Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2011-2018 The plumed team
3 : (see the PEOPLE file at the root of the distribution for a list of names)
4 :
5 : See http://www.plumed.org for more information.
6 :
7 : This file is part of plumed, version 2.
8 :
9 : plumed is free software: you can redistribute it and/or modify
10 : it under the terms of the GNU Lesser General Public License as published by
11 : the Free Software Foundation, either version 3 of the License, or
12 : (at your option) any later version.
13 :
14 : plumed is distributed in the hope that it will be useful,
15 : but WITHOUT ANY WARRANTY; without even the implied warranty of
16 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 : GNU Lesser General Public License for more details.
18 :
19 : You should have received a copy of the GNU Lesser General Public License
20 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 : #ifndef __PLUMED_tools_PDB_h
23 : #define __PLUMED_tools_PDB_h
24 :
25 : #include "AtomNumber.h"
26 : #include "Vector.h"
27 : #include <vector>
28 : #include <string>
29 : #include "Log.h"
30 : #include <map>
31 :
32 :
33 : namespace PLMD {
34 :
35 : /// Minimalistic pdb parser.
36 : /// Contain positions, atomic indexes, occupancy and beta.
37 : /// We should also add other info (e.g. residue name etc).
38 8332 : class PDB {
39 : std::vector<unsigned> block_ends;
40 : std::vector<std::string> atomsymb, chain;
41 : std::vector<unsigned> residue;
42 : std::vector<Vector> positions;
43 : std::vector<double> occupancy;
44 : std::vector<double> beta;
45 : std::vector<std::string> remark;
46 : std::vector<AtomNumber> numbers;
47 : std::map<AtomNumber,unsigned> number2index;
48 : std::vector<std::string> residuenames;
49 : public:
50 : /// Read the pdb from a file, scaling positions by a factor scale
51 : bool read(const std::string&file,bool naturalUnits,double scale);
52 : /// Read from a file pointer
53 : bool readFromFilepointer(FILE *fp,bool naturalUnits,double scale);
54 : /// Access to the position array
55 : const std::vector<Vector> & getPositions()const;
56 : /// Access to the occupancy array
57 : const std::vector<double> & getOccupancy()const;
58 : /// Access to the beta array
59 : const std::vector<double> & getBeta()const;
60 : /// This is used to set the keyword ARG - this is so we
61 : /// we can use a1.* in the input for reference configurations
62 : void setArgKeyword( const std::string& new_args );
63 : /// Add information to the remark
64 : void addRemark( const std::vector<std::string>& v1 );
65 : /// Access to the lines of REMARK
66 : const std::vector<std::string> & getRemark()const;
67 : /// Access to the indexes
68 : const std::vector<AtomNumber> & getAtomNumbers()const;
69 : /// Returns the number of atoms
70 : unsigned size()const;
71 : /// Get the names of all the chains in the pdb file
72 : void getChainNames( std::vector<std::string>& chains ) const;
73 : /// Get the residues in each of the chains
74 : void getResidueRange( const std::string& chainname, unsigned& res_start, unsigned& res_end, std::string& errmsg ) const;
75 : /// Get the atoms in each of the chains
76 : void getAtomRange( const std::string& chainname, AtomNumber& a_start, AtomNumber& a_end, std::string& errmsg ) const;
77 : /// Get the chain ID that a particular residue is a part of
78 : std::string getChainID(const unsigned& resnumber) const;
79 : ///use the log to dump information
80 : friend Log& operator<<(Log& ostr, const PDB& pdb);
81 : /// return the name of a specific atom
82 : std::string getAtomName(AtomNumber a) const;
83 : /// return the residue number for a specific atom
84 : unsigned getResidueNumber(AtomNumber a) const;
85 : /// return the residue name for a specific atom
86 : std::string getResidueName(AtomNumber a) const;
87 : /// get the name of the resnum'th residue
88 : std::string getResidueName(const unsigned& resnum ) const;
89 : /// get the name of the resnum'th residue of chain
90 : /// Chain=="*" matches any chain and makes it equivalent to getResidueName
91 : std::string getResidueName(const unsigned& resnum,const std::string& chain ) const;
92 : /// Check if any of the residues are named name
93 : bool checkForResidue( const std::string& name ) const ;
94 : /// Check if any of the atoms are named atom
95 : bool checkForAtom( const std::string& name ) const ;
96 : /// Return the atom named aname from residue number resnum
97 : AtomNumber getNamedAtomFromResidue( const std::string& aname, const unsigned& resnum ) const;
98 : /// Return the atom named aname from residue number resnum and chain.
99 : /// Chain=="*" matches any chain and makes it equivalent to getNamedAtomFromResidue.
100 : AtomNumber getNamedAtomFromResidueAndChain( const std::string& aname, const unsigned& resnum, const std::string& chain ) const;
101 : /// Access to the atoms of a residue
102 : std::vector<AtomNumber> getAtomsInResidue(const unsigned& resnum,const std::string& chainid)const;
103 : /// Access to the atoms of a chain
104 : std::vector<AtomNumber> getAtomsInChain(const std::string& chainid)const;
105 : /// Get the extents of the blocks containing the atoms
106 : const std::vector<unsigned> & getAtomBlockEnds() const ;
107 : /// Get the number of blocks of atoms in the pdb
108 : unsigned getNumberOfAtomBlocks() const ;
109 : /// Set the position array
110 : void setPositions(const std::vector<Vector> &v);
111 : /// Access to the position array
112 : Vector getPosition(AtomNumber a)const;
113 : };
114 :
115 : }
116 : #endif
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