimplfactory method)": [[3, "openmmml.mlpotential.MLPotentialImplFactory.createImpl"]], "anipotentialimpl (class in openmmml.models.anipotential)": [[4, "openmmml.models.anipotential.ANIPotentialImpl"]], "__init__() (openmmml.models.anipotential.anipotentialimpl method)": [[4, "openmmml.models.anipotential.ANIPotentialImpl.__init__"]], "addforces() (openmmml.models.anipotential.anipotentialimpl method)": [[4, "openmmml.models.anipotential.ANIPotentialImpl.addForces"]]}}) \ No newline at end of file +Search.setIndex({"docnames": ["api", "generated/openmmml.MLPotential", "generated/openmmml.mlpotential.MLPotentialImpl", "generated/openmmml.mlpotential.MLPotentialImplFactory", "generated/openmmml.models.anipotential.ANIPotentialImpl", "index", "userguide"], "filenames": ["api.rst", "generated/openmmml.MLPotential.rst", "generated/openmmml.mlpotential.MLPotentialImpl.rst", "generated/openmmml.mlpotential.MLPotentialImplFactory.rst", "generated/openmmml.models.anipotential.ANIPotentialImpl.rst", "index.rst", "userguide.rst"], "titles": ["API", "openmmml.MLPotential", "openmmml.mlpotential.MLPotentialImpl", "openmmml.mlpotential.MLPotentialImplFactory", "openmmml.models.anipotential.ANIPotentialImpl", "OpenMM-ML", "User Guide"], "terms": {"class": [1, 2, 3, 4], "name": [1, 2, 3, 4, 6], "str": [1, 3, 4], "arg": [1, 2, 3, 4], "A": [1, 4], "potenti": [1, 2, 3, 4, 6], "function": [1, 2, 3, 4, 6], "can": [1, 4, 6], "us": [1, 2, 3, 4, 6], "simul": [1, 6], "To": [1, 6], "thi": [1, 2, 3, 4, 6], "creat": [1, 2, 3, 4, 6], "specifi": [1, 2, 3, 4, 6], "you": [1, 2, 3, 4, 6], "call": [1, 3, 6], "createsystem": [1, 2, 4, 6], "system": [1, 2, 4, 6], "object": [1, 2, 3, 4, 6], "For": [1, 6], "exampl": [1, 6], "ani2x": [1, 4, 6], "topologi": [1, 2, 4, 6], "altern": [1, 6], "createmixedsystem": [1, 6], "where": [1, 6], "part": [1, 6], "i": [1, 2, 3, 4, 6], "model": [1, 5, 6], "rest": [1, 6], "convent": [1, 6], "forc": [1, 2, 4, 6], "field": [1, 6], "As": [1, 6], "an": [1, 3, 6], "suppos": [1, 6], "contain": [1, 6], "three": [1, 6], "chain": [1, 6], "0": [1, 6], "protein": [1, 6], "1": [1, 6], "ligand": [1, 6], "2": [1, 6], "solvent": [1, 6], "The": [1, 4, 6], "follow": [1, 6], "code": [1, 6], "which": [1, 2, 4, 6], "intern": [1, 6], "energi": [1, 6], "comput": [1, 6], "while": [1, 6], "everyth": [1, 6], "els": [1, 6], "includ": [1, 6], "interact": [1, 6], "between": [1, 6], "amber14": [1, 6], "forcefield": [1, 6], "all": [1, 4, 6], "xml": [1, 6], "tip3pfb": [1, 6], "mm_system": [1, 6], "list": [1, 6], "ml_atom": [1, 6], "atom": [1, 2, 4, 6], "index": [1, 6], "ml_system": [1, 6], "__init__": [1, 2, 3, 4], "paramet": [1, 2, 3, 4], "built": 1, "support": [1, 4, 6], "current": [1, 4, 6], "provid": [1, 2, 3, 4], "ani1ccx": [1, 4], "other": 1, "mai": 1, "ad": [1, 2, 4], "registerimplfactori": [1, 3], "particular": 1, "defin": [1, 2, 3], "addit": [1, 2, 3, 4], "argument": [1, 2, 3, 4], "custom": [1, 2, 3, 4], "them": 1, "see": 1, "document": [1, 6], "specif": 1, "more": [1, 4], "inform": 1, "method": [1, 2, 3, 4], "run": 1, "return": [1, 3], "type": [1, 3], "newli": [1, 2, 4], "iter": [1, 2, 4], "int": [1, 2, 4], "removeconstraint": 1, "bool": 1, "true": 1, "forcegroup": [1, 2, 4], "interpol": 1, "fals": 1, "partli": 1, "first": 1, "entir": [1, 2, 4], "pass": [1, 2, 3, 4], "along": 1, "indic": [1, 2, 4], "ml": 1, "subset": 1, "It": 1, "new": [1, 2, 3, 6], "ident": 1, "origin": 1, "one": [1, 4], "except": 1, "chang": 1, "remov": 1, "bond": 1, "angl": 1, "torsion": 1, "ar": [1, 2, 3, 4, 6], "everi": 1, "nonbondedforc": 1, "customnonbondedforc": 1, "exclus": 1, "prevent": 1, "from": [1, 2, 4, 6], "each": 1, "option": [1, 2, 4], "constraint": 1, "both": [1, 4], "necessari": 1, "smoothli": 1, "In": [1, 6], "case": 1, "customcvforc": 1, "were": [1, 2, 3, 4], "abov": 1, "correspond": 1, "custombondforc": 1, "nonbond": 1, "within": 1, "global": 1, "lambda_interpol": 1, "two": 1, "when": [1, 2, 3], "set": [1, 6], "its": 1, "valu": 1, "setparamet": 1, "context": 1, "whose": 1, "should": [1, 2, 4], "pair": 1, "group": [1, 2, 4], "": 1, "place": 1, "static": 1, "factori": [1, 2, 3], "mlpotentialimplfactori": [1, 2], "regist": [1, 2, 3], "constructor": [1, 3], "mlpotentialimpl": [1, 3, 4], "abstract": [2, 3], "interfac": [2, 3], "implement": [2, 3, 4, 6], "If": [2, 3], "need": [2, 3], "subclass": [2, 3, 4], "user": [2, 5], "look": 2, "up": [2, 6], "ha": 2, "been": 2, "appropri": 2, "addforc": [2, 4], "none": [2, 4], "add": [2, 4, 6], "invok": [2, 3, 4], "must": [2, 3, 4], "request": [2, 3, 4], "being": [2, 4], "appli": [2, 4], "ani": [2, 3, 4, 6], "keyword": [2, 3, 4], "allow": [2, 3, 4], "behavior": [2, 3, 4], "base": [2, 3, 4], "extra": [2, 3, 4], "instanc": 3, "createimpl": 3, "correct": 3, "wa": 3, "torchani": [4, 6], "build": 4, "pytorch": 4, "torchforc": 4, "openmm": 4, "version": 4, "ensembl": 4, "eight": 4, "averag": 4, "over": 4, "lead": 4, "slightli": 4, "accur": 4, "result": 4, "than": [4, 6], "individu": 4, "onli": [4, 6], "singl": 4, "modelindex": 4, "select": 4, "larg": 4, "improv": 4, "speed": 4, "cost": 4, "small": [4, 6], "decreas": 4, "accuraci": 4, "nnpop": 4, "mlpotenti": [4, 5, 6], "guid": 5, "api": [5, 6], "openmmml": [5, 6], "develop": 5, "high": 6, "level": 6, "machin": 6, "learn": 6, "With": 6, "just": 6, "few": 6, "line": 6, "standard": 6, "pretrain": 6, "repres": 6, "some": 6, "releas": 6, "1ccx": 6, "2x": 6, "thei": 6, "suitabl": 6, "molecul": 6, "involv": 6, "limit": 6, "element": 6, "charg": 6, "futur": 6, "much": 6, "wider": 6, "rang": 6, "find": 6, "http": 6, "github": 6, "io": 6, "conda": 6, "mamba": 6, "c": 6, "forg": 6, "we": 6, "recommend": 6, "sinc": 6, "faster": 6, "less": 6, "buggi": 6, "packag": 6, "import": 6}, "objects": {"openmmml": [[1, 0, 1, "", "MLPotential"]], "openmmml.MLPotential": [[1, 1, 1, "", "__init__"], [1, 1, 1, "", "createMixedSystem"], [1, 1, 1, "", "createSystem"], [1, 1, 1, "", "registerImplFactory"]], "openmmml.mlpotential": [[2, 0, 1, "", "MLPotentialImpl"], [3, 0, 1, "", "MLPotentialImplFactory"]], "openmmml.mlpotential.MLPotentialImpl": [[2, 1, 1, "", "__init__"], [2, 1, 1, "", "addForces"]], "openmmml.mlpotential.MLPotentialImplFactory": [[3, 1, 1, "", "__init__"], [3, 1, 1, "", "createImpl"]], "openmmml.models.anipotential": [[4, 0, 1, "", "ANIPotentialImpl"]], "openmmml.models.anipotential.ANIPotentialImpl": [[4, 1, 1, "", "__init__"], [4, 1, 1, "", "addForces"]]}, "objtypes": {"0": "py:class", "1": "py:method"}, "objnames": {"0": ["py", "class", "Python class"], "1": ["py", "method", "Python method"]}, "titleterms": {"api": 0, "develop": 0, "model": [0, 4], "openmmml": [1, 2, 3, 4], "mlpotenti": [1, 2, 3], "mlpotentialimpl": 2, "mlpotentialimplfactori": 3, "anipotenti": 4, "anipotentialimpl": 4, "openmm": [5, 6], "ml": [5, 6], "user": 6, "guid": 6, "instal": 6, "usag": 6}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx": 60}, "alltitles": {"API": [[0, "api"]], "Developer API": [[0, "developer-api"]], "Models": [[0, "models"]], "openmmml.MLPotential": [[1, "openmmml-mlpotential"]], "openmmml.mlpotential.MLPotentialImpl": [[2, "openmmml-mlpotential-mlpotentialimpl"]], "openmmml.mlpotential.MLPotentialImplFactory": [[3, "openmmml-mlpotential-mlpotentialimplfactory"]], "openmmml.models.anipotential.ANIPotentialImpl": [[4, "openmmml-models-anipotential-anipotentialimpl"]], "OpenMM-ML": [[5, "openmm-ml"], [6, "openmm-ml"]], "User Guide": [[6, "user-guide"]], "Installation": [[6, "installation"]], "Usage": [[6, "usage"]]}, "indexentries": {"mlpotential (class in openmmml)": [[1, "openmmml.MLPotential"]], "__init__() (openmmml.mlpotential method)": [[1, "openmmml.MLPotential.__init__"]], "createmixedsystem() (openmmml.mlpotential method)": [[1, "openmmml.MLPotential.createMixedSystem"]], "createsystem() (openmmml.mlpotential method)": [[1, "openmmml.MLPotential.createSystem"]], "registerimplfactory() (openmmml.mlpotential static method)": [[1, "openmmml.MLPotential.registerImplFactory"]], "mlpotentialimpl (class in openmmml.mlpotential)": [[2, "openmmml.mlpotential.MLPotentialImpl"]], "__init__() (openmmml.mlpotential.mlpotentialimpl method)": [[2, "openmmml.mlpotential.MLPotentialImpl.__init__"]], "addforces() (openmmml.mlpotential.mlpotentialimpl method)": [[2, "openmmml.mlpotential.MLPotentialImpl.addForces"]], "mlpotentialimplfactory (class in openmmml.mlpotential)": [[3, "openmmml.mlpotential.MLPotentialImplFactory"]], "__init__() (openmmml.mlpotential.mlpotentialimplfactory method)": [[3, "openmmml.mlpotential.MLPotentialImplFactory.__init__"]], "createimpl() (openmmml.mlpotential.mlpotentialimplfactory method)": [[3, "openmmml.mlpotential.MLPotentialImplFactory.createImpl"]], "anipotentialimpl (class in openmmml.models.anipotential)": [[4, "openmmml.models.anipotential.ANIPotentialImpl"]], "__init__() (openmmml.models.anipotential.anipotentialimpl method)": [[4, "openmmml.models.anipotential.ANIPotentialImpl.__init__"]], "addforces() (openmmml.models.anipotential.anipotentialimpl method)": [[4, "openmmml.models.anipotential.ANIPotentialImpl.addForces"]]}}) \ No newline at end of file diff --git a/dev/userguide.html b/dev/userguide.html index 1c224c3..abb11ca 100644 --- a/dev/userguide.html +++ b/dev/userguide.html @@ -8,7 +8,7 @@ - User Guide — OpenMM ML 1.1dev_90984d5 documentation + User Guide — OpenMM ML 1.1dev_3ca70f0 documentation @@ -35,7 +35,7 @@ - + @@ -442,6 +442,7 @@

OpenMM-MLANI-2x, using the implementations in TorchANI. They are suitable for small molecules involving a limited set of elements and no charges. Future releases will add new potential functions that support a much wider range of molecules.

+

You can find the current documentation at https://openmm.github.io/openmm-ml

Installation#

OpenMM-ML can be installed with conda or mamba.