hillclimber 0.1.5a8__cp314-cp314-macosx_15_0_x86_64.whl

plumed/_lib/lib/plumed/scripts/selector.sh

@@ -0,0 +1,234 @@
+#! /usr/bin/env bash
+# vim:ft=python
+
+
+# WARNING: keep these in synch with the python code below:
+if [ "$#" = 1 ]; then
+  if [ "$1" = "--description" ] ; then
+    echo "create lists of serial atom numbers"
+    exit 0
+  fi
+  if [ "$1" = "--options" ] ; then
+    echo "--description --help -h --options --pdb"
+    exit 0
+  fi
+fi
+
+PYTHON_BIN="${PYTHON_BIN-python}"
+PLUMED_PYTHON_BIN="${PLUMED_PYTHON_BIN-${PYTHON_BIN}}"
+TEMP=$(mktemp -t plumed.XXXXXX)
+trap "rm -rf $TEMP" EXIT
+cat > $TEMP << \EOF
+# here's the real script
+
+from __future__ import print_function
+import sys
+import re
+import readline
+
+# When possible, we use python3 specific stuff
+if (sys.version_info > (3, 0)):
+   _HAS_PYTHON3=True
+else:
+   _HAS_PYTHON3=False
+
+def read_mda(path):
+    import MDAnalysis
+    return MDAnalysis.Universe(path)
+
+def read_mdt(path):
+    import mdtraj
+    return mdtraj.load(path).top
+
+def read_vmd(path):
+    import vmd as vmd_python
+    return vmd_python.molecule.load("pdb",path)
+
+def read_vmdexec(path):
+    import subprocess
+    vmdexec = subprocess.Popen(["vmd", "-dispdev", "none",path,"-eofexit"],
+          stdin=subprocess.PIPE, stdout=subprocess.PIPE,universal_newlines=True)
+    # print("fconfigure stdout -buffering none",file=vmd.stdin) # does not work as expected
+    vmdexec.stdin.flush()
+    return vmdexec
+
+dummyline="DUMMYLINE"
+
+def select_vmdexec(vmdexec,selection):
+    import os
+    try:
+        bufferlines=int(os.environ['PLUMED_VMD_BUFFERLINES'])
+    except KeyError:
+        bufferlines=1000
+        
+    print("puts 'NEXT'",file=vmdexec.stdin)
+    print("[atomselect top { " + selection + " }] get index\n",file=vmdexec.stdin)
+    for i in range(bufferlines):
+      print("puts '"+dummyline+"'",file=vmdexec.stdin)
+    # print("for {set i 1} {$i < 2000} {incr i} { puts '" + dummyline +"' }",file=vmdexec.stdin) # does not work
+    print("flush stdout",file=vmdexec.stdin) # useless
+    vmdexec.stdin.flush()
+    is_next=False
+    is_error=False
+    error_msg=""
+    for line in vmdexec.stdout:
+        lines=line.rstrip()
+        if is_error:
+          if(lines=="'"+dummyline+"'"):
+            raise RuntimeError(error_msg)
+          error_msg+=" " + lines
+        elif is_next:
+          if re.match(".*ERROR.*",line):
+            is_error=True
+          else:
+            sel=[]
+            for w in line.split():
+                if not w.isdigit():
+                   sel=[]
+                   break
+                sel.append(int(w))
+            return sel
+        elif(lines=="'NEXT'"):
+          is_next=True
+
+path=None
+
+mda=None
+mdt=None
+vmdexec=None
+vmd=None
+
+help="""
+Example:
+echo "
+mda:nucleic
+mdt:resname RG
+" | selector.sh --pdb ref.pdb
+"""
+
+
+for i in range(1,len(sys.argv)):
+  opt=sys.argv[i]
+  if opt=="-h" or opt=="--help":
+    print(help)
+    sys.exit(0)
+# WARNING: keep these in synch with the bash code above
+  elif opt=="--description":
+    print("create lists of serial atom numbers")
+    sys.exit(0)
+  elif opt=="--options":
+    print("--description --help -h --options --pdb")
+    sys.exit(0)
+  elif opt=="--pdb":
+    path=sys.argv[i+1]
+
+while True:
+    try:
+        if _HAS_PYTHON3:
+            input_=input("")
+        else:
+            input_=raw_input("")
+    except EOFError:
+        break
+    input_=re.sub("#.*","",input_)
+    cmd=re.sub(":.*$","",input_)
+    arg=re.sub("^[^:]*:","",input_)
+    if cmd == "" :
+      continue
+    elif cmd == "quit" :
+        sys.exit(0)
+    elif cmd == "pdb" :
+        path=arg
+        mda=None
+        mdt=None
+        vmd=None
+        vmdexec=None
+    else:
+      if path is None:
+           sys.stdout.write("Error: provide pdb file");
+           sys.stdout.write("\n")
+           sys.stdout.flush()
+      if cmd == "mda" :
+        if mda is None:
+           try:
+               mda=read_mda(path)
+           except Exception as e:
+               sys.stdout.write("Error importing MDAnalysis module: ");
+               sys.stdout.write(str(e));
+               sys.stdout.write("\n")
+               sys.stdout.flush()
+               continue
+        try:
+           sel=mda.select_atoms(arg).indices
+        except Exception as e:
+           sys.stdout.write("Error parsing MDAnalysis expression: ");
+           sys.stdout.write(str(e));
+           sys.stdout.write("\n")
+           sys.stdout.flush()
+           continue
+      elif cmd == "mdt" :
+        if mdt is None:
+           try:
+               mdt=read_mdt(path)
+           except Exception as e:
+               sys.stdout.write("Error importing mdtraj module: ");
+               sys.stdout.write(str(e));
+               sys.stdout.write("\n")
+               sys.stdout.flush()
+               continue
+        try:
+           sel=mdt.select(arg)
+        except Exception as e:
+           sys.stdout.write("Error parsing mdtraj expression: ");
+           sys.stdout.write(str(e));
+           sys.stdout.write("\n")
+           sys.stdout.flush()
+           continue
+      elif cmd == "vmd" :
+        if vmd is None:
+           try:
+               vmd=read_vmd(path)
+           except Exception as e:
+               sys.stdout.write("Error importing vmd_python module: ");
+               sys.stdout.write(str(e));
+               sys.stdout.write("\n")
+               sys.stdout.flush()
+               continue
+        try:
+           import vmd as vmd_python
+           sel=vmd_python.atomsel(arg, vmd).index
+        except Exception as e:
+           sys.stdout.write("Error parsing vmd-python expression: ");
+           sys.stdout.write(str(e));
+           sys.stdout.write("\n")
+           sys.stdout.flush()
+           continue
+      elif cmd == "vmdexec" :
+         if vmdexec is None:
+           vmdexec=read_vmdexec(path)
+         try:
+           sel=select_vmdexec(vmdexec,arg)
+         except Exception as e:
+           sys.stdout.write("Error parsing vmd expression: ");
+           sys.stdout.write(str(e));
+           sys.stdout.write("\n")
+           sys.stdout.flush()
+           continue
+      else:
+         sys.stdout.write("Error: unknown command ")
+         sys.stdout.write(cmd)
+         sys.stdout.write("\n")
+         sys.stdout.flush()
+      outstr="Selection:"
+      for i in range(len(sel)):
+          outstr+=" "
+          outstr+=str(sel[i]+1)
+      outstr+="\n"
+      sys.stdout.write(outstr)
+      sys.stdout.flush()
+
+EOF
+
+set -e
+
+"${PLUMED_PYTHON_BIN}" $TEMP $@

plumed/_lib/lib/plumed/scripts/vim2html.sh

@@ -0,0 +1,190 @@
+#! /usr/bin/env bash
+
+VIMFILE="$PLUMED_ROOT/vim/syntax/plumed.vim"
+
+if [ "$1" = --description ] ; then
+  echo "convert plumed input file to colored html using vim syntax"
+  exit 0
+fi
+
+if [ "$1" = --options ] ; then
+  echo "--description --options --annotate-syntax --pdf --crop --fs --colors"
+  exit 0
+fi
+
+if [ "$1" = --help ] ; then
+cat << EOF
+Usage:
+  plumed vim2html [options] < input > output
+  plumed vim2html [options] input > output
+  plumed vim2html [options] input output
+(one of the three)
+
+Options can be:
+--annotate-syntax Reports annotated syntax on output.
+                  Also reports non-annotated regions on stderr
+--pdf             To produce a pdf file with syntax highlighting.
+--crop            Crop the pdf file to the only written part. Useful to insert the pdf in a LaTex file as image.
+--fs              Specify the fontsize of the pdf output.
+--colors          Specify the color palette. Allowed values are: default/ac
+EOF
+  exit 0
+fi
+
+if [ ! -f "$VIMFILE" ] ; then
+  echo "Cannot find vimfile at $VIMFILE"
+  exit 1
+fi
+
+annotate_syntax=no
+inputfile=""
+outputfile=""
+pdf=no
+crop=no
+fontsize=7.5
+prefix=""
+colors=""
+for opt
+do
+  prefixopt="$prefix$opt"
+  prefix=""
+  case "$prefixopt" in
+    (--annotate-syntax)
+      annotate_syntax=yes ;;
+    (--pdf)
+      pdf=yes;;
+    (--crop)
+      crop=yes;;
+    (--fs)
+      prefix="--fs=";;
+    (--fs=*)
+      fontsize="${prefixopt#--fs=}";;
+    (--colors)
+      prefix="--colors=";;
+    (--colors=*)
+      colors="${prefixopt#--colors=}";;
+    (-*)
+      echo "ERROR: Unknown option $opt. Use -h for help."
+      exit 1 ;;
+    (*)
+      if [ -z "$inputfile" ] ; then
+        inputfile="$opt"
+      elif [ -z "$outputfile" ] ; then
+        outputfile="$opt" ;
+      else
+        echo "ERROR: too many arguments"
+        exit 1
+      fi
+  esac
+done
+temp="$( mktemp -dt plumed.XXXXX)"
+
+{
+if [ -n "$inputfile" ] ; then
+  cat "$inputfile"
+else
+  cat
+# this is to remove \r characters
+fi | tr '\r' ' '
+} | {
+cd $temp
+{
+
+case "$colors" in
+(ac)
+  cat > $temp/colors.vim << EOF
+: set bg=dark
+: hi Statement  ctermfg=5 cterm=bold guifg=#ffff60 gui=none
+: highlight Type ctermfg=2 cterm=bold
+: hi Comment  guifg=#80a0ff ctermfg=darkblue
+: hi Constant ctermfg=red guifg=#ffa0a0 cterm=bold
+EOF
+;;
+(*)
+  echo > $temp/colors.vim
+;;
+esac
+
+if [ "$pdf" = "yes" ]; then
+
+# this is a workaround for a bug in TOhtml
+# that does not color properly when there are empty lines
+  sed "s/^$/ /" |
+  vim - -c ":syntax off" \
+        -c ":source $VIMFILE" \
+        -c ":source $temp/colors.vim" \
+        -c ":set printoptions=header:0" \
+        -c ":set printfont=courier:h$fontsize" \
+        -c ":hardcopy > out.ps" \
+        -c ":q!" 1> /dev/null 2> /dev/null
+else
+  if [ "$annotate_syntax" = "yes" ]; then
+
+    vim - -c ":syntax off" \
+      -c ":source $VIMFILE" \
+      -c ":call PlumedAnnotateSyntax()" \
+      -c ":wq! syntax.log" -c ":q!" 1> /dev/null 2> /dev/null
+
+  else
+    # this is a workaround for a bug in TOhtml
+    # that does not color properly when there are empty lines
+    sed "s/^$/ /" |
+    vim - -c ":syntax off" \
+      -c ":source $VIMFILE" \
+      -c ":source $temp/colors.vim" \
+      -c ":let g:html_use_css = 0" \
+      -c ":let g:html_no_progress" \
+      -c ":let g:html_number_lines = 1" \
+      -c ":TOhtml" \
+      -c ":wq! out.html" -c ":q!" 1> /dev/null 2> /dev/null
+  fi 
+fi
+
+
+}
+}
+
+if [ "$pdf" = "yes" ]; then
+  ps2pdf $temp/out.ps $temp/out.pdf
+  output="$temp/out.pdf"
+  if [ "$crop" = "yes" ]; then
+    (cd $temp;     pdfcrop $temp/out.pdf $temp/outcrop.pdf > /dev/null   )
+    output="$temp/outcrop.pdf"
+  fi
+else
+  if [ "$annotate_syntax" = "yes" ] ; then
+    output="$(awk '{if($1=="ANNOTATION") print}' $temp/syntax.log 2>/dev/null)"
+    error="$(awk '{if($1=="ERROR") print}' $temp/syntax.log >&2 2>/dev/null)"
+  else
+    output="$(cat $temp/out.html | sed 's|^<title>.*</title>$||' | sed 's|^<meta.*$||')"
+  fi
+fi
+
+
+if [ "$pdf" = "yes" ]; then
+  if [ -n "$outputfile" ] ; then
+    cp $output $outputfile
+  else
+    echo "You should specify an output file if using pdf option!"
+    exit 1;
+  fi
+else
+
+  if [ -n "$outputfile" ] ; then
+    echo "$output" > "$outputfile"
+  else
+    echo "$output"
+  fi
+
+fi
+
+echo "$error" >&2
+
+if [ -n "$error" ] ; then
+  exit 1
+fi
+
+
+
+
+

plumed/_lib/lib/plumed/src/colvar/Template.cpp

@@ -0,0 +1,116 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2011-2023 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "Colvar.h"
+#include "core/ActionRegister.h"
+
+namespace PLMD {
+namespace colvar {
+
+//+PLUMEDOC COLVAR TEMPLATE
+/*
+This file provides a template for if you want to introduce a new CV.
+
+The descrition of the CV that you include here will appear in the further details and examples
+section of the manual
+
+You can (and should) include examples showing how to use your CV as follows:
+
+```plumed
+# This should be a sample input.
+t: TEMPLATE ATOMS=1,2
+PRINT ARG=t STRIDE=100 FILE=COLVAR
+```
+
+*/
+//+ENDPLUMEDOC
+
+class Template : public Colvar {
+  bool pbc;
+
+public:
+  explicit Template(const ActionOptions&);
+// active methods:
+  void calculate() override;
+  static void registerKeywords(Keywords& keys);
+};
+
+PLUMED_REGISTER_ACTION(Template,"TEMPLATE")
+
+void Template::registerKeywords(Keywords& keys) {
+  Colvar::registerKeywords(keys);
+  keys.addFlag("TEMPLATE_DEFAULT_OFF_FLAG",false,"flags that are by default not performed should be specified like this");
+  keys.add("compulsory","TEMPLATE_COMPULSORY","all compulsory keywords should be added like this with a description here");
+  keys.add("optional","TEMPLATE_OPTIONAL","all optional keywords that have input should be added like a description here");
+  keys.add("atoms","ATOMS","the keyword with which you specify what atoms to use should be added like this");
+  keys.setValueDescription("scalar","a description of the value that is computed by this colvar should be included here");
+}
+
+Template::Template(const ActionOptions&ao):
+  PLUMED_COLVAR_INIT(ao),
+  pbc(true) {
+  std::vector<AtomNumber> atoms;
+  parseAtomList("ATOMS",atoms);
+  if(atoms.size()!=2) {
+    error("Number of specified atoms should be 2");
+  }
+  bool nopbc=!pbc;
+  parseFlag("NOPBC",nopbc);
+  pbc=!nopbc;
+  checkRead();
+
+  log.printf("  between atoms %d %d\n",atoms[0].serial(),atoms[1].serial());
+  if(pbc) {
+    log.printf("  using periodic boundary conditions\n");
+  } else {
+    log.printf("  without periodic boundary conditions\n");
+  }
+
+  addValueWithDerivatives();
+  setNotPeriodic();
+
+  requestAtoms(atoms);
+}
+
+
+// calculator
+void Template::calculate() {
+
+  Vector distance;
+  if(pbc) {
+    distance=pbcDistance(getPosition(0),getPosition(1));
+  } else {
+    distance=delta(getPosition(0),getPosition(1));
+  }
+  const double value=distance.modulo();
+  const double invvalue=1.0/value;
+
+  setAtomsDerivatives(0,-invvalue*distance);
+  setAtomsDerivatives(1,invvalue*distance);
+  setBoxDerivatives  (-invvalue*Tensor(distance,distance));
+  setValue           (value);
+}
+
+}
+}
+
+
+

plumed/_lib/lib/plumed/src/config/compile_options.sh

@@ -0,0 +1,3 @@
+compile='clang++ -c -I"$PLUMED_INCLUDEDIR/$PLUMED_PROGRAM_NAME"/ -DPACKAGE_NAME="PLUMED" -DPACKAGE_TARNAME="plumed" -DPACKAGE_VERSION="2" -DPACKAGE_STRING="PLUMED 2" -DPACKAGE_BUGREPORT="" -DPACKAGE_URL="" -D__PLUMED_WRAPPER_LIBCXX11=1 -D__PLUMED_CXX17_FILESYSTEM=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_BLAS_RETURNS_FLOAT=double -D__PLUMED_LAPACK_RETURNS_FLOAT=double -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_DLADDR=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1 -D__PLUMED_PROGRAM_NAME="plumed" -D__PLUMED_SOEXT="dylib" -O3 -fPIC -Wall -pedantic -Wno-unknown-pragmas -std=c++17 '
+link_installed='clang++ -dynamiclib -Wl,-headerpad_max_install_names -lstdc++ -lz -ldl -llapack -lblas -Wl,-rpath,@loader_path/../lib /Users/runner/work/hillclimber/hillclimber/src/plumed/_lib/lib/libplumedKernel.dylib'
+soext='dylib'