From c7a1e43ebf23936d015685752390258ad7513a8c Mon Sep 17 00:00:00 2001 From: Amr ALHOSSARY Date: Sun, 11 Oct 2026 19:39:15 -0400 Subject: [PATCH 1/4] MOLINFO WHOLE: check that the reference is not split by the periodic boundary (#1492) With MOLINFO ... WHOLE, WHOLEMOLECULES follows a spanning tree built on the reference coordinates, and the reference is taken as whole on trust. If part of it is wrapped across the periodic boundary, the tree links that part to the wrong atoms through a link that is already its own minimum image, and WHOLEMOLECULES then splits whole molecules in every frame, silently. When the reference pdb has a CRYST1 record that can be the box it was written in (space group P 1, not the 1 A placeholder, not degenerate), Tree now builds the tree a second time on minimum-image distances and walks it over the reference. Atoms that come back moved by a box vector are on the wrong side, and PLUMED stops with an error that names them. A linear-time grid search skips the second tree when no atom comes close to a periodic image of another, which is the usual case for a whole reference. --- CHANGES/v2.11.md | 1 + src/core/GenericMolInfo.cpp | 24 ++++- src/core/GenericMolInfo.h | 7 ++ src/tools/PDB.cpp | 6 ++ src/tools/PDB.h | 3 + src/tools/Tree.cpp | 174 ++++++++++++++++++++++++++++++++++++ src/tools/Tree.h | 6 ++ 7 files changed, 220 insertions(+), 1 deletion(-) diff --git a/CHANGES/v2.11.md b/CHANGES/v2.11.md index a3d9ba4316..188d93c05a 100644 --- a/CHANGES/v2.11.md +++ b/CHANGES/v2.11.md @@ -5,6 +5,7 @@ This page contains changes that will end up in 2.11 ### Changes relevant for users: - When using [MOLINFO](MOLINFO.md) with the `WHOLE` flag, PBCs in the following actions will be reconstructed using a minimum spanning tree based on the coordinates stored in the MOLFILE reference pdb. + - When the reference pdb of [MOLINFO](MOLINFO.md) with the `WHOLE` flag has a CRYST1 record with space group P 1, PLUMED now checks that the reference is really whole in that box, and stops with an error naming the atoms that are on the wrong side of the periodic boundary. Before, a split reference made [WHOLEMOLECULES](WHOLEMOLECULES.md) split whole molecules without any warning. - When using the benchmark now it is possible to scale the atom distances in the synthetic atom distribution (the base atomic distance is 1) - [SAXS](SAXS.md) now accepts the `MARTINI_FF` keyword to select the Martini form-factor generation: `MARTINI_FF=2` (default) keeps the existing Martini 2.2 protein and nucleic-acid form factors, while `MARTINI_FF=3` selects Martini 3 protein form factors. - Added environment variable `PLUMED_LOG_FILE` to control the log file pathname when runnning with GROMACS (the log file was hardcoded as `PLUMED.OUT`) diff --git a/src/core/GenericMolInfo.cpp b/src/core/GenericMolInfo.cpp index 9534f5b780..cfc8ead008 100644 --- a/src/core/GenericMolInfo.cpp +++ b/src/core/GenericMolInfo.cpp @@ -27,6 +27,8 @@ #include "tools/PDB.h" #include "tools/Communicator.h" #include "config/Config.h" +#include +#include namespace PLMD { @@ -47,7 +49,7 @@ void GenericMolInfo::registerKeywords( Keywords& keys ) { keys.add("compulsory","PYTHON_BIN","default","python interpreter"); keys.add("atoms","CHAIN","(for masochists ( mostly Davide Branduardi ) ) The atoms involved in each of the chains of interest in the structure."); keys.add("hidden","STRIDE","frequency for resetting the python interpreter. Should be 1."); - keys.addFlag("WHOLE", false, "The reference structure is whole, i.e. not broken by PBC"); + keys.addFlag("WHOLE", false, "The reference structure is whole, i.e. not broken by PBC. If the pdb file has a CRYST1 record with space group P 1, this is checked for the atoms of each group that is made whole with it"); } GenericMolInfo::~GenericMolInfo() { @@ -89,6 +91,7 @@ GenericMolInfo::GenericMolInfo( const ActionOptions&ao ): if( read_backbone.size()==0 ) { parse("STRUCTURE",reference); + pdbscale_=usingNaturalUnits() ? 1.0 : 0.1/getUnits().getLength(); if( ! pdb.read(reference,usingNaturalUnits(),0.1/getUnits().getLength())) { plumed_merror("missing input file " + reference ); } @@ -419,6 +422,25 @@ bool GenericMolInfo::isWhole() const { return iswhole_; } +Tensor GenericMolInfo::getReferenceBox() const { + const Vector & axs(pdb.getBoxAxs()); + const Vector & ang(pdb.getBoxAng()); + bool unitcube=true; + for(unsigned i=0; i<3; i++) { + if(std::fabs(axs[i]-pdbscale_)>1e-3*pdbscale_ || std::fabs(ang[i]-90.0)>1e-3) { + unitcube=false; + } + } + std::string group=pdb.getSpaceGroup(); + group.erase(std::remove(group.begin(),group.end(),' '),group.end()); + const Tensor & box(pdb.getBoxVec()); + const double det=box.determinant(); + if(unitcube || (group.length()>0 && group!="P1") || !std::isfinite(det) || det<=0.0) { + return Tensor(); + } + return box; +} + void GenericMolInfo::prepare() { if(selector_running) { log<<" MOLINFO "<& atoms ); diff --git a/src/tools/PDB.cpp b/src/tools/PDB.cpp index 765a3932ec..03946b6a89 100644 --- a/src/tools/PDB.cpp +++ b/src/tools/PDB.cpp @@ -274,6 +274,10 @@ const Tensor & PDB::getBoxVec()const { return Box; } +const std::string & PDB::getSpaceGroup()const { + return spaceGroup; +} + std::string PDB::getAtomName(AtomNumber a)const { const auto p=number2index.find(a); if(p==number2index.end()) { @@ -368,6 +372,8 @@ bool PDB::readFromFilepointer(FILE *fp,bool naturalUnits,double scale) { Tools::convert(BoxA,BoxABG[0]); Tools::convert(BoxB,BoxABG[1]); Tools::convert(BoxG,BoxABG[2]); + spaceGroup=line.substr(55,11); + Tools::trim(spaceGroup); BoxXYZ*=scale; double cosA=std::cos(BoxABG[0]*pi/180.); double cosB=std::cos(BoxABG[1]*pi/180.); diff --git a/src/tools/PDB.h b/src/tools/PDB.h index 8e8f56da9e..903be60ab7 100644 --- a/src/tools/PDB.h +++ b/src/tools/PDB.h @@ -55,6 +55,7 @@ class PDB { std::map > arg_data; Vector BoxXYZ,BoxABG; Tensor Box; + std::string spaceGroup; public: /// Read the pdb from a file, scaling positions by a factor scale bool read(const std::string&file,bool naturalUnits,double scale); @@ -146,6 +147,8 @@ class PDB { const Vector & getBoxAng()const; /// Returns box axis vectors const Tensor & getBoxVec()const; +/// Returns the space group of the CRYST1 record (empty if there is none) + const std::string & getSpaceGroup()const; /// Return true if the residue name is one of the allowed reisude names e.g. one of the 20 amino acids for proteins bool allowedResidue( const std::string& type, const std::string& residuename ) const; }; diff --git a/src/tools/Tree.cpp b/src/tools/Tree.cpp index a7bd3aab66..99b6685e4f 100644 --- a/src/tools/Tree.cpp +++ b/src/tools/Tree.cpp @@ -24,9 +24,13 @@ #include "Tools.h" #include "Vector.h" #include "AtomNumber.h" +#include "Pbc.h" +#include "Tensor.h" #include "core/GenericMolInfo.h" #include #include +#include +#include namespace PLMD { @@ -88,6 +92,8 @@ void Tree::buildTree(const std::vector & atoms) { std::vector mindist(newatoms.size(), std::numeric_limits::max()); // initialize tree with first atom mindist[0] = 0.0; + // longest edge of the tree (squared) + double longest2=0.0; // loops for(unsigned i=0; i & atoms) { tree_indexes_.push_back(newatoms[selected_vertex]); tree_.push_back(atoms[newatoms[selected_vertex]]); intree[selected_vertex] = true; + if(i>0) { + longest2=std::max(longest2,mindist[selected_vertex]); + } // update distances double minroot = std::numeric_limits::max(); int iroot = -1; @@ -121,6 +130,8 @@ void Tree::buildTree(const std::vector & atoms) { } } + checkReferenceIsWhole(atoms, newatoms, positions, longest2); + // now re-add atoms not present in the PDB for(unsigned i=0; i & atoms) { } } +namespace { +// True if some atom has a periodic image of an atom (a nonzero lattice translation away) within +// sqrt(cut2) of it. When there is none, minimum-image and plain distances agree on every pair up to +// the longest edge of the plain tree, so the periodic tree is the plain tree and the reference is whole. +// A grid search, linear in the number of atoms. It answers true when the box is too small for that +// search to be cheap, so that the full check decides. +bool hasCloseImage(const std::vector & positions, const Tensor & box, double cut2) { + const double cut=std::sqrt(cut2); + Vector lo(positions[0]), hi(positions[0]); + for(const auto & p : positions) { + for(unsigned k=0; k<3; ++k) { + lo[k]=std::min(lo[k],p[k]); + hi[k]=std::max(hi[k],p[k]); + } + } + // lattice vectors that can bring an atom within cut of the structure + const double reach=(hi-lo).modulo()+cut; + const Tensor inv=inverse(box); + int range[3]; + for(unsigned k=0; k<3; ++k) { + const double col=std::sqrt(inv[0][k]*inv[0][k]+inv[1][k]*inv[1][k]+inv[2][k]*inv[2][k]); + range[k]=static_cast(std::ceil(reach*col)); + } + if((2.0*range[0]+1)*(2.0*range[1]+1)*(2.0*range[2]+1)>4096) { + return true; + } + std::vector shifts; + for(int i=-range[0]; i<=range[0]; ++i) { + for(int j=-range[1]; j<=range[1]; ++j) { + for(int k=-range[2]; k<=range[2]; ++k) { + if(i==0 && j==0 && k==0) { + continue; + } + const Vector n=matmul(Vector(i,j,k),box); + if(n.modulo()<=reach) { + shifts.push_back(n); + } + } + } + } + // atoms in cells of side cut + const double side=std::max(cut,1e-6*(hi-lo).modulo()); + long nc[3]; + for(unsigned k=0; k<3; ++k) { + nc[k]=static_cast((hi[k]-lo[k])/side)+1; + } + if(static_cast(nc[0])*nc[1]*nc[2]>1e8) { + return true; + } + auto cellOf=[&](const Vector & p,unsigned k) { + return static_cast(std::floor((p[k]-lo[k])/side)); + }; + std::vector head(nc[0]*nc[1]*nc[2],-1), next(positions.size(),-1); + for(unsigned a=0; ahi[0]+cut || p[1]hi[1]+cut || p[2]hi[2]+cut) { + continue; + } + long c[3]; + for(unsigned k=0; k<3; ++k) { + c[k]=cellOf(p,k); + } + for(long i=std::max(c[0]-1,0L); i<=std::min(c[0]+1,nc[0]-1); ++i) { + for(long j=std::max(c[1]-1,0L); j<=std::min(c[1]+1,nc[1]-1); ++j) { + for(long k=std::max(c[2]-1,0L); k<=std::min(c[2]+1,nc[2]-1); ++k) { + for(long b=head[(i*nc[1]+j)*nc[2]+k]; b>=0; b=next[b]) { + if(delta(p,positions[b]).modulo2()<=cut2) { + return true; + } + } + } + } + } + } + } + return false; +} +} + +void Tree::checkReferenceIsWhole(const std::vector & atoms, + const std::vector & newatoms, + const std::vector & positions, + double longest2) const { + // The tree is built on plain distances in the reference, so WHOLE is taken on trust: + // if part of the reference is wrapped across the periodic boundary, its link to the rest is + // a long edge that is already its own minimum image, and the walk then moves the same atoms + // across the boundary in every frame. + // Check it with the CRYST1 box: build a second spanning tree on minimum-image distances and + // walk it over the reference. A whole reference comes back unchanged; a wrapped piece comes + // back moved by a lattice vector. + const Tensor box=moldat_->getReferenceBox(); + if(box.determinant()==0.0 || positions.size()<2) { + return; + } + // nearly always, no atom comes close to a periodic image of another: then the reference is whole + if(!hasCloseImage(positions, box, longest2*(1.0+1e-6))) { + return; + } + Pbc pbc; + pbc.setBox(box); + const unsigned n=positions.size(); + std::vector intree(n, false); + std::vector mindist(n, std::numeric_limits::max()); + std::vector parent(n, 0); + std::vector rebuilt(positions); + mindist[0]=0.0; + for(unsigned i=0; i0) { + rebuilt[s]=rebuilt[parent[s]]+pbc.distance(positions[parent[s]],positions[s]); + } + for(unsigned j=0; j::max(); + for(unsigned k=0; k<3; ++k) { + shortest=std::min(shortest,box.getRow(k).modulo()); + } + std::vector moved; + for(unsigned j=0; j1e-3*shortest) { + moved.push_back(j); + } + } + if(moved.size()>0) { + std::string list; + for(unsigned k=0; kgetResidueName(a)+std::to_string(moldat_->getResidueNumber(a))+")"; + } + if(moved.size()>10) { + list+=" and "+std::to_string(moved.size()-10)+" more"; + } + plumed_error()<<"the reference structure in the MOLINFO pdb file is not whole: "< & Tree::getTree(const std::vector & atoms) { buildTree(atoms); return tree_; diff --git a/src/tools/Tree.h b/src/tools/Tree.h index 3b54561591..0cf64dc75b 100644 --- a/src/tools/Tree.h +++ b/src/tools/Tree.h @@ -41,6 +41,12 @@ class Tree { std::vector root_indexes_; std::vector tree_indexes_; +/// Raise an error if the reference structure is split by the periodic boundary + void checkReferenceIsWhole(const std::vector & atoms, + const std::vector & newatoms, + const std::vector & positions, + double longest2) const; + public: /// constructor explicit Tree(GenericMolInfo* moldat); From 7c495a87c07f4468975c92913132d773201a6215 Mon Sep 17 00:00:00 2001 From: Amr ALHOSSARY Date: Sun, 11 Oct 2026 19:39:15 -0400 Subject: [PATCH 2/4] regtest: check of the MOLINFO WHOLE reference, and repair in several cells (#1492) rt-molinfo-whole-check reads a whole and a split copy of trp-cage (1L2Y, model 1) with MOLINFO WHOLE and reports which references are rejected and which atoms are named; copies without a usable CRYST1 record are accepted. rt-molinfo-whole-repair makes five split frames whole (rhombic dodecahedron, truncated octahedron, triclinic and cubic cells; atom- and residue-wise wrapping) with a whole reference. --- regtest/basic/rt-molinfo-whole-check/Makefile | 1 + regtest/basic/rt-molinfo-whole-check/config | 3 + regtest/basic/rt-molinfo-whole-check/main.cpp | 48 + .../rt-molinfo-whole-check/output.reference | 7 + regtest/basic/rt-molinfo-whole-check/torn.pdb | 306 ++++ .../rt-molinfo-whole-check/torn_crystal.pdb | 306 ++++ .../rt-molinfo-whole-check/torn_nocryst.pdb | 305 ++++ .../torn_placeholder.pdb | 306 ++++ .../rt-molinfo-whole-check/torn_zero.pdb | 306 ++++ .../basic/rt-molinfo-whole-check/whole.pdb | 306 ++++ .../basic/rt-molinfo-whole-repair/Makefile | 1 + regtest/basic/rt-molinfo-whole-repair/config | 3 + .../basic/rt-molinfo-whole-repair/plumed.dat | 4 + .../basic/rt-molinfo-whole-repair/traj.gro | 1535 +++++++++++++++++ .../basic/rt-molinfo-whole-repair/whole.pdb | 306 ++++ .../whole.xyz.reference | 1530 ++++++++++++++++ 16 files changed, 5273 insertions(+) create mode 100644 regtest/basic/rt-molinfo-whole-check/Makefile create mode 100644 regtest/basic/rt-molinfo-whole-check/config create mode 100644 regtest/basic/rt-molinfo-whole-check/main.cpp create mode 100644 regtest/basic/rt-molinfo-whole-check/output.reference create mode 100644 regtest/basic/rt-molinfo-whole-check/torn.pdb create mode 100644 regtest/basic/rt-molinfo-whole-check/torn_crystal.pdb create mode 100644 regtest/basic/rt-molinfo-whole-check/torn_nocryst.pdb create mode 100644 regtest/basic/rt-molinfo-whole-check/torn_placeholder.pdb create mode 100644 regtest/basic/rt-molinfo-whole-check/torn_zero.pdb create mode 100644 regtest/basic/rt-molinfo-whole-check/whole.pdb create mode 100644 regtest/basic/rt-molinfo-whole-repair/Makefile create mode 100644 regtest/basic/rt-molinfo-whole-repair/config create mode 100644 regtest/basic/rt-molinfo-whole-repair/plumed.dat create mode 100644 regtest/basic/rt-molinfo-whole-repair/traj.gro create mode 100644 regtest/basic/rt-molinfo-whole-repair/whole.pdb create mode 100644 regtest/basic/rt-molinfo-whole-repair/whole.xyz.reference diff --git a/regtest/basic/rt-molinfo-whole-check/Makefile b/regtest/basic/rt-molinfo-whole-check/Makefile new file mode 100644 index 0000000000..3703b27cea --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-check/Makefile @@ -0,0 +1 @@ +include ../../scripts/test.make diff --git a/regtest/basic/rt-molinfo-whole-check/config b/regtest/basic/rt-molinfo-whole-check/config new file mode 100644 index 0000000000..7e48351687 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-check/config @@ -0,0 +1,3 @@ +type=make +# the test checks exception messages +export PLUMED_STACK_TRACE=no diff --git a/regtest/basic/rt-molinfo-whole-check/main.cpp b/regtest/basic/rt-molinfo-whole-check/main.cpp new file mode 100644 index 0000000000..061ff85738 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-check/main.cpp @@ -0,0 +1,48 @@ +#include "plumed/wrapper/Plumed.h" +#include +#include +#include + +// MOLINFO WHOLE takes the reference structure as whole. Here each reference is read with +// MOLINFO ... WHOLE and used by WHOLEMOLECULES, and we report whether PLUMED accepts it or +// reports it as split by the periodic boundary of its CRYST1 record. +// torn.pdb is whole.pdb with 15 atoms wrapped across a face of its (rhombic dodecahedron) cell. +// Its copies without a usable cell (no CRYST1, the 1 A placeholder, a zero cell, a crystallographic +// space group) cannot be checked and are accepted. +int main(int, char**) { + std::ofstream out("output"); + unsigned natoms=304; + std::vector positions(3*natoms,0.0); + const std::vector> cases{ + {"whole.pdb","1-304"}, + {"torn.pdb","1-304"}, + {"torn.pdb","1-150"}, + {"torn_nocryst.pdb","1-304"}, + {"torn_placeholder.pdb","1-304"}, + {"torn_zero.pdb","1-304"}, + {"torn_crystal.pdb","1-304"} + }; + for(const auto & c : cases) { + PLMD::Plumed plumed; + plumed.cmd("setNatoms",&natoms); + plumed.cmd("setLogFile","test.log"); + plumed.cmd("init"); + out< Date: Mon, 19 Oct 2026 07:30:56 -0400 Subject: [PATCH 3/4] MOLINFO WHOLE: warn, rather than stop, when the reference looks split The check also fires for a group of several molecules that are not in contact, such as a ligand away from the protein, or a membrane, which is continuous across the box. WHOLEMOLECULES handles those correctly, so an error would stop runs that work. The message is now a warning in the log, naming the same atoms, and says when it is expected. New regtests: rt-molinfo-whole-ligand (trp-cage and a ligand closer to a periodic image of the protein) and rt-molinfo-whole-membrane (a small bilayer). Each gives the warning with one group, none with one group per molecule, and the frames are made whole as in the reference. --- CHANGES/v2.11.md | 2 +- regtest/basic/rt-molinfo-whole-check/config | 2 - regtest/basic/rt-molinfo-whole-check/main.cpp | 44 +- .../rt-molinfo-whole-check/output.reference | 2 +- .../basic/rt-molinfo-whole-ligand/Makefile | 1 + regtest/basic/rt-molinfo-whole-ligand/config | 16 + .../basic/rt-molinfo-whole-ligand/plumed.dat | 5 + .../rt-molinfo-whole-ligand/plumed_sep.dat | 3 + regtest/basic/rt-molinfo-whole-ligand/ref.pdb | 316 ++++++ .../basic/rt-molinfo-whole-ligand/traj.gro | 948 ++++++++++++++++++ .../warnings.reference | 5 + .../whole.xyz.reference | 945 +++++++++++++++++ .../basic/rt-molinfo-whole-membrane/Makefile | 1 + .../basic/rt-molinfo-whole-membrane/config | 16 + .../rt-molinfo-whole-membrane/plumed.dat | 5 + .../rt-molinfo-whole-membrane/plumed_sep.dat | 3 + .../basic/rt-molinfo-whole-membrane/ref.pdb | 110 ++ .../basic/rt-molinfo-whole-membrane/traj.gro | 333 ++++++ .../warnings.reference | 5 + .../whole.xyz.reference | 330 ++++++ src/core/GenericMolInfo.cpp | 2 +- src/tools/Tree.cpp | 21 +- src/tools/Tree.h | 2 +- 23 files changed, 3088 insertions(+), 29 deletions(-) create mode 100644 regtest/basic/rt-molinfo-whole-ligand/Makefile create mode 100644 regtest/basic/rt-molinfo-whole-ligand/config create mode 100644 regtest/basic/rt-molinfo-whole-ligand/plumed.dat create mode 100644 regtest/basic/rt-molinfo-whole-ligand/plumed_sep.dat create mode 100644 regtest/basic/rt-molinfo-whole-ligand/ref.pdb create mode 100644 regtest/basic/rt-molinfo-whole-ligand/traj.gro create mode 100644 regtest/basic/rt-molinfo-whole-ligand/warnings.reference create mode 100644 regtest/basic/rt-molinfo-whole-ligand/whole.xyz.reference create mode 100644 regtest/basic/rt-molinfo-whole-membrane/Makefile create mode 100644 regtest/basic/rt-molinfo-whole-membrane/config create mode 100644 regtest/basic/rt-molinfo-whole-membrane/plumed.dat create mode 100644 regtest/basic/rt-molinfo-whole-membrane/plumed_sep.dat create mode 100644 regtest/basic/rt-molinfo-whole-membrane/ref.pdb create mode 100644 regtest/basic/rt-molinfo-whole-membrane/traj.gro create mode 100644 regtest/basic/rt-molinfo-whole-membrane/warnings.reference create mode 100644 regtest/basic/rt-molinfo-whole-membrane/whole.xyz.reference diff --git a/CHANGES/v2.11.md b/CHANGES/v2.11.md index b97173e80d..ceb5c20806 100644 --- a/CHANGES/v2.11.md +++ b/CHANGES/v2.11.md @@ -5,7 +5,7 @@ This page contains changes that will end up in 2.11 ### Changes relevant for users: - When using [MOLINFO](MOLINFO.md) with the `WHOLE` flag, PBCs in the following actions will be reconstructed using a minimum spanning tree based on the coordinates stored in the MOLFILE reference pdb. - - When the reference pdb of [MOLINFO](MOLINFO.md) with the `WHOLE` flag has a CRYST1 record with space group P 1, PLUMED now checks that the reference is really whole in that box, and stops with an error naming the atoms that are on the wrong side of the periodic boundary. Before, a split reference made [WHOLEMOLECULES](WHOLEMOLECULES.md) split whole molecules without any warning. + - When the reference pdb of [MOLINFO](MOLINFO.md) with the `WHOLE` flag has a CRYST1 record with space group P 1, PLUMED now checks that the reference is really whole in that box, and writes a warning to the log naming the atoms that seem to be on the wrong side of the periodic boundary. Before, a split reference made [WHOLEMOLECULES](WHOLEMOLECULES.md) split whole molecules without any warning. - When using the benchmark now it is possible to scale the atom distances in the synthetic atom distribution (the base atomic distance is 1) - [SAXS](SAXS.md) now accepts the `MARTINI_FF` keyword to select the Martini form-factor generation: `MARTINI_FF=2` (default) keeps the existing Martini 2.2 protein and nucleic-acid form factors, while `MARTINI_FF=3` selects Martini 3 protein form factors. - Added environment variable `PLUMED_LOG_FILE` to control the log file pathname when runnning with GROMACS (the log file was hardcoded as `PLUMED.OUT`) diff --git a/regtest/basic/rt-molinfo-whole-check/config b/regtest/basic/rt-molinfo-whole-check/config index 7e48351687..df1f95bf3e 100644 --- a/regtest/basic/rt-molinfo-whole-check/config +++ b/regtest/basic/rt-molinfo-whole-check/config @@ -1,3 +1 @@ type=make -# the test checks exception messages -export PLUMED_STACK_TRACE=no diff --git a/regtest/basic/rt-molinfo-whole-check/main.cpp b/regtest/basic/rt-molinfo-whole-check/main.cpp index 061ff85738..feb64671d0 100644 --- a/regtest/basic/rt-molinfo-whole-check/main.cpp +++ b/regtest/basic/rt-molinfo-whole-check/main.cpp @@ -1,11 +1,12 @@ #include "plumed/wrapper/Plumed.h" #include +#include #include #include // MOLINFO WHOLE takes the reference structure as whole. Here each reference is read with // MOLINFO ... WHOLE and used by WHOLEMOLECULES, and we report whether PLUMED accepts it or -// reports it as split by the periodic boundary of its CRYST1 record. +// writes a warning that it looks split by the periodic boundary of its CRYST1 record. // torn.pdb is whole.pdb with 15 atoms wrapped across a face of its (rhombic dodecahedron) cell. // Its copies without a usable cell (no CRYST1, the 1 A placeholder, a zero cell, a crystallographic // space group) cannot be checked and are accepted. @@ -22,26 +23,37 @@ int main(int, char**) { {"torn_zero.pdb","1-304"}, {"torn_crystal.pdb","1-304"} }; - for(const auto & c : cases) { - PLMD::Plumed plumed; - plumed.cmd("setNatoms",&natoms); - plumed.cmd("setLogFile","test.log"); - plumed.cmd("init"); + for(unsigned i=0; i out_sep 2> err_sep || return 1 +} + +# the WHOLEMOLECULES lines of the log and the warnings, up to the list of atoms +function plumed_regtest_after() { + for f in out_sep out; do + echo "# $f" + grep -E "^PLUMED: (Action WHOLEMOLECULES|WARNING for action MOLINFO)" $f | sed -e "s/^PLUMED: //" -e "s/\\. If these atoms.*//" + done > warnings +} diff --git a/regtest/basic/rt-molinfo-whole-ligand/plumed.dat b/regtest/basic/rt-molinfo-whole-ligand/plumed.dat new file mode 100644 index 0000000000..78d74022e1 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-ligand/plumed.dat @@ -0,0 +1,5 @@ +# trp-cage and a ligand away from it, closer to a periodic image of the protein than to the protein itself +MOLINFO STRUCTURE=ref.pdb WHOLE +# protein and ligand in one group: a warning is written, and the frames are made whole as the reference +WHOLEMOLECULES ENTITY0=1-313 +DUMPATOMS ATOMS=1-313 FILE=whole.xyz PRECISION=3 diff --git a/regtest/basic/rt-molinfo-whole-ligand/plumed_sep.dat b/regtest/basic/rt-molinfo-whole-ligand/plumed_sep.dat new file mode 100644 index 0000000000..0353ca9ec9 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-ligand/plumed_sep.dat @@ -0,0 +1,3 @@ +MOLINFO STRUCTURE=ref.pdb WHOLE +# protein and ligand in separate groups: no warning +WHOLEMOLECULES ENTITY0=1-304 ENTITY1=305-313 diff --git a/regtest/basic/rt-molinfo-whole-ligand/ref.pdb b/regtest/basic/rt-molinfo-whole-ligand/ref.pdb new file mode 100644 index 0000000000..f7e56173c9 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-ligand/ref.pdb @@ -0,0 +1,316 @@ +CRYST1 40.000 40.000 40.000 60.00 60.00 60.00 P 1 1 +ATOM 1 N ASN A 1 30.997 27.202 15.779 1.00 0.00 N +ATOM 2 CA ASN A 1 31.290 26.210 14.716 1.00 0.00 C +ATOM 3 C ASN A 1 32.781 26.039 14.437 1.00 0.00 C +ATOM 4 O ASN A 1 33.264 24.924 14.576 1.00 0.00 O +ATOM 5 CB ASN A 1 30.461 26.471 13.445 1.00 0.00 C +ATOM 6 CG ASN A 1 28.983 26.205 13.723 1.00 0.00 C +ATOM 7 OD1 ASN A 1 28.629 25.775 14.810 1.00 0.00 O +ATOM 8 ND2 ASN A 1 28.092 26.481 12.791 1.00 0.00 N +ATOM 9 H1 ASN A 1 31.568 27.032 16.595 1.00 0.00 H +ATOM 10 H2 ASN A 1 31.158 28.143 15.445 1.00 0.00 H +ATOM 11 H3 ASN A 1 30.021 27.116 16.041 1.00 0.00 H +ATOM 12 HA ASN A 1 30.968 25.237 15.095 1.00 0.00 H +ATOM 13 HB2 ASN A 1 30.588 27.492 13.141 1.00 0.00 H +ATOM 14 HB3 ASN A 1 30.790 25.794 12.655 1.00 0.00 H +ATOM 15 HD21 ASN A 1 28.326 26.866 11.890 1.00 0.00 H +ATOM 16 HD22 ASN A 1 27.141 26.258 13.040 1.00 0.00 H +ATOM 17 N LEU A 2 33.519 27.106 14.106 1.00 0.00 N +ATOM 18 CA LEU A 2 34.975 27.077 13.882 1.00 0.00 C +ATOM 19 C LEU A 2 35.762 26.262 14.930 1.00 0.00 C +ATOM 20 O LEU A 2 36.507 25.349 14.574 1.00 0.00 O +ATOM 21 CB LEU A 2 35.487 28.525 13.715 1.00 0.00 C +ATOM 22 CG LEU A 2 35.103 29.525 14.839 1.00 0.00 C +ATOM 23 CD1 LEU A 2 36.286 29.878 15.735 1.00 0.00 C +ATOM 24 CD2 LEU A 2 34.547 30.823 14.250 1.00 0.00 C +ATOM 25 H LEU A 2 33.077 27.998 13.940 1.00 0.00 H +ATOM 26 HA LEU A 2 35.148 26.569 12.931 1.00 0.00 H +ATOM 27 HB2 LEU A 2 36.558 28.489 13.662 1.00 0.00 H +ATOM 28 HB3 LEU A 2 35.085 28.892 12.770 1.00 0.00 H +ATOM 29 HG LEU A 2 34.330 29.097 15.476 1.00 0.00 H +ATOM 30 HD11 LEU A 2 36.691 28.980 16.188 1.00 0.00 H +ATOM 31 HD12 LEU A 2 37.057 30.379 15.151 1.00 0.00 H +ATOM 32 HD13 LEU A 2 35.969 30.552 16.531 1.00 0.00 H +ATOM 33 HD21 LEU A 2 35.291 31.284 13.598 1.00 0.00 H +ATOM 34 HD22 LEU A 2 33.643 30.619 13.677 1.00 0.00 H +ATOM 35 HD23 LEU A 2 34.306 31.520 15.053 1.00 0.00 H +ATOM 36 N TYR A 3 35.544 26.530 16.223 1.00 0.00 N +ATOM 37 CA TYR A 3 36.208 25.813 17.315 1.00 0.00 C +ATOM 38 C TYR A 3 35.796 24.331 17.408 1.00 0.00 C +ATOM 39 O TYR A 3 36.607 23.484 17.776 1.00 0.00 O +ATOM 40 CB TYR A 3 35.934 26.547 18.636 1.00 0.00 C +ATOM 41 CG TYR A 3 37.074 26.414 19.624 1.00 0.00 C +ATOM 42 CD1 TYR A 3 37.152 25.292 20.472 1.00 0.00 C +ATOM 43 CD2 TYR A 3 38.078 27.401 19.666 1.00 0.00 C +ATOM 44 CE1 TYR A 3 38.241 25.151 21.352 1.00 0.00 C +ATOM 45 CE2 TYR A 3 39.173 27.260 20.539 1.00 0.00 C +ATOM 46 CZ TYR A 3 39.259 26.128 21.377 1.00 0.00 C +ATOM 47 OH TYR A 3 40.331 25.956 22.195 1.00 0.00 O +ATOM 48 H TYR A 3 34.964 27.320 16.454 1.00 0.00 H +ATOM 49 HA TYR A 3 37.283 25.843 17.130 1.00 0.00 H +ATOM 50 HB2 TYR A 3 35.781 27.588 18.425 1.00 0.00 H +ATOM 51 HB3 TYR A 3 35.012 26.171 19.084 1.00 0.00 H +ATOM 52 HD1 TYR A 3 36.385 24.531 20.435 1.00 0.00 H +ATOM 53 HD2 TYR A 3 38.021 28.275 19.029 1.00 0.00 H +ATOM 54 HE1 TYR A 3 38.322 24.296 22.003 1.00 0.00 H +ATOM 55 HE2 TYR A 3 39.931 28.027 20.567 1.00 0.00 H +ATOM 56 HH TYR A 3 41.085 26.470 21.901 1.00 0.00 H +ATOM 57 N ILE A 4 34.556 24.000 17.023 1.00 0.00 N +ATOM 58 CA ILE A 4 34.041 22.626 16.947 1.00 0.00 C +ATOM 59 C ILE A 4 34.809 21.854 15.864 1.00 0.00 C +ATOM 60 O ILE A 4 35.277 20.741 16.108 1.00 0.00 O +ATOM 61 CB ILE A 4 32.512 22.609 16.677 1.00 0.00 C +ATOM 62 CG1 ILE A 4 31.701 23.615 17.531 1.00 0.00 C +ATOM 63 CG2 ILE A 4 31.939 21.191 16.835 1.00 0.00 C +ATOM 64 CD1 ILE A 4 31.879 23.487 19.049 1.00 0.00 C +ATOM 65 H ILE A 4 33.992 24.731 16.617 1.00 0.00 H +ATOM 66 HA ILE A 4 34.228 22.134 17.902 1.00 0.00 H +ATOM 67 HB ILE A 4 32.344 22.883 15.637 1.00 0.00 H +ATOM 68 HG12 ILE A 4 31.998 24.606 17.246 1.00 0.00 H +ATOM 69 HG13 ILE A 4 30.641 23.499 17.298 1.00 0.00 H +ATOM 70 HG21 ILE A 4 32.389 20.520 16.102 1.00 0.00 H +ATOM 71 HG22 ILE A 4 32.139 20.804 17.835 1.00 0.00 H +ATOM 72 HG23 ILE A 4 30.862 21.204 16.666 1.00 0.00 H +ATOM 73 HD11 ILE A 4 31.592 22.490 19.383 1.00 0.00 H +ATOM 74 HD12 ILE A 4 32.915 23.681 19.329 1.00 0.00 H +ATOM 75 HD13 ILE A 4 31.242 24.219 19.547 1.00 0.00 H +ATOM 76 N GLN A 5 34.991 22.474 14.689 1.00 0.00 N +ATOM 77 CA GLN A 5 35.776 21.908 13.591 1.00 0.00 C +ATOM 78 C GLN A 5 37.269 21.754 13.944 1.00 0.00 C +ATOM 79 O GLN A 5 37.912 20.835 13.450 1.00 0.00 O +ATOM 80 CB GLN A 5 35.606 22.762 12.321 1.00 0.00 C +ATOM 81 CG GLN A 5 35.654 21.904 11.044 1.00 0.00 C +ATOM 82 CD GLN A 5 34.322 21.215 10.749 1.00 0.00 C +ATOM 83 OE1 GLN A 5 34.129 20.031 10.999 1.00 0.00 O +ATOM 84 NE2 GLN A 5 33.366 21.929 10.182 1.00 0.00 N +ATOM 85 H GLN A 5 34.571 23.393 14.571 1.00 0.00 H +ATOM 86 HA GLN A 5 35.381 20.913 13.394 1.00 0.00 H +ATOM 87 HB2 GLN A 5 34.660 23.266 12.365 1.00 0.00 H +ATOM 88 HB3 GLN A 5 36.406 23.504 12.281 1.00 0.00 H +ATOM 89 HG2 GLN A 5 35.905 22.536 10.214 1.00 0.00 H +ATOM 90 HG3 GLN A 5 36.440 21.152 11.129 1.00 0.00 H +ATOM 91 HE21 GLN A 5 33.509 22.891 9.926 1.00 0.00 H +ATOM 92 HE22 GLN A 5 32.506 21.440 9.999 1.00 0.00 H +ATOM 93 N TRP A 6 37.824 22.616 14.806 1.00 0.00 N +ATOM 94 CA TRP A 6 39.182 22.444 15.341 1.00 0.00 C +ATOM 95 C TRP A 6 39.267 21.309 16.378 1.00 0.00 C +ATOM 96 O TRP A 6 40.193 20.496 16.330 1.00 0.00 O +ATOM 97 CB TRP A 6 39.677 23.778 15.917 1.00 0.00 C +ATOM 98 CG TRP A 6 41.046 23.727 16.528 1.00 0.00 C +ATOM 99 CD1 TRP A 6 42.217 23.739 15.852 1.00 0.00 C +ATOM 100 CD2 TRP A 6 41.406 23.639 17.940 1.00 0.00 C +ATOM 101 NE1 TRP A 6 43.269 23.635 16.745 1.00 0.00 N +ATOM 102 CE2 TRP A 6 42.826 23.590 18.044 1.00 0.00 C +ATOM 103 CE3 TRP A 6 40.677 23.599 19.146 1.00 0.00 C +ATOM 104 CZ2 TRP A 6 43.497 23.520 19.272 1.00 0.00 C +ATOM 105 CZ3 TRP A 6 41.337 23.508 20.387 1.00 0.00 C +ATOM 106 CH2 TRP A 6 42.740 23.482 20.454 1.00 0.00 C +ATOM 107 H TRP A 6 37.274 23.418 15.092 1.00 0.00 H +ATOM 108 HA TRP A 6 39.846 22.167 14.521 1.00 0.00 H +ATOM 109 HB2 TRP A 6 39.692 24.500 15.123 1.00 0.00 H +ATOM 110 HB3 TRP A 6 38.977 24.119 16.678 1.00 0.00 H +ATOM 111 HD1 TRP A 6 42.310 23.808 14.776 1.00 0.00 H +ATOM 112 HE1 TRP A 6 44.258 23.611 16.490 1.00 0.00 H +ATOM 113 HE3 TRP A 6 39.599 23.646 19.107 1.00 0.00 H +ATOM 114 HZ2 TRP A 6 44.577 23.493 19.295 1.00 0.00 H +ATOM 115 HZ3 TRP A 6 40.760 23.475 21.300 1.00 0.00 H +ATOM 116 HH2 TRP A 6 43.232 23.435 21.415 1.00 0.00 H +ATOM 117 N LEU A 7 38.298 21.215 17.301 1.00 0.00 N +ATOM 118 CA LEU A 7 38.257 20.143 18.297 1.00 0.00 C +ATOM 119 C LEU A 7 38.051 18.756 17.676 1.00 0.00 C +ATOM 120 O LEU A 7 38.754 17.827 18.076 1.00 0.00 O +ATOM 121 CB LEU A 7 37.188 20.430 19.367 1.00 0.00 C +ATOM 122 CG LEU A 7 37.597 21.496 20.403 1.00 0.00 C +ATOM 123 CD1 LEU A 7 36.423 21.752 21.352 1.00 0.00 C +ATOM 124 CD2 LEU A 7 38.805 21.068 21.248 1.00 0.00 C +ATOM 125 H LEU A 7 37.582 21.938 17.328 1.00 0.00 H +ATOM 126 HA LEU A 7 39.232 20.097 18.779 1.00 0.00 H +ATOM 127 HB2 LEU A 7 36.298 20.767 18.871 1.00 0.00 H +ATOM 128 HB3 LEU A 7 36.977 19.504 19.906 1.00 0.00 H +ATOM 129 HG LEU A 7 37.837 22.426 19.894 1.00 0.00 H +ATOM 130 HD11 LEU A 7 35.555 22.083 20.783 1.00 0.00 H +ATOM 131 HD12 LEU A 7 36.173 20.838 21.894 1.00 0.00 H +ATOM 132 HD13 LEU A 7 36.687 22.526 22.073 1.00 0.00 H +ATOM 133 HD21 LEU A 7 38.628 20.086 21.688 1.00 0.00 H +ATOM 134 HD22 LEU A 7 39.703 21.030 20.634 1.00 0.00 H +ATOM 135 HD23 LEU A 7 38.976 21.789 22.046 1.00 0.00 H +ATOM 136 N LYS A 8 37.145 18.594 16.694 1.00 0.00 N +ATOM 137 CA LYS A 8 36.874 17.284 16.065 1.00 0.00 C +ATOM 138 C LYS A 8 38.102 16.648 15.397 1.00 0.00 C +ATOM 139 O LYS A 8 38.179 15.427 15.304 1.00 0.00 O +ATOM 140 CB LYS A 8 35.674 17.378 15.102 1.00 0.00 C +ATOM 141 CG LYS A 8 35.968 18.066 13.757 1.00 0.00 C +ATOM 142 CD LYS A 8 36.216 17.089 12.598 1.00 0.00 C +ATOM 143 CE LYS A 8 36.404 17.876 11.295 1.00 0.00 C +ATOM 144 NZ LYS A 8 35.335 17.592 10.311 1.00 0.00 N +ATOM 145 H LYS A 8 36.577 19.400 16.431 1.00 0.00 H +ATOM 146 HA LYS A 8 36.589 16.597 16.863 1.00 0.00 H +ATOM 147 HB2 LYS A 8 35.333 16.381 14.898 1.00 0.00 H +ATOM 148 HB3 LYS A 8 34.879 17.932 15.603 1.00 0.00 H +ATOM 149 HG2 LYS A 8 35.129 18.685 13.504 1.00 0.00 H +ATOM 150 HG3 LYS A 8 36.836 18.707 13.865 1.00 0.00 H +ATOM 151 HD2 LYS A 8 37.099 16.513 12.798 1.00 0.00 H +ATOM 152 HD3 LYS A 8 35.374 16.401 12.516 1.00 0.00 H +ATOM 153 HE2 LYS A 8 36.396 18.925 11.521 1.00 0.00 H +ATOM 154 HE3 LYS A 8 37.387 17.636 10.877 1.00 0.00 H +ATOM 155 HZ1 LYS A 8 35.277 16.601 10.123 1.00 0.00 H +ATOM 156 HZ2 LYS A 8 34.456 17.951 10.677 1.00 0.00 H +ATOM 157 HZ3 LYS A 8 35.516 18.092 9.453 1.00 0.00 H +ATOM 158 N ASP A 9 39.070 17.468 14.979 1.00 0.00 N +ATOM 159 CA ASP A 9 40.364 17.059 14.429 1.00 0.00 C +ATOM 160 C ASP A 9 41.379 16.611 15.502 1.00 0.00 C +ATOM 161 O ASP A 9 42.443 16.104 15.140 1.00 0.00 O +ATOM 162 CB ASP A 9 40.931 18.236 13.610 1.00 0.00 C +ATOM 163 CG ASP A 9 40.570 18.169 12.124 1.00 0.00 C +ATOM 164 OD1 ASP A 9 39.366 18.024 11.812 1.00 0.00 O +ATOM 165 OD2 ASP A 9 41.525 18.260 11.317 1.00 0.00 O +ATOM 166 H ASP A 9 38.888 18.459 15.043 1.00 0.00 H +ATOM 167 HA ASP A 9 40.217 16.208 13.760 1.00 0.00 H +ATOM 168 HB2 ASP A 9 40.542 19.151 14.014 1.00 0.00 H +ATOM 169 HB3 ASP A 9 42.014 18.238 13.684 1.00 0.00 H +ATOM 170 N GLY A 10 41.083 16.797 16.798 1.00 0.00 N +ATOM 171 CA GLY A 10 41.958 16.457 17.927 1.00 0.00 C +ATOM 172 C GLY A 10 42.526 17.663 18.687 1.00 0.00 C +ATOM 173 O GLY A 10 43.394 17.481 19.542 1.00 0.00 O +ATOM 174 H GLY A 10 40.163 17.167 17.027 1.00 0.00 H +ATOM 175 HA2 GLY A 10 41.384 15.861 18.638 1.00 0.00 H +ATOM 176 HA3 GLY A 10 42.795 15.847 17.586 1.00 0.00 H +ATOM 177 N GLY A 11 42.070 18.888 18.389 1.00 0.00 N +ATOM 178 CA GLY A 11 42.524 20.108 19.057 1.00 0.00 C +ATOM 179 C GLY A 11 44.055 20.273 18.988 1.00 0.00 C +ATOM 180 O GLY A 11 44.608 20.246 17.885 1.00 0.00 O +ATOM 181 H GLY A 11 41.379 18.986 17.653 1.00 0.00 H +ATOM 182 HA2 GLY A 11 42.062 20.966 18.571 1.00 0.00 H +ATOM 183 HA3 GLY A 11 42.178 20.078 20.087 1.00 0.00 H +ATOM 184 N PRO A 12 44.769 20.424 20.128 1.00 0.00 N +ATOM 185 CA PRO A 12 46.231 20.542 20.140 1.00 0.00 C +ATOM 186 C PRO A 12 46.956 19.346 19.499 1.00 0.00 C +ATOM 187 O PRO A 12 48.037 19.513 18.935 1.00 0.00 O +ATOM 188 CB PRO A 12 46.638 20.688 21.613 1.00 0.00 C +ATOM 189 CG PRO A 12 45.358 21.123 22.321 1.00 0.00 C +ATOM 190 CD PRO A 12 44.260 20.460 21.494 1.00 0.00 C +ATOM 191 HA PRO A 12 46.509 21.449 19.601 1.00 0.00 H +ATOM 192 HB2 PRO A 12 46.989 19.752 22.004 1.00 0.00 H +ATOM 193 HB3 PRO A 12 47.429 21.428 21.737 1.00 0.00 H +ATOM 194 HG2 PRO A 12 45.341 20.773 23.335 1.00 0.00 H +ATOM 195 HG3 PRO A 12 45.256 22.208 22.263 1.00 0.00 H +ATOM 196 HD2 PRO A 12 44.071 19.466 21.850 1.00 0.00 H +ATOM 197 HD3 PRO A 12 43.338 21.033 21.580 1.00 0.00 H +ATOM 198 N SER A 13 46.361 18.146 19.539 1.00 0.00 N +ATOM 199 CA SER A 13 46.947 16.896 19.038 1.00 0.00 C +ATOM 200 C SER A 13 46.795 16.706 17.519 1.00 0.00 C +ATOM 201 O SER A 13 46.923 15.587 17.031 1.00 0.00 O +ATOM 202 CB SER A 13 46.356 15.704 19.806 1.00 0.00 C +ATOM 203 OG SER A 13 46.661 15.811 21.184 1.00 0.00 O +ATOM 204 H SER A 13 45.433 18.076 19.947 1.00 0.00 H +ATOM 205 HA SER A 13 48.019 16.916 19.237 1.00 0.00 H +ATOM 206 HB2 SER A 13 45.291 15.693 19.678 1.00 0.00 H +ATOM 207 HB3 SER A 13 46.778 14.773 19.427 1.00 0.00 H +ATOM 208 HG SER A 13 47.605 15.681 21.304 1.00 0.00 H +ATOM 209 N SER A 14 46.535 17.785 16.768 1.00 0.00 N +ATOM 210 CA SER A 14 46.287 17.760 15.319 1.00 0.00 C +ATOM 211 C SER A 14 47.230 18.670 14.511 1.00 0.00 C +ATOM 212 O SER A 14 46.980 18.952 13.341 1.00 0.00 O +ATOM 213 CB SER A 14 44.812 18.082 15.069 1.00 0.00 C +ATOM 214 OG SER A 14 44.329 17.332 13.976 1.00 0.00 O +ATOM 215 H SER A 14 46.407 18.660 17.264 1.00 0.00 H +ATOM 216 HA SER A 14 46.460 16.746 14.956 1.00 0.00 H +ATOM 217 HB2 SER A 14 44.242 17.839 15.945 1.00 0.00 H +ATOM 218 HB3 SER A 14 44.676 19.141 14.877 1.00 0.00 H +ATOM 219 HG SER A 14 43.612 16.751 14.347 1.00 0.00 H +ATOM 220 N GLY A 15 48.317 19.155 15.132 1.00 0.00 N +ATOM 221 CA GLY A 15 49.349 19.959 14.464 1.00 0.00 C +ATOM 222 C GLY A 15 48.882 21.350 14.018 1.00 0.00 C +ATOM 223 O GLY A 15 49.437 21.898 13.067 1.00 0.00 O +ATOM 224 H GLY A 15 48.471 18.865 16.088 1.00 0.00 H +ATOM 225 HA2 GLY A 15 50.195 20.088 15.140 1.00 0.00 H +ATOM 226 HA3 GLY A 15 49.703 19.423 13.582 1.00 0.00 H +ATOM 227 N ARG A 16 47.854 21.911 14.674 1.00 0.00 N +ATOM 228 CA ARG A 16 47.187 23.159 14.280 1.00 0.00 C +ATOM 229 C ARG A 16 46.753 23.991 15.505 1.00 0.00 C +ATOM 230 O ARG A 16 46.120 23.441 16.410 1.00 0.00 O +ATOM 231 CB ARG A 16 46.008 22.832 13.340 1.00 0.00 C +ATOM 232 CG ARG A 16 44.944 21.904 13.956 1.00 0.00 C +ATOM 233 CD ARG A 16 43.821 21.483 12.996 1.00 0.00 C +ATOM 234 NE ARG A 16 44.149 20.264 12.234 1.00 0.00 N +ATOM 235 CZ ARG A 16 44.757 20.161 11.060 1.00 0.00 C +ATOM 236 NH1 ARG A 16 45.187 21.211 10.397 1.00 0.00 N +ATOM 237 NH2 ARG A 16 44.933 18.980 10.525 1.00 0.00 N +ATOM 238 H ARG A 16 47.477 21.399 15.460 1.00 0.00 H +ATOM 239 HA ARG A 16 47.907 23.738 13.704 1.00 0.00 H +ATOM 240 HB2 ARG A 16 45.532 23.753 13.065 1.00 0.00 H +ATOM 241 HB3 ARG A 16 46.422 22.355 12.454 1.00 0.00 H +ATOM 242 HG2 ARG A 16 45.436 21.016 14.303 1.00 0.00 H +ATOM 243 HG3 ARG A 16 44.477 22.423 14.785 1.00 0.00 H +ATOM 244 HD2 ARG A 16 42.931 21.301 13.568 1.00 0.00 H +ATOM 245 HD3 ARG A 16 43.567 22.310 12.331 1.00 0.00 H +ATOM 246 HE ARG A 16 43.861 19.381 12.636 1.00 0.00 H +ATOM 247 HH11 ARG A 16 45.048 22.113 10.813 1.00 0.00 H +ATOM 248 HH12 ARG A 16 45.659 21.113 9.519 1.00 0.00 H +ATOM 249 HH21 ARG A 16 44.547 18.181 11.007 1.00 0.00 H +ATOM 250 HH22 ARG A 16 45.406 18.870 9.650 1.00 0.00 H +ATOM 251 N PRO A 17 47.054 25.305 15.554 1.00 0.00 N +ATOM 252 CA PRO A 17 46.680 26.163 16.679 1.00 0.00 C +ATOM 253 C PRO A 17 45.159 26.406 16.729 1.00 0.00 C +ATOM 254 O PRO A 17 44.484 26.240 15.710 1.00 0.00 O +ATOM 255 CB PRO A 17 47.452 27.469 16.453 1.00 0.00 C +ATOM 256 CG PRO A 17 47.575 27.549 14.933 1.00 0.00 C +ATOM 257 CD PRO A 17 47.718 26.085 14.518 1.00 0.00 C +ATOM 258 HA PRO A 17 47.005 25.703 17.613 1.00 0.00 H +ATOM 259 HB2 PRO A 17 46.907 28.309 16.839 1.00 0.00 H +ATOM 260 HB3 PRO A 17 48.446 27.383 16.895 1.00 0.00 H +ATOM 261 HG2 PRO A 17 46.698 27.989 14.498 1.00 0.00 H +ATOM 262 HG3 PRO A 17 48.438 28.141 14.627 1.00 0.00 H +ATOM 263 HD2 PRO A 17 47.247 25.919 13.568 1.00 0.00 H +ATOM 264 HD3 PRO A 17 48.774 25.814 14.479 1.00 0.00 H +ATOM 265 N PRO A 18 44.608 26.814 17.889 1.00 0.00 N +ATOM 266 CA PRO A 18 43.185 27.106 18.020 1.00 0.00 C +ATOM 267 C PRO A 18 42.799 28.380 17.247 1.00 0.00 C +ATOM 268 O PRO A 18 43.582 29.331 17.205 1.00 0.00 O +ATOM 269 CB PRO A 18 42.933 27.265 19.521 1.00 0.00 C +ATOM 270 CG PRO A 18 44.283 27.730 20.063 1.00 0.00 C +ATOM 271 CD PRO A 18 45.291 27.024 19.157 1.00 0.00 C +ATOM 272 HA PRO A 18 42.617 26.256 17.650 1.00 0.00 H +ATOM 273 HB2 PRO A 18 42.172 27.999 19.706 1.00 0.00 H +ATOM 274 HB3 PRO A 18 42.679 26.298 19.952 1.00 0.00 H +ATOM 275 HG2 PRO A 18 44.380 28.796 19.988 1.00 0.00 H +ATOM 276 HG3 PRO A 18 44.416 27.452 21.109 1.00 0.00 H +ATOM 277 HD2 PRO A 18 46.160 27.637 19.016 1.00 0.00 H +ATOM 278 HD3 PRO A 18 45.560 26.058 19.587 1.00 0.00 H +ATOM 279 N PRO A 19 41.586 28.435 16.670 1.00 0.00 N +ATOM 280 CA PRO A 19 41.083 29.618 15.981 1.00 0.00 C +ATOM 281 C PRO A 19 40.613 30.682 16.989 1.00 0.00 C +ATOM 282 O PRO A 19 39.774 30.399 17.847 1.00 0.00 O +ATOM 283 CB PRO A 19 39.946 29.089 15.105 1.00 0.00 C +ATOM 284 CG PRO A 19 39.379 27.927 15.922 1.00 0.00 C +ATOM 285 CD PRO A 19 40.614 27.350 16.606 1.00 0.00 C +ATOM 286 HA PRO A 19 41.859 30.041 15.343 1.00 0.00 H +ATOM 287 HB2 PRO A 19 39.201 29.845 14.945 1.00 0.00 H +ATOM 288 HB3 PRO A 19 40.361 28.705 14.172 1.00 0.00 H +ATOM 289 HG2 PRO A 19 38.666 28.276 16.644 1.00 0.00 H +ATOM 290 HG3 PRO A 19 38.879 27.189 15.293 1.00 0.00 H +ATOM 291 HD2 PRO A 19 40.368 27.012 17.594 1.00 0.00 H +ATOM 292 HD3 PRO A 19 41.019 26.536 16.005 1.00 0.00 H +ATOM 293 N SER A 20 41.169 31.897 16.883 1.00 0.00 N +ATOM 294 CA SER A 20 40.750 33.102 17.619 1.00 0.00 C +ATOM 295 C SER A 20 39.492 33.732 17.017 1.00 0.00 C +ATOM 296 O SER A 20 39.511 33.991 15.794 1.00 0.00 O +ATOM 297 CB SER A 20 41.870 34.146 17.618 1.00 0.00 C +ATOM 298 OG SER A 20 43.018 33.616 18.245 1.00 0.00 O +ATOM 299 OXT SER A 20 38.557 33.978 17.807 1.00 0.00 O +ATOM 300 H SER A 20 41.867 32.036 16.169 1.00 0.00 H +ATOM 301 HA SER A 20 40.499 32.835 18.644 1.00 0.00 H +ATOM 302 HB2 SER A 20 42.108 34.413 16.606 1.00 0.00 H +ATOM 303 HB3 SER A 20 41.534 35.034 18.158 1.00 0.00 H +ATOM 304 HG SER A 20 42.729 33.115 19.010 1.00 0.00 H +TER +HETATM 305 C1 BEN B 21 39.867 33.011 36.900 1.00 0.00 C +HETATM 306 C2 BEN B 21 40.534 32.219 37.826 1.00 0.00 C +HETATM 307 C3 BEN B 21 41.748 32.641 38.356 1.00 0.00 C +HETATM 308 C4 BEN B 21 42.294 33.857 37.959 1.00 0.00 C +HETATM 309 C5 BEN B 21 41.626 34.649 37.033 1.00 0.00 C +HETATM 310 C6 BEN B 21 40.412 34.227 36.503 1.00 0.00 C +HETATM 311 C7 BEN B 21 38.557 32.555 36.328 1.00 0.00 C +HETATM 312 N1 BEN B 21 38.039 31.396 36.708 1.00 0.00 N +HETATM 313 N2 BEN B 21 37.922 33.314 35.445 1.00 0.00 N +END diff --git a/regtest/basic/rt-molinfo-whole-ligand/traj.gro b/regtest/basic/rt-molinfo-whole-ligand/traj.gro new file mode 100644 index 0000000000..241a7f60de --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-ligand/traj.gro @@ -0,0 +1,948 @@ +trp-cage and a ligand nearer a periodic image of the protein + 313 + 1ASN N 1 5.100 1.565 3.211 + 1ASN CA 2 5.129 1.466 3.105 + 1ASN C 3 5.278 1.449 3.077 + 1ASN O 4 5.326 1.338 3.091 + 1ASN CB 5 5.046 1.492 2.977 + 1ASN CG 6 4.898 1.466 3.005 + 1ASN OD1 7 4.863 1.423 3.114 + 1ASN ND2 8 4.809 1.493 2.912 + 1ASN H1 9 3.157 0.394 0.027 + 1ASN H2 10 5.116 1.660 3.177 + 1ASN H3 11 5.002 1.557 3.237 + 1ASN HA 12 5.097 1.369 3.142 + 1ASN HB2 13 5.059 1.594 2.947 + 1ASN HB3 14 5.079 1.425 2.898 + 1ASN HD21 15 4.833 1.532 2.822 + 1ASN HD22 16 4.714 1.471 2.937 + 2LEU N 17 5.352 1.556 3.044 + 2LEU CA 18 5.497 1.553 3.021 + 2LEU C 19 5.576 1.471 3.126 + 2LEU O 20 5.651 1.380 3.090 + 2LEU CB 21 5.549 1.698 3.004 + 2LEU CG 22 5.510 1.798 3.117 + 2LEU CD1 23 5.629 1.833 3.206 + 2LEU CD2 24 5.455 1.928 3.058 + 2LEU H 25 5.308 1.645 3.027 + 2LEU HA 26 5.515 1.502 2.926 + 2LEU HB2 27 5.656 1.694 2.999 + 2LEU HB3 28 5.509 1.734 2.910 + 2LEU HG 29 5.433 1.755 3.181 + 2LEU HD11 30 5.669 1.743 3.252 + 2LEU HD12 31 5.706 1.883 3.148 + 2LEU HD13 32 3.597 0.746 0.020 + 2LEU HD21 33 5.529 1.974 2.993 + 2LEU HD22 34 5.364 1.907 3.001 + 2LEU HD23 35 5.431 1.997 3.138 + 3TYR N 36 5.554 1.498 3.255 + 3TYR CA 37 3.621 0.272 0.099 + 3TYR C 38 3.580 0.124 0.108 + 3TYR O 39 5.661 3.503 0.145 + 3TYR CB 40 3.593 0.345 0.231 + 3TYR CG 41 3.707 0.332 0.329 + 3TYR CD1 42 3.715 0.220 0.414 + 3TYR CD2 43 3.808 0.431 0.334 + 3TYR CE1 44 3.824 0.206 0.502 + 3TYR CE2 45 3.917 0.417 0.421 + 3TYR CZ 46 3.926 0.303 0.505 + 3TYR OH 47 4.033 0.286 0.587 + 3TYR H 48 3.496 0.423 0.012 + 3TYR HA 49 3.728 0.275 0.080 + 3TYR HB2 50 3.578 0.449 0.210 + 3TYR HB3 51 3.501 0.308 0.275 + 3TYR HD1 52 5.638 3.608 0.411 + 3TYR HD2 53 3.802 0.518 0.270 + 3TYR HE1 54 5.832 3.584 0.567 + 3TYR HE2 55 3.993 0.493 0.424 + 3TYR HH 56 4.109 0.338 0.557 + 4ILE N 57 3.456 0.091 0.069 + 4ILE CA 58 5.404 3.417 0.062 + 4ILE C 59 7.481 4.495 3.219 + 4ILE O 60 7.528 4.384 3.244 + 4ILE CB 61 5.251 3.416 0.035 + 4ILE CG1 62 3.170 0.052 0.120 + 4ILE CG2 63 5.194 3.274 0.051 + 4ILE CD1 64 5.188 3.503 0.272 + 4ILE H 65 3.399 0.164 0.029 + 4ILE HA 66 5.423 3.368 0.157 + 4ILE HB 67 5.234 1.134 3.197 + 4ILE HG12 68 3.200 0.151 0.092 + 4ILE HG13 69 3.064 0.040 0.097 + 4ILE HG21 70 7.239 4.361 3.243 + 4ILE HG22 71 5.214 3.235 0.151 + 4ILE HG23 72 5.086 3.275 0.034 + 4ILE HD11 73 5.159 3.404 0.305 + 4ILE HD12 74 5.292 3.523 0.300 + 4ILE HD13 75 5.124 3.577 0.322 + 5GLN N 76 7.499 4.557 3.102 + 5GLN CA 77 7.578 4.500 2.992 + 5GLN C 78 7.727 4.485 3.027 + 5GLN O 79 3.791 4.393 2.978 + 5GLN CB 80 5.561 1.121 2.865 + 5GLN CG 81 5.565 1.036 2.737 + 5GLN CD 82 5.432 0.967 2.708 + 5GLN OE1 83 7.413 4.313 2.733 + 5GLN NE2 84 5.337 1.038 2.651 + 5GLN H 85 5.457 1.185 3.090 + 5GLN HA 86 7.538 4.401 2.972 + 5GLN HB2 87 5.466 1.172 2.869 + 5GLN HB3 88 5.641 1.196 2.861 + 5GLN HG2 89 5.590 1.099 2.654 + 5GLN HG3 90 7.644 4.425 2.746 + 5GLN HE21 91 5.351 1.134 2.626 + 5GLN HE22 92 5.251 0.989 2.633 + 6TRP N 93 5.782 1.107 3.114 + 6TRP CA 94 7.918 4.554 3.167 + 6TRP C 95 1.927 3.286 0.005 + 6TRP O 96 2.019 3.204 0.000 + 6TRP CB 97 5.968 1.223 3.225 + 6TRP CG 98 0.105 0.063 0.020 + 6TRP CD1 99 2.222 1.219 3.218 + 6TRP CD2 100 2.141 3.519 0.161 + 6TRP NE1 101 0.327 0.054 0.042 + 6TRP CE2 102 2.283 3.514 0.171 + 6TRP CE3 103 6.068 3.515 0.282 + 6TRP CZ2 104 2.350 3.507 0.294 + 6TRP CZ3 105 6.134 3.506 0.406 + 6TRP CH2 106 2.274 3.503 0.412 + 6TRP H 107 5.727 1.187 3.142 + 6TRP HA 108 3.985 4.526 3.085 + 6TRP HB2 109 5.969 1.295 3.145 + 6TRP HB3 110 3.898 0.102 0.035 + 6TRP HD1 111 2.231 1.226 3.111 + 6TRP HE1 112 0.426 0.052 0.016 + 6TRP HE3 113 5.960 3.519 0.278 + 6TRP HZ2 114 2.458 3.504 0.297 + 6TRP HZ3 115 6.076 3.502 0.497 + 6TRP HH2 116 2.323 3.498 0.509 + 7LEU N 117 5.830 3.276 0.097 + 7LEU CA 118 5.826 3.169 0.197 + 7LEU C 119 1.805 3.030 0.135 + 7LEU O 120 1.875 2.937 0.175 + 7LEU CB 121 5.719 3.198 0.304 + 7LEU CG 122 5.760 3.304 0.407 + 7LEU CD1 123 5.642 3.330 0.502 + 7LEU CD2 124 5.881 3.262 0.492 + 7LEU H 125 5.758 3.349 0.100 + 7LEU HA 126 5.923 3.164 0.245 + 7LEU HB2 127 5.630 3.231 0.254 + 7LEU HB3 128 5.698 3.105 0.358 + 7LEU HG 129 5.784 3.397 0.356 + 7LEU HD11 130 5.556 3.363 0.445 + 7LEU HD12 131 5.617 3.239 0.556 + 7LEU HD13 132 5.669 3.407 0.574 + 7LEU HD21 133 5.863 3.163 0.536 + 7LEU HD22 134 5.970 3.258 0.430 + 7LEU HD23 135 5.898 3.334 0.572 + 8LYS N 136 5.715 3.014 0.036 + 8LYS CA 137 3.687 4.038 3.239 + 8LYS C 138 3.810 3.974 3.173 + 8LYS O 139 3.818 3.852 3.163 + 8LYS CB 140 7.567 4.047 3.143 + 8LYS CG 141 7.597 4.116 3.009 + 8LYS CD 142 3.622 4.018 2.893 + 8LYS CE 143 3.640 4.097 2.762 + 8LYS NZ 144 3.534 4.069 2.664 + 8LYS H 145 5.658 3.095 0.010 + 8LYS HA 146 1.659 2.814 0.053 + 8LYS HB2 147 7.533 3.948 3.123 + 8LYS HB3 148 7.488 4.103 3.193 + 8LYS HG2 149 7.513 4.178 2.983 + 8LYS HG3 150 3.684 4.180 3.019 + 8LYS HD2 151 3.710 3.961 2.913 + 8LYS HD3 152 3.537 3.950 2.885 + 8LYS HE2 153 3.640 4.202 2.785 + 8LYS HE3 154 3.739 4.073 2.721 + 8LYS HZ1 155 3.528 3.970 2.645 + 8LYS HZ2 156 7.446 4.105 2.701 + 8LYS HZ3 157 3.552 4.119 2.578 + 9ASP N 158 3.907 4.056 3.131 + 9ASP CA 159 4.036 4.015 3.076 + 9ASP C 160 4.138 3.971 3.183 + 9ASP O 161 4.244 3.920 3.147 + 9ASP CB 162 4.093 4.133 2.994 + 9ASP CG 163 4.057 4.126 2.845 + 9ASP OD1 164 3.937 4.112 2.814 + 9ASP OD2 165 4.153 4.135 2.765 + 9ASP H 166 3.889 4.155 3.137 + 9ASP HA 167 4.022 3.930 3.009 + 9ASP HB2 168 4.054 4.225 3.034 + 9ASP HB3 169 4.201 4.133 3.001 + 10GLY N 170 2.108 2.834 0.047 + 10GLY CA 171 2.196 2.800 0.160 + 10GLY C 172 2.253 2.921 0.236 + 10GLY O 173 2.339 2.903 0.321 + 10GLY H 174 2.016 2.871 0.070 + 10GLY HA2 175 2.138 2.741 0.231 + 10GLY HA3 176 2.280 2.739 0.126 + 11GLY N 177 2.207 3.044 0.206 + 11GLY CA 178 2.252 3.166 0.273 + 11GLY C 179 2.406 3.182 0.266 + 11GLY O 180 2.461 3.179 0.156 + 11GLY H 181 2.138 3.053 0.132 + 11GLY HA2 182 2.206 3.251 0.224 + 11GLY HA3 183 2.218 3.163 0.376 + 12PRO N 184 2.477 3.197 0.380 + 12PRO CA 185 2.623 3.209 0.381 + 12PRO C 186 2.696 3.089 0.317 + 12PRO O 187 2.804 3.106 0.261 + 12PRO CB 188 2.664 3.224 0.528 + 12PRO CG 189 2.536 3.267 0.599 + 12PRO CD 190 2.426 3.201 0.516 + 12PRO HA 191 2.651 3.300 0.327 + 12PRO HB2 192 2.699 3.130 0.567 + 12PRO HB3 193 2.743 3.298 0.541 + 12PRO HG2 194 2.534 3.232 0.701 + 12PRO HG3 195 2.526 3.376 0.593 + 12PRO HD2 196 2.407 3.101 0.552 + 12PRO HD3 197 2.334 3.258 0.525 + 13SER N 198 2.636 2.969 0.321 + 13SER CA 199 2.695 2.844 0.271 + 13SER C 200 2.680 2.825 0.119 + 13SER O 201 2.692 2.713 0.070 + 13SER CB 202 2.636 2.725 0.348 + 13SER OG 203 2.666 2.736 0.485 + 13SER H 204 2.543 2.962 0.362 + 13SER HA 205 2.802 2.846 0.291 + 13SER HB2 206 2.529 2.724 0.335 + 13SER HB3 207 2.678 2.632 0.310 + 13SER HG 208 2.760 2.723 0.497 + 14SER N 209 2.653 2.933 0.044 + 14SER CA 210 4.629 4.085 3.165 + 14SER C 211 4.723 4.176 3.084 + 14SER O 212 4.698 4.205 2.967 + 14SER CB 213 4.481 4.118 3.140 + 14SER OG 214 4.433 4.043 3.031 + 14SER H 215 2.641 3.021 0.093 + 14SER HA 216 4.646 3.984 3.129 + 14SER HB2 217 4.424 4.093 3.227 + 14SER HB3 218 4.468 4.224 3.121 + 14SER HG 219 4.361 3.985 3.068 + 15GLY N 220 4.832 4.225 3.146 + 15GLY CA 221 4.935 4.305 3.079 + 15GLY C 222 4.888 4.444 3.035 + 15GLY O 223 4.944 4.499 2.940 + 15GLY H 224 4.847 4.196 3.242 + 15GLY HA2 225 5.019 4.318 3.147 + 15GLY HA3 226 4.970 4.252 2.991 + 16ARG N 227 4.785 4.501 3.100 + 16ARG CA 228 2.719 1.161 3.061 + 16ARG C 229 2.675 1.244 3.183 + 16ARG O 230 0.612 0.035 0.008 + 16ARG CB 231 2.601 1.128 2.967 + 16ARG CG 232 4.494 4.500 3.029 + 16ARG CD 233 4.382 4.458 2.933 + 16ARG NE 234 4.415 4.336 2.856 + 16ARG CZ 235 4.476 4.326 2.739 + 16ARG NH1 236 2.519 0.966 2.673 + 16ARG NH2 237 4.493 4.207 2.685 + 16ARG H 238 4.748 4.449 3.179 + 16ARG HA 239 2.791 1.219 3.003 + 16ARG HB2 240 2.553 1.221 2.939 + 16ARG HB3 241 2.642 1.081 2.878 + 16ARG HG2 242 4.544 4.411 3.063 + 16ARG HG3 243 4.448 4.552 3.111 + 16ARG HD2 244 4.293 4.440 2.990 + 16ARG HD3 245 2.357 1.076 2.866 + 16ARG HE 246 4.386 4.248 2.897 + 16ARG HH11 247 2.505 1.057 2.714 + 16ARG HH12 248 2.566 0.957 2.585 + 16ARG HH21 249 4.455 4.128 2.734 + 16ARG HH22 250 4.541 4.196 2.598 + 17PRO N 251 2.705 1.376 3.188 + 17PRO CA 252 0.668 0.307 0.035 + 17PRO C 253 0.516 0.331 0.040 + 17PRO O 254 2.448 1.469 3.204 + 17PRO CB 255 0.745 0.437 0.012 + 17PRO CG 256 2.757 1.600 3.126 + 17PRO CD 257 2.772 1.454 3.085 + 17PRO HA 258 0.700 0.261 0.128 + 17PRO HB2 259 0.691 0.521 0.051 + 17PRO HB3 260 0.845 0.429 0.057 + 17PRO HG2 261 2.670 1.644 3.083 + 17PRO HG3 262 2.844 1.659 3.096 + 17PRO HD2 263 2.725 1.437 2.990 + 17PRO HD3 264 2.877 1.427 3.081 + 18PRO N 265 0.461 0.372 0.156 + 18PRO CA 266 0.318 0.401 0.169 + 18PRO C 267 4.280 0.529 0.092 + 18PRO O 268 4.358 0.624 0.088 + 18PRO CB 269 4.293 0.417 0.319 + 18PRO CG 270 0.428 0.464 0.373 + 18PRO CD 271 0.529 0.393 0.283 + 18PRO HA 272 0.262 0.316 0.132 + 18PRO HB2 273 4.217 0.490 0.338 + 18PRO HB3 274 4.268 0.320 0.362 + 18PRO HG2 275 4.438 0.570 0.366 + 18PRO HG3 276 4.442 0.436 0.478 + 18PRO HD2 277 0.616 0.454 0.269 + 18PRO HD3 278 0.556 0.296 0.326 + 19PRO N 279 4.159 0.534 0.034 + 19PRO CA 280 6.108 1.807 3.231 + 19PRO C 281 4.061 0.759 0.066 + 19PRO O 282 3.977 0.730 0.152 + 19PRO CB 283 5.995 1.754 3.143 + 19PRO CG 284 5.938 1.638 3.225 + 19PRO CD 285 4.061 0.426 0.028 + 19PRO HA 286 6.186 1.849 3.167 + 19PRO HB2 287 5.920 1.830 3.127 + 19PRO HB3 288 6.036 1.716 3.050 + 19PRO HG2 289 3.867 0.518 0.031 + 19PRO HG3 290 5.888 1.564 3.162 + 19PRO HD2 291 4.037 0.392 0.126 + 19PRO HD3 292 6.102 1.499 3.233 + 20SER N 293 4.117 0.880 0.055 + 20SER CA 294 4.075 1.001 0.129 + 20SER C 295 3.949 1.064 0.069 + 20SER O 296 5.951 2.244 3.212 + 20SER CB 297 4.187 1.105 0.129 + 20SER OG 298 4.302 1.052 0.192 + 20SER OXT 299 3.856 1.088 0.148 + 20SER H 300 6.187 2.049 3.250 + 20SER HA 301 4.050 0.974 0.231 + 20SER HB2 302 4.211 1.132 0.028 + 20SER HB3 303 4.153 1.194 0.183 + 20SER HG 304 4.273 1.002 0.268 + 21BEN C1 305 3.987 0.992 2.057 + 21BEN C2 306 4.053 0.912 2.150 + 21BEN C3 307 4.175 0.955 2.203 + 21BEN C4 308 4.229 1.076 2.163 + 21BEN C5 309 4.163 1.155 2.070 + 21BEN C6 310 4.041 1.113 2.017 + 21BEN C7 311 3.856 0.946 2.000 + 21BEN N1 312 3.804 0.830 2.038 + 21BEN N2 313 3.792 1.022 1.912 + 4.00000 3.46410 3.26599 0.00000 0.00000 2.00000 0.00000 2.00000 1.15470 +trp-cage and a ligand nearer a periodic image of the protein + 313 + 1ASN N 1 4.311 1.790 2.862 + 1ASN CA 2 4.388 1.679 2.773 + 1ASN C 3 4.481 1.666 2.737 + 1ASN O 4 4.541 1.578 2.784 + 1ASN CB 5 4.258 1.727 2.664 + 1ASN CG 6 4.121 1.683 2.684 + 1ASN OD1 7 4.028 1.674 2.800 + 1ASN ND2 8 3.993 1.726 2.617 + 1ASN H1 9 4.362 1.794 2.978 + 1ASN H2 10 4.350 1.857 2.823 + 1ASN H3 11 4.184 1.773 2.888 + 1ASN HA 12 4.301 1.604 2.805 + 1ASN HB2 13 4.226 1.808 2.638 + 1ASN HB3 14 4.292 1.634 2.560 + 1ASN HD21 15 4.039 1.769 2.550 + 1ASN HD22 16 3.902 1.679 2.603 + 2LEU N 17 4.536 1.806 2.764 + 2LEU CA 18 4.723 1.806 2.691 + 2LEU C 19 4.734 1.689 2.813 + 2LEU O 20 4.880 1.599 2.794 + 2LEU CB 21 4.719 1.961 2.682 + 2LEU CG 22 4.732 2.046 2.812 + 2LEU CD1 23 4.831 2.068 2.892 + 2LEU CD2 24 4.615 2.164 2.755 + 2LEU H 25 4.520 1.880 2.728 + 2LEU HA 26 4.699 1.729 2.576 + 2LEU HB2 27 4.864 1.924 2.657 + 2LEU HB3 28 4.666 1.961 2.613 + 2LEU HG 29 4.659 1.987 2.832 + 2LEU HD11 30 4.889 1.991 2.946 + 2LEU HD12 31 4.875 2.155 2.847 + 2LEU HD13 32 4.785 2.136 2.951 + 2LEU HD21 33 4.730 2.190 2.665 + 2LEU HD22 34 4.572 2.148 2.646 + 2LEU HD23 35 4.620 2.228 2.807 + 3TYR N 36 4.760 1.715 2.899 + 3TYR CA 37 4.800 1.653 3.077 + 3TYR C 38 4.801 1.524 3.040 + 3TYR O 39 4.864 1.425 3.099 + 3TYR CB 40 4.789 1.721 3.198 + 3TYR CG 41 4.928 1.669 3.255 + 3TYR CD1 42 2.886 0.461 0.097 + 3TYR CD2 43 3.001 0.662 0.047 + 3TYR CE1 44 3.003 0.408 0.196 + 3TYR CE2 45 3.116 0.671 0.081 + 3TYR CZ 46 3.113 0.523 0.196 + 3TYR OH 47 3.236 0.499 0.232 + 3TYR H 48 4.704 1.836 2.940 + 3TYR HA 49 4.944 1.655 3.041 + 3TYR HB2 50 4.773 1.843 3.168 + 3TYR HB3 51 4.681 1.699 3.206 + 3TYR HD1 52 2.803 0.369 0.088 + 3TYR HD2 53 5.045 1.903 3.210 + 3TYR HE1 54 3.037 0.354 0.235 + 3TYR HE2 55 3.172 0.728 0.065 + 3TYR HH 56 3.275 0.577 0.243 + 4ILE N 57 4.659 1.511 3.049 + 4ILE CA 58 4.595 1.324 3.029 + 4ILE C 59 4.671 1.265 2.866 + 4ILE O 60 4.716 1.126 2.923 + 4ILE CB 61 4.445 1.335 2.957 + 4ILE CG1 62 4.337 1.465 3.068 + 4ILE CG2 63 4.379 1.189 2.979 + 4ILE CD1 64 4.391 1.428 3.201 + 4ILE H 65 4.588 1.567 2.968 + 4ILE HA 66 4.631 1.275 3.118 + 4ILE HB 67 4.431 1.361 2.849 + 4ILE HG12 68 4.399 1.540 3.039 + 4ILE HG13 69 4.284 1.439 3.055 + 4ILE HG21 70 4.467 1.102 2.921 + 4ILE HG22 71 4.421 1.130 3.072 + 4ILE HG23 72 4.308 1.196 3.008 + 4ILE HD11 73 4.390 1.320 3.257 + 4ILE HD12 74 2.516 0.308 0.004 + 4ILE HD13 75 2.282 0.319 0.005 + 5GLN N 76 4.683 1.323 2.779 + 5GLN CA 77 4.770 1.262 2.648 + 5GLN C 78 4.931 1.256 2.716 + 5GLN O 79 4.996 1.201 2.592 + 5GLN CB 80 4.773 1.373 2.550 + 5GLN CG 81 4.772 1.255 2.407 + 5GLN CD 82 4.636 1.219 2.395 + 5GLN OE1 83 4.593 1.108 2.408 + 5GLN NE2 84 4.547 1.275 2.304 + 5GLN H 85 4.655 1.403 2.718 + 5GLN HA 86 4.706 1.185 2.645 + 5GLN HB2 87 4.669 1.408 2.510 + 5GLN HB3 88 4.860 1.454 2.502 + 5GLN HG2 89 4.797 1.357 2.346 + 5GLN HG3 90 4.832 1.194 2.439 + 5GLN HE21 91 4.555 1.360 2.278 + 5GLN HE22 92 4.464 1.219 2.290 + 6TRP N 93 4.973 1.398 2.778 + 6TRP CA 94 5.108 1.347 2.870 + 6TRP C 95 5.114 1.205 2.923 + 6TRP O 96 5.224 1.083 2.945 + 6TRP CB 97 5.131 1.455 2.875 + 6TRP CG 98 5.324 1.462 2.960 + 6TRP CD1 99 5.433 1.439 2.893 + 6TRP CD2 100 5.314 1.447 3.112 + 6TRP NE1 101 5.543 1.460 3.003 + 6TRP CE2 102 5.510 1.439 3.101 + 6TRP CE3 103 5.262 1.464 3.203 + 6TRP CZ2 104 5.563 1.433 3.228 + 6TRP CZ3 105 3.345 0.272 0.078 + 6TRP CH2 106 3.437 0.298 0.097 + 6TRP H 107 4.965 1.400 2.807 + 6TRP HA 108 5.183 1.280 2.727 + 6TRP HB2 109 5.172 1.510 2.852 + 6TRP HB3 110 5.108 1.470 2.966 + 6TRP HD1 111 5.466 1.477 2.744 + 6TRP HE1 112 5.660 1.445 2.975 + 6TRP HE3 113 5.159 1.417 3.205 + 6TRP HZ2 114 5.656 1.409 3.236 + 6TRP HZ3 115 3.284 0.311 0.133 + 6TRP HH2 116 3.499 0.281 0.204 + 7LEU N 117 5.033 1.186 3.016 + 7LEU CA 118 7.027 4.552 3.137 + 7LEU C 119 7.035 4.401 3.074 + 7LEU O 120 7.028 4.352 3.098 + 7LEU CB 121 6.915 4.593 3.204 + 7LEU CG 122 2.935 0.050 0.076 + 7LEU CD1 123 2.851 0.078 0.167 + 7LEU CD2 124 5.080 3.494 0.169 + 7LEU H 125 4.973 1.262 3.063 + 7LEU HA 126 7.135 4.538 3.204 + 7LEU HB2 127 4.856 1.144 3.193 + 7LEU HB3 128 4.913 3.355 0.030 + 7LEU HG 129 3.001 0.190 0.046 + 7LEU HD11 130 2.766 0.113 0.125 + 7LEU HD12 131 4.855 3.430 0.227 + 7LEU HD13 132 2.876 0.199 0.244 + 7LEU HD21 133 5.072 3.412 0.221 + 7LEU HD22 134 5.168 3.488 0.107 + 7LEU HD23 135 3.073 0.107 0.223 + 8LYS N 136 6.895 4.393 3.029 + 8LYS CA 137 6.891 4.265 2.905 + 8LYS C 138 7.051 4.162 2.853 + 8LYS O 139 7.005 4.087 2.862 + 8LYS CB 140 6.771 4.253 2.821 + 8LYS CG 141 6.795 4.335 2.673 + 8LYS CD 142 6.813 4.267 2.542 + 8LYS CE 143 4.855 0.873 2.400 + 8LYS NZ 144 4.798 0.857 2.343 + 8LYS H 145 6.877 4.470 2.918 + 8LYS HA 146 6.880 4.192 3.011 + 8LYS HB2 147 6.710 4.184 2.813 + 8LYS HB3 148 6.676 4.308 2.844 + 8LYS HG2 149 4.679 0.968 2.667 + 8LYS HG3 150 6.893 4.395 2.692 + 8LYS HD2 151 6.939 4.197 2.547 + 8LYS HD3 152 6.771 4.214 2.575 + 8LYS HE2 153 4.865 1.015 2.436 + 8LYS HE3 154 4.979 0.875 2.401 + 8LYS HZ1 155 6.764 4.181 2.317 + 8LYS HZ2 156 4.661 0.873 2.365 + 8LYS HZ3 157 4.738 0.860 2.250 + 9ASP N 158 7.118 4.283 2.773 + 9ASP CA 159 7.222 4.240 2.789 + 9ASP C 160 7.313 4.216 2.860 + 9ASP O 161 7.476 4.192 2.838 + 9ASP CB 162 7.313 4.335 2.676 + 9ASP CG 163 5.276 0.913 2.504 + 9ASP OD1 164 7.136 4.340 2.479 + 9ASP OD2 165 7.347 4.326 2.455 + 9ASP H 166 7.118 4.391 2.788 + 9ASP HA 167 7.250 4.167 2.634 + 9ASP HB2 168 5.273 0.988 2.737 + 9ASP HB3 169 7.379 4.351 2.684 + 10GLY N 170 7.329 4.194 2.963 + 10GLY CA 171 7.400 4.172 3.140 + 10GLY C 172 7.455 4.285 3.213 + 10GLY O 173 5.552 3.113 0.012 + 10GLY H 174 7.243 4.232 3.017 + 10GLY HA2 175 7.327 4.151 3.163 + 10GLY HA3 176 7.492 4.104 3.096 + 11GLY N 177 7.428 4.459 3.158 + 11GLY CA 178 7.404 4.530 3.205 + 11GLY C 179 7.587 4.581 3.189 + 11GLY O 180 5.688 1.151 3.099 + 11GLY H 181 7.336 4.425 3.050 + 11GLY HA2 182 5.416 1.196 3.148 + 11GLY HA3 183 5.412 3.392 0.056 + 12PRO N 184 5.686 3.434 0.063 + 12PRO CA 185 5.838 3.433 0.036 + 12PRO C 186 7.884 4.462 3.257 + 12PRO O 187 4.010 4.483 3.183 + 12PRO CB 188 5.839 3.445 0.205 + 12PRO CG 189 5.743 3.508 0.273 + 12PRO CD 190 5.625 3.444 0.197 + 12PRO HA 191 3.868 0.064 0.032 + 12PRO HB2 192 5.885 3.354 0.263 + 12PRO HB3 193 5.939 3.521 0.245 + 12PRO HG2 194 5.701 3.490 0.389 + 12PRO HG3 195 3.725 0.099 0.247 + 12PRO HD2 196 5.605 3.339 0.256 + 12PRO HD3 197 5.537 3.509 0.218 + 13SER N 198 5.825 3.238 0.014 + 13SER CA 199 3.879 4.233 3.206 + 13SER C 200 3.867 4.169 3.073 + 13SER O 201 3.884 4.130 3.009 + 13SER CB 202 1.833 2.972 0.014 + 13SER OG 203 1.887 2.936 0.151 + 13SER H 204 5.753 3.177 0.041 + 13SER HA 205 3.991 4.223 3.243 + 13SER HB2 206 5.739 2.994 0.038 + 13SER HB3 207 3.911 3.998 3.222 + 13SER HG 208 1.970 2.949 0.166 + 14SER N 209 3.886 4.318 3.000 + 14SER CA 210 3.857 4.319 2.830 + 14SER C 211 3.880 4.393 2.760 + 14SER O 212 1.907 0.975 2.676 + 14SER CB 213 7.667 4.388 2.797 + 14SER OG 214 3.599 4.268 2.698 + 14SER H 215 3.837 4.385 3.041 + 14SER HA 216 3.831 4.176 2.819 + 14SER HB2 217 7.661 4.360 2.884 + 14SER HB3 218 5.656 1.019 2.810 + 14SER HG 219 3.584 4.209 2.757 + 15GLY N 220 4.017 4.435 2.831 + 15GLY CA 221 2.165 1.067 2.736 + 15GLY C 222 2.064 1.188 2.685 + 15GLY O 223 2.112 1.268 2.619 + 15GLY H 224 4.052 4.421 2.938 + 15GLY HA2 225 2.203 1.070 2.797 + 15GLY HA3 226 2.159 1.010 2.672 + 16ARG N 227 1.984 1.282 2.766 + 16ARG CA 228 1.930 1.394 2.711 + 16ARG C 229 5.879 1.493 2.869 + 16ARG O 230 5.827 1.449 2.960 + 16ARG CB 231 5.806 1.340 2.611 + 16ARG CG 232 5.696 1.310 2.695 + 16ARG CD 233 5.591 1.209 2.619 + 16ARG NE 234 5.607 1.082 2.554 + 16ARG CZ 235 1.690 1.073 2.403 + 16ARG NH1 236 1.707 1.185 2.382 + 16ARG NH2 237 1.672 0.973 2.392 + 16ARG H 238 1.946 1.191 2.841 + 16ARG HA 239 2.020 1.452 2.657 + 16ARG HB2 240 5.764 1.459 2.619 + 16ARG HB3 241 1.851 1.276 2.547 + 16ARG HG2 242 5.716 1.190 2.736 + 16ARG HG3 243 5.669 1.306 2.781 + 16ARG HD2 244 5.521 1.257 2.684 + 16ARG HD3 245 5.555 1.326 2.560 + 16ARG HE 246 5.578 0.996 2.551 + 16ARG HH11 247 5.653 1.285 2.423 + 16ARG HH12 248 1.783 1.183 2.330 + 16ARG HH21 249 1.660 0.904 2.394 + 16ARG HH22 250 1.726 0.969 2.277 + 17PRO N 251 5.866 1.586 2.842 + 17PRO CA 252 5.876 1.689 2.918 + 17PRO C 253 5.731 1.689 2.995 + 17PRO O 254 5.664 1.714 2.905 + 17PRO CB 255 5.966 1.810 2.911 + 17PRO CG 256 5.950 1.839 2.789 + 17PRO CD 257 5.984 1.690 2.734 + 17PRO HA 258 5.888 1.669 3.086 + 17PRO HB2 259 5.898 1.953 2.996 + 17PRO HB3 260 6.033 1.802 2.992 + 17PRO HG2 261 5.863 1.870 2.785 + 17PRO HG3 262 6.047 1.898 2.771 + 17PRO HD2 263 5.906 1.706 2.693 + 17PRO HD3 264 6.066 1.671 2.751 + 18PRO N 265 5.677 1.747 3.086 + 18PRO CA 266 5.482 1.791 3.065 + 18PRO C 267 5.474 1.926 3.003 + 18PRO O 268 5.589 1.983 3.023 + 18PRO CB 269 5.525 1.777 3.266 + 18PRO CG 270 3.606 0.666 0.046 + 18PRO CD 271 5.716 1.792 3.223 + 18PRO HA 272 5.454 1.717 3.068 + 18PRO HB2 273 5.404 1.879 3.249 + 18PRO HB3 274 3.441 0.540 0.018 + 18PRO HG2 275 3.646 0.789 0.025 + 18PRO HG3 276 3.649 0.653 0.154 + 18PRO HD2 277 5.808 1.838 3.199 + 18PRO HD3 278 3.775 0.514 0.042 + 19PRO N 279 5.401 1.932 2.978 + 19PRO CA 280 5.315 2.045 2.888 + 19PRO C 281 5.240 2.121 3.075 + 19PRO O 282 5.171 2.153 3.114 + 19PRO CB 283 5.197 1.974 2.800 + 19PRO CG 284 5.162 1.840 2.882 + 19PRO CD 285 5.282 1.773 2.980 + 19PRO HA 286 5.389 2.089 2.818 + 19PRO HB2 287 5.128 2.105 2.796 + 19PRO HB3 288 5.263 1.983 2.723 + 19PRO HG2 289 5.042 1.905 2.950 + 19PRO HG3 290 5.130 1.776 2.850 + 19PRO HD2 291 5.213 1.782 3.063 + 19PRO HD3 292 5.303 1.706 2.914 + 20SER N 293 5.289 2.256 2.960 + 20SER CA 294 5.272 2.382 3.032 + 20SER C 295 5.183 2.423 3.004 + 20SER O 296 5.190 2.449 2.885 + 20SER CB 297 5.406 2.497 3.051 + 20SER OG 298 5.481 2.457 3.134 + 20SER OXT 299 5.059 2.493 3.067 + 20SER H 300 5.397 2.281 2.950 + 20SER HA 301 5.229 2.360 3.171 + 20SER HB2 302 5.416 2.544 2.977 + 20SER HB3 303 5.362 2.616 3.100 + 20SER HG 304 5.475 2.383 3.229 + 21BEN C1 305 3.375 1.097 1.750 + 21BEN C2 306 3.393 1.062 1.857 + 21BEN C3 307 3.539 1.073 1.918 + 21BEN C4 308 3.596 1.211 1.866 + 21BEN C5 309 3.507 1.313 1.803 + 21BEN C6 310 3.399 1.231 1.722 + 21BEN C7 311 3.183 1.032 1.738 + 21BEN N1 312 3.157 0.951 1.763 + 21BEN N2 313 3.157 1.154 1.639 + 4.00000 3.46410 3.26599 0.00000 0.00000 2.00000 0.00000 2.00000 1.15470 +trp-cage and a ligand nearer a periodic image of the protein + 313 + 1ASN N 1 3.872 2.056 1.020 + 1ASN CA 2 3.882 1.937 0.958 + 1ASN C 3 4.026 1.883 0.908 + 1ASN O 4 4.097 1.808 0.937 + 1ASN CB 5 3.828 1.948 0.813 + 1ASN CG 6 3.655 1.922 0.839 + 1ASN OD1 7 3.659 1.895 0.935 + 1ASN ND2 8 3.583 1.948 0.770 + 1ASN H1 9 3.906 1.978 1.121 + 1ASN H2 10 3.889 2.114 1.015 + 1ASN H3 11 3.803 2.004 1.059 + 1ASN HA 12 3.860 1.844 0.961 + 1ASN HB2 13 3.821 2.035 0.777 + 1ASN HB3 14 3.866 1.850 0.736 + 1ASN HD21 15 3.594 1.979 0.660 + 1ASN HD22 16 3.494 1.916 0.794 + 2LEU N 17 4.152 2.021 0.869 + 2LEU CA 18 4.307 2.010 0.846 + 2LEU C 19 4.381 1.917 0.994 + 2LEU O 20 4.472 1.833 0.971 + 2LEU CB 21 4.342 2.156 0.807 + 2LEU CG 22 4.251 2.280 0.963 + 2LEU CD1 23 4.418 2.286 1.030 + 2LEU CD2 24 4.228 2.359 0.893 + 2LEU H 25 4.060 2.074 0.854 + 2LEU HA 26 4.282 1.922 0.768 + 2LEU HB2 27 4.445 2.138 0.843 + 2LEU HB3 28 4.255 2.194 0.738 + 2LEU HG 29 4.208 2.210 1.006 + 2LEU HD11 30 4.435 2.183 1.103 + 2LEU HD12 31 4.488 2.378 1.016 + 2LEU HD13 32 4.385 2.361 1.122 + 2LEU HD21 33 4.295 2.413 0.808 + 2LEU HD22 34 4.162 2.357 0.813 + 2LEU HD23 35 4.223 2.449 0.984 + 3TYR N 36 4.335 1.947 1.093 + 3TYR CA 37 4.371 1.863 1.203 + 3TYR C 38 4.331 1.723 1.206 + 3TYR O 39 4.463 1.629 1.258 + 3TYR CB 40 4.361 1.984 1.316 + 3TYR CG 41 4.438 1.936 1.392 + 3TYR CD1 42 4.486 1.863 1.533 + 3TYR CD2 43 4.574 2.041 1.422 + 3TYR CE1 44 4.594 1.791 1.583 + 3TYR CE2 45 4.694 2.044 1.532 + 3TYR CZ 46 4.703 1.884 1.566 + 3TYR OH 47 4.830 1.880 1.668 + 3TYR H 48 4.295 2.016 1.103 + 3TYR HA 49 4.563 1.904 1.193 + 3TYR HB2 50 4.376 2.058 1.290 + 3TYR HB3 51 4.301 1.903 1.342 + 3TYR HD1 52 4.391 1.749 1.521 + 3TYR HD2 53 4.554 2.139 1.362 + 3TYR HE1 54 4.640 1.710 1.692 + 3TYR HE2 55 4.778 2.096 1.527 + 3TYR HH 56 4.892 1.942 1.631 + 4ILE N 57 4.222 1.740 1.175 + 4ILE CA 58 4.168 1.551 1.194 + 4ILE C 59 4.296 1.483 1.031 + 4ILE O 60 4.284 1.394 1.046 + 4ILE CB 61 4.002 1.544 1.101 + 4ILE CG1 62 3.904 1.655 1.236 + 4ILE CG2 63 4.019 1.370 1.135 + 4ILE CD1 64 3.953 1.684 1.388 + 4ILE H 65 4.149 1.761 1.090 + 4ILE HA 66 4.177 1.534 1.273 + 4ILE HB 67 4.017 1.575 1.008 + 4ILE HG12 68 3.985 1.739 1.183 + 4ILE HG13 69 3.854 1.632 1.205 + 4ILE HG21 70 3.981 1.325 1.052 + 4ILE HG22 71 3.978 1.396 1.265 + 4ILE HG23 72 3.878 1.404 1.148 + 4ILE HD11 73 3.930 1.559 1.392 + 4ILE HD12 74 4.081 1.662 1.356 + 4ILE HD13 75 3.865 1.712 1.430 + 5GLN N 76 4.309 1.538 0.924 + 5GLN CA 77 4.342 1.488 0.791 + 5GLN C 78 4.511 1.503 0.837 + 5GLN O 79 4.552 1.368 0.770 + 5GLN CB 80 4.368 1.593 0.701 + 5GLN CG 81 4.300 1.504 0.516 + 5GLN CD 82 4.187 1.440 0.499 + 5GLN OE1 83 4.168 1.296 0.577 + 5GLN NE2 84 4.135 1.480 0.489 + 5GLN H 85 4.250 1.641 0.915 + 5GLN HA 86 4.330 1.381 0.797 + 5GLN HB2 87 4.253 1.634 0.703 + 5GLN HB3 88 4.419 1.668 0.686 + 5GLN HG2 89 4.332 1.572 0.468 + 5GLN HG3 90 4.399 1.399 0.591 + 5GLN HE21 91 4.155 1.592 0.462 + 5GLN HE22 92 4.020 1.436 0.473 + 6TRP N 93 4.552 1.607 0.937 + 6TRP CA 94 4.702 1.555 0.966 + 6TRP C 95 4.711 1.448 1.090 + 6TRP O 96 4.809 1.350 1.076 + 6TRP CB 97 4.758 1.685 1.051 + 6TRP CG 98 4.876 1.655 1.127 + 6TRP CD1 99 4.998 1.687 1.037 + 6TRP CD2 100 4.896 1.681 1.238 + 6TRP NE1 101 5.077 1.635 1.151 + 6TRP CE2 102 5.086 1.671 1.308 + 6TRP CE3 103 4.869 1.653 1.391 + 6TRP CZ2 104 5.114 1.646 1.379 + 6TRP CZ3 105 4.898 1.617 1.498 + 6TRP CH2 106 5.031 1.616 1.513 + 6TRP H 107 4.504 1.640 0.980 + 6TRP HA 108 4.773 1.545 0.943 + 6TRP HB2 109 4.702 1.775 0.980 + 6TRP HB3 110 4.659 1.703 1.114 + 6TRP HD1 111 4.973 1.689 0.930 + 6TRP HE1 112 5.181 1.660 1.112 + 6TRP HE3 113 4.755 1.669 1.356 + 6TRP HZ2 114 5.211 1.647 1.402 + 6TRP HZ3 115 4.820 1.598 1.551 + 6TRP HH2 116 5.076 1.658 1.578 + 7LEU N 117 4.602 1.411 1.218 + 7LEU CA 118 4.591 1.307 1.275 + 7LEU C 119 4.573 1.163 1.239 + 7LEU O 120 4.658 1.044 1.255 + 7LEU CB 121 4.503 1.340 1.394 + 7LEU CG 122 4.540 1.434 1.509 + 7LEU CD1 123 4.423 1.493 1.628 + 7LEU CD2 124 4.668 1.432 1.546 + 7LEU H 125 4.535 1.446 1.193 + 7LEU HA 126 4.712 1.291 1.369 + 7LEU HB2 127 4.376 1.376 1.372 + 7LEU HB3 128 4.484 1.249 1.426 + 7LEU HG 129 4.503 1.544 1.435 + 7LEU HD11 130 4.290 1.475 1.483 + 7LEU HD12 131 4.410 1.359 1.637 + 7LEU HD13 132 4.456 1.543 1.661 + 7LEU HD21 133 4.657 1.302 1.651 + 7LEU HD22 134 4.733 1.397 1.528 + 7LEU HD23 135 4.682 1.525 1.688 + 8LYS N 136 4.505 1.134 1.124 + 8LYS CA 137 4.456 1.049 1.046 + 8LYS C 138 4.570 0.972 0.975 + 8LYS O 139 4.604 0.857 0.960 + 8LYS CB 140 4.343 1.018 0.978 + 8LYS CG 141 4.360 1.105 0.847 + 8LYS CD 142 4.412 0.997 0.725 + 8LYS CE 143 4.422 1.072 0.628 + 8LYS NZ 144 4.285 1.095 0.504 + 8LYS H 145 4.454 1.193 1.084 + 8LYS HA 146 4.413 0.949 1.138 + 8LYS HB2 147 4.309 0.930 0.924 + 8LYS HB3 148 4.314 1.068 1.010 + 8LYS HG2 149 4.263 1.182 0.772 + 8LYS HG3 150 4.427 1.181 0.875 + 8LYS HD2 151 4.490 0.946 0.754 + 8LYS HD3 152 4.346 0.927 0.711 + 8LYS HE2 153 4.407 1.179 0.638 + 8LYS HE3 154 4.502 1.059 0.532 + 8LYS HZ1 155 4.315 0.963 0.456 + 8LYS HZ2 156 4.225 1.112 0.529 + 8LYS HZ3 157 4.316 1.052 0.399 + 9ASP N 158 4.689 1.034 0.917 + 9ASP CA 159 4.778 1.023 0.885 + 9ASP C 160 4.878 0.980 1.015 + 9ASP O 161 5.015 0.913 0.971 + 9ASP CB 162 4.866 1.158 0.838 + 9ASP CG 163 4.813 1.118 0.688 + 9ASP OD1 164 4.719 1.085 0.664 + 9ASP OD2 165 4.908 1.117 0.588 + 9ASP H 166 4.668 1.144 0.949 + 9ASP HA 167 4.818 0.909 0.831 + 9ASP HB2 168 4.835 1.205 0.864 + 9ASP HB3 169 4.962 1.135 0.854 + 10GLY N 170 4.920 0.987 1.153 + 10GLY CA 171 4.986 0.965 1.244 + 10GLY C 172 5.038 1.077 1.332 + 10GLY O 173 5.130 1.048 1.410 + 10GLY H 174 4.777 0.995 1.169 + 10GLY HA2 175 4.914 0.908 1.321 + 10GLY HA3 176 5.037 0.880 1.211 + 11GLY N 177 4.958 1.189 1.304 + 11GLY CA 178 5.040 1.318 1.366 + 11GLY C 179 5.175 1.358 1.360 + 11GLY O 180 5.238 1.337 1.263 + 11GLY H 181 4.912 1.220 1.227 + 11GLY HA2 182 4.969 1.399 1.300 + 11GLY HA3 183 4.991 1.311 1.449 + 12PRO N 184 5.258 1.363 1.466 + 12PRO CA 185 5.381 1.358 1.456 + 12PRO C 186 5.472 1.264 1.379 + 12PRO O 187 5.576 1.254 1.340 + 12PRO CB 188 5.438 1.362 1.644 + 12PRO CG 189 5.333 1.420 1.709 + 12PRO CD 190 5.219 1.313 1.601 + 12PRO HA 191 5.424 1.454 1.448 + 12PRO HB2 192 5.458 1.277 1.638 + 12PRO HB3 193 5.501 1.417 1.612 + 12PRO HG2 194 5.343 1.387 1.826 + 12PRO HG3 195 5.313 1.532 1.639 + 12PRO HD2 196 5.193 1.226 1.653 + 12PRO HD3 197 5.102 1.384 1.622 + 13SER N 198 5.409 1.143 1.436 + 13SER CA 199 5.460 0.986 1.377 + 13SER C 200 5.441 1.001 1.192 + 13SER O 201 5.442 0.882 1.188 + 13SER CB 202 5.458 0.849 1.456 + 13SER OG 203 5.447 0.852 1.595 + 13SER H 204 5.310 1.096 1.494 + 13SER HA 205 5.564 0.980 1.409 + 13SER HB2 206 5.279 0.826 1.468 + 13SER HB3 207 3.472 4.208 1.386 + 13SER HG 208 3.528 4.340 1.603 + 14SER N 209 5.456 1.067 1.102 + 14SER CA 210 5.413 1.033 0.981 + 14SER C 211 5.547 1.127 0.907 + 14SER O 212 5.502 1.231 0.782 + 14SER CB 213 5.288 1.080 0.955 + 14SER OG 214 5.227 1.054 0.867 + 14SER H 215 5.427 1.152 1.186 + 14SER HA 216 5.398 1.007 0.937 + 14SER HB2 217 5.180 1.062 1.050 + 14SER HB3 218 5.226 1.228 0.969 + 14SER HG 219 5.129 0.975 0.913 + 15GLY N 220 5.621 1.209 0.996 + 15GLY CA 221 5.673 1.282 0.901 + 15GLY C 222 5.699 1.369 0.863 + 15GLY O 223 5.731 1.466 0.790 + 15GLY H 224 5.627 1.161 1.059 + 15GLY HA2 225 5.786 1.319 0.972 + 15GLY HA3 226 5.729 1.198 0.863 + 16ARG N 227 5.559 1.487 0.945 + 16ARG CA 228 5.484 1.622 0.872 + 16ARG C 229 5.447 1.683 1.011 + 16ARG O 230 5.404 1.617 1.127 + 16ARG CB 231 5.341 1.571 0.802 + 16ARG CG 232 5.246 1.491 0.882 + 16ARG CD 233 5.157 1.443 0.780 + 16ARG NE 234 5.179 1.338 0.682 + 16ARG CZ 235 5.300 1.326 0.584 + 16ARG NH1 236 5.310 1.452 0.487 + 16ARG NH2 237 5.256 1.196 0.533 + 16ARG H 238 5.514 1.412 1.033 + 16ARG HA 239 5.513 1.664 0.823 + 16ARG HB2 240 5.348 1.692 0.768 + 16ARG HB3 241 5.387 1.539 0.712 + 16ARG HG2 242 5.344 1.403 0.871 + 16ARG HG3 243 5.198 1.509 0.956 + 16ARG HD2 244 5.079 1.427 0.819 + 16ARG HD3 245 5.188 1.517 0.669 + 16ARG HE 246 5.147 1.241 0.687 + 16ARG HH11 247 5.291 1.494 0.548 + 16ARG HH12 248 5.350 1.408 0.409 + 16ARG HH21 249 5.252 1.116 0.578 + 16ARG HH22 250 3.298 2.304 3.639 + 17PRO N 251 5.440 1.818 1.013 + 17PRO CA 252 5.486 1.910 1.156 + 17PRO C 253 5.294 1.963 1.173 + 17PRO O 254 5.194 1.883 1.035 + 17PRO CB 255 5.515 2.042 1.131 + 17PRO CG 256 5.503 2.064 0.975 + 17PRO CD 257 5.562 1.866 0.910 + 17PRO HA 258 5.467 1.847 1.198 + 17PRO HB2 259 5.448 2.106 1.118 + 17PRO HB3 260 5.620 2.038 1.156 + 17PRO HG2 261 5.433 2.088 0.906 + 17PRO HG3 262 5.654 2.106 0.934 + 17PRO HD2 263 5.502 1.832 0.811 + 17PRO HD3 264 5.650 1.894 0.896 + 18PRO N 265 5.201 1.965 1.253 + 18PRO CA 266 5.080 1.991 1.277 + 18PRO C 267 5.017 2.149 1.187 + 18PRO O 268 5.134 2.252 1.188 + 18PRO CB 269 5.039 2.044 1.392 + 18PRO CG 270 5.205 2.060 1.449 + 18PRO CD 271 5.298 1.963 1.389 + 18PRO HA 272 5.051 1.935 1.216 + 18PRO HB2 273 4.945 2.068 1.428 + 18PRO HB3 274 5.044 1.947 1.471 + 18PRO HG2 275 5.229 2.167 1.442 + 18PRO HG3 276 5.203 2.014 1.628 + 18PRO HD2 277 5.390 2.075 1.365 + 18PRO HD3 278 5.342 1.882 1.460 + 19PRO N 279 4.947 2.092 1.082 + 19PRO CA 280 4.893 2.264 1.053 + 19PRO C 281 4.825 2.373 1.161 + 19PRO O 282 4.753 2.324 1.252 + 19PRO CB 283 4.752 2.211 0.937 + 19PRO CG 284 4.729 2.090 1.047 + 19PRO CD 285 4.835 2.061 1.105 + 19PRO HA 286 4.949 2.296 0.989 + 19PRO HB2 287 4.692 2.273 0.990 + 19PRO HB3 288 4.789 2.162 0.877 + 19PRO HG2 289 4.656 2.136 1.144 + 19PRO HG3 290 4.631 2.019 0.955 + 19PRO HD2 291 4.795 1.973 1.233 + 19PRO HD3 292 4.897 1.923 1.023 + 20SER N 293 4.918 2.496 1.142 + 20SER CA 294 4.893 2.589 1.218 + 20SER C 295 4.752 2.670 1.161 + 20SER O 296 4.747 2.693 1.043 + 20SER CB 297 4.962 2.728 1.241 + 20SER OG 298 5.054 2.632 1.295 + 20SER OXT 299 4.623 2.683 1.243 + 20SER H 300 4.980 2.453 1.088 + 20SER HA 301 4.825 2.590 1.339 + 20SER HB2 302 4.974 2.728 1.116 + 20SER HB3 303 4.932 2.765 1.309 + 20SER HG 304 5.036 2.585 1.377 + 21BEN C1 305 4.766 2.605 3.151 + 21BEN C2 306 4.837 2.518 3.266 + 21BEN C3 307 4.990 2.568 3.323 + 21BEN C4 308 4.969 2.672 3.243 + 21BEN C5 309 4.976 2.738 3.146 + 21BEN C6 310 4.815 2.713 3.103 + 21BEN C7 311 4.642 2.583 3.078 + 21BEN N1 312 4.608 2.433 3.162 + 21BEN N2 313 4.588 2.601 3.004 + 4.00000 3.46410 3.26599 0.00000 0.00000 2.00000 0.00000 2.00000 1.15470 diff --git a/regtest/basic/rt-molinfo-whole-ligand/warnings.reference b/regtest/basic/rt-molinfo-whole-ligand/warnings.reference new file mode 100644 index 0000000000..3554d28427 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-ligand/warnings.reference @@ -0,0 +1,5 @@ +# out_sep +Action WHOLEMOLECULES +# out +Action WHOLEMOLECULES +WARNING for action MOLINFO with label @0 : the reference structure in the MOLINFO pdb file may not be whole: 9 of its 313 atoms here are closer to a periodic image of the others, in the box of its CRYST1 record, than to the others themselves. Atoms: 305 (BEN21) 306 (BEN21) 307 (BEN21) 308 (BEN21) 309 (BEN21) 310 (BEN21) 311 (BEN21) 312 (BEN21) 313 (BEN21) diff --git a/regtest/basic/rt-molinfo-whole-ligand/whole.xyz.reference b/regtest/basic/rt-molinfo-whole-ligand/whole.xyz.reference new file mode 100644 index 0000000000..485041d7c1 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-ligand/whole.xyz.reference @@ -0,0 +1,945 @@ +313 + 4.000 0.000 0.000 2.000 3.464 0.000 2.000 1.155 3.266 +N 5.100 1.565 3.211 +CA 5.129 1.466 3.105 +C 5.278 1.449 3.077 +O 5.326 1.338 3.091 +CB 5.046 1.492 2.977 +CG 4.898 1.466 3.005 +OD1 4.863 1.423 3.114 +ND2 4.809 1.493 2.912 +H1 5.157 1.549 3.293 +H2 5.116 1.660 3.177 +H3 5.002 1.557 3.237 +HA 5.097 1.369 3.142 +HB2 5.059 1.594 2.947 +HB3 5.079 1.425 2.898 +HD21 4.833 1.532 2.822 +HD22 4.714 1.471 2.937 +N 5.352 1.556 3.044 +CA 5.497 1.553 3.021 +C 5.576 1.471 3.126 +O 5.651 1.380 3.090 +CB 5.549 1.698 3.004 +CG 5.510 1.798 3.117 +CD1 5.629 1.833 3.206 +CD2 5.455 1.928 3.058 +H 5.308 1.645 3.027 +HA 5.515 1.502 2.926 +HB2 5.656 1.694 2.999 +HB3 5.509 1.734 2.910 +HG 5.433 1.755 3.181 +HD11 5.669 1.743 3.252 +HD12 5.706 1.883 3.148 +HD13 5.597 1.901 3.286 +HD21 5.529 1.974 2.993 +HD22 5.364 1.907 3.001 +HD23 5.431 1.997 3.138 +N 5.554 1.498 3.255 +CA 5.621 1.427 3.365 +C 5.580 1.279 3.374 +O 5.661 1.194 3.411 +CB 5.593 1.500 3.497 +CG 5.707 1.487 3.595 +CD1 5.715 1.375 3.680 +CD2 5.808 1.586 3.600 +CE1 5.824 1.361 3.768 +CE2 5.917 1.572 3.687 +CZ 5.926 1.458 3.771 +OH 6.033 1.441 3.853 +H 5.496 1.578 3.278 +HA 5.728 1.430 3.346 +HB2 5.578 1.604 3.476 +HB3 5.501 1.463 3.541 +HD1 5.638 1.299 3.677 +HD2 5.802 1.673 3.536 +HE1 5.832 1.275 3.833 +HE2 5.993 1.648 3.690 +HH 6.109 1.493 3.823 +N 5.456 1.246 3.335 +CA 5.404 1.108 3.328 +C 5.481 1.031 3.219 +O 5.528 0.920 3.244 +CB 5.251 1.107 3.301 +CG1 5.170 1.207 3.386 +CG2 5.194 0.965 3.317 +CD1 5.188 1.194 3.538 +H 5.399 1.319 3.295 +HA 5.423 1.059 3.423 +HB 5.234 1.134 3.197 +HG12 5.200 1.306 3.358 +HG13 5.064 1.195 3.363 +HG21 5.239 0.897 3.243 +HG22 5.214 0.926 3.417 +HG23 5.086 0.966 3.300 +HD11 5.159 1.095 3.571 +HD12 5.292 1.214 3.566 +HD13 5.124 1.268 3.588 +N 5.499 1.093 3.102 +CA 5.578 1.036 2.992 +C 5.727 1.021 3.027 +O 5.791 0.929 2.978 +CB 5.561 1.121 2.865 +CG 5.565 1.036 2.737 +CD 5.432 0.967 2.708 +OE1 5.413 0.849 2.733 +NE2 5.337 1.038 2.651 +H 5.457 1.185 3.090 +HA 5.538 0.937 2.972 +HB2 5.466 1.172 2.869 +HB3 5.641 1.196 2.861 +HG2 5.590 1.099 2.654 +HG3 5.644 0.961 2.746 +HE21 5.351 1.134 2.626 +HE22 5.251 0.989 2.633 +N 5.782 1.107 3.114 +CA 5.918 1.090 3.167 +C 5.927 0.977 3.271 +O 6.019 0.895 3.266 +CB 5.968 1.223 3.225 +CG 6.105 1.218 3.286 +CD1 6.222 1.219 3.218 +CD2 6.141 1.210 3.427 +NE1 6.327 1.209 3.308 +CE2 6.283 1.205 3.437 +CE3 6.068 1.206 3.548 +CZ2 6.350 1.198 3.560 +CZ3 6.134 1.197 3.672 +CH2 6.274 1.194 3.678 +H 5.727 1.187 3.142 +HA 5.985 1.062 3.085 +HB2 5.969 1.295 3.145 +HB3 5.898 1.257 3.301 +HD1 6.231 1.226 3.111 +HE1 6.426 1.207 3.282 +HE3 5.960 1.210 3.544 +HZ2 6.458 1.195 3.563 +HZ3 6.076 1.193 3.763 +HH2 6.323 1.189 3.775 +N 5.830 0.967 3.363 +CA 5.826 0.860 3.463 +C 5.805 0.721 3.401 +O 5.875 0.628 3.441 +CB 5.719 0.889 3.570 +CG 5.760 0.995 3.673 +CD1 5.642 1.021 3.768 +CD2 5.881 0.953 3.758 +H 5.758 1.040 3.366 +HA 5.923 0.855 3.511 +HB2 5.630 0.922 3.520 +HB3 5.698 0.796 3.624 +HG 5.784 1.088 3.622 +HD11 5.556 1.054 3.711 +HD12 5.617 0.930 3.822 +HD13 5.669 1.098 3.840 +HD21 5.863 0.854 3.802 +HD22 5.970 0.949 3.696 +HD23 5.898 1.025 3.838 +N 5.715 0.705 3.302 +CA 5.687 0.574 3.239 +C 5.810 0.510 3.173 +O 5.818 0.388 3.163 +CB 5.567 0.583 3.143 +CG 5.597 0.652 3.009 +CD 5.622 0.554 2.893 +CE 5.640 0.633 2.762 +NZ 5.534 0.605 2.664 +H 5.658 0.786 3.276 +HA 5.659 0.505 3.319 +HB2 5.533 0.484 3.123 +HB3 5.488 0.639 3.193 +HG2 5.513 0.714 2.983 +HG3 5.684 0.716 3.019 +HD2 5.710 0.497 2.913 +HD3 5.537 0.486 2.885 +HE2 5.640 0.738 2.785 +HE3 5.739 0.609 2.721 +HZ1 5.528 0.506 2.645 +HZ2 5.446 0.641 2.701 +HZ3 5.552 0.655 2.578 +N 5.907 0.592 3.131 +CA 6.036 0.551 3.076 +C 6.138 0.507 3.183 +O 6.244 0.456 3.147 +CB 6.093 0.669 2.994 +CG 6.057 0.662 2.845 +OD1 5.937 0.648 2.814 +OD2 6.153 0.671 2.765 +H 5.889 0.691 3.137 +HA 6.022 0.466 3.009 +HB2 6.054 0.761 3.034 +HB3 6.201 0.669 3.001 +N 6.108 0.525 3.313 +CA 6.196 0.491 3.426 +C 6.253 0.612 3.502 +O 6.339 0.594 3.587 +H 6.016 0.562 3.336 +HA2 6.138 0.432 3.497 +HA3 6.280 0.430 3.392 +N 6.207 0.735 3.472 +CA 6.252 0.857 3.539 +C 6.406 0.873 3.532 +O 6.461 0.870 3.422 +H 6.138 0.744 3.398 +HA2 6.206 0.942 3.490 +HA3 6.218 0.854 3.642 +N 6.477 0.888 3.646 +CA 6.623 0.900 3.647 +C 6.696 0.780 3.583 +O 6.804 0.797 3.527 +CB 6.664 0.915 3.794 +CG 6.536 0.958 3.865 +CD 6.426 0.892 3.782 +HA 6.651 0.991 3.593 +HB2 6.699 0.821 3.833 +HB3 6.743 0.989 3.807 +HG2 6.534 0.923 3.967 +HG3 6.526 1.067 3.859 +HD2 6.407 0.792 3.818 +HD3 6.334 0.949 3.791 +N 6.636 0.660 3.587 +CA 6.695 0.535 3.537 +C 6.680 0.516 3.385 +O 6.692 0.404 3.336 +CB 6.636 0.416 3.614 +OG 6.666 0.427 3.751 +H 6.543 0.653 3.628 +HA 6.802 0.537 3.557 +HB2 6.529 0.415 3.601 +HB3 6.678 0.323 3.576 +HG 6.760 0.414 3.763 +N 6.653 0.624 3.310 +CA 6.629 0.621 3.165 +C 6.723 0.712 3.084 +O 6.698 0.741 2.967 +CB 6.481 0.654 3.140 +OG 6.433 0.579 3.031 +H 6.641 0.712 3.359 +HA 6.646 0.520 3.129 +HB2 6.424 0.629 3.227 +HB3 6.468 0.760 3.121 +HG 6.361 0.521 3.068 +N 6.832 0.761 3.146 +CA 6.935 0.841 3.079 +C 6.888 0.980 3.035 +O 6.944 1.035 2.940 +H 6.847 0.732 3.242 +HA2 7.019 0.854 3.147 +HA3 6.970 0.788 2.991 +N 6.785 1.037 3.100 +CA 6.719 1.161 3.061 +C 6.675 1.244 3.183 +O 6.612 1.190 3.274 +CB 6.601 1.128 2.967 +CG 6.494 1.036 3.029 +CD 6.382 0.994 2.933 +NE 6.415 0.872 2.856 +CZ 6.476 0.862 2.739 +NH1 6.519 0.966 2.673 +NH2 6.493 0.743 2.685 +H 6.748 0.985 3.179 +HA 6.791 1.219 3.003 +HB2 6.553 1.221 2.939 +HB3 6.642 1.081 2.878 +HG2 6.544 0.947 3.063 +HG3 6.448 1.088 3.111 +HD2 6.293 0.976 2.990 +HD3 6.357 1.076 2.866 +HE 6.386 0.784 2.897 +HH11 6.505 1.057 2.714 +HH12 6.566 0.957 2.585 +HH21 6.455 0.664 2.734 +HH22 6.541 0.732 2.598 +N 6.705 1.376 3.188 +CA 6.668 1.462 3.301 +C 6.516 1.486 3.306 +O 6.448 1.469 3.204 +CB 6.745 1.592 3.278 +CG 6.757 1.600 3.126 +CD 6.772 1.454 3.085 +HA 6.700 1.416 3.394 +HB2 6.691 1.676 3.317 +HB3 6.845 1.584 3.323 +HG2 6.670 1.644 3.083 +HG3 6.844 1.659 3.096 +HD2 6.725 1.437 2.990 +HD3 6.877 1.427 3.081 +N 6.461 1.527 3.422 +CA 6.318 1.556 3.435 +C 6.280 1.684 3.358 +O 6.358 1.779 3.354 +CB 6.293 1.572 3.585 +CG 6.428 1.619 3.639 +CD 6.529 1.548 3.549 +HA 6.262 1.471 3.398 +HB2 6.217 1.645 3.604 +HB3 6.268 1.475 3.628 +HG2 6.438 1.725 3.632 +HG3 6.442 1.591 3.744 +HD2 6.616 1.609 3.535 +HD3 6.556 1.451 3.592 +N 6.159 1.689 3.300 +CA 6.108 1.807 3.231 +C 6.061 1.914 3.332 +O 5.977 1.885 3.418 +CB 5.995 1.754 3.143 +CG 5.938 1.638 3.225 +CD 6.061 1.581 3.294 +HA 6.186 1.849 3.167 +HB2 5.920 1.830 3.127 +HB3 6.036 1.716 3.050 +HG2 5.867 1.673 3.297 +HG3 5.888 1.564 3.162 +HD2 6.037 1.547 3.392 +HD3 6.102 1.499 3.233 +N 6.117 2.035 3.321 +CA 6.075 2.156 3.395 +C 5.949 2.219 3.335 +O 5.951 2.244 3.212 +CB 6.187 2.260 3.395 +OG 6.302 2.207 3.458 +OXT 5.856 2.243 3.414 +H 6.187 2.049 3.250 +HA 6.050 2.129 3.497 +HB2 6.211 2.287 3.294 +HB3 6.153 2.349 3.449 +HG 6.273 2.157 3.534 +C1 5.987 2.147 5.323 +C2 6.053 2.067 5.416 +C3 6.175 2.110 5.469 +C4 6.229 2.231 5.429 +C5 6.163 2.310 5.336 +C6 6.041 2.268 5.283 +C7 5.856 2.101 5.266 +N1 5.804 1.985 5.304 +N2 5.792 2.177 5.178 +313 + 4.000 0.000 0.000 2.000 3.464 0.000 2.000 1.155 3.266 +N 4.311 1.790 2.862 +CA 4.388 1.679 2.773 +C 4.481 1.666 2.737 +O 4.541 1.578 2.784 +CB 4.258 1.727 2.664 +CG 4.121 1.683 2.684 +OD1 4.028 1.674 2.800 +ND2 3.993 1.726 2.617 +H1 4.362 1.794 2.978 +H2 4.350 1.857 2.823 +H3 4.184 1.773 2.888 +HA 4.301 1.604 2.805 +HB2 4.226 1.808 2.638 +HB3 4.292 1.634 2.560 +HD21 4.039 1.769 2.550 +HD22 3.902 1.679 2.603 +N 4.536 1.806 2.764 +CA 4.723 1.806 2.691 +C 4.734 1.689 2.813 +O 4.880 1.599 2.794 +CB 4.719 1.961 2.682 +CG 4.732 2.046 2.812 +CD1 4.831 2.068 2.892 +CD2 4.615 2.164 2.755 +H 4.520 1.880 2.728 +HA 4.699 1.729 2.576 +HB2 4.864 1.924 2.657 +HB3 4.666 1.961 2.613 +HG 4.659 1.987 2.832 +HD11 4.889 1.991 2.946 +HD12 4.875 2.155 2.847 +HD13 4.785 2.136 2.951 +HD21 4.730 2.190 2.665 +HD22 4.572 2.148 2.646 +HD23 4.620 2.228 2.807 +N 4.760 1.715 2.899 +CA 4.800 1.653 3.077 +C 4.801 1.524 3.040 +O 4.864 1.425 3.099 +CB 4.789 1.721 3.198 +CG 4.928 1.669 3.255 +CD1 4.886 1.616 3.363 +CD2 5.001 1.817 3.313 +CE1 5.003 1.563 3.462 +CE2 5.116 1.826 3.347 +CZ 5.113 1.678 3.462 +OH 5.236 1.654 3.498 +H 4.704 1.836 2.940 +HA 4.944 1.655 3.041 +HB2 4.773 1.843 3.168 +HB3 4.681 1.699 3.206 +HD1 4.803 1.524 3.354 +HD2 5.045 1.903 3.210 +HE1 5.037 1.509 3.501 +HE2 5.172 1.883 3.331 +HH 5.275 1.732 3.509 +N 4.659 1.511 3.049 +CA 4.595 1.324 3.029 +C 4.671 1.265 2.866 +O 4.716 1.126 2.923 +CB 4.445 1.335 2.957 +CG1 4.337 1.465 3.068 +CG2 4.379 1.189 2.979 +CD1 4.391 1.428 3.201 +H 4.588 1.567 2.968 +HA 4.631 1.275 3.118 +HB 4.431 1.361 2.849 +HG12 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4.659 1.703 1.114 +HD1 4.973 1.689 0.930 +HE1 5.181 1.660 1.112 +HE3 4.755 1.669 1.356 +HZ2 5.211 1.647 1.402 +HZ3 4.820 1.598 1.551 +HH2 5.076 1.658 1.578 +N 4.602 1.411 1.218 +CA 4.591 1.307 1.275 +C 4.573 1.163 1.239 +O 4.658 1.044 1.255 +CB 4.503 1.340 1.394 +CG 4.540 1.434 1.509 +CD1 4.423 1.493 1.628 +CD2 4.668 1.432 1.546 +H 4.535 1.446 1.193 +HA 4.712 1.291 1.369 +HB2 4.376 1.376 1.372 +HB3 4.484 1.249 1.426 +HG 4.503 1.544 1.435 +HD11 4.290 1.475 1.483 +HD12 4.410 1.359 1.637 +HD13 4.456 1.543 1.661 +HD21 4.657 1.302 1.651 +HD22 4.733 1.397 1.528 +HD23 4.682 1.525 1.688 +N 4.505 1.134 1.124 +CA 4.456 1.049 1.046 +C 4.570 0.972 0.975 +O 4.604 0.857 0.960 +CB 4.343 1.018 0.978 +CG 4.360 1.105 0.847 +CD 4.412 0.997 0.725 +CE 4.422 1.072 0.628 +NZ 4.285 1.095 0.504 +H 4.454 1.193 1.084 +HA 4.413 0.949 1.138 +HB2 4.309 0.930 0.924 +HB3 4.314 1.068 1.010 +HG2 4.263 1.182 0.772 +HG3 4.427 1.181 0.875 +HD2 4.490 0.946 0.754 +HD3 4.346 0.927 0.711 +HE2 4.407 1.179 0.638 +HE3 4.502 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1.377 +C 5.441 1.001 1.192 +O 5.442 0.882 1.188 +CB 5.458 0.849 1.456 +OG 5.447 0.852 1.595 +H 5.310 1.096 1.494 +HA 5.564 0.980 1.409 +HB2 5.279 0.826 1.468 +HB3 5.472 0.744 1.386 +HG 5.528 0.876 1.603 +N 5.456 1.067 1.102 +CA 5.413 1.033 0.981 +C 5.547 1.127 0.907 +O 5.502 1.231 0.782 +CB 5.288 1.080 0.955 +OG 5.227 1.054 0.867 +H 5.427 1.152 1.186 +HA 5.398 1.007 0.937 +HB2 5.180 1.062 1.050 +HB3 5.226 1.228 0.969 +HG 5.129 0.975 0.913 +N 5.621 1.209 0.996 +CA 5.673 1.282 0.901 +C 5.699 1.369 0.863 +O 5.731 1.466 0.790 +H 5.627 1.161 1.059 +HA2 5.786 1.319 0.972 +HA3 5.729 1.198 0.863 +N 5.559 1.487 0.945 +CA 5.484 1.622 0.872 +C 5.447 1.683 1.011 +O 5.404 1.617 1.127 +CB 5.341 1.571 0.802 +CG 5.246 1.491 0.882 +CD 5.157 1.443 0.780 +NE 5.179 1.338 0.682 +CZ 5.300 1.326 0.584 +NH1 5.310 1.452 0.487 +NH2 5.256 1.196 0.533 +H 5.514 1.412 1.033 +HA 5.513 1.664 0.823 +HB2 5.348 1.692 0.768 +HB3 5.387 1.539 0.712 +HG2 5.344 1.403 0.871 +HG3 5.198 1.509 0.956 +HD2 5.079 1.427 0.819 +HD3 5.188 1.517 0.669 +HE 5.147 1.241 0.687 +HH11 5.291 1.494 0.548 +HH12 5.350 1.408 0.409 +HH21 5.252 1.116 0.578 +HH22 5.298 1.149 0.373 +N 5.440 1.818 1.013 +CA 5.486 1.910 1.156 +C 5.294 1.963 1.173 +O 5.194 1.883 1.035 +CB 5.515 2.042 1.131 +CG 5.503 2.064 0.975 +CD 5.562 1.866 0.910 +HA 5.467 1.847 1.198 +HB2 5.448 2.106 1.118 +HB3 5.620 2.038 1.156 +HG2 5.433 2.088 0.906 +HG3 5.654 2.106 0.934 +HD2 5.502 1.832 0.811 +HD3 5.650 1.894 0.896 +N 5.201 1.965 1.253 +CA 5.080 1.991 1.277 +C 5.017 2.149 1.187 +O 5.134 2.252 1.188 +CB 5.039 2.044 1.392 +CG 5.205 2.060 1.449 +CD 5.298 1.963 1.389 +HA 5.051 1.935 1.216 +HB2 4.945 2.068 1.428 +HB3 5.044 1.947 1.471 +HG2 5.229 2.167 1.442 +HG3 5.203 2.014 1.628 +HD2 5.390 2.075 1.365 +HD3 5.342 1.882 1.460 +N 4.947 2.092 1.082 +CA 4.893 2.264 1.053 +C 4.825 2.373 1.161 +O 4.753 2.324 1.252 +CB 4.752 2.211 0.937 +CG 4.729 2.090 1.047 +CD 4.835 2.061 1.105 +HA 4.949 2.296 0.989 +HB2 4.692 2.273 0.990 +HB3 4.789 2.162 0.877 +HG2 4.656 2.136 1.144 +HG3 4.631 2.019 0.955 +HD2 4.795 1.973 1.233 +HD3 4.897 1.923 1.023 +N 4.918 2.496 1.142 +CA 4.893 2.589 1.218 +C 4.752 2.670 1.161 +O 4.747 2.693 1.043 +CB 4.962 2.728 1.241 +OG 5.054 2.632 1.295 +OXT 4.623 2.683 1.243 +H 4.980 2.453 1.088 +HA 4.825 2.590 1.339 +HB2 4.974 2.728 1.116 +HB3 4.932 2.765 1.309 +HG 5.036 2.585 1.377 +C1 4.766 2.605 3.151 +C2 4.837 2.518 3.266 +C3 4.990 2.568 3.323 +C4 4.969 2.672 3.243 +C5 4.976 2.738 3.146 +C6 4.815 2.713 3.103 +C7 4.642 2.583 3.078 +N1 4.608 2.433 3.162 +N2 4.588 2.601 3.004 diff --git a/regtest/basic/rt-molinfo-whole-membrane/Makefile b/regtest/basic/rt-molinfo-whole-membrane/Makefile new file mode 100644 index 0000000000..3703b27cea --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/Makefile @@ -0,0 +1 @@ +include ../../scripts/test.make diff --git a/regtest/basic/rt-molinfo-whole-membrane/config b/regtest/basic/rt-molinfo-whole-membrane/config new file mode 100644 index 0000000000..5c95d0c38d --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/config @@ -0,0 +1,16 @@ +type=driver +# a small bilayer, continuous across the box, in one group and in separate groups. +# In one group, the reference is reported as maybe not whole (a warning), and the frames are still made whole right. +arg="--plumed plumed.dat --igro traj.gro" + +function plumed_regtest_before() { + $valgrind $plumed driver --plumed plumed_sep.dat --igro traj.gro > out_sep 2> err_sep || return 1 +} + +# the WHOLEMOLECULES lines of the log and the warnings, up to the list of atoms +function plumed_regtest_after() { + for f in out_sep out; do + echo "# $f" + grep -E "^PLUMED: (Action WHOLEMOLECULES|WARNING for action MOLINFO)" $f | sed -e "s/^PLUMED: //" -e "s/\\. If these atoms.*//" + done > warnings +} diff --git a/regtest/basic/rt-molinfo-whole-membrane/plumed.dat b/regtest/basic/rt-molinfo-whole-membrane/plumed.dat new file mode 100644 index 0000000000..5115cb2997 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/plumed.dat @@ -0,0 +1,5 @@ +# a small bilayer: 18 lipids of 6 beads, continuous across the box in x and y +MOLINFO STRUCTURE=ref.pdb WHOLE +# all lipids in one group: a warning is written, and every lipid is still made whole +WHOLEMOLECULES ENTITY0=1-108 +DUMPATOMS ATOMS=1-108 FILE=whole.xyz PRECISION=3 diff --git a/regtest/basic/rt-molinfo-whole-membrane/plumed_sep.dat b/regtest/basic/rt-molinfo-whole-membrane/plumed_sep.dat new file mode 100644 index 0000000000..20d4e8018a --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/plumed_sep.dat @@ -0,0 +1,3 @@ +MOLINFO STRUCTURE=ref.pdb WHOLE +# one group per lipid: no warning +WHOLEMOLECULES ENTITY0=1-6 ENTITY1=7-12 ENTITY2=13-18 ENTITY3=19-24 ENTITY4=25-30 ENTITY5=31-36 ENTITY6=37-42 ENTITY7=43-48 ENTITY8=49-54 ENTITY9=55-60 ENTITY10=61-66 ENTITY11=67-72 ENTITY12=73-78 ENTITY13=79-84 ENTITY14=85-90 ENTITY15=91-96 ENTITY16=97-102 ENTITY17=103-108 diff --git a/regtest/basic/rt-molinfo-whole-membrane/ref.pdb b/regtest/basic/rt-molinfo-whole-membrane/ref.pdb new file mode 100644 index 0000000000..22b370b11c --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/ref.pdb @@ -0,0 +1,110 @@ +CRYST1 24.000 24.000 70.000 90.00 90.00 90.00 P 1 1 +ATOM 1 NC3 LIP A 1 -3.055 0.735 61.000 1.00 0.00 +ATOM 2 PO4 LIP A 1 -2.520 0.673 56.300 1.00 0.00 +ATOM 3 GL1 LIP A 1 -1.984 0.610 51.600 1.00 0.00 +ATOM 4 C1A LIP A 1 -1.449 0.548 46.900 1.00 0.00 +ATOM 5 C2A LIP A 1 -0.914 0.486 42.200 1.00 0.00 +ATOM 6 C3A LIP A 1 -0.378 0.423 37.500 1.00 0.00 +ATOM 7 NC3 LIP A 2 -2.399 9.042 61.000 1.00 0.00 +ATOM 8 PO4 LIP A 2 -1.982 8.886 56.300 1.00 0.00 +ATOM 9 GL1 LIP A 2 -1.565 8.731 51.600 1.00 0.00 +ATOM 10 C1A LIP A 2 -1.149 8.575 46.900 1.00 0.00 +ATOM 11 C2A LIP A 2 -0.732 8.419 42.200 1.00 0.00 +ATOM 12 C3A LIP A 2 -0.315 8.263 37.500 1.00 0.00 +ATOM 13 NC3 LIP A 3 -2.157 18.212 61.000 1.00 0.00 +ATOM 14 PO4 LIP A 3 -1.684 17.729 56.300 1.00 0.00 +ATOM 15 GL1 LIP A 3 -1.210 17.246 51.600 1.00 0.00 +ATOM 16 C1A LIP A 3 -0.737 16.763 46.900 1.00 0.00 +ATOM 17 C2A LIP A 3 -0.263 16.280 42.200 1.00 0.00 +ATOM 18 C3A LIP A 3 0.210 15.797 37.500 1.00 0.00 +ATOM 19 NC3 LIP A 4 9.787 -0.105 61.000 1.00 0.00 +ATOM 20 PO4 LIP A 4 9.387 -0.034 56.300 1.00 0.00 +ATOM 21 GL1 LIP A 4 8.987 0.036 51.600 1.00 0.00 +ATOM 22 C1A LIP A 4 8.586 0.107 46.900 1.00 0.00 +ATOM 23 C2A LIP A 4 8.186 0.178 42.200 1.00 0.00 +ATOM 24 C3A LIP A 4 7.786 0.249 37.500 1.00 0.00 +ATOM 25 NC3 LIP A 5 10.167 9.011 61.000 1.00 0.00 +ATOM 26 PO4 LIP A 5 9.860 8.741 56.300 1.00 0.00 +ATOM 27 GL1 LIP A 5 9.553 8.472 51.600 1.00 0.00 +ATOM 28 C1A LIP A 5 9.246 8.202 46.900 1.00 0.00 +ATOM 29 C2A LIP A 5 8.939 7.932 42.200 1.00 0.00 +ATOM 30 C3A LIP A 5 8.632 7.663 37.500 1.00 0.00 +ATOM 31 NC3 LIP A 6 9.236 15.883 61.000 1.00 0.00 +ATOM 32 PO4 LIP A 6 9.070 15.901 56.300 1.00 0.00 +ATOM 33 GL1 LIP A 6 8.904 15.919 51.600 1.00 0.00 +ATOM 34 C1A LIP A 6 8.738 15.937 46.900 1.00 0.00 +ATOM 35 C2A LIP A 6 8.572 15.954 42.200 1.00 0.00 +ATOM 36 C3A LIP A 6 8.406 15.972 37.500 1.00 0.00 +ATOM 37 NC3 LIP A 7 17.634 -1.408 61.000 1.00 0.00 +ATOM 38 PO4 LIP A 7 17.406 -1.145 56.300 1.00 0.00 +ATOM 39 GL1 LIP A 7 17.178 -0.882 51.600 1.00 0.00 +ATOM 40 C1A LIP A 7 16.950 -0.619 46.900 1.00 0.00 +ATOM 41 C2A LIP A 7 16.722 -0.356 42.200 1.00 0.00 +ATOM 42 C3A LIP A 7 16.494 -0.093 37.500 1.00 0.00 +ATOM 43 NC3 LIP A 8 16.118 8.167 61.000 1.00 0.00 +ATOM 44 PO4 LIP A 8 16.052 8.147 56.300 1.00 0.00 +ATOM 45 GL1 LIP A 8 15.986 8.128 51.600 1.00 0.00 +ATOM 46 C1A LIP A 8 15.920 8.108 46.900 1.00 0.00 +ATOM 47 C2A LIP A 8 15.855 8.088 42.200 1.00 0.00 +ATOM 48 C3A LIP A 8 15.789 8.069 37.500 1.00 0.00 +ATOM 49 NC3 LIP A 9 16.186 16.441 61.000 1.00 0.00 +ATOM 50 PO4 LIP A 9 16.108 16.310 56.300 1.00 0.00 +ATOM 51 GL1 LIP A 9 16.029 16.179 51.600 1.00 0.00 +ATOM 52 C1A LIP A 9 15.951 16.047 46.900 1.00 0.00 +ATOM 53 C2A LIP A 9 15.872 15.916 42.200 1.00 0.00 +ATOM 54 C3A LIP A 9 15.794 15.785 37.500 1.00 0.00 +ATOM 55 NC3 LIP A 10 1.873 8.314 9.000 1.00 0.00 +ATOM 56 PO4 LIP A 10 2.259 7.452 13.700 1.00 0.00 +ATOM 57 GL1 LIP A 10 2.645 6.589 18.400 1.00 0.00 +ATOM 58 C1A LIP A 10 3.031 5.727 23.100 1.00 0.00 +ATOM 59 C2A LIP A 10 3.417 4.865 27.800 1.00 0.00 +ATOM 60 C3A LIP A 10 3.802 4.002 32.500 1.00 0.00 +ATOM 61 NC3 LIP A 11 3.198 11.272 9.000 1.00 0.00 +ATOM 62 PO4 LIP A 11 3.360 11.485 13.700 1.00 0.00 +ATOM 63 GL1 LIP A 11 3.523 11.699 18.400 1.00 0.00 +ATOM 64 C1A LIP A 11 3.686 11.912 23.100 1.00 0.00 +ATOM 65 C2A LIP A 11 3.849 12.125 27.800 1.00 0.00 +ATOM 66 C3A LIP A 11 4.012 12.338 32.500 1.00 0.00 +ATOM 67 NC3 LIP A 12 9.154 18.993 9.000 1.00 0.00 +ATOM 68 PO4 LIP A 12 8.190 19.248 13.700 1.00 0.00 +ATOM 69 GL1 LIP A 12 7.226 19.502 18.400 1.00 0.00 +ATOM 70 C1A LIP A 12 6.262 19.757 23.100 1.00 0.00 +ATOM 71 C2A LIP A 12 5.299 20.011 27.800 1.00 0.00 +ATOM 72 C3A LIP A 12 4.335 20.265 32.500 1.00 0.00 +ATOM 73 NC3 LIP A 13 13.266 6.937 9.000 1.00 0.00 +ATOM 74 PO4 LIP A 13 12.956 6.343 13.700 1.00 0.00 +ATOM 75 GL1 LIP A 13 12.645 5.750 18.400 1.00 0.00 +ATOM 76 C1A LIP A 13 12.334 5.156 23.100 1.00 0.00 +ATOM 77 C2A LIP A 13 12.024 4.563 27.800 1.00 0.00 +ATOM 78 C3A LIP A 13 11.713 3.969 32.500 1.00 0.00 +ATOM 79 NC3 LIP A 14 6.929 13.039 9.000 1.00 0.00 +ATOM 80 PO4 LIP A 14 7.831 12.898 13.700 1.00 0.00 +ATOM 81 GL1 LIP A 14 8.733 12.758 18.400 1.00 0.00 +ATOM 82 C1A LIP A 14 9.636 12.618 23.100 1.00 0.00 +ATOM 83 C2A LIP A 14 10.538 12.477 27.800 1.00 0.00 +ATOM 84 C3A LIP A 14 11.440 12.337 32.500 1.00 0.00 +ATOM 85 NC3 LIP A 15 9.256 18.728 9.000 1.00 0.00 +ATOM 86 PO4 LIP A 15 9.819 18.918 13.700 1.00 0.00 +ATOM 87 GL1 LIP A 15 10.382 19.108 18.400 1.00 0.00 +ATOM 88 C1A LIP A 15 10.946 19.298 23.100 1.00 0.00 +ATOM 89 C2A LIP A 15 11.509 19.488 27.800 1.00 0.00 +ATOM 90 C3A LIP A 15 12.072 19.678 32.500 1.00 0.00 +ATOM 91 NC3 LIP A 16 18.586 3.034 9.000 1.00 0.00 +ATOM 92 PO4 LIP A 16 18.844 3.222 13.700 1.00 0.00 +ATOM 93 GL1 LIP A 16 19.101 3.410 18.400 1.00 0.00 +ATOM 94 C1A LIP A 16 19.358 3.598 23.100 1.00 0.00 +ATOM 95 C2A LIP A 16 19.616 3.786 27.800 1.00 0.00 +ATOM 96 C3A LIP A 16 19.873 3.974 32.500 1.00 0.00 +ATOM 97 NC3 LIP A 17 18.304 13.126 9.000 1.00 0.00 +ATOM 98 PO4 LIP A 17 18.640 12.968 13.700 1.00 0.00 +ATOM 99 GL1 LIP A 17 18.977 12.810 18.400 1.00 0.00 +ATOM 100 C1A LIP A 17 19.313 12.651 23.100 1.00 0.00 +ATOM 101 C2A LIP A 17 19.649 12.493 27.800 1.00 0.00 +ATOM 102 C3A LIP A 17 19.986 12.335 32.500 1.00 0.00 +ATOM 103 NC3 LIP A 18 21.363 18.683 9.000 1.00 0.00 +ATOM 104 PO4 LIP A 18 21.117 18.913 13.700 1.00 0.00 +ATOM 105 GL1 LIP A 18 20.872 19.144 18.400 1.00 0.00 +ATOM 106 C1A LIP A 18 20.626 19.374 23.100 1.00 0.00 +ATOM 107 C2A LIP A 18 20.380 19.605 27.800 1.00 0.00 +ATOM 108 C3A LIP A 18 20.135 19.836 32.500 1.00 0.00 +END diff --git a/regtest/basic/rt-molinfo-whole-membrane/traj.gro b/regtest/basic/rt-molinfo-whole-membrane/traj.gro new file mode 100644 index 0000000000..79523e7351 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/traj.gro @@ -0,0 +1,333 @@ +a small bilayer, each lipid moved and wrapped atom by atom + 108 + 1LIP NC3 1 2.374 0.135 1.087 + 1LIP PO4 2 2.377 0.135 0.572 + 1LIP GL1 3 0.080 0.160 0.143 + 1LIP C1A 4 0.095 0.121 6.655 + 1LIP C2A 5 0.175 0.115 6.180 + 1LIP C3A 6 0.225 0.114 5.688 + 2LIP NC3 7 2.047 0.894 1.137 + 2LIP PO4 8 2.103 0.831 0.671 + 2LIP GL1 9 2.128 0.838 0.184 + 2LIP C1A 10 2.202 0.874 6.707 + 2LIP C2A 11 2.214 0.815 6.265 + 2LIP C3A 12 2.295 0.804 5.799 + 3LIP NC3 13 2.354 2.071 1.062 + 3LIP PO4 14 2.354 1.995 0.576 + 3LIP GL1 15 0.025 1.919 0.114 + 3LIP C1A 16 0.030 1.881 6.661 + 3LIP C2A 17 0.116 1.852 6.170 + 3LIP C3A 18 0.092 1.830 5.708 + 4LIP NC3 19 1.371 2.323 1.185 + 4LIP PO4 20 1.297 2.284 0.678 + 4LIP GL1 21 1.275 2.296 0.229 + 4LIP C1A 22 1.267 2.334 6.736 + 4LIP C2A 23 1.232 2.303 6.249 + 4LIP C3A 24 1.185 2.303 5.750 + 5LIP NC3 25 1.486 0.681 1.119 + 5LIP PO4 26 1.432 0.678 0.643 + 5LIP GL1 27 1.450 0.682 0.139 + 5LIP C1A 28 1.381 0.613 6.690 + 5LIP C2A 29 1.289 0.611 6.217 + 5LIP C3A 30 1.286 0.594 5.765 + 6LIP NC3 31 1.630 1.314 1.137 + 6LIP PO4 32 1.594 1.327 0.659 + 6LIP GL1 33 1.600 1.312 0.172 + 6LIP C1A 34 1.581 1.303 6.728 + 6LIP C2A 35 1.563 1.364 6.274 + 6LIP C3A 36 1.511 1.322 5.765 + 7LIP NC3 37 0.058 0.051 1.098 + 7LIP PO4 38 2.369 0.076 0.613 + 7LIP GL1 39 2.370 0.052 0.158 + 7LIP C1A 40 2.287 0.136 6.717 + 7LIP C2A 41 2.277 0.144 6.233 + 7LIP C3A 42 2.317 0.211 5.720 + 8LIP NC3 43 1.724 0.920 1.104 + 8LIP PO4 44 1.698 0.890 0.638 + 8LIP GL1 45 1.683 0.941 0.141 + 8LIP C1A 46 1.700 0.934 6.647 + 8LIP C2A 47 1.674 0.915 6.209 + 8LIP C3A 48 1.678 0.928 5.768 + 9LIP NC3 49 1.704 1.872 1.091 + 9LIP PO4 50 1.735 1.908 0.632 + 9LIP GL1 51 1.692 1.835 0.167 + 9LIP C1A 52 1.727 1.855 6.704 + 9LIP C2A 53 1.647 1.851 6.244 + 9LIP C3A 54 1.686 1.838 5.753 + 10LIP NC3 55 0.770 1.306 2.842 + 10LIP PO4 56 0.796 1.239 3.308 + 10LIP GL1 57 0.864 1.077 3.809 + 10LIP C1A 58 0.845 1.054 4.244 + 10LIP C2A 59 0.900 0.949 4.723 + 10LIP C3A 60 0.989 0.881 5.190 + 11LIP NC3 61 0.592 0.833 2.919 + 11LIP PO4 62 0.562 0.843 3.335 + 11LIP GL1 63 0.625 0.856 3.824 + 11LIP C1A 64 0.603 0.896 4.311 + 11LIP C2A 65 0.640 0.916 4.785 + 11LIP C3A 66 0.639 0.973 5.247 + 12LIP NC3 67 1.319 2.090 2.877 + 12LIP PO4 68 1.255 2.086 3.319 + 12LIP GL1 69 1.133 2.155 3.841 + 12LIP C1A 70 1.096 2.213 4.254 + 12LIP C2A 71 0.969 2.183 4.764 + 12LIP C3A 72 0.855 2.221 5.215 + 13LIP NC3 73 1.519 0.339 2.929 + 13LIP PO4 74 1.470 0.256 3.380 + 13LIP GL1 75 1.395 0.212 3.859 + 13LIP C1A 76 1.392 0.104 4.326 + 13LIP C2A 77 1.318 0.085 4.820 + 13LIP C3A 78 1.370 0.004 5.261 + 14LIP NC3 79 1.104 1.326 2.901 + 14LIP PO4 80 1.192 1.309 3.384 + 14LIP GL1 81 1.210 1.299 3.879 + 14LIP C1A 82 1.339 1.274 4.305 + 14LIP C2A 83 1.410 1.302 4.803 + 14LIP C3A 84 1.510 1.265 5.236 + 15LIP NC3 85 1.099 1.738 2.988 + 15LIP PO4 86 1.136 1.751 3.439 + 15LIP GL1 87 1.157 1.795 3.922 + 15LIP C1A 88 1.227 1.783 4.419 + 15LIP C2A 89 1.303 1.850 4.914 + 15LIP C3A 90 1.371 1.881 5.355 + 16LIP NC3 91 1.952 0.348 2.878 + 16LIP PO4 92 2.015 0.387 3.406 + 16LIP GL1 93 2.031 0.433 3.816 + 16LIP C1A 94 2.076 0.421 4.307 + 16LIP C2A 95 2.092 0.443 4.766 + 16LIP C3A 96 2.046 0.475 5.269 + 17LIP NC3 97 2.112 1.210 2.994 + 17LIP PO4 98 2.139 1.202 3.426 + 17LIP GL1 99 2.166 1.196 3.915 + 17LIP C1A 100 2.218 1.170 4.336 + 17LIP C2A 101 2.256 1.098 4.854 + 17LIP C3A 102 2.260 1.145 5.278 + 18LIP NC3 103 2.309 2.019 2.930 + 18LIP PO4 104 2.328 1.999 3.398 + 18LIP GL1 105 2.340 2.046 3.861 + 18LIP C1A 106 2.303 2.059 4.361 + 18LIP C2A 107 2.268 2.089 4.809 + 18LIP C3A 108 2.217 2.095 5.332 + 2.40000 2.40000 7.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 +a small bilayer, each lipid moved and wrapped atom by atom + 108 + 1LIP NC3 1 0.026 0.918 4.147 + 1LIP PO4 2 0.081 0.897 3.661 + 1LIP GL1 3 0.127 0.936 3.210 + 1LIP C1A 4 0.180 0.878 2.726 + 1LIP C2A 5 0.254 0.922 2.250 + 1LIP C3A 6 0.268 0.887 1.749 + 2LIP NC3 7 2.255 1.289 4.083 + 2LIP PO4 8 2.311 1.289 3.626 + 2LIP GL1 9 2.359 1.265 3.136 + 2LIP C1A 10 0.002 1.262 2.623 + 2LIP C2A 11 0.048 1.258 2.207 + 2LIP C3A 12 0.095 1.214 1.688 + 3LIP NC3 13 2.040 0.118 4.105 + 3LIP PO4 14 2.074 0.109 3.607 + 3LIP GL1 15 2.143 0.039 3.148 + 3LIP C1A 16 2.202 0.004 2.682 + 3LIP C2A 17 2.217 2.343 2.179 + 3LIP C3A 18 2.251 2.274 1.728 + 4LIP NC3 19 0.860 0.239 4.066 + 4LIP PO4 20 0.790 0.230 3.552 + 4LIP GL1 21 0.780 0.230 3.081 + 4LIP C1A 22 0.724 0.242 2.607 + 4LIP C2A 23 0.696 0.232 2.161 + 4LIP C3A 24 0.639 0.261 1.713 + 5LIP NC3 25 1.028 1.275 4.117 + 5LIP PO4 26 0.994 1.234 3.693 + 5LIP GL1 27 1.003 1.237 3.208 + 5LIP C1A 28 0.946 1.226 2.736 + 5LIP C2A 29 0.876 1.153 2.258 + 5LIP C3A 30 0.841 1.142 1.759 + 6LIP NC3 31 0.812 1.933 4.168 + 6LIP PO4 32 0.822 1.992 3.630 + 6LIP GL1 33 0.810 2.001 3.194 + 6LIP C1A 34 0.827 1.993 2.724 + 6LIP C2A 35 0.767 2.019 2.284 + 6LIP C3A 36 0.738 1.975 1.792 + 7LIP NC3 37 1.637 0.106 4.081 + 7LIP PO4 38 1.644 0.129 3.647 + 7LIP GL1 39 1.642 0.166 3.151 + 7LIP C1A 40 1.601 0.193 2.681 + 7LIP C2A 41 1.569 0.225 2.208 + 7LIP C3A 42 1.558 0.279 1.776 + 8LIP NC3 43 1.650 1.382 4.244 + 8LIP PO4 44 1.656 1.377 3.804 + 8LIP GL1 45 1.624 1.368 3.292 + 8LIP C1A 46 1.596 1.379 2.825 + 8LIP C2A 47 1.598 1.359 2.397 + 8LIP C3A 48 1.565 1.378 1.891 + 9LIP NC3 49 1.464 1.710 4.086 + 9LIP PO4 50 1.456 1.722 3.626 + 9LIP GL1 51 1.482 1.697 3.172 + 9LIP C1A 52 1.432 1.695 2.695 + 9LIP C2A 53 1.451 1.680 2.179 + 9LIP C3A 54 1.446 1.660 1.726 + 10LIP NC3 55 2.286 1.693 5.868 + 10LIP PO4 56 2.328 1.601 6.339 + 10LIP GL1 57 2.343 1.523 6.839 + 10LIP C1A 58 0.001 1.407 0.258 + 10LIP C2A 59 0.026 1.358 0.702 + 10LIP C3A 60 0.063 1.252 1.208 + 11LIP NC3 61 0.053 1.723 5.830 + 11LIP PO4 62 0.059 1.765 6.367 + 11LIP GL1 63 0.063 1.747 6.808 + 11LIP C1A 64 0.077 1.751 0.298 + 11LIP C2A 65 0.069 1.800 0.739 + 11LIP C3A 66 0.104 1.823 1.236 + 12LIP NC3 67 1.171 2.194 5.861 + 12LIP PO4 68 1.048 2.233 6.367 + 12LIP GL1 69 0.979 2.260 6.809 + 12LIP C1A 70 0.854 2.292 0.282 + 12LIP C2A 71 0.743 2.318 0.779 + 12LIP C3A 72 0.673 2.374 1.215 + 13LIP NC3 73 1.267 1.369 5.866 + 13LIP PO4 74 1.247 1.305 6.366 + 13LIP GL1 75 1.219 1.260 6.830 + 13LIP C1A 76 1.165 1.169 0.286 + 13LIP C2A 77 1.153 1.158 0.769 + 13LIP C3A 78 1.126 1.075 1.244 + 14LIP NC3 79 0.841 1.785 5.939 + 14LIP PO4 80 0.917 1.761 6.395 + 14LIP GL1 81 1.029 1.697 6.853 + 14LIP C1A 82 1.138 1.700 0.337 + 14LIP C2A 83 1.221 1.684 0.816 + 14LIP C3A 84 1.269 1.699 1.308 + 15LIP NC3 85 1.169 2.105 5.882 + 15LIP PO4 86 1.175 2.108 6.393 + 15LIP GL1 87 1.230 2.136 6.856 + 15LIP C1A 88 1.333 2.124 0.356 + 15LIP C2A 89 1.381 2.184 0.805 + 15LIP C3A 90 1.446 2.222 1.295 + 16LIP NC3 91 1.745 0.775 5.926 + 16LIP PO4 92 1.789 0.777 6.389 + 16LIP GL1 93 1.826 0.824 6.859 + 16LIP C1A 94 1.863 0.829 0.349 + 16LIP C2A 95 1.866 0.817 0.841 + 16LIP C3A 96 1.890 0.851 1.277 + 17LIP NC3 97 1.853 1.493 5.937 + 17LIP PO4 98 1.847 1.522 6.406 + 17LIP GL1 99 1.842 1.490 6.843 + 17LIP C1A 100 1.907 1.514 0.304 + 17LIP C2A 101 1.964 1.473 0.753 + 17LIP C3A 102 1.979 1.461 1.222 + 18LIP NC3 103 2.078 0.152 5.914 + 18LIP PO4 104 2.010 0.202 6.348 + 18LIP GL1 105 1.980 0.216 6.821 + 18LIP C1A 106 1.967 0.262 0.314 + 18LIP C2A 107 1.978 0.269 0.765 + 18LIP C3A 108 1.940 0.251 1.240 + 2.40000 2.40000 7.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 +a small bilayer, each lipid moved and wrapped atom by atom + 108 + 1LIP NC3 1 0.146 0.735 1.117 + 1LIP PO4 2 0.195 0.704 0.653 + 1LIP GL1 3 0.196 0.673 0.163 + 1LIP C1A 4 0.272 0.694 6.698 + 1LIP C2A 5 0.338 0.674 6.229 + 1LIP C3A 6 0.350 0.694 5.781 + 2LIP NC3 7 2.331 1.390 1.002 + 2LIP PO4 8 0.009 1.401 0.580 + 2LIP GL1 9 0.029 1.381 0.100 + 2LIP C1A 10 0.053 1.337 6.602 + 2LIP C2A 11 0.080 1.364 6.159 + 2LIP C3A 12 0.103 1.315 5.713 + 3LIP NC3 13 0.198 0.100 1.130 + 3LIP PO4 14 0.248 0.062 0.658 + 3LIP GL1 15 0.335 0.033 0.179 + 3LIP C1A 16 0.354 2.345 6.741 + 3LIP C2A 17 0.425 2.289 6.269 + 3LIP C3A 18 0.449 2.248 5.786 + 4LIP NC3 19 1.160 0.553 1.127 + 4LIP PO4 20 1.122 0.554 0.675 + 4LIP GL1 21 1.083 0.577 0.162 + 4LIP C1A 22 1.061 0.584 6.747 + 4LIP C2A 23 1.002 0.580 6.323 + 4LIP C3A 24 0.980 0.628 5.787 + 5LIP NC3 25 1.520 1.548 1.097 + 5LIP PO4 26 1.481 1.561 0.605 + 5LIP GL1 27 1.450 1.527 0.198 + 5LIP C1A 28 1.448 1.475 6.667 + 5LIP C2A 29 1.443 1.458 6.220 + 5LIP C3A 30 1.343 1.432 5.750 + 6LIP NC3 31 1.027 1.686 1.137 + 6LIP PO4 32 1.041 1.721 0.667 + 6LIP GL1 33 1.023 1.700 0.183 + 6LIP C1A 34 0.961 1.664 6.698 + 6LIP C2A 35 0.970 1.702 6.229 + 6LIP C3A 36 0.984 1.743 5.765 + 7LIP NC3 37 2.052 2.303 1.061 + 7LIP PO4 38 2.014 2.334 0.622 + 7LIP GL1 39 2.005 2.375 0.173 + 7LIP C1A 40 1.968 0.014 6.640 + 7LIP C2A 41 1.932 0.056 6.221 + 7LIP C3A 42 1.975 0.045 5.729 + 8LIP NC3 43 2.188 0.880 1.096 + 8LIP PO4 44 2.181 0.863 0.632 + 8LIP GL1 45 2.219 0.861 0.169 + 8LIP C1A 46 2.191 0.920 6.693 + 8LIP C2A 47 2.160 0.894 6.232 + 8LIP C3A 48 2.121 0.877 5.766 + 9LIP NC3 49 1.990 2.075 1.061 + 9LIP PO4 50 1.937 2.086 0.602 + 9LIP GL1 51 1.929 2.038 0.130 + 9LIP C1A 52 1.941 2.061 6.708 + 9LIP C2A 53 1.938 2.073 6.207 + 9LIP C3A 54 1.898 2.039 5.708 + 10LIP NC3 55 0.626 1.564 2.824 + 10LIP PO4 56 0.699 1.441 3.302 + 10LIP GL1 57 0.733 1.364 3.753 + 10LIP C1A 58 0.747 1.245 4.262 + 10LIP C2A 59 0.803 1.176 4.691 + 10LIP C3A 60 0.852 1.090 5.171 + 11LIP NC3 61 1.263 1.473 2.845 + 11LIP PO4 62 1.279 1.531 3.334 + 11LIP GL1 63 1.288 1.542 3.762 + 11LIP C1A 64 1.306 1.572 4.272 + 11LIP C2A 65 1.338 1.547 4.746 + 11LIP C3A 66 1.350 1.617 5.157 + 12LIP NC3 67 1.217 0.076 2.961 + 12LIP PO4 68 1.088 0.170 3.470 + 12LIP GL1 69 0.999 0.214 3.940 + 12LIP C1A 70 0.927 0.210 4.342 + 12LIP C2A 71 0.824 0.218 4.859 + 12LIP C3A 72 0.709 0.241 5.282 + 13LIP NC3 73 1.565 1.371 2.895 + 13LIP PO4 74 1.495 1.338 3.359 + 13LIP GL1 75 1.456 1.251 3.857 + 13LIP C1A 76 1.453 1.205 4.310 + 13LIP C2A 77 1.453 1.126 4.764 + 13LIP C3A 78 1.403 1.070 5.232 + 14LIP NC3 79 1.346 1.542 2.890 + 14LIP PO4 80 1.412 1.546 3.315 + 14LIP GL1 81 1.538 1.547 3.796 + 14LIP C1A 82 1.606 1.518 4.268 + 14LIP C2A 83 1.645 1.491 4.744 + 14LIP C3A 84 1.773 1.478 5.225 + 15LIP NC3 85 1.572 0.121 2.829 + 15LIP PO4 86 1.656 0.095 3.288 + 15LIP GL1 87 1.727 0.161 3.803 + 15LIP C1A 88 1.743 0.127 4.250 + 15LIP C2A 89 1.784 0.166 4.756 + 15LIP C3A 90 1.864 0.196 5.201 + 16LIP NC3 91 1.989 0.911 2.892 + 16LIP PO4 92 2.064 1.015 3.344 + 16LIP GL1 93 2.040 0.965 3.816 + 16LIP C1A 94 2.119 0.965 4.264 + 16LIP C2A 95 2.128 1.012 4.785 + 16LIP C3A 96 2.122 1.097 5.235 + 17LIP NC3 97 2.159 1.345 2.890 + 17LIP PO4 98 2.194 1.283 3.362 + 17LIP GL1 99 2.248 1.276 3.827 + 17LIP C1A 100 2.263 1.273 4.281 + 17LIP C2A 101 2.282 1.236 4.755 + 17LIP C3A 102 2.319 1.257 5.256 + 18LIP NC3 103 0.409 2.225 2.970 + 18LIP PO4 104 0.367 2.283 3.391 + 18LIP GL1 105 0.387 2.268 3.889 + 18LIP C1A 106 0.336 2.302 4.365 + 18LIP C2A 107 0.325 2.345 4.798 + 18LIP C3A 108 0.321 2.359 5.268 + 2.40000 2.40000 7.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 diff --git a/regtest/basic/rt-molinfo-whole-membrane/warnings.reference b/regtest/basic/rt-molinfo-whole-membrane/warnings.reference new file mode 100644 index 0000000000..5087c9864a --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/warnings.reference @@ -0,0 +1,5 @@ +# out_sep +Action WHOLEMOLECULES +# out +Action WHOLEMOLECULES +WARNING for action MOLINFO with label @0 : the reference structure in the MOLINFO pdb file may not be whole: 102 of its 108 atoms here are closer to a periodic image of the others, in the box of its CRYST1 record, than to the others themselves. Atoms: 7 (LIP2) 8 (LIP2) 9 (LIP2) 10 (LIP2) 11 (LIP2) 12 (LIP2) 13 (LIP3) 14 (LIP3) 15 (LIP3) 16 (LIP3) and 92 more diff --git a/regtest/basic/rt-molinfo-whole-membrane/whole.xyz.reference b/regtest/basic/rt-molinfo-whole-membrane/whole.xyz.reference new file mode 100644 index 0000000000..8e4d6af5b0 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/whole.xyz.reference @@ -0,0 +1,330 @@ +108 + 2.400 2.400 7.000 +NC3 2.374 0.135 1.087 +PO4 2.377 0.135 0.572 +GL1 2.480 0.160 0.143 +C1A 2.495 0.121 -0.345 +C2A 2.575 0.115 -0.820 +C3A 2.625 0.114 -1.312 +NC3 2.047 0.894 1.137 +PO4 2.103 0.831 0.671 +GL1 2.128 0.838 0.184 +C1A 2.202 0.874 -0.293 +C2A 2.214 0.815 -0.735 +C3A 2.295 0.804 -1.201 +NC3 2.354 2.071 1.062 +PO4 2.354 1.995 0.576 +GL1 2.425 1.919 0.114 +C1A 2.430 1.881 -0.339 +C2A 2.516 1.852 -0.830 +C3A 2.492 1.830 -1.292 +NC3 3.771 -0.077 1.185 +PO4 3.697 -0.116 0.678 +GL1 3.675 -0.104 0.229 +C1A 3.667 -0.066 -0.264 +C2A 3.632 -0.097 -0.751 +C3A 3.585 -0.097 -1.250 +NC3 3.886 0.681 1.119 +PO4 3.832 0.678 0.643 +GL1 3.850 0.682 0.139 +C1A 3.781 0.613 -0.310 +C2A 3.689 0.611 -0.783 +C3A 3.686 0.594 -1.235 +NC3 4.030 1.314 1.137 +PO4 3.994 1.327 0.659 +GL1 4.000 1.312 0.172 +C1A 3.981 1.303 -0.272 +C2A 3.963 1.364 -0.726 +C3A 3.911 1.322 -1.235 +NC3 4.858 0.051 1.098 +PO4 4.769 0.076 0.613 +GL1 4.770 0.052 0.158 +C1A 4.687 0.136 -0.283 +C2A 4.677 0.144 -0.767 +C3A 4.717 0.211 -1.280 +NC3 4.124 0.920 1.104 +PO4 4.098 0.890 0.638 +GL1 4.083 0.941 0.141 +C1A 4.100 0.934 -0.353 +C2A 4.074 0.915 -0.791 +C3A 4.078 0.928 -1.232 +NC3 4.104 1.872 1.091 +PO4 4.135 1.908 0.632 +GL1 4.092 1.835 0.167 +C1A 4.127 1.855 -0.296 +C2A 4.047 1.851 -0.756 +C3A 4.086 1.838 -1.247 +NC3 3.170 1.306 -4.158 +PO4 3.196 1.239 -3.692 +GL1 3.264 1.077 -3.191 +C1A 3.245 1.054 -2.756 +C2A 3.300 0.949 -2.277 +C3A 3.389 0.881 -1.810 +NC3 2.992 0.833 -4.081 +PO4 2.962 0.843 -3.665 +GL1 3.025 0.856 -3.176 +C1A 3.003 0.896 -2.689 +C2A 3.040 0.916 -2.215 +C3A 3.039 0.973 -1.753 +NC3 3.719 2.090 -4.123 +PO4 3.655 2.086 -3.681 +GL1 3.533 2.155 -3.159 +C1A 3.496 2.213 -2.746 +C2A 3.369 2.183 -2.236 +C3A 3.255 2.221 -1.785 +NC3 3.919 0.339 -4.071 +PO4 3.870 0.256 -3.620 +GL1 3.795 0.212 -3.141 +C1A 3.792 0.104 -2.674 +C2A 3.718 0.085 -2.180 +C3A 3.770 0.004 -1.739 +NC3 3.504 1.326 -4.099 +PO4 3.592 1.309 -3.616 +GL1 3.610 1.299 -3.121 +C1A 3.739 1.274 -2.695 +C2A 3.810 1.302 -2.197 +C3A 3.910 1.265 -1.764 +NC3 3.499 1.738 -4.012 +PO4 3.536 1.751 -3.561 +GL1 3.557 1.795 -3.078 +C1A 3.627 1.783 -2.581 +C2A 3.703 1.850 -2.086 +C3A 3.771 1.881 -1.645 +NC3 4.352 0.348 -4.122 +PO4 4.415 0.387 -3.594 +GL1 4.431 0.433 -3.184 +C1A 4.476 0.421 -2.693 +C2A 4.492 0.443 -2.234 +C3A 4.446 0.475 -1.731 +NC3 4.512 1.210 -4.006 +PO4 4.539 1.202 -3.574 +GL1 4.566 1.196 -3.085 +C1A 4.618 1.170 -2.664 +C2A 4.656 1.098 -2.146 +C3A 4.660 1.145 -1.722 +NC3 4.709 2.019 -4.070 +PO4 4.728 1.999 -3.602 +GL1 4.740 2.046 -3.139 +C1A 4.703 2.059 -2.639 +C2A 4.668 2.089 -2.191 +C3A 4.617 2.095 -1.668 +108 + 2.400 2.400 7.000 +NC3 0.026 0.918 4.147 +PO4 0.081 0.897 3.661 +GL1 0.127 0.936 3.210 +C1A 0.180 0.878 2.726 +C2A 0.254 0.922 2.250 +C3A 0.268 0.887 1.749 +NC3 -0.145 1.289 4.083 +PO4 -0.089 1.289 3.626 +GL1 -0.041 1.265 3.136 +C1A 0.002 1.262 2.623 +C2A 0.048 1.258 2.207 +C3A 0.095 1.214 1.688 +NC3 -0.360 2.518 4.105 +PO4 -0.326 2.509 3.607 +GL1 -0.257 2.439 3.148 +C1A -0.198 2.404 2.682 +C2A -0.183 2.343 2.179 +C3A -0.149 2.274 1.728 +NC3 0.860 0.239 4.066 +PO4 0.790 0.230 3.552 +GL1 0.780 0.230 3.081 +C1A 0.724 0.242 2.607 +C2A 0.696 0.232 2.161 +C3A 0.639 0.261 1.713 +NC3 1.028 1.275 4.117 +PO4 0.994 1.234 3.693 +GL1 1.003 1.237 3.208 +C1A 0.946 1.226 2.736 +C2A 0.876 1.153 2.258 +C3A 0.841 1.142 1.759 +NC3 0.812 1.933 4.168 +PO4 0.822 1.992 3.630 +GL1 0.810 2.001 3.194 +C1A 0.827 1.993 2.724 +C2A 0.767 2.019 2.284 +C3A 0.738 1.975 1.792 +NC3 1.637 0.106 4.081 +PO4 1.644 0.129 3.647 +GL1 1.642 0.166 3.151 +C1A 1.601 0.193 2.681 +C2A 1.569 0.225 2.208 +C3A 1.558 0.279 1.776 +NC3 1.650 1.382 4.244 +PO4 1.656 1.377 3.804 +GL1 1.624 1.368 3.292 +C1A 1.596 1.379 2.825 +C2A 1.598 1.359 2.397 +C3A 1.565 1.378 1.891 +NC3 1.464 1.710 4.086 +PO4 1.456 1.722 3.626 +GL1 1.482 1.697 3.172 +C1A 1.432 1.695 2.695 +C2A 1.451 1.680 2.179 +C3A 1.446 1.660 1.726 +NC3 -0.114 1.693 -1.132 +PO4 -0.072 1.601 -0.661 +GL1 -0.057 1.523 -0.161 +C1A 0.001 1.407 0.258 +C2A 0.026 1.358 0.702 +C3A 0.063 1.252 1.208 +NC3 0.053 1.723 -1.170 +PO4 0.059 1.765 -0.633 +GL1 0.063 1.747 -0.192 +C1A 0.077 1.751 0.298 +C2A 0.069 1.800 0.739 +C3A 0.104 1.823 1.236 +NC3 1.171 2.194 -1.139 +PO4 1.048 2.233 -0.633 +GL1 0.979 2.260 -0.191 +C1A 0.854 2.292 0.282 +C2A 0.743 2.318 0.779 +C3A 0.673 2.374 1.215 +NC3 1.267 1.369 -1.134 +PO4 1.247 1.305 -0.634 +GL1 1.219 1.260 -0.170 +C1A 1.165 1.169 0.286 +C2A 1.153 1.158 0.769 +C3A 1.126 1.075 1.244 +NC3 0.841 1.785 -1.061 +PO4 0.917 1.761 -0.605 +GL1 1.029 1.697 -0.147 +C1A 1.138 1.700 0.337 +C2A 1.221 1.684 0.816 +C3A 1.269 1.699 1.308 +NC3 1.169 2.105 -1.118 +PO4 1.175 2.108 -0.607 +GL1 1.230 2.136 -0.144 +C1A 1.333 2.124 0.356 +C2A 1.381 2.184 0.805 +C3A 1.446 2.222 1.295 +NC3 1.745 0.775 -1.074 +PO4 1.789 0.777 -0.611 +GL1 1.826 0.824 -0.141 +C1A 1.863 0.829 0.349 +C2A 1.866 0.817 0.841 +C3A 1.890 0.851 1.277 +NC3 1.853 1.493 -1.063 +PO4 1.847 1.522 -0.594 +GL1 1.842 1.490 -0.157 +C1A 1.907 1.514 0.304 +C2A 1.964 1.473 0.753 +C3A 1.979 1.461 1.222 +NC3 2.078 2.552 -1.086 +PO4 2.010 2.602 -0.652 +GL1 1.980 2.616 -0.179 +C1A 1.967 2.662 0.314 +C2A 1.978 2.669 0.765 +C3A 1.940 2.651 1.240 +108 + 2.400 2.400 7.000 +NC3 0.146 0.735 1.117 +PO4 0.195 0.704 0.653 +GL1 0.196 0.673 0.163 +C1A 0.272 0.694 -0.302 +C2A 0.338 0.674 -0.771 +C3A 0.350 0.694 -1.219 +NC3 -0.069 1.390 1.002 +PO4 0.009 1.401 0.580 +GL1 0.029 1.381 0.100 +C1A 0.053 1.337 -0.398 +C2A 0.080 1.364 -0.841 +C3A 0.103 1.315 -1.287 +NC3 0.198 2.500 1.130 +PO4 0.248 2.462 0.658 +GL1 0.335 2.433 0.179 +C1A 0.354 2.345 -0.259 +C2A 0.425 2.289 -0.731 +C3A 0.449 2.248 -1.214 +NC3 1.160 0.553 1.127 +PO4 1.122 0.554 0.675 +GL1 1.083 0.577 0.162 +C1A 1.061 0.584 -0.253 +C2A 1.002 0.580 -0.677 +C3A 0.980 0.628 -1.213 +NC3 1.520 1.548 1.097 +PO4 1.481 1.561 0.605 +GL1 1.450 1.527 0.198 +C1A 1.448 1.475 -0.333 +C2A 1.443 1.458 -0.780 +C3A 1.343 1.432 -1.250 +NC3 1.027 1.686 1.137 +PO4 1.041 1.721 0.667 +GL1 1.023 1.700 0.183 +C1A 0.961 1.664 -0.302 +C2A 0.970 1.702 -0.771 +C3A 0.984 1.743 -1.235 +NC3 2.052 -0.097 1.061 +PO4 2.014 -0.066 0.622 +GL1 2.005 -0.025 0.173 +C1A 1.968 0.014 -0.360 +C2A 1.932 0.056 -0.779 +C3A 1.975 0.045 -1.271 +NC3 2.188 0.880 1.096 +PO4 2.181 0.863 0.632 +GL1 2.219 0.861 0.169 +C1A 2.191 0.920 -0.307 +C2A 2.160 0.894 -0.768 +C3A 2.121 0.877 -1.234 +NC3 1.990 2.075 1.061 +PO4 1.937 2.086 0.602 +GL1 1.929 2.038 0.130 +C1A 1.941 2.061 -0.292 +C2A 1.938 2.073 -0.793 +C3A 1.898 2.039 -1.292 +NC3 0.626 1.564 -4.176 +PO4 0.699 1.441 -3.698 +GL1 0.733 1.364 -3.247 +C1A 0.747 1.245 -2.738 +C2A 0.803 1.176 -2.309 +C3A 0.852 1.090 -1.829 +NC3 1.263 1.473 -4.155 +PO4 1.279 1.531 -3.666 +GL1 1.288 1.542 -3.238 +C1A 1.306 1.572 -2.728 +C2A 1.338 1.547 -2.254 +C3A 1.350 1.617 -1.843 +NC3 1.217 2.476 -4.039 +PO4 1.088 2.570 -3.530 +GL1 0.999 2.614 -3.060 +C1A 0.927 2.610 -2.658 +C2A 0.824 2.618 -2.141 +C3A 0.709 2.641 -1.718 +NC3 1.565 1.371 -4.105 +PO4 1.495 1.338 -3.641 +GL1 1.456 1.251 -3.143 +C1A 1.453 1.205 -2.690 +C2A 1.453 1.126 -2.236 +C3A 1.403 1.070 -1.768 +NC3 1.346 1.542 -4.110 +PO4 1.412 1.546 -3.685 +GL1 1.538 1.547 -3.204 +C1A 1.606 1.518 -2.732 +C2A 1.645 1.491 -2.256 +C3A 1.773 1.478 -1.775 +NC3 1.572 2.521 -4.171 +PO4 1.656 2.495 -3.712 +GL1 1.727 2.561 -3.197 +C1A 1.743 2.527 -2.750 +C2A 1.784 2.566 -2.244 +C3A 1.864 2.596 -1.799 +NC3 1.989 0.911 -4.108 +PO4 2.064 1.015 -3.656 +GL1 2.040 0.965 -3.184 +C1A 2.119 0.965 -2.736 +C2A 2.128 1.012 -2.215 +C3A 2.122 1.097 -1.765 +NC3 2.159 1.345 -4.110 +PO4 2.194 1.283 -3.638 +GL1 2.248 1.276 -3.173 +C1A 2.263 1.273 -2.719 +C2A 2.282 1.236 -2.245 +C3A 2.319 1.257 -1.744 +NC3 2.809 2.225 -4.030 +PO4 2.767 2.283 -3.609 +GL1 2.787 2.268 -3.111 +C1A 2.736 2.302 -2.635 +C2A 2.725 2.345 -2.202 +C3A 2.721 2.359 -1.732 diff --git a/src/core/GenericMolInfo.cpp b/src/core/GenericMolInfo.cpp index cfc8ead008..63e93d407d 100644 --- a/src/core/GenericMolInfo.cpp +++ b/src/core/GenericMolInfo.cpp @@ -49,7 +49,7 @@ void GenericMolInfo::registerKeywords( Keywords& keys ) { keys.add("compulsory","PYTHON_BIN","default","python interpreter"); keys.add("atoms","CHAIN","(for masochists ( mostly Davide Branduardi ) ) The atoms involved in each of the chains of interest in the structure."); keys.add("hidden","STRIDE","frequency for resetting the python interpreter. Should be 1."); - keys.addFlag("WHOLE", false, "The reference structure is whole, i.e. not broken by PBC. If the pdb file has a CRYST1 record with space group P 1, this is checked for the atoms of each group that is made whole with it"); + keys.addFlag("WHOLE", false, "The reference structure is whole, i.e. not broken by PBC. If the pdb file has a CRYST1 record with space group P 1, this is checked for the atoms of each group that is made whole with it, and a warning is written to the log if some of them are closer to a periodic image of the others than to the others themselves"); } GenericMolInfo::~GenericMolInfo() { diff --git a/src/tools/Tree.cpp b/src/tools/Tree.cpp index 99b6685e4f..92e3449038 100644 --- a/src/tools/Tree.cpp +++ b/src/tools/Tree.cpp @@ -31,6 +31,7 @@ #include #include #include +#include namespace PLMD { @@ -294,13 +295,19 @@ void Tree::checkReferenceIsWhole(const std::vector & atoms, if(moved.size()>10) { list+=" and "+std::to_string(moved.size()-10)+" more"; } - plumed_error()<<"the reference structure in the MOLINFO pdb file is not whole: "<warning(msg.str()); } } diff --git a/src/tools/Tree.h b/src/tools/Tree.h index 0cf64dc75b..b7f3ee0c48 100644 --- a/src/tools/Tree.h +++ b/src/tools/Tree.h @@ -41,7 +41,7 @@ class Tree { std::vector root_indexes_; std::vector tree_indexes_; -/// Raise an error if the reference structure is split by the periodic boundary +/// Write a warning to the log if the reference structure looks split by the periodic boundary void checkReferenceIsWhole(const std::vector & atoms, const std::vector & newatoms, const std::vector & positions, From a2515433cd3e92d094079e77f3707b2bbaf9eb83 Mon Sep 17 00:00:00 2001 From: Amr ALHOSSARY Date: Mon, 19 Oct 2026 15:22:03 -0400 Subject: [PATCH 4/4] MOLINFO WHOLE: check the reference along each chain As suggested in the review: replace the second, minimum-image spanning tree with a short check when MOLINFO reads the pdb. Along each chain, the step between two consecutive atoms of a residue, or of two consecutive protein or nucleic-acid residues, must be its own minimum image in the box of the CRYST1 record. If not, a warning names the atoms that are across the periodic boundary from the atom before them. The check no longer looks at the groups of WHOLEMOLECULES, so a ligand in its own chain, or a membrane whose lipids are each a residue, gives no warning. Tree is unchanged from master. rt-molinfo-whole-check gains a DNA chain (chain A of 1BNA) wrapped nucleotide by nucleotide, so that only steps between residues cross the boundary. PDB keeps residue names as written (" DA"), so they are trimmed on both sides before MolDataClass::allowedResidue. --- CHANGES/v2.11.md | 2 +- .../basic/rt-molinfo-whole-check/dna_torn.pdb | 245 ++++++++++++++++++ .../rt-molinfo-whole-check/dna_whole.pdb | 245 ++++++++++++++++++ regtest/basic/rt-molinfo-whole-check/main.cpp | 16 +- .../rt-molinfo-whole-check/output.reference | 5 +- regtest/basic/rt-molinfo-whole-ligand/config | 4 +- .../basic/rt-molinfo-whole-ligand/plumed.dat | 2 +- .../warnings.reference | 1 - .../basic/rt-molinfo-whole-membrane/config | 4 +- .../rt-molinfo-whole-membrane/plumed.dat | 2 +- .../warnings.reference | 1 - src/core/GenericMolInfo.cpp | 89 +++++-- src/core/GenericMolInfo.h | 7 - src/tools/Tree.cpp | 181 ------------- src/tools/Tree.h | 6 - 15 files changed, 577 insertions(+), 233 deletions(-) create mode 100644 regtest/basic/rt-molinfo-whole-check/dna_torn.pdb create mode 100644 regtest/basic/rt-molinfo-whole-check/dna_whole.pdb diff --git a/CHANGES/v2.11.md b/CHANGES/v2.11.md index ceb5c20806..aaf421e666 100644 --- a/CHANGES/v2.11.md +++ b/CHANGES/v2.11.md @@ -5,7 +5,7 @@ This page contains changes that will end up in 2.11 ### Changes relevant for users: - When using [MOLINFO](MOLINFO.md) with the `WHOLE` flag, PBCs in the following actions will be reconstructed using a minimum spanning tree based on the coordinates stored in the MOLFILE reference pdb. - - When the reference pdb of [MOLINFO](MOLINFO.md) with the `WHOLE` flag has a CRYST1 record with space group P 1, PLUMED now checks that the reference is really whole in that box, and writes a warning to the log naming the atoms that seem to be on the wrong side of the periodic boundary. Before, a split reference made [WHOLEMOLECULES](WHOLEMOLECULES.md) split whole molecules without any warning. + - When the reference pdb of [MOLINFO](MOLINFO.md) with the `WHOLE` flag has a CRYST1 record with space group P 1, PLUMED now checks along each chain that the reference is whole in that box, and writes a warning to the log naming the atoms that are across the periodic boundary from the atom before them. Before, a split reference made [WHOLEMOLECULES](WHOLEMOLECULES.md) split whole molecules without any warning. - When using the benchmark now it is possible to scale the atom distances in the synthetic atom distribution (the base atomic distance is 1) - [SAXS](SAXS.md) now accepts the `MARTINI_FF` keyword to select the Martini form-factor generation: `MARTINI_FF=2` (default) keeps the existing Martini 2.2 protein and nucleic-acid form factors, while `MARTINI_FF=3` selects Martini 3 protein form factors. - Added environment variable `PLUMED_LOG_FILE` to control the log file pathname when runnning with GROMACS (the log file was hardcoded as `PLUMED.OUT`) diff --git a/regtest/basic/rt-molinfo-whole-check/dna_torn.pdb b/regtest/basic/rt-molinfo-whole-check/dna_torn.pdb new file mode 100644 index 0000000000..060cf91ff4 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-check/dna_torn.pdb @@ -0,0 +1,245 @@ +CRYST1 47.018 47.018 47.018 60.00 60.00 90.00 P 1 1 +ATOM 1 O5' DC A 1 31.610 35.993 16.129 1.00 64.35 O +ATOM 2 C5' DC A 1 31.805 35.719 14.731 1.00 44.69 C +ATOM 3 C4' DC A 1 32.636 34.466 14.612 1.00 31.28 C +ATOM 4 O4' DC A 1 32.035 33.381 15.364 1.00 37.45 O +ATOM 5 C3' DC A 1 32.847 33.920 13.206 1.00 46.72 C +ATOM 6 O3' DC A 1 34.025 33.123 13.193 1.00 48.89 O +ATOM 7 C2' DC A 1 31.623 33.021 13.159 1.00 30.88 C +ATOM 8 C1' DC A 1 31.906 32.280 14.456 1.00 36.58 C +ATOM 9 N1 DC A 1 30.745 31.459 14.892 1.00 40.51 N +ATOM 10 C2 DC A 1 30.899 30.252 15.527 1.00 16.62 C +ATOM 11 O2 DC A 1 32.035 29.812 15.726 1.00 27.75 O +ATOM 12 N3 DC A 1 29.818 29.559 15.889 1.00 20.55 N +ATOM 13 C4 DC A 1 28.592 30.024 15.632 1.00 34.72 C +ATOM 14 N4 DC A 1 27.503 29.275 15.956 1.00 40.31 N +ATOM 15 C5 DC A 1 28.394 31.240 14.983 1.00 30.78 C +ATOM 16 C6 DC A 1 29.518 31.969 14.613 1.00 25.90 C +ATOM 17 P DG A 2 35.084 33.084 11.995 1.00 58.85 P +ATOM 18 OP1 DG A 2 36.211 33.955 12.363 1.00 57.82 O +ATOM 19 OP2 DG A 2 34.497 33.257 10.651 1.00 78.33 O +ATOM 20 O5' DG A 2 35.515 31.549 12.010 1.00 40.36 O +ATOM 21 C5' DG A 2 36.218 30.973 13.106 1.00 47.19 C +ATOM 22 C4' DG A 2 36.169 29.507 12.791 1.00 47.81 C +ATOM 23 O4' DG A 2 34.868 29.050 13.186 1.00 38.76 O +ATOM 24 C3' DG A 2 36.368 29.123 11.319 1.00 28.58 C +ATOM 25 O3' DG A 2 37.398 28.118 11.165 1.00 40.44 O +ATOM 26 C2' DG A 2 34.948 28.683 10.928 1.00 21.14 C +ATOM 27 C1' DG A 2 34.396 28.102 12.228 1.00 33.95 C +ATOM 28 N9 DG A 2 32.912 28.268 12.292 1.00 34.00 N +ATOM 29 C8 DG A 2 32.201 29.382 11.941 1.00 36.47 C +ATOM 30 N7 DG A 2 30.882 29.253 12.148 1.00 32.37 N +ATOM 31 C5 DG A 2 30.758 28.010 12.654 1.00 15.06 C +ATOM 32 C6 DG A 2 29.579 27.323 13.057 1.00 11.88 C +ATOM 33 O6 DG A 2 28.414 27.714 13.030 1.00 21.30 O +ATOM 34 N1 DG A 2 29.872 26.077 13.549 1.00 15.44 N +ATOM 35 C2 DG A 2 31.109 25.515 13.667 1.00 9.63 C +ATOM 36 N2 DG A 2 31.183 24.254 14.180 1.00 16.69 N +ATOM 37 N3 DG A 2 32.212 26.158 13.282 1.00 30.98 N +ATOM 38 C4 DG A 2 31.965 27.392 12.786 1.00 18.56 C +ATOM 39 P DC A 3 37.739 27.419 9.764 1.00 44.67 P +ATOM 40 OP1 DC A 3 39.181 27.114 9.732 1.00 53.89 O +ATOM 41 OP2 DC A 3 37.234 28.210 8.627 1.00 57.79 O +ATOM 42 O5' DC A 3 36.935 26.044 9.839 1.00 35.42 O +ATOM 43 C5' DC A 3 37.259 25.083 10.847 1.00 45.75 C +ATOM 44 C4' DC A 3 36.198 24.031 10.757 1.00 43.02 C +ATOM 45 O4' DC A 3 34.931 24.642 10.965 1.00 36.85 O +ATOM 46 C3' DC A 3 36.099 23.355 9.415 1.00 40.14 C +ATOM 47 O3' DC A 3 36.796 22.107 9.440 1.00 49.62 O +ATOM 48 C2' DC A 3 34.605 23.204 9.173 1.00 53.79 C +ATOM 49 C1' DC A 3 33.953 23.764 10.421 1.00 22.18 C +ATOM 50 N1 DC A 3 32.871 24.687 10.033 1.00 25.44 N +ATOM 51 C2 DC A 3 31.584 24.382 10.328 1.00 19.81 C +ATOM 52 O2 DC A 3 31.360 23.310 10.894 1.00 29.92 O +ATOM 53 N3 DC A 3 30.610 25.245 10.014 1.00 21.59 N +ATOM 54 C4 DC A 3 30.892 26.401 9.409 1.00 14.01 C +ATOM 55 N4 DC A 3 29.896 27.297 9.141 1.00 26.88 N +ATOM 56 C5 DC A 3 32.201 26.743 9.083 1.00 27.59 C +ATOM 57 C6 DC A 3 33.212 25.846 9.411 1.00 27.05 C +ATOM 58 P DG A 4 36.924 21.210 8.129 1.00 44.54 P +ATOM 59 OP1 DG A 4 38.095 20.333 8.277 1.00 61.90 O +ATOM 60 OP2 DG A 4 36.883 22.094 6.952 1.00 37.36 O +ATOM 61 O5' DG A 4 35.606 20.335 8.182 1.00 32.01 O +ATOM 62 C5' DG A 4 35.389 19.423 9.265 1.00 37.89 C +ATOM 63 C4' DG A 4 34.068 18.758 9.017 1.00 53.00 C +ATOM 64 O4' DG A 4 33.028 19.750 9.008 1.00 38.79 O +ATOM 65 C3' DG A 4 33.939 18.027 7.688 1.00 56.72 C +ATOM 66 O3' DG A 4 32.959 17.012 7.750 1.00 64.12 O +ATOM 67 C2' DG A 4 33.468 19.166 6.800 1.00 40.81 C +ATOM 68 C1' DG A 4 32.391 19.699 7.730 1.00 30.52 C +ATOM 69 N9 DG A 4 31.980 21.079 7.381 1.00 28.53 N +ATOM 70 C8 DG A 4 32.692 22.061 6.744 1.00 27.82 C +ATOM 71 N7 DG A 4 31.988 23.192 6.589 1.00 28.01 N +ATOM 72 C5 DG A 4 30.796 22.898 7.147 1.00 23.22 C +ATOM 73 C6 DG A 4 29.627 23.702 7.261 1.00 29.21 C +ATOM 74 O6 DG A 4 29.444 24.855 6.880 1.00 38.58 O +ATOM 75 N1 DG A 4 28.608 23.012 7.864 1.00 27.94 N +ATOM 76 C2 DG A 4 28.647 21.728 8.328 1.00 23.44 C +ATOM 77 N2 DG A 4 27.506 21.214 8.865 1.00 42.64 N +ATOM 78 N3 DG A 4 29.743 20.977 8.229 1.00 21.56 N +ATOM 79 C4 DG A 4 30.759 21.623 7.633 1.00 23.44 C +ATOM 80 P DA A 5 33.031 15.767 6.757 1.00 57.01 P +ATOM 81 OP1 DA A 5 33.791 14.689 7.404 1.00 58.59 O +ATOM 82 OP2 DA A 5 33.512 16.221 5.422 1.00 51.96 O +ATOM 83 O5' DA A 5 31.485 15.379 6.673 1.00 47.12 O +ATOM 84 C5' DA A 5 30.690 15.367 7.874 1.00 47.67 C +ATOM 85 C4' DA A 5 29.347 15.886 7.469 1.00 64.79 C +ATOM 86 O4' DA A 5 29.517 17.245 7.073 1.00 47.60 O +ATOM 87 C3' DA A 5 28.694 15.191 6.276 1.00 51.50 C +ATOM 88 O3' DA A 5 27.437 14.594 6.632 1.00 52.18 O +ATOM 89 C2' DA A 5 28.627 16.296 5.208 1.00 45.00 C +ATOM 90 C1' DA A 5 28.526 17.530 6.081 1.00 26.88 C +ATOM 91 N9 DA A 5 29.066 18.714 5.379 1.00 16.69 N +ATOM 92 C8 DA A 5 30.333 18.901 4.894 1.00 28.14 C +ATOM 93 N7 DA A 5 30.538 20.144 4.425 1.00 34.85 N +ATOM 94 C5 DA A 5 29.348 20.751 4.610 1.00 22.49 C +ATOM 95 C6 DA A 5 28.905 22.077 4.331 1.00 18.12 C +ATOM 96 N6 DA A 5 29.720 23.020 3.780 1.00 29.30 N +ATOM 97 N1 DA A 5 27.641 22.376 4.630 1.00 27.61 N +ATOM 98 C2 DA A 5 26.853 21.450 5.181 1.00 18.53 C +ATOM 99 N3 DA A 5 27.138 20.190 5.496 1.00 29.16 N +ATOM 100 C4 DA A 5 28.425 19.908 5.173 1.00 15.08 C +ATOM 101 P DA A 6 26.541 13.804 5.575 1.00 43.68 P +ATOM 102 OP1 DA A 6 25.703 12.837 6.312 1.00 42.55 O +ATOM 103 OP2 DA A 6 27.390 13.297 4.480 1.00 54.20 O +ATOM 104 O5' DA A 6 25.554 14.909 4.992 1.00 28.20 O +ATOM 105 C5' DA A 6 24.477 15.395 5.802 1.00 42.29 C +ATOM 106 C4' DA A 6 23.786 16.401 4.947 1.00 33.23 C +ATOM 107 O4' DA A 6 24.827 17.258 4.474 1.00 41.48 O +ATOM 108 C3' DA A 6 23.092 15.868 3.699 1.00 18.16 C +ATOM 109 O3' DA A 6 21.682 16.167 3.693 1.00 30.42 O +ATOM 110 C2' DA A 6 23.915 16.490 2.573 1.00 52.97 C +ATOM 111 C1' DA A 6 24.374 17.772 3.231 1.00 38.93 C +ATOM 112 N9 DA A 6 25.593 18.324 2.590 1.00 19.06 N +ATOM 113 C8 DA A 6 26.790 17.697 2.380 1.00 17.83 C +ATOM 114 N7 DA A 6 27.724 18.512 1.868 1.00 29.55 N +ATOM 115 C5 DA A 6 27.091 19.699 1.758 1.00 19.88 C +ATOM 116 C6 DA A 6 27.548 20.985 1.327 1.00 17.26 C +ATOM 117 N6 DA A 6 28.836 21.216 0.939 1.00 19.85 N +ATOM 118 N1 DA A 6 26.674 21.989 1.364 1.00 17.93 N +ATOM 119 C2 DA A 6 25.428 21.760 1.784 1.00 23.00 C +ATOM 120 N3 DA A 6 24.885 20.622 2.210 1.00 21.37 N +ATOM 121 C4 DA A 6 25.791 19.621 2.169 1.00 15.93 C +ATOM 122 P DT A 7 44.265 39.357 35.674 1.00 40.72 P +ATOM 123 OP1 DT A 7 42.852 39.267 36.101 1.00 46.75 O +ATOM 124 OP2 DT A 7 44.784 38.201 34.896 1.00 42.53 O +ATOM 125 O5' DT A 7 44.423 40.694 34.835 1.00 35.21 O +ATOM 126 C5' DT A 7 44.091 41.942 35.445 1.00 34.88 C +ATOM 127 C4' DT A 7 44.346 42.935 34.357 1.00 31.45 C +ATOM 128 O4' DT A 7 45.727 42.887 34.038 1.00 46.82 O +ATOM 129 C3' DT A 7 43.645 42.591 33.055 1.00 23.76 C +ATOM 130 O3' DT A 7 42.435 43.341 32.921 1.00 44.27 O +ATOM 131 C2' DT A 7 44.716 42.834 31.982 1.00 26.30 C +ATOM 132 C1' DT A 7 45.828 43.516 32.778 1.00 28.96 C +ATOM 133 N1 DT A 7 47.205 43.210 32.324 1.00 20.47 N +ATOM 134 C2 DT A 7 48.006 44.230 31.935 1.00 28.01 C +ATOM 135 O2 DT A 7 47.567 45.384 31.902 1.00 40.01 O +ATOM 136 N3 DT A 7 49.303 43.948 31.611 1.00 27.94 N +ATOM 137 C4 DT A 7 49.817 42.679 31.641 1.00 15.14 C +ATOM 138 O4 DT A 7 51.014 42.529 31.378 1.00 32.54 O +ATOM 139 C5 DT A 7 48.965 41.632 31.994 1.00 10.83 C +ATOM 140 C7 DT A 7 49.453 40.209 31.995 1.00 36.33 C +ATOM 141 C6 DT A 7 47.649 41.923 32.353 1.00 12.19 C +ATOM 142 P DT A 8 41.568 43.297 31.583 1.00 49.10 P +ATOM 143 OP1 DT A 8 40.209 43.751 31.939 1.00 41.11 O +ATOM 144 OP2 DT A 8 41.642 41.975 30.919 1.00 39.21 O +ATOM 145 O5' DT A 8 42.270 44.425 30.686 1.00 48.80 O +ATOM 146 C5' DT A 8 42.330 45.785 31.177 1.00 34.73 C +ATOM 147 C4' DT A 8 43.179 46.536 30.197 1.00 28.73 C +ATOM 148 O4' DT A 8 44.372 45.765 30.043 1.00 39.07 O +ATOM 149 C3' DT A 8 42.602 46.639 28.788 1.00 37.88 C +ATOM 150 O3' DT A 8 42.151 47.974 28.455 1.00 52.04 O +ATOM 151 C2' DT A 8 43.697 46.025 27.898 1.00 32.80 C +ATOM 152 C1' DT A 8 44.920 46.162 28.793 1.00 36.58 C +ATOM 153 N1 DT A 8 46.007 45.183 28.518 1.00 24.57 N +ATOM 154 C2 DT A 8 47.270 45.623 28.253 1.00 19.41 C +ATOM 155 O2 DT A 8 47.508 46.823 28.148 1.00 32.74 O +ATOM 156 N3 DT A 8 48.278 44.710 28.171 1.00 25.12 N +ATOM 157 C4 DT A 8 48.060 43.367 28.310 1.00 31.35 C +ATOM 158 O4 DT A 8 49.042 42.624 28.262 1.00 28.53 O +ATOM 159 C5 DT A 8 46.753 42.918 28.524 1.00 22.80 C +ATOM 160 C7 DT A 8 46.445 41.447 28.655 1.00 24.98 C +ATOM 161 C6 DT A 8 45.729 43.855 28.663 1.00 20.28 C +ATOM 162 P DC A 9 41.715 48.378 26.968 1.00 48.97 P +ATOM 163 OP1 DC A 9 40.832 49.551 27.028 1.00 62.33 O +ATOM 164 OP2 DC A 9 41.194 47.212 26.229 1.00 51.53 O +ATOM 165 O5' DC A 9 43.110 48.854 26.370 1.00 43.99 O +ATOM 166 C5' DC A 9 43.820 49.934 27.008 1.00 50.86 C +ATOM 167 C4' DC A 9 45.081 50.160 26.216 1.00 46.66 C +ATOM 168 O4' DC A 9 45.822 48.934 26.207 1.00 42.69 O +ATOM 169 C3' DC A 9 44.901 50.547 24.757 1.00 56.96 C +ATOM 170 O3' DC A 9 45.654 51.721 24.426 1.00 63.54 O +ATOM 171 C2' DC A 9 45.310 49.272 24.012 1.00 50.41 C +ATOM 172 C1' DC A 9 46.425 48.790 24.916 1.00 41.08 C +ATOM 173 N1 DC A 9 46.708 47.329 24.774 1.00 37.23 N +ATOM 174 C2 DC A 9 47.998 46.910 24.599 1.00 40.54 C +ATOM 175 O2 DC A 9 48.875 47.754 24.429 1.00 43.89 O +ATOM 176 N3 DC A 9 48.290 45.604 24.632 1.00 32.57 N +ATOM 177 C4 DC A 9 47.325 44.702 24.805 1.00 24.65 C +ATOM 178 N4 DC A 9 47.645 43.382 24.848 1.00 27.84 N +ATOM 179 C5 DC A 9 45.987 45.082 24.936 1.00 17.61 C +ATOM 180 C6 DC A 9 45.683 46.440 24.926 1.00 30.63 C +ATOM 181 P DG A 10 45.239 52.640 23.178 1.00 65.48 P +ATOM 182 OP1 DG A 10 45.680 54.024 23.501 1.00 59.09 O +ATOM 183 OP2 DG A 10 43.816 52.413 22.812 1.00 45.71 O +ATOM 184 O5' DG A 10 46.138 52.072 21.988 1.00 70.30 O +ATOM 185 C5' DG A 10 47.566 52.247 22.039 1.00 71.73 C +ATOM 186 C4' DG A 10 48.156 51.397 20.957 1.00 58.69 C +ATOM 187 O4' DG A 10 47.986 50.031 21.355 1.00 41.03 O +ATOM 188 C3' DG A 10 47.511 51.485 19.571 1.00 45.61 C +ATOM 189 O3' DG A 10 48.495 51.403 18.545 1.00 52.70 O +ATOM 190 C2' DG A 10 46.598 50.269 19.573 1.00 36.02 C +ATOM 191 C1' DG A 10 47.613 49.335 20.172 1.00 50.90 C +ATOM 192 N9 DG A 10 47.074 48.020 20.559 1.00 45.86 N +ATOM 193 C8 DG A 10 45.800 47.622 20.849 1.00 44.49 C +ATOM 194 N7 DG A 10 45.725 46.316 21.146 1.00 39.96 N +ATOM 195 C5 DG A 10 47.002 45.895 21.041 1.00 38.99 C +ATOM 196 C6 DG A 10 47.560 44.599 21.248 1.00 35.78 C +ATOM 197 O6 DG A 10 46.997 43.559 21.580 1.00 34.90 O +ATOM 198 N1 DG A 10 48.913 44.606 21.039 1.00 23.54 N +ATOM 199 C2 DG A 10 49.682 45.672 20.677 1.00 8.73 C +ATOM 200 N2 DG A 10 51.018 45.476 20.522 1.00 23.15 N +ATOM 201 N3 DG A 10 49.166 46.880 20.492 1.00 24.68 N +ATOM 202 C4 DG A 10 47.840 46.908 20.698 1.00 31.53 C +ATOM 203 P DC A 11 48.947 52.728 17.779 1.00 60.62 P +ATOM 204 OP1 DC A 11 48.980 53.879 18.710 1.00 63.74 O +ATOM 205 OP2 DC A 11 48.070 52.849 16.595 1.00 52.44 O +ATOM 206 O5' DC A 11 50.456 52.393 17.393 1.00 57.57 O +ATOM 207 C5' DC A 11 51.459 52.415 18.441 1.00 54.70 C +ATOM 208 C4' DC A 11 52.406 51.253 18.249 1.00 72.51 C +ATOM 209 O4' DC A 11 51.627 50.061 18.362 1.00 47.18 O +ATOM 210 C3' DC A 11 53.126 51.134 16.911 1.00 29.82 C +ATOM 211 O3' DC A 11 54.524 50.818 17.058 1.00 43.53 O +ATOM 212 C2' DC A 11 52.302 50.074 16.181 1.00 51.34 C +ATOM 213 C1' DC A 11 52.040 49.143 17.345 1.00 30.07 C +ATOM 214 N1 DC A 11 50.856 48.282 17.122 1.00 23.25 N +ATOM 215 C2 DC A 11 50.986 46.935 17.230 1.00 20.38 C +ATOM 216 O2 DC A 11 52.108 46.485 17.445 1.00 38.77 O +ATOM 217 N3 DC A 11 49.907 46.149 17.132 1.00 15.92 N +ATOM 218 C4 DC A 11 48.699 46.680 16.923 1.00 15.82 C +ATOM 219 N4 DC A 11 47.594 45.881 16.887 1.00 28.04 N +ATOM 220 C5 DC A 11 48.532 48.051 16.781 1.00 26.17 C +ATOM 221 C6 DC A 11 49.654 48.865 16.890 1.00 35.50 C +ATOM 222 P DG A 12 55.515 51.081 15.834 1.00 55.98 P +ATOM 223 OP1 DG A 12 56.888 51.283 16.351 1.00 45.83 O +ATOM 224 OP2 DG A 12 54.947 52.158 15.001 1.00 44.26 O +ATOM 225 O5' DG A 12 55.486 49.719 14.996 1.00 62.63 O +ATOM 226 C5' DG A 12 56.293 48.591 15.400 1.00 69.50 C +ATOM 227 C4' DG A 12 55.932 47.474 14.460 1.00 39.92 C +ATOM 228 O4' DG A 12 54.534 47.276 14.620 1.00 32.00 O +ATOM 229 C3' DG A 12 56.105 47.711 12.944 1.00 50.39 C +ATOM 230 O3' DG A 12 57.169 46.942 12.358 1.00 64.13 O +ATOM 231 C2' DG A 12 54.719 47.369 12.378 1.00 36.18 C +ATOM 232 C1' DG A 12 54.149 46.507 13.490 1.00 24.79 C +ATOM 233 N9 DG A 12 52.677 46.527 13.494 1.00 28.44 N +ATOM 234 C8 DG A 12 51.847 47.596 13.281 1.00 31.85 C +ATOM 235 N7 DG A 12 50.552 47.265 13.369 1.00 38.26 N +ATOM 236 C5 DG A 12 50.572 45.947 13.657 1.00 28.99 C +ATOM 237 C6 DG A 12 49.485 45.049 13.903 1.00 42.63 C +ATOM 238 O6 DG A 12 48.275 45.274 13.902 1.00 49.17 O +ATOM 239 N1 DG A 12 49.934 43.773 14.134 1.00 40.15 N +ATOM 240 C2 DG A 12 51.226 43.350 14.154 1.00 33.42 C +ATOM 241 N2 DG A 12 51.443 42.024 14.353 1.00 40.53 N +ATOM 242 N3 DG A 12 52.245 44.192 13.967 1.00 37.34 N +ATOM 243 C4 DG A 12 51.844 45.463 13.732 1.00 31.14 C +END diff --git a/regtest/basic/rt-molinfo-whole-check/dna_whole.pdb b/regtest/basic/rt-molinfo-whole-check/dna_whole.pdb new file mode 100644 index 0000000000..2123faf43b --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-check/dna_whole.pdb @@ -0,0 +1,245 @@ +CRYST1 47.018 47.018 47.018 60.00 60.00 90.00 P 1 1 +ATOM 1 O5' DC A 1 55.119 59.502 49.376 1.00 64.35 O +ATOM 2 C5' DC A 1 55.314 59.228 47.978 1.00 44.69 C +ATOM 3 C4' DC A 1 56.145 57.975 47.859 1.00 31.28 C +ATOM 4 O4' DC A 1 55.544 56.890 48.611 1.00 37.45 O +ATOM 5 C3' DC A 1 56.356 57.429 46.453 1.00 46.72 C +ATOM 6 O3' DC A 1 57.534 56.632 46.440 1.00 48.89 O +ATOM 7 C2' DC A 1 55.132 56.530 46.406 1.00 30.88 C +ATOM 8 C1' DC A 1 55.415 55.789 47.703 1.00 36.58 C +ATOM 9 N1 DC A 1 54.254 54.968 48.139 1.00 40.51 N +ATOM 10 C2 DC A 1 54.408 53.761 48.774 1.00 16.62 C +ATOM 11 O2 DC A 1 55.544 53.321 48.973 1.00 27.75 O +ATOM 12 N3 DC A 1 53.327 53.068 49.136 1.00 20.55 N +ATOM 13 C4 DC A 1 52.101 53.533 48.879 1.00 34.72 C +ATOM 14 N4 DC A 1 51.012 52.784 49.203 1.00 40.31 N +ATOM 15 C5 DC A 1 51.903 54.749 48.230 1.00 30.78 C +ATOM 16 C6 DC A 1 53.027 55.478 47.860 1.00 25.90 C +ATOM 17 P DG A 2 58.593 56.593 45.242 1.00 58.85 P +ATOM 18 OP1 DG A 2 59.720 57.464 45.610 1.00 57.82 O +ATOM 19 OP2 DG A 2 58.006 56.766 43.898 1.00 78.33 O +ATOM 20 O5' DG A 2 59.024 55.058 45.257 1.00 40.36 O +ATOM 21 C5' DG A 2 59.727 54.482 46.353 1.00 47.19 C +ATOM 22 C4' DG A 2 59.678 53.016 46.038 1.00 47.81 C +ATOM 23 O4' DG A 2 58.377 52.559 46.433 1.00 38.76 O +ATOM 24 C3' DG A 2 59.877 52.632 44.566 1.00 28.58 C +ATOM 25 O3' DG A 2 60.907 51.627 44.412 1.00 40.44 O +ATOM 26 C2' DG A 2 58.457 52.192 44.175 1.00 21.14 C +ATOM 27 C1' DG A 2 57.905 51.611 45.475 1.00 33.95 C +ATOM 28 N9 DG A 2 56.421 51.777 45.539 1.00 34.00 N +ATOM 29 C8 DG A 2 55.710 52.891 45.188 1.00 36.47 C +ATOM 30 N7 DG A 2 54.391 52.762 45.395 1.00 32.37 N +ATOM 31 C5 DG A 2 54.267 51.519 45.901 1.00 15.06 C +ATOM 32 C6 DG A 2 53.088 50.832 46.304 1.00 11.88 C +ATOM 33 O6 DG A 2 51.923 51.223 46.277 1.00 21.30 O +ATOM 34 N1 DG A 2 53.381 49.586 46.796 1.00 15.44 N +ATOM 35 C2 DG A 2 54.618 49.024 46.914 1.00 9.63 C +ATOM 36 N2 DG A 2 54.692 47.763 47.427 1.00 16.69 N +ATOM 37 N3 DG A 2 55.721 49.667 46.529 1.00 30.98 N +ATOM 38 C4 DG A 2 55.474 50.901 46.033 1.00 18.56 C +ATOM 39 P DC A 3 61.248 50.928 43.011 1.00 44.67 P +ATOM 40 OP1 DC A 3 62.690 50.623 42.979 1.00 53.89 O +ATOM 41 OP2 DC A 3 60.743 51.719 41.874 1.00 57.79 O +ATOM 42 O5' DC A 3 60.444 49.553 43.086 1.00 35.42 O +ATOM 43 C5' DC A 3 60.768 48.592 44.094 1.00 45.75 C +ATOM 44 C4' DC A 3 59.707 47.540 44.004 1.00 43.02 C +ATOM 45 O4' DC A 3 58.440 48.151 44.212 1.00 36.85 O +ATOM 46 C3' DC A 3 59.608 46.864 42.662 1.00 40.14 C +ATOM 47 O3' DC A 3 60.305 45.616 42.687 1.00 49.62 O +ATOM 48 C2' DC A 3 58.114 46.713 42.420 1.00 53.79 C +ATOM 49 C1' DC A 3 57.462 47.273 43.668 1.00 22.18 C +ATOM 50 N1 DC A 3 56.380 48.196 43.280 1.00 25.44 N +ATOM 51 C2 DC A 3 55.093 47.891 43.575 1.00 19.81 C +ATOM 52 O2 DC A 3 54.869 46.819 44.141 1.00 29.92 O +ATOM 53 N3 DC A 3 54.119 48.754 43.261 1.00 21.59 N +ATOM 54 C4 DC A 3 54.401 49.910 42.656 1.00 14.01 C +ATOM 55 N4 DC A 3 53.405 50.806 42.388 1.00 26.88 N +ATOM 56 C5 DC A 3 55.710 50.252 42.330 1.00 27.59 C +ATOM 57 C6 DC A 3 56.721 49.355 42.658 1.00 27.05 C +ATOM 58 P DG A 4 60.433 44.719 41.376 1.00 44.54 P +ATOM 59 OP1 DG A 4 61.604 43.842 41.524 1.00 61.90 O +ATOM 60 OP2 DG A 4 60.392 45.603 40.199 1.00 37.36 O +ATOM 61 O5' DG A 4 59.115 43.844 41.429 1.00 32.01 O +ATOM 62 C5' DG A 4 58.898 42.932 42.512 1.00 37.89 C +ATOM 63 C4' DG A 4 57.577 42.267 42.264 1.00 53.00 C +ATOM 64 O4' DG A 4 56.537 43.259 42.255 1.00 38.79 O +ATOM 65 C3' DG A 4 57.448 41.536 40.935 1.00 56.72 C +ATOM 66 O3' DG A 4 56.468 40.521 40.997 1.00 64.12 O +ATOM 67 C2' DG A 4 56.977 42.675 40.047 1.00 40.81 C +ATOM 68 C1' DG A 4 55.900 43.208 40.977 1.00 30.52 C +ATOM 69 N9 DG A 4 55.489 44.588 40.628 1.00 28.53 N +ATOM 70 C8 DG A 4 56.201 45.570 39.991 1.00 27.82 C +ATOM 71 N7 DG A 4 55.497 46.701 39.836 1.00 28.01 N +ATOM 72 C5 DG A 4 54.305 46.407 40.394 1.00 23.22 C +ATOM 73 C6 DG A 4 53.136 47.211 40.508 1.00 29.21 C +ATOM 74 O6 DG A 4 52.953 48.364 40.127 1.00 38.58 O +ATOM 75 N1 DG A 4 52.117 46.521 41.111 1.00 27.94 N +ATOM 76 C2 DG A 4 52.156 45.237 41.575 1.00 23.44 C +ATOM 77 N2 DG A 4 51.015 44.723 42.112 1.00 42.64 N +ATOM 78 N3 DG A 4 53.252 44.486 41.476 1.00 21.56 N +ATOM 79 C4 DG A 4 54.268 45.132 40.880 1.00 23.44 C +ATOM 80 P DA A 5 56.540 39.276 40.004 1.00 57.01 P +ATOM 81 OP1 DA A 5 57.300 38.198 40.651 1.00 58.59 O +ATOM 82 OP2 DA A 5 57.021 39.730 38.669 1.00 51.96 O +ATOM 83 O5' DA A 5 54.994 38.888 39.920 1.00 47.12 O +ATOM 84 C5' DA A 5 54.199 38.876 41.121 1.00 47.67 C +ATOM 85 C4' DA A 5 52.856 39.395 40.716 1.00 64.79 C +ATOM 86 O4' DA A 5 53.026 40.754 40.320 1.00 47.60 O +ATOM 87 C3' DA A 5 52.203 38.700 39.523 1.00 51.50 C +ATOM 88 O3' DA A 5 50.946 38.103 39.879 1.00 52.18 O +ATOM 89 C2' DA A 5 52.136 39.805 38.455 1.00 45.00 C +ATOM 90 C1' DA A 5 52.035 41.039 39.328 1.00 26.88 C +ATOM 91 N9 DA A 5 52.575 42.223 38.626 1.00 16.69 N +ATOM 92 C8 DA A 5 53.842 42.410 38.141 1.00 28.14 C +ATOM 93 N7 DA A 5 54.047 43.653 37.672 1.00 34.85 N +ATOM 94 C5 DA A 5 52.857 44.260 37.857 1.00 22.49 C +ATOM 95 C6 DA A 5 52.414 45.586 37.578 1.00 18.12 C +ATOM 96 N6 DA A 5 53.229 46.529 37.027 1.00 29.30 N +ATOM 97 N1 DA A 5 51.150 45.885 37.877 1.00 27.61 N +ATOM 98 C2 DA A 5 50.362 44.959 38.428 1.00 18.53 C +ATOM 99 N3 DA A 5 50.647 43.699 38.743 1.00 29.16 N +ATOM 100 C4 DA A 5 51.934 43.417 38.420 1.00 15.08 C +ATOM 101 P DA A 6 50.050 37.313 38.822 1.00 43.68 P +ATOM 102 OP1 DA A 6 49.212 36.346 39.559 1.00 42.55 O +ATOM 103 OP2 DA A 6 50.899 36.806 37.727 1.00 54.20 O +ATOM 104 O5' DA A 6 49.063 38.418 38.239 1.00 28.20 O +ATOM 105 C5' DA A 6 47.986 38.904 39.049 1.00 42.29 C +ATOM 106 C4' DA A 6 47.295 39.910 38.194 1.00 33.23 C +ATOM 107 O4' DA A 6 48.336 40.767 37.721 1.00 41.48 O +ATOM 108 C3' DA A 6 46.601 39.377 36.946 1.00 18.16 C +ATOM 109 O3' DA A 6 45.191 39.676 36.940 1.00 30.42 O +ATOM 110 C2' DA A 6 47.424 39.999 35.820 1.00 52.97 C +ATOM 111 C1' DA A 6 47.883 41.281 36.478 1.00 38.93 C +ATOM 112 N9 DA A 6 49.102 41.833 35.837 1.00 19.06 N +ATOM 113 C8 DA A 6 50.299 41.206 35.627 1.00 17.83 C +ATOM 114 N7 DA A 6 51.233 42.021 35.115 1.00 29.55 N +ATOM 115 C5 DA A 6 50.600 43.208 35.005 1.00 19.88 C +ATOM 116 C6 DA A 6 51.057 44.494 34.574 1.00 17.26 C +ATOM 117 N6 DA A 6 52.345 44.725 34.186 1.00 19.85 N +ATOM 118 N1 DA A 6 50.183 45.498 34.611 1.00 17.93 N +ATOM 119 C2 DA A 6 48.937 45.269 35.031 1.00 23.00 C +ATOM 120 N3 DA A 6 48.394 44.131 35.457 1.00 21.37 N +ATOM 121 C4 DA A 6 49.300 43.130 35.416 1.00 15.93 C +ATOM 122 P DT A 7 44.265 39.357 35.674 1.00 40.72 P +ATOM 123 OP1 DT A 7 42.852 39.267 36.101 1.00 46.75 O +ATOM 124 OP2 DT A 7 44.784 38.201 34.896 1.00 42.53 O +ATOM 125 O5' DT A 7 44.423 40.694 34.835 1.00 35.21 O +ATOM 126 C5' DT A 7 44.091 41.942 35.445 1.00 34.88 C +ATOM 127 C4' DT A 7 44.346 42.935 34.357 1.00 31.45 C +ATOM 128 O4' DT A 7 45.727 42.887 34.038 1.00 46.82 O +ATOM 129 C3' DT A 7 43.645 42.591 33.055 1.00 23.76 C +ATOM 130 O3' DT A 7 42.435 43.341 32.921 1.00 44.27 O +ATOM 131 C2' DT A 7 44.716 42.834 31.982 1.00 26.30 C +ATOM 132 C1' DT A 7 45.828 43.516 32.778 1.00 28.96 C +ATOM 133 N1 DT A 7 47.205 43.210 32.324 1.00 20.47 N +ATOM 134 C2 DT A 7 48.006 44.230 31.935 1.00 28.01 C +ATOM 135 O2 DT A 7 47.567 45.384 31.902 1.00 40.01 O +ATOM 136 N3 DT A 7 49.303 43.948 31.611 1.00 27.94 N +ATOM 137 C4 DT A 7 49.817 42.679 31.641 1.00 15.14 C +ATOM 138 O4 DT A 7 51.014 42.529 31.378 1.00 32.54 O +ATOM 139 C5 DT A 7 48.965 41.632 31.994 1.00 10.83 C +ATOM 140 C7 DT A 7 49.453 40.209 31.995 1.00 36.33 C +ATOM 141 C6 DT A 7 47.649 41.923 32.353 1.00 12.19 C +ATOM 142 P DT A 8 41.568 43.297 31.583 1.00 49.10 P +ATOM 143 OP1 DT A 8 40.209 43.751 31.939 1.00 41.11 O +ATOM 144 OP2 DT A 8 41.642 41.975 30.919 1.00 39.21 O +ATOM 145 O5' DT A 8 42.270 44.425 30.686 1.00 48.80 O +ATOM 146 C5' DT A 8 42.330 45.785 31.177 1.00 34.73 C +ATOM 147 C4' DT A 8 43.179 46.536 30.197 1.00 28.73 C +ATOM 148 O4' DT A 8 44.372 45.765 30.043 1.00 39.07 O +ATOM 149 C3' DT A 8 42.602 46.639 28.788 1.00 37.88 C +ATOM 150 O3' DT A 8 42.151 47.974 28.455 1.00 52.04 O +ATOM 151 C2' DT A 8 43.697 46.025 27.898 1.00 32.80 C +ATOM 152 C1' DT A 8 44.920 46.162 28.793 1.00 36.58 C +ATOM 153 N1 DT A 8 46.007 45.183 28.518 1.00 24.57 N +ATOM 154 C2 DT A 8 47.270 45.623 28.253 1.00 19.41 C +ATOM 155 O2 DT A 8 47.508 46.823 28.148 1.00 32.74 O +ATOM 156 N3 DT A 8 48.278 44.710 28.171 1.00 25.12 N +ATOM 157 C4 DT A 8 48.060 43.367 28.310 1.00 31.35 C +ATOM 158 O4 DT A 8 49.042 42.624 28.262 1.00 28.53 O +ATOM 159 C5 DT A 8 46.753 42.918 28.524 1.00 22.80 C +ATOM 160 C7 DT A 8 46.445 41.447 28.655 1.00 24.98 C +ATOM 161 C6 DT A 8 45.729 43.855 28.663 1.00 20.28 C +ATOM 162 P DC A 9 41.715 48.378 26.968 1.00 48.97 P +ATOM 163 OP1 DC A 9 40.832 49.551 27.028 1.00 62.33 O +ATOM 164 OP2 DC A 9 41.194 47.212 26.229 1.00 51.53 O +ATOM 165 O5' DC A 9 43.110 48.854 26.370 1.00 43.99 O +ATOM 166 C5' DC A 9 43.820 49.934 27.008 1.00 50.86 C +ATOM 167 C4' DC A 9 45.081 50.160 26.216 1.00 46.66 C +ATOM 168 O4' DC A 9 45.822 48.934 26.207 1.00 42.69 O +ATOM 169 C3' DC A 9 44.901 50.547 24.757 1.00 56.96 C +ATOM 170 O3' DC A 9 45.654 51.721 24.426 1.00 63.54 O +ATOM 171 C2' DC A 9 45.310 49.272 24.012 1.00 50.41 C +ATOM 172 C1' DC A 9 46.425 48.790 24.916 1.00 41.08 C +ATOM 173 N1 DC A 9 46.708 47.329 24.774 1.00 37.23 N +ATOM 174 C2 DC A 9 47.998 46.910 24.599 1.00 40.54 C +ATOM 175 O2 DC A 9 48.875 47.754 24.429 1.00 43.89 O +ATOM 176 N3 DC A 9 48.290 45.604 24.632 1.00 32.57 N +ATOM 177 C4 DC A 9 47.325 44.702 24.805 1.00 24.65 C +ATOM 178 N4 DC A 9 47.645 43.382 24.848 1.00 27.84 N +ATOM 179 C5 DC A 9 45.987 45.082 24.936 1.00 17.61 C +ATOM 180 C6 DC A 9 45.683 46.440 24.926 1.00 30.63 C +ATOM 181 P DG A 10 45.239 52.640 23.178 1.00 65.48 P +ATOM 182 OP1 DG A 10 45.680 54.024 23.501 1.00 59.09 O +ATOM 183 OP2 DG A 10 43.816 52.413 22.812 1.00 45.71 O +ATOM 184 O5' DG A 10 46.138 52.072 21.988 1.00 70.30 O +ATOM 185 C5' DG A 10 47.566 52.247 22.039 1.00 71.73 C +ATOM 186 C4' DG A 10 48.156 51.397 20.957 1.00 58.69 C +ATOM 187 O4' DG A 10 47.986 50.031 21.355 1.00 41.03 O +ATOM 188 C3' DG A 10 47.511 51.485 19.571 1.00 45.61 C +ATOM 189 O3' DG A 10 48.495 51.403 18.545 1.00 52.70 O +ATOM 190 C2' DG A 10 46.598 50.269 19.573 1.00 36.02 C +ATOM 191 C1' DG A 10 47.613 49.335 20.172 1.00 50.90 C +ATOM 192 N9 DG A 10 47.074 48.020 20.559 1.00 45.86 N +ATOM 193 C8 DG A 10 45.800 47.622 20.849 1.00 44.49 C +ATOM 194 N7 DG A 10 45.725 46.316 21.146 1.00 39.96 N +ATOM 195 C5 DG A 10 47.002 45.895 21.041 1.00 38.99 C +ATOM 196 C6 DG A 10 47.560 44.599 21.248 1.00 35.78 C +ATOM 197 O6 DG A 10 46.997 43.559 21.580 1.00 34.90 O +ATOM 198 N1 DG A 10 48.913 44.606 21.039 1.00 23.54 N +ATOM 199 C2 DG A 10 49.682 45.672 20.677 1.00 8.73 C +ATOM 200 N2 DG A 10 51.018 45.476 20.522 1.00 23.15 N +ATOM 201 N3 DG A 10 49.166 46.880 20.492 1.00 24.68 N +ATOM 202 C4 DG A 10 47.840 46.908 20.698 1.00 31.53 C +ATOM 203 P DC A 11 48.947 52.728 17.779 1.00 60.62 P +ATOM 204 OP1 DC A 11 48.980 53.879 18.710 1.00 63.74 O +ATOM 205 OP2 DC A 11 48.070 52.849 16.595 1.00 52.44 O +ATOM 206 O5' DC A 11 50.456 52.393 17.393 1.00 57.57 O +ATOM 207 C5' DC A 11 51.459 52.415 18.441 1.00 54.70 C +ATOM 208 C4' DC A 11 52.406 51.253 18.249 1.00 72.51 C +ATOM 209 O4' DC A 11 51.627 50.061 18.362 1.00 47.18 O +ATOM 210 C3' DC A 11 53.126 51.134 16.911 1.00 29.82 C +ATOM 211 O3' DC A 11 54.524 50.818 17.058 1.00 43.53 O +ATOM 212 C2' DC A 11 52.302 50.074 16.181 1.00 51.34 C +ATOM 213 C1' DC A 11 52.040 49.143 17.345 1.00 30.07 C +ATOM 214 N1 DC A 11 50.856 48.282 17.122 1.00 23.25 N +ATOM 215 C2 DC A 11 50.986 46.935 17.230 1.00 20.38 C +ATOM 216 O2 DC A 11 52.108 46.485 17.445 1.00 38.77 O +ATOM 217 N3 DC A 11 49.907 46.149 17.132 1.00 15.92 N +ATOM 218 C4 DC A 11 48.699 46.680 16.923 1.00 15.82 C +ATOM 219 N4 DC A 11 47.594 45.881 16.887 1.00 28.04 N +ATOM 220 C5 DC A 11 48.532 48.051 16.781 1.00 26.17 C +ATOM 221 C6 DC A 11 49.654 48.865 16.890 1.00 35.50 C +ATOM 222 P DG A 12 55.515 51.081 15.834 1.00 55.98 P +ATOM 223 OP1 DG A 12 56.888 51.283 16.351 1.00 45.83 O +ATOM 224 OP2 DG A 12 54.947 52.158 15.001 1.00 44.26 O +ATOM 225 O5' DG A 12 55.486 49.719 14.996 1.00 62.63 O +ATOM 226 C5' DG A 12 56.293 48.591 15.400 1.00 69.50 C +ATOM 227 C4' DG A 12 55.932 47.474 14.460 1.00 39.92 C +ATOM 228 O4' DG A 12 54.534 47.276 14.620 1.00 32.00 O +ATOM 229 C3' DG A 12 56.105 47.711 12.944 1.00 50.39 C +ATOM 230 O3' DG A 12 57.169 46.942 12.358 1.00 64.13 O +ATOM 231 C2' DG A 12 54.719 47.369 12.378 1.00 36.18 C +ATOM 232 C1' DG A 12 54.149 46.507 13.490 1.00 24.79 C +ATOM 233 N9 DG A 12 52.677 46.527 13.494 1.00 28.44 N +ATOM 234 C8 DG A 12 51.847 47.596 13.281 1.00 31.85 C +ATOM 235 N7 DG A 12 50.552 47.265 13.369 1.00 38.26 N +ATOM 236 C5 DG A 12 50.572 45.947 13.657 1.00 28.99 C +ATOM 237 C6 DG A 12 49.485 45.049 13.903 1.00 42.63 C +ATOM 238 O6 DG A 12 48.275 45.274 13.902 1.00 49.17 O +ATOM 239 N1 DG A 12 49.934 43.773 14.134 1.00 40.15 N +ATOM 240 C2 DG A 12 51.226 43.350 14.154 1.00 33.42 C +ATOM 241 N2 DG A 12 51.443 42.024 14.353 1.00 40.53 N +ATOM 242 N3 DG A 12 52.245 44.192 13.967 1.00 37.34 N +ATOM 243 C4 DG A 12 51.844 45.463 13.732 1.00 31.14 C +END diff --git a/regtest/basic/rt-molinfo-whole-check/main.cpp b/regtest/basic/rt-molinfo-whole-check/main.cpp index feb64671d0..b7094a8624 100644 --- a/regtest/basic/rt-molinfo-whole-check/main.cpp +++ b/regtest/basic/rt-molinfo-whole-check/main.cpp @@ -6,10 +6,12 @@ // MOLINFO WHOLE takes the reference structure as whole. Here each reference is read with // MOLINFO ... WHOLE and used by WHOLEMOLECULES, and we report whether PLUMED accepts it or -// writes a warning that it looks split by the periodic boundary of its CRYST1 record. +// writes a warning that a chain looks split by the periodic boundary of its CRYST1 record. // torn.pdb is whole.pdb with 15 atoms wrapped across a face of its (rhombic dodecahedron) cell. // Its copies without a usable cell (no CRYST1, the 1 A placeholder, a zero cell, a crystallographic // space group) cannot be checked and are accepted. +// dna_torn.pdb is dna_whole.pdb (chain A of 1BNA) wrapped nucleotide by nucleotide: each nucleotide is +// whole, and the chain is split between them. int main(int, char**) { std::ofstream out("output"); unsigned natoms=304; @@ -17,11 +19,12 @@ int main(int, char**) { const std::vector> cases{ {"whole.pdb","1-304"}, {"torn.pdb","1-304"}, - {"torn.pdb","1-150"}, {"torn_nocryst.pdb","1-304"}, {"torn_placeholder.pdb","1-304"}, {"torn_zero.pdb","1-304"}, - {"torn_crystal.pdb","1-304"} + {"torn_crystal.pdb","1-304"}, + {"dna_whole.pdb","1-243"}, + {"dna_torn.pdb","1-243"} }; for(unsigned i=0; i warnings } diff --git a/regtest/basic/rt-molinfo-whole-ligand/plumed.dat b/regtest/basic/rt-molinfo-whole-ligand/plumed.dat index 78d74022e1..a05e51816a 100644 --- a/regtest/basic/rt-molinfo-whole-ligand/plumed.dat +++ b/regtest/basic/rt-molinfo-whole-ligand/plumed.dat @@ -1,5 +1,5 @@ # trp-cage and a ligand away from it, closer to a periodic image of the protein than to the protein itself MOLINFO STRUCTURE=ref.pdb WHOLE -# protein and ligand in one group: a warning is written, and the frames are made whole as the reference +# protein and ligand in one group: no warning (the ligand is a chain of its own), and the frames are made whole as the reference WHOLEMOLECULES ENTITY0=1-313 DUMPATOMS ATOMS=1-313 FILE=whole.xyz PRECISION=3 diff --git a/regtest/basic/rt-molinfo-whole-ligand/warnings.reference b/regtest/basic/rt-molinfo-whole-ligand/warnings.reference index 3554d28427..99de63f898 100644 --- a/regtest/basic/rt-molinfo-whole-ligand/warnings.reference +++ b/regtest/basic/rt-molinfo-whole-ligand/warnings.reference @@ -2,4 +2,3 @@ Action WHOLEMOLECULES # out Action WHOLEMOLECULES -WARNING for action MOLINFO with label @0 : the reference structure in the MOLINFO pdb file may not be whole: 9 of its 313 atoms here are closer to a periodic image of the others, in the box of its CRYST1 record, than to the others themselves. Atoms: 305 (BEN21) 306 (BEN21) 307 (BEN21) 308 (BEN21) 309 (BEN21) 310 (BEN21) 311 (BEN21) 312 (BEN21) 313 (BEN21) diff --git a/regtest/basic/rt-molinfo-whole-membrane/config b/regtest/basic/rt-molinfo-whole-membrane/config index 5c95d0c38d..3bac19a409 100644 --- a/regtest/basic/rt-molinfo-whole-membrane/config +++ b/regtest/basic/rt-molinfo-whole-membrane/config @@ -1,6 +1,6 @@ type=driver # a small bilayer, continuous across the box, in one group and in separate groups. -# In one group, the reference is reported as maybe not whole (a warning), and the frames are still made whole right. +# There is no warning, and the frames are made whole right. arg="--plumed plumed.dat --igro traj.gro" function plumed_regtest_before() { @@ -11,6 +11,6 @@ function plumed_regtest_before() { function plumed_regtest_after() { for f in out_sep out; do echo "# $f" - grep -E "^PLUMED: (Action WHOLEMOLECULES|WARNING for action MOLINFO)" $f | sed -e "s/^PLUMED: //" -e "s/\\. If these atoms.*//" + grep -E "^PLUMED: (Action WHOLEMOLECULES|WARNING for action MOLINFO)" $f | sed -e "s/^PLUMED: //" -e "s/\\. WHOLEMOLECULES will.*//" done > warnings } diff --git a/regtest/basic/rt-molinfo-whole-membrane/plumed.dat b/regtest/basic/rt-molinfo-whole-membrane/plumed.dat index 5115cb2997..81db707076 100644 --- a/regtest/basic/rt-molinfo-whole-membrane/plumed.dat +++ b/regtest/basic/rt-molinfo-whole-membrane/plumed.dat @@ -1,5 +1,5 @@ # a small bilayer: 18 lipids of 6 beads, continuous across the box in x and y MOLINFO STRUCTURE=ref.pdb WHOLE -# all lipids in one group: a warning is written, and every lipid is still made whole +# all lipids in one group: no warning (the check does not go from one lipid to the next), and every lipid is made whole WHOLEMOLECULES ENTITY0=1-108 DUMPATOMS ATOMS=1-108 FILE=whole.xyz PRECISION=3 diff --git a/regtest/basic/rt-molinfo-whole-membrane/warnings.reference b/regtest/basic/rt-molinfo-whole-membrane/warnings.reference index 5087c9864a..99de63f898 100644 --- a/regtest/basic/rt-molinfo-whole-membrane/warnings.reference +++ b/regtest/basic/rt-molinfo-whole-membrane/warnings.reference @@ -2,4 +2,3 @@ Action WHOLEMOLECULES # out Action WHOLEMOLECULES -WARNING for action MOLINFO with label @0 : the reference structure in the MOLINFO pdb file may not be whole: 102 of its 108 atoms here are closer to a periodic image of the others, in the box of its CRYST1 record, than to the others themselves. Atoms: 7 (LIP2) 8 (LIP2) 9 (LIP2) 10 (LIP2) 11 (LIP2) 12 (LIP2) 13 (LIP3) 14 (LIP3) 15 (LIP3) 16 (LIP3) and 92 more diff --git a/src/core/GenericMolInfo.cpp b/src/core/GenericMolInfo.cpp index 63e93d407d..7e9b9249bc 100644 --- a/src/core/GenericMolInfo.cpp +++ b/src/core/GenericMolInfo.cpp @@ -26,6 +26,8 @@ #include "tools/MolDataClass.h" #include "tools/PDB.h" #include "tools/Communicator.h" +#include "tools/Pbc.h" +#include "tools/Tools.h" #include "config/Config.h" #include #include @@ -49,13 +51,72 @@ void GenericMolInfo::registerKeywords( Keywords& keys ) { keys.add("compulsory","PYTHON_BIN","default","python interpreter"); keys.add("atoms","CHAIN","(for masochists ( mostly Davide Branduardi ) ) The atoms involved in each of the chains of interest in the structure."); keys.add("hidden","STRIDE","frequency for resetting the python interpreter. Should be 1."); - keys.addFlag("WHOLE", false, "The reference structure is whole, i.e. not broken by PBC. If the pdb file has a CRYST1 record with space group P 1, this is checked for the atoms of each group that is made whole with it, and a warning is written to the log if some of them are closer to a periodic image of the others than to the others themselves"); + keys.addFlag("WHOLE", false, "The reference structure is whole, i.e. not broken by PBC. If the pdb file has a CRYST1 record with space group P 1, this is checked along each chain, and a warning is written to the log if consecutive atoms of a residue, or of two consecutive protein or nucleic-acid residues, are on opposite sides of the periodic boundary"); } GenericMolInfo::~GenericMolInfo() { // empty destructor to delete unique_ptr } +namespace { +// MOLINFO WHOLE takes the reference structure as whole. Check it along each chain in the box of the +// CRYST1 record: consecutive atoms of a residue, or of two consecutive protein or nucleic-acid residues, +// are close, so a step between them that is not its own minimum image crosses the periodic boundary. +// Returns a warning, or an empty string. +std::string checkWhole(const PDB & pdb,double scale) { + // skip a cell that cannot be the periodic box: none or degenerate, the 1 A cube written when there + // is no unit cell, or a crystallographic cell (simulation programs write the space group P 1) + const Tensor & box(pdb.getBoxVec()); + const double det=box.determinant(); + bool unitcube=true; + for(unsigned k=0; k<3; k++) { + unitcube=unitcube && std::fabs(pdb.getBoxAxs()[k]-scale)<1e-3*scale && std::fabs(pdb.getBoxAng()[k]-90.0)<1e-3; + } + std::string group=pdb.getSpaceGroup(); + group.erase(std::remove(group.begin(),group.end(),' '),group.end()); + if(unitcube || (group.length()>0 && group!="P1") || !std::isfinite(det) || det<=0.0) { + return ""; + } + Pbc pbc; + pbc.setBox(box); + auto polymer=[](std::string r) { + Tools::ltrim(r); + Tools::trim(r); + return MolDataClass::allowedResidue("protein",r) || MolDataClass::allowedResidue("dna",r) || MolDataClass::allowedResidue("rna",r); + }; + const auto & at(pdb.getAtomNumbers()); + const auto & pos(pdb.getPositions()); + unsigned n=0; + std::string list; + for(unsigned i=1; i1e-3*std::cbrt(det)) { + if(++n<=10) { + std::string r=pdb.getResidueName(at[i]); + Tools::ltrim(r); + Tools::trim(r); + list+=" "+std::to_string(at[i].serial())+" ("+r+std::to_string(pdb.getResidueNumber(at[i]))+")"; + } + } + } + if(n==0) { + return ""; + } + return "the reference structure in the MOLINFO pdb file may not be whole: in the box of its CRYST1 record, " + +std::to_string(n)+" atoms are across the periodic boundary from the atom before them in their chain:"+list + +(n>10 ? " and "+std::to_string(n-10)+" more" : "") + +". WHOLEMOLECULES will then split these molecules in every frame: make the pdb whole" + +" (for example with gmx trjconv -pbc whole), or check that its CRYST1 record is the box the structure was written in"; +} +} + GenericMolInfo::GenericMolInfo( const ActionOptions&ao ): Action(ao), ActionAnyorder(ao), @@ -91,10 +152,15 @@ GenericMolInfo::GenericMolInfo( const ActionOptions&ao ): if( read_backbone.size()==0 ) { parse("STRUCTURE",reference); - pdbscale_=usingNaturalUnits() ? 1.0 : 0.1/getUnits().getLength(); if( ! pdb.read(reference,usingNaturalUnits(),0.1/getUnits().getLength())) { plumed_merror("missing input file " + reference ); } + if( iswhole_ ) { + const std::string msg=checkWhole(pdb,usingNaturalUnits() ? 1.0 : 0.1/getUnits().getLength()); + if( msg.length()>0 ) { + warning(msg); + } + } std::vector chains; pdb.getChainNames( chains ); @@ -422,25 +488,6 @@ bool GenericMolInfo::isWhole() const { return iswhole_; } -Tensor GenericMolInfo::getReferenceBox() const { - const Vector & axs(pdb.getBoxAxs()); - const Vector & ang(pdb.getBoxAng()); - bool unitcube=true; - for(unsigned i=0; i<3; i++) { - if(std::fabs(axs[i]-pdbscale_)>1e-3*pdbscale_ || std::fabs(ang[i]-90.0)>1e-3) { - unitcube=false; - } - } - std::string group=pdb.getSpaceGroup(); - group.erase(std::remove(group.begin(),group.end(),' '),group.end()); - const Tensor & box(pdb.getBoxVec()); - const double det=box.determinant(); - if(unitcube || (group.length()>0 && group!="P1") || !std::isfinite(det) || det<=0.0) { - return Tensor(); - } - return box; -} - void GenericMolInfo::prepare() { if(selector_running) { log<<" MOLINFO "<& atoms ); diff --git a/src/tools/Tree.cpp b/src/tools/Tree.cpp index 92e3449038..a7bd3aab66 100644 --- a/src/tools/Tree.cpp +++ b/src/tools/Tree.cpp @@ -24,14 +24,9 @@ #include "Tools.h" #include "Vector.h" #include "AtomNumber.h" -#include "Pbc.h" -#include "Tensor.h" #include "core/GenericMolInfo.h" #include #include -#include -#include -#include namespace PLMD { @@ -93,8 +88,6 @@ void Tree::buildTree(const std::vector & atoms) { std::vector mindist(newatoms.size(), std::numeric_limits::max()); // initialize tree with first atom mindist[0] = 0.0; - // longest edge of the tree (squared) - double longest2=0.0; // loops for(unsigned i=0; i & atoms) { tree_indexes_.push_back(newatoms[selected_vertex]); tree_.push_back(atoms[newatoms[selected_vertex]]); intree[selected_vertex] = true; - if(i>0) { - longest2=std::max(longest2,mindist[selected_vertex]); - } // update distances double minroot = std::numeric_limits::max(); int iroot = -1; @@ -131,8 +121,6 @@ void Tree::buildTree(const std::vector & atoms) { } } - checkReferenceIsWhole(atoms, newatoms, positions, longest2); - // now re-add atoms not present in the PDB for(unsigned i=0; i & atoms) { } } -namespace { -// True if some atom has a periodic image of an atom (a nonzero lattice translation away) within -// sqrt(cut2) of it. When there is none, minimum-image and plain distances agree on every pair up to -// the longest edge of the plain tree, so the periodic tree is the plain tree and the reference is whole. -// A grid search, linear in the number of atoms. It answers true when the box is too small for that -// search to be cheap, so that the full check decides. -bool hasCloseImage(const std::vector & positions, const Tensor & box, double cut2) { - const double cut=std::sqrt(cut2); - Vector lo(positions[0]), hi(positions[0]); - for(const auto & p : positions) { - for(unsigned k=0; k<3; ++k) { - lo[k]=std::min(lo[k],p[k]); - hi[k]=std::max(hi[k],p[k]); - } - } - // lattice vectors that can bring an atom within cut of the structure - const double reach=(hi-lo).modulo()+cut; - const Tensor inv=inverse(box); - int range[3]; - for(unsigned k=0; k<3; ++k) { - const double col=std::sqrt(inv[0][k]*inv[0][k]+inv[1][k]*inv[1][k]+inv[2][k]*inv[2][k]); - range[k]=static_cast(std::ceil(reach*col)); - } - if((2.0*range[0]+1)*(2.0*range[1]+1)*(2.0*range[2]+1)>4096) { - return true; - } - std::vector shifts; - for(int i=-range[0]; i<=range[0]; ++i) { - for(int j=-range[1]; j<=range[1]; ++j) { - for(int k=-range[2]; k<=range[2]; ++k) { - if(i==0 && j==0 && k==0) { - continue; - } - const Vector n=matmul(Vector(i,j,k),box); - if(n.modulo()<=reach) { - shifts.push_back(n); - } - } - } - } - // atoms in cells of side cut - const double side=std::max(cut,1e-6*(hi-lo).modulo()); - long nc[3]; - for(unsigned k=0; k<3; ++k) { - nc[k]=static_cast((hi[k]-lo[k])/side)+1; - } - if(static_cast(nc[0])*nc[1]*nc[2]>1e8) { - return true; - } - auto cellOf=[&](const Vector & p,unsigned k) { - return static_cast(std::floor((p[k]-lo[k])/side)); - }; - std::vector head(nc[0]*nc[1]*nc[2],-1), next(positions.size(),-1); - for(unsigned a=0; ahi[0]+cut || p[1]hi[1]+cut || p[2]hi[2]+cut) { - continue; - } - long c[3]; - for(unsigned k=0; k<3; ++k) { - c[k]=cellOf(p,k); - } - for(long i=std::max(c[0]-1,0L); i<=std::min(c[0]+1,nc[0]-1); ++i) { - for(long j=std::max(c[1]-1,0L); j<=std::min(c[1]+1,nc[1]-1); ++j) { - for(long k=std::max(c[2]-1,0L); k<=std::min(c[2]+1,nc[2]-1); ++k) { - for(long b=head[(i*nc[1]+j)*nc[2]+k]; b>=0; b=next[b]) { - if(delta(p,positions[b]).modulo2()<=cut2) { - return true; - } - } - } - } - } - } - } - return false; -} -} - -void Tree::checkReferenceIsWhole(const std::vector & atoms, - const std::vector & newatoms, - const std::vector & positions, - double longest2) const { - // The tree is built on plain distances in the reference, so WHOLE is taken on trust: - // if part of the reference is wrapped across the periodic boundary, its link to the rest is - // a long edge that is already its own minimum image, and the walk then moves the same atoms - // across the boundary in every frame. - // Check it with the CRYST1 box: build a second spanning tree on minimum-image distances and - // walk it over the reference. A whole reference comes back unchanged; a wrapped piece comes - // back moved by a lattice vector. - const Tensor box=moldat_->getReferenceBox(); - if(box.determinant()==0.0 || positions.size()<2) { - return; - } - // nearly always, no atom comes close to a periodic image of another: then the reference is whole - if(!hasCloseImage(positions, box, longest2*(1.0+1e-6))) { - return; - } - Pbc pbc; - pbc.setBox(box); - const unsigned n=positions.size(); - std::vector intree(n, false); - std::vector mindist(n, std::numeric_limits::max()); - std::vector parent(n, 0); - std::vector rebuilt(positions); - mindist[0]=0.0; - for(unsigned i=0; i0) { - rebuilt[s]=rebuilt[parent[s]]+pbc.distance(positions[parent[s]],positions[s]); - } - for(unsigned j=0; j::max(); - for(unsigned k=0; k<3; ++k) { - shortest=std::min(shortest,box.getRow(k).modulo()); - } - std::vector moved; - for(unsigned j=0; j1e-3*shortest) { - moved.push_back(j); - } - } - if(moved.size()>0) { - std::string list; - for(unsigned k=0; kgetResidueName(a)+std::to_string(moldat_->getResidueNumber(a))+")"; - } - if(moved.size()>10) { - list+=" and "+std::to_string(moved.size()-10)+" more"; - } - // A warning, not an error: a group of several molecules that are not in contact (a ligand away - // from the protein, a membrane) is reported too, and WHOLEMOLECULES can still handle it. - std::ostringstream msg; - msg<<"the reference structure in the MOLINFO pdb file may not be whole: "<warning(msg.str()); - } -} - const std::vector & Tree::getTree(const std::vector & atoms) { buildTree(atoms); return tree_; diff --git a/src/tools/Tree.h b/src/tools/Tree.h index b7f3ee0c48..3b54561591 100644 --- a/src/tools/Tree.h +++ b/src/tools/Tree.h @@ -41,12 +41,6 @@ class Tree { std::vector root_indexes_; std::vector tree_indexes_; -/// Write a warning to the log if the reference structure looks split by the periodic boundary - void checkReferenceIsWhole(const std::vector & atoms, - const std::vector & newatoms, - const std::vector & positions, - double longest2) const; - public: /// constructor explicit Tree(GenericMolInfo* moldat);