From 3c55c8cfc610932d0a5e794c0dc7b0fd1c78e094 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Thu, 5 Jul 2012 02:17:32 +0200
Subject: [PATCH] Molck missing files
---
modules/conop/src/diag.cc | 98 ++++++++++++++++++++
modules/conop/src/diag.hh | 134 +++++++++++++++++++++++++++
modules/conop/src/model_check.cc | 150 +++++++++++++++++++++++++++++++
modules/conop/src/model_check.hh | 30 +++++++
4 files changed, 412 insertions(+)
create mode 100644 modules/conop/src/diag.cc
create mode 100644 modules/conop/src/diag.hh
create mode 100644 modules/conop/src/model_check.cc
create mode 100644 modules/conop/src/model_check.hh
diff --git a/modules/conop/src/diag.cc b/modules/conop/src/diag.cc
new file mode 100644
index 000000000..75245fc93
--- /dev/null
+++ b/modules/conop/src/diag.cc
@@ -0,0 +1,98 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include "diag.hh"
+
+namespace ost { namespace conop {
+
+String Diag::Format(bool colored) const
+{
+ std::stringstream ss;
+ std::vector<String> strings;
+ for (std::vector<ArgDesc>::const_iterator
+ i=args_.begin(), e=args_.end(); i!=e; ++i) {
+ switch (i->type) {
+ case DIAG_ARG_TYPE_ATOM:
+ if (colored) {
+ strings.push_back("\033[0;30m"+
+ atoms_[i->index].GetQualifiedName()+"\033[0m");
+ } else {
+ strings.push_back(atoms_[i->index].GetQualifiedName());
+ }
+ break;
+ case DIAG_ARG_TYPE_RESIDUE:
+ if (colored) {
+ strings.push_back("\033[0;30m"+
+ residues_[i->index].GetQualifiedName()+"\033[0m");
+ } else {
+ strings.push_back(residues_[i->index].GetQualifiedName());
+ }
+ break;
+ case DIAG_ARG_TYPE_CHAIN:
+ if (colored) {
+ strings.push_back("\033[0;30m"+
+ chains_[i->index].GetName()+"\033[0m");
+ } else {
+ strings.push_back(chains_[i->index].GetName());
+ }
+ break;
+ case DIAG_ARG_TYPE_STRING:
+ strings.push_back(strings_[i->index]);
+ break;
+ case DIAG_ARG_TYPE_INT:
+ ss << ints_[i->index];
+ strings.push_back(ss.str());
+ ss.str("");
+ break;
+ }
+ }
+ for (size_t i=0; i<format_.size(); ++i) {
+ if (format_[i]=='%') {
+ // scan for number
+ ++i;
+ assert(i<format_.size());
+ if (format_[i]=='%' ) {
+ ss << '%';
+ continue;
+ }
+ bool plural_s=false;
+ if (format_[i]=='s') {
+ plural_s=true;
+ ++i;
+ }
+ const char *start=&format_[i];
+ char *end=NULL;
+ long int id=strtol(start, &end, 10);
+ assert(start!=end);
+ assert(id>=0 && id<strings.size());
+ if (plural_s) {
+ if (ints_[args_[id].index]!=1) {
+ ss << "s";
+ }
+ } else {
+ ss << strings[id];
+ }
+ i+=end-start-1;
+ continue;
+ }
+ ss << format_[i];
+ }
+ return ss.str();
+}
+
+}} /* ost::conop */
diff --git a/modules/conop/src/diag.hh b/modules/conop/src/diag.hh
new file mode 100644
index 000000000..58f476554
--- /dev/null
+++ b/modules/conop/src/diag.hh
@@ -0,0 +1,134 @@
+#//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_CONOP_DIAG_HH
+#define OST_CONOP_DIAG_HH
+#include <ost/mol/atom_handle.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/chain_handle.hh>
+#include <ost/conop/module_config.hh>
+
+namespace ost { namespace conop {
+
+typedef enum {
+ DIAG_ARG_TYPE_ATOM,
+ DIAG_ARG_TYPE_RESIDUE,
+ DIAG_ARG_TYPE_CHAIN,
+ DIAG_ARG_TYPE_STRING,
+ DIAG_ARG_TYPE_INT
+} DiagArgType;
+
+typedef enum {
+ DIAG_UNK_ATOM,
+ DIAG_UNK_RESIDUE,
+ DIAG_MISSING_ATOM,
+ DIAG_NONSTD_RESIDUE
+} DiagType;
+
+class DLLEXPORT_OST_CONOP Diag {
+public:
+ Diag(DiagType typ, const char* fmt): type_(typ), format_(fmt) {}
+ DiagType GetType() const { return type_; }
+ Diag& AddAtom(mol::AtomHandle atom)
+ {
+ atoms_.push_back(atom);
+ args_.push_back(ArgDesc(atoms_.size()-1, DIAG_ARG_TYPE_ATOM));
+ return *this;
+ }
+
+ Diag& AddResidue(mol::ResidueHandle res)
+ {
+ residues_.push_back(res);
+ args_.push_back(ArgDesc(residues_.size()-1, DIAG_ARG_TYPE_RESIDUE));
+ return *this;
+ }
+ Diag& AddChain(mol::ChainHandle chain)
+ {
+ chains_.push_back(chain);
+ args_.push_back(ArgDesc(chains_.size()-1, DIAG_ARG_TYPE_CHAIN));
+ return *this;
+ }
+ Diag& AddInt(int int_val)
+ {
+ ints_.push_back(int_val);
+ args_.push_back(ArgDesc(ints_.size()-1, DIAG_ARG_TYPE_INT));
+ return *this;
+ }
+ Diag& AddString(const String& str)
+ {
+ strings_.push_back(str);
+ args_.push_back(ArgDesc(strings_.size()-1, DIAG_ARG_TYPE_STRING));
+ return *this;
+ }
+ mol::AtomHandle GetAtom(size_t index) const
+ {
+ assert(index<args_.size());
+ return atoms_[args_[index].index];
+ }
+ mol::ResidueHandle GetResidue(size_t index) const
+ {
+ assert(index<args_.size());
+ return residues_[args_[index].index];
+ }
+ mol::ChainHandle GetChain(size_t index) const
+ {
+ assert(index<args_.size());
+ return chains_[args_[index].index];
+ }
+ String Format(bool colored=true) const;
+private:
+ struct ArgDesc {
+ ArgDesc(size_t i, DiagArgType t): index(i), type(t) { }
+ size_t index;
+ DiagArgType type;
+ };
+ DiagType type_;
+ String format_;
+ mol::AtomHandleList atoms_;
+ mol::ResidueHandleList residues_;
+ mol::ChainHandleList chains_;
+ std::vector<String> strings_;
+ std::vector<int> ints_;
+ std::vector<ArgDesc> args_;
+};
+
+class DLLEXPORT_OST_CONOP DiagEngine {
+public:
+ DiagEngine() {}
+
+ ~DiagEngine()
+ {
+ for(std::vector<Diag*>::iterator
+ i=diags_.begin(), e=diags_.end(); i!=e;++i) {
+ delete *i;
+ }
+ }
+
+ Diag& AddDiag(DiagType type, const char* fmt)
+ {
+ diags_.push_back(new Diag(type, fmt));
+ return *diags_.back();
+ }
+
+ const std::vector<Diag*>& GetDiags() const { return diags_; }
+private:
+ std::vector<Diag*> diags_;
+};
+
+}} /* ost::conop */
+#endif
diff --git a/modules/conop/src/model_check.cc b/modules/conop/src/model_check.cc
new file mode 100644
index 000000000..cb5d710b6
--- /dev/null
+++ b/modules/conop/src/model_check.cc
@@ -0,0 +1,150 @@
+#include <ost/mol/iterator.hh>
+#include "model_check.hh"
+#include "amino_acids.hh"
+
+using namespace ost::mol;
+
+namespace ost { namespace conop {
+
+void Checker::CheckForCompleteness(bool require_hydrogens)
+{
+ for (ResidueHandleIter i=ent_.ResiduesBegin(), e=ent_.ResiduesEnd();
+ i!=e; ++i) {
+ ResidueHandle res=*i;
+ String anames="";
+ CompoundPtr compound=lib_->FindCompound(res.GetName(),Compound::PDB);
+ if (!compound) {
+ if (checked_unk_res_) {
+ continue;
+ }
+ diags_.AddDiag(DIAG_UNK_RESIDUE, "unknown residue %0")
+ .AddResidue(res);
+ continue;
+ }
+ int missing_atoms=0;
+ const AtomSpecList& atom_specs=compound->GetAtomSpecs();
+ for (AtomSpecList::const_iterator
+ j=atom_specs.begin(), e2=atom_specs.end(); j!=e2; ++j) {
+ if (j->is_leaving) {
+ continue;
+ }
+ if (!require_hydrogens && (j->element=="H" || j->element=="D")) {
+ continue;
+ }
+ if (!res.FindAtom(j->name) && !res.FindAtom(j->alt_name)) {
+ if (!anames.empty()) {
+ anames+=", ";
+ }
+ anames+="'"+j->name+"'";
+ missing_atoms+=1;
+ }
+ }
+ if (missing_atoms>0) {
+ diags_.AddDiag(DIAG_MISSING_ATOM, "residue %0 is missing %1 atom%s1: %2")
+ .AddResidue(res)
+ .AddInt(missing_atoms)
+ .AddString(anames);
+ }
+ }
+ checked_unk_res_=true;
+}
+
+mol::AtomHandleList Checker::GetHydrogens()
+{
+ AtomHandleList hydlist;
+ for (ResidueHandleIter i=ent_.ResiduesBegin(), e=ent_.ResiduesEnd();
+ i!=e; ++i) {
+ ResidueHandle res=*i;
+ CompoundPtr compound=lib_->FindCompound(res.GetName(),Compound::PDB);
+ if (!compound) {
+ continue;
+ }
+ AtomHandleList atoms=res.GetAtomList();
+ for (AtomHandleList::const_iterator
+ j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
+ int specindx=compound->GetAtomSpecIndex(j->GetName());
+ if (specindx!=-1) {
+ if (compound->GetAtomSpecs()[specindx].element=="H" || compound->GetAtomSpecs()[specindx].element=="D") {
+ hydlist.push_back(*j);
+ }
+ }
+ }
+ }
+ return hydlist;
+}
+
+mol::AtomHandleList Checker::GetZeroOccupancy()
+{
+ AtomHandleList zerolist;
+ for (ResidueHandleIter i=ent_.ResiduesBegin(), e=ent_.ResiduesEnd();
+ i!=e; ++i) {
+ ResidueHandle res=*i;
+ AtomHandleList atoms=res.GetAtomList();
+ for (AtomHandleList::const_iterator j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
+ if (j->GetOccupancy()==0.0) {
+ zerolist.push_back(*j);
+ }
+ }
+ }
+ return zerolist;
+}
+
+void Checker::CheckForNonStandard()
+{
+ for (ResidueHandleIter i=ent_.ResiduesBegin(), e=ent_.ResiduesEnd();
+ i!=e; ++i) {
+ ResidueHandle res=*i;
+ CompoundPtr compound=lib_->FindCompound(res.GetName(),Compound::PDB);
+ if (!compound) {
+ if (checked_unk_res_) {
+ continue;
+ }
+ diags_.AddDiag(DIAG_UNK_RESIDUE, "unknown residue %0")
+ .AddResidue(res);
+ continue;
+ }
+ if (ResidueToAminoAcid(res)==XXX) {
+ diags_.AddDiag(DIAG_NONSTD_RESIDUE, "%0 is not a standard amino acid")
+ .AddResidue(res);
+ }
+ }
+ checked_unk_res_=true;
+}
+
+void Checker::CheckForUnknownAtoms()
+{
+ for (ResidueHandleIter i=ent_.ResiduesBegin(), e=ent_.ResiduesEnd();
+ i!=e; ++i) {
+ ResidueHandle res=*i;
+ String anames="";
+ CompoundPtr compound=lib_->FindCompound(res.GetName(),Compound::PDB);
+ if (!compound) {
+ if (checked_unk_res_) {
+ continue;
+ }
+ diags_.AddDiag(DIAG_UNK_RESIDUE, "unknown residue %0")
+ .AddResidue(res);
+ continue;
+ }
+ AtomHandleList atoms=res.GetAtomList();
+ const AtomSpecList& atom_specs=compound->GetAtomSpecs();
+ for (AtomHandleList::const_iterator
+ j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
+ bool found=false;
+ for (AtomSpecList::const_iterator
+ k=atom_specs.begin(), e3=atom_specs.end(); k!=e3; ++k) {
+ if (k->name==j->GetName() || k->alt_name==j->GetName()) {
+ found=true;
+ break;
+ }
+ }
+ if (!found) {
+ diags_.AddDiag(DIAG_UNK_ATOM, "residue %0 contains unknown atom %1")
+ .AddResidue(res)
+ .AddAtom(*j);
+ }
+ }
+ }
+ checked_unk_res_=true;
+}
+}} /* ost::conop */
diff --git a/modules/conop/src/model_check.hh b/modules/conop/src/model_check.hh
new file mode 100644
index 000000000..25bdfb88b
--- /dev/null
+++ b/modules/conop/src/model_check.hh
@@ -0,0 +1,30 @@
+#ifndef OST_CONOP_MODEL_CHECK_HH
+#define OST_CONOP_MODEL_CHECK_HH
+
+#include <ost/mol/entity_handle.hh>
+#include <ost/conop/diag.hh>
+#include <ost/conop/compound_lib.hh>
+namespace ost { namespace conop {
+
+class DLLEXPORT_OST_CONOP Checker {
+public:
+ Checker(CompoundLibPtr lib, const mol::EntityHandle& ent,
+ DiagEngine& diags): lib_(lib), ent_(ent), diags_(diags),
+ checked_unk_res_(false)
+ {}
+ void CheckForUnknownAtoms();
+ void CheckForCompleteness(bool require_hydrogens=false);
+ void CheckForNonStandard();
+ mol::AtomHandleList GetHydrogens();
+ mol::AtomHandleList GetZeroOccupancy();
+
+ const std::vector<Diag*>& GetDiags() const { return diags_.GetDiags(); }
+private:
+ CompoundLibPtr lib_;
+ mol::EntityHandle ent_;
+ DiagEngine& diags_;
+ bool checked_unk_res_;
+};
+
+}} /* ost::conop */
+#endif
--
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