Initial Commit

README.md

+# Tinker Parser
+[NOMAD Laboratory CoE](http://nomad-coe.eu) parser for [TINKER](https://dasher.wustl.edu/tinker/)
+## Version 0.0.1
+
+This is the parser for Tinker in [TINKER](https://dasher.wustl.edu/tinker/).
+The official version lives at:
+
+    git@gitlab.mpcdf.mpg.de:nomad-lab/parser-tinker.git
+
+You can browse it at:
+
+    https://gitlab.rzg.mpg.de/nomad-lab/parser-tinker
+
+It relies on having the nomad-meta-info and the python-common repositories one level higher.
+The simplest way to have this is to check out nomad-lab-base recursively:
+
+    git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git
+
+This parser will be in the directory parsers/tinker of this repository.
+
+## Running and Testing the Parser
+### Requirements
+The required python packages can be installed with (see [python-common](https://gitlab.rzg.mpg.de/nomad-lab/python-common)):
+
+    pip install -r nomad-lab-base/python-common/requirements.txt
+
+### Usage
+Tinker MD log output files can be parsed with:
+
+    python TINKERParser.py [path/toFile]
+
+### Test Files
+Example log output files of Tinker can be found in the directory test/examples.
+More details about the calculations and files are explained in README file of test/examples.
+

parser/parser-tinker/.idea/misc.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.6.1 virtualenv at /labEnv3" project-jdk-type="Python SDK" />
+</project>
\ No newline at end of file

parser/parser-tinker/.idea/modules.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/parser-amber.iml" filepath="$PROJECT_DIR$/.idea/parser-amber.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file

parser/parser-tinker/.idea/parser-amber.iml

+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+  <component name="TestRunnerService">
+    <option name="projectConfiguration" value="Nosetests" />
+    <option name="PROJECT_TEST_RUNNER" value="Nosetests" />
+  </component>
+</module>
\ No newline at end of file

parser/parser-tinker/TINKERCommon.py

+import logging
+import os
+
+PARSERNAME = "TINKER"
+PROGRAMNAME = "tinker"
+PARSERVERSION = "0.0.1"
+PARSERMETANAME = PARSERNAME.lower()
+PARSERTAG = 'x_' + PARSERMETANAME
+
+PARSER_INFO_DEFAULT = {
+        'name'   : PARSERMETANAME+'-parser', 
+        'version': PARSERVERSION
+}
+
+META_INFO_PATH = os.path.normpath(os.path.join(
+    os.path.dirname(os.path.abspath(__file__)), 
+    "../../../../nomad-meta-info/meta_info/nomad_meta_info/"+PARSERMETANAME+".nomadmetainfo.json"))
+
+LOGGER = logging.getLogger("nomad."+PROGRAMNAME+"Parser")
+
+def set_excludeList(self):
+    """Sets the exclude list for x_
+
+    Returns:
+        the list of names
+    """
+    excludelist = [
+        PARSERTAG+'_mdin_verbatim_writeout',
+        PARSERTAG+'_dumm_text',
+        PARSERTAG+'_dummy',
+        PARSERTAG+'_mdin_wt'
+        ]
+    excludelist.extend([PARSERTAG+'_mdin_file_%s' % fileNL.lower() for fileNL in self.fileDict.keys()])
+    excludelist.extend([PARSERTAG+'_mdin_%s' % cntrlNL.lower() for cntrlNL in self.cntrlDict.keys()])
+    excludelist.extend([PARSERTAG+'_mdin_%s' % ewaldNL.lower() for ewaldNL in self.ewaldDict.keys()])
+    excludelist.extend([PARSERTAG+'_mdin_%s' % qmmmNL.lower() for qmmmNL in self.qmmmDict.keys()])
+    return excludelist
+
+def set_includeList():
+    """Sets the include list for x_
+
+    Returns:
+        the list of names
+    """
+    includelist = []
+    return includelist
+
+

parser/parser-tinker/setup_paths.py

+import sys
+import os
+import os.path
+basedir = os.path.dirname(os.path.abspath(__file__))
+commondir = os.path.normpath(os.path.join(basedir,"../../../../python-common/common/python"))
+
+if not commondir in sys.path:
+    sys.path.insert(0, commondir)

src/main/scala/eu/nomad_lab/parsers/TinkerParser.scala

+package eu.nomad_lab.parsers
+
+import eu.nomad_lab
+import eu.nomad_lab.DefaultPythonInterpreter
+import org.{ json4s => jn }
+import eu.{ nomad_lab => lab }
+import scala.collection.breakOut
+
+object TinkerParser extends SimpleExternalParserGenerator(
+  name = "TinkerParser",
+  parserInfo = jn.JObject(
+    ("name" -> jn.JString("TinkerParser")) ::
+      ("parserId" -> jn.JString("TinkerParser" + lab.TinkerVersionInfo.version)) ::
+      ("versionInfo" -> jn.JObject(
+        ("nomadCoreVersion" -> jn.JObject(lab.NomadCoreVersionInfo.toMap.map {
+          case (k, v) => k -> jn.JString(v.toString)
+        }(breakOut): List[(String, jn.JString)])) ::
+          (lab.TinkerVersionInfo.toMap.map {
+            case (key, value) =>
+              (key -> jn.JString(value.toString))
+          }(breakOut): List[(String, jn.JString)])
+      )) :: Nil
+  ),
+  mainFileTypes = Seq("text/.*"),
+  mainFileRe = """\s*#+\s*TINKER\s*---\s*Software\s*Tools\s*for\s*Molecular\s*Design\s*#+\s*""".r,
+  cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/tinker/parser/parser-tinker/TINKERParser.py",
+    "${mainFilePath}"),
+  resList = Seq(
+    "parser-tinker/TINKERParser.py",
+    "parser-tinker/TINKERDictionary.py",
+    "parser-tinker/TINKERCommon.py",
+    "parser-tinker/setup_paths.py",
+    "nomad_meta_info/public.nomadmetainfo.json",
+    "nomad_meta_info/common.nomadmetainfo.json",
+    "nomad_meta_info/meta_types.nomadmetainfo.json"
+    "nomad_meta_info/tinker.nomadmetainfo.json"
+  ) ++ DefaultPythonInterpreter.commonFiles(),
+  dirMap = Map(
+    "parser-tinker" -> "parsers/tinker/parser/parser-tinker",
+    "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info",
+    "python" -> "python-common/common/python/nomadcore"
+  ) ++ DefaultPythonInterpreter.commonDirMapping(),
+  metaInfoEnv = Some(lab.meta.KnownMetaInfoEnvs.tinker)
+)
+

src/test/scala/eu/nomad_lab/parsers/TinkerParserSpec.scala

+package eu.nomad_lab.parsers
+
+import org.specs2.mutable.Specification
+
+object TinkerParserTests extends Specification {
+  "TinkerParserTest" >> {
+    "[Anion in Water (xyz sequence of outputs with 643 atoms)] test with json-events" >> {
+      ParserRun.parse(TinkerParser, "parsers/tinker/test/examples/anion/anion.log", "json-events") must_== ParseResult.ParseSuccess
+    }
+    "[Anion in Water (xyz sequence of outputs with 643 atoms)] test with json" >> {
+      ParserRun.parse(TinkerParser, "parsers/tinker/test/examples/anion/anion.log", "json") must_== ParseResult.ParseSuccess
+    }
+    "[Ice (.arc trajectory with 3024 atoms)] test with json-events" >> {
+      ParserRun.parse(TinkerParser, "parsers/tinker/test/examples/ice/ice.log", "json-events") must_== ParseResult.ParseSuccess
+    }
+    "[Ice (.arc trajectory with 3024 atoms)] test with json" >> {
+      ParserRun.parse(TinkerParser, "parsers/tinker/test/examples/ice/ice.log", "json") must_== ParseResult.ParseSuccess
+    }
+  }
+}

test/examples/README.md

+# Tests:
+### Source of Tests:
+
+The tests are taken from Tinker (version 8.1) examples in [TINKER](http://dasher.wustl.edu/tinker/).
+
+### TEST Directory for the TINKER Package
+
+This directory contains some test casess illustrating use of
+several of the programs in the TINKER package.
+
+For example, the argon.run file contains the commands to run
+the first test case. The resulting output is found in the file
+argon.log.
+
+#### ANION       
+estimation of the free energy of hydration
+of Cl- anion vs. Br- anion via a 2 picosecond
+simulation on a "hybrid" anion in a box of
+water, followed by free energy perturbation
+
+#### ARGON
+minimization followed by 6 picoseconds
+of a molecular dynamics run on a periodic
+box containing 150 argon atoms
+
+#### ENKEPHALIN
+generation of coordinates from the
+amino acid sequence and phi/psi angles,
+followed by energy minimization and
+determination of the lowest frequency
+normal mode
+
+#### ICE/WATER
+short MD simulation of the monoclinic ice V
+crystal form using the iAMOEBA water model,
+neighbor lists and PME electrostatics
+

test/examples/anion/anion.dat

+anion
+1 20
+0.5
+300.0
+4
+y

test/examples/anion/anion.run

+cp anion.dyn0 anion.dyn
+../bin/dynamic anion 1000 2.0 0.1 2 300.0
+../bin/alchemy < anion.dat

test/examples/argon/argon.key

+########################################################################
+##                                                                    ##
+##    Keyfile for the argon box TINKER molecular dynamics example.    ##
+##    Note the use of "lights" to speed vdw computation, and the      ##
+##    fixed random number seed forcing the calculation to generate    ##
+##    the same trajectory each time for validation purposes.          ##
+##                                                                    ##
+########################################################################
+
+parameters       ../params/mm3
+lights
+randomseed       123456789
+
+a-axis           26.0206
+vdw-cutoff       12.0
+tau-pressure     1.0e+20

test/examples/argon/argon.run

+cp argon.1st argon.xyz
+../bin/minimize argon 1.0
+../bin/dynamic argon 3000 2.0 1.0 4 150.87 49.0
+#rm argon.xyz* argon.dyn argon.0*

test/examples/enkephalin/enkephalin.key

+parameters    oplsaa
+printout             100
+digits               8

test/examples/enkephalin/enkephalin.run

+../bin/protein < enkephalin.dat
+../bin/minimize enkephalin 0.00001
+../bin/vibrate enkephalin -7 8