Contact map files¶
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class mdk::cmap::ContactMap
A POD representing a contact map (a.k.a. structured part), as represented in the legacy contact map file): specifically, the location and extent of the structured part, associated native bond and dihedral angles and Go-model contacts.
This data structure doesn’t provide its own means of parsing (
cmap::LegacyParsermust be used, for example), since a change of format shouldn’t influence this POD.Public Members
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int len
Length of the structured part.
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int offset
Offset of the structured part (w.r.t. the chain beginning).
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std::vector<double> angle
angle[i] denotes the native bond angle value for triple (i-1, i, i+1), relative to the position as indicated by /p off, i.e. if (i+off-1, i+off, i+off+1) relative to the start of the chain. Note: the native angles near the ends of the structured part are undefined.
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std::vector<double> dihedral
dihedral[i] denotes the native dihedral angle value for quadruple (i-2, i-1, i, i+1), relative to the position as indicated by /p off, i.e. if (i+off-2, i+off-1, i+off, i+off+1) relative to the start of the chain. Note: the native angles near the ends of the structured part are undefined.
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struct Contact
Public Members
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int res[2]
Residues forming the contact.
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double dist0
Native length of the contact.
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int res[2]
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int len
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class mdk::cmap::LegacyParser
A parser of contact map files in the legacy format (as described in legacy README.txt).
Public Functions
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ContactMap read(std::istream &is)
Read contact map from a stream.
- Parameters
is – Input stream wherefrom to read the contact map
- Returns
Parsed contact map.
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std::ostream &write(std::ostream &os, ContactMap const &cmap)
Write contact map to a stream.
- Parameters
os – Output stream whereto to write the contact map
cmap – Contact map to write
- Returns
os
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ContactMap read(std::istream &is)