mirror of https://github.com/CGAL/cgal
124 lines
3.4 KiB
C++
124 lines
3.4 KiB
C++
/* Copyright 2004
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Stanford University
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This file is part of the DSR PDB Library.
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The DSR PDB Library is free software; you can redistribute it and/or modify
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it under the terms of the GNU Lesser General Public License as published by
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the Free Software Foundation; either version 2.1 of the License, or (at your
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option) any later version.
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The DSR PDB Library is distributed in the hope that it will be useful, but
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WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
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or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
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License for more details.
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You should have received a copy of the GNU Lesser General Public License
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along with the DSR PDB Library; see the file LICENSE.LGPL. If not, write to
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the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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MA 02110-1301, USA. */
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#ifndef DSR_MODEL_H_
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#define DSR_MODEL_H_
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#include <CGAL/PDB/Protein.h>
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#include <vector>
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#include <string>
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CGAL_PDB_BEGIN_NAMESPACE
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class PDB;
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//! A class representing a single model from a PDB file.
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/*!
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You can iterator through the chains and soon the heterogens.
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*/
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class Model {
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friend class PDB;
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public:
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//! Construct an empty model
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Model();
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//! Construct an empty model with a number
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Model(unsigned int i);
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//! The number of strands
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size_t number_of_chains() const;
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//! get the ith strand
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Protein &chain(unsigned int i);
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//! get the ith strand
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const Protein &chain(unsigned int i) const;
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//! add a strand
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void new_chain(const Protein &p);
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//! write to a pdb
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void write(std::ostream &out) const;
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//! return the index or -1 if it is not valid
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int index() const{return index_;}
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//! set the index
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void set_index(int ind) {index_=ind;}
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typedef std::vector<Protein>::const_iterator Const_chains_iterator;
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//! Begin iterating through the chains.
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Const_chains_iterator chains_begin() const {
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return chains_.begin();
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}
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//! End iterating through the chains.
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Const_chains_iterator chains_end() const {
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return chains_.end();
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}
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class Hetatom_data {
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public:
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Hetatom_data(const char *rnm,
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const char *anm, int rn, char ch): resname_(rnm),
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atomname_(anm),
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rnum_(rn), chain_(ch){
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}
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const char *molecule_name() const {
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return resname_.c_str();
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}
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const char *atom_name() const {
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return atomname_.c_str();
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}
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int molecule_number() const {
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return rnum_;
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}
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char chain() const {
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return chain_;
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}
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protected:
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std::string resname_;
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std::string atomname_;
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int rnum_;
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char chain_;
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};
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//! An iterator through CGAL::PDB::Atom values for the HETATM records.
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typedef std::vector<std::pair<Hetatom_data, Atom> >::const_iterator Const_hetatoms_iterator;
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//! Begin iterating through CGAL:PDB::Atom values for the HETATM records.
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Const_hetatoms_iterator hetatoms_begin() const {
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return hetatoms_.begin();
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}
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Const_hetatoms_iterator hetatoms_end() const {
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return hetatoms_.end();
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}
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//! The number of hetatoms
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unsigned int hetatoms_size() const {
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return hetatoms_.size();
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}
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protected:
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void process_line(const char *c);
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std::vector<std::string> extra_;
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std::vector<Protein> chains_;
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std::vector<std::pair<Hetatom_data, Atom> > hetatoms_;
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int index_;
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};
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CGAL_PDB_END_NAMESPACE
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#endif
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